From ea9b00ce56bdc78db6e5b46af9b6bbebf74ad138 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 20 May 2021 15:31:42 +0200 Subject: [PATCH 01/92] adjusted test --- .../dnetlib/dhp/actionmanager/project/utils/EXCELParser.java | 2 +- .../dnetlib/dhp/actionmanager/project/EXCELParserTest.java | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java index cc18c6f54c..1a6ebb9e86 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java @@ -32,7 +32,7 @@ public class EXCELParser { XSSFSheet sheet = wb.getSheet(sheetName); - if(sheetName == null){ + if (sheetName == null) { throw new RuntimeException("Sheet name " + sheetName + " not present in current file"); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java index 59b536cd54..72ba48f418 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java @@ -35,8 +35,9 @@ public class EXCELParserTest { EXCELParser excelParser = new EXCELParser(); - List pl = excelParser - .parse(httpConnector.getInputSourceAsStream(URL), "eu.dnetlib.dhp.actionmanager.project.utils.ExcelTopic"); + final String classForName = "eu.dnetlib.dhp.actionmanager.project.utils.ExcelTopic"; + final String sheetName = "Topics"; + List pl = excelParser.parse(httpConnector.getInputSourceAsStream(URL), classForName, sheetName); Assertions.assertEquals(3837, pl.size()); From 4d6c473bf18a42a1e0fac7863eddae017d1a7eff Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 20 May 2021 18:26:42 +0200 Subject: [PATCH 02/92] removed redundant classes contained now in dhp-schema --- .../dhp/schema/orcid/AuthorHistory.java | 79 ------------- .../dhp/schema/orcid/AuthorSummary.java | 25 ---- .../dnetlib/dhp/schema/orcid/Contributor.java | 58 ---------- .../dnetlib/dhp/schema/orcid/ExternalId.java | 38 ------ .../dnetlib/dhp/schema/orcid/OrcidData.java | 34 ------ .../dhp/schema/orcid/PublicationDate.java | 38 ------ .../eu/dnetlib/dhp/schema/orcid/Work.java | 16 --- .../dnetlib/dhp/schema/orcid/WorkDetail.java | 109 ------------------ 8 files changed, 397 deletions(-) delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorHistory.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorSummary.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Contributor.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/ExternalId.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidData.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/PublicationDate.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Work.java delete mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/WorkDetail.java diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorHistory.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorHistory.java deleted file mode 100644 index 554aae82cf..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorHistory.java +++ /dev/null @@ -1,79 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -public class AuthorHistory implements Serializable { - private String creationMethod; - private String completionDate; - private String submissionDate; - private String lastModifiedDate; - private boolean claimed; - private String deactivationDate; - private boolean verifiedEmail; - private boolean verifiedPrimaryEmail; - - public String getCreationMethod() { - return creationMethod; - } - - public void setCreationMethod(String creationMethod) { - this.creationMethod = creationMethod; - } - - public String getCompletionDate() { - return completionDate; - } - - public void setCompletionDate(String completionDate) { - this.completionDate = completionDate; - } - - public String getSubmissionDate() { - return submissionDate; - } - - public void setSubmissionDate(String submissionDate) { - this.submissionDate = submissionDate; - } - - public String getLastModifiedDate() { - return lastModifiedDate; - } - - public void setLastModifiedDate(String lastModifiedDate) { - this.lastModifiedDate = lastModifiedDate; - } - - public boolean isClaimed() { - return claimed; - } - - public void setClaimed(boolean claimed) { - this.claimed = claimed; - } - - public String getDeactivationDate() { - return deactivationDate; - } - - public void setDeactivationDate(String deactivationDate) { - this.deactivationDate = deactivationDate; - } - - public boolean isVerifiedEmail() { - return verifiedEmail; - } - - public void setVerifiedEmail(boolean verifiedEmail) { - this.verifiedEmail = verifiedEmail; - } - - public boolean isVerifiedPrimaryEmail() { - return verifiedPrimaryEmail; - } - - public void setVerifiedPrimaryEmail(boolean verifiedPrimaryEmail) { - this.verifiedPrimaryEmail = verifiedPrimaryEmail; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorSummary.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorSummary.java deleted file mode 100644 index 813aead490..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorSummary.java +++ /dev/null @@ -1,25 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -public class AuthorSummary extends OrcidData implements Serializable { - AuthorData authorData; - AuthorHistory authorHistory; - - public AuthorData getAuthorData() { - return authorData; - } - - public void setAuthorData(AuthorData authorData) { - this.authorData = authorData; - } - - public AuthorHistory getAuthorHistory() { - return authorHistory; - } - - public void setAuthorHistory(AuthorHistory authorHistory) { - this.authorHistory = authorHistory; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Contributor.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Contributor.java deleted file mode 100644 index 3b543db4b0..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Contributor.java +++ /dev/null @@ -1,58 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -import eu.dnetlib.dhp.schema.orcid.AuthorData; - -/** - * This class models the data related to a contributor, that are retrieved from an orcid publication - */ - -public class Contributor extends AuthorData implements Serializable { - private String sequence; - private String role; - private transient boolean simpleMatch; - private transient Double score; - private transient boolean bestMatch; - - public String getSequence() { - return sequence; - } - - public void setSequence(String sequence) { - this.sequence = sequence; - } - - public String getRole() { - return role; - } - - public void setRole(String role) { - this.role = role; - } - - public boolean isSimpleMatch() { - return simpleMatch; - } - - public void setSimpleMatch(boolean simpleMatch) { - this.simpleMatch = simpleMatch; - } - - public Double getScore() { - return score; - } - - public void setScore(Double score) { - this.score = score; - } - - public boolean isBestMatch() { - return bestMatch; - } - - public void setBestMatch(boolean bestMatch) { - this.bestMatch = bestMatch; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/ExternalId.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/ExternalId.java deleted file mode 100644 index d8f001aa5a..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/ExternalId.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -/** - * This class models the data related to external id, that are retrieved from an orcid publication - */ - -public class ExternalId implements Serializable { - private String type; - private String value; - private String relationShip; - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - public String getValue() { - return value; - } - - public void setValue(String value) { - this.value = value; - } - - public String getRelationShip() { - return relationShip; - } - - public void setRelationShip(String relationShip) { - this.relationShip = relationShip; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidData.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidData.java deleted file mode 100644 index 606eea6a8e..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidData.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -public class OrcidData implements Serializable { - protected String base64CompressData; - protected String statusCode; - protected String downloadDate; - - public String getBase64CompressData() { - return base64CompressData; - } - - public void setBase64CompressData(String base64CompressData) { - this.base64CompressData = base64CompressData; - } - - public String getStatusCode() { - return statusCode; - } - - public void setStatusCode(String statusCode) { - this.statusCode = statusCode; - } - - public String getDownloadDate() { - return downloadDate; - } - - public void setDownloadDate(String downloadDate) { - this.downloadDate = downloadDate; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/PublicationDate.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/PublicationDate.java deleted file mode 100644 index 01972ce95a..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/PublicationDate.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -/** - * This class models the data related to a publication date, that are retrieved from an orcid publication - */ - -public class PublicationDate implements Serializable { - private String year; - private String month; - private String day; - - public String getYear() { - return year; - } - - public void setYear(String year) { - this.year = year; - } - - public String getMonth() { - return month; - } - - public void setMonth(String month) { - this.month = month; - } - - public String getDay() { - return day; - } - - public void setDay(String day) { - this.day = day; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Work.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Work.java deleted file mode 100644 index c557eb5d2f..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/Work.java +++ /dev/null @@ -1,16 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; - -public class Work extends OrcidData implements Serializable { - WorkDetail workDetail; - - public WorkDetail getWorkDetail() { - return workDetail; - } - - public void setWorkDetail(WorkDetail workDetail) { - this.workDetail = workDetail; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/WorkDetail.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/WorkDetail.java deleted file mode 100644 index 614d415c15..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/WorkDetail.java +++ /dev/null @@ -1,109 +0,0 @@ - -package eu.dnetlib.dhp.schema.orcid; - -import java.io.Serializable; -import java.util.List; - -import eu.dnetlib.dhp.schema.orcid.Contributor; -import eu.dnetlib.dhp.schema.orcid.ExternalId; -import eu.dnetlib.dhp.schema.orcid.OrcidData; -import eu.dnetlib.dhp.schema.orcid.PublicationDate; - -/** - * This class models the data that are retrieved from orcid publication - */ - -public class WorkDetail implements Serializable { - - private String oid; - private String id; - private String sourceName; - private String type; - private List titles; - private List urls; - List extIds; - List publicationDates; - List contributors; - - public String getOid() { - return oid; - } - - public void setOid(String oid) { - this.oid = oid; - } - - public String getErrorCode() { - return errorCode; - } - - public void setErrorCode(String errorCode) { - this.errorCode = errorCode; - } - - private String errorCode; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public List getTitles() { - return titles; - } - - public void setTitles(List titles) { - this.titles = titles; - } - - public String getSourceName() { - return sourceName; - } - - public void setSourceName(String sourceName) { - this.sourceName = sourceName; - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - public List getUrls() { - return urls; - } - - public void setUrls(List urls) { - this.urls = urls; - } - - public List getExtIds() { - return extIds; - } - - public void setExtIds(List extIds) { - this.extIds = extIds; - } - - public List getPublicationDates() { - return publicationDates; - } - - public void setPublicationDates(List publicationDates) { - this.publicationDates = publicationDates; - } - - public List getContributors() { - return contributors; - } - - public void setContributors(List contributors) { - this.contributors = contributors; - } -} From ae7bd24d79ccd30d978f080da3b623f5090a8d5a Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 20 May 2021 18:32:22 +0200 Subject: [PATCH 03/92] removed old workflows --- .../oozie_app/config-default.xml | 31 - .../orcid_activities/oozie_app/workflow.xml | 542 ------------------ .../oozie_app/config-default.xml | 22 - .../oozie_app/workflow.xml | 505 ---------------- .../oozie_app/workflow.xml | 99 ---- .../oozie_app/workflow.xml | 232 -------- .../oozie_app/config-default.xml | 26 - .../oozie_app/workflow.xml | 40 -- .../oozie_app/config-default.xml | 26 - .../orcid_summaries/oozie_app/workflow.xml | 68 --- 10 files changed, 1591 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml deleted file mode 100644 index 05fe6d014f..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - oozie.action.sharelib.for.java - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx2g - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml deleted file mode 100644 index ea4d33296c..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml +++ /dev/null @@ -1,542 +0,0 @@ - - - - workingPath - the working dir base path - - - shell_cmd_0 - wget -O /tmp/ORCID_2020_10_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/25002232 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_0.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_0.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_0.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 0 - - - shell_cmd_1 - wget -O /tmp/ORCID_2020_10_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/25002088 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_1.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_1.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_1.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 1 - - - shell_cmd_2 - wget -O /tmp/ORCID_2020_10_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/25000596 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_2.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_2.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_2.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 2 - - - shell_cmd_3 - wget -O /tmp/ORCID_2020_10_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/25015150 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_3.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_3.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_3.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 3 - - - shell_cmd_4 - wget -O /tmp/ORCID_2020_10_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/25033643 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_4.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_4.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_4.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 4 - - - shell_cmd_5 - wget -O /tmp/ORCID_2020_10_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/25005483 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_5.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_5.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_5.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 5 - - - shell_cmd_6 - wget -O /tmp/ORCID_2020_10_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/25005425 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_6.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_6.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_6.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 6 - - - shell_cmd_7 - wget -O /tmp/ORCID_2020_10_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/25012016 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_7.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_7.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_7.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 7 - - - shell_cmd_8 - wget -O /tmp/ORCID_2020_10_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/25012079 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_8.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_8.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_8.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 8 - - - shell_cmd_9 - wget -O /tmp/ORCID_2020_10_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/25010727 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_9.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_9.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_9.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 9 - - - shell_cmd_X - wget -O /tmp/ORCID_2020_10_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/25011025 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_X.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_X.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_X.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file X - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_0.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_0} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_0.tar.gz - -owno_doi_works/works_0.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_1.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_1} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_1.tar.gz - -owno_doi_works/works_1.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_2.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_2} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_2.tar.gz - -owno_doi_works/works_2.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_3.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_3} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_3.tar.gz - -owno_doi_works/works_3.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_4.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_4} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_4.tar.gz - -owno_doi_works/works_4.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_5.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_5} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_5.tar.gz - -owno_doi_works/works_5.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_6.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_6} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_6.tar.gz - -owno_doi_works/works_6.seq - -oewno_doi_enriched_works/ - - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_7.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_7} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_7.tar.gz - -owno_doi_works/works_7.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_8.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_8} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_8.tar.gz - -owno_doi_works/works_8.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_9.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_9} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_9.tar.gz - -owno_doi_works/works_9.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_X.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_X} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_X.tar.gz - -owno_doi_works/works_X.seq - -oewno_doi_enriched_works/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml deleted file mode 100644 index 5621415d97..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.action.sharelib.for.java - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx4g - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml deleted file mode 100644 index 1c2ae89ddc..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml +++ /dev/null @@ -1,505 +0,0 @@ - - - - workingPath_activities - the working dir base path - - - shell_cmd_0 - wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 0 - - - shell_cmd_1 - wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 1 - - - shell_cmd_2 - wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 2 - - - shell_cmd_3 - wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 3 - - - shell_cmd_4 - wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 4 - - - shell_cmd_5 - wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 5 - - - shell_cmd_6 - wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 6 - - - shell_cmd_7 - wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 7 - - - shell_cmd_8 - wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 8 - - - shell_cmd_9 - wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 9 - - - shell_cmd_X - wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file X - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_0} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_0.tar.gz - -ooutput/authors_dois_0.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_1} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_1.tar.gz - -ooutput/authors_dois_1.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_2} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_2.tar.gz - -ooutput/authors_dois_2.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_3} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_3.tar.gz - -ooutput/authors_dois_3.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_4} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_4.tar.gz - -ooutput/authors_dois_4.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_5} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_5.tar.gz - -ooutput/authors_dois_5.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_6} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_6.tar.gz - -ooutput/authors_dois_6.seq - - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_7} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_7.tar.gz - -ooutput/authors_dois_7.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_8} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_8.tar.gz - -ooutput/authors_dois_8.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_9} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_9.tar.gz - -ooutput/authors_dois_9.seq - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_X} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen - -d${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_X.tar.gz - -ooutput/authors_dois_X.seq - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml deleted file mode 100644 index 133a6f4bd2..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml +++ /dev/null @@ -1,99 +0,0 @@ - - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - spark2MaxExecutors - 20 - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - workingPath - the working dir base path - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - yarn-cluster - cluster - GenDoiAuthorList - eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - -w${workingPath}/ - -aauthors/authors.seq - -xwxml/works/*.seq - -odoi_author_list/ - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml deleted file mode 100644 index 6f629c7540..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml +++ /dev/null @@ -1,232 +0,0 @@ - - - - workingPath - the working dir base path - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.java - ${oozieActionShareLibForSpark2} - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx2g - - - oozie.use.system.libpath - true - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_0.tar.gz - -owxml/works/xml_works_0.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_1.tar.gz - -owxml/works/xml_works_1.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_2.tar.gz - -owxml/works/xml_works_2.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_3.tar.gz - -owxml/works/xml_works_3.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_4.tar.gz - -owxml/works/xml_works_4.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_5.tar.gz - -owxml/works/xml_works_5.seq - -oew--- - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_6.tar.gz - -owxml/works/xml_works_6.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_7.tar.gz - -owxml/works/xml_works_7.seq - -oew--- - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_8.tar.gz - -owxml/works/xml_works_8.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_9.tar.gz - -owxml/works/xml_works_9.seq - -oew--- - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_activites_X.tar.gz - -owxml/works/xml_works_X.seq - -oew--- - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml deleted file mode 100644 index 191654378a..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx8g - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml deleted file mode 100644 index 68d468ab33..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml +++ /dev/null @@ -1,40 +0,0 @@ - - - - workingPath - the working dir base path - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLSummariesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_summaries.tar.gz - -oxml/authors/ - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml deleted file mode 100644 index 191654378a..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx8g - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml deleted file mode 100644 index 8517f35ee0..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - - workingPath - the working dir base path - - - shell_cmd_0 - wget -O /tmp/ORCID_2020_10_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/25032905 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_summaries.tar.gz /data/orcid_activities_2020/ORCID_2020_10_summaries.tar.gz ; rm -f /tmp/ORCID_2020_10_summaries.tar.gz - - the shell command that downloads and puts to hdfs orcid summaries - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2020_10_summaries.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_0} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidDSManager - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_summaries.tar.gz - -oauthors/ - - - - - - - \ No newline at end of file From 1265dadc90686ad9a687a8bf7e20fd739d663ae9 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 20 May 2021 19:01:28 +0200 Subject: [PATCH 04/92] workflow aligned with stable_ids --- .../orcid/SparkDownloadOrcidAuthors.java | 2 +- .../orcidnodoi/oaf/PublicationToOaf.java | 4 +- .../oozie_app/workflow.xml | 42 ------------------- .../orcidnodoi/oozie_app/workflow.xml | 31 ++++++++++---- 4 files changed, 27 insertions(+), 52 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_orcid_no_doi/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java index 36b4b073db..8cf070213c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -62,7 +62,7 @@ public class SparkDownloadOrcidAuthors { isSparkSessionManaged, spark -> { String lastUpdate = HDFSUtil.readFromTextFile(hdfsServerUri, workingPath, "last_update.txt"); - logger.info("lastUpdate: ", lastUpdate); + logger.info("lastUpdate: {}", lastUpdate); if (StringUtils.isBlank(lastUpdate)) { throw new RuntimeException("last update info not found"); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 5c32362223..ccae4d9768 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -174,7 +174,9 @@ public class PublicationToOaf implements Serializable { publication .getExternalReference() .add( - convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types")); + convertExtRef( + extId, classid, classname, ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES)); } }); diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_orcid_no_doi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_orcid_no_doi/oozie_app/workflow.xml deleted file mode 100644 index becdf0974e..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_orcid_no_doi/oozie_app/workflow.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - - inputPath - /data/orcid_activities_2020/no_doi_dataset - path where retrieve the already generated action set - - - outputPath - /data/orcid_activities_2020/test_import_orcid_no_doi - path where to store the action set - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${inputPath}/* - ${outputPath} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 6513ff7e1a..365c4d5b4f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -1,5 +1,15 @@ + + workingPath + /data/orcid_activities_2020 + path where the collection workflow stores the ORCID data + + + outputPath + path where to store the action set + + spark2GenNoDoiDatasetMaxExecutors 40 @@ -35,10 +45,6 @@ spark2EventLogDir spark 2.* event log dir location - - workingPath - the working dir base path - @@ -83,11 +89,20 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - -w${workingPath}/ - -n${nameNode} - -ilast_orcid_dataset - -oewno_doi_dataset + --workingPath${workingPath}/ + --hdfsServerUri${nameNode} + --orcidDataFolderlast_orcid_dataset + --outputEnrichedWorksPathno_doi_dataset + + + + + + + ${workingPath}/no_doi_dataset/* + ${outputPath} + From d0945c3c7817d7081b6fb214b6ec7ee227e3a396 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 20 May 2021 19:14:31 +0200 Subject: [PATCH 05/92] added temporary output folder, because of folder access rights are different on beta and prod --- .../dhp/doiboost/orcidnodoi/oozie_app/workflow.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 365c4d5b4f..68f370a20e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -9,7 +9,10 @@ outputPath path where to store the action set - + + processOutputFolder + temporary path where to store the action set + spark2GenNoDoiDatasetMaxExecutors 40 @@ -66,7 +69,7 @@ - + @@ -92,7 +95,7 @@ --workingPath${workingPath}/ --hdfsServerUri${nameNode} --orcidDataFolderlast_orcid_dataset - --outputEnrichedWorksPathno_doi_dataset + --outputEnrichedWorksPath${processOutputFolder} @@ -100,7 +103,7 @@ - ${workingPath}/no_doi_dataset/* + ${workingPath}/${processOutputFolder}/* ${outputPath} From abdd0ade1fd154cbacedfea928788f600b3ba4a7 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 21 May 2021 12:08:16 +0200 Subject: [PATCH 06/92] added temporary output folder as workflow parameter --- .../eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 68f370a20e..f7ac04821e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -7,10 +7,12 @@ outputPath + /data/orcid_activities_2020/no_doi_dataset_prod/ path where to store the action set processOutputFolder + process_no_doi_dataset_prod temporary path where to store the action set From 783988af06de0efd44ef7b5f0d5578bda7ed9ed9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 11:17:25 +0200 Subject: [PATCH 07/92] depending on dhp-schemas:2.6.14 (release) --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 45e230c4fc..9396eeeb66 100644 --- a/pom.xml +++ b/pom.xml @@ -736,7 +736,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.7.14] + [2.6.14] [4.0.3] [6.0.5] [3.1.6] From 28a66af425a3128d6e3922831a49c954ccc729d6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 11:52:24 +0200 Subject: [PATCH 08/92] updated URL in the issueManagement tag --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 9396eeeb66..19d00d6375 100644 --- a/pom.xml +++ b/pom.xml @@ -25,7 +25,7 @@ Redmine - https://issue.openaire.research-infrastructures.eu/projects/openaire + https://support.openaire.eu/projects/openaire From e0061232e96b8f3b4d20781ba794484366438cb4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 13:41:21 +0200 Subject: [PATCH 09/92] [aggregation] datacite wf: conditional creation of links, optional resume from intermediate phases --- .../datacite/oozie_app/workflow.xml | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml index 036178b37b..3e0c2bba64 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml @@ -13,15 +13,26 @@ 100 The request block size + + exportLinks + false + instructs the transformation phase to produce the links or not + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + ${wf:conf('resumeFrom') eq 'TransformDatacite'} + + + @@ -49,8 +60,7 @@ - - + yarn-cluster cluster @@ -70,7 +80,7 @@ --sourcePath${mainPath}/datacite_dump --targetPath${mainPath}/datacite_oaf --isLookupUrl${isLookupUrl} - --exportLinkstrue + --exportLinks${exportLinks} --masteryarn-cluster From f5486ffb1413031c28c22b9453c9b376a4aaff00 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:07:45 +0200 Subject: [PATCH 10/92] Fixed issues to tests --- .../eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index 7628fb8535..d620c4ef3d 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -61,7 +61,7 @@ class MappingORCIDToOAFTest { assertTrue(oA == p.count()) println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p.first())) - + spark.close() } @@ -78,7 +78,7 @@ class MappingORCIDToOAFTest { val oaf = ORCIDToOAF.convertTOOAF(orcid) assert(oaf.getPid.size() == 1) oaf.getPid.toList.foreach(pid => assert(pid.getQualifier.getClassid.equals("doi"))) - oaf.getPid.toList.foreach(pid => assert(pid.getValue.equals("10.1042/BCJ20160876".toLowerCase()))) + oaf.getPid.toList.foreach(pid => assert(pid.getValue.equals("10.1042/BCJ20160876"))) //println(mapper.writeValueAsString(ORCIDToOAF.convertTOOAF(orcid))) From 2f66fedfec8f393bb5b9b299ae32459c13f856a2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:22:23 +0200 Subject: [PATCH 11/92] changed the logic to verify if a community is contained in the list of context of a result --- .../dhp/oa/graph/dump/community/CommunitySplit.java | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 55f075e954..9e071a3565 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -57,16 +57,13 @@ public class CommunitySplit implements Serializable { Dataset community_products = result .filter((FilterFunction) r -> containsCommunity(r, c)); - try { - community_products.first(); + community_products .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath + "/" + c); - } catch (Exception e) { - } } @@ -75,9 +72,9 @@ public class CommunitySplit implements Serializable { return r .getContext() .stream() - .filter(con -> con.getCode().equals(c)) - .collect(Collectors.toList()) - .size() > 0; + .map(con -> con.getCode()) + .collect(Collectors.toList()) + .contains(c) } return false; } From da88c850c61899e02278fa40b4a9a6fd7d5dacbb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:22:44 +0200 Subject: [PATCH 12/92] changed the logic to verify if a community is contained in the list of context of a result --- .../eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 9e071a3565..088ca1eaa8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -74,7 +74,7 @@ public class CommunitySplit implements Serializable { .stream() .map(con -> con.getCode()) .collect(Collectors.toList()) - .contains(c) + .contains(c); } return false; } From 86e50f7311f9b914a01c0bbd1eaee54b925225ad Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:31:45 +0200 Subject: [PATCH 13/92] modified code to split the Croatian funder --- .../funderresults/SparkDumpFunderResults.java | 31 ++++++++++++++++--- 1 file changed, 26 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 00f604b14b..261fb68bb1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -8,6 +8,7 @@ import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -102,29 +103,49 @@ public class SparkDumpFunderResults implements Serializable { } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } - writeFunderResult(funder, result, outputPath + "/" + funderdump); + writeFunderResult(funder, result, outputPath , funderdump); }); } - private static void writeFunderResult(String funder, Dataset results, String outputPath) { + private static void dumpResults(String nsp, Dataset results, String outputPath, String funderName, String funderDump) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { return null; } for (Project p : r.getProjects()) { - if (p.getId().startsWith(funder)) { + if (p.getId().startsWith(nsp)) { + + if (nsp.equals("40|irb")) { + if (p.getFunder().getShortName().equals(funderName)) + return r; + else + return null; + } return r; } } return null; }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) + .filter((FilterFunction) r -> r!= null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath); + .json(outputPath + "/" + funderDump); } + + private static void writeFunderResult(String funder, Dataset results, String outputPath, + String funderDump) { + + if (funder.equals("40|irb")) { + dumpResults(funder, results, outputPath, "CSF", "HRZZ"); + dumpResults(funder, results, outputPath, "MSES", "MZOS"); + } else + dumpResults(funder, results, outputPath, funderDump, null); + + } + + } From 69fd40fd308a7d9806c7ef801c57782ba91c0d8d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:35:26 +0200 Subject: [PATCH 14/92] modified code to split the Croatian funder --- .../dump/funderresults/SparkDumpFunderResults.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 261fb68bb1..b124b76ce0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -108,7 +108,7 @@ public class SparkDumpFunderResults implements Serializable { } - private static void dumpResults(String nsp, Dataset results, String outputPath, String funderName, String funderDump) { + private static void dumpResults(String nsp, Dataset results, String outputPath, String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { @@ -117,7 +117,7 @@ public class SparkDumpFunderResults implements Serializable { for (Project p : r.getProjects()) { if (p.getId().startsWith(nsp)) { - if (nsp.equals("40|irb")) { + if (nsp.startsWith("40|irb")) { if (p.getFunder().getShortName().equals(funderName)) return r; else @@ -132,18 +132,18 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath + "/" + funderDump); + .json(outputPath + "/" + funderName); } private static void writeFunderResult(String funder, Dataset results, String outputPath, String funderDump) { - if (funder.equals("40|irb")) { - dumpResults(funder, results, outputPath, "CSF", "HRZZ"); - dumpResults(funder, results, outputPath, "MSES", "MZOS"); + if (funder.startsWith("40|irb")) { + dumpResults(funder, results, outputPath, "HRZZ"); + dumpResults(funder, results, outputPath, "MZOS"); } else - dumpResults(funder, results, outputPath, funderDump, null); + dumpResults(funder, results, outputPath, funderDump); } From 87a6e2b967bd27a1e3a226b18e315b7a203a8bbc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:38:28 +0200 Subject: [PATCH 15/92] extended test class --- .../dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 71bf5d9421..eefb0b9cbe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -137,5 +137,11 @@ public class SplitPerFunderTest { .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); + // MZOS 1 + tmp = sc + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + } } From 4b432fbee8293f57afa3bc75d4d7416315bafcc0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 14:40:39 +0200 Subject: [PATCH 16/92] extended test class --- .../dhp/oa/graph/dump/funderresource/extendeddump/relation | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation index 3ed91f4513..f886784376 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation @@ -5,4 +5,5 @@ 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GmbH"},"relevantdate":[{"dataInfo":null,"qualifier":{"classid":"created","classname":"created","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"value":"2017-03-26T10:09:50Z"},{"dataInfo":null,"qualifier":{"classid":"published-print","classname":"published-print","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"value":"1866-01-01"}],"resourcetype":{"classid":"Other","classname":"Other","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":null,"value":"Crossref"},{"dataInfo":null,"value":null}],"subject":[{"dataInfo":null,"qualifier":{"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Theology"},{"dataInfo":null,"qualifier":{"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"History"},{"dataInfo":null,"qualifier":{"classid":"keywords","classname":"keywords","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Art history"}],"title":[{"dataInfo":null,"qualifier":{"classid":"alternative title","classname":"alternative title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"XIV. Die wörter άγαλμα, είχών, ξόανον, ανδρuις und verwandte, in ihren verschiedenen beziehungen. Nach Pausanias"},{"dataInfo":null,"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"xiv die worter άγαλμα eίχών ξόανον ανδρuις und verwandte in ihren verschiedenen beziehungen nach pausanias"}],"journal":{"conferencedate":null,"conferenceplace":null,"dataInfo":null,"edition":null,"ep":null,"iss":null,"issnLinking":null,"issnOnline":"2196-7008","issnPrinted":"0031-7985","name":"Philologus","sp":null,"vol":"24"}} \ No newline at end of file From 6410ab71d8bf6f936503ad760f0a00e040fae80f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:13:58 +0200 Subject: [PATCH 18/92] added APC in the dump and test method --- .../dhp/oa/graph/dump/ResultMapper.java | 8 +++ .../dhp/oa/graph/dump/DumpJobTest.java | 54 +++++++++++++++++++ 2 files changed, 62 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index d30b3122c0..1a4e7c42a9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -423,6 +423,14 @@ public class ResultMapper implements Serializable { .ofNullable(i.getInstancetype()) .ifPresent(value -> instance.setType(value.getClassname())); Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); + Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); + if (oPca.isPresent() && oPcc.isPresent()) { + APC apc = new APC(); + apc.setCurrency(oPcc.get().getValue()); + apc.setAmount(oPca.get().getValue()); + instance.setArticleprocessingcharge(apc); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 7c69c9635f..f0842c8445 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -13,6 +13,7 @@ import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.slf4j.Logger; @@ -408,4 +409,57 @@ public class DumpJobTest { } + @Test + public void testArticlePCA() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(23, verificationDataset.count()); + //verificationDataset.show(false); + + Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); + + verificationDataset.createOrReplaceTempView("check"); + + org.apache.spark.sql.Dataset temp = spark.sql("select id " + + "from check " + + "lateral view explode (instance) i as inst " + + "where inst.articleprocessingcharge is not null"); + + Assertions.assertTrue(temp.count() == 2); + + Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); + + Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); + + + +// verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset +// .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") +// .count() + +//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + } + } From 13c66e16be2ce8503ffe48c002adee17637ab2e5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:15:27 +0200 Subject: [PATCH 19/92] changed logic to split for communities --- .../graph/dump/community/CommunitySplit.java | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 088ca1eaa8..ec16a65e0d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -57,13 +57,11 @@ public class CommunitySplit implements Serializable { Dataset community_products = result .filter((FilterFunction) r -> containsCommunity(r, c)); - - community_products - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/" + c); - + community_products + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath + "/" + c); } @@ -72,9 +70,9 @@ public class CommunitySplit implements Serializable { return r .getContext() .stream() - .map(con -> con.getCode()) - .collect(Collectors.toList()) - .contains(c); + .map(con -> con.getCode()) + .collect(Collectors.toList()) + .contains(c); } return false; } From 9a58f1b93ddc0b68415452772cf7f5f167fa0c46 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:20:39 +0200 Subject: [PATCH 20/92] added logic to select only the valid relations: those not deletedbyinference and having both part of the relation as entities in the graph --- .../SparkSelectValidRelationsJob.java | 127 ++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java new file mode 100644 index 0000000000..fdd545ff72 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -0,0 +1,127 @@ +package eu.dnetlib.dhp.oa.graph.dump.complete; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.oaf.*; + +public class SparkSelectValidRelationsJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkSelectValidRelationsJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + selectValidRelation(spark, inputPath, outputPath); + + }); + + } + + private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { + Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); + Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); + Dataset dataset = Utils + .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); + Dataset other = Utils + .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); + Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); + Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); + Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); + + relation.createOrReplaceTempView("relation"); + publication.createOrReplaceTempView("publication"); + dataset.createOrReplaceTempView("dataset"); + other.createOrReplaceTempView("other"); + software.createOrReplaceTempView("software"); + organization.createOrReplaceTempView("organization"); + project.createOrReplaceTempView("project"); + datasource.createOrReplaceTempView("datasource"); + + spark + .sql( + "SELECT id " + + "FROM publication " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM dataset " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM other " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM software " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM organization " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM project " + + "UNION ALL " + + "SELECT id " + + "FROM datasource ") + .createOrReplaceTempView("identifiers"); + + spark + .sql( + "SELECT relation.* " + + "FROM relation " + + "JOIN identifiers i1 " + + "ON source = i1.id " + + "JOIN identifiers i2 " + + "ON target = i2.id " + + "WHERE datainfo.deletedbyinference = false") + .as(Encoders.bean(Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + ; + + } +} \ No newline at end of file From 39b1a6edf6fae8c2be7d0f5a604e9f05135fba55 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:23:09 +0200 Subject: [PATCH 21/92] added test class for the selection of valid relations and description --- .../SparkSelectValidRelationsJob.java | 8 ++ .../dump/complete/SelectRelationTest.java | 99 +++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java index fdd545ff72..8b477b34d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -18,6 +18,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.oaf.*; +/** + * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference + * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. + * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists + * with this view for both the source and the target + */ + + public class SparkSelectValidRelationsJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java new file mode 100644 index 0000000000..248bd72568 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java @@ -0,0 +1,99 @@ +package eu.dnetlib.dhp.oa.graph.dump.complete; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Relation; +import net.sf.saxon.expr.instruct.ForEach; + +public class SelectRelationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(SelectRelationTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SelectRelationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SelectRelationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SelectRelationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") + .getPath(); + + SparkSelectValidRelationsJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); + + Assertions.assertTrue(verificationDataset.count() == 7); + + } + +} \ No newline at end of file From 8429aed6c61294f00c3a874f6b9c90c4688189df Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:49:38 +0200 Subject: [PATCH 22/92] Added resource for testing selection of valid relations --- .../dhp/oa/graph/dump/selectrelations/dataset | 10 ++++++++++ .../oa/graph/dump/selectrelations/datasource | 7 +++++++ .../graph/dump/selectrelations/organization | 19 +++++++++++++++++++ .../dump/selectrelations/otherresearchproduct | 3 +++ .../dhp/oa/graph/dump/selectrelations/project | 12 ++++++++++++ .../oa/graph/dump/selectrelations/publication | 9 +++++++++ .../oa/graph/dump/selectrelations/relation | 15 +++++++++++++++ .../oa/graph/dump/selectrelations/software | 6 ++++++ 8 files changed, 81 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/dataset create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/datasource create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/organization create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/relation create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/software diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/dataset b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/dataset new file mode 100644 index 0000000000..2b62b5f0d0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/selectrelations/dataset @@ -0,0 +1,10 @@ +{"author":[{"affiliation":[],"fullname":"Kooi, M.","name":"M.","pid":[],"rank":1,"surname":"Kooi"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for Community - 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\ No newline at end of file From e9a17ec8997099eaf391f30f00bc0fe4c8c95e61 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 15:53:35 +0200 Subject: [PATCH 23/92] added check to verify not to add void APC --- .../eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 1a4e7c42a9..47baee30d4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -426,10 +426,15 @@ public class ResultMapper implements Serializable { Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); if (oPca.isPresent() && oPcc.isPresent()) { - APC apc = new APC(); - apc.setCurrency(oPcc.get().getValue()); - apc.setAmount(oPca.get().getValue()); - instance.setArticleprocessingcharge(apc); + Field pca = oPca.get(); + Field pcc = oPcc.get(); + if(!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")){ + APC apc = new APC(); + apc.setCurrency(oPcc.get().getValue()); + apc.setAmount(oPca.get().getValue()); + instance.setArticleprocessingcharge(apc); + } + } } From f13e11e3f761c2835695ec21e698d99c454249d5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 16:04:02 +0200 Subject: [PATCH 24/92] [aggregation] datacite wf: defined parameter declaring the path used to store the OAF objects produced by the transformation phase --- .../dhp/actionmanager/datacite/oozie_app/workflow.xml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml index 3e0c2bba64..69fc959578 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml @@ -4,6 +4,10 @@ mainPath the working path of Datacite stores + + oafTargetPath + the target path where the OAF records are stored + isLookupUrl The IS lookUp service endopoint @@ -56,7 +60,7 @@ --masteryarn-cluster --blocksize${blocksize} - + @@ -78,7 +82,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${mainPath}/datacite_dump - --targetPath${mainPath}/datacite_oaf + --targetPath${oafTargetPath} --isLookupUrl${isLookupUrl} --exportLinks${exportLinks} --masteryarn-cluster From 5295d106914ca9bbe4e0b34e9689f5dcd45b0159 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 16:11:46 +0200 Subject: [PATCH 25/92] added check not to dump deletedByInference entities --- .../dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java | 3 +++ .../oa/graph/dump/complete/SparkSelectValidRelationsJob.java | 4 +++- .../dump/complete/DumpOrganizationProjectDatasourceTest.java | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 36ced3a4ab..530f7a003f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -453,6 +453,7 @@ public class DumpGraphEntities implements Serializable { .map( (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class)) + .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") @@ -460,6 +461,8 @@ public class DumpGraphEntities implements Serializable { } private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + if(org.getDataInfo().getDeletedbyinference()) + return null; Organization organization = new Organization(); Optional diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java index 8b477b34d6..77402ea1b9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -110,9 +110,11 @@ public class SparkSelectValidRelationsJob implements Serializable { "UNION ALL " + "SELECT id " + "FROM project " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + "UNION ALL " + "SELECT id " + - "FROM datasource ") + "FROM datasource " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " ) .createOrReplaceTempView("identifiers"); spark diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 69100a114e..89ecdfb2b4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -88,7 +88,7 @@ public class DumpOrganizationProjectDatasourceTest { org.apache.spark.sql.Dataset verificationDataset = spark .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - Assertions.assertEquals(34, verificationDataset.count()); + Assertions.assertEquals(15, verificationDataset.count()); verificationDataset .foreach( From 72397ea1ba4c03f306f49d5e2fe522f0503deb05 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 16:18:35 +0200 Subject: [PATCH 26/92] Added fix for community of arbitrary name length --- .../main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index d20a3036e8..f5b8f1c768 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -89,7 +89,7 @@ public class DumpProducts implements Serializable { return c.getId(); } if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, 3); + return c.getId().substring(0, c.getId().indexOf("::")); } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); From 8f322a73cba044338329eecfc00cfa38bf5eaeca Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 16:22:58 +0200 Subject: [PATCH 27/92] change because of the renaming of originalId in acronym --- .../java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java index 31d105b66f..a6757d18d4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java @@ -35,7 +35,7 @@ public class Process implements Serializable { ri.setType(Constants.RESEARCH_INFRASTRUCTURE); } ri.setId(Utils.getContextId(ci.getId())); - ri.setOriginalId(ci.getId()); + ri.setAcronym(ci.getId()); ri.setDescription(ci.getDescription()); ri.setName(ci.getName()); From fa720c1da44c78ea08784a32c44b71a3899f349f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 16:59:30 +0200 Subject: [PATCH 28/92] [doiboost] added workflow for the ActionSet update dedicated to production --- .../process/oozie_app/config-default.xml | 42 +++ .../doiboost/process/oozie_app/workflow.xml | 259 ++++++++++++++++++ 2 files changed, 301 insertions(+) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/config-default.xml new file mode 100644 index 0000000000..508202e301 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml new file mode 100644 index 0000000000..cf1cd97f7a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -0,0 +1,259 @@ + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorIntersectionMemory + memory for individual executor + + + + sparkExecutorCores + number of cores used by single executor + + + + workingPath + the working Path + + + + hostedByMapPath + the hostedByMap Path + + + outputPath + the Path of the sequence file action set + + + + + + inputPathCrossref + the Crossref input path + + + + + inputPathMAG + the MAG working path + + + + + + inputPathUnpayWall + the UnpayWall working path + + + + + workingPathOrcid + the ORCID working path + + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + ${wf:conf('resumeFrom') eq 'PreprocessMag'} + ${wf:conf('resumeFrom') eq 'PreprocessUW'} + ${wf:conf('resumeFrom') eq 'ProcessORCID'} + ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} + ${wf:conf('resumeFrom') eq 'GenerateActionSet'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + ConvertCrossrefToOAF + eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${inputPathCrossref}/crossref_ds + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + yarn-cluster + cluster + Convert Mag to OAF Dataset + eu.dnetlib.doiboost.mag.SparkProcessMAG + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorIntersectionMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${inputPathMAG}/dataset + --workingPath${inputPathMAG}/process_p + --targetPath${workingPath} + --masteryarn-cluster + + + + + + + + + + yarn-cluster + cluster + Convert UnpayWall to Dataset + eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${inputPathUnpayWall}/uw_extracted + --targetPath${workingPath}/uwPublication + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --workingPath${workingPathOrcid} + --targetPath${workingPath}/orcidPublication + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Create DOIBoost Infospace + eu.dnetlib.doiboost.SparkGenerateDoiBoost + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorIntersectionMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --hostedByMapPath${hostedByMapPath} + --affiliationPath${inputPathMAG}/dataset/Affiliations + --paperAffiliationPath${inputPathMAG}/dataset/PaperAuthorAffiliations + --workingPath${workingPath} + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Generate DOIBoost ActionSet + eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --dbPublicationPath${workingPath}/doiBoostPublicationFiltered + --dbDatasetPath${workingPath}/crossrefDataset + --crossRefRelation${workingPath}/crossrefRelation + --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation + --dbOrganizationPath${workingPath}/doiBoostOrganization + --targetPath${workingPath}/actionDataSet + --sFilePath${outputPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file From 084b4ef999eccd94a2c16eaffb372c2cf87c6950 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:07:46 +0200 Subject: [PATCH 29/92] added the creation of the openaireId from funder and grant number if the element is not present in the context profile --- .../dump/complete/QueryInformationSystem.java | 68 +++++++++++++++++-- 1 file changed, 63 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index c33a693a54..7a69c1a0dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -14,6 +14,7 @@ import org.jetbrains.annotations.NotNull; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.dhp.utils.DHPUtils; public class QueryInformationSystem { @@ -113,14 +114,71 @@ public class QueryInformationSystem { @NotNull private List getCategoryList(Element el, String prefix) { List datasourceList = new ArrayList<>(); - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - if (n.valueOf("./@name").equals("openaireId")) { - datasourceList.add(prefix + "|" + n.getText()); - } + for (Object node : el.selectNodes(".//concept")) { + String oid = getOpenaireId((Node) node, prefix); + if (oid != null) + datasourceList.add(oid); } return datasourceList; } + private String getOpenaireId(Node el, String prefix) { + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + if (n.valueOf("./@name").equals("openaireId")) { + return prefix + "|" + n.getText(); + } + } + + return makeOpenaireId(el, prefix); + + } + + private String makeOpenaireId(Node el, String prefix) { + String funder = null; + String grantId = null; + String funding = null; + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + switch (n.valueOf("./@name")) { + case "funding": + funding = n.getText(); + break; + case "funder": + funder = n.getText(); + break; + case "CD_PROJECT_NUMBER": + grantId = n.getText(); + break; + } + } + String nsp = null; + switch (funder.toLowerCase()) { + case "ec": + if (funding == null) { + return null; + } + if (funding.toLowerCase().startsWith("h2020")) { + nsp = "corda__h2020::"; + } else { + nsp = "corda_______::"; + } + break; + case "tubitak": + nsp = "tubitakf____::"; + break; + case "dfg": + nsp = "dfgf________::"; + break; + default: + nsp = funder.toLowerCase(); + for (int i = funder.length(); i < 12; i++) + nsp += "_"; + nsp += "::"; + } + + return prefix + "|" + nsp + DHPUtils.md5(grantId); + } + } From 59615da65e1a6984e82d23dff5b860800d5939f6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:09:15 +0200 Subject: [PATCH 30/92] Add test to verify the creation of relation between context and projects --- .../dump/complete/CreateRelationTest.java | 152 +++++++++++++++++- 1 file changed, 150 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java index b556fa2d66..5f21e0bc5a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; + +import eu.dnetlib.dhp.schema.oaf.Project; import java.util.*; import java.util.function.Consumer; import java.util.stream.Collectors; @@ -203,6 +205,7 @@ public class CreateRelationTest { " \n" + " oac_ni\n" + " 2018-03-01T12:00:00\n" + + " \n" + " \n" + " \n" + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + @@ -437,8 +440,58 @@ public class CreateRelationTest { " \n" + " oaa_elixir-gr\n" + " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + " \n" + + " \n" + + " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" + + " \n" + + " 1U24RR025736-01\n" + + " NIH\n" + + " \n" + + " \n" + + " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" + + " \n" + + " 0223843\n" + + " NSF\n" + + " \n" + + " \n" + + " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" + + " \n" + + " 5R01MH082795-05\n" + + " NIH\n" + + " \n" + + " \n" + + " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" + + " \n" + + " 1P50MH096889-01A1\n" + + " NIH\n" + + " \n" + + " \n" + + " Enhancement of the 1000 Functional Connectome Project\n" + + " \n" + + " 1R03MH096321-01A1\n" + + " TUBITAK\n" + + " \n" + + " \n" + + " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" + + " \n" + + " 1131441\n" + + " NSF\n" + + " \n" + + " \n" + + " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" + + " \n" + + " 0121950\n" + + " NSF\n" + + " \n" + + " \n" + + " Transforming statistical methodology for neuroimaging meta-analysis.\n" + + " \n" + + " 100309\n" + + " WT\n" + + " \n" + + " " + + + " \n" + " \n" + " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + @@ -566,4 +619,99 @@ public class CreateRelationTest { tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); } + + @Test + public void test2() { + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + + queryInformationSystem + .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); + + cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); + + + List rList = new ArrayList<>(); + + cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); + + Assertions.assertEquals(44 , rList.size()); + + Assertions + .assertFalse( + rList + .stream() + .map(r -> r.getSource().getId()) + .collect(Collectors.toSet()) + .contains( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getTarget() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Set tmp = rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .map(r -> r.getTarget().getId()) + .collect(Collectors.toSet()); + + Assertions + .assertTrue( + tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && + tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4") ); + + rList.forEach(rel -> { + if (rel.getSource().getId().startsWith("40|")){ + String proj = rel.getSource().getId().substring(3); + Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); + } + }); + + } } From 618d2de2da0b9749b5eca6097faee25706d08956 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:10:02 +0200 Subject: [PATCH 31/92] minor changes and refactoring --- .../dhp/oa/graph/dump/ResultMapper.java | 2 +- .../dump/complete/CreateContextRelation.java | 8 +- .../dump/complete/DumpGraphEntities.java | 4 +- .../dhp/oa/graph/dump/complete/Extractor.java | 4 +- .../SparkSelectValidRelationsJob.java | 188 +++++++++--------- .../dhp/oa/graph/dump/DumpJobTest.java | 36 ++-- .../graph/dump/complete/CreateEntityTest.java | 10 +- .../dump/complete/SelectRelationTest.java | 99 ++++----- 8 files changed, 176 insertions(+), 175 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 47baee30d4..fe9b4e443d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -428,7 +428,7 @@ public class ResultMapper implements Serializable { if (oPca.isPresent() && oPcc.isPresent()) { Field pca = oPca.get(); Field pcc = oPcc.get(); - if(!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")){ + if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { APC apc = new APC(); apc.setCurrency(oPcc.get().getValue()); apc.setAmount(oPca.get().getValue()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java index 102406315b..59f660525f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java @@ -70,10 +70,10 @@ public class CreateContextRelation implements Serializable { cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); log.info("Creating relations for projects... "); -// cce -// .execute( -// Process::getRelation, CONTEX_RELATION_PROJECT, -// ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); + cce + .execute( + Process::getRelation, CONTEX_RELATION_PROJECT, + ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); cce.close(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 530f7a003f..b843ec3657 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -453,7 +453,7 @@ public class DumpGraphEntities implements Serializable { .map( (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") @@ -461,7 +461,7 @@ public class DumpGraphEntities implements Serializable { } private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { - if(org.getDataInfo().getDeletedbyinference()) + if (org.getDataInfo().getDeletedbyinference()) return null; Organization organization = new Organization(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index 31886d1b13..f76f920137 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -129,7 +129,7 @@ public class Extractor implements Serializable { return relationList.iterator(); }, Encoders.bean(Relation.class)) - .write() + .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath); @@ -147,7 +147,7 @@ public class Extractor implements Serializable { .map( paction -> Provenance .newInstance( - paction.getClassid(), + paction.getClassname(), dinfo.getTrust())) .orElse( Provenance diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java index 77402ea1b9..e729e13dfa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.oa.graph.dump.complete; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; @@ -25,113 +26,112 @@ import eu.dnetlib.dhp.schema.oaf.*; * with this view for both the source and the target */ - public class SparkSelectValidRelationsJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); + private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelationsJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkSelectValidRelationsJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); + SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - selectValidRelation(spark, inputPath, outputPath); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + selectValidRelation(spark, inputPath, outputPath); - }); + }); - } + } - private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { - Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); - Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); - Dataset dataset = Utils - .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); - Dataset other = Utils - .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); - Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); - Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); - Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); + private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { + Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); + Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); + Dataset dataset = Utils + .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); + Dataset other = Utils + .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); + Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); + Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); + Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); - relation.createOrReplaceTempView("relation"); - publication.createOrReplaceTempView("publication"); - dataset.createOrReplaceTempView("dataset"); - other.createOrReplaceTempView("other"); - software.createOrReplaceTempView("software"); - organization.createOrReplaceTempView("organization"); - project.createOrReplaceTempView("project"); - datasource.createOrReplaceTempView("datasource"); + relation.createOrReplaceTempView("relation"); + publication.createOrReplaceTempView("publication"); + dataset.createOrReplaceTempView("dataset"); + other.createOrReplaceTempView("other"); + software.createOrReplaceTempView("software"); + organization.createOrReplaceTempView("organization"); + project.createOrReplaceTempView("project"); + datasource.createOrReplaceTempView("datasource"); - spark - .sql( - "SELECT id " + - "FROM publication " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM dataset " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM other " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM software " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM organization " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM project " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM datasource " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " ) - .createOrReplaceTempView("identifiers"); + spark + .sql( + "SELECT id " + + "FROM publication " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM dataset " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM other " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM software " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM organization " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM project " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM datasource " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ") + .createOrReplaceTempView("identifiers"); - spark - .sql( - "SELECT relation.* " + - "FROM relation " + - "JOIN identifiers i1 " + - "ON source = i1.id " + - "JOIN identifiers i2 " + - "ON target = i2.id " + - "WHERE datainfo.deletedbyinference = false") - .as(Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - ; + spark + .sql( + "SELECT relation.* " + + "FROM relation " + + "JOIN identifiers i1 " + + "ON source = i1.id " + + "JOIN identifiers i2 " + + "ON target = i2.id " + + "WHERE datainfo.deletedbyinference = false") + .as(Encoders.bean(Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + ; - } -} \ No newline at end of file + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index f0842c8445..6b64a4124d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -412,40 +412,42 @@ public class DumpJobTest { @Test public void testArticlePCA() { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(23, verificationDataset.count()); - //verificationDataset.show(false); + // verificationDataset.show(false); Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); verificationDataset.createOrReplaceTempView("check"); - org.apache.spark.sql.Dataset temp = spark.sql("select id " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); + org.apache.spark.sql.Dataset temp = spark + .sql( + "select id " + + "from check " + + "lateral view explode (instance) i as inst " + + "where inst.articleprocessingcharge is not null"); Assertions.assertTrue(temp.count() == 2); @@ -453,8 +455,6 @@ public class DumpJobTest { Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - - // verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset // .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") // .count() diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java index 3ecbd18943..679c093936 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java @@ -97,7 +97,7 @@ public class CreateEntityTest { Assertions.assertEquals(12, riList.size()); riList.stream().forEach(c -> { - switch (c.getOriginalId()) { + switch (c.getAcronym()) { case "mes": Assertions .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY)); @@ -115,9 +115,9 @@ public class CreateEntityTest { String .format( "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getOriginalId())))); + DHPUtils.md5(c.getAcronym())))); Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes")); - Assertions.assertTrue("mes".equals(c.getOriginalId())); + Assertions.assertTrue("mes".equals(c.getAcronym())); break; case "clarin": Assertions @@ -130,9 +130,9 @@ public class CreateEntityTest { String .format( "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getOriginalId())))); + DHPUtils.md5(c.getAcronym())))); Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin")); - Assertions.assertTrue("clarin".equals(c.getOriginalId())); + Assertions.assertTrue("clarin".equals(c.getAcronym())); break; } // TODO add check for all the others Entities diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java index 248bd72568..3e4ab93c55 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.oa.graph.dump.complete; import java.io.IOException; @@ -28,72 +29,72 @@ import net.sf.saxon.expr.instruct.ForEach; public class SelectRelationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(SelectRelationTest.class); + private static final Logger log = LoggerFactory + .getLogger(SelectRelationTest.class); - private static HashMap map = new HashMap<>(); + private static HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SelectRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SelectRelationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(SelectRelationTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(SelectRelationTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(SelectRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(SelectRelationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void test1() throws Exception { + @Test + public void test1() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") - .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") + .getPath(); - SparkSelectValidRelationsJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); + SparkSelectValidRelationsJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); // dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); - Assertions.assertTrue(verificationDataset.count() == 7); + Assertions.assertTrue(verificationDataset.count() == 7); - } + } -} \ No newline at end of file +} From d418c309f57518a7e1d25fb45c36b145b4dac902 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:11:49 +0200 Subject: [PATCH 32/92] removed the part after part-x- in the file name generated by spark. It was too long and created problems while creating the tar entries --- .../main/java/eu/dnetlib/dhp/common/MakeTarArchive.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index 7dc0e44177..518dfefe09 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -90,6 +90,13 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); + if (name.startsWith("part-") & name.length() > 10) { + String tmp = name.substring(0, 10); + if (name.contains(".")) { + tmp += name.substring(name.indexOf(".")); + } + name = tmp; + } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); From 734de62474089e7111debe5b39be0b1da05c8a43 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 13 Jul 2021 17:26:04 +0200 Subject: [PATCH 33/92] [doiboost] added workflow for the ActionSet update dedicated to production --- .../eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index cf1cd97f7a..f845d97f30 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -106,8 +106,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${inputPathCrossref}/crossref_ds - --targetPath${workingPath} + --targetPath${workingPath} --masteryarn-cluster @@ -195,8 +194,7 @@ - + yarn-cluster cluster From 5e38c7f42da63cd2be6078ea1b443eecf5944fb2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:32:38 +0200 Subject: [PATCH 34/92] dumping only communities with status all --- .../eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index d118accbae..fe40369250 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -20,7 +20,7 @@ public class QueryInformationSystem { private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + From d70f8c96fdb6bde8b5b2e1e4fb74a86beae80276 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 17:34:53 +0200 Subject: [PATCH 35/92] funding contains and not starts with h2020 --- .../dhp/oa/graph/dump/complete/QueryInformationSystem.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 7a69c1a0dc..3736b73807 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -159,7 +159,7 @@ public class QueryInformationSystem { if (funding == null) { return null; } - if (funding.toLowerCase().startsWith("h2020")) { + if (funding.toLowerCase().contains("h2020")) { nsp = "corda__h2020::"; } else { nsp = "corda_______::"; From c028feef4f5664002a8733bfac072a6652889d93 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:06:44 +0200 Subject: [PATCH 36/92] workflow for the dump as sub workflows --- .../dump/wf/main/oozie_app/config-default.xml | 30 + .../graph/dump/wf/main/oozie_app/import.txt | 4 + .../graph/dump/wf/main/oozie_app/workflow.xml | 306 ++++++++++ .../oozie_app/config-default.xml | 30 + .../oozie_app/workflow.xml | 347 +++++++++++ .../community/oozie_app/config-default.xml | 30 + .../community/oozie_app/import.txt | 2 + .../community/oozie_app/workflow.xml | 145 +++++ .../complete/oozie_app/config-default.xml | 30 + .../complete/oozie_app/workflow.xml | 537 ++++++++++++++++++ .../funder/oozie_app/config-default.xml | 0 .../subworkflows/funder/oozie_app/import.txt | 2 + .../funder/oozie_app/workflow.xml | 256 +++++++++ 13 files changed, 1719 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml new file mode 100644 index 0000000000..d262cb6e05 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt new file mode 100644 index 0000000000..bf55947d14 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt @@ -0,0 +1,4 @@ +## This is a classpath-based import file (this header is required) +dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app +dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app +dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml new file mode 100644 index 0000000000..2a612dec59 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml @@ -0,0 +1,306 @@ + + + + + singleDeposition + Indicates if it is a single community deposition + + + communityId + the id of the community to be dumped if a dump for a single community should be done + + + dumpType + the type of the dump one of {complete, community, funder} + + + onlyUpload + true if the dump is already done and should only be upload in zenodo + + + upload + true if the dump should be upload in zenodo + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:conf('onlyUpload') eq true} + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + --singleDeposition${singleDeposition} + --communityId${communityId} + + + + + + + + ${wf:conf('dumpType') eq "funder"} + ${wf:conf('dumpType') eq "community"} + + + + + + + + ${wf:appPath()}/dump_complete + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + organizationCommunityMap + ${organizationCommunityMap} + + + isLookUpUrl + ${isLookUpUrl} + + + resultAggregation + ${resultAggregation} + + + + + + + + + + + ${wf:appPath()}/dump_community + + + + + sourcePath + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + + + + + + + + ${wf:appPath()}/dump_funder + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + dumpType + ${dumpType} + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + + ${wf:conf('upload') eq true} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml new file mode 100644 index 0000000000..5f954ff38a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml @@ -0,0 +1,347 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + communityMapPath + the path to the community map + + + selectedResults + the path the the possible subset ot results to be dumped + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt new file mode 100644 index 0000000000..15387e988d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml new file mode 100644 index 0000000000..319517026a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + + + yarn + cluster + Split dumped result for community + eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --communityMapPath${communityMapPath} + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml new file mode 100644 index 0000000000..f84ab7e1ad --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -0,0 +1,537 @@ + + + + sourcePath + the source path + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table organization + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/organization + --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization + --outputPath${outputPath}/organization + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${outputPath}/project + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table datasource + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/datasource + --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputPath${outputPath}/datasource + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Select valid table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/validrelation + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/validrelation + --outputPath${workingDir}/relation/relation + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities + --hdfsPath${outputPath}/communities_infrastructures/communities_infrastructure.json.gz + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation + --hdfsPath${workingDir}/relation/context + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/relation/contextOrg + --organizationCommunityMap${organizationCommunityMap} + --communityMapPath${communityMapPath} + + + + + + + + + + + + + + + + + yarn + cluster + Extract Relations from publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/relation/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/relation/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/relation/orp + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/relation/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Collect Results and Relations and put them in the right path + eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir} + --outputPath${outputPath} + --resultAggregation${resultAggregation} + + + + + + + + + Sub-workflow dump complete failed with error message ${wf:errorMessage()} + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt new file mode 100644 index 0000000000..15387e988d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml new file mode 100644 index 0000000000..b990f4e49b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -0,0 +1,256 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --graphPath${sourcePath} + + + + + + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${workingDir}/result + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --graphPath${sourcePath} + + + + + + + + + \ No newline at end of file From eae10c58943a6c0d7797facb69531dc442ae5b30 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:07:25 +0200 Subject: [PATCH 37/92] modification to allow the dump for a single community --- .../oa/graph/dump/QueryInformationSystem.java | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index fe40369250..d1f295fcf6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -17,7 +17,7 @@ public class QueryInformationSystem { private ISLookUpService isLookUp; - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + " and ($x//context/param[./@name = 'status']/text() = 'all') " @@ -28,9 +28,22 @@ public class QueryInformationSystem { "{$x//CONFIGURATION/context/@label}" + ""; - public CommunityMap getCommunityMap() + private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//CONFIGURATION/context[./@id=%s] " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + public CommunityMap getCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, DocumentException { - return getMap(isLookUp.quickSearchProfile(XQUERY)); + if (singleCommunity) + return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + community_id + "'"))); + return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); } From 970b387b8dfa34592bbbf2f62c8ec1eae27d272e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:08:10 +0200 Subject: [PATCH 38/92] modification to allow dump of a single community --- .../dhp/oa/graph/dump/SaveCommunityMap.java | 21 ++++++++++++------- .../oa/graph/dump/input_cm_parameters.json | 14 ++++++++++++- 2 files changed, 26 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 6ac626518c..7db19f7719 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -1,4 +1,3 @@ - package eu.dnetlib.dhp.oa.graph.dump; import java.io.BufferedWriter; @@ -6,6 +5,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.Serializable; import java.nio.charset.StandardCharsets; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; @@ -54,10 +54,10 @@ public class SaveCommunityMap implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SaveCommunityMap.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); + .toString( + SaveCommunityMap.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -71,14 +71,19 @@ public class SaveCommunityMap implements Serializable { final String isLookUpUrl = parser.get("isLookUpUrl"); log.info("isLookUpUrl: {}", isLookUpUrl); + final Boolean singleCommunity = Optional.ofNullable(parser.get("singleDeposition")) + .map(Boolean::valueOf).orElse(false); + + final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); + final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); - scm.saveCommunityMap(); + scm.saveCommunityMap(singleCommunity, community_id); } - private void saveCommunityMap() throws ISLookUpException, IOException, DocumentException { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap())); + private void saveCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, IOException, DocumentException { + writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); writer.close(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json index 6e42bfa643..8062205101 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json @@ -18,7 +18,19 @@ "paramLongName": "outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true - } + }, + { + "paramName": "sd", + "paramLongName": "singleDeposition", + "paramDescription": "true if the dump should be created for a single community", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "communityId", + "paramDescription": "the id of the community for which to create the dump", + "paramRequired": true + } } ] From 52ce35d57b7c3e4b28996f2147182cf93099f969 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:08:46 +0200 Subject: [PATCH 39/92] - --- .../eu/dnetlib/dhp/oa/graph/dump/input_parameters.json | 7 ++++++- .../eu/dnetlib/dhp/oa/graph/dump/split_parameters.json | 7 ++++++- .../eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json | 7 +------ 3 files changed, 13 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index 1d986fc261..e86f6e3d25 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -35,7 +35,12 @@ "paramLongName":"dumpType", "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", "paramRequired": false - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json index 29812188a5..dec82bc973 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json @@ -25,7 +25,12 @@ "paramLongName": "isSparkSessionManaged", "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json index 683b6f4b73..b02062ede7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json @@ -12,12 +12,7 @@ "paramDescription": "The id of the concept record for a new version", "paramRequired": false }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": false - }, + { "paramName":"di", "paramLongName":"depositionId", From 320cf02d967f86aa7f2971d5bb81aef714621d13 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:13:32 +0200 Subject: [PATCH 40/92] Changed the way to find results linked to projects. We verify to actually have the project on the graph before selecting the result --- .../SparkResultLinkedToProject.java | 35 +++++++++---------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 1a28a21f43..9c4c73d851 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -24,7 +24,8 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; - +import org.apache.spark.sql.*; +import eu.dnetlib.dhp.schema.oaf.Project; /** * Selects the results linked to projects. Only for these results the dump will be performed. * The code to perform the dump and to expend the dumped results with the informaiton related to projects @@ -59,8 +60,8 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("graphPath: {}", graphPath); Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); @@ -70,34 +71,32 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); }); } private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + String inputPath, String outputPath, String graphPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils - .readPath(spark, relationPath, Relation.class) + .readPath(spark, graphPath + "/relation", Relation.class) .filter( "dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - relations - .joinWith( - results, relations.col("source").equalTo(results.col("id")), - "inner") - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction, R>) (k, it) -> { - return it.next()._2(); - }, Encoders.bean(inputClazz)) + spark + .sql( + "Select res.* " + + "from relation rel " + + "join result res " + + "on rel.source = res.id " + + "join project p " + + "on rel.target = p.id " + + "") + .as(Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") From 886617afd0243075836815cb6cef59e9e2c096ae Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:15:35 +0200 Subject: [PATCH 41/92] One result linked to more than on project is saved just once --- .../graph/dump/funderresults/SparkResultLinkedToProject.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 9c4c73d851..e0355d6d61 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -97,6 +97,11 @@ public class SparkResultLinkedToProject implements Serializable { "on rel.target = p.id " + "") .as(Encoders.bean(inputClazz)) + .groupByKey( + (MapFunction< R, String>) value -> value + .getId(), + Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") From 774cdb190e498da204f162d1497f27dd68fb880a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Jul 2021 18:57:24 +0200 Subject: [PATCH 42/92] changes to mirror the last dump of the graph with the ols data model. --- .../dnetlib/doiboost/mag/MAGMappingTest.scala | 24 +++++-- .../dhp/oa/graph/dump/DumpProducts.java | 3 +- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 12 ++-- .../graph/dump/community/CommunitySplit.java | 10 +-- .../funderresults/SparkDumpFunderResults.java | 17 +++-- .../dump/complete/schema/result_schema.json | 70 ++++++++++++++++++- .../dump/QueryInformationSystemTest.java | 2 +- .../dump/complete/CreateRelationTest.java | 2 +- .../dump/funderresult/SplitPerFunderTest.java | 4 +- 9 files changed, 113 insertions(+), 31 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala index 7eb50665e2..d43e7ed378 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala @@ -70,9 +70,15 @@ class MAGMappingTest { implicit val formats = DefaultFormats - val conf = new SparkConf().setAppName("test").setMaster("local[2]") - val sc = new SparkContext(conf) - val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + + val conf = new SparkConf().setAppName("test").setMaster("local[*]").set("spark.driver.host", "localhost") + + val spark: SparkSession = + SparkSession + .builder() + .appName(getClass.getSimpleName) + .config(conf) + .getOrCreate() val path = getClass.getResource("magPapers.json").getPath import org.apache.spark.sql.Encoders @@ -95,9 +101,15 @@ class MAGMappingTest { implicit val formats = DefaultFormats - val conf = new SparkConf().setAppName("test").setMaster("local[2]") - val sc = new SparkContext(conf) - val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + + val conf = new SparkConf().setAppName("test").setMaster("local[*]").set("spark.driver.host", "localhost") + + val spark: SparkSession = + SparkSession + .builder() + .appName(getClass.getSimpleName) + .config(conf) + .getOrCreate() val path = getClass.getResource("duplicatedMagPapers.json").getPath import org.apache.spark.sql.Encoders diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index f5b8f1c768..4ddcea9e8f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -37,7 +37,8 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); + execDump( + spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index fd8262544c..28881b253a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -48,14 +48,14 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - final String communityMapPath = parser.get("communityMapPath"); + //final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); + //CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); RemoteIterator fileStatusListIterator = fileSystem .listFiles( @@ -87,10 +87,10 @@ public class SendToZenodoHDFS implements Serializable { if (!p_string.endsWith("_SUCCESS")) { // String tmp = p_string.substring(0, p_string.lastIndexOf("/")); String name = p_string.substring(p_string.lastIndexOf("/") + 1); - log.info("Sending information for community: " + name); - if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { - name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; - } +// log.info("Sending information for community: " + name); +// if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { +// name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; +// } FSDataInputStream inputStream = fileSystem.open(p); zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index ec16a65e0d..d64c265034 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -34,12 +34,13 @@ public class CommunitySplit implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execSplit(spark, inputPath, outputPath, Utils.getCommunityMap(spark, communityMapPath).keySet()); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + execSplit(spark, inputPath, outputPath, communityMap); }); } private static void execSplit(SparkSession spark, String inputPath, String outputPath, - Set communities) { + CommunityMap communities) { Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -48,8 +49,9 @@ public class CommunitySplit implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); communities + .keySet() .stream() - .forEach(c -> printResult(c, result, outputPath)); + .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); } @@ -61,7 +63,7 @@ public class CommunitySplit implements Serializable { .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) - .json(outputPath + "/" + c); + .json(outputPath); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index b124b76ce0..9fcdcaf78d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -103,12 +103,13 @@ public class SparkDumpFunderResults implements Serializable { } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } - writeFunderResult(funder, result, outputPath , funderdump); + writeFunderResult(funder, result, outputPath, funderdump); }); } - private static void dumpResults(String nsp, Dataset results, String outputPath, String funderName) { + private static void dumpResults(String nsp, Dataset results, String outputPath, + String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { @@ -128,24 +129,22 @@ public class SparkDumpFunderResults implements Serializable { } return null; }, Encoders.bean(CommunityResult.class)) - .filter((FilterFunction) r -> r!= null) + .filter((FilterFunction) r -> r != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath + "/" + funderName); } - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { + String funderDump) { if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); + dumpResults(funder, results, outputPath, "HRZZ"); + dumpResults(funder, results, outputPath, "MZOS"); } else - dumpResults(funder, results, outputPath, funderDump); + dumpResults(funder, results, outputPath, funderDump); } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json index 867fd5a779..03cbfb0744 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json @@ -1,6 +1,23 @@ { "$schema": "http://json-schema.org/draft-07/schema#", "definitions": { + "AccessRight":{ + "type":"object", + "properties":{ + "code": { + "type": "string", + "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" + }, + "label": { + "type": "string", + "description": "Label for the access mode" + }, + "scheme": { + "type": "string", + "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" + } + } + }, "ControlledField": { "type": "object", "properties": { @@ -266,6 +283,57 @@ ] } }, + "instance":{ + "type":"array", + "items":{ + "type":"object", + "properties":{ + "accessright":{ + "allOf":[ + { + "$ref":"#/definitions/AccessRight" + }, + { + "description":"The accessright of this materialization of the result" + } + ] + }, + "articleprocessingcharge":{ + "type":"object", + "properties":{ + "amount":{ + "type":"string" + }, + "currency":{ + "type":"string" + } + } + }, + "license":{ + "type":"string" + }, + "publicationdate":{ + "type":"string" + }, + "refereed":{ + "type":"string" + }, + "type":{ + "type":"string", + "description":"The specific sub-type of this materialization of the result (see https://api.openaire.eu/vocabularies/dnet:result_typologies following the links)" + }, + "url":{ + "description":"Description of url", + "type":"array", + "items":{ + "type":"string", + "description":"urls where it is possible to access the materialization of the result" + } + } + }, + "description":"One of the materialization for this result" + } + }, "programmingLanguage": { "type": "string", "description": "Only for results with type 'software': the programming language" @@ -302,7 +370,7 @@ "subject": { "allOf": [ {"$ref": "#/definitions/ControlledField"}, - {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."}, + {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."} ] } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java index c6666342a0..499df3a097 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java @@ -70,7 +70,7 @@ public class QueryInformationSystemTest { lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); queryInformationSystem = new QueryInformationSystem(); queryInformationSystem.setIsLookUp(isLookUpService); - map = queryInformationSystem.getCommunityMap(); + map = queryInformationSystem.getCommunityMap(false, null); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java index 5f21e0bc5a..448034d0cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java @@ -379,7 +379,7 @@ public class CreateRelationTest { " \n" + " 675858\n" + " \n" + - " H2020-EINFRA-2015-1\n" + + " EC | H2020 | RIA\n" + " EC\n" + " West-Life\n" + " \n" + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index eefb0b9cbe..26187f0a32 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -139,8 +139,8 @@ public class SplitPerFunderTest { // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); } From 4cb65bc64af4d4cf0b76ea3cc6ca9e67d200af83 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 14 Jul 2021 09:44:32 +0200 Subject: [PATCH 43/92] fixed process doiboost workflow: - splitted OrcidToOAF into two phase preprocess and process - updated workflow used in production --- .../crossref/SparkMapDumpIntoOAF.scala | 2 +- .../orcid/SparkConvertORCIDToOAF.scala | 56 +++------------ .../doiboost/orcid/SparkPreprocessORCID.scala | 70 +++++++++++++++++++ .../doiboost/uw/SparkMapUnpayWallToOAF.scala | 2 +- .../convert_crossref_dump_to_oaf_params.json | 6 ++ .../doiboost/convert_orcid_to_oaf_params.json | 6 ++ .../doiboost/convert_uw_to_oaf_params.json | 6 ++ .../dhp/doiboost/oozie_app/workflow.xml | 2 +- .../doiboost/orcid_oaf/oozie_app/workflow.xml | 2 +- ...rams.json => preprocess_orcid_params.json} | 3 +- .../orcid/MappingORCIDToOAFTest.scala | 2 +- 11 files changed, 103 insertions(+), 54 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_crossref_dump_to_oaf_params.json create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_uw_to_oaf_params.json rename dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/{convert_map_to_oaf_params.json => preprocess_orcid_params.json} (59%) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala index 57acaf404d..c65916610c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala @@ -21,7 +21,7 @@ object SparkMapDumpIntoOAF { val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_crossref_dump_to_oaf_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala index a359eb3c6e..9117bcb347 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -1,61 +1,18 @@ package eu.dnetlib.doiboost.orcid -import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.oaf.Publication -import eu.dnetlib.dhp.schema.orcid.OrcidDOI import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.rdd.RDD -import org.apache.spark.sql.functions._ -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} object SparkConvertORCIDToOAF { val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) - def fixORCIDItem(item :ORCIDItem):ORCIDItem = { - new ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList) - - } - - - def run(spark:SparkSession,sourcePath:String,workingPath:String, targetPath:String):Unit = { - import spark.implicits._ - implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] - - val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s)) - - spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author") - - val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null) - - spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works") - - val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor] - - val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork] - - works.joinWith(authors, authors("oid").equalTo(works("oid"))) - .map(i =>{ - val doi = i._1.doi - var author = i._2 - (doi, author) - }).groupBy(col("_1").alias("doi")) - .agg(collect_list(col("_2")).alias("authors")).as[ORCIDItem] - .map(s => fixORCIDItem(s)) - .write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor") - - val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem] - - logger.info("Converting ORCID to OAF") - dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath) - } - def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -64,11 +21,16 @@ object SparkConvertORCIDToOAF { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + import spark.implicits._ - val sourcePath = parser.get("sourcePath") val workingPath = parser.get("workingPath") val targetPath = parser.get("targetPath") - run(spark, sourcePath, workingPath, targetPath) + + val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem] + + logger.info("Converting ORCID to OAF") + dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath) } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala new file mode 100644 index 0000000000..d6911cfa78 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala @@ -0,0 +1,70 @@ +package eu.dnetlib.doiboost.orcid + +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.dhp.schema.orcid.OrcidDOI +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.functions._ +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkPreprocessORCID { + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + + def fixORCIDItem(item :ORCIDItem):ORCIDItem = { + ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList) + + } + + + def run(spark:SparkSession,sourcePath:String,workingPath:String):Unit = { + import spark.implicits._ + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + + val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s)) + + spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author") + + val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null) + + spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works") + + val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor] + + val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork] + + works.joinWith(authors, authors("oid").equalTo(works("oid"))) + .map(i =>{ + val doi = i._1.doi + val author = i._2 + (doi, author) + }).groupBy(col("_1").alias("doi")) + .agg(collect_list(col("_2")).alias("authors")).as[ORCIDItem] + .map(s => fixORCIDItem(s)) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor") + } + + def main(args: Array[String]): Unit = { + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val sourcePath = parser.get("sourcePath") + val workingPath = parser.get("workingPath") + + run(spark, sourcePath, workingPath) + + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala index a72e4b0d6e..4530926f10 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala @@ -18,7 +18,7 @@ object SparkMapUnpayWallToOAF { val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass) val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_uw_to_oaf_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_crossref_dump_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_crossref_dump_to_oaf_params.json new file mode 100644 index 0000000000..da324f8c45 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_crossref_dump_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the OAF Orcid transformed", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source path ", "paramRequired": false}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json new file mode 100644 index 0000000000..6c9ca5ede1 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the OAF Orcid transformed", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": false}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_uw_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_uw_to_oaf_params.json new file mode 100644 index 0000000000..da324f8c45 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_uw_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the OAF Orcid transformed", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source path ", "paramRequired": false}, + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index fa47e142d0..34b4b5c5e3 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -368,7 +368,7 @@ yarn-cluster cluster Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + eu.dnetlib.doiboost.orcid.SparkPreprocessORCID dhp-doiboost-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml index bffde793ba..0670e18de4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml @@ -34,7 +34,7 @@ yarn-cluster cluster Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF + eu.dnetlib.doiboost.orcid.SparkPreprocessORCID dhp-doiboost-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json similarity index 59% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json index 1521035705..fdc1e2f20e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json @@ -1,7 +1,6 @@ [ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the Orcid Input file", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": false}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true}, - {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} + {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index d620c4ef3d..5fced8edb6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -46,7 +46,7 @@ class MappingORCIDToOAFTest { implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] import spark.implicits._ - SparkConvertORCIDToOAF.run( spark,sourcePath, workingPath, targetPath) + SparkPreprocessORCID.run( spark,sourcePath, workingPath) val mapper = new ObjectMapper() From 1cdd09cd8ed069c2d2dc2d5856faf154c15a3558 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 14 Jul 2021 11:14:59 +0200 Subject: [PATCH 44/92] Tentative fix for testing of Jenkins --- .../dnetlib/doiboost/mag/MAGMappingTest.scala | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala index 7eb50665e2..dbdedcbd06 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala @@ -70,9 +70,15 @@ class MAGMappingTest { implicit val formats = DefaultFormats - val conf = new SparkConf().setAppName("test").setMaster("local[2]") - val sc = new SparkContext(conf) - val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + val conf = new SparkConf() + conf.setMaster("local[*]") + conf.set("spark.driver.host", "localhost") + val spark: SparkSession = + SparkSession + .builder() + .appName(getClass.getSimpleName) + .config(conf) + .getOrCreate() val path = getClass.getResource("magPapers.json").getPath import org.apache.spark.sql.Encoders @@ -95,9 +101,15 @@ class MAGMappingTest { implicit val formats = DefaultFormats - val conf = new SparkConf().setAppName("test").setMaster("local[2]") - val sc = new SparkContext(conf) - val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + val conf = new SparkConf() + conf.setMaster("local[*]") + conf.set("spark.driver.host", "localhost") + val spark: SparkSession = + SparkSession + .builder() + .appName(getClass.getSimpleName) + .config(conf) + .getOrCreate() val path = getClass.getResource("duplicatedMagPapers.json").getPath import org.apache.spark.sql.Encoders From 10068c00ea1dc757262b4bbe2307fcb1b0e3fd30 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 14 Jul 2021 14:37:06 +0200 Subject: [PATCH 45/92] Code refactor: - removed old workflows in doiboost - splitted workflow of doiboost in preprocess and process --- .../orcid/SparkConvertORCIDToOAF.scala | 17 +- .../doiboost/orcid/SparkPreprocessORCID.scala | 2 +- .../doiboost/crossref/oozie_app/workflow.xml | 101 ---- .../intersection/oozie_app/config-default.xml | 38 -- .../intersection/oozie_app/workflow.xml | 96 ---- .../doiboost/mag/oozie_app/config-default.xml | 42 -- .../dhp/doiboost/mag/oozie_app/workflow.xml | 92 ---- .../dhp/doiboost/oozie_app/config-default.xml | 42 -- .../dhp/doiboost/oozie_app/workflow.xml | 453 ------------------ .../oozie_app/config-default.xml | 0 .../preprocess/oozie_app/workflow.xml | 216 +++++++++ .../unpaywall/oozie_app/config-default.xml | 38 -- .../doiboost/unpaywall/oozie_app/workflow.xml | 55 --- .../dnetlib/doiboost/mag/MAGMappingTest.scala | 25 +- .../orcid/MappingORCIDToOAFTest.scala | 4 + 15 files changed, 240 insertions(+), 981 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml rename dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/{crossref => preprocess}/oozie_app/config-default.xml (100%) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala index 9117bcb347..fa4a93e008 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala @@ -10,6 +10,16 @@ import org.slf4j.{Logger, LoggerFactory} object SparkConvertORCIDToOAF { val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + + def run(spark:SparkSession, workingPath:String, targetPath:String) :Unit = { + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + import spark.implicits._ + val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem] + + logger.info("Converting ORCID to OAF") + dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath) + } + def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) @@ -21,16 +31,11 @@ object SparkConvertORCIDToOAF { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] - import spark.implicits._ val workingPath = parser.get("workingPath") val targetPath = parser.get("targetPath") - val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem] - - logger.info("Converting ORCID to OAF") - dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath) + run(spark,workingPath, targetPath) } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala index d6911cfa78..31f3319122 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala @@ -50,7 +50,7 @@ object SparkPreprocessORCID { def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml deleted file mode 100644 index 63c2e9ef29..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml +++ /dev/null @@ -1,101 +0,0 @@ - - - - workingPath - the working dir base path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - timestamp - Timestamp for incremental Harvesting - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.crossref.CrossrefImporter - -t${workingPath}/input/crossref/index_update - -n${nameNode} - -ts${timestamp} - - - - - - - - yarn-cluster - cluster - ExtractCrossrefToOAF - eu.dnetlib.doiboost.crossref.CrossrefDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --workingPath/data/doiboost/input/crossref - --masteryarn-cluster - - - - - - - - - - - - - - - - - - yarn-cluster - cluster - ConvertCrossrefToOAF - eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --sourcePath${workingPath}/input/crossref/crossref_ds - --targetPath${workingPath}/process/ - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml deleted file mode 100644 index cf617a84c4..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml deleted file mode 100644 index dcde62c9d9..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml +++ /dev/null @@ -1,96 +0,0 @@ - - - - hostedByMapPath - the Hosted By Map Path - - - affiliationPath - the Affliation Path - - - paperAffiliationPath - the paperAffiliation Path - - - workingDirPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - yarn-cluster - cluster - Create DOIBoost Infospace - eu.dnetlib.doiboost.SparkGenerateDoiBoost - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --hostedByMapPath${hostedByMapPath} - --affiliationPath${affiliationPath} - --paperAffiliationPath${paperAffiliationPath} - --workingDirPath${workingDirPath} - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Generate DOIBoost ActionSet - eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --dbPublicationPath${workingDirPath}/doiBoostPublicationFiltered - --dbDatasetPath${workingDirPath}/crossrefDataset - --crossRefRelation${workingDirPath}/crossrefRelation - --dbaffiliationRelationPath${workingDirPath}/doiBoostPublicationAffiliation - -do${workingDirPath}/doiBoostOrganization - --targetPath${workingDirPath}/actionDataSet - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml deleted file mode 100644 index 59e5c059fc..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.wf.rerun.failnodes - false - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml deleted file mode 100644 index 9d19dddc71..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml +++ /dev/null @@ -1,92 +0,0 @@ - - - - sourcePath - the working dir base path - - - targetPath - the working dir base path - - - workingPath - the working dir base path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - yarn-cluster - cluster - Convert Mag to Dataset - eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - ${sparkExtraOPT} - - --sourcePath${sourcePath} - --targetPath${workingPath} - --masteryarn-cluster - - - - - - - - - - yarn-cluster - cluster - Convert Mag to OAF Dataset - eu.dnetlib.doiboost.mag.SparkPreProcessMAG - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --sourcePath${workingPath} - --workingPath${workingPath}/process - --targetPath${targetPath} - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml deleted file mode 100644 index 508202e301..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml deleted file mode 100644 index 34b4b5c5e3..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ /dev/null @@ -1,453 +0,0 @@ - - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorIntersectionMemory - memory for individual executor - - - - sparkExecutorCores - number of cores used by single executor - - - - - - workingPath - the working Path - - - - hostedByMapPath - the hostedByMap Path - - - outputPath - the Path of the sequence file action set - - - - - - inputPathCrossref - the Crossref input path - - - crossrefDumpPath - the Crossref dump path - - - - - - - - - - - - - - - - - MAGDumpPath - the MAG dump working path - - - - inputPathMAG - the MAG working path - - - - - - inputPathUnpayWall - the UnpayWall working path - - - - - inputPathOrcid - the ORCID input path - - - - workingPathOrcid - the ORCID working path - - - - - - ${jobTracker} - ${nameNode} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - ${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'} - ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} - ${wf:conf('resumeFrom') eq 'PreprocessMag'} - ${wf:conf('resumeFrom') eq 'PreprocessUW'} - ${wf:conf('resumeFrom') eq 'PreprocessORCID'} - ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} - ${wf:conf('resumeFrom') eq 'GenerateActionSet'} - ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords - --hdfsServerUri${nameNode} - --crossrefFileNameTarGz${crossrefDumpPath}/crossref.tar.gz - --workingPath${crossrefDumpPath} - --outputPath${crossrefDumpPath}/files/ - - - - - - - - yarn-cluster - cluster - SparkUnpackCrossrefEntries - eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${crossrefDumpPath}/files - --targetPath${crossrefDumpPath}/crossref_unpack/ - - - - - - - - - yarn-cluster - cluster - SparkGenerateCrossrefDataset - eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=7G - --executor-cores=2 - --driver-memory=7G - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn-cluster - --sourcePath${crossrefDumpPath}/crossref_unpack/ - --targetPath${inputPathCrossref}/crossref_ds - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - yarn-cluster - cluster - Convert Mag to Dataset - eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${MAGDumpPath} - --targetPath${inputPathMAG}/dataset - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - ConvertCrossrefToOAF - eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathCrossref}/crossref_ds - --targetPath${workingPath} - --masteryarn-cluster - - - - - - - - yarn-cluster - cluster - Convert Mag to OAF Dataset - eu.dnetlib.doiboost.mag.SparkProcessMAG - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorIntersectionMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathMAG}/dataset - --workingPath${inputPathMAG}/process - --targetPath${workingPath} - --masteryarn-cluster - - - - - - - - - - yarn-cluster - cluster - Convert UnpayWall to Dataset - eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathUnpayWall}/uw_extracted - --targetPath${workingPath}/uwPublication - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkPreprocessORCID - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathOrcid} - --workingPath${workingPathOrcid} - --targetPath${workingPath}/orcidPublication - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Create DOIBoost Infospace - eu.dnetlib.doiboost.SparkGenerateDoiBoost - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorIntersectionMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --hostedByMapPath${hostedByMapPath} - --affiliationPath${inputPathMAG}/dataset/Affiliations - --paperAffiliationPath${inputPathMAG}/dataset/PaperAuthorAffiliations - --workingPath${workingPath} - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - Generate DOIBoost ActionSet - eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --dbPublicationPath${workingPath}/doiBoostPublicationFiltered - --dbDatasetPath${workingPath}/crossrefDataset - --crossRefRelation${workingPath}/crossrefRelation - --dbaffiliationRelationPath${workingPath}/doiBoostPublicationAffiliation - --dbOrganizationPath${workingPath}/doiBoostOrganization - --targetPath${workingPath}/actionDataSet - --sFilePath${outputPath} - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml new file mode 100644 index 0000000000..03f7b7566c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -0,0 +1,216 @@ + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + inputPathCrossref + the Crossref input path + + + crossrefDumpPath + the Crossref dump path + + + + + MAGDumpPath + the MAG dump working path + + + + inputPathMAG + the MAG working path + + + + + + inputPathOrcid + the ORCID input path + + + + workingPathOrcid + the ORCID working path + + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + ${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'} + ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} + ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} + ${wf:conf('resumeFrom') eq 'ConvertMagToDataset'} + ${wf:conf('resumeFrom') eq 'PreProcessORCID'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords + --hdfsServerUri${nameNode} + --crossrefFileNameTarGz${crossrefDumpPath}/crossref.tar.gz + --workingPath${crossrefDumpPath} + --outputPath${crossrefDumpPath}/files/ + + + + + + + + yarn-cluster + cluster + SparkUnpackCrossrefEntries + eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn-cluster + --sourcePath${crossrefDumpPath}/files + --targetPath${crossrefDumpPath}/crossref_unpack/ + + + + + + + + + yarn-cluster + cluster + SparkGenerateCrossrefDataset + eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=7G + --executor-cores=2 + --driver-memory=7G + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn-cluster + --sourcePath${crossrefDumpPath}/crossref_unpack/ + --targetPath${inputPathCrossref}/crossref_ds + + + + + + + + + + + + + + + + + + + + + + + + + + + + yarn-cluster + cluster + Convert Mag to Dataset + eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${MAGDumpPath} + --targetPath${inputPathMAG}/dataset + --masteryarn-cluster + + + + + + + + + yarn-cluster + cluster + Convert ORCID to Dataset + eu.dnetlib.doiboost.orcid.SparkPreprocessORCID + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${inputPathOrcid} + --workingPath${workingPathOrcid} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml deleted file mode 100644 index cf617a84c4..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml deleted file mode 100644 index d2a69752ea..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - sourcePath - the working dir base path - - - targetPath - the working dir base path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn-cluster - cluster - Convert UnpayWall to Dataset - eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - ${sparkExtraOPT} - - --sourcePath${sourcePath}/uw_extracted - --targetPath${targetPath} - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala index dbdedcbd06..46d4ec08d6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala @@ -1,22 +1,15 @@ package eu.dnetlib.doiboost.mag -import java.sql.Timestamp - -import eu.dnetlib.dhp.schema.oaf.Publication -import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature -import org.apache.spark.{SparkConf, SparkContext} -import org.apache.spark.api.java.function.MapFunction -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} -import org.junit.jupiter.api.Test -import org.slf4j.{Logger, LoggerFactory} +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, SparkSession} +import org.codehaus.jackson.map.ObjectMapper import org.junit.jupiter.api.Assertions._ -import org.apache.spark.sql.functions._ +import org.junit.jupiter.api.Test +import org.json4s.DefaultFormats +import org.slf4j.{Logger, LoggerFactory} -import scala.collection.JavaConverters._ +import java.sql.Timestamp import scala.io.Source -import scala.reflect.ClassTag -import scala.util.matching.Regex @@ -65,8 +58,7 @@ class MAGMappingTest { @Test def normalizeDoiTest():Unit = { - import org.json4s.jackson.Serialization.write - import org.json4s.DefaultFormats + implicit val formats = DefaultFormats @@ -96,7 +88,6 @@ class MAGMappingTest { @Test def normalizeDoiTest2():Unit = { - import org.json4s.jackson.Serialization.write import org.json4s.DefaultFormats implicit val formats = DefaultFormats diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index 5fced8edb6..b484dc0878 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -48,6 +48,8 @@ class MappingORCIDToOAFTest { SparkPreprocessORCID.run( spark,sourcePath, workingPath) + SparkConvertORCIDToOAF.run(spark, workingPath,targetPath) + val mapper = new ObjectMapper() @@ -62,6 +64,8 @@ class MappingORCIDToOAFTest { println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p.first())) spark.close() + + } From a65667d2175d2b6a83a04462699d74b7aee13305 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 14 Jul 2021 15:07:07 +0200 Subject: [PATCH 46/92] added publication to dataset even if no contributors --- .../SparkGenEnrichedOrcidWorks.java | 27 +++++++++++++++---- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 5bcec72246..ca39f99cc9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -4,6 +4,7 @@ package eu.dnetlib.doiboost.orcidnodoi; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; +import java.util.Arrays; import java.util.List; import java.util.Objects; import java.util.Optional; @@ -32,10 +33,7 @@ import com.google.gson.JsonParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.orcid.AuthorData; -import eu.dnetlib.dhp.schema.orcid.AuthorSummary; -import eu.dnetlib.dhp.schema.orcid.Work; -import eu.dnetlib.dhp.schema.orcid.WorkDetail; +import eu.dnetlib.dhp.schema.orcid.*; import eu.dnetlib.doiboost.orcid.json.JsonHelper; import eu.dnetlib.doiboost.orcid.util.HDFSUtil; import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; @@ -111,6 +109,10 @@ public class SparkGenEnrichedOrcidWorks { Encoders.bean(WorkDetail.class)); logger.info("Works data loaded: " + workDataset.count()); + final LongAccumulator warnNotFoundContributors = spark + .sparkContext() + .longAccumulator("warnNotFoundContributors"); + JavaRDD> enrichedWorksRDD = workDataset .joinWith( authorDataset, @@ -119,7 +121,21 @@ public class SparkGenEnrichedOrcidWorks { (MapFunction, Tuple2>) value -> { WorkDetail w = value._1; AuthorData a = value._2; - AuthorMatcher.match(a, w.getContributors()); + if (w.getContributors() == null + || (w.getContributors() != null && w.getContributors().size() == 0)) { + Contributor c = new Contributor(); + c.setName(a.getName()); + c.setSurname(a.getSurname()); + c.setCreditName(a.getCreditName()); + c.setOid(a.getOid()); + List contributors = Arrays.asList(c); + w.setContributors(contributors); + if (warnNotFoundContributors != null) { + warnNotFoundContributors.add(1); + } + } else { + AuthorMatcher.match(a, w.getContributors()); + } return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w)); }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())) @@ -180,6 +196,7 @@ public class SparkGenEnrichedOrcidWorks { logger.info("parsedPublications: " + parsedPublications.value().toString()); logger.info("enrichedPublications: " + enrichedPublications.value().toString()); + logger.info("warnNotFoundContributors: " + warnNotFoundContributors.value().toString()); logger.info("errorsGeneric: " + errorsGeneric.value().toString()); logger.info("errorsInvalidTitle: " + errorsInvalidTitle.value().toString()); logger.info("errorsNotFoundAuthors: " + errorsNotFoundAuthors.value().toString()); From 66604bb2b4fe045858b1d54ac3fc2df93bbbdeba Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 14 Jul 2021 16:44:51 +0200 Subject: [PATCH 47/92] added absolute path to process folder --- .../doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java | 2 +- .../dhp/doiboost/orcidnodoi/oozie_app/workflow.xml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index c342d2e790..1d47808ef1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -188,7 +188,7 @@ public class SparkGenEnrichedOrcidWorks { OBJECT_MAPPER.writeValueAsString(new AtomicAction<>(Publication.class, p)))) .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) .saveAsNewAPIHadoopFile( - workingPath.concat(outputEnrichedWorksPath), + outputEnrichedWorksPath, Text.class, Text.class, SequenceFileOutputFormat.class, diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index f7ac04821e..05492d50d1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -11,7 +11,7 @@ path where to store the action set - processOutputFolder + processOutputPath process_no_doi_dataset_prod temporary path where to store the action set @@ -71,7 +71,7 @@ - + @@ -97,7 +97,7 @@ --workingPath${workingPath}/ --hdfsServerUri${nameNode} --orcidDataFolderlast_orcid_dataset - --outputEnrichedWorksPath${processOutputFolder} + --outputEnrichedWorksPath${processOutputPath} @@ -105,7 +105,7 @@ - ${workingPath}/${processOutputFolder}/* + ${processOutputPath}/* ${outputPath} From 2dc50c0999738eb3051fb8570f3e3a0b4bb81c7e Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 14 Jul 2021 17:02:22 +0200 Subject: [PATCH 48/92] added default value to process path --- .../eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 05492d50d1..04ca05af2b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -12,7 +12,7 @@ processOutputPath - process_no_doi_dataset_prod + /data/orcid_activities_2020/process_no_doi_dataset_prod temporary path where to store the action set From 5e5f65a3c313bbd985a9504b657251da43fb525c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 19 Jul 2021 15:56:55 +0200 Subject: [PATCH 49/92] contents mapped from the stores with 'claim' interpretation will not change their identifier along their way towards the graph --- .../raw/AbstractMdRecordToOafMapper.java | 24 +++++++++++++++---- .../raw/GenerateEntitiesApplication.java | 6 +++-- .../dhp/oa/graph/raw/OafToOafMapper.java | 5 ++++ .../dhp/oa/graph/raw/OdfToOafMapper.java | 5 ++++ 4 files changed, 34 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 1e80dfd46c..cbaadf85c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -71,6 +71,8 @@ public abstract class AbstractMdRecordToOafMapper { private final boolean shouldHashId; + private final boolean forceOriginalId; + protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; @@ -98,11 +100,20 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId, final boolean forceOriginalId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = forceOriginalId; + } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { this.vocs = vocs; this.invisible = invisible; this.shouldHashId = shouldHashId; + this.forceOriginalId = false; } public List processMdRecord(final String xml) { @@ -190,10 +201,15 @@ public abstract class AbstractMdRecordToOafMapper { final long lastUpdateTimestamp) { final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); - if (!id.equals(entity.getId())) { - entity.getOriginalId().add(entity.getId()); - entity.setId(id); + + if (!forceOriginalId) { + final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); + if (!id.equals(entity.getId())) { + final Set originalId = Sets.newHashSet(entity.getOriginalId()); + originalId.add(entity.getId()); + entity.setOriginalId(Lists.newArrayList(originalId)); + entity.setId(id); + } } final List oafs = Lists.newArrayList(entity); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index fcd6f459a7..bbfb7429f3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -163,11 +163,13 @@ public class GenerateEntitiesApplication { switch (type.toLowerCase()) { case "oaf-store-cleaned": - case "oaf-store-claim": return new OafToOafMapper(vocs, false, shouldHashId).processMdRecord(s); + case "oaf-store-claim": + return new OafToOafMapper(vocs, false, shouldHashId, true).processMdRecord(s); case "odf-store-cleaned": - case "odf-store-claim": return new OdfToOafMapper(vocs, false, shouldHashId).processMdRecord(s); + case "odf-store-claim": + return new OdfToOafMapper(vocs, false, shouldHashId, true).processMdRecord(s); case "oaf-store-intersection": return new OafToOafMapper(vocs, true, shouldHashId).processMdRecord(s); case "odf-store-intersection": diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 06aeab3451..d753cddeb4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -27,6 +27,11 @@ import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; public class OafToOafMapper extends AbstractMdRecordToOafMapper { + public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, + final boolean forceOrginalId) { + super(vocs, invisible, shouldHashId, forceOrginalId); + } + public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { super(vocs, invisible, shouldHashId); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index b7400873b6..7925a78269 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -22,6 +22,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; + public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, + final boolean forceOrginalId) { + super(vocs, invisible, shouldHashId, forceOrginalId); + } + public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId) { super(vocs, invisible, shouldHashId); } From 5947cddafc11a26026a2a4cf1906ce395348b0c5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 19 Jul 2021 17:52:24 +0200 Subject: [PATCH 50/92] adding record identifier among the originalIds regardless of what IdentifierFactory produces --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index cbaadf85c0..03c3eeb3ce 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -202,12 +202,13 @@ public abstract class AbstractMdRecordToOafMapper { final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final Set originalId = Sets.newHashSet(entity.getOriginalId()); + originalId.add(entity.getId()); + entity.setOriginalId(Lists.newArrayList(originalId)); + if (!forceOriginalId) { final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); if (!id.equals(entity.getId())) { - final Set originalId = Sets.newHashSet(entity.getOriginalId()); - originalId.add(entity.getId()); - entity.setOriginalId(Lists.newArrayList(originalId)); entity.setId(id); } } From 77e8c6c7f7688078bb459da07566a6d75f03dccd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 20 Jul 2021 11:51:33 +0200 Subject: [PATCH 51/92] filtering 'old' OpenAIRE ids from the entity.originalId[] array in the OAF -> XML searialization procedure --- .../eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 86bbae99ec..a985d23718 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -16,6 +16,7 @@ import javax.xml.transform.*; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import org.apache.commons.lang3.StringUtils; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; @@ -183,6 +184,7 @@ public class XmlRecordFactory implements Serializable { .getOriginalId() .stream() .filter(Objects::nonNull) + .filter(id -> !id.matches("^\\d{2}" + IdentifierFactory.ID_PREFIX_SEPARATOR)) .map(s -> XmlSerializationUtils.asXmlElement("originalId", s)) .collect(Collectors.toList())); } From 906995847955881606e357abd4ebbd244f149eff Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 20 Jul 2021 19:31:43 +0200 Subject: [PATCH 52/92] tests for enermaps --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 25 +++++++ .../eu/dnetlib/dhp/oa/graph/raw/enermaps.xml | 72 +++++++++++++++++++ .../oa/provision/XmlRecordFactoryTest.java | 29 ++++++++ .../eu/dnetlib/dhp/oa/provision/enermaps.json | 1 + 4 files changed, 127 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 5b229a6255..495dc4a045 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -567,6 +567,31 @@ public class MappersTest { assertNotNull(d.getInstance().get(0).getUrl()); } + @Test + void testEnermaps() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml")); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Dataset); + + final Dataset d = (Dataset) list.get(0); + + assertValidId(d.getId()); + assertValidId(d.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertEquals(1, d.getAuthor().size()); + assertEquals(1, d.getInstance().size()); + assertNotNull(d.getInstance().get(0).getUrl()); + assertNotNull(d.getContext()); + assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId())); + assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId()); + } + @Test void testClaimFromCrossref() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml new file mode 100644 index 0000000000..362b40c85c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/enermaps.xml @@ -0,0 +1,72 @@ + + + + enermaps____::04149ee428d07360314c2cb3ba95d41e + tgs00004 + 2021-07-20T18:43:12.096+02:00 + enermaps____ + + + + https://ec.europa.eu/eurostat/web/products-datasets/-/tgs00004 + + + Statistical Office of the European Union (Eurostat) + + + + + Regional GDP + + + Statistical Office of the European Union (Eurostat) + 2020 + + 2020-10-07 + + + + OPEN + Creative Commons Attribution 4.0 International + + + GDP expressed in PPS (purchasing power standards) eliminates differences in price levels between countries. Calculations on a per inhabitant basis allow for the comparison of economies and regions significantly different in absolute size. GDP per inhabitant in PPS is the key variable for determining the eligibility of NUTS 2 regions in the framework of the European Unions structural policy. + + 0021 + 2020-10-07 + OPEN + Creative Commons Attribution 4.0 International + + + + + + + + + https%3A%2F%2Flab.idiap.ch%2Fenermaps%2Fapi%2Fdatacite + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 6631cb4da6..a5a1563aa0 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -7,6 +7,8 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; +import eu.dnetlib.dhp.oa.provision.utils.ContextDef; +import eu.dnetlib.dhp.schema.oaf.Dataset; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -131,4 +133,31 @@ public class XmlRecordFactoryTest { System.out.println(doc.asXML()); assertEquals("", doc.valueOf("//rel/validated")); } + + @Test + public void testEnermapsRecord() throws IOException, DocumentException { + + String contextmap = "" + + ""+ + ""+ + ""; + + ContextMapper contextMapper = ContextMapper.fromXml(contextmap); + XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, + otherDsTypeId); + + Dataset d = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class); + + JoinedEntity je = new JoinedEntity<>(d); + + String xml = xmlRecordFactory.build(je); + + assertNotNull(xml); + + Document doc = new SAXReader().read(new StringReader(xml)); + assertNotNull(doc); + System.out.println(doc.asXML()); + assertEquals("enermaps::selection::tgs00004", doc.valueOf("//concept/@id")); + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json new file mode 100644 index 0000000000..dcd4c2ee17 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/enermaps.json @@ -0,0 +1 @@ +{"collectedfrom":[{"key":"10|enermaps____::d77d5e503ad1439f585ac494268b351b","value":"Enermaps","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626800904248,"id":"50|enermaps____::04149ee428d07360314c2cb3ba95d41e","originalId":["50|enermaps____::04149ee428d07360314c2cb3ba95d41e","tgs00004"],"pid":[],"dateofcollection":"2021-07-20T18:43:12.096+02:00","dateoftransformation":"","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2021-07-20T18:43:12.096+02:00","altered":true,"baseURL":"https%3A%2F%2Flab.idiap.ch%2Fenermaps%2Fapi%2Fdatacite","identifier":"","datestamp":"","metadataNamespace":""}},"measures":null,"author":[{"fullname":"Statistical Office of the European Union (Eurostat)","name":"","surname":"","rank":1,"pid":[],"affiliation":[]}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[],"title":[{"value":"\n Regional GDP\n ","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[{"value":"2020-10-07","qualifier":{"classid":"Issued","classname":"Issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"description":[{"value":"GDP expressed in PPS (purchasing power standards) eliminates differences in price levels between countries. Calculations on a per inhabitant basis allow for the comparison of economies and regions significantly different in absolute size. GDP per inhabitant in PPS is the key variable for determining the eligibility of NUTS 2 regions in the framework of the European Unions structural policy.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Statistical Office of the European Union (Eurostat)","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"coverage":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[{"id":"enermaps::selection::tgs00004","dataInfo":[{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}]}],"externalReference":[],"instance":[{"license":{"value":"Creative Commons Attribution 4.0 International","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0021","classname":"Dataset","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository","dataInfo":null},"url":["https://ec.europa.eu/eurostat/web/products-datasets/-/tgs00004"],"distributionlocation":null,"collectedfrom":{"key":"10|enermaps____::d77d5e503ad1439f585ac494268b351b","value":"Enermaps","dataInfo":null},"pid":[],"alternateIdentifier":[],"dateofacceptance":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"}}],"storagedate":{"value":"2020-10-07","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"device":null,"size":null,"version":null,"lastmetadataupdate":null,"metadataversionnumber":null,"geolocation":[]} From ffdb2a3ea39823e04062d05f4ce50d6e0f9cf0f0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 23 Jul 2021 11:55:55 +0200 Subject: [PATCH 53/92] [cleaning] fixed filtering function for missing titles --- .../eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index a75cc52e6a..e5181b1119 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -98,7 +98,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { Result r = (Result) value; - if (Objects.nonNull(r.getTitle()) && r.getTitle().isEmpty()) { + if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) { return false; } From 5b6844b969ba4bff22b2f38e9aaf414aa6ac5056 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 23 Jul 2021 18:14:37 +0200 Subject: [PATCH 54/92] mapping funding relations from Datacite should be done according to the actual result identifier --- .../actionmanager/datacite/DataciteToOAFTransformation.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala index 0cdf0accb1..045927bed1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala @@ -532,11 +532,11 @@ object DataciteToOAFTransformation { JField("awardUri", JString(awardUri)) <- fundingReferences } yield awardUri + result.setId(IdentifierFactory.createIdentifier(result)) var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null) - fix_figshare(result) - result.setId(IdentifierFactory.createIdentifier(result)) + if (result.getId == null) return List() From 998b66855abcfe828f670586793b5dbefafa442d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Jul 2021 15:11:37 +0200 Subject: [PATCH 55/92] updated assertions in eu.dnetlib.dhp.oa.graph.raw.MappersTest --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 58 ++++++++----------- 1 file changed, 24 insertions(+), 34 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 495dc4a045..aeeceaeb58 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,17 +1,13 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.Mockito.lenient; - -import java.io.IOException; -import java.util.List; -import java.util.Optional; - +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -20,22 +16,12 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import com.fasterxml.jackson.databind.ObjectMapper; +import java.io.IOException; +import java.util.List; +import java.util.Optional; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -74,7 +60,7 @@ public class MappersTest { assertValidId(p.getId()); - assertEquals(1, p.getOriginalId().size()); + assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718")); assertValidId(p.getCollectedfrom().get(0).getKey()); @@ -261,8 +247,8 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); - assertEquals(1, d.getOriginalId().size()); - assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526")); + assertEquals(2, d.getOriginalId().size()); + assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); @@ -351,8 +337,11 @@ public class MappersTest { final Publication p = (Publication) list.get(0); assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); - assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + assertEquals(2, p.getOriginalId().size()); + + assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739"))); + //assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); @@ -413,7 +402,8 @@ public class MappersTest { assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename()); assertValidId(d.getId()); - assertTrue(d.getOriginalId().size() == 1); + assertEquals(2, d.getOriginalId().size()); + assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0)); assertValidId(d.getCollectedfrom().get(0).getKey()); @@ -688,8 +678,8 @@ public class MappersTest { final Dataset p = (Dataset) list.get(0); assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); - assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0)); + assertEquals(2, p.getOriginalId().size()); + assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); From d267dce52009efb3e7db40548fcc7f8337b18d70 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Jul 2021 17:18:29 +0200 Subject: [PATCH 56/92] [raw_all] added extra workflow step for patching the identifiers in the relations, given an id mapping dataset --- .../graph/raw/PatchRelationsApplication.java | 117 ++++++++++++++++++ .../graph/raw/common/RelationIdMapping.java | 24 ++++ .../oa/graph/patch_relations_parameters.json | 26 ++++ .../oa/graph/raw_all/oozie_app/workflow.xml | 47 ++++++- 4 files changed, 213 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java new file mode 100644 index 0000000000..151f5ba3f9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -0,0 +1,117 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; +import eu.dnetlib.dhp.schema.oaf.Relation; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.io.FileNotFoundException; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class PatchRelationsApplication { + + private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Optional.ofNullable( + PatchRelationsApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json")) + .orElseThrow(FileNotFoundException::new) + )); + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String graphBasePath = parser.get("graphBasePath"); + log.info("graphBasePath: {}", graphBasePath); + + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); + + final String idMappingPath = parser.get("idMappingPath"); + log.info("idMappingPath: {}", idMappingPath); + + final SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath)); + } + + /** + * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the + * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location. + * + * @param spark the SparkSession + * @param graphBasePath base graph path providing the set of relations to patch + * @param workingDir intermediate storage location + * @param idMappingPath dataset providing the old -> new identifier mapping + */ + private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) { + + final String relationPath = graphBasePath + "/relation"; + + final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); + final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + + rels + .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "full") + .filter((FilterFunction>) t -> Objects.nonNull(t._1())) + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional.ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setSource); + return r; + }, Encoders.bean(Relation.class)) + .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "full") + .filter((FilterFunction>) t -> Objects.nonNull(t._1())) + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional.ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setTarget); + return r; + }, Encoders.bean(Relation.class)) + .map( + (MapFunction) OBJECT_MAPPER::writeValueAsString, + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(workingDir); + + spark.read().textFile(workingDir) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(relationPath); + } + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java new file mode 100644 index 0000000000..f251da8c33 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java @@ -0,0 +1,24 @@ +package eu.dnetlib.dhp.oa.graph.raw.common; + +public class RelationIdMapping { + + private String oldId; + + private String newId; + + public String getOldId() { + return oldId; + } + + public void setOldId(final String oldId) { + this.oldId = oldId; + } + + public String getNewId() { + return newId; + } + + public void setNewId(final String newId) { + this.newId = newId; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json new file mode 100644 index 0000000000..178c2d69bf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "g", + "paramLongName": "graphBasePath", + "paramDescription": "base graph path providing the set of relations to patch", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDir", + "paramDescription": "intermediate storage location", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "idMappingPath", + "paramDescription": "dataset providing the old -> new identifier mapping", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index 7f1ecb39fb..e7320de3b3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -100,6 +100,16 @@ a blacklist of nsprefixes (comma separeted) + + shouldPatchRelations + false + activates the relation patching phase, driven by the content in ${idMappingPath} + + + idMappingPath + + path pointing to the relations identifiers mapping dataset + sparkDriverMemory memory for driver process @@ -538,7 +548,42 @@ - + + + + + + ${(shouldPatchRelations eq "true") and + (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")} + + + + + + + + yarn + cluster + PatchRelations + eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --graphBasePath${workingDir}/graph_raw + --workingDir${workingDir}/patch_relations + --idMappingPath${idMappingPath} + + + + From 9594343725ca1bf512da19aff1c2bdd4e98c6557 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 28 Jul 2021 11:41:34 +0200 Subject: [PATCH 57/92] code formatting after mvn compile --- .../dhp/oa/provision/utils/XmlRecordFactory.java | 2 +- .../dhp/oa/provision/XmlRecordFactoryTest.java | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index a985d23718..2c82402900 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -16,7 +16,6 @@ import javax.xml.transform.*; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import org.apache.commons.lang3.StringUtils; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; @@ -43,6 +42,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class XmlRecordFactory implements Serializable { diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index a5a1563aa0..897e507e19 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -7,8 +7,6 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; -import eu.dnetlib.dhp.oa.provision.utils.ContextDef; -import eu.dnetlib.dhp.schema.oaf.Dataset; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -25,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -137,17 +136,18 @@ public class XmlRecordFactoryTest { @Test public void testEnermapsRecord() throws IOException, DocumentException { - String contextmap = "" + - ""+ - ""+ - ""; + String contextmap = "" + + + "" + + "" + + ""; ContextMapper contextMapper = ContextMapper.fromXml(contextmap); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, - otherDsTypeId); + otherDsTypeId); Dataset d = OBJECT_MAPPER - .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class); + .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class); JoinedEntity je = new JoinedEntity<>(d); From a9961a183598e77434831b5e24a4c1932a75f6f7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 28 Jul 2021 16:21:29 +0200 Subject: [PATCH 58/92] [cleaning] title cleaning based on the me.xuender:unidecode library --- dhp-common/pom.xml | 5 ++ .../oaf/utils/GraphCleaningFunctions.java | 19 ++--- .../schema/oaf/utils/OafMapperUtilsTest.java | 25 ++++-- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 79 ++++++++++--------- .../eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml | 70 ++++++++++++++++ pom.xml | 5 ++ 6 files changed, 151 insertions(+), 52 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 74f31cf357..4c7810c47c 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -25,6 +25,11 @@ com.github.sisyphsu dateparser + + me.xuender + unidecode + + org.apache.spark spark-core_2.11 diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index e5181b1119..1d002ed7ec 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; -import java.util.regex.Matcher; -import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; -import org.jetbrains.annotations.NotNull; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; -import com.google.common.collect.Maps; import com.google.common.collect.Sets; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import me.xuender.unidecode.Unidecode; public class GraphCleaningFunctions extends CleaningFunctions { @@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(Objects::nonNull) .filter(sp -> StringUtils.isNotBlank(sp.getValue())) .filter( - sp -> sp - .getValue() - .toLowerCase() - .replaceAll(TITLE_FILTER_REGEX, "") - .length() > TITLE_FILTER_RESIDUAL_LENGTH) + sp -> { + final String title = sp + .getValue() + .toLowerCase(); + final String residual = Unidecode + .decode(title) + .replaceAll(TITLE_FILTER_REGEX, ""); + return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH; + }) .map(GraphCleaningFunctions::cleanValue) .collect(Collectors.toList())); } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index eefa1e9a31..8d519a93f6 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; -import java.time.LocalDate; -import java.time.format.DateTimeFormatter; import java.util.HashSet; import java.util.List; -import java.util.Locale; -import java.util.Optional; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; @@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; +import me.xuender.unidecode.Unidecode; public class OafMapperUtilsTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + @Test + public void testUnidecode() { + + assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ")); + assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛")); + assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼")); + assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい")); + assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի")); + assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики")); + assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ")); + assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης")); + assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية")); + assertEquals("abc def ghi", Unidecode.decode("abc def ghi")); + } + @Test public void testDateValidation() { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index aeeceaeb58..ba4211a3f2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,13 +1,15 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup; +import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.List; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -16,12 +18,14 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import java.io.IOException; -import java.util.List; -import java.util.Optional; +import com.fasterxml.jackson.databind.ObjectMapper; -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.lenient; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -340,7 +344,7 @@ public class MappersTest { assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739"))); - //assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); @@ -557,31 +561,6 @@ public class MappersTest { assertNotNull(d.getInstance().get(0).getUrl()); } - @Test - void testEnermaps() throws IOException { - final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml")); - final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); - - System.out.println("***************"); - System.out.println(new ObjectMapper().writeValueAsString(list)); - System.out.println("***************"); - - assertEquals(1, list.size()); - assertTrue(list.get(0) instanceof Dataset); - - final Dataset d = (Dataset) list.get(0); - - assertValidId(d.getId()); - assertValidId(d.getCollectedfrom().get(0).getKey()); - assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertEquals(1, d.getAuthor().size()); - assertEquals(1, d.getInstance().size()); - assertNotNull(d.getInstance().get(0).getUrl()); - assertNotNull(d.getContext()); - assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId())); - assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId()); - } - @Test void testClaimFromCrossref() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml")); @@ -663,6 +642,30 @@ public class MappersTest { System.out.println(p.getTitle().get(0).getValue()); } + @Test + void testJairo() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_jairo.xml")); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertFalse(p.getTitle().isEmpty()); + assertTrue(p.getTitle().size() == 1); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + + final Publication p_cleaned = cleanup(fixVocabularyNames(p)); + + assertNotNull(p_cleaned.getTitle()); + assertFalse(p_cleaned.getTitle().isEmpty()); + } + @Test void testOdfFromHdfs() throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml new file mode 100644 index 0000000000..9ec696256f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml @@ -0,0 +1,70 @@ + + +
+ jairo_______::000012e58ed836576ef2a0d38b0f726f + oai:irdb.nii.ac.jp:01221:0000010198 + + + + + + 2021-05-10T11:31:09.424Z + 2021-06-03T01:45:42.536Z + jairo_______ +
+ + 多項式GCDを用いた復号法に関する研究 + 上原, 剛 + 甲斐, 博 + 野田, 松太郎 + application/pdf + http://hdl.handle.net/2433/25934 + jpn + 京都大学数理解析研究所 + 410 + Departmental Bulletin Paper + 0014 + 2004-10-01 + + openaire____::554c7c2873 + OPEN + + + 2433/25934 + AN00061013 + http://hdl.handle.net/2433/25934 + http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf + 数理解析研究所講究録 + + + + + https%3A%2F%2Firdb.nii.ac.jp%2Foai + oai:irdb.nii.ac.jp:01221:0000010198 + 2021-04-13T13:36:29Z + + + http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request + oai:repository.kulib.kyoto-u.ac.jp:2433/25934 + 2012-07-12T14:15:41Z + http://irdb.nii.ac.jp/oai + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 19d00d6375..075a45c9f6 100644 --- a/pom.xml +++ b/pom.xml @@ -205,6 +205,11 @@ dateparser 1.0.7 + + me.xuender + unidecode + 0.0.7 + com.google.guava From 1923c1ce21658c05e9822c9363a3509e4b63eb32 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 29 Jul 2021 11:36:20 +0200 Subject: [PATCH 59/92] replaced full join + filtering with a left join --- .../dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index 151f5ba3f9..c2bcf69f09 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -80,8 +80,7 @@ public class PatchRelationsApplication { final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); rels - .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "full") - .filter((FilterFunction>) t -> Objects.nonNull(t._1())) + .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") .map((MapFunction, Relation>) t -> { final Relation r = t._1(); Optional.ofNullable(t._2()) @@ -89,8 +88,7 @@ public class PatchRelationsApplication { .ifPresent(r::setSource); return r; }, Encoders.bean(Relation.class)) - .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "full") - .filter((FilterFunction>) t -> Objects.nonNull(t._1())) + .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left") .map((MapFunction, Relation>) t -> { final Relation r = t._1(); Optional.ofNullable(t._2()) From e725c88ebb6eedea235abfc07af932756c9e2397 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 29 Jul 2021 13:03:16 +0200 Subject: [PATCH 60/92] [raw_all] patching relation identifier phase to be run at the end, i.e. includes also claimed relations --- .../oa/graph/raw_all/oozie_app/workflow.xml | 75 +++++++++---------- 1 file changed, 37 insertions(+), 38 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index e7320de3b3..321ca40909 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -548,42 +548,7 @@ - - - - - - ${(shouldPatchRelations eq "true") and - (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")} - - - - - - - - yarn - cluster - PatchRelations - eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 - - --graphBasePath${workingDir}/graph_raw - --workingDir${workingDir}/patch_relations - --idMappingPath${idMappingPath} - - - - + @@ -596,7 +561,6 @@ - yarn @@ -805,7 +769,42 @@ - + + + + + + ${(shouldPatchRelations eq "true") and + (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")} + + + + + + + + yarn + cluster + PatchRelations + eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --graphBasePath${graphOutputPath} + --workingDir${workingDir}/patch_relations + --idMappingPath${idMappingPath} + + + + \ No newline at end of file From 6e3554a45e4ac1598b3a6177c9d3a85f687b7325 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 29 Jul 2021 13:56:37 +0200 Subject: [PATCH 61/92] [provision] lowercase relation filter --- .../java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index 7d53d35549..b3f7854924 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -10,6 +10,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -81,6 +82,7 @@ public class PrepareRelationsJob { Set relationFilter = Optional .ofNullable(parser.get("relationFilter")) + .map(String::toLowerCase) .map(s -> Sets.newHashSet(Splitter.on(",").split(s))) .orElse(new HashSet<>()); log.info("relationFilter: {}", relationFilter); @@ -130,7 +132,7 @@ public class PrepareRelationsJob { JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath) .filter(rel -> rel.getDataInfo().getDeletedbyinference() == false) - .filter(rel -> relationFilter.contains(rel.getRelClass()) == false); + .filter(rel -> relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())) == false); JavaRDD pruned = pruneRels( pruneRels( From 576693d782d2ff51908168a519f19a4f70097136 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 30 Jul 2021 10:13:33 +0200 Subject: [PATCH 62/92] added unit test for PatchRelationsApplication --- .../graph/raw/PatchRelationsApplication.java | 3 + .../raw/PatchRelationApplicationTest.java | 89 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/id_mapping.json | 5 ++ .../dhp/oa/graph/raw/relations_to_patch.json | 6 ++ 4 files changed, 103 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index c2bcf69f09..dddc53bc8e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -79,6 +79,9 @@ public class PatchRelationsApplication { final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + log.info("relations: {}", rels.count()); + log.info("idMapping: {}", idMapping.count()); + rels .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") .map((MapFunction, Relation>) t -> { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java new file mode 100644 index 0000000000..def53c085e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java @@ -0,0 +1,89 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import com.fasterxml.jackson.databind.ObjectMapper; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Optional; + +public class PatchRelationApplicationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final String ID_MAPPING_PATH = "map/id_mapping.json"; + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(PatchRelationApplicationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(PatchRelationApplicationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PatchRelationApplicationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + FileUtils.copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"), + workingDir.resolve(ID_MAPPING_PATH).toFile() + ); + + FileUtils.copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"), + workingDir.resolve("graphBasePath/relation/rels.json").toFile() + ); + + } + + @BeforeEach + public void setUp() throws IOException { + + + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testPatchRelationApplication() throws Exception { + + PatchRelationsApplication.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-graphBasePath", workingDir.toString() + "/graphBasePath", + "-workingDir", workingDir.toString() + "/workingDir", + "-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH + }); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json new file mode 100644 index 0000000000..640d042b1d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/id_mapping.json @@ -0,0 +1,5 @@ +{"oldId": "1a", "newId": "1b"} +{"oldId": "2a", "newId": "2b"} +{"oldId": "3a", "newId": "3b"} +{"oldId": "4a", "newId": "4b"} +{"oldId": "5a", "newId": "5b"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json new file mode 100644 index 0000000000..3e1203b183 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json @@ -0,0 +1,6 @@ +{"source":"1a","target":"10a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"10a","target":"1a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} From 9bc4fd3b69981716c6a6b96b1234871539bf2f79 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 30 Jul 2021 10:34:05 +0200 Subject: [PATCH 63/92] Patch FCT relations - fixed issue with join --- .../dhp/oa/graph/raw/PatchRelationsApplication.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index dddc53bc8e..5bbc8a975d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -82,7 +82,7 @@ public class PatchRelationsApplication { log.info("relations: {}", rels.count()); log.info("idMapping: {}", idMapping.count()); - rels + Dataset fj = rels .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") .map((MapFunction, Relation>) t -> { final Relation r = t._1(); @@ -90,8 +90,9 @@ public class PatchRelationsApplication { .map(RelationIdMapping::getNewId) .ifPresent(r::setSource); return r; - }, Encoders.bean(Relation.class)) - .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left") + }, Encoders.bean(Relation.class)); + + fj.joinWith(idMapping, fj.col("target").equalTo(idMapping.col("oldId")), "left") .map((MapFunction, Relation>) t -> { final Relation r = t._1(); Optional.ofNullable(t._2()) From a6a38cca9ec383e992cbafe82b30159f573e3f2b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 30 Jul 2021 11:06:11 +0200 Subject: [PATCH 64/92] fixed implementation of PatchRelationsApplication, refined the relative unit test --- .../graph/raw/PatchRelationsApplication.java | 181 +++++++++--------- .../graph/raw/common/RelationIdMapping.java | 29 +-- .../raw/PatchRelationApplicationTest.java | 148 ++++++++------ .../dhp/oa/graph/raw/relations_to_patch.json | 2 +- 4 files changed, 198 insertions(+), 162 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index dddc53bc8e..5523863ff0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -1,10 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.raw; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; -import eu.dnetlib.dhp.schema.oaf.Relation; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.FileNotFoundException; +import java.util.Objects; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -15,104 +17,111 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; +import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; -import java.io.FileNotFoundException; -import java.util.Objects; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class PatchRelationsApplication { - private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class); + private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - Optional.ofNullable( - PatchRelationsApplication.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json")) - .orElseThrow(FileNotFoundException::new) - )); - parser.parseArgument(args); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Optional + .ofNullable( + PatchRelationsApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json")) + .orElseThrow(FileNotFoundException::new))); + parser.parseArgument(args); - final Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String graphBasePath = parser.get("graphBasePath"); - log.info("graphBasePath: {}", graphBasePath); + final String graphBasePath = parser.get("graphBasePath"); + log.info("graphBasePath: {}", graphBasePath); - final String workingDir = parser.get("workingDir"); - log.info("workingDir: {}", workingDir); + final String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); - final String idMappingPath = parser.get("idMappingPath"); - log.info("idMappingPath: {}", idMappingPath); + final String idMappingPath = parser.get("idMappingPath"); + log.info("idMappingPath: {}", idMappingPath); - final SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath)); - } + final SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath)); + } - /** - * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the - * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location. - * - * @param spark the SparkSession - * @param graphBasePath base graph path providing the set of relations to patch - * @param workingDir intermediate storage location - * @param idMappingPath dataset providing the old -> new identifier mapping - */ - private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) { + /** + * Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the + * mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location. + * + * @param spark the SparkSession + * @param graphBasePath base graph path providing the set of relations to patch + * @param workingDir intermediate storage location + * @param idMappingPath dataset providing the old -> new identifier mapping + */ + private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, + final String idMappingPath) { - final String relationPath = graphBasePath + "/relation"; + final String relationPath = graphBasePath + "/relation"; - final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); - final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); + final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); - log.info("relations: {}", rels.count()); - log.info("idMapping: {}", idMapping.count()); + log.info("relations: {}", rels.count()); + log.info("idMapping: {}", idMapping.count()); - rels - .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") - .map((MapFunction, Relation>) t -> { - final Relation r = t._1(); - Optional.ofNullable(t._2()) - .map(RelationIdMapping::getNewId) - .ifPresent(r::setSource); - return r; - }, Encoders.bean(Relation.class)) - .joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left") - .map((MapFunction, Relation>) t -> { - final Relation r = t._1(); - Optional.ofNullable(t._2()) - .map(RelationIdMapping::getNewId) - .ifPresent(r::setTarget); - return r; - }, Encoders.bean(Relation.class)) - .map( - (MapFunction) OBJECT_MAPPER::writeValueAsString, - Encoders.STRING()) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(workingDir); + final Dataset bySource = rels + .joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left") + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional + .ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setSource); + return r; + }, Encoders.bean(Relation.class)); - spark.read().textFile(workingDir) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .text(relationPath); - } + bySource + .joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left") + .map((MapFunction, Relation>) t -> { + final Relation r = t._1(); + Optional + .ofNullable(t._2()) + .map(RelationIdMapping::getNewId) + .ifPresent(r::setTarget); + return r; + }, Encoders.bean(Relation.class)) + .map( + (MapFunction) OBJECT_MAPPER::writeValueAsString, + Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(workingDir); + spark + .read() + .textFile(workingDir) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(relationPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java index f251da8c33..d5852ab709 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/RelationIdMapping.java @@ -1,24 +1,25 @@ + package eu.dnetlib.dhp.oa.graph.raw.common; public class RelationIdMapping { - private String oldId; + private String oldId; - private String newId; + private String newId; - public String getOldId() { - return oldId; - } + public String getOldId() { + return oldId; + } - public void setOldId(final String oldId) { - this.oldId = oldId; - } + public void setOldId(final String oldId) { + this.oldId = oldId; + } - public String getNewId() { - return newId; - } + public String getNewId() { + return newId; + } - public void setNewId(final String newId) { - this.newId = newId; - } + public void setNewId(final String newId) { + this.newId = newId; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java index def53c085e..3fd3654161 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationApplicationTest.java @@ -1,89 +1,115 @@ + package eu.dnetlib.dhp.oa.graph.raw; -import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import static org.junit.jupiter.api.Assertions.assertEquals; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.Optional; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Relation; public class PatchRelationApplicationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String ID_MAPPING_PATH = "map/id_mapping.json"; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final String ID_MAPPING_PATH = "map/id_mapping.json"; - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class); + private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(PatchRelationApplicationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(PatchRelationApplicationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(PatchRelationApplicationTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(PatchRelationApplicationTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(PatchRelationApplicationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + spark = SparkSession + .builder() + .appName(PatchRelationApplicationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); - FileUtils.copyInputStreamToFile( - PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"), - workingDir.resolve(ID_MAPPING_PATH).toFile() - ); + FileUtils + .copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"), + workingDir.resolve(ID_MAPPING_PATH).toFile()); - FileUtils.copyInputStreamToFile( - PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"), - workingDir.resolve("graphBasePath/relation/rels.json").toFile() - ); + FileUtils + .copyInputStreamToFile( + PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"), + workingDir.resolve("graphBasePath/relation/rels.json").toFile()); - } + } - @BeforeEach - public void setUp() throws IOException { + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + public void testPatchRelationApplication() throws Exception { - } + final String graphBasePath = workingDir.toString() + "/graphBasePath"; + PatchRelationsApplication.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-graphBasePath", graphBasePath, + "-workingDir", workingDir.toString() + "/workingDir", + "-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH + }); - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + final List rels = spark + .read() + .textFile(graphBasePath + "/relation") + .map( + (MapFunction) s -> OBJECT_MAPPER.readValue(s, Relation.class), + Encoders.bean(Relation.class)) + .collectAsList(); - @Test - public void testPatchRelationApplication() throws Exception { + assertEquals(6, rels.size()); - PatchRelationsApplication.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-graphBasePath", workingDir.toString() + "/graphBasePath", - "-workingDir", workingDir.toString() + "/workingDir", - "-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH - }); + assertEquals(0, getCount(rels, "1a"), "should be patched to 1b"); + assertEquals(0, getCount(rels, "2a"), "should be patched to 2b"); - } + assertEquals(2, getCount(rels, "10a"), "not included in patching"); + assertEquals(2, getCount(rels, "20a"), "not included in patching"); + + assertEquals(2, getCount(rels, "15a"), "not included in patching"); + assertEquals(2, getCount(rels, "25a"), "not included in patching"); + + assertEquals(2, getCount(rels, "1b"), "patched from 1a"); + assertEquals(2, getCount(rels, "2b"), "patched from 2a"); + } + + private long getCount(List rels, final String id) { + return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count(); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json index 3e1203b183..31755c53d5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relations_to_patch.json @@ -3,4 +3,4 @@ {"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} {"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} {"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} -{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} +{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} \ No newline at end of file From 11e26c020a85b874bec96e870cd9856c7a204000 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 30 Jul 2021 11:54:13 +0200 Subject: [PATCH 65/92] Update 'README.md' --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 39d4d98e4a..0a0bd82ab5 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,2 @@ # dnet-hadoop -Dnet-hadoop is a tool for \ No newline at end of file +Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning. \ No newline at end of file From 74afe43c3abaca564998f3bf91840276c03d4c85 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 4 Aug 2021 10:16:17 +0200 Subject: [PATCH 66/92] fixed wrong test file --- .../eu/dnetlib/dhp/sx/graph/oaf_to_summary | 30 +++++++------------ 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary index 4d581044a2..e1fd758b41 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary @@ -1,20 +1,10 @@ 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Unfortunately, conventional wave theories based on Stokes-type expansions do not consider fluid motions at levels above the unperturbed fluid level. The usual practice of extrapolating the fluid kinematics from the unperturbed free surface to higher points in the fluid is generally reasonable for narrowband waves, but for broadband ocean waves this results in dramatic (and nonphysical) overestimation of surface velocities. Consequently, practical approximations for random waves are at best empirical and are often only loosely constrained by physical principles. In the present work, the authors formulate the governing equations for water waves in an incompressible and inviscid fluid, using a boundary-fitted coordinate system (i.e., sigma or s coordinates) to derive expressions for near-surface kinematics in nonlinear random waves from first principles. Comparison to a numerical model valid for highly nonlinear waves shows that the new results 1) are consistent with second-order Stokes theory, 2) are similar to extrapolation methods in narrowband waves, and 3) greatly improve estimates of surface kinematics in random seas.","dataInfo":null}],"dateofacceptance":{"value":"2017-05-09T19:33:59Z","dataInfo":null},"publisher":{"value":"American Meteorological 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(ISSCC)","issnPrinted":null,"issnOnline":null,"issnLinking":null,"ep":null,"iss":null,"sp":null,"vol":null,"edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":null}} \ No newline at end of file From 73dc082927a1bd2561bac10073c075a4575df690 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 5 Aug 2021 15:20:50 +0200 Subject: [PATCH 67/92] added new dumped field (openaccessroute, pid and alternate identifier at the level of the instance) and the bipFinder measure at the level of the result --- .../dhp/oa/graph/dump/ResultMapper.java | 52 ++++++++++++++++--- 1 file changed, 46 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index fe9b4e443d..9f665c06dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -5,6 +5,16 @@ import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; +import eu.dnetlib.dhp.schema.dump.oaf.Author; +import eu.dnetlib.dhp.schema.dump.oaf.Country; +import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.ModelConstants; @@ -13,10 +23,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ResultMapper implements Serializable { @@ -130,6 +136,13 @@ public class ResultMapper implements Serializable { break; } + Optional> mes = Optional.ofNullable(input.getMeasures()); + if(mes.isPresent()){ + List measure = new ArrayList<>(); + mes.get().forEach(m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(u.getKey(), u.getValue())))); + out.setMeasures(measure); + } + Optional .ofNullable(input.getAuthor()) .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); @@ -395,11 +408,12 @@ public class ResultMapper implements Serializable { } private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional - .ofNullable(i.getAccessright()); + Optional opAr = Optional.ofNullable(i.getAccessright()); + if (opAr.isPresent()) { if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance .setAccessright( AccessRight @@ -407,9 +421,35 @@ public class ResultMapper implements Serializable { code, Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); + if (opAr.get().getOpenAccessRoute() != null){ + switch (opAr.get().getOpenAccessRoute()){ + case hybrid: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); + break; + case gold: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); + break; + case green: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); + break; + case bronze: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); + break; + + } + } } } + Optional.ofNullable(i.getPid()) + .ifPresent(pid -> instance.setPid( + pid.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + Optional.ofNullable(i.getAlternateIdentifier()) + .ifPresent(ai -> instance.setAlternateIdentifier(ai.stream().map(p -> ControlledField. + newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()))); + Optional .ofNullable(i.getLicense()) .ifPresent(value -> instance.setLicense(value.getValue())); From c3931557e3985c70a99159b414d138576aaf278b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 6 Aug 2021 18:56:18 +0200 Subject: [PATCH 68/92] extended the logic of the dump to consider the validation date in the relation (also in the dumped result for communities and funders at the level of the project), the extention on the instance for the APC, the pid, the alternate identifiers, and the extention of the AccessRight to store the OpenAccessRoute. Added new resourec for testing and extended the old class to verify the new dump. Fixed also issue on relation dump: only relation whose source and target are entities in the graph are dumped. The same hold for references to projects --- .../dhp/oa/graph/dump/DumpProducts.java | 4 +- .../oa/graph/dump/QueryInformationSystem.java | 18 +- .../dhp/oa/graph/dump/ResultMapper.java | 133 ++++++---- .../dhp/oa/graph/dump/SaveCommunityMap.java | 23 +- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 4 +- .../graph/dump/community/CommunitySplit.java | 2 +- .../community/SparkPrepareResultProject.java | 14 +- .../dump/complete/DumpGraphEntities.java | 26 +- .../dhp/oa/graph/dump/complete/Extractor.java | 2 +- .../dump/complete/QueryInformationSystem.java | 7 +- .../dump/complete/SparkDumpRelationJob.java | 11 +- .../funderresults/SparkDumpFunderResults.java | 65 +++-- .../SparkResultLinkedToProject.java | 43 ++-- .../graph/dump/funder_result_parameters.json | 4 +- .../graph/dump/input_parameters_link_prj.json | 4 +- .../dhp/oa/graph/dump/DumpJobTest.java | 182 +++++++++++++- .../dump/PrepareResultProjectJobTest.java | 109 ++++++++ .../dump/QueryInformationSystemTest.java | 2 +- .../oa/graph/dump/SplitForCommunityTest.java | 8 +- .../dump/complete/CreateRelationTest.java | 238 +++++++++--------- .../graph/dump/complete/DumpRelationTest.java | 76 +++++- .../complete/QueryInformationSystemTest.java | 5 +- .../ResultLinkedToProjectTest.java | 10 +- .../dump/funderresult/SplitPerFunderTest.java | 8 +- .../dump/funderresource/extendeddump/project | 12 + .../funderresource/extendeddump/publication | 3 +- .../dump/funderresource/extendeddump/relation | 9 - .../graph/dump/funderresource/match/project | 12 + .../match/{relations.json => relation} | 4 +- .../graph/dump/funderresource/nomatch/project | 12 + .../nomatch/{relations.json => relation} | 0 .../oa/graph/dump/relation/relation_validated | 30 +++ .../resultDump/publication_extendedinstance | 1 + .../resultProject/match_validatedRels/project | 23 ++ .../match_validatedRels/relation | 8 + pom.xml | 2 +- 36 files changed, 820 insertions(+), 294 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/project delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/relation create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/project rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/{relations.json => relation} (95%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/project rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/{relations.json => relation} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels/relation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index 4ddcea9e8f..d09e584a33 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -37,8 +37,8 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump( - spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); + execDump( + spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index d1f295fcf6..7b661ac668 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -29,15 +29,15 @@ public class QueryInformationSystem { ""; private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//CONFIGURATION/context[./@id=%s] " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//CONFIGURATION/context[./@id=%s] " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; public CommunityMap getCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, DocumentException { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 9f665c06dd..e381173383 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -5,6 +5,10 @@ import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; import eu.dnetlib.dhp.schema.dump.oaf.Author; import eu.dnetlib.dhp.schema.dump.oaf.Country; @@ -14,15 +18,13 @@ import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; import eu.dnetlib.dhp.schema.dump.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; public class ResultMapper implements Serializable { @@ -137,9 +139,12 @@ public class ResultMapper implements Serializable { } Optional> mes = Optional.ofNullable(input.getMeasures()); - if(mes.isPresent()){ + if (mes.isPresent()) { List measure = new ArrayList<>(); - mes.get().forEach(m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(u.getKey(), u.getValue())))); + mes + .get() + .forEach( + m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue())))); out.setMeasures(measure); } @@ -271,18 +276,17 @@ public class ResultMapper implements Serializable { } - List pids = new ArrayList<>(); + Optional .ofNullable(input.getPid()) .ifPresent( - value -> value + value -> out.setPid(value .stream() - .forEach( - p -> pids - .add( + .map( + p -> ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())))); - out.setPid(pids); + .newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()))); + oStr = Optional.ofNullable(input.getDateofacceptance()); if (oStr.isPresent()) { out.setPublicationdate(oStr.get().getValue()); @@ -292,10 +296,11 @@ public class ResultMapper implements Serializable { out.setPublisher(oStr.get().getValue()); } - List sourceList = new ArrayList<>(); + Optional .ofNullable(input.getSource()) - .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()) )); + // value.stream().forEach(s -> sourceList.add(s.getValue()))); // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); List subjectList = new ArrayList<>(); Optional @@ -421,8 +426,8 @@ public class ResultMapper implements Serializable { code, Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); - if (opAr.get().getOpenAccessRoute() != null){ - switch (opAr.get().getOpenAccessRoute()){ + if (opAr.get().getOpenAccessRoute() != null) { + switch (opAr.get().getOpenAccessRoute()) { case hybrid: instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); break; @@ -441,14 +446,25 @@ public class ResultMapper implements Serializable { } } - Optional.ofNullable(i.getPid()) - .ifPresent(pid -> instance.setPid( - pid.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); + Optional + .ofNullable(i.getPid()) + .ifPresent( + pid -> instance + .setPid( + pid + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); - Optional.ofNullable(i.getAlternateIdentifier()) - .ifPresent(ai -> instance.setAlternateIdentifier(ai.stream().map(p -> ControlledField. - newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()))); + Optional + .ofNullable(i.getAlternateIdentifier()) + .ifPresent( + ai -> instance + .setAlternateIdentifier( + ai + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); Optional .ofNullable(i.getLicense()) @@ -554,34 +570,55 @@ public class ResultMapper implements Serializable { return a; } - private static Pid getOrcid(List p) { - for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return Pid - .newInstance( + private static Pid getAuthorPid(StructuredProperty pid) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid - .newInstance( + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - ); - } - - } + ); } + } + + private static Pid getOrcid(List p) { + List pid_list = p.stream().map(pid -> { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || + (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))){ + return pid; + } + return null; + }).filter(pid -> pid != null).collect(Collectors.toList()); + + if(pid_list.size() == 1){ + return getAuthorPid(pid_list.get(0)); + } + + List orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid() + .equals(ModelConstants.ORCID)).collect(Collectors.toList()); + if(orcid.size() == 1){ + return getAuthorPid(orcid.get(0)); + } + orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid() + .equals(ModelConstants.ORCID_PENDING)).collect(Collectors.toList()); + if(orcid.size() == 1){ + return getAuthorPid(orcid.get(0)); + } + return null; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 7db19f7719..71bea60478 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.oa.graph.dump; import java.io.BufferedWriter; @@ -54,10 +55,10 @@ public class SaveCommunityMap implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SaveCommunityMap.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); + .toString( + SaveCommunityMap.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -71,8 +72,10 @@ public class SaveCommunityMap implements Serializable { final String isLookUpUrl = parser.get("isLookUpUrl"); log.info("isLookUpUrl: {}", isLookUpUrl); - final Boolean singleCommunity = Optional.ofNullable(parser.get("singleDeposition")) - .map(Boolean::valueOf).orElse(false); + final Boolean singleCommunity = Optional + .ofNullable(parser.get("singleDeposition")) + .map(Boolean::valueOf) + .orElse(false); final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); @@ -82,8 +85,12 @@ public class SaveCommunityMap implements Serializable { } - private void saveCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, IOException, DocumentException { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); + private void saveCommunityMap(boolean singleCommunity, String community_id) + throws ISLookUpException, IOException, DocumentException { + writer + .write( + Utils.OBJECT_MAPPER + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); writer.close(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index 28881b253a..e0b7cf5d73 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -48,14 +48,14 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - //final String communityMapPath = parser.get("communityMapPath"); + // final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - //CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); + // CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); RemoteIterator fileStatusListIterator = fileSystem .listFiles( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index d64c265034..6abca22559 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -49,7 +49,7 @@ public class CommunitySplit implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); communities - .keySet() + .keySet() .stream() .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 2d43888b46..6b4baafde8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -8,6 +8,8 @@ import java.io.StringReader; import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -76,7 +78,7 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); @@ -96,7 +98,7 @@ public class SparkPrepareResultProject implements Serializable { rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); - Project ps = getProject(p); + Project ps = getProject(p, first._2); List projList = new ArrayList<>(); projList.add(ps); @@ -105,7 +107,7 @@ public class SparkPrepareResultProject implements Serializable { eu.dnetlib.dhp.schema.oaf.Project op = c._1(); if (!projectSet.contains(op.getId())) { projList - .add(getProject(op)); + .add(getProject(op, c._2)); projectSet.add(op.getId()); @@ -120,7 +122,7 @@ public class SparkPrepareResultProject implements Serializable { .json(outputPath); } - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) { + private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { Project p = Project .newInstance( op.getId(), @@ -155,7 +157,9 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - + if (relation.getValidated()){ + p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); + } return p; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index b843ec3657..7441baaef1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; +import static com.jayway.jsonpath.Filter.filter; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; @@ -8,8 +9,12 @@ import java.io.StringReader; import java.util.*; import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -448,19 +453,18 @@ public class DumpGraphEntities implements Serializable { private static void organizationMap(SparkSession spark, String inputPath, String outputPath, Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), - Encoders.bean(Organization.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + Utils.readPath(spark, inputPath, inputClazz) + .map( + (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), + Encoders.bean(Organization.class)) + .filter((FilterFunction) o -> o!= null) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } - private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { if (org.getDataInfo().getDeletedbyinference()) return null; Organization organization = new Organization(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index f76f920137..7e8ddfaf8c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -129,7 +129,7 @@ public class Extractor implements Serializable { return relationList.iterator(); }, Encoders.bean(Relation.class)) - .write() + .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 3736b73807..ecb5881985 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -5,6 +5,8 @@ import java.io.StringReader; import java.util.*; import java.util.function.Consumer; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Element; @@ -12,9 +14,9 @@ import org.dom4j.Node; import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; +import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.dhp.utils.DHPUtils; public class QueryInformationSystem { @@ -136,6 +138,9 @@ public class QueryInformationSystem { } private String makeOpenaireId(Node el, String prefix) { + if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))){ + return null; + } String funder = null; String grantId = null; String funding = null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index 11c3600dd9..7370b43f8f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -107,13 +107,10 @@ public class SparkDumpRelationJob implements Serializable { } } } -// Optional -// .ofNullable(relation.getDataInfo()) -// .ifPresent( -// datainfo -> rel_new -// .setProvenance( -// Provenance -// .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust()))); + if(relation.getValidated()){ + rel_new.setValidated(relation.getValidated()); + rel_new.setValidationDate(relation.getValidationDate()); + } return rel_new; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 9fcdcaf78d..1c70525539 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -44,9 +44,9 @@ public class SparkDumpFunderResults implements Serializable { parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -55,40 +55,38 @@ public class SparkDumpFunderResults implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("relationPath: {}", graphPath); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, relationPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath, graphPath); + }); } private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String relationPath) { + String graphPath) { - Dataset relation = Utils - .readPath(spark, relationPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils + .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - List funderList = relation - .select("target") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); + + List funderList = project + .select("id") + .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) + .distinct() + .collectAsList(); funderList.forEach(funder -> { String fundernsp = funder.substring(3); @@ -109,7 +107,7 @@ public class SparkDumpFunderResults implements Serializable { } private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { + String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { @@ -117,7 +115,6 @@ public class SparkDumpFunderResults implements Serializable { } for (Project p : r.getProjects()) { if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { if (p.getFunder().getShortName().equals(funderName)) return r; @@ -129,15 +126,15 @@ public class SparkDumpFunderResults implements Serializable { } return null; }, Encoders.bean(CommunityResult.class)) - .filter((FilterFunction) r -> r != null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funderName); } private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { + String funderDump) { if (funder.startsWith("40|irb")) { dumpResults(funder, results, outputPath, "HRZZ"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index e0355d6d61..55578fdaba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -21,14 +22,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; -import org.apache.spark.sql.*; -import eu.dnetlib.dhp.schema.oaf.Project; + /** * Selects the results linked to projects. Only for these results the dump will be performed. - * The code to perform the dump and to expend the dumped results with the informaiton related to projects + * The code to perform the dump and to expend the dumped results with the information related to projects * is the one used for the dump of the community products */ public class SparkResultLinkedToProject implements Serializable { @@ -78,6 +79,7 @@ public class SparkResultLinkedToProject implements Serializable { private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, String inputPath, String outputPath, String graphPath) { + Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); @@ -86,25 +88,32 @@ public class SparkResultLinkedToProject implements Serializable { .filter( "dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)) - .groupByKey( - (MapFunction< R, String>) value -> value - .getId(), + results.createOrReplaceTempView("result"); + relations.createOrReplaceTempView("relation"); + project.createOrReplaceTempView("project"); + + Dataset tmp = spark + .sql( + "Select res.* " + + "from relation rel " + + "join result res " + + "on rel.source = res.id " + + "join project p " + + "on rel.target = p.id " + + "") + .as(Encoders.bean(inputClazz)); + tmp + .groupByKey( + (MapFunction) value -> value + .getId(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) + .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 9a5a553b1f..5dc8e8910e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -18,8 +18,8 @@ "paramRequired": false }, { - "paramName": "rp", - "paramLongName": "relationPath", + "paramName": "gp", + "paramLongName": "graphPath", "paramDescription": "the relationPath", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index fdd9492fe7..f5641bc456 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -24,8 +24,8 @@ "paramRequired": true }, { - "paramName":"rp", - "paramLongName":"relationPath", + "paramName":"gp", + "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 6b64a4124d..39454192eb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -7,7 +7,13 @@ import java.nio.file.Path; import java.util.Arrays; import java.util.List; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.sun.xml.internal.ws.policy.AssertionSet; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import org.apache.commons.io.FileUtils; +import org.apache.neethi.Assertion; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -199,7 +205,7 @@ public class DumpJobTest { Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + } @@ -302,6 +308,178 @@ public class DumpJobTest { //TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + } + + @Test + public void testPublicationExtendedInstance(){ + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + verificationDataset.show(false); + + GraphResult gr = verificationDataset.first(); + + + Assertions.assertEquals(2, gr.getMeasures().size()); + Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("influence") + && m.getValue().equals("1.62759106106e-08"))); + Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("popularity") + && m.getValue().equals("0.22519296"))); + + Assertions.assertEquals(6, gr.getAuthor().size()); + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Nikolaidou,Charitini") && + a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") + && a.getRank() == 1 && a.getPid() == null)); + + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Votsi,Nefta") && + a.getName().equals("Nefta") && a.getSurname().equals("Votsi") + && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Sgardelis,Steanos") && + a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") + && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Halley,John") && + a.getName().equals("John") && a.getSurname().equals("Halley") + && a.getRank() == 4 && a.getPid() == null)); + + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Pantis,John") && + a.getName().equals("John") && a.getSurname().equals("Pantis") + && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + + Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Tsiafouli,Maria") && + a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") + && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + + Assertions.assertEquals("publication", gr.getType()); + + Assertions.assertEquals("eng", gr.getLanguage().getCode()); + Assertions.assertEquals("English", gr.getLanguage().getLabel()); + + Assertions.assertEquals(1, gr.getCountry().size()); + Assertions.assertEquals("IT" , gr.getCountry().get(0).getCode()); + Assertions.assertEquals("Italy" , gr.getCountry().get(0).getLabel()); + Assertions.assertTrue( gr.getCountry().get(0).getProvenance() == null); + + Assertions.assertEquals(12, gr.getSubjects().size()); + Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") + && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Natura 2000") + && s.getSubject().getScheme().equals("") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + + Assertions.assertEquals("Ecosystem Service capacity is higher in areas of multiple designation types", + gr.getMaintitle()); + + Assertions.assertEquals(null, gr.getSubtitle()); + + Assertions.assertEquals(1, gr.getDescription().size()); + + Assertions.assertTrue(gr.getDescription().get(0).startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); + Assertions.assertTrue(gr.getDescription().get(0).endsWith("start complying with new standards and demands for nature conservation and environmental management.")); + + Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); + + Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); + + Assertions.assertEquals(null, gr.getEmbargoenddate()); + + Assertions.assertEquals(1, gr.getSource().size()); + Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); + + Assertions.assertEquals(1, gr.getFormat().size()); + Assertions.assertEquals("text/html", gr.getFormat().get(0)); + + Assertions.assertEquals(0, gr.getContributor().size()); + + Assertions.assertEquals(0, gr.getCoverage().size()); + + Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); + Assertions.assertEquals(Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); + Assertions.assertEquals(null, gr.getBestaccessright().getOpenAccessRoute()); + + Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); + Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); + Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); + Assertions.assertEquals("", gr.getContainer().getIssnLinking()); + + Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); + + Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); + + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + + Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); + + Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); + + Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); + + Assertions.assertEquals(null, gr.getSize()); + + Assertions.assertEquals(null, gr.getVersion()); + + Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); + + Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); + + Assertions.assertEquals(2, gr.getOriginalId().size()); + Assertions.assertTrue(gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") + && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); + + Assertions.assertEquals(1, gr.getPid().size()); + Assertions.assertTrue(gr.getPid().get(0).getScheme().equals("doi") + && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); + + Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); + + Assertions.assertEquals(1, gr.getInstance().size()); + + Instance instance = gr.getInstance().get(0); + Assertions.assertEquals(0, instance.getPid().size()); + Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); + Assertions.assertTrue(instance.getAlternateIdentifier().get(0).getScheme().equals("doi") + && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); + Assertions.assertEquals(null, instance.getLicense()); + Assertions.assertTrue(instance.getAccessright().getCode().equals(Constants.accessRightsCoarMap + .get(ModelConstants.ACCESS_RIGHT_OPEN))); + Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); + Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); + Assertions.assertEquals(2, instance.getUrl().size()); + Assertions.assertTrue(instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") + && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); + Assertions.assertEquals("2017-01-01",instance.getPublicationdate()); + Assertions.assertEquals(null,instance.getArticleprocessingcharge()); + Assertions.assertEquals("peerReviewed", instance.getRefereed()); + + } @Test @@ -455,6 +633,8 @@ public class DumpJobTest { Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); + + // verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset // .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") // .count() diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index d5a9ba8ddb..2fbd37db7b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -7,9 +7,11 @@ import java.nio.file.Path; import java.util.HashMap; import org.apache.commons.io.FileUtils; +import org.apache.neethi.Assertion; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; @@ -236,4 +238,111 @@ public class PrepareResultProjectJobTest { } + @Test + public void testMatchValidated() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + Assertions.assertTrue(verificationDataset.count() == 2); + + Assertions + .assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + Assertions + .assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + Assertions.assertEquals(3, resultExplodedProvenance.count()); + Assertions.assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); + Assertions + .assertEquals( + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); + + Assertions + .assertEquals( + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java index 499df3a097..729e78844a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java @@ -24,7 +24,7 @@ public class QueryInformationSystemTest { private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java index 42ad5634a7..946e136555 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java @@ -79,7 +79,7 @@ public class SplitForCommunityTest { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/dh-ch") + .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark @@ -92,7 +92,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/egi") + .textFile(workingDir.toString() + "/split/EGI_Federation") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -105,7 +105,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/ni") + .textFile(workingDir.toString() + "/split/Neuroinformatics") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -118,7 +118,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/science-innovation-policy") + .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java index 448034d0cf..76d4064229 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java @@ -1,8 +1,6 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; - -import eu.dnetlib.dhp.schema.oaf.Project; import java.util.*; import java.util.function.Consumer; import java.util.stream.Collectors; @@ -16,6 +14,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; public class CreateRelationTest { @@ -205,7 +204,7 @@ public class CreateRelationTest { " \n" + " oac_ni\n" + " 2018-03-01T12:00:00\n" + - " \n" + + " \n" + " \n" + " \n" + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + @@ -441,57 +440,65 @@ public class CreateRelationTest { " oaa_elixir-gr\n" + " 2018-03-01T12:00:00\n" + " \n" + - " \n" + - " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" + - " \n" + - " 1U24RR025736-01\n" + - " NIH\n" + - " \n" + - " \n" + - " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" + - " \n" + - " 0223843\n" + - " NSF\n" + - " \n" + - " \n" + - " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" + - " \n" + - " 5R01MH082795-05\n" + - " NIH\n" + - " \n" + - " \n" + - " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" + - " \n" + - " 1P50MH096889-01A1\n" + - " NIH\n" + - " \n" + - " \n" + - " Enhancement of the 1000 Functional Connectome Project\n" + - " \n" + - " 1R03MH096321-01A1\n" + - " TUBITAK\n" + - " \n" + - " \n" + - " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" + - " \n" + - " 1131441\n" + - " NSF\n" + - " \n" + - " \n" + - " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" + - " \n" + - " 0121950\n" + - " NSF\n" + - " \n" + - " \n" + - " Transforming statistical methodology for neuroimaging meta-analysis.\n" + - " \n" + - " 100309\n" + - " WT\n" + - " \n" + - " " + + " \n" + + " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" + + + " \n" + + " 1U24RR025736-01\n" + + " NIH\n" + + " \n" + + " \n" + + " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" + + + " \n" + + " 0223843\n" + + " NSF\n" + + " \n" + + " \n" + + " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" + + + " \n" + + " 5R01MH082795-05\n" + + " NIH\n" + + " \n" + + " \n" + + " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" + + + " \n" + + " 1P50MH096889-01A1\n" + + " NIH\n" + + " \n" + + " \n" + + " Enhancement of the 1000 Functional Connectome Project\n" + + + " \n" + + " 1R03MH096321-01A1\n" + + " TUBITAK\n" + + " \n" + + " \n" + + " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" + + + " \n" + + " 1131441\n" + + " NSF\n" + + " \n" + + " \n" + + " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" + + + " \n" + + " 0121950\n" + + " NSF\n" + + " \n" + + " \n" + + " Transforming statistical methodology for neuroimaging meta-analysis.\n" + + + " \n" + + " 100309\n" + + " WT\n" + + " \n" + + " " + - " \n" + " \n" + " \n" + " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + @@ -626,88 +633,87 @@ public class CreateRelationTest { final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem - .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); + .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); - List rList = new ArrayList<>(); cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - Assertions.assertEquals(44 , rList.size()); + Assertions.assertEquals(44, rList.size()); Assertions - .assertFalse( - rList - .stream() - .map(r -> r.getSource().getId()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))); + .assertFalse( + rList + .stream() + .map(r -> r.getSource().getId()) + .collect(Collectors.toSet()) + .contains( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))); Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getTarget() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getTarget() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .map(r -> r.getTarget().getId()) - .collect(Collectors.toSet()); + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .map(r -> r.getTarget().getId()) + .collect(Collectors.toSet()); Assertions - .assertTrue( - tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && - tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4") ); + .assertTrue( + tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && + tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4")); rList.forEach(rel -> { - if (rel.getSource().getId().startsWith("40|")){ + if (rel.getSource().getId().startsWith("40|")) { String proj = rel.getSource().getId().substring(3); Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java index d80eb3ec6e..a310448a43 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java @@ -10,6 +10,7 @@ import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; @@ -71,7 +72,7 @@ public class DumpRelationTest { public void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") .getPath(); SparkDumpRelationJob.main(new String[] { @@ -93,6 +94,8 @@ public class DumpRelationTest { verificationDataset.createOrReplaceTempView("table"); + verificationDataset.foreach((ForeachFunction)r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + Dataset check = spark .sql( "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " @@ -127,4 +130,75 @@ public class DumpRelationTest { .count()); } + @Test + public void test2() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + verificationDataset.createOrReplaceTempView("table"); + + verificationDataset.foreach((ForeachFunction)r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + Dataset check = spark + .sql( + "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " + + + "from table "); + + Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 20, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); + Assertions + .assertEquals( + 7, check + .filter( + "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + + "and provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); + Assertions + .assertEquals( + 1, check + .filter( + "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + + "and provenance = 'Inferred by OpenAIRE'") + .count()); + + Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); + Assertions + .assertEquals( + 2, check + .filter( + "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + + "and provenance = 'Harvested' and validated = true " + + "and validationDate = '2021-08-06'") + .count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java index d769aa138a..fa1528e90f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java @@ -6,6 +6,7 @@ import static org.mockito.Mockito.lenient; import java.util.*; import java.util.function.Consumer; +import eu.dnetlib.dhp.schema.common.ModelSupport; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -528,7 +529,7 @@ public class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|"); + queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); Assertions.assertEquals(5, cInfoList.size()); } @@ -539,7 +540,7 @@ public class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10"); + queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); cInfoList.forEach(contextInfo -> { switch (contextInfo.getId()) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 6c5ebbab36..0b062abd5c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -75,8 +75,8 @@ public class ResultLinkedToProjectTest { .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -84,7 +84,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", graphPath }); @@ -109,7 +109,7 @@ public class ResultLinkedToProjectTest { .getPath(); final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -117,7 +117,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", relationPath }); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 26187f0a32..9dd2aa41eb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -75,7 +75,7 @@ public class SplitPerFunderTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-outputPath", workingDir.toString() + "/split", "-sourcePath", sourcePath, - "-relationPath", sourcePath + "-graphPath", sourcePath }); @@ -143,5 +143,11 @@ public class SplitPerFunderTest { .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); + // CONICYT 0 + tmp = sc + .textFile(workingDir.toString() + "/split/CONICYTF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(0, tmp.count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/project b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/project new file mode 100644 index 0000000000..f68cead77a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/project @@ -0,0 +1,12 @@ 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It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)","New York University [Abu Dhabi] ; NYU System (NYU)","Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Muséum National d'Histoire Naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)","University of Washington [Seattle]","Université Libre de Bruxelles [Bruxelles] (ULB)","ANR-09-CEXC-0006,FOCEA,Excellence pour une synergie observation-modèle et l'évaluation de l'état écologique de la Méditerranée Nord Occidentale(2009)","ANR: 11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)","ANR: 11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011)","European Project: 624170,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IEF,SEAQUEST(2015)","Institut méditerranéen d'océanologie (MIO) ; Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)","Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)","Université libre de Bruxelles (ULB)","Processus et interactions de fine échelle océanique (PROTEO) ; Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN) ; Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)","ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011)"],"country":[{"code":"FR","label":"France","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2019-10-11T09:44:42.348Z","description":["International audience; Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Pensoft 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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels/relation b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels/relation new file mode 100644 index 0000000000..d829e66abb --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels/relation @@ -0,0 +1,8 @@ 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.../dhp/oa/graph/dump/DumpJobTest.java | 56 ++++++++++++++++++- .../resultDump/publication_extendedinstance | 2 +- 2 files changed, 56 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 39454192eb..d7c247499a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -308,6 +308,60 @@ public class DumpJobTest { //TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + } + + @Test + public void testPublicationExtendedInstance2Community() throws JsonProcessingException { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run(false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); + + //the common fields in the result have been checked with the test below. Now checking only + // community specific fields + + CommunityResult cr = verificationDataset.first(); + + Assertions.assertEquals(1, cr.getContext().size()); + Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); + Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); + Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); + Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); + Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); + + Assertions.assertEquals(1, cr.getCollectedfrom().size()); + Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); + Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); + + Assertions.assertEquals(1, cr.getInstance().size()); + Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getInstance().get(0).getCollectedfrom().getKey()); + Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); + Assertions.assertEquals("10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); + Assertions.assertEquals("One Ecosystem",cr.getInstance().get(0).getHostedby().getValue()); + + } @Test @@ -337,7 +391,6 @@ public class DumpJobTest { .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(1, verificationDataset.count()); - verificationDataset.show(false); GraphResult gr = verificationDataset.first(); @@ -472,6 +525,7 @@ public class DumpJobTest { .get(ModelConstants.ACCESS_RIGHT_OPEN))); Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); + Assertions.assertTrue(instance.getType().equals("Article")); Assertions.assertEquals(2, instance.getUrl().size()); Assertions.assertTrue(instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance index 92d7e53c0b..043be7b1a9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance @@ -1 +1 @@ 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Pensoft 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Service trade-offs and synergies","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":" cultural services","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"provisioning services","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"regulating services","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"supporting services","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Ecosystem Service capacity is higher in areas of multiple designation types","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Pensoft Publishers","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[{"value":"One Ecosystem 2: e13718","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"fulltext":[],"format":[{"value":"text/html","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"}],"id":"dh-ch"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":"green"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd","value":"One Ecosystem","dataInfo":null},"url":["https://doi.org/10.3897/oneeco.2.e13718","https://oneecosystem.pensoft.net/article/13718/"],"distributionlocation":"","collectedfrom":{"key":"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db","value":"Pensoft","dataInfo":null},"pid":[],"alternateIdentifier":[{"value":"10.3897/oneeco.2.e13718","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":{"classid":"0001","classname":"peerReviewed","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"}}],"journal":{"name":"One Ecosystem","issnPrinted":"","issnOnline":"2367-8194","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":null,"conferencedate":null,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}} \ No newline at end of file From bc9e3a06ba9a436d2bbe00d56accd78f55508abd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Aug 2021 15:46:06 +0200 Subject: [PATCH 70/92] Graph Dump - extended the test class --- .../dhp/oa/graph/dump/DumpJobTest.java | 609 +++++++++++------- 1 file changed, 374 insertions(+), 235 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index d7c247499a..3a4f05fb59 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -145,227 +145,7 @@ public class DumpJobTest { } @Test - public void testDataset() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(90, verificationDataset.count()); - -// verificationDataset -// .filter("id = '50|DansKnawCris::1a960e20087cb46b93588e4e184e8a58'") -// .foreach((ForeachFunction) rec -> System.out.println(OBJECT_MAPPER.writeValueAsString(rec))); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset - .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset - .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset - .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset - .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") - .count()); - - Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); - - Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - - - } - - @Test - public void testDataset2All() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - verificationDataset - .foreach((ForeachFunction) res -> System.out.println(OBJECT_MAPPER.writeValueAsString(res))); - } - - @Test - public void testDataset2Communities() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(0, verificationDataset.count()); - - verificationDataset.show(false); - } - - @Test - public void testPublication() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(74, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) - - } - - @Test - public void testPublicationExtendedInstance2Community() throws JsonProcessingException { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run(false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - - //the common fields in the result have been checked with the test below. Now checking only - // community specific fields - - CommunityResult cr = verificationDataset.first(); - - Assertions.assertEquals(1, cr.getContext().size()); - Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); - Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); - Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); - Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); - Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); - - Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); - Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); - - Assertions.assertEquals(1, cr.getInstance().size()); - Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getInstance().get(0).getCollectedfrom().getKey()); - Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions.assertEquals("10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem",cr.getInstance().get(0).getHostedby().getValue()); - - - } - - @Test - public void testPublicationExtendedInstance(){ + public void testPublicationDump(){ final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") .getPath(); @@ -519,7 +299,7 @@ public class DumpJobTest { Assertions.assertEquals(0, instance.getPid().size()); Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); Assertions.assertTrue(instance.getAlternateIdentifier().get(0).getScheme().equals("doi") - && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); + && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); Assertions.assertEquals(null, instance.getLicense()); Assertions.assertTrue(instance.getAccessright().getCode().equals(Constants.accessRightsCoarMap .get(ModelConstants.ACCESS_RIGHT_OPEN))); @@ -532,8 +312,379 @@ public class DumpJobTest { Assertions.assertEquals("2017-01-01",instance.getPublicationdate()); Assertions.assertEquals(null,instance.getArticleprocessingcharge()); Assertions.assertEquals("peerReviewed", instance.getRefereed()); + } + @Test + public void testDatasetDump(){ + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run(false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Dataset.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); + + //the common fields in the result have been already checked. Now checking only + // community specific fields + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getGeolocation().size()); + Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")).count()); + + Assertions.assertEquals("1024Gb", gr.getSize()); + + Assertions.assertEquals("1.01", gr.getVersion()); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + + } + + @Test + public void testSoftwareDump(){ + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run(false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Software.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getDocumentationUrl().size()); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); + + Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); + + Assertions.assertEquals("perl", gr.getProgrammingLanguage()); + + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testOrpDump(){ + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run(false, sourcePath, workingDir.toString() + "/result", + communityMapPath, OtherResearchProduct.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getContactperson().size()); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); + + Assertions.assertEquals(1, gr.getContactgroup().size()); + Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); + + Assertions.assertEquals(2, gr.getTool().size()); + Assertions.assertTrue(gr.getTool().contains("tool1")); + Assertions.assertTrue(gr.getTool().contains("tool2")); + + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testPublicationDumpCommunity() throws JsonProcessingException { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run(false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); + + //the common fields in the result have been already checked. Now checking only + // community specific fields + + CommunityResult cr = verificationDataset.first(); + + Assertions.assertEquals(1, cr.getContext().size()); + Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); + Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); + Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); + Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); + Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); + + Assertions.assertEquals(1, cr.getCollectedfrom().size()); + Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); + Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); + + Assertions.assertEquals(1, cr.getInstance().size()); + Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getInstance().get(0).getCollectedfrom().getKey()); + Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); + Assertions.assertEquals("10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); + Assertions.assertEquals("One Ecosystem",cr.getInstance().get(0).getHostedby().getValue()); + + + } + + @Test + public void testDataset() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(90, verificationDataset.count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset + .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset + .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset + .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset + .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") + .count()); + + Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); + + Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); + + + + } + + @Test + public void testDataset2All() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); + + Assertions.assertEquals(5, verificationDataset.count()); + + } + + @Test + public void testDataset2Communities() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + + } + + @Test + public void testPublication() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(74, verificationDataset.count()); + verificationDataset.show(false); + + Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); + } @Test @@ -566,9 +717,7 @@ public class DumpJobTest { Assertions.assertEquals(6, verificationDataset.count()); Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - verificationDataset.show(false); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -602,9 +751,6 @@ public class DumpJobTest { Assertions.assertEquals(3, verificationDataset.count()); Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - verificationDataset.show(false); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -621,7 +767,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -668,7 +813,7 @@ public class DumpJobTest { .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(23, verificationDataset.count()); - // verificationDataset.show(false); + Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); @@ -688,12 +833,6 @@ public class DumpJobTest { Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - -// verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset -// .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") -// .count() - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } } From 8daaa32e90f1ddc88a24c2603723230ae57cec9a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Aug 2021 15:46:29 +0200 Subject: [PATCH 71/92] Graph Dump - added resources for testing --- .../dhp/oa/graph/dump/resultDump/dataset_extendedinstance | 1 + .../eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance | 1 + .../dhp/oa/graph/dump/resultDump/software_extendedinstance | 1 + 3 files changed, 3 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance new file mode 100644 index 0000000000..14ca9c10cd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance @@ -0,0 +1 @@ +{"author":[{"affiliation":[],"fullname":"Santana Quintero, Mario","name":"Mario","pid":[],"rank":1,"surname":"Santana Quintero"},{"affiliation":[],"fullname":"Giansante, Christian","name":"Christian","pid":[],"rank":2,"surname":"Giansante"},{"affiliation":[],"fullname":"Sharp, Rachel","name":"Rachel","pid":[],"rank":3,"surname":"Sharp"},{"affiliation":[],"fullname":"Bernard, Tristan","name":"Tristan","pid":[],"rank":4,"surname":"Bernard"},{"affiliation":[],"fullname":"Waheed, Khadija","name":"Khadija","pid":[],"rank":5,"surname":"Waheed"},{"affiliation":[],"fullname":"Merchant, Arkoun","name":"Arkoun","pid":[],"rank":6,"surname":"Merchant"},{"affiliation":[],"fullname":"Lapko, Spencer","name":"Spencer","pid":[],"rank":7,"surname":"Lapko"}],"bestaccessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::e783372970a1dc066ce99c673090ff88","value":"Federated Research Data Repository / Dépôt fédéré de données de 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It's architect, J. Bowes, designed approximately 30 other buildings in the Ottawa area during his career. The four-storey, masonry clad building was originally designed to house L'Institut Canadien Français d'Ottawa. This organization played a key role in the advancement to officially make Ottawa a bilingual city. Nearly a century later, 18 York St was acquired by the NCC after it had been gutted by a fire in 1970, and was rehabilitated into a Franco-Ontarian theatre. 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+{"measures":[{"key":"influence","value":"1.62759106106e-08"},{"key":"popularity","value":"0.22519296"}],"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem Services hotspots"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Natura 2000"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Quiet Protected Areas"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Biodiversity"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Agriculture"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Elevation"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Slope"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Ecosystem Service trade-offs and synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management."],"publicationdate":"2017-01-01","publisher":"Pensoft Publishers","embargoenddate":null,"source":["One Ecosystem 2: e13718"],"format":["text/html"],"contributor":[],"coverage":[],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/","openAccessRoute":null},"container":{"name":"One 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+{"measures":[{"key":"influence","value":"1.62759106106e-08"},{"key":"popularity","value":"0.22519296"}],"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem 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synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management."],"publicationdate":"2017-01-01","publisher":"Pensoft Publishers","embargoenddate":null,"source":["One Ecosystem 2: e13718"],"format":["text/html"],"contributor":[],"coverage":[],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/","openAccessRoute":null},"container":{"name":"One Ecosystem","issnPrinted":"","issnOnline":"2367-8194","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":null,"conferencedate":null},"documentationUrl":null,"codeRepositoryUrl":null,"programmingLanguage":null,"contactperson":null,"contactgroup":null,"tool":null,"size":null,"version":null,"geolocation":null,"id":"50|fakeoft_____::00ea4a1cd53806a97d62ea6bf268f2a2","originalId":["50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2","10.3897/oneeco.2.e13718"],"pid":[{"scheme":"doi","value":"10.1016/j.triboint.2014.05.004"}],"dateofcollection":"2020-03-23T00:20:51.392Z","lastupdatetimestamp":1628257970612,"projects":null,"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.9"}]}],"collectedfrom":[{"key":"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db","value":"Pensoft"}],"instance":[{"pid":[],"alternateIdentifier":[{"scheme":"doi","value":"10.3897/oneeco.2.e13718"}],"license":null,"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/","openAccessRoute":"green"},"type":"Article","url":["https://doi.org/10.3897/oneeco.2.e13718","https://oneecosystem.pensoft.net/article/13718/"],"articleprocessingcharge":null,"publicationdate":"2017-01-01","refereed":"peerReviewed","hostedby":{"key":"10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd","value":"One Ecosystem"},"collectedfrom":{"key":"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db","value":"Pensoft"}}]} \ No newline at end of file From a90bac3bc92d44f1628dd309ee5e7404b4b06e09 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Aug 2021 16:36:54 +0200 Subject: [PATCH 73/92] Graph Dump - added method to test class to verify addition of validation date in projects for community result --- .../oa/graph/dump/UpdateProjectInfoTest.java | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java index 20a46cee08..fd34433c6e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java @@ -5,11 +5,17 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; +import java.util.logging.Filter; +import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -135,4 +141,85 @@ public class UpdateProjectInfoTest { resultExplodedProvenance.show(false); } + @Test + public void testValidatedRelation() throws Exception{ + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") + .getPath(); + + SparkUpdateProjectInfo.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-preparedInfoPath", sourcePath + "/preparedInfoValidated", + "-outputPath", workingDir.toString() + "/result", + "-sourcePath", sourcePath + "/publication_extendedmodel" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + verificationDataset.show(false); + + Assertions.assertEquals(2, verificationDataset.count()); + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " + + + "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " + + "from dataset " + + "lateral view explode(projects) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + + Assertions.assertEquals(2, resultExplodedProvenance.count()); + resultExplodedProvenance.show(false); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") + .count()); + + Project project = verificationDataset + .map((MapFunction) cr -> cr.getProjects().stream().filter(p -> p.getValidated() != null).collect(Collectors.toList()).get(0) + , Encoders.bean(Project.class)).first(); + + Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); + Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); + Assertions.assertTrue(project.getFunder().getFundingStream() == null); + Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); + + + project = verificationDataset + .map((MapFunction) cr -> cr.getProjects().stream().filter(p -> p.getValidated() == null).collect(Collectors.toList()).get(0) + , Encoders.bean(Project.class)).first(); + + + Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); + Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); + Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); + + + } + } From c4ccd7b32c3ee272188bad034b6f0264c074bd88 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 1 Oct 2021 12:59:47 +0200 Subject: [PATCH 74/92] - --- .../dhp/oa/dedup/SparkWhitelistSimRels.java | 196 +-- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 1266 +++++++++-------- .../eu/dnetlib/dhp/PropagationConstant.java | 11 +- .../SparkOrcidToResultFromSemRelJob.java | 7 +- ...kResultToCommunityFromOrganizationJob.java | 4 +- ...parkResultToCommunityThroughSemRelJob.java | 4 +- .../dhp/oa/graph/dump/ResultMapper.java | 84 +- .../dhp/oa/graph/dump/SaveCommunityMap.java | 10 +- .../community/SparkPrepareResultProject.java | 10 +- .../dump/complete/DumpGraphEntities.java | 25 +- .../dump/complete/QueryInformationSystem.java | 6 +- .../dump/complete/SparkDumpRelationJob.java | 2 +- .../funderresults/SparkDumpFunderResults.java | 53 +- .../SparkResultLinkedToProject.java | 1 - .../dhp/oa/graph/dump/DumpJobTest.java | 380 +++-- .../dump/PrepareResultProjectJobTest.java | 152 +- .../oa/graph/dump/UpdateProjectInfoTest.java | 83 +- .../graph/dump/complete/DumpRelationTest.java | 80 +- .../complete/QueryInformationSystemTest.java | 8 +- .../dump/funderresult/SplitPerFunderTest.java | 4 +- .../provision/IndexRecordTransformerTest.java | 3 +- pom.xml | 2 +- 22 files changed, 1273 insertions(+), 1118 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java index fa7d335700..48ba8a6f6d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.oa.dedup; import java.io.IOException; @@ -35,117 +36,124 @@ import scala.Tuple3; public class SparkWhitelistSimRels extends AbstractSparkAction { - private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class); + private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class); - private static final String WHITELIST_SEPARATOR = "####"; + private static final String WHITELIST_SEPARATOR = "####"; - public SparkWhitelistSimRels(ArgumentApplicationParser parser, SparkSession spark) { - super(parser, spark); - } + public SparkWhitelistSimRels(ArgumentApplicationParser parser, SparkSession spark) { + super(parser, spark); + } - public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); - parser.parseArgument(args); + public static void main(String[] args) throws Exception { + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkCreateSimRels.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); + parser.parseArgument(args); - SparkConf conf = new SparkConf(); - new SparkWhitelistSimRels(parser, getSparkSession(conf)) - .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); - } + SparkConf conf = new SparkConf(); + new SparkWhitelistSimRels(parser, getSparkSession(conf)) + .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); + } - @Override - public void run(ISLookUpService isLookUpService) - throws DocumentException, IOException, ISLookUpException, SAXException { + @Override + public void run(ISLookUpService isLookUpService) + throws DocumentException, IOException, ISLookUpException, SAXException { - // read oozie parameters - final String graphBasePath = parser.get("graphBasePath"); - final String isLookUpUrl = parser.get("isLookUpUrl"); - final String actionSetId = parser.get("actionSetId"); - final String workingPath = parser.get("workingPath"); - final int numPartitions = Optional - .ofNullable(parser.get("numPartitions")) - .map(Integer::valueOf) - .orElse(NUM_PARTITIONS); - final String whiteListPath = parser.get("whiteListPath"); + // read oozie parameters + final String graphBasePath = parser.get("graphBasePath"); + final String isLookUpUrl = parser.get("isLookUpUrl"); + final String actionSetId = parser.get("actionSetId"); + final String workingPath = parser.get("workingPath"); + final int numPartitions = Optional + .ofNullable(parser.get("numPartitions")) + .map(Integer::valueOf) + .orElse(NUM_PARTITIONS); + final String whiteListPath = parser.get("whiteListPath"); - log.info("numPartitions: '{}'", numPartitions); - log.info("graphBasePath: '{}'", graphBasePath); - log.info("isLookUpUrl: '{}'", isLookUpUrl); - log.info("actionSetId: '{}'", actionSetId); - log.info("workingPath: '{}'", workingPath); - log.info("whiteListPath: '{}'", whiteListPath); + log.info("numPartitions: '{}'", numPartitions); + log.info("graphBasePath: '{}'", graphBasePath); + log.info("isLookUpUrl: '{}'", isLookUpUrl); + log.info("actionSetId: '{}'", actionSetId); + log.info("workingPath: '{}'", workingPath); + log.info("whiteListPath: '{}'", whiteListPath); - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - //file format: source####target - Dataset> whiteListRels = spark.createDataset(sc - .textFile(whiteListPath) - //check if the line is in the correct format: id1####id2 - .filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2) - .map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1])) - .rdd(), - Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + // file format: source####target + Dataset> whiteListRels = spark + .createDataset( + sc + .textFile(whiteListPath) + // check if the line is in the correct format: id1####id2 + .filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2) + .map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1])) + .rdd(), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - // for each dedup configuration - for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) { + // for each dedup configuration + for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) { - final String entity = dedupConf.getWf().getEntityType(); - final String subEntity = dedupConf.getWf().getSubEntityValue(); - log.info("Adding whitelist simrels for: '{}'", subEntity); + final String entity = dedupConf.getWf().getEntityType(); + final String subEntity = dedupConf.getWf().getSubEntityValue(); + log.info("Adding whitelist simrels for: '{}'", subEntity); - final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); + final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity); - Dataset> entities = spark.createDataset(sc - .textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) - .repartition(numPartitions) - .mapToPair( - (PairFunction) s -> { - MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); - return new Tuple2<>(d.getIdentifier(), "present"); - }) - .rdd(), - Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + Dataset> entities = spark + .createDataset( + sc + .textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) + .repartition(numPartitions) + .mapToPair( + (PairFunction) s -> { + MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); + return new Tuple2<>(d.getIdentifier(), "present"); + }) + .rdd(), + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - Dataset> whiteListRels1 = whiteListRels - .joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner") - .map((MapFunction, Tuple2>, Tuple2>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + Dataset> whiteListRels1 = whiteListRels + .joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner") + .map( + (MapFunction, Tuple2>, Tuple2>) Tuple2::_1, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - Dataset> whiteListRels2 = whiteListRels1 - .joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner") - .map((MapFunction, Tuple2>, Tuple2>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + Dataset> whiteListRels2 = whiteListRels1 + .joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner") + .map( + (MapFunction, Tuple2>, Tuple2>) Tuple2::_1, + Encoders.tuple(Encoders.STRING(), Encoders.STRING())); - Dataset whiteListSimRels = whiteListRels2 - .map((MapFunction, Relation>) - r -> createSimRel(r._1(), r._2(), entity), - Encoders.bean(Relation.class) - ); + Dataset whiteListSimRels = whiteListRels2 + .map( + (MapFunction, Relation>) r -> createSimRel(r._1(), r._2(), entity), + Encoders.bean(Relation.class)); - saveParquet(whiteListSimRels, outputPath, SaveMode.Append); - } - } + saveParquet(whiteListSimRels, outputPath, SaveMode.Append); + } + } - private Relation createSimRel(String source, String target, String entity) { - final Relation r = new Relation(); - r.setSource(source); - r.setTarget(target); - r.setSubRelType("dedupSimilarity"); - r.setRelClass("isSimilarTo"); - r.setDataInfo(new DataInfo()); + private Relation createSimRel(String source, String target, String entity) { + final Relation r = new Relation(); + r.setSource(source); + r.setTarget(target); + r.setSubRelType("dedupSimilarity"); + r.setRelClass("isSimilarTo"); + r.setDataInfo(new DataInfo()); - switch (entity) { - case "result": - r.setRelType("resultResult"); - break; - case "organization": - r.setRelType("organizationOrganization"); - break; - default: - throw new IllegalArgumentException("unmanaged entity type: " + entity); - } - return r; - } + switch (entity) { + case "result": + r.setRelType("resultResult"); + break; + case "organization": + r.setRelType("organizationOrganization"); + break; + default: + throw new IllegalArgumentException("unmanaged entity type: " + entity); + } + return r; + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index fa03f93a6b..549988767f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -48,634 +48,640 @@ import scala.Tuple2; @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest implements Serializable { - @Mock(serializable = true) - ISLookUpService isLookUpService; - - private static SparkSession spark; - private static JavaSparkContext jsc; - - private static String testGraphBasePath; - private static String testOutputBasePath; - private static String testDedupGraphBasePath; - private static final String testActionSetId = "test-orchestrator"; - private static String whitelistPath; - private static List whiteList; - - private static String WHITELIST_SEPARATOR = "####"; - - @BeforeAll - public static void cleanUp() throws IOException, URISyntaxException { - - testGraphBasePath = Paths - .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()) - .toFile() - .getAbsolutePath(); - testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); - - testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); - - whitelistPath = Paths - .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI()) - .toFile() - .getAbsolutePath(); - whiteList = IOUtils.readLines(new FileReader(whitelistPath)); - - FileUtils.deleteDirectory(new File(testOutputBasePath)); - FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - - final SparkConf conf = new SparkConf(); - conf.set("spark.sql.shuffle.partitions", "200"); - spark = SparkSession - .builder() - .appName(SparkDedupTest.class.getSimpleName()) - .master("local[*]") - .config(conf) - .getOrCreate(); - - jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - } - - @BeforeEach - public void setUp() throws IOException, ISLookUpException { - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"))); - - lenient() - .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"))); - } - - @Test - @Order(1) - void createSimRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); - - parser - .parseArgument( - new String[]{ - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath, - "-np", "50" - }); - - new SparkCreateSimRels(parser, spark).run(isLookUpService); - - long orgs_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) - .count(); - - long pubs_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) - .count(); - - long sw_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software")) - .count(); - - long ds_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset")) - .count(); - - long orp_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) - .count(); - - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); - assertEquals(336, sw_simrel); - assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); - } - - @Test - @Order(2) - void whitelistSimRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkWhitelistSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); - - parser - .parseArgument( - new String[]{ - "-i", testGraphBasePath, - "-asi", testActionSetId, - "-la", "lookupurl", - "-w", testOutputBasePath, - "-np", "50", - "-wl", whitelistPath - }); - - new SparkWhitelistSimRels(parser, spark).run(isLookUpService); - - long orgs_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) - .count(); - - long pubs_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) - .count(); - - long ds_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset")) - .count(); - - long orp_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) - .count(); - - //entities simrels supposed to be equal to the number of previous step (no rels in whitelist) - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); - assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); - - //entities simrels to be different from the number of previous step (new simrels in the whitelist) - Dataset sw_simrel = spark - .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software")); - - //check if the first relation in the whitelist exists - assertTrue(sw_simrel - .as(Encoders.bean(Relation.class)) - .toJavaRDD() - .filter(rel -> - rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1])).count() > 0); - //check if the second relation in the whitelist exists - assertTrue(sw_simrel - .as(Encoders.bean(Relation.class)) - .toJavaRDD() - .filter(rel -> - rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1])).count() > 0); - - assertEquals(338, sw_simrel.count()); - - } - - @Test - @Order(3) - void cutMergeRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - - parser - .parseArgument( - new String[]{ - "-i", - testGraphBasePath, - "-asi", - testActionSetId, - "-la", - "lookupurl", - "-w", - testOutputBasePath, - "-cc", - "3" - }); - - new SparkCreateMergeRels(parser, spark).run(isLookUpService); - - long orgs_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") - .as(Encoders.bean(Relation.class)) - .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) - .groupBy("source") - .agg(count("target").alias("cnt")) - .select("source", "cnt") - .where("cnt > 3") - .count(); - - long pubs_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .as(Encoders.bean(Relation.class)) - .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) - .groupBy("source") - .agg(count("target").alias("cnt")) - .select("source", "cnt") - .where("cnt > 3") - .count(); - long sw_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") - .as(Encoders.bean(Relation.class)) - .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) - .groupBy("source") - .agg(count("target").alias("cnt")) - .select("source", "cnt") - .where("cnt > 3") - .count(); - - long ds_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") - .as(Encoders.bean(Relation.class)) - .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) - .groupBy("source") - .agg(count("target").alias("cnt")) - .select("source", "cnt") - .where("cnt > 3") - .count(); - - long orp_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") - .as(Encoders.bean(Relation.class)) - .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) - .groupBy("source") - .agg(count("target").alias("cnt")) - .select("source", "cnt") - .where("cnt > 3") - .count(); - - assertEquals(0, orgs_mergerel); - assertEquals(0, pubs_mergerel); - assertEquals(0, sw_mergerel); - assertEquals(0, ds_mergerel); - assertEquals(0, orp_mergerel); - - FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")); - FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")); - FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")); - FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")); - FileUtils - .deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")); - } - - @Test - @Order(4) - void createMergeRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); - - parser - .parseArgument( - new String[]{ - "-i", - testGraphBasePath, - "-asi", - testActionSetId, - "-la", - "lookupurl", - "-w", - testOutputBasePath - }); - - new SparkCreateMergeRels(parser, spark).run(isLookUpService); - - long orgs_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") - .count(); - long pubs_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .count(); - long sw_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") - .count(); - long ds_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") - .count(); - - long orp_mergerel = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") - .count(); - - assertEquals(1272, orgs_mergerel); - assertEquals(1438, pubs_mergerel); - assertEquals(286, sw_mergerel); - assertEquals(472, ds_mergerel); - assertEquals(718, orp_mergerel); - - } - - @Test - @Order(5) - void createDedupRecordTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateDedupRecord.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); - parser - .parseArgument( - new String[]{ - "-i", - testGraphBasePath, - "-asi", - testActionSetId, - "-la", - "lookupurl", - "-w", - testOutputBasePath - }); - - new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - - long orgs_deduprecord = jsc - .textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord") - .count(); - long pubs_deduprecord = jsc - .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") - .count(); - long sw_deduprecord = jsc - .textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") - .count(); - long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count(); - long orp_deduprecord = jsc - .textFile( - testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord") - .count(); - - assertEquals(85, orgs_deduprecord); - assertEquals(65, pubs_deduprecord); - assertEquals(49, sw_deduprecord); - assertEquals(97, ds_deduprecord); - assertEquals(89, orp_deduprecord); - } - - @Test - @Order(6) - void updateEntityTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkUpdateEntity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); - parser - .parseArgument( - new String[]{ - "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath - }); - - new SparkUpdateEntity(parser, spark).run(isLookUpService); - - long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); - long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); - long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); - long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); - long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); - long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count(); - long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count(); - - long mergedOrgs = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); - - long mergedPubs = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); - - long mergedSw = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); - - long mergedDs = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); - - long mergedOrp = spark - .read() - .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") - .as(Encoders.bean(Relation.class)) - .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) - .distinct() - .count(); - - assertEquals(896, publications); - assertEquals(838, organizations); - assertEquals(100, projects); - assertEquals(100, datasource); - assertEquals(198, softwares); - assertEquals(389, dataset); - assertEquals(517, otherresearchproduct); - - long deletedOrgs = jsc - .textFile(testDedupGraphBasePath + "/organization") - .filter(this::isDeletedByInference) - .count(); - - long deletedPubs = jsc - .textFile(testDedupGraphBasePath + "/publication") - .filter(this::isDeletedByInference) - .count(); - - long deletedSw = jsc - .textFile(testDedupGraphBasePath + "/software") - .filter(this::isDeletedByInference) - .count(); - - long deletedDs = jsc - .textFile(testDedupGraphBasePath + "/dataset") - .filter(this::isDeletedByInference) - .count(); - - long deletedOrp = jsc - .textFile(testDedupGraphBasePath + "/otherresearchproduct") - .filter(this::isDeletedByInference) - .count(); - - assertEquals(mergedOrgs, deletedOrgs); - assertEquals(mergedPubs, deletedPubs); - assertEquals(mergedSw, deletedSw); - assertEquals(mergedDs, deletedDs); - assertEquals(mergedOrp, deletedOrp); - } - - @Test - @Order(7) - void propagateRelationTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkPropagateRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); - parser - .parseArgument( - new String[]{ - "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath - }); - - new SparkPropagateRelation(parser, spark).run(isLookUpService); - - long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); - - assertEquals(4860, relations); - - // check deletedbyinference - final Dataset mergeRels = spark - .read() - .load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")) - .as(Encoders.bean(Relation.class)); - final JavaPairRDD mergedIds = mergeRels - .where("relClass == 'merges'") - .select(mergeRels.col("target")) - .distinct() - .toJavaRDD() - .mapToPair( - (PairFunction) r -> new Tuple2(r.getString(0), "d")); - - JavaRDD toCheck = jsc - .textFile(testDedupGraphBasePath + "/relation") - .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json)) - .join(mergedIds) - .map(t -> t._2()._1()) - .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json)) - .join(mergedIds) - .map(t -> t._2()._1()); - - long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); - long updated = toCheck.count(); - - assertEquals(updated, deletedbyinference); - } - - @Test - @Order(8) - void testRelations() throws Exception { - testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10); - testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2); - } - - private void testUniqueness(String path, int expected_total, int expected_unique) { - Dataset rel = spark - .read() - .textFile(getClass().getResource(path).getPath()) - .map( - (MapFunction) s -> new ObjectMapper().readValue(s, Relation.class), - Encoders.bean(Relation.class)); - - assertEquals(expected_total, rel.count()); - assertEquals(expected_unique, rel.distinct().count()); - } - - @AfterAll - public static void finalCleanUp() throws IOException { - FileUtils.deleteDirectory(new File(testOutputBasePath)); - FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - } - - public boolean isDeletedByInference(String s) { - return s.contains("\"deletedbyinference\":true"); - } + @Mock(serializable = true) + ISLookUpService isLookUpService; + + private static SparkSession spark; + private static JavaSparkContext jsc; + + private static String testGraphBasePath; + private static String testOutputBasePath; + private static String testDedupGraphBasePath; + private static final String testActionSetId = "test-orchestrator"; + private static String whitelistPath; + private static List whiteList; + + private static String WHITELIST_SEPARATOR = "####"; + + @BeforeAll + public static void cleanUp() throws IOException, URISyntaxException { + + testGraphBasePath = Paths + .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()) + .toFile() + .getAbsolutePath(); + testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + whitelistPath = Paths + .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI()) + .toFile() + .getAbsolutePath(); + whiteList = IOUtils.readLines(new FileReader(whitelistPath)); + + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + + final SparkConf conf = new SparkConf(); + conf.set("spark.sql.shuffle.partitions", "200"); + spark = SparkSession + .builder() + .appName(SparkDedupTest.class.getSimpleName()) + .master("local[*]") + .config(conf) + .getOrCreate(); + + jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + } + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset"))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"))); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct"))) + .thenReturn( + IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"))); + } + + @Test + @Order(1) + void createSimRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkCreateSimRels.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + + parser + .parseArgument( + new String[] { + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath, + "-np", "50" + }); + + new SparkCreateSimRels(parser, spark).run(isLookUpService); + + long orgs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) + .count(); + + long pubs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) + .count(); + + long sw_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software")) + .count(); + + long ds_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset")) + .count(); + + long orp_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) + .count(); + + assertEquals(3082, orgs_simrel); + assertEquals(7036, pubs_simrel); + assertEquals(336, sw_simrel); + assertEquals(442, ds_simrel); + assertEquals(6750, orp_simrel); + } + + @Test + @Order(2) + void whitelistSimRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkWhitelistSimRels.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); + + parser + .parseArgument( + new String[] { + "-i", testGraphBasePath, + "-asi", testActionSetId, + "-la", "lookupurl", + "-w", testOutputBasePath, + "-np", "50", + "-wl", whitelistPath + }); + + new SparkWhitelistSimRels(parser, spark).run(isLookUpService); + + long orgs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) + .count(); + + long pubs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) + .count(); + + long ds_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset")) + .count(); + + long orp_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) + .count(); + + // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) + assertEquals(3082, orgs_simrel); + assertEquals(7036, pubs_simrel); + assertEquals(442, ds_simrel); + assertEquals(6750, orp_simrel); + + // entities simrels to be different from the number of previous step (new simrels in the whitelist) + Dataset sw_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software")); + + // check if the first relation in the whitelist exists + assertTrue( + sw_simrel + .as(Encoders.bean(Relation.class)) + .toJavaRDD() + .filter( + rel -> rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0]) + && rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1])) + .count() > 0); + // check if the second relation in the whitelist exists + assertTrue( + sw_simrel + .as(Encoders.bean(Relation.class)) + .toJavaRDD() + .filter( + rel -> rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0]) + && rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1])) + .count() > 0); + + assertEquals(338, sw_simrel.count()); + + } + + @Test + @Order(3) + void cutMergeRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkCreateMergeRels.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + + parser + .parseArgument( + new String[] { + "-i", + testGraphBasePath, + "-asi", + testActionSetId, + "-la", + "lookupurl", + "-w", + testOutputBasePath, + "-cc", + "3" + }); + + new SparkCreateMergeRels(parser, spark).run(isLookUpService); + + long orgs_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + long pubs_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + long sw_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + long ds_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + long orp_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + assertEquals(0, orgs_mergerel); + assertEquals(0, pubs_mergerel); + assertEquals(0, sw_mergerel); + assertEquals(0, ds_mergerel); + assertEquals(0, orp_mergerel); + + FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")); + FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")); + FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")); + FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")); + FileUtils + .deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")); + } + + @Test + @Order(4) + void createMergeRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkCreateMergeRels.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + + parser + .parseArgument( + new String[] { + "-i", + testGraphBasePath, + "-asi", + testActionSetId, + "-la", + "lookupurl", + "-w", + testOutputBasePath + }); + + new SparkCreateMergeRels(parser, spark).run(isLookUpService); + + long orgs_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .count(); + long pubs_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .count(); + long sw_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .count(); + long ds_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") + .count(); + + long orp_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") + .count(); + + assertEquals(1272, orgs_mergerel); + assertEquals(1438, pubs_mergerel); + assertEquals(286, sw_mergerel); + assertEquals(472, ds_mergerel); + assertEquals(718, orp_mergerel); + + } + + @Test + @Order(5) + void createDedupRecordTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkCreateDedupRecord.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + parser + .parseArgument( + new String[] { + "-i", + testGraphBasePath, + "-asi", + testActionSetId, + "-la", + "lookupurl", + "-w", + testOutputBasePath + }); + + new SparkCreateDedupRecord(parser, spark).run(isLookUpService); + + long orgs_deduprecord = jsc + .textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord") + .count(); + long pubs_deduprecord = jsc + .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") + .count(); + long sw_deduprecord = jsc + .textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") + .count(); + long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count(); + long orp_deduprecord = jsc + .textFile( + testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord") + .count(); + + assertEquals(85, orgs_deduprecord); + assertEquals(65, pubs_deduprecord); + assertEquals(49, sw_deduprecord); + assertEquals(97, ds_deduprecord); + assertEquals(89, orp_deduprecord); + } + + @Test + @Order(6) + void updateEntityTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkUpdateEntity.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + parser + .parseArgument( + new String[] { + "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath + }); + + new SparkUpdateEntity(parser, spark).run(isLookUpService); + + long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count(); + long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); + long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); + long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); + long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count(); + long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count(); + + long mergedOrgs = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + long mergedPubs = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + long mergedSw = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + long mergedDs = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + long mergedOrp = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + assertEquals(896, publications); + assertEquals(838, organizations); + assertEquals(100, projects); + assertEquals(100, datasource); + assertEquals(198, softwares); + assertEquals(389, dataset); + assertEquals(517, otherresearchproduct); + + long deletedOrgs = jsc + .textFile(testDedupGraphBasePath + "/organization") + .filter(this::isDeletedByInference) + .count(); + + long deletedPubs = jsc + .textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference) + .count(); + + long deletedSw = jsc + .textFile(testDedupGraphBasePath + "/software") + .filter(this::isDeletedByInference) + .count(); + + long deletedDs = jsc + .textFile(testDedupGraphBasePath + "/dataset") + .filter(this::isDeletedByInference) + .count(); + + long deletedOrp = jsc + .textFile(testDedupGraphBasePath + "/otherresearchproduct") + .filter(this::isDeletedByInference) + .count(); + + assertEquals(mergedOrgs, deletedOrgs); + assertEquals(mergedPubs, deletedPubs); + assertEquals(mergedSw, deletedSw); + assertEquals(mergedDs, deletedDs); + assertEquals(mergedOrp, deletedOrp); + } + + @Test + @Order(7) + void propagateRelationTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkPropagateRelation.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + parser + .parseArgument( + new String[] { + "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath + }); + + new SparkPropagateRelation(parser, spark).run(isLookUpService); + + long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); + + assertEquals(4860, relations); + + // check deletedbyinference + final Dataset mergeRels = spark + .read() + .load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")) + .as(Encoders.bean(Relation.class)); + final JavaPairRDD mergedIds = mergeRels + .where("relClass == 'merges'") + .select(mergeRels.col("target")) + .distinct() + .toJavaRDD() + .mapToPair( + (PairFunction) r -> new Tuple2(r.getString(0), "d")); + + JavaRDD toCheck = jsc + .textFile(testDedupGraphBasePath + "/relation") + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()) + .mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json)) + .join(mergedIds) + .map(t -> t._2()._1()); + + long deletedbyinference = toCheck.filter(this::isDeletedByInference).count(); + long updated = toCheck.count(); + + assertEquals(updated, deletedbyinference); + } + + @Test + @Order(8) + void testRelations() throws Exception { + testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10); + testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2); + } + + private void testUniqueness(String path, int expected_total, int expected_unique) { + Dataset rel = spark + .read() + .textFile(getClass().getResource(path).getPath()) + .map( + (MapFunction) s -> new ObjectMapper().readValue(s, Relation.class), + Encoders.bean(Relation.class)); + + assertEquals(expected_total, rel.count()); + assertEquals(expected_unique, rel.distinct().count()); + } + + @AfterAll + public static void finalCleanUp() throws IOException { + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + } + + public boolean isDeletedByInference(String s) { + return s.contains("\"deletedbyinference\":true"); + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 0d7c74475e..23e97a97a8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -69,7 +69,7 @@ public class PropagationConstant { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_COUNTRY_INSTREPO_CLASS_ID, PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS)); + ModelConstants.DNET_PROVENANCE_ACTIONS)); return nc; } @@ -84,7 +84,8 @@ public class PropagationConstant { return di; } - public static Qualifier getQualifier(String inference_class_id, String inference_class_name, String qualifierSchema) { + public static Qualifier getQualifier(String inference_class_id, String inference_class_name, + String qualifierSchema) { Qualifier pa = new Qualifier(); pa.setClassid(inference_class_id); pa.setClassname(inference_class_name); @@ -108,7 +109,11 @@ public class PropagationConstant { r.setRelClass(rel_class); r.setRelType(rel_type); r.setSubRelType(subrel_type); - r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name, ModelConstants.DNET_PROVENANCE_ACTIONS)); + r + .setDataInfo( + getDataInfo( + inference_provenance, inference_class_id, inference_class_name, + ModelConstants.DNET_PROVENANCE_ACTIONS)); return r; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 68949b9004..a38b4da2e8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -173,14 +173,17 @@ public class SparkOrcidToResultFromSemRelJob { if (toaddpid) { StructuredProperty p = new StructuredProperty(); p.setValue(autoritative_author.getOrcid()); - p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES)); + p + .setQualifier( + getQualifier( + ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES)); p .setDataInfo( getDataInfo( PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS)); + ModelConstants.DNET_PROVENANCE_ACTIONS)); Optional> authorPid = Optional.ofNullable(author.getPid()); if (authorPid.isPresent()) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 1289ff644f..50df08f8c8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -10,7 +10,6 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -22,6 +21,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; @@ -130,7 +130,7 @@ public class SparkResultToCommunityFromOrganizationJob { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); + ModelConstants.DNET_PROVENANCE_ACTIONS))); propagatedContexts.add(newContext); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 7f76ead94b..f31a262307 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; @@ -126,7 +126,7 @@ public class SparkResultToCommunityThroughSemRelJob { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); + ModelConstants.DNET_PROVENANCE_ACTIONS))); return newContext; } return null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index f4bf8d52a4..988a8c7a41 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -6,6 +6,8 @@ import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; @@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; public class ResultMapper implements Serializable { @@ -278,16 +278,17 @@ public class ResultMapper implements Serializable { } - Optional .ofNullable(input.getPid()) .ifPresent( - value -> out.setPid(value - .stream() - .map( - p -> - ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList()))); + value -> out + .setPid( + value + .stream() + .map( + p -> ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); oStr = Optional.ofNullable(input.getDateofacceptance()); if (oStr.isPresent()) { @@ -298,11 +299,10 @@ public class ResultMapper implements Serializable { out.setPublisher(oStr.get().getValue()); } - Optional .ofNullable(input.getSource()) - .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()) )); - // value.stream().forEach(s -> sourceList.add(s.getValue()))); + .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()))); + // value.stream().forEach(s -> sourceList.add(s.getValue()))); // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); List subjectList = new ArrayList<>(); Optional @@ -577,48 +577,60 @@ public class ResultMapper implements Serializable { Optional di = Optional.ofNullable(pid.getDataInfo()); if (di.isPresent()) { return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); } else { return Pid - .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - ); + ); } } private static Pid getOrcid(List p) { List pid_list = p.stream().map(pid -> { if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || - (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))){ + (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { return pid; } - return null; + return null; }).filter(pid -> pid != null).collect(Collectors.toList()); - if(pid_list.size() == 1){ + if (pid_list.size() == 1) { return getAuthorPid(pid_list.get(0)); } - List orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid() - .equals(ModelConstants.ORCID)).collect(Collectors.toList()); - if(orcid.size() == 1){ + List orcid = pid_list + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } - orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid() - .equals(ModelConstants.ORCID_PENDING)).collect(Collectors.toList()); - if(orcid.size() == 1){ + orcid = pid_list + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID_PENDING)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 6cdd741ea1..9713247446 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -86,10 +86,10 @@ public class SaveCommunityMap implements Serializable { private void saveCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, IOException, DocumentException, SAXException { - writer - .write( - Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); - } + writer + .write( + Utils.OBJECT_MAPPER + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index edd6d9b234..3508e41262 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -8,8 +8,6 @@ import java.io.StringReader; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -28,9 +26,11 @@ import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; +import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -80,7 +80,9 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); @@ -159,7 +161,7 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - if (relation.getValidated()){ + if (relation.getValidated()) { p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); } return p; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 7441baaef1..7f64db41cc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -9,7 +9,6 @@ import java.io.StringReader; import java.util.*; import java.util.stream.Collectors; -import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.ForeachFunction; @@ -23,6 +22,8 @@ import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -453,18 +454,20 @@ public class DumpGraphEntities implements Serializable { private static void organizationMap(SparkSession spark, String inputPath, String outputPath, Class inputClazz) { - Utils.readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), - Encoders.bean(Organization.class)) - .filter((FilterFunction) o -> o!= null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + Utils + .readPath(spark, inputPath, inputClazz) + .map( + (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), + Encoders.bean(Organization.class)) + .filter((FilterFunction) o -> o != null) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } - private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization( + eu.dnetlib.dhp.schema.oaf.Organization org) { if (org.getDataInfo().getDeletedbyinference()) return null; Organization organization = new Organization(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index be1f211710..88c92da53d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -5,8 +5,6 @@ import java.io.StringReader; import java.util.*; import java.util.function.Consumer; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Element; @@ -15,6 +13,8 @@ import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -140,7 +140,7 @@ public class QueryInformationSystem { } private String makeOpenaireId(Node el, String prefix) { - if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))){ + if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { return null; } String funder = null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index 7370b43f8f..ab7e7e595d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -107,7 +107,7 @@ public class SparkDumpRelationJob implements Serializable { } } } - if(relation.getValidated()){ + if (relation.getValidated()) { rel_new.setValidated(relation.getValidated()); rel_new.setValidationDate(relation.getValidationDate()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index d520a9c6ab..9cddba3c54 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -41,9 +41,9 @@ public class SparkDumpFunderResults implements Serializable { parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -58,32 +58,31 @@ public class SparkDumpFunderResults implements Serializable { SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath, graphPath); + }); } private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { + String graphPath) { Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); + .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); + .select("id") + .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) + .distinct() + .collectAsList(); funderList.forEach(funder -> { String fundernsp = funder.substring(3); @@ -104,7 +103,7 @@ public class SparkDumpFunderResults implements Serializable { } private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { + String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { @@ -123,15 +122,15 @@ public class SparkDumpFunderResults implements Serializable { } return null; }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funderName); } private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { + String funderDump) { if (funder.startsWith("40|irb")) { dumpResults(funder, results, outputPath, "HRZZ"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index e17aa285c0..156ae6d633 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -80,7 +80,6 @@ public class SparkResultLinkedToProject implements Serializable { private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, String inputPath, String outputPath, String graphPath) { - Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 3a4f05fb59..bf6301ec47 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -7,17 +7,10 @@ import java.nio.file.Path; import java.util.Arrays; import java.util.List; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.sun.xml.internal.ws.policy.AssertionSet; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import org.apache.commons.io.FileUtils; -import org.apache.neethi.Assertion; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -25,10 +18,14 @@ import org.junit.jupiter.api.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -145,70 +142,121 @@ public class DumpJobTest { } @Test - public void testPublicationDump(){ + public void testPublicationDump() { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(1, verificationDataset.count()); GraphResult gr = verificationDataset.first(); - Assertions.assertEquals(2, gr.getMeasures().size()); - Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("influence") - && m.getValue().equals("1.62759106106e-08"))); - Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("popularity") - && m.getValue().equals("0.22519296"))); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("influence") + && m.getValue().equals("1.62759106106e-08"))); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("popularity") + && m.getValue().equals("0.22519296"))); Assertions.assertEquals(6, gr.getAuthor().size()); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Nikolaidou,Charitini") && - a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") - && a.getRank() == 1 && a.getPid() == null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Nikolaidou,Charitini") && + a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") + && a.getRank() == 1 && a.getPid() == null)); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Votsi,Nefta") && - a.getName().equals("Nefta") && a.getSurname().equals("Votsi") - && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Votsi,Nefta") && + a.getName().equals("Nefta") && a.getSurname().equals("Votsi") + && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Sgardelis,Steanos") && - a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") - && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Sgardelis,Steanos") && + a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") + && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Halley,John") && - a.getName().equals("John") && a.getSurname().equals("Halley") - && a.getRank() == 4 && a.getPid() == null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Halley,John") && + a.getName().equals("John") && a.getSurname().equals("Halley") + && a.getRank() == 4 && a.getPid() == null)); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Pantis,John") && - a.getName().equals("John") && a.getSurname().equals("Pantis") - && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Pantis,John") && + a.getName().equals("John") && a.getSurname().equals("Pantis") + && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); - Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Tsiafouli,Maria") && - a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") - && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null)); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Tsiafouli,Maria") && + a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") + && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); Assertions.assertEquals("publication", gr.getType()); @@ -216,27 +264,52 @@ public class DumpJobTest { Assertions.assertEquals("English", gr.getLanguage().getLabel()); Assertions.assertEquals(1, gr.getCountry().size()); - Assertions.assertEquals("IT" , gr.getCountry().get(0).getCode()); - Assertions.assertEquals("Italy" , gr.getCountry().get(0).getLabel()); - Assertions.assertTrue( gr.getCountry().get(0).getProvenance() == null); + Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); + Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); + Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); Assertions.assertEquals(12, gr.getSubjects().size()); - Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") - && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Natura 2000") - && s.getSubject().getScheme().equals("") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") + && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Natura 2000") + && s.getSubject().getScheme().equals("") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - Assertions.assertEquals("Ecosystem Service capacity is higher in areas of multiple designation types", + Assertions + .assertEquals( + "Ecosystem Service capacity is higher in areas of multiple designation types", gr.getMaintitle()); Assertions.assertEquals(null, gr.getSubtitle()); Assertions.assertEquals(1, gr.getDescription().size()); - Assertions.assertTrue(gr.getDescription().get(0).startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); - Assertions.assertTrue(gr.getDescription().get(0).endsWith("start complying with new standards and demands for nature conservation and environmental management.")); + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .endsWith( + "start complying with new standards and demands for nature conservation and environmental management.")); Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); @@ -255,7 +328,9 @@ public class DumpJobTest { Assertions.assertEquals(0, gr.getCoverage().size()); Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); - Assertions.assertEquals(Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); + Assertions + .assertEquals( + Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); Assertions.assertEquals(null, gr.getBestaccessright().getOpenAccessRoute()); Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); @@ -284,12 +359,16 @@ public class DumpJobTest { Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); Assertions.assertEquals(2, gr.getOriginalId().size()); - Assertions.assertTrue(gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") - && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); + Assertions + .assertTrue( + gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") + && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); Assertions.assertEquals(1, gr.getPid().size()); - Assertions.assertTrue(gr.getPid().get(0).getScheme().equals("doi") - && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); + Assertions + .assertTrue( + gr.getPid().get(0).getScheme().equals("doi") + && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); @@ -298,53 +377,63 @@ public class DumpJobTest { Instance instance = gr.getInstance().get(0); Assertions.assertEquals(0, instance.getPid().size()); Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); - Assertions.assertTrue(instance.getAlternateIdentifier().get(0).getScheme().equals("doi") - && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); + Assertions + .assertTrue( + instance.getAlternateIdentifier().get(0).getScheme().equals("doi") + && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); Assertions.assertEquals(null, instance.getLicense()); - Assertions.assertTrue(instance.getAccessright().getCode().equals(Constants.accessRightsCoarMap - .get(ModelConstants.ACCESS_RIGHT_OPEN))); + Assertions + .assertTrue( + instance + .getAccessright() + .getCode() + .equals( + Constants.accessRightsCoarMap + .get(ModelConstants.ACCESS_RIGHT_OPEN))); Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); Assertions.assertTrue(instance.getType().equals("Article")); Assertions.assertEquals(2, instance.getUrl().size()); - Assertions.assertTrue(instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") - && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); - Assertions.assertEquals("2017-01-01",instance.getPublicationdate()); - Assertions.assertEquals(null,instance.getArticleprocessingcharge()); + Assertions + .assertTrue( + instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") + && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); + Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); + Assertions.assertEquals(null, instance.getArticleprocessingcharge()); Assertions.assertEquals("peerReviewed", instance.getRefereed()); } - @Test - public void testDatasetDump(){ + public void testDatasetDump() { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run(false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Dataset.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(1, verificationDataset.count()); Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); - //the common fields in the result have been already checked. Now checking only + // the common fields in the result have been already checked. Now checking only // community specific fields GraphResult gr = verificationDataset.first(); @@ -353,10 +442,33 @@ public class DumpJobTest { Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) + .count()); + Assertions + .assertEquals( + 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) + .count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) + .count()); Assertions.assertEquals("1024Gb", gr.getSize()); @@ -373,30 +485,30 @@ public class DumpJobTest { } @Test - public void testSoftwareDump(){ + public void testSoftwareDump() { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run(false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Software.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Software.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(1, verificationDataset.count()); @@ -412,7 +524,6 @@ public class DumpJobTest { Assertions.assertEquals("perl", gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getContainer()); Assertions.assertEquals(null, gr.getContactperson()); Assertions.assertEquals(null, gr.getContactgroup()); @@ -424,30 +535,30 @@ public class DumpJobTest { } @Test - public void testOrpDump(){ + public void testOrpDump() { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run(false, sourcePath, workingDir.toString() + "/result", - communityMapPath, OtherResearchProduct.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, OtherResearchProduct.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); Assertions.assertEquals(1, verificationDataset.count()); @@ -466,7 +577,6 @@ public class DumpJobTest { Assertions.assertTrue(gr.getTool().contains("tool1")); Assertions.assertTrue(gr.getTool().contains("tool2")); - Assertions.assertEquals(null, gr.getContainer()); Assertions.assertEquals(null, gr.getDocumentationUrl()); Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); @@ -481,32 +591,33 @@ public class DumpJobTest { public void testPublicationDumpCommunity() throws JsonProcessingException { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); DumpProducts dump = new DumpProducts(); dump - .run(false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + .run( + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(1, verificationDataset.count()); Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - //the common fields in the result have been already checked. Now checking only + // the common fields in the result have been already checked. Now checking only // community specific fields CommunityResult cr = verificationDataset.first(); @@ -519,15 +630,20 @@ public class DumpJobTest { Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); + Assertions + .assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); Assertions.assertEquals(1, cr.getInstance().size()); - Assertions.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getInstance().get(0).getCollectedfrom().getKey()); + Assertions + .assertEquals( + "10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", + cr.getInstance().get(0).getCollectedfrom().getKey()); Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions.assertEquals("10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem",cr.getInstance().get(0).getHostedby().getValue()); - + Assertions + .assertEquals( + "10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); + Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); } @@ -587,8 +703,6 @@ public class DumpJobTest { Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - } @Test @@ -650,7 +764,6 @@ public class DumpJobTest { Assertions.assertEquals(0, verificationDataset.count()); - } @Test @@ -718,7 +831,6 @@ public class DumpJobTest { Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - } @Test @@ -814,7 +926,6 @@ public class DumpJobTest { Assertions.assertEquals(23, verificationDataset.count()); - Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); verificationDataset.createOrReplaceTempView("check"); @@ -832,7 +943,6 @@ public class DumpJobTest { Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index c950f1c91d..a17861ad71 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -8,16 +8,17 @@ import java.nio.file.Files; import java.nio.file.Path; import org.apache.commons.io.FileUtils; -import org.apache.neethi.Assertion; + import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; + import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; + import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; @@ -229,107 +230,98 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - Assertions.assertTrue(verificationDataset.count() == 2); + assertEquals(2, verificationDataset.count() ); - Assertions - .assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - Assertions - .assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - Assertions.assertEquals(3, resultExplodedProvenance.count()); - Assertions.assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); - Assertions - .assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + assertEquals(3, resultExplodedProvenance.count()); + assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); + assertEquals( + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + assertEquals( + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); - Assertions - .assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + assertEquals( + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + assertEquals( + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); - Assertions - .assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + assertEquals( + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java index 61102232e5..9710e45537 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java @@ -8,8 +8,6 @@ import java.util.HashMap; import java.util.logging.Filter; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -31,6 +29,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; public class UpdateProjectInfoTest { @@ -142,26 +142,26 @@ public class UpdateProjectInfoTest { } @Test - public void testValidatedRelation() throws Exception{ + public void testValidatedRelation() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") + .getPath(); SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfoValidated", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/publication_extendedmodel" + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-preparedInfoPath", sourcePath + "/preparedInfoValidated", + "-outputPath", workingDir.toString() + "/result", + "-sourcePath", sourcePath + "/publication_extendedmodel" }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); verificationDataset.show(false); @@ -169,10 +169,10 @@ public class UpdateProjectInfoTest { verificationDataset.createOrReplaceTempView("dataset"); String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " - + "from dataset " + - "lateral view explode(projects) p as MyT "; + + + "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " + + "from dataset " + + "lateral view explode(projects) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); @@ -180,27 +180,34 @@ public class UpdateProjectInfoTest { resultExplodedProvenance.show(false); Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); + .assertEquals( + 2, + resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") - .count()); + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") + .count()); Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") - .count()); + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") + .count()); Project project = verificationDataset - .map((MapFunction) cr -> cr.getProjects().stream().filter(p -> p.getValidated() != null).collect(Collectors.toList()).get(0) - , Encoders.bean(Project.class)).first(); + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() != null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); @@ -208,18 +215,22 @@ public class UpdateProjectInfoTest { Assertions.assertTrue(project.getFunder().getFundingStream() == null); Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); - project = verificationDataset - .map((MapFunction) cr -> cr.getProjects().stream().filter(p -> p.getValidated() == null).collect(Collectors.toList()).get(0) - , Encoders.bean(Project.class)).first(); - + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() == null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java index a310448a43..fe178795d7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java @@ -94,7 +94,8 @@ public class DumpRelationTest { verificationDataset.createOrReplaceTempView("table"); - verificationDataset.foreach((ForeachFunction)r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); Dataset check = spark .sql( @@ -134,13 +135,13 @@ public class DumpRelationTest { public void test2() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") + .getPath(); SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath }); // dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); @@ -148,57 +149,58 @@ public class DumpRelationTest { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); verificationDataset.createOrReplaceTempView("table"); - verificationDataset.foreach((ForeachFunction)r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); + .sql( + "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " + + + "from table "); Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); Assertions - .assertEquals( - 20, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); + .assertEquals( + 20, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); + .assertEquals( + 7, check + .filter( + "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + + "and provenance = 'Harvested'") + .count()); Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); + .assertEquals( + 1, check + .filter( + "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + + "and provenance = 'Inferred by OpenAIRE'") + .count()); Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); Assertions - .assertEquals( - 2, check - .filter( - "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + - "and provenance = 'Harvested' and validated = true " + - "and validationDate = '2021-08-06'") - .count()); + .assertEquals( + 2, check + .filter( + "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + + "and provenance = 'Harvested' and validated = true " + + "and validationDate = '2021-08-06'") + .count()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java index 7bb6b9ea94..08fcd49a86 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java @@ -6,7 +6,6 @@ import static org.mockito.Mockito.lenient; import java.util.*; import java.util.function.Consumer; -import eu.dnetlib.dhp.schema.common.ModelSupport; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -14,6 +13,7 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -529,7 +529,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); Assertions.assertEquals(5, cInfoList.size()); } @@ -540,7 +541,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); cInfoList.forEach(contextInfo -> { switch (contextInfo.getId()) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index ad4ea36c44..477481c080 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -145,8 +145,8 @@ public class SplitPerFunderTest { // CONICYT 0 tmp = sc - .textFile(workingDir.toString() + "/split/CONICYTF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CONICYTF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(0, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index 8daf318bea..6229ad19b4 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -84,7 +84,8 @@ public class IndexRecordTransformerTest { @Test public void testForEOSCFutureTraining() throws IOException, TransformerException { - final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml")); + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml")); testRecordTransformation(record); } diff --git a/pom.xml b/pom.xml index 4d3bcee607..4be4257791 100644 --- a/pom.xml +++ b/pom.xml @@ -753,7 +753,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.7.18] + [2.7.19] [4.0.3] [6.0.5] [3.1.6] From e653756e3d855ae7c838afdb8c09b61cfb17d749 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 4 Oct 2021 18:40:07 +0200 Subject: [PATCH 75/92] applied some suggestiond from Sonar Lint --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 27 ++-- .../dhp/oa/graph/dump/DumpProducts.java | 5 +- .../eu/dnetlib/dhp/oa/graph/dump/MakeTar.java | 12 +- .../oa/graph/dump/QueryInformationSystem.java | 4 +- .../dhp/oa/graph/dump/ResultMapper.java | 122 +++++++++--------- .../dhp/oa/graph/dump/SaveCommunityMap.java | 8 +- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 23 +--- .../graph/dump/community/CommunitySplit.java | 8 +- .../community/SparkPrepareResultProject.java | 6 +- .../dump/complete/CreateContextRelation.java | 3 +- .../dhp/oa/graph/dump/complete/Extractor.java | 43 +++--- .../dhp/oa/graph/dump/complete/Process.java | 5 +- .../dump/complete/QueryInformationSystem.java | 18 ++- .../dump/complete/SparkDumpRelationJob.java | 33 +++-- .../complete/SparkOrganizationRelation.java | 3 +- .../SparkSelectValidRelationsJob.java | 1 - .../dump/exceptions/MyRuntimeException.java | 30 +++++ .../NoAvailableEntityTypeException.java | 29 +++++ .../funderresults/SparkDumpFunderResults.java | 3 - .../SparkResultLinkedToProject.java | 3 - .../dump/PrepareResultProjectJobTest.java | 91 +++++++------ ...DumpOrganizationProjectDatasourceTest.java | 5 +- .../dhp/oa/graph/hostedbymap/TestApply.scala | 2 +- .../complete/organization/organization.json | 4 +- 24 files changed, 274 insertions(+), 214 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 6dca09b632..61167639ca 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -5,37 +5,40 @@ import java.util.Map; import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.common.ModelConstants; + public class Constants { - public static final Map accessRightsCoarMap = Maps.newHashMap(); - public static final Map coarCodeLabelMap = Maps.newHashMap(); + protected static final Map accessRightsCoarMap = Maps.newHashMap(); + protected static final Map coarCodeLabelMap = Maps.newHashMap(); public static final String INFERRED = "Inferred by OpenAIRE"; + public static final String CABF2 = "c_abf2"; public static final String HARVESTED = "Harvested"; public static final String DEFAULT_TRUST = "0.9"; public static final String USER_CLAIM = "Linked by user"; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - public static String RESEARCH_COMMUNITY = "Research Community"; + public static final String RESEARCH_COMMUNITY = "Research Community"; - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; static { - accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); - accessRightsCoarMap.put("CLOSED", "c_14cb"); - accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + accessRightsCoarMap.put("OPEN SOURCE", CABF2); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); } static { - coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index d09e584a33..68e1e8402f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -17,6 +17,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -66,7 +67,7 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - String dumpType) { + String dumpType) throws NoAvailableEntityTypeException { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { @@ -94,7 +95,7 @@ public class DumpProducts implements Serializable { } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.size() == 0) { + if (toDumpFor.isEmpty()) { return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java index 0d2df11fe6..b56849a3ab 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java @@ -57,16 +57,16 @@ public class MakeTar implements Serializable { public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) throws IOException { - RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - while (dir_iterator.hasNext()) { - LocatedFileStatus fileStatus = dir_iterator.next(); + while (dirIterator.hasNext()) { + LocatedFileStatus fileStatus = dirIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + String pathString = p.toString(); + String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - MakeTarArchive.tarMaxSize(fileSystem, p_string, outputPath + "/" + entity, entity, gBperSplit); + MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index 4d0c59955c..b972de6e9a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -40,10 +40,10 @@ public class QueryInformationSystem { "{$x//CONFIGURATION/context/@label}" + ""; - public CommunityMap getCommunityMap(boolean singleCommunity, String community_id) + public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, DocumentException, SAXException { if (singleCommunity) - return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + community_id + "'"))); + return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 988a8c7a41..0f3192c25c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -6,9 +6,8 @@ import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; @@ -29,7 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.*; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, String dumpType) { + E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { Result out; if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { @@ -136,6 +135,8 @@ public class ResultMapper implements Serializable { out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); break; + default: + throw new NoAvailableEntityTypeException(); } Optional> mes = Optional.ofNullable(input.getMeasures()); @@ -156,17 +157,15 @@ public class ResultMapper implements Serializable { // I do not map Access Right UNKNOWN or OTHER Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } + if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); } final List contributorList = new ArrayList<>(); @@ -263,7 +262,7 @@ public class ResultMapper implements Serializable { .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) .collect(Collectors.toList()); - if (iTitle.size() > 0) { + if (!iTitle.isEmpty()) { out.setMaintitle(iTitle.get(0).getValue()); } @@ -272,7 +271,7 @@ public class ResultMapper implements Serializable { .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) .collect(Collectors.toList()); - if (iTitle.size() > 0) { + if (!iTitle.isEmpty()) { out.setSubtitle(iTitle.get(0).getValue()); } @@ -301,9 +300,8 @@ public class ResultMapper implements Serializable { Optional .ofNullable(input.getSource()) - .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()))); - // value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + .ifPresent(value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); + List subjectList = new ArrayList<>(); Optional .ofNullable(input.getSubject()) @@ -334,14 +332,14 @@ public class ResultMapper implements Serializable { value -> value .stream() .map(c -> { - String community_id = c.getId(); - if (community_id.indexOf("::") > 0) { - community_id = community_id.substring(0, community_id.indexOf("::")); + String communityId = c.getId(); + if (communityId.contains("::")) { + communityId = communityId.substring(0, communityId.indexOf("::")); } - if (communities.contains(community_id)) { + if (communities.contains(communityId)) { Context context = new Context(); - context.setCode(community_id); - context.setLabel(communityMap.get(community_id)); + context.setCode(communityId); + context.setLabel(communityMap.get(communityId)); Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); if (dataInfo.isPresent()) { List provenance = new ArrayList<>(); @@ -361,7 +359,11 @@ public class ResultMapper implements Serializable { .filter(Objects::nonNull) .collect(Collectors.toSet())); - context.setProvenance(getUniqueProvenance(provenance)); + try { + context.setProvenance(getUniqueProvenance(provenance)); + } catch (NoAvailableEntityTypeException e) { + e.printStackTrace(); + } } return context; } @@ -371,7 +373,7 @@ public class ResultMapper implements Serializable { .collect(Collectors.toList())) .orElse(new ArrayList<>()); - if (contextList.size() > 0) { + if (!contextList.isEmpty()) { Set hashValue = new HashSet<>(); List remainigContext = new ArrayList<>(); contextList.forEach(c -> { @@ -417,35 +419,34 @@ public class ResultMapper implements Serializable { private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { Optional opAr = Optional.ofNullable(i.getAccessright()); - if (opAr.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - if (opAr.get().getOpenAccessRoute() != null) { - switch (opAr.get().getOpenAccessRoute()) { - case hybrid: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); - break; - case gold: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); - break; - case green: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); - break; - case bronze: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); - break; + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + if (opAr.get().getOpenAccessRoute() != null) { + switch (opAr.get().getOpenAccessRoute()) { + case hybrid: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); + break; + case gold: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); + break; + case green: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); + break; + case bronze: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); + break; - } } } + } Optional @@ -498,7 +499,8 @@ public class ResultMapper implements Serializable { } - private static List getUniqueProvenance(List provenance) { + private static List getUniqueProvenance(List provenance) + throws NoAvailableEntityTypeException { Provenance iProv = new Provenance(); Provenance hProv = new Provenance(); @@ -520,6 +522,8 @@ public class ResultMapper implements Serializable { case Constants.USER_CLAIM: lProv = getHighestTrust(lProv, p); break; + default: + throw new NoAvailableEntityTypeException(); } } @@ -599,19 +603,19 @@ public class ResultMapper implements Serializable { } private static Pid getOrcid(List p) { - List pid_list = p.stream().map(pid -> { + List pidList = p.stream().map(pid -> { if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { return pid; } return null; - }).filter(pid -> pid != null).collect(Collectors.toList()); + }).filter(Objects::nonNull).collect(Collectors.toList()); - if (pid_list.size() == 1) { - return getAuthorPid(pid_list.get(0)); + if (pidList.size() == 1) { + return getAuthorPid(pidList.get(0)); } - List orcid = pid_list + List orcid = pidList .stream() .filter( ap -> ap @@ -622,7 +626,7 @@ public class ResultMapper implements Serializable { if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } - orcid = pid_list + orcid = pidList .stream() .filter( ap -> ap diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 9713247446..1eff998920 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -31,9 +31,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; public class SaveCommunityMap implements Serializable { private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final QueryInformationSystem queryInformationSystem; + private final transient QueryInformationSystem queryInformationSystem; - private final BufferedWriter writer; + private final transient BufferedWriter writer; public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { final Configuration conf = new Configuration(); @@ -84,12 +84,12 @@ public class SaveCommunityMap implements Serializable { } - private void saveCommunityMap(boolean singleCommunity, String community_id) + private void saveCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, IOException, DocumentException, SAXException { writer .write( Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId))); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index 09e3015725..a19a3a5b60 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -5,15 +5,13 @@ import java.io.Serializable; import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.MissingConceptDoiException; import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; public class SendToZenodoHDFS implements Serializable { @@ -21,8 +19,6 @@ public class SendToZenodoHDFS implements Serializable { private static final String VERSION = "version"; // to be used to upload a new version of a published deposition private static final String UPDATE = "update"; // to upload content to an open deposition not published - private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); - public static void main(final String[] args) throws Exception, MissingConceptDoiException { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -48,15 +44,12 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - // final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - // CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); - RemoteIterator fileStatusListIterator = fileSystem .listFiles( new Path(hdfsPath), true); @@ -77,19 +70,17 @@ public class SendToZenodoHDFS implements Serializable { } zenodoApiClient.uploadOpenDeposition(depositionId); break; + default: + throw new NoAvailableEntityTypeException(); } while (fileStatusListIterator.hasNext()) { LocatedFileStatus fileStatus = fileStatusListIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - if (!p_string.endsWith("_SUCCESS")) { - String name = p_string.substring(p_string.lastIndexOf("/") + 1); -// log.info("Sending information for community: " + name); -// if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { -// name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; -// } + String pString = p.toString(); + if (!pString.endsWith("_SUCCESS")) { + String name = pString.substring(pString.lastIndexOf("/") + 1); FSDataInputStream inputStream = fileSystem.open(p); zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); @@ -101,7 +92,7 @@ public class SendToZenodoHDFS implements Serializable { zenodoApiClient.sendMretadata(metadata); } - if (publish) { + if (Boolean.TRUE.equals(publish)) { zenodoApiClient.publish(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 6abca22559..ee6341f843 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -5,7 +5,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; @@ -16,6 +15,7 @@ import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Context; /** * This class splits the dumped results according to the research community - research initiative/infrastructure they @@ -56,10 +56,10 @@ public class CommunitySplit implements Serializable { } private static void printResult(String c, Dataset result, String outputPath) { - Dataset community_products = result + Dataset communityProducts = result .filter((FilterFunction) r -> containsCommunity(r, c)); - community_products + communityProducts .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) @@ -72,7 +72,7 @@ public class CommunitySplit implements Serializable { return r .getContext() .stream() - .map(con -> con.getCode()) + .map(Context::getCode) .collect(Collectors.toList()) .contains(c); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 3508e41262..87ac20948a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -161,7 +161,7 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - if (relation.getValidated()) { + if (Boolean.TRUE.equals(relation.getValidated())) { p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); } return p; @@ -179,8 +179,8 @@ public class SparkPrepareResultProject implements Serializable { f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream(((Node) node.get(0)).getText()); + List node = ((Node) o).selectNodes("./name"); + f.setFundingStream((node.get(0)).getText()); } return f; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java index 0c8f5dba4e..a468e334da 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.*; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -120,7 +121,7 @@ public class CreateContextRelation implements Serializable { writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); writer.newLine(); } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index 7e8ddfaf8c..3e47ee6648 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -62,22 +62,7 @@ public class Extractor implements Serializable { .readPath(spark, inputPath, inputClazz) .flatMap((FlatMapFunction) value -> { List relationList = new ArrayList<>(); - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); + extractRelationsFromInstance(hashCodes, value, relationList); Set communities = communityMap.keySet(); Optional .ofNullable(value.getContext()) @@ -136,8 +121,28 @@ public class Extractor implements Serializable { } + private void extractRelationsFromInstance(Set hashCodes, R value, + List relationList) { + Optional + .ofNullable(value.getInstance()) + .ifPresent(inst -> inst.forEach(instance -> { + Optional + .ofNullable(instance.getCollectedfrom()) + .ifPresent( + cf -> getRelatioPair( + value, relationList, cf, + ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); + Optional + .ofNullable(instance.getHostedby()) + .ifPresent( + hb -> getRelatioPair( + value, relationList, hb, + Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); + })); + } + private static void getRelatioPair(R value, List relationList, KeyValue cf, - String result_dtasource, String datasource_result, + String resultDatasource, String datasourceResult, Set hashCodes) { Provenance provenance = Optional .ofNullable(cf.getDataInfo()) @@ -162,7 +167,7 @@ public class Extractor implements Serializable { Relation r = getRelation( value.getId(), cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - result_dtasource, ModelConstants.PROVISION, + resultDatasource, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { relationList @@ -173,7 +178,7 @@ public class Extractor implements Serializable { r = getRelation( cf.getKey(), value.getId(), Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasource_result, ModelConstants.PROVISION, + datasourceResult, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java index b0b8b8acdc..e1cb0e753f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java @@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; @@ -43,7 +44,7 @@ public class Process implements Serializable { return (R) ri; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } @@ -91,7 +92,7 @@ public class Process implements Serializable { return relationList; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 88c92da53d..fcc4bf39ce 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -13,7 +13,6 @@ import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -94,9 +93,9 @@ public class QueryInformationSystem { Element root = doc.getRootElement(); cinfo.setId(root.attributeValue("id")); - Iterator it = root.elementIterator(); + Iterator it = root.elementIterator(); while (it.hasNext()) { - Element el = (Element) it.next(); + Element el = it.next(); if (el.getName().equals("category")) { String categoryId = el.attributeValue("id"); categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); @@ -143,7 +142,7 @@ public class QueryInformationSystem { if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { return null; } - String funder = null; + String funder = ""; String grantId = null; String funding = null; for (Object node : el.selectNodes(".//param")) { @@ -158,9 +157,12 @@ public class QueryInformationSystem { case "CD_PROJECT_NUMBER": grantId = n.getText(); break; + default: + break; } } String nsp = null; + switch (funder.toLowerCase()) { case "ec": if (funding == null) { @@ -179,10 +181,12 @@ public class QueryInformationSystem { nsp = "dfgf________::"; break; default: - nsp = funder.toLowerCase(); + StringBuilder bld = new StringBuilder(); + bld.append(funder.toLowerCase()); for (int i = funder.length(); i < 12; i++) - nsp += "_"; - nsp += "::"; + bld.append("_"); + bld.append("::"); + nsp = bld.toString(); } return prefix + "|" + nsp + DHPUtils.md5(grantId); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index ab7e7e595d..ddfd6592f9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -71,22 +71,22 @@ public class SparkDumpRelationJob implements Serializable { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel_new = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - rel_new + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); + relNew .setSource( Node .newInstance( relation.getSource(), ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - rel_new + relNew .setTarget( Node .newInstance( relation.getTarget(), ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - rel_new + relNew .setReltype( RelType .newInstance( @@ -96,23 +96,22 @@ public class SparkDumpRelationJob implements Serializable { Optional odInfo = Optional.ofNullable(relation.getDataInfo()); if (odInfo.isPresent()) { DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent()) { - if (Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - rel_new - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } + if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && + Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { + relNew + .setProvenance( + Provenance + .newInstance( + dInfo.getProvenanceaction().getClassname(), + dInfo.getTrust())); } } - if (relation.getValidated()) { - rel_new.setValidated(relation.getValidated()); - rel_new.setValidationDate(relation.getValidationDate()); + if (Boolean.TRUE.equals(relation.getValidated())) { + relNew.setValidated(relation.getValidated()); + relNew.setValidationDate(relation.getValidationDate()); } - return rel_new; + return relNew; }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) .write() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java index 4365e861fe..f9d2123e2c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java @@ -58,7 +58,8 @@ public class SparkOrganizationRelation implements Serializable { final OrganizationMap organizationMap = new Gson() .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - log.info("organization map : {}", new Gson().toJson(organizationMap)); + final String serializedOrganizationMap = new Gson().toJson(organizationMap); + log.info("organization map : {}", serializedOrganizationMap); final String communityMapPath = parser.get("communityMapPath"); log.info("communityMapPath: {}", communityMapPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java index e729e13dfa..20f3fc4a7e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -131,7 +131,6 @@ public class SparkSelectValidRelationsJob implements Serializable { .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath); - ; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java new file mode 100644 index 0000000000..e325c43347 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class MyRuntimeException extends RuntimeException { + + public MyRuntimeException() { + super(); + } + + public MyRuntimeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public MyRuntimeException(final String message, final Throwable cause) { + super(message, cause); + } + + public MyRuntimeException(final String message) { + super(message); + } + + public MyRuntimeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java new file mode 100644 index 0000000000..f3fbf740a3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class NoAvailableEntityTypeException extends Exception { + public NoAvailableEntityTypeException() { + super(); + } + + public NoAvailableEntityTypeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public NoAvailableEntityTypeException(final String message, final Throwable cause) { + super(message, cause); + } + + public NoAvailableEntityTypeException(final String message) { + super(message); + } + + public NoAvailableEntityTypeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 9cddba3c54..6aed9d7a8c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -10,7 +10,6 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -18,10 +17,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 156ae6d633..d89b9e86dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -10,7 +10,6 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -19,13 +18,11 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index a17861ad71..86d2f93c9c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -8,17 +8,14 @@ import java.nio.file.Files; import java.nio.file.Path; import org.apache.commons.io.FileUtils; - import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; - import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; - import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; @@ -248,14 +245,14 @@ public class PrepareResultProjectJobTest { org.apache.spark.sql.Dataset verificationDataset = spark .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - assertEquals(2, verificationDataset.count() ); + assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); @@ -269,59 +266,59 @@ public class PrepareResultProjectJobTest { assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 89ecdfb2b4..051141e183 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -6,6 +6,7 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -98,7 +99,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpProjectTest() { + public void dumpProjectTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") @@ -127,7 +128,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpDatasourceTest() { + public void dumpDatasourceTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") .getPath(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index 1bdcb60aaf..4613d56369 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -54,7 +54,7 @@ class TestApply extends java.io.Serializable{ assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy")) assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) - assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.gold)) assertTrue(pa.getBestaccessright.getClassid.equals("OPEN")) assertTrue(pa.getBestaccessright.getClassname.equals("Open Access")) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json index d172419bf7..e141af7872 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json @@ -1,6 +1,5 @@ {"alternativeNames":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"value":"한국초등도덕교육학회"}],"collectedfrom":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"key":"10|openaire____::ff4a008470319a22d9cf3d14af485977","value":"GRID - Global Research Identifier Database"}],"country":{"classid":"KR","classname":"Korea (Republic 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dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml new file mode 100644 index 0000000000..668332b28a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml @@ -0,0 +1,31 @@ +Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + --> + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt new file mode 100644 index 0000000000..307a85f913 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt @@ -0,0 +1,8 @@ +# Set of Catalan contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +l +m +n +s +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt new file mode 100644 index 0000000000..f1bba51b23 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt @@ -0,0 +1,15 @@ +# Set of French contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +l +m +t +qu +n +s +j +d +c +jusqu +quoiqu +lorsqu +puisqu diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt new file mode 100644 index 0000000000..9ebe7fa349 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +m +b diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt new file mode 100644 index 0000000000..cac0409537 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt @@ -0,0 +1,23 @@ +# Set of Italian contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +c +l +all +dall +dell +nell +sull +coll +pell +gl +agl +dagl +degl +negl +sugl +un +m +t +s +v +d diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt new file mode 100644 index 0000000000..4d2642cc5a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish hyphenations for StopFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +h +n +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt new file mode 100644 index 0000000000..441072971d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt @@ -0,0 +1,6 @@ +# Set of overrides for the dutch stemmer +# TODO: load this as a resource from the analyzer and sync it in build.xml +fiets fiets +bromfiets bromfiets +ei eier +kind kinder diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt new file mode 100644 index 0000000000..71b750845e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt @@ -0,0 +1,420 @@ +# +# This file defines a Japanese stoptag set for JapanesePartOfSpeechStopFilter. +# +# Any token with a part-of-speech tag that exactly matches those defined in this +# file are removed from the token stream. +# +# Set your own stoptags by uncommenting the lines below. Note that comments are +# not allowed on the same line as a stoptag. See LUCENE-3745 for frequency lists, +# etc. that can be useful for building you own stoptag set. +# +# The entire possible tagset is provided below for convenience. +# +##### +# noun: unclassified nouns +#名詞 +# +# noun-common: Common nouns or nouns where the sub-classification is undefined +#名詞-一般 +# +# noun-proper: Proper nouns where the sub-classification is undefined +#名詞-固有名詞 +# +# noun-proper-misc: miscellaneous proper nouns +#名詞-固有名詞-一般 +# +# noun-proper-person: Personal names where the sub-classification is undefined +#名詞-固有名詞-人名 +# +# noun-proper-person-misc: names that cannot be divided into surname and +# given name; foreign names; names where the surname or given name is unknown. +# e.g. お市の方 +#名詞-固有名詞-人名-一般 +# +# noun-proper-person-surname: Mainly Japanese surnames. +# e.g. 山田 +#名詞-固有名詞-人名-姓 +# +# noun-proper-person-given_name: Mainly Japanese given names. +# e.g. 太郎 +#名詞-固有名詞-人名-名 +# +# noun-proper-organization: Names representing organizations. +# e.g. 通産省, NHK +#名詞-固有名詞-組織 +# +# noun-proper-place: Place names where the sub-classification is undefined +#名詞-固有名詞-地域 +# +# noun-proper-place-misc: Place names excluding countries. +# e.g. アジア, バルセロナ, 京都 +#名詞-固有名詞-地域-一般 +# +# noun-proper-place-country: Country names. +# e.g. 日本, オーストラリア +#名詞-固有名詞-地域-国 +# +# noun-pronoun: Pronouns where the sub-classification is undefined +#名詞-代名詞 +# +# noun-pronoun-misc: miscellaneous pronouns: +# e.g. それ, ここ, あいつ, あなた, あちこち, いくつ, どこか, なに, みなさん, みんな, わたくし, われわれ +#名詞-代名詞-一般 +# +# noun-pronoun-contraction: Spoken language contraction made by combining a +# pronoun and the particle 'wa'. +# e.g. ありゃ, こりゃ, こりゃあ, そりゃ, そりゃあ +#名詞-代名詞-縮約 +# +# noun-adverbial: Temporal nouns such as names of days or months that behave +# like adverbs. Nouns that represent amount or ratios and can be used adverbially, +# e.g. 金曜, 一月, 午後, 少量 +#名詞-副詞可能 +# +# noun-verbal: Nouns that take arguments with case and can appear followed by +# 'suru' and related verbs (する, できる, なさる, くださる) +# e.g. インプット, 愛着, 悪化, 悪戦苦闘, 一安心, 下取り +#名詞-サ変接続 +# +# noun-adjective-base: The base form of adjectives, words that appear before な ("na") +# e.g. 健康, 安易, 駄目, だめ +#名詞-形容動詞語幹 +# +# noun-numeric: Arabic numbers, Chinese numerals, and counters like 何 (回), 数. +# e.g. 0, 1, 2, 何, 数, 幾 +#名詞-数 +# +# noun-affix: noun affixes where the sub-classification is undefined +#名詞-非自立 +# +# noun-affix-misc: Of adnominalizers, the case-marker の ("no"), and words that +# attach to the base form of inflectional words, words that cannot be classified +# into any of the other categories below. This category includes indefinite nouns. +# e.g. あかつき, 暁, かい, 甲斐, 気, きらい, 嫌い, くせ, 癖, こと, 事, ごと, 毎, しだい, 次第, +# 順, せい, 所為, ついで, 序で, つもり, 積もり, 点, どころ, の, はず, 筈, はずみ, 弾み, +# 拍子, ふう, ふり, 振り, ほう, 方, 旨, もの, 物, 者, ゆえ, 故, ゆえん, 所以, わけ, 訳, +# わり, 割り, 割, ん-口語/, もん-口語/ +#名詞-非自立-一般 +# +# noun-affix-adverbial: noun affixes that that can behave as adverbs. +# e.g. あいだ, 間, あげく, 挙げ句, あと, 後, 余り, 以外, 以降, 以後, 以上, 以前, 一方, うえ, +# 上, うち, 内, おり, 折り, かぎり, 限り, きり, っきり, 結果, ころ, 頃, さい, 際, 最中, さなか, +# 最中, じたい, 自体, たび, 度, ため, 為, つど, 都度, とおり, 通り, とき, 時, ところ, 所, +# とたん, 途端, なか, 中, のち, 後, ばあい, 場合, 日, ぶん, 分, ほか, 他, まえ, 前, まま, +# 儘, 侭, みぎり, 矢先 +#名詞-非自立-副詞可能 +# +# noun-affix-aux: noun affixes treated as 助動詞 ("auxiliary verb") in school grammars +# with the stem よう(だ) ("you(da)"). +# e.g. よう, やう, 様 (よう) +#名詞-非自立-助動詞語幹 +# +# noun-affix-adjective-base: noun affixes that can connect to the indeclinable +# connection form な (aux "da"). +# e.g. みたい, ふう +#名詞-非自立-形容動詞語幹 +# +# noun-special: special nouns where the sub-classification is undefined. +#名詞-特殊 +# +# noun-special-aux: The そうだ ("souda") stem form that is used for reporting news, is +# treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the base +# form of inflectional words. +# e.g. そう +#名詞-特殊-助動詞語幹 +# +# noun-suffix: noun suffixes where the sub-classification is undefined. +#名詞-接尾 +# +# noun-suffix-misc: Of the nouns or stem forms of other parts of speech that connect +# to ガル or タイ and can combine into compound nouns, words that cannot be classified into +# any of the other categories below. In general, this category is more inclusive than +# 接尾語 ("suffix") and is usually the last element in a compound noun. +# e.g. おき, かた, 方, 甲斐 (がい), がかり, ぎみ, 気味, ぐるみ, (～した) さ, 次第, 済 (ず) み, +# よう, (でき)っこ, 感, 観, 性, 学, 類, 面, 用 +#名詞-接尾-一般 +# +# noun-suffix-person: Suffixes that form nouns and attach to person names more often +# than other nouns. +# e.g. 君, 様, 著 +#名詞-接尾-人名 +# +# noun-suffix-place: Suffixes that form nouns and attach to place names more often +# than other nouns. +# e.g. 町, 市, 県 +#名詞-接尾-地域 +# +# noun-suffix-verbal: Of the suffixes that attach to nouns and form nouns, those that +# can appear before スル ("suru"). +# e.g. 化, 視, 分け, 入り, 落ち, 買い +#名詞-接尾-サ変接続 +# +# noun-suffix-aux: The stem form of そうだ (様態) that is used to indicate conditions, +# is treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the +# conjunctive form of inflectional words. +# e.g. そう +#名詞-接尾-助動詞語幹 +# +# noun-suffix-adjective-base: Suffixes that attach to other nouns or the conjunctive +# form of inflectional words and appear before the copula だ ("da"). +# e.g. 的, げ, がち +#名詞-接尾-形容動詞語幹 +# +# noun-suffix-adverbial: Suffixes that attach to other nouns and can behave as adverbs. +# e.g. 後 (ご), 以後, 以降, 以前, 前後, 中, 末, 上, 時 (じ) +#名詞-接尾-副詞可能 +# +# noun-suffix-classifier: Suffixes that attach to numbers and form nouns. This category +# is more inclusive than 助数詞 ("classifier") and includes common nouns that attach +# to numbers. +# e.g. 個, つ, 本, 冊, パーセント, cm, kg, カ月, か国, 区画, 時間, 時半 +#名詞-接尾-助数詞 +# +# noun-suffix-special: Special suffixes that mainly attach to inflecting words. +# e.g. (楽し) さ, (考え) 方 +#名詞-接尾-特殊 +# +# noun-suffix-conjunctive: Nouns that behave like conjunctions and join two words +# together. +# e.g. (日本) 対 (アメリカ), 対 (アメリカ), (3) 対 (5), (女優) 兼 (主婦) +#名詞-接続詞的 +# +# noun-verbal_aux: Nouns that attach to the conjunctive particle て ("te") and are +# semantically verb-like. +# e.g. ごらん, ご覧, 御覧, 頂戴 +#名詞-動詞非自立的 +# +# noun-quotation: text that cannot be segmented into words, proverbs, Chinese poetry, +# dialects, English, etc. Currently, the only entry for 名詞 引用文字列 ("noun quotation") +# is いわく ("iwaku"). +#名詞-引用文字列 +# +# noun-nai_adjective: Words that appear before the auxiliary verb ない ("nai") and +# behave like an adjective. +# e.g. 申し訳, 仕方, とんでも, 違い +#名詞-ナイ形容詞語幹 +# +##### +# prefix: unclassified prefixes +#接頭詞 +# +# prefix-nominal: Prefixes that attach to nouns (including adjective stem forms) +# excluding numerical expressions. +# e.g. お (水), 某 (氏), 同 (社), 故 (～氏), 高 (品質), お (見事), ご (立派) +#接頭詞-名詞接続 +# +# prefix-verbal: Prefixes that attach to the imperative form of a verb or a verb +# in conjunctive form followed by なる/なさる/くださる. +# e.g. お (読みなさい), お (座り) +#接頭詞-動詞接続 +# +# prefix-adjectival: Prefixes that attach to adjectives. +# e.g. お (寒いですねえ), バカ (でかい) +#接頭詞-形容詞接続 +# +# prefix-numerical: Prefixes that attach to numerical expressions. +# e.g. 約, およそ, 毎時 +#接頭詞-数接続 +# +##### +# verb: unclassified verbs +#動詞 +# +# verb-main: +#動詞-自立 +# +# verb-auxiliary: +#動詞-非自立 +# +# verb-suffix: +#動詞-接尾 +# +##### +# adjective: unclassified adjectives +#形容詞 +# +# adjective-main: +#形容詞-自立 +# +# adjective-auxiliary: +#形容詞-非自立 +# +# adjective-suffix: +#形容詞-接尾 +# +##### +# adverb: unclassified adverbs +#副詞 +# +# adverb-misc: Words that can be segmented into one unit and where adnominal +# modification is not possible. +# e.g. あいかわらず, 多分 +#副詞-一般 +# +# adverb-particle_conjunction: Adverbs that can be followed by の, は, に, +# な, する, だ, etc. +# e.g. こんなに, そんなに, あんなに, なにか, なんでも +#副詞-助詞類接続 +# +##### +# adnominal: Words that only have noun-modifying forms. +# e.g. この, その, あの, どの, いわゆる, なんらかの, 何らかの, いろんな, こういう, そういう, ああいう, +# どういう, こんな, そんな, あんな, どんな, 大きな, 小さな, おかしな, ほんの, たいした, +# 「(, も) さる (ことながら)」, 微々たる, 堂々たる, 単なる, いかなる, 我が」「同じ, 亡き +#連体詞 +# +##### +# conjunction: Conjunctions that can occur independently. +# e.g. が, けれども, そして, じゃあ, それどころか +接続詞 +# +##### +# particle: unclassified particles. +助詞 +# +# particle-case: case particles where the subclassification is undefined. +助詞-格助詞 +# +# particle-case-misc: Case particles. +# e.g. から, が, で, と, に, へ, より, を, の, にて +助詞-格助詞-一般 +# +# particle-case-quote: the "to" that appears after nouns, a person’s speech, +# quotation marks, expressions of decisions from a meeting, reasons, judgements, +# conjectures, etc. +# e.g. ( だ) と (述べた.), ( である) と (して執行猶予...) +助詞-格助詞-引用 +# +# particle-case-compound: Compounds of particles and verbs that mainly behave +# like case particles. +# e.g. という, といった, とかいう, として, とともに, と共に, でもって, にあたって, に当たって, に当って, +# にあたり, に当たり, に当り, に当たる, にあたる, において, に於いて,に於て, における, に於ける, +# にかけ, にかけて, にかんし, に関し, にかんして, に関して, にかんする, に関する, に際し, +# に際して, にしたがい, に従い, に従う, にしたがって, に従って, にたいし, に対し, にたいして, +# に対して, にたいする, に対する, について, につき, につけ, につけて, につれ, につれて, にとって, +# にとり, にまつわる, によって, に依って, に因って, により, に依り, に因り, による, に依る, に因る, +# にわたって, にわたる, をもって, を以って, を通じ, を通じて, を通して, をめぐって, をめぐり, をめぐる, +# って-口語/, ちゅう-関西弁「という」/, (何) ていう (人)-口語/, っていう-口語/, といふ, とかいふ +助詞-格助詞-連語 +# +# particle-conjunctive: +# e.g. から, からには, が, けれど, けれども, けど, し, つつ, て, で, と, ところが, どころか, とも, ども, +# ながら, なり, ので, のに, ば, ものの, や ( した), やいなや, (ころん) じゃ(いけない)-口語/, +# (行っ) ちゃ(いけない)-口語/, (言っ) たって (しかたがない)-口語/, (それがなく)ったって (平気)-口語/ +助詞-接続助詞 +# +# particle-dependency: +# e.g. こそ, さえ, しか, すら, は, も, ぞ +助詞-係助詞 +# +# particle-adverbial: +# e.g. がてら, かも, くらい, 位, ぐらい, しも, (学校) じゃ(これが流行っている)-口語/, +# (それ)じゃあ (よくない)-口語/, ずつ, (私) なぞ, など, (私) なり (に), (先生) なんか (大嫌い)-口語/, +# (私) なんぞ, (先生) なんて (大嫌い)-口語/, のみ, だけ, (私) だって-口語/, だに, +# (彼)ったら-口語/, (お茶) でも (いかが), 等 (とう), (今後) とも, ばかり, ばっか-口語/, ばっかり-口語/, +# ほど, 程, まで, 迄, (誰) も (が)([助詞-格助詞] および [助詞-係助詞] の前に位置する「も」) +助詞-副助詞 +# +# particle-interjective: particles with interjective grammatical roles. +# e.g. (松島) や +助詞-間投助詞 +# +# particle-coordinate: +# e.g. と, たり, だの, だり, とか, なり, や, やら +助詞-並立助詞 +# +# particle-final: +# e.g. かい, かしら, さ, ぜ, (だ)っけ-口語/, (とまってる) で-方言/, な, ナ, なあ-口語/, ぞ, ね, ネ, +# ねぇ-口語/, ねえ-口語/, ねん-方言/, の, のう-口語/, や, よ, ヨ, よぉ-口語/, わ, わい-口語/ +助詞-終助詞 +# +# particle-adverbial/conjunctive/final: The particle "ka" when unknown whether it is +# adverbial, conjunctive, or sentence final. For example: +# (a) 「A か B か」. Ex:「(国内で運用する) か,(海外で運用する) か (.)」 +# (b) Inside an adverb phrase. Ex:「(幸いという) か (, 死者はいなかった.)」 +# 「(祈りが届いたせい) か (, 試験に合格した.)」 +# (c) 「かのように」. Ex:「(何もなかった) か (のように振る舞った.)」 +# e.g. か +助詞-副助詞／並立助詞／終助詞 +# +# particle-adnominalizer: The "no" that attaches to nouns and modifies +# non-inflectional words. +助詞-連体化 +# +# particle-adnominalizer: The "ni" and "to" that appear following nouns and adverbs +# that are giongo, giseigo, or gitaigo. +# e.g. に, と +助詞-副詞化 +# +# particle-special: A particle that does not fit into one of the above classifications. +# This includes particles that are used in Tanka, Haiku, and other poetry. +# e.g. かな, けむ, ( しただろう) に, (あんた) にゃ(わからん), (俺) ん (家) +助詞-特殊 +# +##### +# auxiliary-verb: +助動詞 +# +##### +# interjection: Greetings and other exclamations. +# e.g. おはよう, おはようございます, こんにちは, こんばんは, ありがとう, どうもありがとう, ありがとうございます, +# いただきます, ごちそうさま, さよなら, さようなら, はい, いいえ, ごめん, ごめんなさい +#感動詞 +# +##### +# symbol: unclassified Symbols. +記号 +# +# symbol-misc: A general symbol not in one of the categories below. +# e.g. [○◎@$〒→+] +記号-一般 +# +# symbol-comma: Commas +# e.g. [,、] +記号-読点 +# +# symbol-period: Periods and full stops. +# e.g. [.．。] +記号-句点 +# +# symbol-space: Full-width whitespace. +記号-空白 +# +# symbol-open_bracket: +# e.g. [({‘“『【] +記号-括弧開 +# +# symbol-close_bracket: +# e.g. [)}’”』」】] +記号-括弧閉 +# +# symbol-alphabetic: +#記号-アルファベット +# +##### +# other: unclassified other +#その他 +# +# other-interjection: Words that are hard to classify as noun-suffixes or +# sentence-final particles. +# e.g. (だ)ァ +その他-間投 +# +##### +# filler: Aizuchi that occurs during a conversation or sounds inserted as filler. +# e.g. あの, うんと, えと +フィラー +# +##### +# non-verbal: non-verbal sound. +非言語音 +# +##### +# fragment: +#語断片 +# +##### +# unknown: unknown part of speech. +#未知語 +# +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt new file mode 100644 index 0000000000..046829db6a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt @@ -0,0 +1,125 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Cleaned on October 11, 2009 (not normalized, so use before normalization) +# This means that when modifying this list, you might need to add some +# redundant entries, for example containing forms with both أ and ا +من +ومن +منها +منه +في +وفي +فيها +فيه +و +ف +ثم +او +أو +ب +بها +به +ا +أ +اى +اي +أي +أى +لا +ولا +الا +ألا +إلا +لكن +ما +وما +كما +فما +عن +مع +اذا +إذا +ان +أن +إن +انها +أنها +إنها +انه +أنه +إنه +بان +بأن +فان +فأن +وان +وأن +وإن +التى +التي +الذى +الذي +الذين +الى +الي +إلى +إلي +على +عليها +عليه +اما +أما +إما +ايضا +أيضا +كل +وكل +لم +ولم +لن +ولن +هى +هي +هو +وهى +وهي +وهو +فهى +فهي +فهو +انت +أنت +لك +لها +له +هذه +هذا +تلك +ذلك +هناك +كانت +كان +يكون +تكون +وكانت +وكان +غير +بعض +قد +نحو +بين +بينما +منذ +ضمن +حيث +الان +الآن +خلال +بعد +قبل +حتى +عند +عندما +لدى +جميع diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt new file mode 100644 index 0000000000..1ae4ba2ae3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt @@ -0,0 +1,193 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +а +аз +ако +ала +бе +без +беше +би +бил +била +били +било +близо +бъдат +бъде +бяха +в +вас +ваш +ваша +вероятно +вече +взема +ви +вие +винаги +все +всеки +всички +всичко +всяка +във +въпреки +върху +г +ги +главно +го +д +да +дали +до +докато +докога +дори +досега +доста +е +едва +един +ето +за +зад +заедно +заради +засега +затова +защо +защото +и +из +или +им +има +имат +иска +й +каза +как +каква +какво +както +какъв +като +кога +когато +което +които +кой +който +колко +която +къде +където +към +ли +м +ме +между +мен +ми +мнозина +мога +могат +може +моля +момента +му +н +на +над +назад +най +направи +напред +например +нас +не +него +нея +ни +ние +никой +нито +но +някои +някой +няма +обаче +около +освен +особено +от +отгоре +отново +още +пак +по +повече +повечето +под +поне +поради +после +почти +прави +пред +преди +през +при +пък +първо +с +са +само +се +сега +си +скоро +след +сме +според +сред +срещу +сте +съм +със +също +т +тази +така +такива +такъв +там +твой +те +тези +ти +тн +то +това +тогава +този +той +толкова +точно +трябва +тук +тъй +тя +тях +у +харесва +ч +че +често +чрез +ще +щом +я diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt new file mode 100644 index 0000000000..3da65deafe --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt @@ -0,0 +1,220 @@ +# Catalan stopwords from http://github.com/vcl/cue.language (Apache 2 Licensed) +a +abans +ací +ah +així +això +al +als +aleshores +algun +alguna +algunes +alguns +alhora +allà +allí +allò +altra +altre +altres +amb +ambdós +ambdues +apa +aquell +aquella +aquelles +aquells +aquest +aquesta +aquestes +aquests +aquí +baix +cada +cadascú +cadascuna +cadascunes +cadascuns +com +contra +d'un +d'una +d'unes +d'uns +dalt +de +del +dels +des +després +dins +dintre +donat +doncs +durant +e +eh +el +els +em +en +encara +ens +entre +érem +eren +éreu +es +és +esta +està +estàvem +estaven +estàveu +esteu +et +etc +ets +fins +fora +gairebé +ha +han +has +havia +he +hem +heu +hi +ho +i +igual +iguals +ja +l'hi +la +les +li +li'n +llavors +m'he +ma +mal +malgrat +mateix +mateixa +mateixes +mateixos +me +mentre +més +meu +meus +meva +meves +molt +molta +moltes +molts +mon +mons +n'he +n'hi +ne +ni +no +nogensmenys +només +nosaltres +nostra +nostre +nostres +o +oh +oi +on +pas +pel +pels +per +però +perquè +poc +poca +pocs +poques +potser +propi +qual +quals +quan +quant +que +què +quelcom +qui +quin +quina +quines +quins +s'ha +s'han +sa +semblant +semblants +ses +seu +seus +seva +seva +seves +si +sobre +sobretot +sóc +solament +sols +son +són +sons +sota +sou +t'ha +t'han +t'he +ta +tal +també +tampoc +tan +tant +tanta +tantes +teu +teus +teva +teves +ton +tons +tot +tota +totes +tots +un +una +unes +uns +us +va +vaig +vam +van +vas +veu +vosaltres +vostra +vostre +vostres diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt new file mode 100644 index 0000000000..53c6097dac --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt @@ -0,0 +1,172 @@ +a +s +k +o +i +u +v +z +dnes +cz +tímto +budeš +budem +byli +jseš +můj +svým +ta +tomto +tohle +tuto +tyto +jej +zda +proč +máte +tato +kam +tohoto +kdo +kteří +mi +nám +tom +tomuto +mít +nic +proto +kterou +byla +toho +protože +asi +ho +naši +napište +re +což +tím +takže +svých +její +svými +jste +aj +tu +tedy +teto +bylo +kde +ke +pravé +ji +nad +nejsou +či +pod +téma +mezi +přes +ty +pak +vám +ani +když +však +neg +jsem +tento +článku +články +aby +jsme +před +pta +jejich +byl +ještě +až +bez +také +pouze +první +vaše +která +nás +nový +tipy +pokud +může +strana +jeho +své +jiné +zprávy +nové +není +vás +jen +podle +zde +už +být +více +bude +již +než +který +by +které +co +nebo +ten +tak +má +při +od +po +jsou +jak +další +ale +si +se +ve +to +jako +za +zpět +ze +do +pro +je +na +atd +atp +jakmile +přičemž +já +on +ona +ono +oni +ony +my +vy +jí +ji +mě +mne +jemu +tomu +těm +těmu +němu +němuž +jehož +jíž +jelikož +jež +jakož +načež diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt new file mode 100644 index 0000000000..42e6145b98 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt @@ -0,0 +1,110 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/danish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Danish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + +og | and +i | in +jeg | I +det | that (dem. pronoun)/it (pers. pronoun) +at | that (in front of a sentence)/to (with infinitive) +en | a/an +den | it (pers. pronoun)/that (dem. pronoun) +til | to/at/for/until/against/by/of/into, more +er | present tense of "to be" +som | who, as +på | on/upon/in/on/at/to/after/of/with/for, on +de | they +med | with/by/in, along +han | he +af | of/by/from/off/for/in/with/on, off +for | at/for/to/from/by/of/ago, in front/before, because +ikke | not +der | who/which, there/those +var | past tense of "to be" +mig | me/myself +sig | oneself/himself/herself/itself/themselves +men | but +et | a/an/one, one (number), someone/somebody/one +har | present tense of "to have" +om | round/about/for/in/a, about/around/down, if +vi | we +min | my +havde | past tense of "to have" +ham | him +hun | she +nu | now +over | over/above/across/by/beyond/past/on/about, over/past +da | then, when/as/since +fra | from/off/since, off, since +du | you +ud | out +sin | his/her/its/one's +dem | them +os | us/ourselves +op | up +man | you/one +hans | his +hvor | where +eller | or +hvad | what +skal | must/shall etc. +selv | myself/youself/herself/ourselves etc., even +her | here +alle | all/everyone/everybody etc. +vil | will (verb) +blev | past tense of "to stay/to remain/to get/to become" +kunne | could +ind | in +når | when +være | present tense of "to be" +dog | however/yet/after all +noget | something +ville | would +jo | you know/you see (adv), yes +deres | their/theirs +efter | after/behind/according to/for/by/from, later/afterwards +ned | down +skulle | should +denne | this +end | than +dette | this +mit | my/mine +også | also +under | under/beneath/below/during, below/underneath +have | have +dig | you +anden | other +hende | her +mine | my +alt | everything +meget | much/very, plenty of +sit | his, her, its, one's +sine | his, her, its, one's +vor | our +mod | against +disse | these +hvis | if +din | your/yours +nogle | some +hos | by/at +blive | be/become +mange | many +ad | by/through +bliver | present tense of "to be/to become" +hendes | her/hers +været | be +thi | for (conj) +jer | you +sådan | such, like this/like that diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt new file mode 100644 index 0000000000..86525e7ae0 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt @@ -0,0 +1,294 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/german/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A German stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | The number of forms in this list is reduced significantly by passing it + | through the German stemmer. + + +aber | but + +alle | all +allem +allen +aller +alles + +als | than, as +also | so +am | an + dem +an | at + +ander | other +andere +anderem +anderen +anderer +anderes +anderm +andern +anderr +anders + +auch | also +auf | on +aus | out of +bei | by +bin | am +bis | until +bist | art +da | there +damit | with it +dann | then + +der | the +den +des +dem +die +das + +daß | that + +derselbe | the same +derselben +denselben +desselben +demselben +dieselbe +dieselben +dasselbe + +dazu | to that + +dein | thy +deine +deinem +deinen +deiner +deines + +denn | because + +derer | of those +dessen | of him + +dich | thee +dir | to thee +du | thou + +dies | this +diese +diesem +diesen +dieser +dieses + + +doch | (several meanings) +dort | (over) there + + +durch | through + +ein | a +eine +einem +einen +einer +eines + +einig | some +einige +einigem +einigen +einiger +einiges + +einmal | once + +er | he +ihn | him +ihm | to him + +es | it +etwas | something + +euer | your +eure +eurem +euren +eurer +eures + +für | for +gegen | towards +gewesen | p.p. of sein +hab | have +habe | have +haben | have +hat | has +hatte | had +hatten | had +hier | here +hin | there +hinter | behind + +ich | I +mich | me +mir | to me + + +ihr | you, to her +ihre +ihrem +ihren +ihrer +ihres +euch | to you + +im | in + dem +in | in +indem | while +ins | in + das +ist | is + +jede | each, every +jedem +jeden +jeder +jedes + +jene | that +jenem +jenen +jener +jenes + +jetzt | now +kann | can + +kein | no +keine +keinem +keinen +keiner +keines + +können | can +könnte | could +machen | do +man | one + +manche | some, many a +manchem +manchen +mancher +manches + +mein | my +meine +meinem +meinen +meiner +meines + +mit | with +muss | must +musste | had to +nach | to(wards) +nicht | not +nichts | nothing +noch | still, yet +nun | now +nur | only +ob | whether +oder | or +ohne | without +sehr | very + +sein | his +seine +seinem +seinen +seiner +seines + +selbst | self +sich | herself + +sie | they, she +ihnen | to them + +sind | are +so | so + +solche | such +solchem +solchen +solcher +solches + +soll | shall +sollte | should +sondern | but +sonst | else +über | over +um | about, around +und | and + +uns | us +unse +unsem +unsen +unser +unses + +unter | under +viel | much +vom | von + dem +von | from +vor | before +während | while +war | was +waren | were +warst | wast +was | what +weg | away, off +weil | because +weiter | further + +welche | which +welchem +welchen +welcher +welches + +wenn | when +werde | will +werden | will +wie | how +wieder | again +will | want +wir | we +wird | will +wirst | willst +wo | where +wollen | want +wollte | wanted +würde | would +würden | would +zu | to +zum | zu + dem +zur | zu + der +zwar | indeed +zwischen | between + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt new file mode 100644 index 0000000000..232681f5bd --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt @@ -0,0 +1,78 @@ +# Lucene Greek Stopwords list +# Note: by default this file is used after GreekLowerCaseFilter, +# so when modifying this file use 'σ' instead of 'ς' +ο +η +το +οι +τα +του +τησ +των +τον +την +και +κι +κ +ειμαι +εισαι +ειναι +ειμαστε +ειστε +στο +στον +στη +στην +μα +αλλα +απο +για +προσ +με +σε +ωσ +παρα +αντι +κατα +μετα +θα +να +δε +δεν +μη +μην +επι +ενω +εαν +αν +τοτε +που +πωσ +ποιοσ +ποια +ποιο +ποιοι +ποιεσ +ποιων +ποιουσ +αυτοσ +αυτη +αυτο +αυτοι +αυτων +αυτουσ +αυτεσ +αυτα +εκεινοσ +εκεινη +εκεινο +εκεινοι +εκεινεσ +εκεινα +εκεινων +εκεινουσ +οπωσ +ομωσ +ισωσ +οσο +οτι diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt new file mode 100644 index 0000000000..2c164c0b2a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt @@ -0,0 +1,54 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +# a couple of test stopwords to test that the words are really being +# configured from this file: +stopworda +stopwordb + +# Standard english stop words taken from Lucene's StopAnalyzer +a +an +and +are +as +at +be +but +by +for +if +in +into +is +it +no +not +of +on +or +such +that +the +their +then +there +these +they +this +to +was +will +with diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt new file mode 100644 index 0000000000..487d78c8d5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt @@ -0,0 +1,356 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/spanish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Spanish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | from, of +la | the, her +que | who, that +el | the +en | in +y | and +a | to +los | the, them +del | de + el +se | himself, from him etc +las | the, them +por | for, by, etc +un | a +para | for +con | with +no | no +una | a +su | his, her +al | a + el + | es from SER +lo | him +como | how +más | more +pero | pero +sus | su plural +le | to him, her +ya | already +o | or + | fue from SER +este | this + | ha from HABER +sí | himself etc +porque | because +esta | this + | son from SER +entre | between + | está from ESTAR +cuando | when +muy | very +sin | without +sobre | on + | ser from SER + | tiene from TENER +también | also +me | me +hasta | until +hay | there is/are +donde | where + | han from HABER +quien | whom, that + | están from ESTAR + | estado from ESTAR +desde | from +todo | all +nos | us +durante | during + | estados from ESTAR +todos | all +uno | a +les | to them +ni | nor +contra | against +otros | other + | fueron from SER +ese | that +eso | that + | había from HABER +ante | before +ellos | they +e | and (variant of y) +esto | this +mí | me +antes | before +algunos | some +qué | what? +unos | a +yo | I +otro | other +otras | other +otra | other +él | he +tanto | so much, many +esa | that +estos | these +mucho | much, many +quienes | who +nada | nothing +muchos | many +cual | who + | sea from SER +poco | few +ella | she +estar | to be + | haber from HABER +estas | these + | estaba from ESTAR + | estamos from ESTAR +algunas | some +algo | something +nosotros | we + + | other forms + +mi | me +mis | mi plural +tú | thou +te | thee +ti | thee +tu | thy +tus | tu plural +ellas | they +nosotras | we +vosotros | you +vosotras | you +os | you +mío | mine +mía | +míos | +mías | +tuyo | thine +tuya | +tuyos | +tuyas | +suyo | his, hers, theirs +suya | +suyos | +suyas | +nuestro | ours +nuestra | +nuestros | +nuestras | +vuestro | yours +vuestra | +vuestros | +vuestras | +esos | those +esas | those + + | forms of estar, to be (not including the infinitive): +estoy +estás +está +estamos +estáis +están +esté +estés +estemos +estéis +estén +estaré +estarás +estará +estaremos +estaréis +estarán +estaría +estarías +estaríamos +estaríais +estarían +estaba +estabas +estábamos +estabais +estaban +estuve +estuviste +estuvo +estuvimos +estuvisteis +estuvieron +estuviera +estuvieras +estuviéramos +estuvierais +estuvieran +estuviese +estuvieses +estuviésemos +estuvieseis +estuviesen +estando +estado +estada +estados +estadas +estad + + | forms of haber, to have (not including the infinitive): +he +has +ha +hemos +habéis +han +haya +hayas +hayamos +hayáis +hayan +habré +habrás +habrá +habremos +habréis +habrán +habría +habrías +habríamos +habríais +habrían +había +habías +habíamos +habíais +habían +hube +hubiste +hubo +hubimos +hubisteis +hubieron +hubiera +hubieras +hubiéramos +hubierais +hubieran +hubiese +hubieses +hubiésemos +hubieseis +hubiesen +habiendo +habido +habida +habidos +habidas + + | forms of ser, to be (not including the infinitive): +soy +eres +es +somos +sois +son +sea +seas +seamos +seáis +sean +seré +serás +será +seremos +seréis +serán +sería +serías +seríamos +seríais +serían +era +eras +éramos +erais +eran +fui +fuiste +fue +fuimos +fuisteis +fueron +fuera +fueras +fuéramos +fuerais +fueran +fuese +fueses +fuésemos +fueseis +fuesen +siendo +sido + | sed also means 'thirst' + + | forms of tener, to have (not including the infinitive): +tengo +tienes +tiene +tenemos +tenéis +tienen +tenga +tengas +tengamos +tengáis +tengan +tendré +tendrás +tendrá +tendremos +tendréis +tendrán +tendría +tendrías +tendríamos +tendríais +tendrían +tenía +tenías +teníamos +teníais +tenían +tuve +tuviste +tuvo +tuvimos +tuvisteis +tuvieron +tuviera +tuvieras +tuviéramos +tuvierais +tuvieran +tuviese +tuvieses +tuviésemos +tuvieseis +tuviesen +teniendo +tenido +tenida +tenidos +tenidas +tened + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt new file mode 100644 index 0000000000..25f1db9346 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt @@ -0,0 +1,99 @@ +# example set of basque stopwords +al +anitz +arabera +asko +baina +bat +batean +batek +bati +batzuei +batzuek +batzuetan +batzuk +bera +beraiek +berau +berauek +bere +berori +beroriek +beste +bezala +da +dago +dira +ditu +du +dute +edo +egin +ere +eta +eurak +ez +gainera +gu +gutxi +guzti +haiei +haiek +haietan +hainbeste +hala +han +handik +hango +hara +hari +hark +hartan +hau +hauei +hauek +hauetan +hemen +hemendik +hemengo +hi +hona +honek +honela +honetan +honi +hor +hori +horiei +horiek +horietan +horko +horra +horrek +horrela +horretan +horri +hortik +hura +izan +ni +noiz +nola +non +nondik +nongo +nor +nora +ze +zein +zen +zenbait +zenbat +zer +zergatik +ziren +zituen +zu +zuek +zuen +zuten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt new file mode 100644 index 0000000000..723641c6da --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt @@ -0,0 +1,313 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Note: by default this file is used after normalization, so when adding entries +# to this file, use the arabic 'ي' instead of 'ی' +انان +نداشته +سراسر +خياه +ايشان +وي +تاكنون +بيشتري +دوم +پس +ناشي +وگو +يا +داشتند +سپس +هنگام +هرگز +پنج +نشان +امسال +ديگر +گروهي +شدند +چطور +ده +و +دو +نخستين +ولي +چرا +چه +وسط +ه +كدام +قابل +يك +رفت +هفت +همچنين +در +هزار +بله +بلي +شايد +اما +شناسي +گرفته +دهد +داشته +دانست +داشتن +خواهيم +ميليارد +وقتيكه +امد +خواهد +جز +اورده +شده +بلكه +خدمات +شدن +برخي +نبود +بسياري +جلوگيري +حق +كردند +نوعي +بعري +نكرده +نظير +نبايد +بوده +بودن +داد +اورد +هست +جايي +شود +دنبال +داده +بايد +سابق +هيچ +همان +انجا +كمتر +كجاست +گردد +كسي +تر +مردم +تان +دادن +بودند +سري +جدا +ندارند +مگر +يكديگر +دارد +دهند +بنابراين +هنگامي +سمت +جا +انچه +خود +دادند +زياد +دارند +اثر +بدون +بهترين +بيشتر +البته +به +براساس +بيرون +كرد +بعضي +گرفت +توي +اي +ميليون +او +جريان +تول +بر +مانند +برابر +باشيم +مدتي +گويند +اكنون +تا +تنها +جديد +چند +بي +نشده +كردن +كردم +گويد +كرده +كنيم +نمي +نزد +روي +قصد +فقط +بالاي +ديگران +اين +ديروز +توسط +سوم +ايم +دانند +سوي +استفاده +شما +كنار +داريم +ساخته +طور +امده +رفته +نخست +بيست +نزديك +طي +كنيد +از +انها +تمامي +داشت +يكي +طريق +اش +چيست +روب +نمايد +گفت +چندين +چيزي +تواند +ام +ايا +با +ان +ايد +ترين +اينكه +ديگري +راه +هايي +بروز +همچنان +پاعين +كس +حدود +مختلف +مقابل +چيز +گيرد +ندارد +ضد +همچون +سازي +شان +مورد +باره +مرسي +خويش +برخوردار +چون +خارج +شش +هنوز +تحت +ضمن +هستيم +گفته +فكر +بسيار +پيش +براي +روزهاي +انكه +نخواهد +بالا +كل +وقتي +كي +چنين +كه +گيري +نيست +است +كجا +كند +نيز +يابد +بندي +حتي +توانند +عقب +خواست +كنند +بين +تمام +همه +ما +باشند +مثل +شد +اري +باشد +اره +طبق +بعد +اگر +صورت +غير +جاي +بيش +ريزي +اند +زيرا +چگونه +بار +لطفا +مي +درباره +من +ديده +همين +گذاري +برداري +علت +گذاشته +هم +فوق +نه +ها +شوند +اباد +همواره +هر +اول +خواهند +چهار +نام +امروز +مان +هاي +قبل +كنم +سعي +تازه +را +هستند +زير +جلوي +عنوان +بود diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt new file mode 100644 index 0000000000..4372c9a055 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt @@ -0,0 +1,97 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/finnish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| forms of BE + +olla +olen +olet +on +olemme +olette +ovat +ole | negative form + +oli +olisi +olisit +olisin +olisimme +olisitte +olisivat +olit +olin +olimme +olitte +olivat +ollut +olleet + +en | negation +et +ei +emme +ette +eivät + +|Nom Gen Acc Part Iness Elat Illat Adess Ablat Allat Ess Trans +minä minun minut minua minussa minusta minuun minulla minulta minulle | I +sinä sinun sinut sinua sinussa sinusta sinuun sinulla sinulta sinulle | you +hän hänen hänet häntä hänessä hänestä häneen hänellä häneltä hänelle | he she +me meidän meidät meitä meissä meistä meihin meillä meiltä meille | we +te teidän teidät teitä teissä teistä teihin teillä teiltä teille | you +he heidän heidät heitä heissä heistä heihin heillä heiltä heille | they + +tämä tämän tätä tässä tästä tähän tallä tältä tälle tänä täksi | this +tuo tuon tuotä tuossa tuosta tuohon tuolla tuolta tuolle tuona tuoksi | that +se sen sitä siinä siitä siihen sillä siltä sille sinä siksi | it +nämä näiden näitä näissä näistä näihin näillä näiltä näille näinä näiksi | these +nuo noiden noita noissa noista noihin noilla noilta noille noina noiksi | those +ne niiden niitä niissä niistä niihin niillä niiltä niille niinä niiksi | they + +kuka kenen kenet ketä kenessä kenestä keneen kenellä keneltä kenelle kenenä keneksi| who +ketkä keiden ketkä keitä keissä keistä keihin keillä keiltä keille keinä keiksi | (pl) +mikä minkä minkä mitä missä mistä mihin millä miltä mille minä miksi | which what +mitkä | (pl) + +joka jonka jota jossa josta johon jolla jolta jolle jona joksi | who which +jotka joiden joita joissa joista joihin joilla joilta joille joina joiksi | (pl) + +| conjunctions + +että | that +ja | and +jos | if +koska | because +kuin | than +mutta | but +niin | so +sekä | and +sillä | for +tai | or +vaan | but +vai | or +vaikka | although + + +| prepositions + +kanssa | with +mukaan | according to +noin | about +poikki | across +yli | over, across + +| other + +kun | when +niin | so +nyt | now +itse | self + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt new file mode 100644 index 0000000000..749abae684 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt @@ -0,0 +1,186 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/french/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A French stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +au | a + le +aux | a + les +avec | with +ce | this +ces | these +dans | with +de | of +des | de + les +du | de + le +elle | she +en | `of them' etc +et | and +eux | them +il | he +je | I +la | the +le | the +leur | their +lui | him +ma | my (fem) +mais | but +me | me +même | same; as in moi-même (myself) etc +mes | me (pl) +moi | me +mon | my (masc) +ne | not +nos | our (pl) +notre | our +nous | we +on | one +ou | where +par | by +pas | not +pour | for +qu | que before vowel +que | that +qui | who +sa | his, her (fem) +se | oneself +ses | his (pl) +son | his, her (masc) +sur | on +ta | thy (fem) +te | thee +tes | thy (pl) +toi | thee +ton | thy (masc) +tu | thou +un | a +une | a +vos | your (pl) +votre | your +vous | you + + | single letter forms + +c | c' +d | d' +j | j' +l | l' +à | to, at +m | m' +n | n' +s | s' +t | t' +y | there + + | forms of être (not including the infinitive): +été +étée +étées +étés +étant +suis +es +est +sommes +êtes +sont +serai +seras +sera +serons +serez +seront +serais +serait +serions +seriez +seraient +étais +était +étions +étiez +étaient +fus +fut +fûmes +fûtes +furent +sois +soit +soyons +soyez +soient +fusse +fusses +fût +fussions +fussiez +fussent + + | forms of avoir (not including the infinitive): +ayant +eu +eue +eues +eus +ai +as +avons +avez +ont +aurai +auras +aura +aurons +aurez +auront +aurais +aurait +aurions +auriez +auraient +avais +avait +avions +aviez +avaient +eut +eûmes +eûtes +eurent +aie +aies +ait +ayons +ayez +aient +eusse +eusses +eût +eussions +eussiez +eussent + + | Later additions (from Jean-Christophe Deschamps) +ceci | this +cela | that +celà | that +cet | this +cette | this +ici | here +ils | they +les | the (pl) +leurs | their (pl) +quel | which +quels | which +quelle | which +quelles | which +sans | without +soi | oneself + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt new file mode 100644 index 0000000000..9ff88d747e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt @@ -0,0 +1,110 @@ + +a +ach +ag +agus +an +aon +ar +arna +as +b' +ba +beirt +bhúr +caoga +ceathair +ceathrar +chomh +chtó +chuig +chun +cois +céad +cúig +cúigear +d' +daichead +dar +de +deich +deichniúr +den +dhá +do +don +dtí +dá +dár +dó +faoi +faoin +faoina +faoinár +fara +fiche +gach +gan +go +gur +haon +hocht +i +iad +idir +in +ina +ins +inár +is +le +leis +lena +lenár +m' +mar +mo +mé +na +nach +naoi +naonúr +ná +ní +níor +nó +nócha +ocht +ochtar +os +roimh +sa +seacht +seachtar +seachtó +seasca +seisear +siad +sibh +sinn +sna +sé +sí +tar +thar +thú +triúr +trí +trína +trínár +tríocha +tú +um +ár +é +éis +í +ó +ón +óna +ónár diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt new file mode 100644 index 0000000000..d8760b12c1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt @@ -0,0 +1,161 @@ +# galican stopwords +a +aínda +alí +aquel +aquela +aquelas +aqueles +aquilo +aquí +ao +aos +as +así +á +ben +cando +che +co +coa +comigo +con +connosco +contigo +convosco +coas +cos +cun +cuns +cunha +cunhas +da +dalgunha +dalgunhas +dalgún +dalgúns +das +de +del +dela +delas +deles +desde +deste +do +dos +dun +duns +dunha +dunhas +e +el +ela +elas +eles +en +era +eran +esa +esas +ese +eses +esta +estar +estaba +está +están +este +estes +estiven +estou +eu +é +facer +foi +foron +fun +había +hai +iso +isto +la +las +lle +lles +lo +los +mais +me +meu +meus +min +miña +miñas +moi +na +nas +neste +nin +no +non +nos +nosa +nosas +noso +nosos +nós +nun +nunha +nuns +nunhas +o +os +ou +ó +ós +para +pero +pode +pois +pola +polas +polo +polos +por +que +se +senón +ser +seu +seus +sexa +sido +sobre +súa +súas +tamén +tan +te +ten +teñen +teño +ter +teu +teus +ti +tido +tiña +tiven +túa +túas +un +unha +unhas +uns +vos +vosa +vosas +voso +vosos +vós diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt new file mode 100644 index 0000000000..86286bb083 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt @@ -0,0 +1,235 @@ +# Also see http://www.opensource.org/licenses/bsd-license.html +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# This file was created by Jacques Savoy and is distributed under the BSD license. +# Note: by default this file also contains forms normalized by HindiNormalizer +# for spelling variation (see section below), such that it can be used whether or +# not you enable that feature. When adding additional entries to this list, +# please add the normalized form as well. +अंदर +अत +अपना +अपनी +अपने +अभी +आदि +आप +इत्यादि +इन +इनका +इन्हीं +इन्हें +इन्हों +इस +इसका +इसकी +इसके +इसमें +इसी +इसे +उन +उनका +उनकी +उनके +उनको +उन्हीं +उन्हें +उन्हों +उस +उसके +उसी +उसे +एक +एवं +एस +ऐसे +और +कई +कर +करता +करते +करना +करने +करें +कहते +कहा +का +काफ़ी +कि +कितना +किन्हें +किन्हों +किया +किर +किस +किसी +किसे +की +कुछ +कुल +के +को +कोई +कौन +कौनसा +गया +घर +जब +जहाँ +जा +जितना +जिन +जिन्हें +जिन्हों +जिस +जिसे +जीधर +जैसा +जैसे +जो +तक +तब +तरह +तिन +तिन्हें +तिन्हों +तिस +तिसे +तो +था +थी +थे +दबारा +दिया +दुसरा +दूसरे +दो +द्वारा +न +नहीं +ना +निहायत +नीचे +ने +पर +पर +पहले +पूरा +पे +फिर +बनी +बही +बहुत +बाद +बाला +बिलकुल +भी +भीतर +मगर +मानो +मे +में +यदि +यह +यहाँ +यही +या +यिह +ये +रखें +रहा +रहे +ऱ्वासा +लिए +लिये +लेकिन +व +वर्ग +वह +वह +वहाँ +वहीं +वाले +वुह +वे +वग़ैरह +संग +सकता +सकते +सबसे +सभी +साथ +साबुत +साभ +सारा +से +सो +ही +हुआ +हुई +हुए +है +हैं +हो +होता +होती +होते +होना +होने +# additional normalized forms of the above +अपनि +जेसे +होति +सभि +तिंहों +इंहों +दवारा +इसि +किंहें +थि +उंहों +ओर +जिंहें +वहिं +अभि +बनि +हि +उंहिं +उंहें +हें +वगेरह +एसे +रवासा +कोन +निचे +काफि +उसि +पुरा +भितर +हे +बहि +वहां +कोइ +यहां +जिंहों +तिंहें +किसि +कइ +यहि +इंहिं +जिधर +इंहें +अदि +इतयादि +हुइ +कोनसा +इसकि +दुसरे +जहां +अप +किंहों +उनकि +भि +वरग +हुअ +जेसा +नहिं diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt new file mode 100644 index 0000000000..37526da8aa --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt @@ -0,0 +1,211 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/hungarian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| Hungarian stop word list +| prepared by Anna Tordai + +a +ahogy +ahol +aki +akik +akkor +alatt +által +általában +amely +amelyek +amelyekben +amelyeket +amelyet +amelynek +ami +amit +amolyan +amíg +amikor +át +abban +ahhoz +annak +arra +arról +az +azok +azon +azt +azzal +azért +aztán +azután +azonban +bár +be +belül +benne +cikk +cikkek +cikkeket +csak +de +e +eddig +egész +egy +egyes +egyetlen +egyéb +egyik +egyre +ekkor +el +elég +ellen +elő +először +előtt +első +én +éppen +ebben +ehhez +emilyen +ennek +erre +ez +ezt +ezek +ezen +ezzel +ezért +és +fel +felé +hanem +hiszen +hogy +hogyan +igen +így +illetve +ill. +ill +ilyen +ilyenkor +ison +ismét +itt +jó +jól +jobban +kell +kellett +keresztül +keressünk +ki +kívül +között +közül +legalább +lehet +lehetett +legyen +lenne +lenni +lesz +lett +maga +magát +majd +majd +már +más +másik +meg +még +mellett +mert +mely +melyek +mi +mit +míg +miért +milyen +mikor +minden +mindent +mindenki +mindig +mint +mintha +mivel +most +nagy +nagyobb +nagyon +ne +néha +nekem +neki +nem +néhány +nélkül +nincs +olyan +ott +össze +ő +ők +őket +pedig +persze +rá +s +saját +sem +semmi +sok +sokat +sokkal +számára +szemben +szerint +szinte +talán +tehát +teljes +tovább +továbbá +több +úgy +ugyanis +új +újabb +újra +után +utána +utolsó +vagy +vagyis +valaki +valami +valamint +való +vagyok +van +vannak +volt +voltam +voltak +voltunk +vissza +vele +viszont +volna diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt new file mode 100644 index 0000000000..60c1c50fbc --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt @@ -0,0 +1,46 @@ +# example set of Armenian stopwords. +այդ +այլ +այն +այս +դու +դուք +եմ +են +ենք +ես +եք +է +էի +էին +էինք +էիր +էիք +էր +ըստ +թ +ի +ին +իսկ +իր +կամ +համար +հետ +հետո +մենք +մեջ +մի +ն +նա +նաև +նրա +նրանք +որ +որը +որոնք +որպես +ու +ում +պիտի +վրա +և diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt new file mode 100644 index 0000000000..4617f83a5c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt @@ -0,0 +1,359 @@ +# from appendix D of: A Study of Stemming Effects on Information +# Retrieval in Bahasa Indonesia +ada +adanya +adalah +adapun +agak +agaknya +agar +akan +akankah +akhirnya +aku +akulah +amat +amatlah +anda +andalah +antar +diantaranya +antara +antaranya +diantara +apa +apaan +mengapa +apabila +apakah +apalagi +apatah +atau +ataukah +ataupun +bagai +bagaikan +sebagai +sebagainya +bagaimana +bagaimanapun +sebagaimana +bagaimanakah +bagi +bahkan +bahwa +bahwasanya +sebaliknya +banyak +sebanyak +beberapa +seberapa +begini +beginian +beginikah +beginilah +sebegini +begitu +begitukah +begitulah +begitupun +sebegitu +belum +belumlah +sebelum +sebelumnya +sebenarnya +berapa +berapakah +berapalah +berapapun +betulkah +sebetulnya +biasa +biasanya +bila +bilakah +bisa +bisakah +sebisanya +boleh +bolehkah +bolehlah +buat +bukan +bukankah +bukanlah +bukannya +cuma +percuma +dahulu +dalam +dan +dapat +dari +daripada +dekat +demi +demikian +demikianlah +sedemikian +dengan +depan +di +dia +dialah +dini +diri +dirinya +terdiri +dong +dulu +enggak +enggaknya +entah +entahlah +terhadap +terhadapnya +hal +hampir +hanya +hanyalah +harus +haruslah +harusnya +seharusnya +hendak +hendaklah +hendaknya +hingga +sehingga +ia +ialah +ibarat +ingin +inginkah +inginkan +ini +inikah +inilah +itu +itukah +itulah +jangan +jangankan +janganlah +jika +jikalau +juga +justru +kala +kalau +kalaulah +kalaupun +kalian +kami +kamilah +kamu +kamulah +kan +kapan +kapankah +kapanpun +dikarenakan +karena +karenanya +ke +kecil +kemudian +kenapa +kepada +kepadanya +ketika +seketika +khususnya +kini +kinilah +kiranya +sekiranya +kita +kitalah +kok +lagi +lagian +selagi +lah +lain +lainnya +melainkan +selaku +lalu +melalui +terlalu +lama +lamanya +selama +selama +selamanya +lebih +terlebih +bermacam +macam +semacam +maka +makanya +makin +malah +malahan +mampu +mampukah +mana +manakala +manalagi +masih +masihkah +semasih +masing +mau +maupun +semaunya +memang +mereka +merekalah +meski +meskipun +semula +mungkin +mungkinkah +nah +namun +nanti +nantinya +nyaris +oleh +olehnya +seorang +seseorang +pada +padanya +padahal +paling +sepanjang +pantas +sepantasnya +sepantasnyalah +para +pasti +pastilah +per +pernah +pula +pun +merupakan +rupanya +serupa +saat +saatnya +sesaat +saja +sajalah +saling +bersama +sama +sesama +sambil +sampai +sana +sangat +sangatlah +saya +sayalah +se +sebab +sebabnya +sebuah +tersebut +tersebutlah +sedang +sedangkan +sedikit +sedikitnya +segala +segalanya +segera +sesegera +sejak +sejenak +sekali +sekalian +sekalipun +sesekali +sekaligus +sekarang +sekarang +sekitar +sekitarnya +sela +selain +selalu +seluruh +seluruhnya +semakin +sementara +sempat +semua +semuanya +sendiri +sendirinya +seolah +seperti +sepertinya +sering +seringnya +serta +siapa +siapakah +siapapun +disini +disinilah +sini +sinilah +sesuatu +sesuatunya +suatu +sesudah +sesudahnya +sudah +sudahkah +sudahlah +supaya +tadi +tadinya +tak +tanpa +setelah +telah +tentang +tentu +tentulah +tentunya +tertentu +seterusnya +tapi +tetapi +setiap +tiap +setidaknya +tidak +tidakkah +tidaklah +toh +waduh +wah +wahai +sewaktu +walau +walaupun +wong +yaitu +yakni +yang diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt new file mode 100644 index 0000000000..1219cc773a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt @@ -0,0 +1,303 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/italian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | An Italian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +ad | a (to) before vowel +al | a + il +allo | a + lo +ai | a + i +agli | a + gli +all | a + l' +agl | a + gl' +alla | a + la +alle | a + le +con | with +col | con + il +coi | con + i (forms collo, cogli etc are now very rare) +da | from +dal | da + il +dallo | da + lo +dai | da + i +dagli | da + gli +dall | da + l' +dagl | da + gll' +dalla | da + la +dalle | da + le +di | of +del | di + il +dello | di + lo +dei | di + i +degli | di + gli +dell | di + l' +degl | di + gl' +della | di + la +delle | di + le +in | in +nel | in + el +nello | in + lo +nei | in + i +negli | in + gli +nell | in + l' +negl | in + gl' +nella | in + la +nelle | in + le +su | on +sul | su + il +sullo | su + lo +sui | su + i +sugli | su + gli +sull | su + l' +sugl | su + gl' +sulla | su + la +sulle | su + le +per | through, by +tra | among +contro | against +io | I +tu | thou +lui | he +lei | she +noi | we +voi | you +loro | they +mio | my +mia | +miei | +mie | +tuo | +tua | +tuoi | thy +tue | +suo | +sua | +suoi | his, her +sue | +nostro | our +nostra | +nostri | +nostre | +vostro | your +vostra | +vostri | +vostre | +mi | me +ti | thee +ci | us, there +vi | you, there +lo | him, the +la | her, the +li | them +le | them, the +gli | to him, the +ne | from there etc +il | the +un | a +uno | a +una | a +ma | but +ed | and +se | if +perché | why, because +anche | also +come | how +dov | where (as dov') +dove | where +che | who, that +chi | who +cui | whom +non | not +più | more +quale | who, that +quanto | how much +quanti | +quanta | +quante | +quello | that +quelli | +quella | +quelle | +questo | this +questi | +questa | +queste | +si | yes +tutto | all +tutti | all + + | single letter forms: + +a | at +c | as c' for ce or ci +e | and +i | the +l | as l' +o | or + + | forms of avere, to have (not including the infinitive): + +ho +hai +ha +abbiamo +avete +hanno +abbia +abbiate +abbiano +avrò +avrai +avrà +avremo +avrete +avranno +avrei +avresti +avrebbe +avremmo +avreste +avrebbero +avevo +avevi +aveva +avevamo +avevate +avevano +ebbi +avesti +ebbe +avemmo +aveste +ebbero +avessi +avesse +avessimo +avessero +avendo +avuto +avuta +avuti +avute + + | forms of essere, to be (not including the infinitive): +sono +sei +è +siamo +siete +sia +siate +siano +sarò +sarai +sarà +saremo +sarete +saranno +sarei +saresti +sarebbe +saremmo +sareste +sarebbero +ero +eri +era +eravamo +eravate +erano +fui +fosti +fu +fummo +foste +furono +fossi +fosse +fossimo +fossero +essendo + + | forms of fare, to do (not including the infinitive, fa, fat-): +faccio +fai +facciamo +fanno +faccia +facciate +facciano +farò +farai +farà +faremo +farete +faranno +farei +faresti +farebbe +faremmo +fareste +farebbero +facevo +facevi +faceva +facevamo +facevate +facevano +feci +facesti +fece +facemmo +faceste +fecero +facessi +facesse +facessimo +facessero +facendo + + | forms of stare, to be (not including the infinitive): +sto +stai +sta +stiamo +stanno +stia +stiate +stiano +starò +starai +starà +staremo +starete +staranno +starei +staresti +starebbe +staremmo +stareste +starebbero +stavo +stavi +stava +stavamo +stavate +stavano +stetti +stesti +stette +stemmo +steste +stettero +stessi +stesse +stessimo +stessero +stando diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt new file mode 100644 index 0000000000..d4321be6b1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt @@ -0,0 +1,127 @@ +# +# This file defines a stopword set for Japanese. +# +# This set is made up of hand-picked frequent terms from segmented Japanese Wikipedia. +# Punctuation characters and frequent kanji have mostly been left out. See LUCENE-3745 +# for frequency lists, etc. that can be useful for making your own set (if desired) +# +# Note that there is an overlap between these stopwords and the terms stopped when used +# in combination with the JapanesePartOfSpeechStopFilter. When editing this file, note +# that comments are not allowed on the same line as stopwords. +# +# Also note that stopping is done in a case-insensitive manner. Change your StopFilter +# configuration if you need case-sensitive stopping. Lastly, note that stopping is done +# using the same character width as the entries in this file. Since this StopFilter is +# normally done after a CJKWidthFilter in your chain, you would usually want your romaji +# entries to be in half-width and your kana entries to be in full-width. +# +の +に +は +を +た +が +で +て +と +し +れ +さ +ある +いる +も +する +から +な +こと +として +い +や +れる +など +なっ +ない +この +ため +その +あっ +よう +また +もの +という +あり +まで +られ +なる +へ +か +だ +これ +によって +により +おり +より +による +ず +なり +られる +において +ば +なかっ +なく +しかし +について +せ +だっ +その後 +できる +それ +う +ので +なお +のみ +でき +き +つ +における +および +いう +さらに +でも +ら +たり +その他 +に関する +たち +ます +ん +なら +に対して +特に +せる +及び +これら +とき +では +にて +ほか +ながら +うち +そして +とともに +ただし +かつて +それぞれ +または +お +ほど +ものの +に対する +ほとんど +と共に +といった +です +とも +ところ +ここ +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt new file mode 100644 index 0000000000..e21a23c06c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt @@ -0,0 +1,172 @@ +# Set of Latvian stopwords from A Stemming Algorithm for Latvian, Karlis Kreslins +# the original list of over 800 forms was refined: +# pronouns, adverbs, interjections were removed +# +# prepositions +aiz +ap +ar +apakš +ārpus +augšpus +bez +caur +dēļ +gar +iekš +iz +kopš +labad +lejpus +līdz +no +otrpus +pa +par +pār +pēc +pie +pirms +pret +priekš +starp +šaipus +uz +viņpus +virs +virspus +zem +apakšpus +# Conjunctions +un +bet +jo +ja +ka +lai +tomēr +tikko +turpretī +arī +kaut +gan +tādēļ +tā +ne +tikvien +vien +kā +ir +te +vai +kamēr +# Particles +ar +diezin +droši +diemžēl +nebūt +ik +it +taču +nu +pat +tiklab +iekšpus +nedz +tik +nevis +turpretim +jeb +iekam +iekām +iekāms +kolīdz +līdzko +tiklīdz +jebšu +tālab +tāpēc +nekā +itin +jā +jau +jel +nē +nezin +tad +tikai +vis +tak +iekams +vien +# modal verbs +būt +biju +biji +bija +bijām +bijāt +esmu +esi +esam +esat +būšu +būsi +būs +būsim +būsiet +tikt +tiku +tiki +tika +tikām +tikāt +tieku +tiec +tiek +tiekam +tiekat +tikšu +tiks +tiksim +tiksiet +tapt +tapi +tapāt +topat +tapšu +tapsi +taps +tapsim +tapsiet +kļūt +kļuvu +kļuvi +kļuva +kļuvām +kļuvāt +kļūstu +kļūsti +kļūst +kļūstam +kļūstat +kļūšu +kļūsi +kļūs +kļūsim +kļūsiet +# verbs +varēt +varēju +varējām +varēšu +varēsim +var +varēji +varējāt +varēsi +varēsiet +varat +varēja +varēs diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt new file mode 100644 index 0000000000..47a2aeacf6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt @@ -0,0 +1,119 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/dutch/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Dutch stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large sample of Dutch text. + + | Dutch stop words frequently exhibit homonym clashes. These are indicated + | clearly below. + +de | the +en | and +van | of, from +ik | I, the ego +te | (1) chez, at etc, (2) to, (3) too +dat | that, which +die | that, those, who, which +in | in, inside +een | a, an, one +hij | he +het | the, it +niet | not, nothing, naught +zijn | (1) to be, being, (2) his, one's, its +is | is +was | (1) was, past tense of all persons sing. of 'zijn' (to be) (2) wax, (3) the washing, (4) rise of river +op | on, upon, at, in, up, used up +aan | on, upon, to (as dative) +met | with, by +als | like, such as, when +voor | (1) before, in front of, (2) furrow +had | had, past tense all persons sing. of 'hebben' (have) +er | there +maar | but, only +om | round, about, for etc +hem | him +dan | then +zou | should/would, past tense all persons sing. of 'zullen' +of | or, whether, if +wat | what, something, anything +mijn | possessive and noun 'mine' +men | people, 'one' +dit | this +zo | so, thus, in this way +door | through by +over | over, across +ze | she, her, they, them +zich | oneself +bij | (1) a bee, (2) by, near, at +ook | also, too +tot | till, until +je | you +mij | me +uit | out of, from +der | Old Dutch form of 'van der' still found in surnames +daar | (1) there, (2) because +haar | (1) her, their, them, (2) hair +naar | (1) unpleasant, unwell etc, (2) towards, (3) as +heb | present first person sing. of 'to have' +hoe | how, why +heeft | present third person sing. of 'to have' +hebben | 'to have' and various parts thereof +deze | this +u | you +want | (1) for, (2) mitten, (3) rigging +nog | yet, still +zal | 'shall', first and third person sing. of verb 'zullen' (will) +me | me +zij | she, they +nu | now +ge | 'thou', still used in Belgium and south Netherlands +geen | none +omdat | because +iets | something, somewhat +worden | to become, grow, get +toch | yet, still +al | all, every, each +waren | (1) 'were' (2) to wander, (3) wares, (3) +veel | much, many +meer | (1) more, (2) lake +doen | to do, to make +toen | then, when +moet | noun 'spot/mote' and present form of 'to must' +ben | (1) am, (2) 'are' in interrogative second person singular of 'to be' +zonder | without +kan | noun 'can' and present form of 'to be able' +hun | their, them +dus | so, consequently +alles | all, everything, anything +onder | under, beneath +ja | yes, of course +eens | once, one day +hier | here +wie | who +werd | imperfect third person sing. of 'become' +altijd | always +doch | yet, but etc +wordt | present third person sing. of 'become' +wezen | (1) to be, (2) 'been' as in 'been fishing', (3) orphans +kunnen | to be able +ons | us/our +zelf | self +tegen | against, towards, at +na | after, near +reeds | already +wil | (1) present tense of 'want', (2) 'will', noun, (3) fender +kon | could; past tense of 'to be able' +niets | nothing +uw | your +iemand | somebody +geweest | been; past participle of 'be' +andere | other diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt new file mode 100644 index 0000000000..a7a2c28ba5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt @@ -0,0 +1,194 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/norwegian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Norwegian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This stop word list is for the dominant bokmål dialect. Words unique + | to nynorsk are marked *. + + | Revised by Jan Bruusgaard , Jan 2005 + +og | and +i | in +jeg | I +det | it/this/that +at | to (w. inf.) +en | a/an +et | a/an +den | it/this/that +til | to +er | is/am/are +som | who/that +på | on +de | they / you(formal) +med | with +han | he +av | of +ikke | not +ikkje | not * +der | there +så | so +var | was/were +meg | me +seg | you +men | but +ett | one +har | have +om | about +vi | we +min | my +mitt | my +ha | have +hadde | had +hun | she +nå | now +over | over +da | when/as +ved | by/know +fra | from +du | you +ut | out +sin | your +dem | them +oss | us +opp | up +man | you/one +kan | can +hans | his +hvor | where +eller | or +hva | what +skal | shall/must +selv | self (reflective) +sjøl | self (reflective) +her | here +alle | all +vil | will +bli | become +ble | became +blei | became * +blitt | have become +kunne | could +inn | in +når | when +være | be +kom | come +noen | some +noe | some +ville | would +dere | you +som | who/which/that +deres | their/theirs +kun | only/just +ja | yes +etter | after +ned | down +skulle | should +denne | this +for | for/because +deg | you +si | hers/his +sine | hers/his +sitt | hers/his +mot | against +å | to +meget | much +hvorfor | why +dette | this +disse | these/those +uten | without +hvordan | how +ingen | none +din | your +ditt | your +blir | become +samme | same +hvilken | which +hvilke | which (plural) +sånn | such a +inni | inside/within +mellom | between +vår | our +hver | each +hvem | who +vors | us/ours +hvis | whose +både | both +bare | only/just +enn | than +fordi | as/because +før | before +mange | many +også | also +slik | just +vært | been +være | to be +båe | both * +begge | both +siden | since +dykk | your * +dykkar | yours * +dei | they * +deira | them * +deires | theirs * +deim | them * +di | your (fem.) * +då | as/when * +eg | I * +ein | a/an * +eit | a/an * +eitt | a/an * +elles | or * +honom | he * +hjå | at * +ho | she * +hoe | she * +henne | her +hennar | her/hers +hennes | hers +hoss | how * +hossen | how * +ikkje | not * +ingi | noone * +inkje | noone * +korleis | how * +korso | how * +kva | what/which * +kvar | where * +kvarhelst | where * +kven | who/whom * +kvi | why * +kvifor | why * +me | we * +medan | while * +mi | my * +mine | my * +mykje | much * +no | now * +nokon | some (masc./neut.) * +noka | some (fem.) * +nokor | some * +noko | some * +nokre | some * +si | his/hers * +sia | since * +sidan | since * +so | so * +somt | some * +somme | some * +um | about* +upp | up * +vere | be * +vore | was * +verte | become * +vort | become * +varte | became * +vart | became * + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt new file mode 100644 index 0000000000..acfeb01af6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt @@ -0,0 +1,253 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/portuguese/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Portuguese stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | of, from +a | the; to, at; her +o | the; him +que | who, that +e | and +do | de + o +da | de + a +em | in +um | a +para | for + | é from SER +com | with +não | not, no +uma | a +os | the; them +no | em + o +se | himself etc +na | em + a +por | for +mais | more +as | the; them +dos | de + os +como | as, like +mas | but + | foi from SER +ao | a + o +ele | he +das | de + as + | tem from TER +à | a + a +seu | his +sua | her +ou | or + | ser from SER +quando | when +muito | much + | há from HAV +nos | em + os; us +já | already, now + | está from EST +eu | I +também | also +só | only, just +pelo | per + o +pela | per + a +até | up to +isso | that +ela | he +entre | between + | era from SER +depois | after +sem | without +mesmo | same +aos | a + os + | ter from TER +seus | his +quem | whom +nas | em + as +me | me +esse | that +eles | they + | estão from EST +você | you + | tinha from TER + | foram from SER +essa | that +num | em + um +nem | nor +suas | her +meu | my +às | a + as +minha | my + | têm from TER +numa | em + uma +pelos | per + os +elas | they + | havia from HAV + | seja from SER +qual | which + | será from SER +nós | we + | tenho from TER +lhe | to him, her +deles | of them +essas | those +esses | those +pelas | per + as +este | this + | fosse from SER +dele | of him + + | other words. There are many contractions such as naquele = em+aquele, + | mo = me+o, but they are rare. + | Indefinite article plural forms are also rare. + +tu | thou +te | thee +vocês | you (plural) +vos | you +lhes | to them +meus | my +minhas +teu | thy +tua +teus +tuas +nosso | our +nossa +nossos +nossas + +dela | of her +delas | of them + +esta | this +estes | these +estas | these +aquele | that +aquela | that +aqueles | those +aquelas | those +isto | this +aquilo | that + + | forms of estar, to be (not including the infinitive): +estou +está +estamos +estão +estive +esteve +estivemos +estiveram +estava +estávamos +estavam +estivera +estivéramos +esteja +estejamos +estejam +estivesse +estivéssemos +estivessem +estiver +estivermos +estiverem + + | forms of haver, to have (not including the infinitive): +hei +há +havemos +hão +houve +houvemos +houveram +houvera +houvéramos +haja +hajamos +hajam +houvesse +houvéssemos +houvessem +houver +houvermos +houverem +houverei +houverá +houveremos +houverão +houveria +houveríamos +houveriam + + | forms of ser, to be (not including the infinitive): +sou +somos +são +era +éramos +eram +fui +foi +fomos +foram +fora +fôramos +seja +sejamos +sejam +fosse +fôssemos +fossem +for +formos +forem +serei +será +seremos +serão +seria +seríamos +seriam + + | forms of ter, to have (not including the infinitive): +tenho +tem +temos +tém +tinha +tínhamos +tinham +tive +teve +tivemos +tiveram +tivera +tivéramos +tenha +tenhamos +tenham +tivesse +tivéssemos +tivessem +tiver +tivermos +tiverem +terei +terá +teremos +terão +teria +teríamos +teriam diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt new file mode 100644 index 0000000000..4fdee90a5b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt @@ -0,0 +1,233 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +acea +aceasta +această +aceea +acei +aceia +acel +acela +acele +acelea +acest +acesta +aceste +acestea +aceşti +aceştia +acolo +acum +ai +aia +aibă +aici +al +ăla +ale +alea +ălea +altceva +altcineva +am +ar +are +aş +aşadar +asemenea +asta +ăsta +astăzi +astea +ăstea +ăştia +asupra +aţi +au +avea +avem +aveţi +azi +bine +bucur +bună +ca +că +căci +când +care +cărei +căror +cărui +cât +câte +câţi +către +câtva +ce +cel +ceva +chiar +cînd +cine +cineva +cît +cîte +cîţi +cîtva +contra +cu +cum +cumva +curând +curînd +da +dă +dacă +dar +datorită +de +deci +deja +deoarece +departe +deşi +din +dinaintea +dintr +dintre +drept +după +ea +ei +el +ele +eram +este +eşti +eu +face +fără +fi +fie +fiecare +fii +fim +fiţi +iar +ieri +îi +îl +îmi +împotriva +în +înainte +înaintea +încât +încît +încotro +între +întrucât +întrucît +îţi +la +lângă +le +li +lîngă +lor +lui +mă +mâine +mea +mei +mele +mereu +meu +mi +mine +mult +multă +mulţi +ne +nicăieri +nici +nimeni +nişte +noastră +noastre +noi +noştri +nostru +nu +ori +oricând +oricare +oricât +orice +oricînd +oricine +oricît +oricum +oriunde +până +pe +pentru +peste +pînă +poate +pot +prea +prima +primul +prin +printr +sa +să +săi +sale +sau +său +se +şi +sînt +sîntem +sînteţi +spre +sub +sunt +suntem +sunteţi +ta +tăi +tale +tău +te +ţi +ţie +tine +toată +toate +tot +toţi +totuşi +tu +un +una +unde +undeva +unei +unele +uneori +unor +vă +vi +voastră +voastre +voi +voştri +vostru +vouă +vreo +vreun diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt new file mode 100644 index 0000000000..55271400c6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt @@ -0,0 +1,243 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/russian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | a russian stop word list. comments begin with vertical bar. each stop + | word is at the start of a line. + + | this is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | letter `ё' is translated to `е'. + +и | and +в | in/into +во | alternative form +не | not +что | what/that +он | he +на | on/onto +я | i +с | from +со | alternative form +как | how +а | milder form of `no' (but) +то | conjunction and form of `that' +все | all +она | she +так | so, thus +его | him +но | but +да | yes/and +ты | thou +к | towards, by +у | around, chez +же | intensifier particle +вы | you +за | beyond, behind +бы | conditional/subj. particle +по | up to, along +только | only +ее | her +мне | to me +было | it was +вот | here is/are, particle +от | away from +меня | me +еще | still, yet, more +нет | no, there isnt/arent +о | about +из | out of +ему | to him +теперь | now +когда | when +даже | even +ну | so, well +вдруг | suddenly +ли | interrogative particle +если | if +уже | already, but homonym of `narrower' +или | or +ни | neither +быть | to be +был | he was +него | prepositional form of его +до | up to +вас | you accusative +нибудь | indef. suffix preceded by hyphen +опять | again +уж | already, but homonym of `adder' +вам | to you +сказал | he said +ведь | particle `after all' +там | there +потом | then +себя | oneself +ничего | nothing +ей | to her +может | usually with `быть' as `maybe' +они | they +тут | here +где | where +есть | there is/are +надо | got to, must +ней | prepositional form of ей +для | for +мы | we +тебя | thee +их | them, their +чем | than +была | she was +сам | self +чтоб | in order to +без | without +будто | as if +человек | man, person, one +чего | genitive form of `what' +раз | once +тоже | also +себе | to oneself +под | beneath +жизнь | life +будет | will be +ж | short form of intensifer particle `же' +тогда | then +кто | who +этот | this +говорил | was saying +того | genitive form of `that' +потому | for that reason +этого | genitive form of `this' +какой | which +совсем | altogether +ним | prepositional form of `его', `они' +здесь | here +этом | prepositional form of `этот' +один | one +почти | almost +мой | my +тем | instrumental/dative plural of `тот', `то' +чтобы | full form of `in order that' +нее | her (acc.) +кажется | it seems +сейчас | now +были | they were +куда | where to +зачем | why +сказать | to say +всех | all (acc., gen. preposn. plural) +никогда | never +сегодня | today +можно | possible, one can +при | by +наконец | finally +два | two +об | alternative form of `о', about +другой | another +хоть | even +после | after +над | above +больше | more +тот | that one (masc.) +через | across, in +эти | these +нас | us +про | about +всего | in all, only, of all +них | prepositional form of `они' (they) +какая | which, feminine +много | lots +разве | interrogative particle +сказала | she said +три | three +эту | this, acc. fem. sing. +моя | my, feminine +впрочем | moreover, besides +хорошо | good +свою | ones own, acc. fem. sing. +этой | oblique form of `эта', fem. `this' +перед | in front of +иногда | sometimes +лучше | better +чуть | a little +том | preposn. form of `that one' +нельзя | one must not +такой | such a one +им | to them +более | more +всегда | always +конечно | of course +всю | acc. fem. sing of `all' +между | between + + + | b: some paradigms + | + | personal pronouns + | + | я меня мне мной [мною] + | ты тебя тебе тобой [тобою] + | он его ему им [него, нему, ним] + | она ее эи ею [нее, нэи, нею] + | оно его ему им [него, нему, ним] + | + | мы нас нам нами + | вы вас вам вами + | они их им ими [них, ним, ними] + | + | себя себе собой [собою] + | + | demonstrative pronouns: этот (this), тот (that) + | + | этот эта это эти + | этого эты это эти + | этого этой этого этих + | этому этой этому этим + | этим этой этим [этою] этими + | этом этой этом этих + | + | тот та то те + | того ту то те + | того той того тех + | тому той тому тем + | тем той тем [тою] теми + | том той том тех + | + | determinative pronouns + | + | (a) весь (all) + | + | весь вся все все + | всего всю все все + | всего всей всего всех + | всему всей всему всем + | всем всей всем [всею] всеми + | всем всей всем всех + | + | (b) сам (himself etc) + | + | сам сама само сами + | самого саму само самих + | самого самой самого самих + | самому самой самому самим + | самим самой самим [самою] самими + | самом самой самом самих + | + | stems of verbs `to be', `to have', `to do' and modal + | + | быть бы буд быв есть суть + | име + | дел + | мог мож мочь + | уме + | хоч хот + | долж + | можн + | нужн + | нельзя + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt new file mode 100644 index 0000000000..096f87f676 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt @@ -0,0 +1,133 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/swedish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Swedish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | Swedish stop words occasionally exhibit homonym clashes. For example + | så = so, but also seed. These are indicated clearly below. + +och | and +det | it, this/that +att | to (with infinitive) +i | in, at +en | a +jag | I +hon | she +som | who, that +han | he +på | on +den | it, this/that +med | with +var | where, each +sig | him(self) etc +för | for +så | so (also: seed) +till | to +är | is +men | but +ett | a +om | if; around, about +hade | had +de | they, these/those +av | of +icke | not, no +mig | me +du | you +henne | her +då | then, when +sin | his +nu | now +har | have +inte | inte någon = no one +hans | his +honom | him +skulle | 'sake' +hennes | her +där | there +min | my +man | one (pronoun) +ej | nor +vid | at, by, on (also: vast) +kunde | could +något | some etc +från | from, off +ut | out +när | when +efter | after, behind +upp | up +vi | we +dem | them +vara | be +vad | what +över | over +än | than +dig | you +kan | can +sina | his +här | here +ha | have +mot | towards +alla | all +under | under (also: wonder) +någon | some etc +eller | or (else) +allt | all +mycket | much +sedan | since +ju | why +denna | this/that +själv | myself, yourself etc +detta | this/that +åt | to +utan | without +varit | was +hur | how +ingen | no +mitt | my +ni | you +bli | to be, become +blev | from bli +oss | us +din | thy +dessa | these/those +några | some etc +deras | their +blir | from bli +mina | my +samma | (the) same +vilken | who, that +er | you, your +sådan | such a +vår | our +blivit | from bli +dess | its +inom | within +mellan | between +sådant | such a +varför | why +varje | each +vilka | who, that +ditt | thy +vem | who +vilket | who, that +sitta | his +sådana | such a +vart | each +dina | thy +vars | whose +vårt | our +våra | our +ert | your +era | your +vilkas | whose + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt new file mode 100644 index 0000000000..07f0fabe69 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt @@ -0,0 +1,119 @@ +# Thai stopwords from: +# "Opinion Detection in Thai Political News Columns +# Based on Subjectivity Analysis" +# Khampol Sukhum, Supot Nitsuwat, and Choochart Haruechaiyasak +ไว้ +ไม่ +ไป +ได้ +ให้ +ใน +โดย +แห่ง +แล้ว +และ +แรก +แบบ +แต่ +เอง +เห็น +เลย +เริ่ม +เรา +เมื่อ +เพื่อ +เพราะ +เป็นการ +เป็น +เปิดเผย +เปิด +เนื่องจาก +เดียวกัน +เดียว +เช่น +เฉพาะ +เคย +เข้า +เขา +อีก +อาจ +อะไร +ออก +อย่าง +อยู่ +อยาก +หาก +หลาย +หลังจาก +หลัง +หรือ +หนึ่ง +ส่วน +ส่ง +สุด +สําหรับ +ว่า +วัน +ลง +ร่วม +ราย +รับ +ระหว่าง +รวม +ยัง +มี +มาก +มา +พร้อม +พบ +ผ่าน +ผล +บาง +น่า +นี้ +นํา +นั้น +นัก +นอกจาก +ทุก +ที่สุด +ที่ +ทําให้ +ทํา +ทาง +ทั้งนี้ +ทั้ง +ถ้า +ถูก +ถึง +ต้อง +ต่างๆ +ต่าง +ต่อ +ตาม +ตั้งแต่ +ตั้ง +ด้าน +ด้วย +ดัง +ซึ่ง +ช่วง +จึง +จาก +จัด +จะ +คือ +ความ +ครั้ง +คง +ขึ้น +ของ +ขอ +ขณะ +ก่อน +ก็ +การ +กับ +กัน +กว่า +กล่าว diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt new file mode 100644 index 0000000000..84d9408d4e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt @@ -0,0 +1,212 @@ +# Turkish stopwords from LUCENE-559 +# merged with the list from "Information Retrieval on Turkish Texts" +# (http://www.users.muohio.edu/canf/papers/JASIST2008offPrint.pdf) +acaba +altmış +altı +ama +ancak +arada +aslında +ayrıca +bana +bazı +belki +ben +benden +beni +benim +beri +beş +bile +bin +bir +birçok +biri +birkaç +birkez +birşey +birşeyi +biz +bize +bizden +bizi +bizim +böyle +böylece +bu +buna +bunda +bundan +bunlar +bunları +bunların +bunu +bunun +burada +çok +çünkü +da +daha +dahi +de +defa +değil +diğer +diye +doksan +dokuz +dolayı +dolayısıyla +dört +edecek +eden +ederek +edilecek +ediliyor +edilmesi +ediyor +eğer +elli +en +etmesi +etti +ettiği +ettiğini +gibi +göre +halen +hangi +hatta +hem +henüz +hep +hepsi +her +herhangi +herkesin +hiç +hiçbir +için +iki +ile +ilgili +ise +işte +itibaren +itibariyle +kadar +karşın +katrilyon +kendi +kendilerine +kendini +kendisi +kendisine +kendisini +kez +ki +kim +kimden +kime +kimi +kimse +kırk +milyar +milyon +mu +mü +mı +nasıl +ne +neden +nedenle +nerde +nerede +nereye +niye +niçin +o +olan +olarak +oldu +olduğu +olduğunu +olduklarını +olmadı +olmadığı +olmak +olması +olmayan +olmaz +olsa +olsun +olup +olur +olursa +oluyor +on +ona +ondan +onlar +onlardan +onları +onların +onu +onun +otuz +oysa +öyle +pek +rağmen +sadece +sanki +sekiz +seksen +sen +senden +seni +senin +siz +sizden +sizi +sizin +şey +şeyden +şeyi +şeyler +şöyle +şu +şuna +şunda +şundan +şunları +şunu +tarafından +trilyon +tüm +üç +üzere +var +vardı +ve +veya +ya +yani +yapacak +yapılan +yapılması +yapıyor +yapmak +yaptı +yaptığı +yaptığını +yaptıkları +yedi +yerine +yetmiş +yine +yirmi +yoksa +yüz +zaten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt new file mode 100644 index 0000000000..6f0368e4d8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt @@ -0,0 +1,29 @@ +# +# This is a sample user dictionary for Kuromoji (JapaneseTokenizer) +# +# Add entries to this file in order to override the statistical model in terms +# of segmentation, readings and part-of-speech tags. Notice that entries do +# not have weights since they are always used when found. This is by-design +# in order to maximize ease-of-use. +# +# Entries are defined using the following CSV format: +# , ... , ... , +# +# Notice that a single half-width space separates tokens and readings, and +# that the number tokens and readings must match exactly. +# +# Also notice that multiple entries with the same is undefined. +# +# Whitespace only lines are ignored. Comments are not allowed on entry lines. +# + +# Custom segmentation for kanji compounds +日本経済新聞,日本 経済 新聞,ニホン ケイザイ シンブン,カスタム名詞 +関西国際空港,関西 国際 空港,カンサイ コクサイ クウコウ,カスタム名詞 + +# Custom segmentation for compound katakana +トートバッグ,トート バッグ,トート バッグ,かずカナ名詞 +ショルダーバッグ,ショルダー バッグ,ショルダー バッグ,かずカナ名詞 + +# Custom reading for former sumo wrestler +朝青龍,朝青龍,アサショウリュウ,カスタム人名 diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema new file mode 100644 index 0000000000..bcf4e189d6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema @@ -0,0 +1,411 @@ + + + + __indexrecordidentifier + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json new file mode 100644 index 0000000000..06114ef257 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json @@ -0,0 +1,20 @@ +{"params":{ + "query":{ + "defType":"edismax", + "q.alt":"*:*", + "rows":"10", + "fl":"*,score", + "":{"v":0} + }, + "facets":{ + "facet":"on", + "facet.mincount": "1", + "":{"v":0} + }, + "velocity":{ + "wt": "velocity", + "v.template":"browse", + "v.layout": "layout", + "":{"v":0} + } +}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt new file mode 100644 index 0000000000..1dfc0abecb --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt @@ -0,0 +1,21 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +# Use a protected word file to protect against the stemmer reducing two +# unrelated words to the same base word. + +# Some non-words that normally won't be encountered, +# just to test that they won't be stemmed. +dontstems +zwhacky + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml new file mode 100644 index 0000000000..de38e73071 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml @@ -0,0 +1,1506 @@ + + + + + + + + + 7.5.0 + + + + + + + + + + + + + + + + + + + + + ${solr.data.dir:} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.lock.type:native} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.ulog.dir:} + ${solr.ulog.numVersionBuckets:65536} + + + + + ${solr.autoCommit.maxTime:15000} + false + + + + + + ${solr.autoSoftCommit.maxTime:-1} + + + + + + + + + + + + + + + + 1024 + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + 20 + + + 200 + + + + + + + + + + + + + + + + false + + + + + + + + + + + + + + + + + + + + + + + explicit + AND + 10 + + + + + + + + + + + + + + + + explicit + AND + 10 + + + edismax + + + 1.0 + + + + resultidentifier^100 + resultauthor^34 + resultacceptanceyear^21 + resultsubject^13 + resulttitle^8 + relprojectname^5 + resultdescription^3 + __all + + + + + + + + + + + + + + + + + + + + + + + + + + + explicit + json + true + + + + + + + + explicit + + + + + + __all + + + + + + + + + true + ignored_ + __all + + + + + + + + text_general + + + + + + default + __all + solr.DirectSolrSpellChecker + + internal + + 0.5 + + 2 + + 1 + + 5 + + 4 + + 0.01 + + + + + + + + + + + + default + on + true + 10 + 5 + 5 + true + true + 10 + 5 + + + spellcheck + + + + + + + + + + true + + + tvComponent + + + + + + + + + + + + true + false + + + terms + + + + + + + + string + elevate.xml + + + + + + explicit + + + elevator + + + + + + + + + + + 100 + + + + + + + + 70 + + 0.5 + + [-\w ,/\n\"']{20,200} + + + + + + + ]]> + ]]> + + + + + + + + + + + + + + + + + + + + + + + + ,, + ,, + ,, + ,, + ,]]> + ]]> + + + + + + 10 + .,!? + + + + + + + WORD + + + en + US + + + + + + + + + + + + + + [^\w-\.] + _ + + + + + + + yyyy-MM-dd'T'HH:mm:ss.SSSZ + yyyy-MM-dd'T'HH:mm:ss,SSSZ + yyyy-MM-dd'T'HH:mm:ss.SSS + yyyy-MM-dd'T'HH:mm:ss,SSS + yyyy-MM-dd'T'HH:mm:ssZ + yyyy-MM-dd'T'HH:mm:ss + yyyy-MM-dd'T'HH:mmZ + yyyy-MM-dd'T'HH:mm + yyyy-MM-dd HH:mm:ss.SSSZ + yyyy-MM-dd HH:mm:ss,SSSZ + yyyy-MM-dd HH:mm:ss.SSS + yyyy-MM-dd HH:mm:ss,SSS + yyyy-MM-dd HH:mm:ssZ + yyyy-MM-dd HH:mm:ss + yyyy-MM-dd HH:mmZ + yyyy-MM-dd HH:mm + yyyy-MM-dd + + + + strings + + java.lang.Boolean + booleans + + + java.util.Date + tdates + + + java.lang.Long + java.lang.Integer + tlongs + + + java.lang.Number + tdoubles + + + + + + + + + + + + + + + + + + + + + + + + text/plain; charset=UTF-8 + + + + + ${velocity.template.base.dir:} + ${velocity.solr.resource.loader.enabled:true} + ${velocity.params.resource.loader.enabled:false} + + + + + 5 + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt new file mode 100644 index 0000000000..ae1e83eeb3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt @@ -0,0 +1,14 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt new file mode 100644 index 0000000000..eab4ee8753 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt @@ -0,0 +1,29 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +#some test synonym mappings unlikely to appear in real input text +aaafoo => aaabar +bbbfoo => bbbfoo bbbbar +cccfoo => cccbar cccbaz +fooaaa,baraaa,bazaaa + +# Some synonym groups specific to this example +GB,gib,gigabyte,gigabytes +MB,mib,megabyte,megabytes +Television, Televisions, TV, TVs +#notice we use "gib" instead of "GiB" so any WordDelimiterGraphFilter coming +#after us won't split it into two words. + +# Synonym mappings can be used for spelling correction too +pixima => pixma + From e468a7b96b99fe9ac717a9038f5bc222c5f557e4 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Fri, 8 Oct 2021 16:58:51 +0300 Subject: [PATCH 77/92] Add tests to query Solr with different configurations --- .../oa/provision/SolrConfigExploreTest.java | 126 +++++++++++++++++ .../dhp/oa/provision/SolrConfigTest.java | 131 ++++++++++++++++++ .../dhp/oa/provision/SolrExploreTest.java | 109 +++++++++++++++ 3 files changed, 366 insertions(+) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java new file mode 100644 index 0000000000..9bc2924c3e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java @@ -0,0 +1,126 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.net.URI; + +import org.apache.commons.io.IOUtils; +import org.apache.solr.client.solrj.SolrQuery; +import org.apache.solr.client.solrj.response.QueryResponse; +import org.apache.solr.common.SolrDocument; +import org.apache.solr.common.params.CommonParams; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class SolrConfigExploreTest extends SolrExploreTest { + + protected static SparkSession spark; + + private static final Integer batchSize = 100; + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private ISLookupClient isLookupClient; + + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); + + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } + + @BeforeAll + public static void before() { + + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + + } + + @AfterAll + public static void tearDown() { + spark.stop(); + } + + @Test + public void testSolrConfig() throws Exception { + + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; + + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.setRequestHandler("/exploreSearch"); + query.add(CommonParams.Q, q); + query.set("debugQuery", "on"); + + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); +// System.out.println(rsp.getHighlighting()); +// System.out.println(rsp.getExplainMap()); + + for (SolrDocument doc : rsp.getResults()) { + System.out.println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t" + ); + } + } + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java new file mode 100644 index 0000000000..e20ecf1523 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java @@ -0,0 +1,131 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.io.StringReader; +import java.net.URI; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.solr.client.solrj.SolrQuery; +import org.apache.solr.client.solrj.response.QueryResponse; +import org.apache.solr.common.SolrDocument; +import org.apache.solr.common.SolrInputField; +import org.apache.solr.common.params.CommonParams; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class SolrConfigTest extends SolrTest { + + protected static SparkSession spark; + + private static final Integer batchSize = 100; + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private ISLookupClient isLookupClient; + + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); + + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } + + @BeforeAll + public static void before() { + + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + + } + + @AfterAll + public static void tearDown() { + spark.stop(); + } + + @Test + public void testSolrConfig() throws Exception { + + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; + + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.add(CommonParams.Q, q); + + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); + + for (SolrDocument doc : rsp.getResults()) { + System.out.println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t" + ); + } + } + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java new file mode 100644 index 0000000000..b86fd8ac83 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java @@ -0,0 +1,109 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.File; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.solr.client.solrj.embedded.JettyConfig; +import org.apache.solr.client.solrj.impl.CloudSolrClient; +import org.apache.solr.client.solrj.request.CollectionAdminRequest; +import org.apache.solr.client.solrj.request.ConfigSetAdminRequest; +import org.apache.solr.client.solrj.request.QueryRequest; +import org.apache.solr.cloud.MiniSolrCloudCluster; +import org.apache.solr.common.params.CollectionParams; +import org.apache.solr.common.params.CoreAdminParams; +import org.apache.solr.common.params.ModifiableSolrParams; +import org.apache.solr.common.util.NamedList; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.io.TempDir; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public abstract class SolrExploreTest { + + protected static final Logger log = LoggerFactory.getLogger(SolrTest.class); + + protected static final String FORMAT = "test"; + protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire"; + protected static final String CONFIG_NAME = "testConfig"; + + protected static MiniSolrCloudCluster miniCluster; + + @TempDir + public static Path workingDir; + + @BeforeAll + public static void setup() throws Exception { + + // random unassigned HTTP port + final int jettyPort = 0; + final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build(); + + log.info(String.format("working directory: %s", workingDir.toString())); + System.setProperty("solr.log.dir", workingDir.resolve("logs").toString()); + + // create a MiniSolrCloudCluster instance + miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig); + + // Upload Solr configuration directory to ZooKeeper + String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig"; + File configDir = new File(solrZKConfigDir); + + miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); + + // override settings in the solrconfig include + System.setProperty("solr.tests.maxBufferedDocs", "100000"); + System.setProperty("solr.tests.maxIndexingThreads", "-1"); + System.setProperty("solr.tests.ramBufferSizeMB", "100"); + + // use non-test classes so RandomizedRunner isn't necessary + System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); + System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); + System.setProperty("solr.lock.type", "single"); + + log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString()); + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); + + NamedList res = createCollection( + miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME); + res.forEach(o -> log.info(o.toString())); + + miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION); + + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); + + } + + @AfterAll + public static void shutDown() throws Exception { + miniCluster.shutdown(); + FileUtils.deleteDirectory(workingDir.toFile()); + } + + protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, + int replicationFactor, int maxShardsPerNode, String configName) throws Exception { + ModifiableSolrParams modParams = new ModifiableSolrParams(); + modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); + modParams.set("name", name); + modParams.set("numShards", numShards); + modParams.set("replicationFactor", replicationFactor); + modParams.set("collection.configName", configName); + modParams.set("maxShardsPerNode", maxShardsPerNode); + QueryRequest request = new QueryRequest(modParams); + request.setPath("/admin/collections"); + return client.request(request); + } + +} From 201ce71cc184c87e1b6df23fd2cc5430cb4e4309 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Mon, 11 Oct 2021 13:16:39 +0300 Subject: [PATCH 78/92] Add resultsubject, relprojectname and resultacceptanceyear to __all field --- .../conf/exploreTestConfig/managed-schema | 39 ++++++++++++------- 1 file changed, 26 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema index bcf4e189d6..39c811f83f 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema @@ -369,15 +369,15 @@ - + + + - - - - + + @@ -390,22 +390,35 @@ + + + + + + + + + + + + + + + + + + + + - - - - - - - - + \ No newline at end of file From 83f51f1812212cd7d5587cf6e5597945ae619b5c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 12 Oct 2021 09:14:43 +0200 Subject: [PATCH 79/92] refactoring --- .../dump/complete/DumpOrganizationProjectDatasourceTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 051141e183..80b5fd89e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -6,7 +6,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -23,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Project; From 63933808d4e89b683f06036c78170e4be37d36a2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 13 Oct 2021 11:28:28 +0200 Subject: [PATCH 80/92] added fix for mixing result types, added configuration default to funder subworkflow --- .../dhp/oa/graph/dump/DumpProducts.java | 3 +- .../oa/graph/dump/QueryInformationSystem.java | 2 +- .../dhp/oa/graph/dump/ResultMapper.java | 682 +++++++++--------- .../dhp/oa/graph/dump/SaveCommunityMap.java | 8 +- .../oa/graph/dump/input_cm_parameters.json | 2 +- .../funder/oozie_app/config-default.xml | 30 + 6 files changed, 389 insertions(+), 338 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index 68e1e8402f..a714cea207 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,6 +11,7 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -57,7 +58,7 @@ public class DumpProducts implements Serializable { Utils .readPath(spark, inputPath, inputClazz) .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) - .filter(Objects::nonNull) + .filter((FilterFunction) value -> value != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index b972de6e9a..ab5434ed0c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -62,7 +62,7 @@ public class QueryInformationSystem { for (String xml : communityMap) { final Document doc; final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); + // reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); doc = reader.read(new StringReader(xml)); Element root = doc.getRootElement(); map.put(root.attribute("id").getValue(), root.attribute("label").getValue()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 0f3192c25c..49468540d9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -40,355 +40,371 @@ public class ResultMapper implements Serializable { eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; Optional ort = Optional.ofNullable(input.getResulttype()); if (ort.isPresent()) { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + try { - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": - - eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); - - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - default: - throw new NoAvailableEntityTypeException(); - } - - Optional> mes = Optional.ofNullable(input.getMeasures()); - if (mes.isPresent()) { - List measure = new ArrayList<>(); - mes - .get() - .forEach( - m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue())))); - out.setMeasures(measure); - } - - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); - - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - Country country = new Country(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - - out.setDateofcollection(input.getDateofcollection()); - - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); - - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getCommunityInstance).collect(Collectors.toList())); - } - } - - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setMaintitle(iTitle.get(0).getValue()); + addTypeSpecificInformation(out, input, ort); + Optional> mes = Optional.ofNullable(input.getMeasures()); + if (mes.isPresent()) { + List measure = new ArrayList<>(); + mes + .get() + .forEach( + m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue())))); + out.setMeasures(measure); } - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setSubtitle(iTitle.get(0).getValue()); + Optional + .ofNullable(input.getAuthor()) + .ifPresent( + ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); + + // I do not map Access Right UNKNOWN or OTHER + + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); } - } + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> out - .setPid( - value - .stream() - .map( - p -> ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - - Optional - .ofNullable(input.getSource()) - .ifPresent(value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); - - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - - out.setType(input.getResulttype().getClassid()); - } - - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((CommunityResult) out) - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String communityId = c.getId(); - if (communityId.contains("::")) { - communityId = communityId.substring(0, communityId.indexOf("::")); - } - if (communities.contains(communityId)) { - Context context = new Context(); - context.setCode(communityId); - context.setLabel(communityMap.get(communityId)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance .newInstance( - provenanceaction.getClassname(), di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); - try { - context.setProvenance(getUniqueProvenance(provenance)); - } catch (NoAvailableEntityTypeException e) { - e.printStackTrace(); - } - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); - if (!contextList.isEmpty()) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + Optional> oInst = Optional + .ofNullable(input.getInstance()); + + if (oInst.isPresent()) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((GraphResult) out) + .setInstance( + oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); + } else { + ((CommunityResult) out) + .setInstance( + oInst + .get() + .stream() + .map(ResultMapper::getCommunityInstance) + .collect(Collectors.toList())); } - }); - ((CommunityResult) out).setContext(remainigContext); + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> out + .setPid( + value + .stream() + .map( + p -> ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + Optional + .ofNullable(input.getSource()) + .ifPresent( + value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); + + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((CommunityResult) out) + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + Set communities = communityMap.keySet(); + List contextList = Optional + .ofNullable( + input + .getContext()) + .map( + value -> value + .stream() + .map(c -> { + String communityId = c.getId(); + if (communityId.contains("::")) { + communityId = communityId.substring(0, communityId.indexOf("::")); + } + if (communities.contains(communityId)) { + Context context = new Context(); + context.setCode(communityId); + context.setLabel(communityMap.get(communityId)); + Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); + if (dataInfo.isPresent()) { + List provenance = new ArrayList<>(); + provenance + .addAll( + dataInfo + .get() + .stream() + .map( + di -> Optional + .ofNullable(di.getProvenanceaction()) + .map( + provenanceaction -> Provenance + .newInstance( + provenanceaction.getClassname(), + di.getTrust())) + .orElse(null)) + .filter(Objects::nonNull) + .collect(Collectors.toSet())); + + try { + context.setProvenance(getUniqueProvenance(provenance)); + } catch (NoAvailableEntityTypeException e) { + e.printStackTrace(); + } + } + return context; + } + return null; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); + + if (!contextList.isEmpty()) { + Set hashValue = new HashSet<>(); + List remainigContext = new ArrayList<>(); + contextList.forEach(c -> { + if (!hashValue.contains(c.hashCode())) { + remainigContext.add(c); + hashValue.add(c.hashCode()); + } + }); + ((CommunityResult) out).setContext(remainigContext); + } + } + } catch (ClassCastException cce) { + return out; } } + return out; } + private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, + Optional ort) throws NoAvailableEntityTypeException { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + Dataset id = (Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + Software is = (Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(Field::getValue) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + OtherResearchProduct ir = (OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + default: + throw new NoAvailableEntityTypeException(); + } + } + private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { Instance instance = new Instance(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 1eff998920..a6595d756d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory; import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; /** @@ -86,10 +87,13 @@ public class SaveCommunityMap implements Serializable { private void saveCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, IOException, DocumentException, SAXException { + final String communityMapString = Utils.OBJECT_MAPPER + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); + log.info("communityMap {} ", communityMapString); writer .write( - Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId))); + communityMapString); + writer.close(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json index 8062205101..677715847c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json @@ -30,7 +30,7 @@ "paramLongName": "communityId", "paramDescription": "the id of the community for which to create the dump", "paramRequired": true - } } + } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml index e69de29bb2..e5ec3d0aee 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file From 5d9cc2452dc76452fbb45f326315ec5061f2feae Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 13 Oct 2021 15:33:50 +0200 Subject: [PATCH 81/92] changed the working path parameter value as dependant from the dnet-workflow working dir parameter --- .../eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index 282c06f4e4..29a12f4df4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -50,10 +50,6 @@ inputPathMAG the MAG input path - - workingPathMAG - the MAG working path where to store the intermediate process results - @@ -142,7 +138,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${inputPathMAG}/dataset - --workingPath${workingPathMAG} + --workingPath${workingPath}/MAG --targetPath${workingPath} --masteryarn-cluster From b292e4a700eed70b8a94542245610b88f53e9ac3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 Oct 2021 17:31:53 +0200 Subject: [PATCH 82/92] [stats wf] added extra logging in the context data retrieval phase --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh index 6d42ab13d4..c60d67b1a2 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh @@ -11,9 +11,13 @@ TARGET_DB=$2 TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 contexts.csv + +echo "Downloading categories data" cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv + +echo "Downloading concepts data" cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv cat categories.csv | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv From 51a03c0a50bd1a546865892698f840a97479b16e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Oct 2021 14:23:05 +0200 Subject: [PATCH 83/92] refactor code for EBI from dhp-graph-mapper into dhp-aggregation --- .../sx/bio/ebi/SparkDownloadEBILinks.scala | 4 +- .../dhp/sx/bio/ebi/SparkEBILinksToOaf.scala | 4 +- .../sx/bio}/ebi/oozie_app/config-default.xml | 0 .../dhp/sx/bio/ebi/oozie_app/workflow.xml | 105 ++++++++++++++++++ .../dhp/sx/graph/ebi/oozie_app/workflow.xml | 99 ----------------- .../ebi/update/oozie_app/config-default.xml | 68 ------------ .../graph/ebi/update/oozie_app/workflow.xml | 67 ----------- 7 files changed, 109 insertions(+), 238 deletions(-) rename dhp-workflows/{dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph => dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio}/ebi/oozie_app/config-default.xml (100%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala index 578db1ea94..85fbd99c47 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala @@ -66,7 +66,7 @@ object SparkDownloadEBILinks { val log: Logger = LoggerFactory.getLogger(getClass) val MAX_ITEM_PER_PARTITION = 20000 val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -86,7 +86,7 @@ object SparkDownloadEBILinks { val workingPath = parser.get("workingPath") log.info(s"workingPath -> $workingPath") - log.info("Getting max pubmedId where the links have been requested") + log.info("Getting max pubmedId where the links have already requested") val links: Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem] val lastPMIDRequested = links.map(l => l.id).select(max("value")).first.getLong(0) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index 0db469769c..10467884cd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -14,7 +14,7 @@ object SparkEBILinksToOaf { def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -31,7 +31,7 @@ object SparkEBILinksToOaf { log.info(s"targetPath -> $targetPath") implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - val ebLinks: Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links != null) + val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{")) ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml new file mode 100644 index 0000000000..73b1a3b608 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml @@ -0,0 +1,105 @@ + + + + sourcePath + the Working Path + + + workingPath + the Working Path + + + targetPath + the OAF MDStore Path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + resumeFrom + DownloadEBILinks + node to start + + + + + + + + ${wf:conf('resumeFrom') eq 'DownloadEBILinks'} + ${wf:conf('resumeFrom') eq 'CreateEBIDataSet'} + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn-cluster + cluster + Incremental Download EBI Links + eu.dnetllib.dhp.sx.bio.ebi.SparkDownloadEBILinks + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${sourcePath} + --workingPath${workingPath} + --masteryarn + + + + + + + + + + + + + + + + yarn-cluster + cluster + Create OAF DataSet + eu.dnetllib.dhp.sx.bio.ebi.SparkEBILinksToOaf + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=2000 + ${sparkExtraOPT} + + --sourcePath${sourcePath}/ebi_links_dataset + --targetPath${targetPath} + --masteryarn + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml deleted file mode 100644 index 7612321c04..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml +++ /dev/null @@ -1,99 +0,0 @@ - - - - workingPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn-cluster - cluster - Create Baselnie DataSet - - eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=1 - --driver-memory=${sparkDriverMemory} - --executor-cores=${sparkExecutorCores} - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - --hdfsServerUri${nameNode} - - - - - - - - yarn-cluster - cluster - Create EBI DataSet - - eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=1000 - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - - - - - - - - yarn-cluster - cluster - Create Baseline DataSet - - eu.dnetlib.dhp.sx.ebi.SparkAddLinkUpdates - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=1 - --driver-memory=${sparkDriverMemory} - --executor-cores=${sparkExecutorCores} - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml deleted file mode 100644 index 17cd6c9a33..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - - - - - - - - - - - - - - - - - - - - - - - oozie.launcher.mapreduce.user.classpath.first - true - - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml deleted file mode 100644 index cd3bb8c714..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml +++ /dev/null @@ -1,67 +0,0 @@ - - - - sourcePath - the Working Path - - - workingPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - Incremental Download EBI Links - eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath} - --workingPath${workingPath} - --masteryarn - - - - - - - - - - - - - - - \ No newline at end of file From 7b15b88d4cdc60daf7cc7e60badea8f844abb57e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 15 Oct 2021 15:00:15 +0200 Subject: [PATCH 84/92] renamed wrong package, implemented last aggregation workflow for scholexplorer --- .../dhp/sx/bio/BioDBToOAF.scala | 2 +- .../bio/SparkTransformBioDatabaseToOAF.scala | 6 +- .../ebi/SparkCreateBaselineDataFrame.scala | 4 +- .../sx/bio/ebi/SparkDownloadEBILinks.scala | 7 +- .../dhp/sx/bio/ebi/SparkEBILinksToOaf.scala | 7 +- .../dhp/sx/bio/pubmed/PMArticle.java | 2 +- .../dhp/sx/bio/pubmed/PMAuthor.java | 2 +- .../dhp/sx/bio/pubmed/PMGrant.java | 2 +- .../dhp/sx/bio/pubmed/PMJournal.java | 2 +- .../dhp/sx/bio/pubmed/PMParser.scala | 2 +- .../dhp/sx/bio/pubmed/PMSubject.java | 2 +- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 2 +- .../sx/bio/db}/oozie_app/config-default.xml | 0 .../dhp/sx/bio/db/oozie_app/workflow.xml | 51 +++++ .../dhp/sx/bio/ebi}/bio_to_oaf_params.json | 0 .../dhp/sx/bio/BioScholixTest.scala | 6 +- .../dhp/sx/graph/bio/oozie_app/workflow.xml | 177 ------------------ 17 files changed, 75 insertions(+), 199 deletions(-) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/BioDBToOAF.scala (99%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala (91%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala (98%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala (95%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala (90%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMArticle.java (97%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMAuthor.java (93%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMGrant.java (94%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMJournal.java (95%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMParser.scala (99%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PMSubject.java (94%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/pubmed/PubMedToOaf.scala (99%) rename dhp-workflows/{dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio => dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db}/oozie_app/config-default.xml (100%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml rename dhp-workflows/{dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio => dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi}/bio_to_oaf_params.json (100%) rename dhp-workflows/dhp-aggregation/src/test/java/eu/{dnetllib => dnetlib}/dhp/sx/bio/BioScholixTest.scala (97%) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/BioDBToOAF.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index dffc88c6ca..70dcc0184c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -1,4 +1,4 @@ -package eu.dnetllib.dhp.sx.bio +package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala similarity index 91% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index 16d2b25a62..7a62437a36 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -1,8 +1,8 @@ -package eu.dnetllib.dhp.sx.bio +package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.Oaf -import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved +import BioDBToOAF.ScholixResolved import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} @@ -13,7 +13,7 @@ object SparkTransformBioDatabaseToOAF { def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val log: Logger = LoggerFactory.getLogger(getClass) - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json"))) parser.parseArgument(args) val database: String = parser.get("database") log.info("database: {}", database) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index 17bf3fa6b3..17d21f19c6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -1,10 +1,10 @@ -package eu.dnetllib.dhp.sx.bio.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.oaf.Result +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} import eu.dnetlib.dhp.utils.ISLookupClientFactory -import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} import org.apache.commons.io.IOUtils import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala index 85fbd99c47..eab6b1dc6a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala @@ -1,8 +1,9 @@ -package eu.dnetllib.dhp.sx.bio.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem -import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal} +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal import org.apache.commons.io.IOUtils import org.apache.http.client.config.RequestConfig import org.apache.http.client.methods.HttpGet diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index 10467884cd..b19bfc23a5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -1,9 +1,10 @@ -package eu.dnetllib.dhp.sx.bio.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.Oaf -import eu.dnetllib.dhp.sx.bio.BioDBToOAF -import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.sx.bio.BioDBToOAF +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import BioDBToOAF.EBILinkItem import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql._ diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java similarity index 97% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMArticle.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index 305bb89be0..8815284255 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -1,5 +1,5 @@ -package eu.dnetllib.dhp.sx.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; import java.io.Serializable; import java.util.ArrayList; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java similarity index 93% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMAuthor.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java index c89929981b..cef92d0031 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMAuthor.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java @@ -1,5 +1,5 @@ -package eu.dnetllib.dhp.sx.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; import java.io.Serializable; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMGrant.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java similarity index 94% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMGrant.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java index 7df5dd5f2f..ce9420cc13 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMGrant.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java @@ -1,5 +1,5 @@ -package eu.dnetllib.dhp.sx.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; public class PMGrant { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMJournal.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMJournal.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java index 6065416f8d..863a23bd50 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMJournal.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java @@ -1,5 +1,5 @@ -package eu.dnetllib.dhp.sx.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; import java.io.Serializable; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMParser.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 8fa226b7d5..80cb0667cb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -1,4 +1,4 @@ -package eu.dnetllib.dhp.sx.bio.pubmed +package eu.dnetlib.dhp.sx.bio.pubmed import scala.xml.MetaData import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMSubject.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java similarity index 94% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMSubject.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java index e6ab61b875..862d39a940 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PMSubject.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java @@ -1,5 +1,5 @@ -package eu.dnetllib.dhp.sx.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; public class PMSubject { private String value; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PubMedToOaf.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index a1777a230c..13f38408ed 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetllib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -1,4 +1,4 @@ -package eu.dnetllib.dhp.sx.bio.pubmed +package eu.dnetlib.dhp.sx.bio.pubmed import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml new file mode 100644 index 0000000000..071d202b6f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml @@ -0,0 +1,51 @@ + + + + sourcePath + the PDB Database Working Path + + + database + the PDB Database Working Path + + + + targetPath + the Target Working dir path + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Convert Bio DB to OAF Dataset + eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --dbPath${sourcePath} + --database${database} + --targetPath${targetPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetllib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala similarity index 97% rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetllib/dhp/sx/bio/BioScholixTest.scala rename to dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index c072f149ce..893a6e628e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetllib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -1,10 +1,10 @@ -package eu.dnetllib.dhp.sx.bio +package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} -import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml deleted file mode 100644 index 0df085ee1f..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml +++ /dev/null @@ -1,177 +0,0 @@ - - - - PDBPath - the PDB Database Working Path - - - - UNIPROTDBPath - the UNIPROT Database Working Path - - - - EBIDataset - the EBI Links Dataset Path - - - - ScholixResolvedDBPath - the Scholix Resolved Dataset Path - - - - CrossrefLinksPath - the CrossrefLinks Path - - - targetPath - the Target Working dir path - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn - cluster - Convert PDB to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${PDBPath} - --databasePDB - --targetPath${targetPath}/pdb_OAF - - - - - - - - - yarn - cluster - Convert UNIPROT to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${UNIPROTDBPath} - --databaseUNIPROT - --targetPath${targetPath}/uniprot_OAF - - - - - - - - - yarn - cluster - Convert EBI Links to OAF Dataset - eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --sourcePath${EBIDataset} - --targetPath${targetPath}/ebi_OAF - - - - - - - - - yarn - cluster - Convert Scholix to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${ScholixResolvedDBPath} - --databaseSCHOLIX - --targetPath${targetPath}/scholix_resolved_OAF - - - - - - - - - yarn - cluster - Convert Crossref Links to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${CrossrefLinksPath} - --databaseCROSSREF_LINKS - --targetPath${targetPath}/crossref_unresolved_relation_OAF - - - - - - - - - - - \ No newline at end of file From 46f82c7c8fecadd36754e0caf04fa2ef09c889ee Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 Oct 2021 10:53:16 +0200 Subject: [PATCH 85/92] removed not needed folder deletion --- .../eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index ab3b9593ed..40a17b4869 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -107,7 +107,6 @@ - From a894d7adf3dd104f56bdfbbe8e4797813a9f168a Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 19 Oct 2021 10:02:55 +0200 Subject: [PATCH 86/92] updated version of dhp-schemas --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3e8d6bc190..02bc5d8d4e 100644 --- a/pom.xml +++ b/pom.xml @@ -753,7 +753,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.8.20] + [2.8.21] [4.0.3] [6.0.5] [3.1.6] From c7f6cd2591ddc7b6e9f6a1ca4eb29c62a73869f5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 19 Oct 2021 10:15:26 +0200 Subject: [PATCH 87/92] added again the setting for saXReader --- .../eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index ab5434ed0c..b972de6e9a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -62,7 +62,7 @@ public class QueryInformationSystem { for (String xml : communityMap) { final Document doc; final SAXReader reader = new SAXReader(); - // reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); + reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); doc = reader.read(new StringReader(xml)); Element root = doc.getRootElement(); map.put(root.attribute("id").getValue(), root.attribute("label").getValue()); From 7a73010acdd93ca7f7d470c8f732315b54482acc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 Oct 2021 11:59:16 +0200 Subject: [PATCH 88/92] WIP: worflow nodes for including Scholexplorer records in the RAW graph --- .../oa/graph/raw/CopyHdfsOafApplication.java | 143 ++++++++++++++++++ .../raw/MigrateHdfsMdstoresApplication.java | 26 ---- .../common/AbstractMigrationApplication.java | 47 ++++++ .../oa/graph/copy_hdfs_oaf_parameters.json | 38 +++++ .../oa/graph/raw_all/oozie_app/workflow.xml | 27 ++++ 5 files changed, 255 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java new file mode 100644 index 0000000000..2e06114751 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java @@ -0,0 +1,143 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import com.clearspring.analytics.util.Lists; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class CopyHdfsOafApplication extends AbstractMigrationApplication { + + private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + CopyHdfsOafApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json"))); + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); + + final String mdFormat = parser.get("mdFormat"); + log.info("mdFormat: {}", mdFormat); + + final String mdLayout = parser.get("mdLayout"); + log.info("mdLayout: {}", mdLayout); + + final String mdInterpretation = parser.get("mdInterpretation"); + log.info("mdInterpretation: {}", mdInterpretation); + + final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + + final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); + + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths)); + } + + public static void processPaths(final SparkSession spark, + final VocabularyGroup vocs, + final String outputPath, + final Set paths) { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + log.info("Found {} mdstores", paths.size()); + paths.forEach(log::info); + + final String[] validPaths = paths + .stream() + .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) + .toArray(String[]::new); + log.info("Non empty mdstores {}", validPaths.length); + + if (validPaths.length > 0) { + // load the dataset + Dataset oaf = spark + .read() + .load(validPaths) + .as(Encoders.kryo(Oaf.class)); + + // dispatch each entity type individually in the respective graph subdirectory in append mode + for(Map.Entry e : ModelSupport.entityTypes.entrySet()) { + oaf + .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey().toString())) + .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue())) + .write() + .option("compression", "gzip") + .mode(SaveMode.Append) + .text(outputPath + "/" + e.getKey()); + } + + oaf + .flatMap((FlatMapFunction) o -> { + Relation rel = (Relation) o; + List rels = Lists.newArrayList(); + rels.add(getInverse(rel, vocs)); + + return rels.iterator(); + }, Encoders.bean(Relation.class)); + } + } + + private static Relation getInverse(Relation rel, VocabularyGroup vocs) { + final Relation inverse = new Relation(); + + inverse.setProperties(rel.getProperties()); + inverse.setValidated(rel.getValidated()); + inverse.setValidationDate(rel.getValidationDate()); + inverse.setCollectedfrom(rel.getCollectedfrom()); + inverse.setDataInfo(rel.getDataInfo()); + inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp()); + + inverse.setSource(rel.getTarget()); + inverse.setTarget(rel.getSource()); + inverse.setRelType(rel.getRelType()); + inverse.setSubRelType(rel.getSubRelType()); + + return inverse; + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 4110bd8067..6c72e4dfc4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -135,30 +135,4 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication } } - private static Set mdstorePaths(final String mdstoreManagerUrl, - final String format, - final String layout, - final String interpretation) throws IOException { - final String url = mdstoreManagerUrl + "/mdstores/"; - final ObjectMapper objectMapper = new ObjectMapper(); - - final HttpGet req = new HttpGet(url); - - try (final CloseableHttpClient client = HttpClients.createDefault()) { - try (final CloseableHttpResponse response = client.execute(req)) { - final String json = IOUtils.toString(response.getEntity().getContent()); - final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); - return Arrays - .stream(mdstores) - .filter(md -> md.getFormat().equalsIgnoreCase(format)) - .filter(md -> md.getLayout().equalsIgnoreCase(layout)) - .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) - .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) - .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) - .filter(md -> md.getSize() > 0) - .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") - .collect(Collectors.toSet()); - } - } - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index 5d32fe926d..7c88dbd9d9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -3,8 +3,14 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Closeable; import java.io.IOException; +import java.util.Arrays; +import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; @@ -16,6 +22,10 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Oaf; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; public class AbstractMigrationApplication implements Closeable { @@ -47,6 +57,43 @@ public class AbstractMigrationApplication implements Closeable { SequenceFile.Writer.valueClass(Text.class)); } + /** + * Retrieves from the metadata store manager application the list of paths associated with mdstores characterized + * by he given format, layout, interpretation + * @param mdstoreManagerUrl the URL of the mdstore manager service + * @param format the mdstore format + * @param layout the mdstore layout + * @param interpretation the mdstore interpretation + * @return the set of hdfs paths + * @throws IOException in case of HTTP communication issues + */ + protected static Set mdstorePaths(final String mdstoreManagerUrl, + final String format, + final String layout, + final String interpretation) throws IOException { + final String url = mdstoreManagerUrl + "/mdstores/"; + final ObjectMapper objectMapper = new ObjectMapper(); + + final HttpGet req = new HttpGet(url); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + final String json = IOUtils.toString(response.getEntity().getContent()); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); + return Arrays + .stream(mdstores) + .filter(md -> md.getFormat().equalsIgnoreCase(format)) + .filter(md -> md.getLayout().equalsIgnoreCase(layout)) + .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) + .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) + .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) + .filter(md -> md.getSize() > 0) + .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") + .collect(Collectors.toSet()); + } + } + } + private Configuration getConf() { return new Configuration(); /* diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json new file mode 100644 index 0000000000..1e862198f1 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json @@ -0,0 +1,38 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "mdstoreManagerUrl", + "paramDescription": "the MdstoreManager url", + "paramRequired": true + }, + { + "paramName": "f", + "paramLongName": "mdFormat", + "paramDescription": "metadata format", + "paramRequired": true + }, + { + "paramName": "l", + "paramLongName": "mdLayout", + "paramDescription": "metadata layout", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "mdInterpretation", + "paramDescription": "metadata interpretation", + "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the url of the ISLookupService", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index 321ca40909..563923a5a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -544,6 +544,33 @@ --sourcePath${workingDir}/entities --graphRawPath${workingDir}/graph_raw + + + + + + + yarn + cluster + ImportOAF_hdfs_graph + eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --hdfsPath${workingDir}/graph_raw + --mdstoreManagerUrl${mdstoreManagerUrl} + --mdFormatOAF + --mdLayoutstore + --mdInterpretationgraph + --isLookupUrl${isLookupUrl} + From f8329bc11052f327336089b70a85ccbe90bca511 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 19 Oct 2021 15:24:22 +0200 Subject: [PATCH 89/92] since dhp-schemas changed, introducing new Relation inverse model, this class has been updated --- .../java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java index 38ffd28fef..7d0d6b0b86 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java @@ -91,8 +91,8 @@ public class ReadBlacklistFromDB implements Closeable { String encoding = rs.getString("relationship"); RelationInverse ri = ModelSupport.relationInverseMap.get(encoding); - direct.setRelClass(ri.getRelation()); - inverse.setRelClass(ri.getInverse()); + direct.setRelClass(ri.getRelClass()); + inverse.setRelClass(ri.getInverseRelClass()); direct.setRelType(ri.getRelType()); inverse.setRelType(ri.getRelType()); direct.setSubRelType(ri.getSubReltype()); From c9870c5122d2d59ece2a4500dc2e75490c176202 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 19 Oct 2021 15:24:59 +0200 Subject: [PATCH 90/92] code formatted --- .../oa/provision/SolrConfigExploreTest.java | 154 +++++++++--------- .../dhp/oa/provision/SolrConfigTest.java | 150 ++++++++--------- .../dhp/oa/provision/SolrExploreTest.java | 128 +++++++-------- 3 files changed, 216 insertions(+), 216 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java index 9bc2924c3e..3beca7e7e2 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java @@ -25,102 +25,102 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class SolrConfigExploreTest extends SolrExploreTest { - protected static SparkSession spark; + protected static SparkSession spark; - private static final Integer batchSize = 100; + private static final Integer batchSize = 100; - @Mock - private ISLookUpService isLookUpService; + @Mock + private ISLookUpService isLookUpService; - @Mock - private ISLookupClient isLookupClient; + @Mock + private ISLookupClient isLookupClient; - @BeforeEach - public void prepareMocks() throws ISLookUpException, IOException { - isLookupClient.setIsLookup(isLookUpService); + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); - int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); - Mockito - .when(isLookupClient.getDsId(Mockito.anyString())) - .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); - Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); - Mockito - .when(isLookupClient.getLayoutSource(Mockito.anyString())) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); - Mockito - .when(isLookupClient.getLayoutTransformer()) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); - } + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } - @BeforeAll - public static void before() { + @BeforeAll + public static void before() { - SparkConf conf = new SparkConf(); - conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); - conf.registerKryoClasses(new Class[] { - SerializableSolrInputDocument.class - }); + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); - conf.setMaster("local[1]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); - spark = SparkSession - .builder() - .appName(XmlIndexingJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - } + @AfterAll + public static void tearDown() { + spark.stop(); + } - @AfterAll - public static void tearDown() { - spark.stop(); - } + @Test + public void testSolrConfig() throws Exception { - @Test - public void testSolrConfig() throws Exception { + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + .run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient); - Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; - String[] queryStrings = { - "cancer", - "graph", - "graphs" - }; + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.setRequestHandler("/exploreSearch"); + query.add(CommonParams.Q, q); + query.set("debugQuery", "on"); - for (String q : queryStrings) { - SolrQuery query = new SolrQuery(); - query.setRequestHandler("/exploreSearch"); - query.add(CommonParams.Q, q); - query.set("debugQuery", "on"); - - log.info("Submit query to Solr with params: {}", query.toString()); - QueryResponse rsp = miniCluster.getSolrClient().query(query); + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); // System.out.println(rsp.getHighlighting()); // System.out.println(rsp.getExplainMap()); - for (SolrDocument doc : rsp.getResults()) { - System.out.println( - doc.get("score") + "\t" + - doc.get("__indexrecordidentifier") + "\t" + - doc.get("resultidentifier") + "\t" + - doc.get("resultauthor") + "\t" + - doc.get("resultacceptanceyear") + "\t" + - doc.get("resultsubject") + "\t" + - doc.get("resulttitle") + "\t" + - doc.get("relprojectname") + "\t" + - doc.get("resultdescription") + "\t" + - doc.get("__all") + "\t" - ); - } - } - } + for (SolrDocument doc : rsp.getResults()) { + System.out + .println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t"); + } + } + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java index e20ecf1523..ab98b1da29 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java @@ -34,98 +34,98 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class SolrConfigTest extends SolrTest { - protected static SparkSession spark; + protected static SparkSession spark; - private static final Integer batchSize = 100; + private static final Integer batchSize = 100; - @Mock - private ISLookUpService isLookUpService; + @Mock + private ISLookUpService isLookUpService; - @Mock - private ISLookupClient isLookupClient; + @Mock + private ISLookupClient isLookupClient; - @BeforeEach - public void prepareMocks() throws ISLookUpException, IOException { - isLookupClient.setIsLookup(isLookUpService); + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); - int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); - Mockito - .when(isLookupClient.getDsId(Mockito.anyString())) - .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); - Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); - Mockito - .when(isLookupClient.getLayoutSource(Mockito.anyString())) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); - Mockito - .when(isLookupClient.getLayoutTransformer()) - .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); - } + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } - @BeforeAll - public static void before() { + @BeforeAll + public static void before() { - SparkConf conf = new SparkConf(); - conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); - conf.registerKryoClasses(new Class[] { - SerializableSolrInputDocument.class - }); + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); - conf.setMaster("local[1]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); - spark = SparkSession - .builder() - .appName(XmlIndexingJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - } + @AfterAll + public static void tearDown() { + spark.stop(); + } - @AfterAll - public static void tearDown() { - spark.stop(); - } + @Test + public void testSolrConfig() throws Exception { - @Test - public void testSolrConfig() throws Exception { + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + .run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null).run(isLookupClient); - Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; - String[] queryStrings = { - "cancer", - "graph", - "graphs" - }; + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.add(CommonParams.Q, q); - for (String q : queryStrings) { - SolrQuery query = new SolrQuery(); - query.add(CommonParams.Q, q); + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); - log.info("Submit query to Solr with params: {}", query.toString()); - QueryResponse rsp = miniCluster.getSolrClient().query(query); - - for (SolrDocument doc : rsp.getResults()) { - System.out.println( - doc.get("score") + "\t" + - doc.get("__indexrecordidentifier") + "\t" + - doc.get("resultidentifier") + "\t" + - doc.get("resultauthor") + "\t" + - doc.get("resultacceptanceyear") + "\t" + - doc.get("resultsubject") + "\t" + - doc.get("resulttitle") + "\t" + - doc.get("relprojectname") + "\t" + - doc.get("resultdescription") + "\t" + - doc.get("__all") + "\t" - ); - } - } - } + for (SolrDocument doc : rsp.getResults()) { + System.out + .println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t"); + } + } + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java index b86fd8ac83..34a9465a72 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java @@ -23,87 +23,87 @@ import org.slf4j.LoggerFactory; public abstract class SolrExploreTest { - protected static final Logger log = LoggerFactory.getLogger(SolrTest.class); + protected static final Logger log = LoggerFactory.getLogger(SolrTest.class); - protected static final String FORMAT = "test"; - protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire"; - protected static final String CONFIG_NAME = "testConfig"; + protected static final String FORMAT = "test"; + protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire"; + protected static final String CONFIG_NAME = "testConfig"; - protected static MiniSolrCloudCluster miniCluster; + protected static MiniSolrCloudCluster miniCluster; - @TempDir - public static Path workingDir; + @TempDir + public static Path workingDir; - @BeforeAll - public static void setup() throws Exception { + @BeforeAll + public static void setup() throws Exception { - // random unassigned HTTP port - final int jettyPort = 0; - final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build(); + // random unassigned HTTP port + final int jettyPort = 0; + final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build(); - log.info(String.format("working directory: %s", workingDir.toString())); - System.setProperty("solr.log.dir", workingDir.resolve("logs").toString()); + log.info(String.format("working directory: %s", workingDir.toString())); + System.setProperty("solr.log.dir", workingDir.resolve("logs").toString()); - // create a MiniSolrCloudCluster instance - miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig); + // create a MiniSolrCloudCluster instance + miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig); - // Upload Solr configuration directory to ZooKeeper - String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig"; - File configDir = new File(solrZKConfigDir); + // Upload Solr configuration directory to ZooKeeper + String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig"; + File configDir = new File(solrZKConfigDir); - miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); + miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); - // override settings in the solrconfig include - System.setProperty("solr.tests.maxBufferedDocs", "100000"); - System.setProperty("solr.tests.maxIndexingThreads", "-1"); - System.setProperty("solr.tests.ramBufferSizeMB", "100"); + // override settings in the solrconfig include + System.setProperty("solr.tests.maxBufferedDocs", "100000"); + System.setProperty("solr.tests.maxIndexingThreads", "-1"); + System.setProperty("solr.tests.ramBufferSizeMB", "100"); - // use non-test classes so RandomizedRunner isn't necessary - System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); - System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); - System.setProperty("solr.lock.type", "single"); + // use non-test classes so RandomizedRunner isn't necessary + System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); + System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); + System.setProperty("solr.lock.type", "single"); - log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString()); - log - .info( - CollectionAdminRequest.ClusterStatus - .getClusterStatus() - .process(miniCluster.getSolrClient()) - .toString()); + log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString()); + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); - NamedList res = createCollection( - miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME); - res.forEach(o -> log.info(o.toString())); + NamedList res = createCollection( + miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME); + res.forEach(o -> log.info(o.toString())); - miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION); + miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION); - log - .info( - CollectionAdminRequest.ClusterStatus - .getClusterStatus() - .process(miniCluster.getSolrClient()) - .toString()); + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); - } + } - @AfterAll - public static void shutDown() throws Exception { - miniCluster.shutdown(); - FileUtils.deleteDirectory(workingDir.toFile()); - } + @AfterAll + public static void shutDown() throws Exception { + miniCluster.shutdown(); + FileUtils.deleteDirectory(workingDir.toFile()); + } - protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, - int replicationFactor, int maxShardsPerNode, String configName) throws Exception { - ModifiableSolrParams modParams = new ModifiableSolrParams(); - modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); - modParams.set("name", name); - modParams.set("numShards", numShards); - modParams.set("replicationFactor", replicationFactor); - modParams.set("collection.configName", configName); - modParams.set("maxShardsPerNode", maxShardsPerNode); - QueryRequest request = new QueryRequest(modParams); - request.setPath("/admin/collections"); - return client.request(request); - } + protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, + int replicationFactor, int maxShardsPerNode, String configName) throws Exception { + ModifiableSolrParams modParams = new ModifiableSolrParams(); + modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); + modParams.set("name", name); + modParams.set("numShards", numShards); + modParams.set("replicationFactor", replicationFactor); + modParams.set("collection.configName", configName); + modParams.set("maxShardsPerNode", maxShardsPerNode); + QueryRequest request = new QueryRequest(modParams); + request.setPath("/admin/collections"); + return client.request(request); + } } From 98f37c8d81222bce8cb4870850e65dcf52fc375a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 Oct 2021 16:14:40 +0200 Subject: [PATCH 91/92] WIP: worflow nodes for including Scholexplorer records in the RAW graph --- .../dhp/oa/graph/raw/CopyHdfsOafApplication.java | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java index 2e06114751..c0accd25a0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java @@ -101,24 +101,15 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { .as(Encoders.kryo(Oaf.class)); // dispatch each entity type individually in the respective graph subdirectory in append mode - for(Map.Entry e : ModelSupport.entityTypes.entrySet()) { + for(Map.Entry e : ModelSupport.oafTypes.entrySet()) { oaf - .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey().toString())) + .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey())) .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue())) .write() .option("compression", "gzip") .mode(SaveMode.Append) .text(outputPath + "/" + e.getKey()); } - - oaf - .flatMap((FlatMapFunction) o -> { - Relation rel = (Relation) o; - List rels = Lists.newArrayList(); - rels.add(getInverse(rel, vocs)); - - return rels.iterator(); - }, Encoders.bean(Relation.class)); } } From 512e7b01707690d4539fad1d444da92055678c5e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 Oct 2021 16:19:29 +0200 Subject: [PATCH 92/92] code formatting --- .../oa/graph/raw/CopyHdfsOafApplication.java | 38 ++++++++++--------- .../common/AbstractMigrationApplication.java | 36 +++++++++--------- 2 files changed, 38 insertions(+), 36 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java index c0accd25a0..4cff88d820 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java @@ -1,18 +1,10 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.clearspring.analytics.util.Lists; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.*; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; @@ -26,9 +18,19 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.*; +import com.clearspring.analytics.util.Lists; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CopyHdfsOafApplication extends AbstractMigrationApplication { @@ -96,12 +98,12 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { if (validPaths.length > 0) { // load the dataset Dataset oaf = spark - .read() - .load(validPaths) - .as(Encoders.kryo(Oaf.class)); + .read() + .load(validPaths) + .as(Encoders.kryo(Oaf.class)); // dispatch each entity type individually in the respective graph subdirectory in append mode - for(Map.Entry e : ModelSupport.oafTypes.entrySet()) { + for (Map.Entry e : ModelSupport.oafTypes.entrySet()) { oaf .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey())) .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue())) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index 7c88dbd9d9..8cd495e08a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -8,7 +8,6 @@ import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -17,16 +16,17 @@ import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Oaf; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; +import eu.dnetlib.dhp.schema.oaf.Oaf; + public class AbstractMigrationApplication implements Closeable { private final AtomicInteger counter = new AtomicInteger(0); @@ -68,9 +68,9 @@ public class AbstractMigrationApplication implements Closeable { * @throws IOException in case of HTTP communication issues */ protected static Set mdstorePaths(final String mdstoreManagerUrl, - final String format, - final String layout, - final String interpretation) throws IOException { + final String format, + final String layout, + final String interpretation) throws IOException { final String url = mdstoreManagerUrl + "/mdstores/"; final ObjectMapper objectMapper = new ObjectMapper(); @@ -81,15 +81,15 @@ public class AbstractMigrationApplication implements Closeable { final String json = IOUtils.toString(response.getEntity().getContent()); final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); return Arrays - .stream(mdstores) - .filter(md -> md.getFormat().equalsIgnoreCase(format)) - .filter(md -> md.getLayout().equalsIgnoreCase(layout)) - .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) - .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) - .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) - .filter(md -> md.getSize() > 0) - .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") - .collect(Collectors.toSet()); + .stream(mdstores) + .filter(md -> md.getFormat().equalsIgnoreCase(format)) + .filter(md -> md.getLayout().equalsIgnoreCase(layout)) + .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) + .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) + .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) + .filter(md -> md.getSize() > 0) + .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") + .collect(Collectors.toSet()); } } }