From ea9b00ce56bdc78db6e5b46af9b6bbebf74ad138 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 20 May 2021 15:31:42 +0200 Subject: [PATCH 001/106] 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 cc18c6f54..1a6ebb9e8 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 59b536cd5..72ba48f41 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 002/106] 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 554aae82c..000000000 --- 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 813aead49..000000000 --- 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 3b543db4b..000000000 --- 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 d8f001aa5..000000000 --- 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 606eea6a8..000000000 --- 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 01972ce95..000000000 --- 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 c557eb5d2..000000000 --- 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 614d415c1..000000000 --- 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 003/106] 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 05fe6d014..000000000 --- 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 ea4d33296..000000000 --- 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 5621415d9..000000000 --- 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 1c2ae89dd..000000000 --- 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 133a6f4bd..000000000 --- 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 6f629c754..000000000 --- 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${nameNode} - -fORCID_2020_10_activites_X.tar.gz - -owxml/works/xml_works_X.seq - -oew--- - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml deleted file mode 100644 index 191654378..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx8g - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml deleted file mode 100644 index 68d468ab3..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml +++ /dev/null @@ -1,40 +0,0 @@ - - - - workingPath - the working dir base path - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.ExtractXMLSummariesData - -w${workingPath}/ - -n${nameNode} - -fORCID_2020_10_summaries.tar.gz - -oxml/authors/ - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml deleted file mode 100644 index 191654378..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx8g - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml deleted file mode 100644 index 8517f35ee..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - - workingPath - the working dir base path - - - shell_cmd_0 - wget -O /tmp/ORCID_2020_10_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/25032905 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_summaries.tar.gz /data/orcid_activities_2020/ORCID_2020_10_summaries.tar.gz ; rm -f /tmp/ORCID_2020_10_summaries.tar.gz - - the shell command that downloads and puts to hdfs orcid summaries - - - - - - - - Action failed, error message[${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 004/106] 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 36b4b073d..8cf070213 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 5c3236222..ccae4d976 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 becdf0974..000000000 --- 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}/* - ${outputPath} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 6513ff7e1..365c4d5b4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -1,5 +1,15 @@ + + workingPath + /data/orcid_activities_2020 + path where the collection workflow stores the ORCID data + + + outputPath + path where to store the action set + + spark2GenNoDoiDatasetMaxExecutors 40 @@ -35,10 +45,6 @@ spark2EventLogDir spark 2.* event log dir location - - workingPath - the working dir base path - @@ -83,11 +89,20 @@ --conf spark.eventLog.dir=${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/* + ${outputPath} + From d0945c3c7817d7081b6fb214b6ec7ee227e3a396 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 20 May 2021 19:14:31 +0200 Subject: [PATCH 005/106] added temporary output folder, because of folder access rights are different on beta and prod --- .../dhp/doiboost/orcidnodoi/oozie_app/workflow.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index 365c4d5b4..68f370a20 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -9,7 +9,10 @@ outputPath path where to store the action set - + + processOutputFolder + temporary path where to store the action set + spark2GenNoDoiDatasetMaxExecutors 40 @@ -66,7 +69,7 @@ - + @@ -92,7 +95,7 @@ --workingPath${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 006/106] 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 68f370a20..f7ac04821 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 007/106] 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 45e230c4f..9396eeeb6 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 008/106] 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 9396eeeb6..19d00d637 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 009/106] [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 036178b37..3e0c2bba6 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 010/106] 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 7628fb853..d620c4ef3 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 011/106] 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 55f075e95..9e071a356 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 012/106] 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 9e071a356..088ca1eaa 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 013/106] 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 00f604b14..261fb68bb 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 014/106] 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 261fb68bb..b124b76ce 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 015/106] 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 71bf5d942..eefb0b9cb 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 016/106] 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 3ed91f451..f88678437 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 018/106] 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 d30b3122c..1a4e7c42a 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 7c69c9635..f0842c844 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 019/106] 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 088ca1eaa..ec16a65e0 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 020/106] 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 000000000..fdd545ff7 --- /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 021/106] 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 fdd545ff7..8b477b34d 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 000000000..248bd7256 --- /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 022/106] 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 000000000..2b62b5f0d --- /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 023/106] 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 1a4e7c42a..47baee30d 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 024/106] [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 3e0c2bba6..69fc95957 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 025/106] 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 36ced3a4a..530f7a003 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 8b477b34d..77402ea1b 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 69100a114..89ecdfb2b 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 026/106] 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 d20a3036e..f5b8f1c76 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 027/106] 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 31d105b66..a6757d18d 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 028/106] [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 000000000..508202e30 --- /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 000000000..cf1cd97f7 --- /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 029/106] 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 c33a693a5..7a69c1a0d 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 030/106] 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 b556fa2d6..5f21e0bc5 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 031/106] 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 47baee30d..fe9b4e443 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 102406315..59f660525 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 530f7a003..b843ec365 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 31886d1b1..f76f92013 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 77402ea1b..e729e13df 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 f0842c844..6b64a4124 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 3ecbd1894..679c09393 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 248bd7256..3e4ab93c5 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 032/106] 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 7dc0e4417..518dfefe0 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 033/106] [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 cf1cd97f7..f845d97f3 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 034/106] 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 d118accba..fe4036925 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 035/106] 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 7a69c1a0d..3736b7380 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 036/106] 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 000000000..d262cb6e0 --- /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 000000000..bf55947d1 --- /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 000000000..2a612dec5 --- /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 000000000..e5ec3d0ae --- /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 000000000..5f954ff38 --- /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 000000000..e5ec3d0ae --- /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 000000000..15387e988 --- /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 000000000..319517026 --- /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 000000000..e5ec3d0ae --- /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 000000000..f84ab7e1a --- /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 000000000..e69de29bb 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 000000000..15387e988 --- /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 000000000..b990f4e49 --- /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 037/106] 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 fe4036925..d1f295fcf 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 038/106] 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 6ac626518..7db19f771 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 6e42bfa64..806220510 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 039/106] - --- .../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 1d986fc26..e86f6e3d2 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 29812188a..dec82bc97 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 683b6f4b7..b02062ede 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 040/106] 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 1a28a21f4..9c4c73d85 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 041/106] 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 9c4c73d85..e0355d6d6 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 042/106] 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 7eb50665e..d43e7ed37 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 f5b8f1c76..4ddcea9e8 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 fd8262544..28881b253 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 ec16a65e0..d64c26503 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 b124b76ce..9fcdcaf78 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 867fd5a77..03cbfb074 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 c6666342a..499df3a09 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 5f21e0bc5..448034d0c 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 eefb0b9cb..26187f0a3 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 043/106] 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 57acaf404..c65916610 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 a359eb3c6..9117bcb34 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"$workingPath/orcidworksWithAuthor").as[ORCIDItem] + + logger.info("Converting ORCID to OAF") + dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath) } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala new file mode 100644 index 000000000..d6911cfa7 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala @@ -0,0 +1,70 @@ +package eu.dnetlib.doiboost.orcid + +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.dhp.schema.orcid.OrcidDOI +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.functions._ +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkPreprocessORCID { + val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) + + def fixORCIDItem(item :ORCIDItem):ORCIDItem = { + ORCIDItem(item.doi, item.authors.groupBy(_.oid).map(_._2.head).toList) + + } + + + def run(spark:SparkSession,sourcePath:String,workingPath:String):Unit = { + import spark.implicits._ + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication] + + val inputRDD:RDD[OrcidAuthor] = spark.sparkContext.textFile(s"$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 a72e4b0d6..4530926f1 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 000000000..da324f8c4 --- /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 000000000..6c9ca5ede --- /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 000000000..da324f8c4 --- /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 fa47e142d..34b4b5c5e 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 bffde793b..0670e18de 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 152103570..fdc1e2f20 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 d620c4ef3..5fced8edb 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 044/106] 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 7eb50665e..dbdedcbd0 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 045/106] 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 9117bcb34..fa4a93e00 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 d6911cfa7..31f331912 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 63c2e9ef2..000000000 --- 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${workingPath}/process/ - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml deleted file mode 100644 index cf617a84c..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml +++ /dev/null @@ -1,38 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml deleted file mode 100644 index dcde62c9d..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml +++ /dev/null @@ -1,96 +0,0 @@ - - - - hostedByMapPath - the Hosted By Map Path - - - affiliationPath - the Affliation Path - - - paperAffiliationPath - the paperAffiliation Path - - - workingDirPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - - - Action failed, error message[${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${workingDirPath}/actionDataSet - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml deleted file mode 100644 index 59e5c059f..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.wf.rerun.failnodes - false - - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml deleted file mode 100644 index 9d19dddc7..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml +++ /dev/null @@ -1,92 +0,0 @@ - - - - sourcePath - the working dir base path - - - targetPath - the working dir base path - - - workingPath - the working dir base path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${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 508202e30..000000000 --- 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 34b4b5c5e..000000000 --- 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 000000000..03f7b7566 --- /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 cf617a84c..000000000 --- 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 d2a69752e..000000000 --- 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 dbdedcbd0..46d4ec08d 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 5fced8edb..b484dc087 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 046/106] 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 5bcec7224..ca39f99cc 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 047/106] 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 c342d2e79..1d47808ef 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 f7ac04821..05492d50d 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 048/106] 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 05492d50d..04ca05af2 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 049/106] 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 1e80dfd46..cbaadf85c 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 fcd6f459a..bbfb7429f 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 06aeab345..d753cddeb 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 b7400873b..7925a7826 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 050/106] 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 cbaadf85c..03c3eeb3c 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 051/106] 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 86bbae99e..a985d2371 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 052/106] 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 5b229a625..495dc4a04 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 000000000..362b40c85 --- /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 6631cb4da..a5a1563aa 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 000000000..dcd4c2ee1 --- /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 053/106] [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 a75cc52e6..e5181b111 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 054/106] 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 0cdf0accb..045927bed 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 055/106] 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 495dc4a04..aeeceaeb5 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 056/106] [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 000000000..151f5ba3f --- /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 000000000..f251da8c3 --- /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 000000000..178c2d69b --- /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 7f1ecb39f..e7320de3b 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 057/106] 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 a985d2371..2c8240290 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 a5a1563aa..897e507e1 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 058/106] [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 74f31cf35..4c7810c47 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 e5181b111..1d002ed7e 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 eefa1e9a3..8d519a93f 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 aeeceaeb5..ba4211a3f 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 000000000..9ec696256 --- /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 19d00d637..075a45c9f 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 059/106] 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 151f5ba3f..c2bcf69f0 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 060/106] [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 e7320de3b..321ca4090 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 061/106] [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 7d53d3554..b3f785492 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 062/106] 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 c2bcf69f0..dddc53bc8 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 000000000..def53c085 --- /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 000000000..640d042b1 --- /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 000000000..3e1203b18 --- /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 063/106] 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 dddc53bc8..5bbc8a975 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 064/106] 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 dddc53bc8..5523863ff 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 f251da8c3..d5852ab70 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 def53c085..3fd365416 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 3e1203b18..31755c53d 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 065/106] Update 'README.md' --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 39d4d98e4..0a0bd82ab 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 066/106] 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 4d581044a..e1fd758b4 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 067/106] 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 fe9b4e443..9f665c06d 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 068/106] 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 4ddcea9e8..d09e584a3 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 d1f295fcf..7b661ac66 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 9f665c06d..e38117338 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 7db19f771..71bea6047 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 28881b253..e0b7cf5d7 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 d64c26503..6abca2255 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 2d43888b4..6b4baafde 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 b843ec365..7441baaef 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 f76f92013..7e8ddfaf8 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 3736b7380..ecb588198 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 11c3600dd..7370b43f8 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 9fcdcaf78..1c7052553 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 e0355d6d6..55578fdab 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 9a5a553b1..5dc8e8910 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 fdd9492fe..f5641bc45 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 6b64a4124..39454192e 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 d5a9ba8dd..2fbd37db7 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 499df3a09..729e78844 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 42ad5634a..946e13655 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 448034d0c..76d406422 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 d80eb3ec6..a310448a4 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 d769aa138..fa1528e90 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 6c5ebbab3..0b062abd5 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 26187f0a3..9dd2aa41e 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 000000000..f68cead77 --- /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 000000000..d829e66ab --- /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 @@ +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","source":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb","validated":true, 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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 39454192e..d7c247499 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 92d7e53c0..043be7b1a 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 070/106] 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 d7c247499..3a4f05fb5 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 071/106] 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 000000000..14ca9c10c --- /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 073/106] 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 20a46cee0..fd34433c6 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 074/106] - --- .../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 fa7d33570..48ba8a6f6 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 fa03f93a6..549988767 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 0d7c74475..23e97a97a 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 68949b900..a38b4da2e 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 1289ff644..50df08f8c 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 7f76ead94..f31a26230 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 f4bf8d52a..988a8c7a4 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 6cdd741ea..971324744 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 edd6d9b23..3508e4126 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 7441baaef..7f64db41c 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 be1f21171..88c92da53 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 7370b43f8..ab7e7e595 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 d520a9c6a..9cddba3c5 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 e17aa285c..156ae6d63 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 3a4f05fb5..bf6301ec4 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 c950f1c91..a17861ad7 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 61102232e..9710e4553 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 a310448a4..fe178795d 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 7bb6b9ea9..08fcd49a8 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 ad4ea36c4..477481c08 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 8daf318be..6229ad19b 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 4d3bcee60..4be425779 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 075/106] 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 6dca09b63..61167639c 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 d09e584a3..68e1e8402 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 0d2df11fe..b56849a3a 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 4d0c59955..b972de6e9 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 988a8c7a4..0f3192c25 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 971324744..1eff99892 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 09e301572..a19a3a5b6 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 6abca2255..ee6341f84 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 3508e4126..87ac20948 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 0c8f5dba4..a468e334d 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 7e8ddfaf8..3e47ee664 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 b0b8b8acd..e1cb0e753 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 88c92da53..fcc4bf39c 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 ab7e7e595..ddfd6592f 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 4365e861f..f9d2123e2 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 e729e13df..20f3fc4a7 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 000000000..e325c4334 --- /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 000000000..f3fbf740a --- /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 9cddba3c5..6aed9d7a8 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 156ae6d63..d89b9e86d 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 a17861ad7..86d2f93c9 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 89ecdfb2b..051141e18 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 1bdcb60aa..4613d5636 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 d172419bf..e141af787 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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076/106] 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 051141e18..80b5fd89e 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 077/106] 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 68e1e8402..a714cea20 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 b972de6e9..ab5434ed0 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 0f3192c25..49468540d 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 1eff99892..a6595d756 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 806220510..677715847 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 e69de29bb..e5ec3d0ae 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 326bf63775db8e3ef896a2aa1a091ec6e1d2b0ce Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 13 Oct 2021 12:24:48 +0200 Subject: [PATCH 078/106] integration of parent child orgs relations --- .../raw/MigrateDbEntitiesApplication.java | 28 +++++++++++++++++++ .../sql/queryParentChildRelsOpenOrgs.sql | 13 +++++++++ 2 files changed, 41 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index d78732f9b..29df17f1b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -186,6 +186,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i log.info("Processing Openorgs Merge Rels..."); smdbe.execute("queryOpenOrgsSimilarityForProvision.sql", smdbe::processOrgOrgMergeRels); + + log.info("Processing Openorgs Parent/Child Rels..."); + smdbe.execute("queryParentChildRelsOpenOrgs.sql", smdbe::processOrgOrgParentChildRels); break; case openaire_organizations: @@ -689,6 +692,31 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } + public List processOrgOrgParentChildRels(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); // TODO + + final String orgId1 = createOpenaireId(20, rs.getString("source"), true); + final String orgId2 = createOpenaireId(20, rs.getString("target"), true); + + final List collectedFrom = listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); + + final Relation r = new Relation(); + r.setRelType(ORG_ORG_RELTYPE); + r.setSubRelType(ModelConstants.RELATIONSHIP); + r.setRelClass(rs.getString("reltype").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF : ModelConstants.IS_CHILD_OF); + r.setSource(orgId1); + r.setTarget(orgId2); + r.setCollectedfrom(collectedFrom); + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + public List processOrgOrgSimRels(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); // TODO diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql new file mode 100644 index 000000000..388fee3f5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -0,0 +1,13 @@ +SELECT + id1 AS source, + id2 AS target, + reltype AS type, + false AS inferred, + false AS deletedbyinference, + 0.95 AS trust, + '' AS inferenceprovenance, + 'openaire____::openorgs' AS collectedfromid, + 'OpenOrgs Database' AS collectedfromname, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction +FROM relationships +WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file From 995c1eddaf6adcf3a3a24136fc948cd939a5e7d0 Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 13 Oct 2021 17:07:10 +0200 Subject: [PATCH 079/106] minor change --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 29df17f1b..00184bc9d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -699,12 +699,16 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final String orgId1 = createOpenaireId(20, rs.getString("source"), true); final String orgId2 = createOpenaireId(20, rs.getString("target"), true); - final List collectedFrom = listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); + final List collectedFrom = listKeyValues( + createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r.setRelClass(rs.getString("reltype").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF : ModelConstants.IS_CHILD_OF); + r + .setRelClass( + rs.getString("reltype").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF + : ModelConstants.IS_CHILD_OF); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom); From 4b7c8dff2dec9fae75f73dca36b2f3c87de4441f Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 14 Oct 2021 18:53:35 +0300 Subject: [PATCH 080/106] fetching affiliated results for 4 orgs in monitor. fixed affiliated orgs in stats db --- .../oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 2 +- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 9ea50d488..d39af37d5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -17,7 +17,7 @@ create table TARGET.result as union all select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) union all - select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on p.id=rp.project join SOURCE.project_organizations po on po.id=p.id where rp.id=r.id and po.organization in ( + select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( 'openorgs____::759d59f05d77188faee99b7493b46805', 'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index b3cbc9b41..d461bd343 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -126,7 +126,7 @@ FROM ${stats_db_name}.otherresearchproduct_topics; CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'resultOrganization' +WHERE r.reltype = 'resultOrganization' and r.relclass='hasAuthorInstitution' and r.subreltype='affiliation' and r.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.result_projects AS From 41ecb1eb61e2d7a4285d60749c1ee0146b3436f9 Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 15 Oct 2021 13:42:55 +0300 Subject: [PATCH 081/106] invalidating medatadata before context thingies --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 2 ++ 1 file changed, 2 insertions(+) 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 6d42ab13d..2a40eb920 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 @@ -26,6 +26,8 @@ hdfs dfs -copyFromLocal concepts.csv ${TMP} hdfs dfs -chmod -R 777 ${TMP} echo "Creating and populating impala tables" +impala-shell -q "invalidate metadata" +impala-shell -d ${TARGET_DB} -q "invalidate metadata" impala-shell -q "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ','" impala-shell -q "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ','" impala-shell -q "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ','" From 7b15b88d4cdc60daf7cc7e60badea8f844abb57e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 15 Oct 2021 15:00:15 +0200 Subject: [PATCH 082/106] 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 dffc88c6c..70dcc0184 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 16d2b25a6..7a62437a3 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 17bf3fa6b..17d21f19c 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 85fbd99c4..eab6b1dc6 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 10467884c..b19bfc23a 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 305bb89be..881528425 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 c89929981..cef92d003 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 7df5dd5f2..ce9420cc1 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 6065416f8..863a23bd5 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 8fa226b7d..80cb0667c 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 e6ab61b87..862d39a94 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 a1777a230..13f38408e 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 000000000..071d202b6 --- /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 c072f149c..893a6e628 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 0df085ee1..000000000 --- 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 5f780a6ba19233edf20014cb0b81a8246e962384 Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 18 Oct 2021 23:30:40 +0200 Subject: [PATCH 083/106] bug fix in migrate entities: parameter name was wrong --- .../dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 2 +- .../eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 00184bc9d..e453f7918 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -707,7 +707,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i r.setSubRelType(ModelConstants.RELATIONSHIP); r .setRelClass( - rs.getString("reltype").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF + rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF : ModelConstants.IS_CHILD_OF); r.setSource(orgId1); r.setTarget(orgId2); 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 321ca4090..8139ecf7e 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 @@ -258,7 +258,7 @@ ${wf:conf('reuseDB') eq false} ${wf:conf('reuseDB') eq true} - + From a894d7adf3dd104f56bdfbbe8e4797813a9f168a Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 19 Oct 2021 10:02:55 +0200 Subject: [PATCH 084/106] updated version of dhp-schemas --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3e8d6bc19..02bc5d8d4 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 085/106] 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 ab5434ed0..b972de6e9 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 086/106] 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 000000000..2e0611475 --- /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 4110bd806..6c72e4dfc 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 5d32fe926..7c88dbd9d 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 000000000..1e862198f --- /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 321ca4090..563923a5a 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 087/106] 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 38ffd28fe..7d0d6b0b8 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 088/106] 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 9bc2924c3..3beca7e7e 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 e20ecf152..ab98b1da2 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 b86fd8ac8..34a9465a7 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 089/106] 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 2e0611475..c0accd25a 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 090/106] 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 c0accd25a..4cff88d82 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 7c88dbd9d..8cd495e08 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()); } } } From c01dd0c92524c21bfe8f06649a6d75f942ffbcc7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 20 Oct 2021 13:55:07 +0200 Subject: [PATCH 091/106] registered oaf model classes for the KryoSerializer --- .../eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java | 3 +++ 1 file changed, 3 insertions(+) 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 4cff88d82..25b343c1a 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 @@ -76,6 +76,9 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); final SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths)); } From 00b78b9c588e0c36264a3cd128419d91b6dd91c4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 20 Oct 2021 14:04:45 +0200 Subject: [PATCH 092/106] cleanup: mapping contents in the graph already defined in the OAF graph model doesn't require to be aware of the vocabularies --- .../dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java | 9 +-------- .../dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json | 6 ------ .../dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml | 1 - 3 files changed, 1 insertion(+), 15 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 25b343c1a..c016e2156 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 @@ -67,23 +67,16 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { 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(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths)); + runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, hdfsPath, paths)); } public static void processPaths(final SparkSession spark, - final VocabularyGroup vocs, final String outputPath, final Set paths) { 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 index 1e862198f..1d89017c5 100644 --- 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 @@ -28,11 +28,5 @@ "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 c4cca52f6..137c69ed8 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 @@ -569,7 +569,6 @@ --mdFormatOAF --mdLayoutstore --mdInterpretationgraph - --isLookupUrl${isLookupUrl} From 4f8970f8ed73acd2c89c23af6c209d0d4443c59c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 20 Oct 2021 14:14:53 +0200 Subject: [PATCH 093/106] [stats] reducing the step22 wait time --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh index dc19f84b4..03aa535e1 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash curl --request GET $1/cache/updateCache -sleep 20h \ No newline at end of file +sleep 6h \ No newline at end of file From ae4e99a4715811e193ee7892f679125cd8dbbdaa Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Oct 2021 17:12:08 +0200 Subject: [PATCH 094/106] Adapted workflow of resolution of PID to work into OpenAIRE data workflow - Added relations in both verse on all Scholexplorer datasources --- .../java/eu/dnetlib/dhp/utils/DHPUtils.java | 9 + .../DataciteToOAFTransformation.scala | 11 +- .../GenerateDataciteDatasetSpark.scala | 19 ++- .../dhp/collection/CollectionUtils.scala | 43 +++++ .../bio/SparkTransformBioDatabaseToOAF.scala | 9 +- .../dhp/sx/bio/ebi/SparkEBILinksToOaf.scala | 2 + .../collection/oozie_app/config-default.xml | 23 +++ .../collection/oozie_app/workflow.xml | 52 ++++++ .../datacite/generate_dataset_params.json | 4 +- .../oozie_app/config-default.xml | 23 +++ .../transformation/oozie_app/workflow.xml | 126 ++++++++++++++ .../resolution/SparkResolveRelation.scala | 152 +++++++++++++++++ .../dhp/sx/graph/SparkResolveRelation.scala | 154 ------------------ .../resolution}/oozie_app/config-default.xml | 0 .../graph/resolution}/oozie_app/workflow.xml | 34 +--- .../resolution}/resolve_relations_params.json | 3 +- .../sx/graph/scholix/ScholixGraphTest.scala | 2 +- 17 files changed, 468 insertions(+), 198 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/{sx/graph/resolverelation => oa/graph/resolution}/oozie_app/config-default.xml (100%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/{sx/graph/resolverelation => oa/graph/resolution}/oozie_app/workflow.xml (54%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/{sx/graph => oa/graph/resolution}/resolve_relations_params.json (50%) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 6a86f30df..c53affbad 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -10,6 +10,7 @@ import java.util.Properties; import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import org.apache.commons.codec.binary.Base64; import org.apache.commons.codec.binary.Base64OutputStream; import org.apache.commons.codec.binary.Hex; @@ -56,6 +57,14 @@ public class DHPUtils { return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); } + + public static String generateUnresolvedIdentifier(final String pid, final String pidType) { + + final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid); + + return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim()); + } + public static String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); 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 cfdd98d30..e3729e5b7 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 @@ -325,8 +325,9 @@ object DataciteToOAFTransformation { val grantId = m.matcher(awardUri).replaceAll("$2") val targetId = s"$p${DHPUtils.md5(grantId)}" List( - generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo), - generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo) + generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo) +// REMOVED INVERSE RELATION since there is a specific method that should generate later +// generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo) ) } else @@ -580,11 +581,11 @@ object DataciteToOAFTransformation { rel.setProperties(List(dateProps).asJava) rel.setSource(id) - rel.setTarget(s"unresolved::${r.relatedIdentifier}::${r.relatedIdentifierType}") + rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType)) rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava) - rel.getCollectedfrom.asScala.map(c => c.getValue)(collection.breakOut) + rel.getCollectedfrom.asScala.map(c => c.getValue).toList rel - })(collection breakOut) + }).toList } def generateDataInfo(trust: String): DataInfo = { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala index 2cabc7879..65d00c4d1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala @@ -1,9 +1,13 @@ package eu.dnetlib.dhp.actionmanager.datacite +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup -import eu.dnetlib.dhp.schema.mdstore.MetadataRecord +import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations +import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord} import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile import eu.dnetlib.dhp.utils.ISLookupClientFactory import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} @@ -21,7 +25,6 @@ object GenerateDataciteDatasetSpark { parser.parseArgument(args) val master = parser.get("master") val sourcePath = parser.get("sourcePath") - val targetPath = parser.get("targetPath") val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks")) val isLookupUrl: String = parser.get("isLookupUrl") log.info("isLookupUrl: {}", isLookupUrl) @@ -39,10 +42,22 @@ object GenerateDataciteDatasetSpark { import spark.implicits._ + val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") + val mapper = new ObjectMapper() + val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) + val outputBasePath = cleanedMdStoreVersion.getHdfsPath + + log.info("outputBasePath: {}", outputBasePath) + val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH" + spark.read.load(sourcePath).as[DataciteType] .filter(d => d.isActive) .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) .filter(d => d != null) + .flatMap(i=> fixRelations(i)).filter(i => i != null) .write.mode(SaveMode.Overwrite).save(targetPath) + + val total_items =spark.read.load(targetPath).as[Oaf].count() + writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH) } } \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala new file mode 100644 index 000000000..e212d7e2a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -0,0 +1,43 @@ +package eu.dnetlib.dhp.collection + +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation} + +object CollectionUtils { + + /** + * This method in pipeline to the transformation phase, + * generates relations in both verse, typically it should be a phase of flatMap + * + * @param i input OAF + * @return + * If the input OAF is an entity -> List(i) + * If the input OAF is a relation -> List(relation, inverseRelation) + * + */ + + def fixRelations(i: Oaf): List[Oaf] = { + if (i.isInstanceOf[OafEntity]) + return List(i) + else { + val r: Relation = i.asInstanceOf[Relation] + val currentRel = ModelSupport.findRelation(r.getRelClass) + if (currentRel != null) { + + // Cleaning relation + r.setRelType(currentRel.getRelType) + r.setSubRelType(currentRel.getSubReltype) + r.setRelClass(currentRel.getRelClass) + val inverse = new Relation + inverse.setSource(r.getTarget) + inverse.setTarget(r.getSource) + inverse.setRelType(currentRel.getRelType) + inverse.setSubRelType(currentRel.getSubReltype) + inverse.setRelClass(currentRel.getInverseRelClass) + return List(r, inverse) + } + } + List() + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index 7a62437a3..8ae8285e3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.Oaf import BioDBToOAF.ScholixResolved +import eu.dnetlib.dhp.collection.CollectionUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} @@ -35,13 +36,13 @@ object SparkTransformBioDatabaseToOAF { import spark.implicits._ database.toUpperCase() match { case "UNIPROT" => - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath) + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) case "PDB" => - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) case "SCHOLIX" => - spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).write.mode(SaveMode.Overwrite).save(targetPath) + spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) case "CROSSREF_LINKS" => - spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) + spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index b19bfc23a..8da617ca0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -5,6 +5,7 @@ import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.sx.bio.BioDBToOAF import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem import BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.collection.CollectionUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql._ @@ -37,6 +38,7 @@ object SparkEBILinksToOaf { ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)) + .flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null) .write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml new file mode 100644 index 000000000..41a2e2291 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml @@ -0,0 +1,52 @@ + + + + mainPath + the working path of Datacite stores + + + isLookupUrl + The IS lookUp service endopoint + + + blocksize + 100 + The request block size + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn-cluster + cluster + ImportDatacite + eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite + dhp-aggregation-${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} + + --targetPath${mainPath}/datacite_update + --dataciteDumpPath${mainPath}/datacite_dump + --namenode${nameNode} + --masteryarn-cluster + --blocksize${blocksize} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json index 67e7f37dc..04dc8b942 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json @@ -7,8 +7,8 @@ }, { - "paramName": "t", - "paramLongName": "targetPath", + "paramName": "mo", + "paramLongName": "mdstoreOutputVersion", "paramDescription": "the target mdstore path", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml new file mode 100644 index 000000000..aeb824a41 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml @@ -0,0 +1,126 @@ + + + + mainPath + the working path of Datacite stores + + + isLookupUrl + The IS lookUp service endopoint + + + mdStoreOutputId + the identifier of the cleaned MDStore + + + mdStoreManagerURI + the path of the cleaned mdstore + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionNEW_VERSION + --mdStoreID${mdStoreOutputId} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + yarn-cluster + cluster + TransformJob + eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark + dhp-aggregation-${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${mainPath}/datacite_dump + --mdstoreOutputVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --isLookupUrl${isLookupUrl} + --exportLinkstrue + --masteryarn-cluster + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionCOMMIT + --namenode${nameNode} + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionREAD_UNLOCK + --mdStoreManagerURI${mdStoreManagerURI} + --readMDStoreId${wf:actionData('BeginRead')['mdStoreReadLockVersion']} + + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionROLLBACK + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala new file mode 100644 index 000000000..e87f46b00 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala @@ -0,0 +1,152 @@ +package eu.dnetlib.dhp.oa.graph.resolution + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport +import eu.dnetlib.dhp.schema.oaf.{Relation, Result} +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.io.IOUtils +import org.apache.hadoop.fs.{FileSystem, Path} +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql._ +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +object SparkResolveRelation { + 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/oa/graph/resolution/resolve_relations_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphBasePath = parser.get("graphBasePath") + log.info(s"graphBasePath -> $graphBasePath") + val workingPath = parser.get("workingPath") + log.info(s"workingPath -> $workingPath") + + implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) + import spark.implicits._ + + + //CLEANING TEMPORARY FOLDER + HdfsSupport.remove(workingPath, spark.sparkContext.hadoopConfiguration) + val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration) + fs.mkdirs(new Path(workingPath)) + + extractPidResolvedTableFromJsonRDD(spark, graphBasePath, workingPath) + + val mapper: ObjectMapper = new ObjectMapper() + + val rPid: Dataset[(String, String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String, String)] + + val relationDs: Dataset[(String, Relation)] = spark.read.text(s"$graphBasePath/relation").as[String] + .map(s => mapper.readValue(s, classOf[Relation])).as[Relation] + .map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + + relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map { + m => + val sourceResolved = m._2 + val currentRelation = m._1._2 + if (sourceResolved != null && sourceResolved._1 != null && sourceResolved._1.nonEmpty) + currentRelation.setSource(sourceResolved._1) + currentRelation + }.write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedSource") + + + val relationSourceResolved: Dataset[(String, Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation] + .map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map { + m => + val targetResolved = m._2 + val currentRelation = m._1._2 + if (targetResolved != null && targetResolved._1.nonEmpty) + currentRelation.setTarget(targetResolved._1) + currentRelation + }.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")) + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relation_resolved") + + + // TO BE conservative we keep the original relation in the working dir + // and save the relation resolved on the graphBasePath + //In future this two line of code should be removed + + fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation")) + + spark.read.load(s"$workingPath/relation_resolved").as[Relation] + .map(r => mapper.writeValueAsString(r)) + .write + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .text(s"$graphBasePath/relation") + } + + + def extractPidsFromRecord(input: String): (String, List[(String, String)]) = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val id: String = (json \ "id").extract[String] + val result: List[(String, String)] = for { + JObject(pids) <- json \\ "instance" \ "pid" + JField("value", JString(pidValue)) <- pids + JField("qualifier", JObject(qualifier)) <- pids + JField("classname", JString(pidType)) <- qualifier + } yield (pidValue, pidType) + + val alternateIds: List[(String, String)] = for { + JObject(pids) <- json \\ "alternateIdentifier" + JField("value", JString(pidValue)) <- pids + JField("qualifier", JObject(qualifier)) <- pids + JField("classname", JString(pidType)) <- qualifier + } yield (pidValue, pidType) + + (id, result ::: alternateIds) + } + + + private def isRelation(input: String): Boolean = { + + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val source = (json \ "source").extractOrElse[String](null) + + source != null + } + + private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, graphPath: String, workingPath: String) = { + import spark.implicits._ + + val d: RDD[(String, String)] = spark.sparkContext.textFile(s"$graphPath/*") + .filter(i => !isRelation(i)) + .map(i => extractPidsFromRecord(i)) + .filter(s => s != null && s._1 != null && s._2 != null && s._2.nonEmpty) + .flatMap { p => + p._2.map(pid => + (p._1, DHPUtils.generateUnresolvedIdentifier(pid._1, pid._2)) + ) + }.filter(r => r._1 != null || r._2 != null) + + spark.createDataset(d) + .groupByKey(_._2) + .reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y) + .map(s => s._2) + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedPid") + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala deleted file mode 100644 index 1b13b81c7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala +++ /dev/null @@ -1,154 +0,0 @@ -package eu.dnetlib.dhp.sx.graph - -import com.fasterxml.jackson.databind.ObjectMapper -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Relation, Result} -import org.apache.commons.io.IOUtils -import org.apache.hadoop.io.compress.GzipCodec -import org.apache.spark.SparkConf -import org.apache.spark.rdd.RDD -import org.apache.spark.sql._ -import org.json4s -import org.json4s.DefaultFormats -import org.json4s.JsonAST.{JField, JObject, JString} -import org.json4s.jackson.JsonMethods.parse -import org.slf4j.{Logger, LoggerFactory} - -import scala.collection.JavaConverters._ -object SparkResolveRelation { - 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/resolve_relations_params.json"))) - parser.parseArgument(args) - val spark: SparkSession = - SparkSession - .builder() - .config(conf) - .appName(getClass.getSimpleName) - .master(parser.get("master")).getOrCreate() - - - val relationPath = parser.get("relationPath") - log.info(s"sourcePath -> $relationPath") - val entityPath = parser.get("entityPath") - log.info(s"entityPath -> $entityPath") - val workingPath = parser.get("workingPath") - log.info(s"workingPath -> $workingPath") - - implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) - import spark.implicits._ - - - extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath) - - val mappper = new ObjectMapper() - - val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)] - - val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - - relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{ - m => - val sourceResolved = m._2 - val currentRelation = m._1._2 - if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty) - currentRelation.setSource(sourceResolved._1) - currentRelation - }.write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedSource") - - - val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{ - m => - val targetResolved = m._2 - val currentRelation = m._1._2 - if (targetResolved!=null && targetResolved._1.nonEmpty) - currentRelation.setTarget(targetResolved._1) - currentRelation - }.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50")) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relation_resolved") - - spark.read.load(s"$workingPath/relation_resolved").as[Relation] - .map(r => mappper.writeValueAsString(r)) - .rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec]) - - } - - - def extractPidsFromRecord(input:String):(String,List[(String,String)]) = { - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json: json4s.JValue = parse(input) - val id:String = (json \ "id").extract[String] - val result: List[(String,String)] = for { - JObject(pids) <- json \ "pid" - JField("value", JString(pidValue)) <- pids - JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier - } yield (pidValue, pidType) - - val alternateIds: List[(String,String)] = for { - JObject(pids) <- json \\ "alternateIdentifier" - JField("value", JString(pidValue)) <- pids - JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier - } yield (pidValue, pidType) - - (id,result:::alternateIds) - } - - private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = { - import spark.implicits._ - - val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*") - .map(i => extractPidsFromRecord(i)) - .filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty) - .flatMap{ p => - p._2.map(pid => - (p._1, convertPidToDNETIdentifier(pid._1, pid._2)) - ) - }.filter(r =>r._1 != null || r._2 != null) - - spark.createDataset(d) - .groupByKey(_._2) - .reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedPid") - } - - - /* - This method should be used once we finally convert everythings in Kryo dataset - instead of using rdd of json - */ - private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = { - import spark.implicits._ - implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) - val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result] - entities.flatMap(e => e.getPid.asScala - .map(p => - convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid)) - .filter(s => s != null) - .map(s => (s, e.getId)) - ).groupByKey(_._1) - .reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedPid") - } - - def convertPidToDNETIdentifier(pid:String, pidType: String):String = { - if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty) - null - else - s"unresolved::${pid.toLowerCase}::${pidType.toLowerCase}" - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml similarity index 54% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml index 7683ff94c..e9e1a8ede 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml @@ -1,44 +1,23 @@ - entityPath - the path of deduplicate Entities + graphBasePath + the path of the graph - - relationPath - the path of relation unresolved - - - targetPath - the path of relation unresolved - - - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - yarn cluster Resolve Relations in raw graph - eu.dnetlib.dhp.sx.graph.SparkResolveRelation + eu.dnetlib.dhp.oa.graph.resolution.SparkResolveRelation dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -51,9 +30,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --masteryarn - --relationPath${relationPath} - --workingPath${targetPath} - --entityPath${entityPath} + --graphBasePath${graphBasePath} + --workingPath${workingDir} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json similarity index 50% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json index f211adb9a..1fbe20648 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json @@ -1,6 +1,5 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"e", "paramLongName":"entityPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala index 5b7fbe1cf..bd7e4fd09 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.sx.graph.scholix import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} +import eu.dnetlib.dhp.oa.graph.resolution.SparkResolveRelation import eu.dnetlib.dhp.schema.oaf.{Relation, Result} import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary -import eu.dnetlib.dhp.sx.graph.SparkResolveRelation import eu.dnetlib.dhp.sx.graph.bio.pubmed.AbstractVocabularyTest import org.json4s import org.json4s.DefaultFormats From ab3a99d3e9463fce361dc3cd1f2872ddbaefdac0 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Oct 2021 17:19:47 +0200 Subject: [PATCH 095/106] removed old datacite oozie workflow --- .../actionset/oozie_app/config-default.xml | 23 ----- .../datacite/actionset/oozie_app/workflow.xml | 46 ---------- .../datacite/oozie_app/config-default.xml | 23 ----- .../datacite/oozie_app/workflow.xml | 81 ------------------ .../scholix/oozie_app/config-default.xml | 23 ----- .../datacite/scholix/oozie_app/workflow.xml | 84 ------------------- 6 files changed, 280 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml deleted file mode 100644 index dd3c32c62..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml +++ /dev/null @@ -1,23 +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 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml deleted file mode 100644 index 3c58ace7b..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml +++ /dev/null @@ -1,46 +0,0 @@ - - - - sourcePath - the working path of Datacite stores - - - outputPath - the path of Datacite ActionSet - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - ExportDataset - eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${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}${spark2EventLogDir} - - --sourcePath${sourcePath} - --targetPath${outputPath} - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml deleted file mode 100644 index dd3c32c62..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml deleted file mode 100644 index c6332ff7d..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ /dev/null @@ -1,81 +0,0 @@ - - - - mainPath - the working path of Datacite stores - - - isLookupUrl - The IS lookUp service endopoint - - - blocksize - 100 - The request block size - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - ImportDatacite - eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${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}${spark2EventLogDir} - - --targetPath${mainPath}/datacite_update - --dataciteDumpPath${mainPath}/datacite_dump - --namenode${nameNode} - --masteryarn-cluster - --blocksize${blocksize} - - - - - - - - - yarn-cluster - cluster - TransformJob - eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark - dhp-aggregation-${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${mainPath}/datacite_dump - --targetPath${mainPath}/datacite_oaf - --isLookupUrl${isLookupUrl} - --exportLinksfalse - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml deleted file mode 100644 index dd3c32c62..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml deleted file mode 100644 index 397288c69..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml +++ /dev/null @@ -1,84 +0,0 @@ - - - - datacitePath - the path of Datacite spark dataset - - - isLookupUrl - The IS lookUp service endopoint - - - crossrefPath - the path of Crossref spark dataset - - - - targetPath - the path of Crossref spark dataset - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - ImportDatacite - eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${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}${spark2EventLogDir} - - --sourcePath${datacitePath} - --targetPath${targetPath}/datacite_oaf - --isLookupUrl${isLookupUrl} - --exportLinkstrue - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - FilterCrossrefEntities - eu.dnetlib.dhp.actionmanager.datacite.FilterCrossrefEntitiesSpark - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${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}${spark2EventLogDir} - - --sourcePath${crossrefPath} - --targetPath${targetPath}/crossref_oaf - --masteryarn-cluster - - - - - - - \ No newline at end of file From aeeebd573b2538e78c81ec8b9680ab5f4b4a794d Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Oct 2021 17:37:42 +0200 Subject: [PATCH 096/106] code refactor renamed datacite package --- .../datacite/ExportActionSetJobNode.scala | 41 ----------------- .../FilterCrossrefEntitiesSpark.scala | 46 ------------------- .../datacite/AbstractRestClient.scala | 8 ++-- .../datacite/DataciteAPIImporter.scala | 4 +- .../DataciteToOAFTransformation.scala | 2 +- .../GenerateDataciteDatasetSpark.scala | 19 ++++---- .../datacite/ImportDatacite.scala | 21 ++++----- .../SparkDownloadUpdateDatacite.scala | 16 +++---- .../collection/oozie_app/config-default.xml | 0 .../collection/oozie_app/workflow.xml | 2 +- .../datacite/datacite_filter | 0 .../datacite/exportDataset_parameters.json | 0 .../datacite/filter_crossref_param.json | 0 .../datacite/generate_dataset_params.json | 0 .../datacite/hostedBy_map.json | 0 .../datacite/import_from_api.json | 0 .../oozie_app/config-default.xml | 0 .../transformation/oozie_app/workflow.xml | 2 +- .../datacite/DataciteToOAFTest.scala | 5 +- 19 files changed, 36 insertions(+), 130 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/AbstractRestClient.scala (90%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/DataciteAPIImporter.scala (95%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/DataciteToOAFTransformation.scala (99%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/GenerateDataciteDatasetSpark.scala (86%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/ImportDatacite.scala (93%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionmanager => }/datacite/SparkDownloadUpdateDatacite.scala (68%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/collection/oozie_app/config-default.xml (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/collection/oozie_app/workflow.xml (95%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/datacite_filter (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/exportDataset_parameters.json (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/filter_crossref_param.json (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/generate_dataset_params.json (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/hostedBy_map.json (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/import_from_api.json (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/transformation/oozie_app/config-default.xml (100%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionmanager => }/datacite/transformation/oozie_app/workflow.xml (97%) rename dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/{actionmanager => }/datacite/DataciteToOAFTest.scala (88%) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala deleted file mode 100644 index 9f0d25735..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala +++ /dev/null @@ -1,41 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.Oaf -import org.apache.hadoop.io.Text -import org.apache.hadoop.io.compress.GzipCodec -import org.apache.hadoop.mapred.SequenceFileOutputFormat -import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.slf4j.{Logger, LoggerFactory} - -import scala.io.Source - -object ExportActionSetJobNode { - - val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass) - - def main(args: Array[String]): Unit = { - val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString) - parser.parseArgument(args) - val master = parser.get("master") - val sourcePath = parser.get("sourcePath") - val targetPath = parser.get("targetPath") - - val spark: SparkSession = SparkSession.builder().config(conf) - .appName(ExportActionSetJobNode.getClass.getSimpleName) - .master(master) - .getOrCreate() - implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING) - - spark.read.load(sourcePath).as[Oaf] - .map(o =>DataciteToOAFTransformation.toActionSet(o)) - .filter(o => o!= null) - .rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) - - - } - -} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala deleted file mode 100644 index 5860c50ac..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala +++ /dev/null @@ -1,46 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup -import eu.dnetlib.dhp.schema.mdstore.MetadataRecord -import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} -import eu.dnetlib.dhp.utils.ISLookupClientFactory -import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.slf4j.{Logger, LoggerFactory} - -import scala.io.Source - -object FilterCrossrefEntitiesSpark { - - val log: Logger = LoggerFactory.getLogger(getClass.getClass) - - def main(args: Array[String]): Unit = { - val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json")).mkString) - parser.parseArgument(args) - val master = parser.get("master") - val sourcePath = parser.get("sourcePath") - log.info("sourcePath: {}", sourcePath) - val targetPath = parser.get("targetPath") - log.info("targetPath: {}", targetPath) - - - - val spark: SparkSession = SparkSession.builder().config(conf) - .appName(getClass.getSimpleName) - .master(master) - .getOrCreate() - - - - implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result] - - val d:Dataset[Oaf]= spark.read.load(sourcePath).as[Oaf] - - d.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]).write.mode(SaveMode.Overwrite).save(targetPath) - - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala index bae41b218..6a9b8e3e5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala @@ -1,12 +1,10 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite import org.apache.commons.io.IOUtils import org.apache.http.client.config.RequestConfig -import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest} +import org.apache.http.client.methods.{HttpGet, HttpPost, HttpUriRequest} import org.apache.http.entity.StringEntity -import org.apache.http.impl.client.{HttpClientBuilder, HttpClients} - -import java.io.IOException +import org.apache.http.impl.client.HttpClientBuilder abstract class AbstractRestClient extends Iterator[String] { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala index 36ec9e8c3..7ec44a6ff 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala @@ -1,7 +1,7 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite -import org.json4s.{DefaultFormats, JValue} import org.json4s.jackson.JsonMethods.{compact, parse, render} +import org.json4s.{DefaultFormats, JValue} class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient { 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/datacite/DataciteToOAFTransformation.scala similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index e3729e5b7..6ce4920ed 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/datacite/DataciteToOAFTransformation.scala @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala similarity index 86% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala index 65d00c4d1..a63627d1c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala @@ -1,10 +1,11 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations +import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH +import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord} import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile @@ -21,7 +22,7 @@ object GenerateDataciteDatasetSpark { def main(args: Array[String]): Unit = { val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString) + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString) parser.parseArgument(args) val master = parser.get("master") val sourcePath = parser.get("sourcePath") @@ -36,12 +37,12 @@ object GenerateDataciteDatasetSpark { .master(master) .getOrCreate() + import spark.implicits._ + implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord] implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - import spark.implicits._ - val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") val mapper = new ObjectMapper() val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) @@ -54,10 +55,10 @@ object GenerateDataciteDatasetSpark { .filter(d => d.isActive) .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) .filter(d => d != null) - .flatMap(i=> fixRelations(i)).filter(i => i != null) + .flatMap(i => fixRelations(i)).filter(i => i != null) .write.mode(SaveMode.Overwrite).save(targetPath) - val total_items =spark.read.load(targetPath).as[Oaf].count() + val total_items = spark.read.load(targetPath).as[Oaf].count() writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH) } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala similarity index 93% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala index 2b73d2955..018b4958a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala @@ -1,6 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite -import eu.dnetlib.dhp.actionmanager.datacite.DataciteToOAFTransformation.df_it import eu.dnetlib.dhp.application.ArgumentApplicationParser import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.{FileSystem, LocalFileSystem, Path} @@ -9,14 +8,14 @@ import org.apache.hadoop.io.{IntWritable, SequenceFile, Text} import org.apache.spark.SparkContext import org.apache.spark.rdd.RDD import org.apache.spark.sql.expressions.Aggregator +import org.apache.spark.sql.functions.max import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession} import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse -import org.apache.spark.sql.functions.max import org.slf4j.{Logger, LoggerFactory} -import java.time.format.DateTimeFormatter._ -import java.time.{LocalDate, LocalDateTime, ZoneOffset} +import java.time.format.DateTimeFormatter.ISO_DATE_TIME +import java.time.{LocalDateTime, ZoneOffset} import scala.io.Source object ImportDatacite { @@ -138,11 +137,11 @@ object ImportDatacite { } } - private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = { - var from:Long = timestamp * 1000 - val delta:Long = 100000000L + private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs: Int): Long = { + var from: Long = timestamp * 1000 + val delta: Long = 100000000L var client: DataciteAPIImporter = null - val now :Long =System.currentTimeMillis() + val now: Long = System.currentTimeMillis() var i = 0 try { val writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfsTargetPath), SequenceFile.Writer.keyClass(classOf[IntWritable]), SequenceFile.Writer.valueClass(classOf[Text])) @@ -168,7 +167,7 @@ object ImportDatacite { start = System.currentTimeMillis } } - println(s"updating from value: $from -> ${from+delta}") + println(s"updating from value: $from -> ${from + delta}") from = from + delta } } catch { @@ -183,4 +182,4 @@ object ImportDatacite { i } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala similarity index 68% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala index 0b459fcf6..d46e5423d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala @@ -1,18 +1,14 @@ -package eu.dnetlib.dhp.actionmanager.datacite - +package eu.dnetlib.dhp.datacite import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} -import org.apache.hadoop.conf.Configuration -import org.apache.hadoop.fs.LocalFileSystem -import org.apache.hadoop.hdfs.DistributedFileSystem import org.apache.spark.SparkConf -import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.apache.spark.sql.functions.max +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.slf4j.{Logger, LoggerFactory} import java.text.SimpleDateFormat -import java.util.{Date, Locale} +import java.util.Locale import scala.io.Source object SparkDownloadUpdateDatacite { @@ -21,7 +17,7 @@ object SparkDownloadUpdateDatacite { def main(args: Array[String]): Unit = { val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString) + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString) parser.parseArgument(args) val master = parser.get("master") val sourcePath = parser.get("sourcePath") @@ -42,9 +38,9 @@ object SparkDownloadUpdateDatacite { import spark.implicits._ - val maxDate:String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0) + val maxDate: String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0) val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) - val string_to_date =ISO8601FORMAT.parse(maxDate) + val string_to_date = ISO8601FORMAT.parse(maxDate) val ts = string_to_date.getTime diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml index 41a2e2291..6989eed66 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/collection/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml @@ -28,7 +28,7 @@ yarn-cluster cluster ImportDatacite - eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite + eu.dnetlib.dhp.datacite.ImportDatacite dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/datacite_filter similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/datacite_filter diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/exportDataset_parameters.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/exportDataset_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/filter_crossref_param.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/filter_crossref_param.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/generate_dataset_params.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/generate_dataset_params.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/import_from_api.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/import_from_api.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml similarity index 97% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml index aeb824a41..d5bae7305 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/transformation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml @@ -47,7 +47,7 @@ yarn-cluster cluster TransformJob - eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark + eu.dnetlib.dhp.datacite.GenerateDataciteDatasetSpark dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala similarity index 88% rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala rename to dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index a795a910d..f21e9eab1 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -1,8 +1,7 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite -import com.fasterxml.jackson.databind.ObjectMapper -import com.fasterxml.jackson.databind.SerializationFeature +import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.Oaf import org.junit.jupiter.api.extension.ExtendWith From ac36aa7d1c9324b1b018a71eeb3b4f94b05165a6 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Oct 2021 11:35:02 +0200 Subject: [PATCH 097/106] fixed wrong Encoding during a map phase --- .../eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.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/raw/CopyHdfsOafApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java index c016e2156..77971a5a4 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 @@ -102,7 +102,7 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { 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())) + .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.STRING()) .write() .option("compression", "gzip") .mode(SaveMode.Append) From 3702fe478d2082cd28b1f27bf0d094600d2e8b9b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 Oct 2021 12:05:02 +0200 Subject: [PATCH 098/106] cleanup --- .../oa/graph/raw/CopyHdfsOafApplication.java | 20 +------------------ 1 file changed, 1 insertion(+), 19 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 77971a5a4..792264e18 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 @@ -110,23 +110,5 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { } } } - - 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; - } - + } From d147295c2f9b531b8da7973436694c0354c79ba9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 Oct 2021 14:15:57 +0200 Subject: [PATCH 099/106] avoiding java.io.NotSerializableException: java.util.HashMap --- .../dhp/oa/graph/raw/CopyHdfsOafApplication.java | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 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 792264e18..31ebcbc6e 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 @@ -31,6 +31,7 @@ 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 scala.Tuple2; public class CopyHdfsOafApplication extends AbstractMigrationApplication { @@ -73,10 +74,13 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication { conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, hdfsPath, paths)); + final List oafTypes = Lists.newArrayList(ModelSupport.oafTypes.keySet()); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, oafTypes, hdfsPath, paths)); } public static void processPaths(final SparkSession spark, + final List oafTypes, final String outputPath, final Set paths) { @@ -99,16 +103,16 @@ 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.oafTypes.entrySet()) { + for (String type : oafTypes) { oaf - .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey())) + .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(type)) .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.STRING()) .write() .option("compression", "gzip") .mode(SaveMode.Append) - .text(outputPath + "/" + e.getKey()); + .text(outputPath + "/" + type); } } } - + } From 6b34ba737eae62a3c8c61dc279fbfdd17233aa18 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 Oct 2021 14:16:18 +0200 Subject: [PATCH 100/106] minor --- .../src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java | 2 +- dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java index 0b2cd571f..654fdd5ac 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java @@ -28,7 +28,7 @@ public class HdfsSupport { * @param configuration Configuration of hadoop env */ public static boolean exists(String path, Configuration configuration) { - logger.info("Removing path: {}", path); + logger.info("Checking existence for path: {}", path); return rethrowAsRuntimeException( () -> { Path f = new Path(path); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index c53affbad..4fee87ed7 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -10,7 +10,6 @@ import java.util.Properties; import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import org.apache.commons.codec.binary.Base64; import org.apache.commons.codec.binary.Base64OutputStream; import org.apache.commons.codec.binary.Hex; @@ -27,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import net.minidev.json.JSONArray; import scala.collection.JavaConverters; import scala.collection.Seq; @@ -57,7 +57,6 @@ public class DHPUtils { return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); } - public static String generateUnresolvedIdentifier(final String pid, final String pidType) { final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid); From 034304b33af2b8fdec46cafc8f3c81f4fb704c2e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Oct 2021 09:40:47 +0200 Subject: [PATCH 101/106] conflict resolved on merge --- .../java/eu/dnetlib/dhp/utils/DHPUtils.java | 82 ++++++++---- .../dhp/sx/bio/ebi/oozie_app/workflow.xml | 4 +- .../dhp/sx/bio/pubmed/oozie_app/workflow.xml | 2 +- .../oa/graph/raw/CopyHdfsOafApplication.java | 118 ------------------ .../raw/CopyHdfsOafSparkApplication.scala | 74 +++++++++++ .../common/AbstractMigrationApplication.java | 23 +--- .../oa/graph/copy_hdfs_oaf_parameters.json | 6 + .../oa/graph/raw_all/oozie_app/workflow.xml | 3 +- 8 files changed, 147 insertions(+), 165 deletions(-) delete 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/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 4fee87ed7..66e4cb780 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -1,36 +1,35 @@ package eu.dnetlib.dhp.utils; -import java.io.*; -import java.nio.charset.StandardCharsets; -import java.security.MessageDigest; -import java.util.List; -import java.util.Map; -import java.util.Properties; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; - -import org.apache.commons.codec.binary.Base64; -import org.apache.commons.codec.binary.Base64OutputStream; -import org.apache.commons.codec.binary.Hex; -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.SaveMode; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import com.jayway.jsonpath.JsonPath; - +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import net.minidev.json.JSONArray; +import org.apache.commons.codec.binary.Hex; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +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 org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SaveMode; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.collection.JavaConverters; import scala.collection.Seq; +import java.io.*; +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.util.*; +import java.util.stream.Collectors; + public class DHPUtils { private static final Logger log = LoggerFactory.getLogger(DHPUtils.class); @@ -53,6 +52,45 @@ public class DHPUtils { } } + /** + * 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 + * @param includeEmpty include Empty mdstores + * @return the set of hdfs paths + * @throws IOException in case of HTTP communication issues + */ + public static Set mdstorePaths(final String mdstoreManagerUrl, + final String format, + final String layout, + final String interpretation, + boolean includeEmpty) 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 -> includeEmpty || md.getSize() > 0) + .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") + .collect(Collectors.toSet()); + } + } + } + public static String generateIdentifier(final String originalId, final String nsPrefix) { return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); } 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 index 73b1a3b60..4b47ae38e 100644 --- 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 @@ -52,7 +52,7 @@ yarn-cluster cluster Incremental Download EBI Links - eu.dnetllib.dhp.sx.bio.ebi.SparkDownloadEBILinks + eu.dnetlib.dhp.sx.bio.ebi.SparkDownloadEBILinks dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -85,7 +85,7 @@ yarn-cluster cluster Create OAF DataSet - eu.dnetllib.dhp.sx.bio.ebi.SparkEBILinksToOaf + eu.dnetlib.dhp.sx.bio.ebi.SparkEBILinksToOaf dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml index 21fd2d153..8915a090b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml @@ -30,7 +30,7 @@ yarn cluster Convert Baseline to OAF Dataset - eu.dnetllib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame + eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} 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 deleted file mode 100644 index 31ebcbc6e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java +++ /dev/null @@ -1,118 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.raw; - -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; -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 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 scala.Tuple2; - -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 Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); - - final SparkConf conf = new SparkConf(); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - - final List oafTypes = Lists.newArrayList(ModelSupport.oafTypes.keySet()); - - runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, oafTypes, hdfsPath, paths)); - } - - public static void processPaths(final SparkSession spark, - final List oafTypes, - 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 (String type : oafTypes) { - oaf - .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(type)) - .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.STRING()) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .text(outputPath + "/" + type); - } - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala new file mode 100644 index 000000000..c7ad1890d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala @@ -0,0 +1,74 @@ +package eu.dnetlib.dhp.oa.graph.raw + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils +import org.apache.http.client.methods.HttpGet +import org.apache.http.impl.client.HttpClients +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.{SparkConf, SparkContext} +import org.slf4j.LoggerFactory + +import scala.collection.JavaConverters._ +import scala.io.Source + +object CopyHdfsOafSparkApplication { + + def main(args: Array[String]): Unit = { + val log = LoggerFactory.getLogger(getClass) + val conf = new SparkConf() + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")).mkString) + parser.parseArgument(args) + + val spark = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val sc: SparkContext = spark.sparkContext + + val mdstoreManagerUrl = parser.get("mdstoreManagerUrl") + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl) + + val mdFormat = parser.get("mdFormat") + log.info("mdFormat: {}", mdFormat) + + val mdLayout = parser.get("mdLayout") + log.info("mdLayout: {}", mdLayout) + + val mdInterpretation = parser.get("mdInterpretation") + log.info("mdInterpretation: {}", mdInterpretation) + + val hdfsPath = parser.get("hdfsPath") + log.info("hdfsPath: {}", hdfsPath) + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + + val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala + + val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList + + if (validPaths.nonEmpty) { + val oaf = spark.read.load(validPaths: _*).as[Oaf] + val mapper = new ObjectMapper() + val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList + l.foreach( + e => + oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .write + .option("compression", "gzip") + .mode(SaveMode.Append) + .text(s"$hdfsPath/${e}") + ) + } + } +} 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 8cd495e08..cba64899b 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 @@ -26,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.utils.DHPUtils; public class AbstractMigrationApplication implements Closeable { @@ -71,27 +72,7 @@ public class AbstractMigrationApplication implements Closeable { 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()); - } - } + return DHPUtils.mdstorePaths(mdstoreManagerUrl, format, layout, interpretation, false); } private Configuration getConf() { 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 index 1d89017c5..d1b16b09a 100644 --- 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 @@ -23,6 +23,12 @@ "paramDescription": "metadata layout", "paramRequired": true }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "should be yarn or local", + "paramRequired": true + }, { "paramName": "i", "paramLongName": "mdInterpretation", 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 137c69ed8..307e26267 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 @@ -553,7 +553,7 @@ yarn cluster ImportOAF_hdfs_graph - eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafApplication + eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafSparkApplication dhp-graph-mapper-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} @@ -568,6 +568,7 @@ --mdstoreManagerUrl${mdstoreManagerUrl} --mdFormatOAF --mdLayoutstore + --masteryarn --mdInterpretationgraph From aafdffa6b3c3d423a1b9a0085b4d6540bb723e13 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Oct 2021 09:45:46 +0200 Subject: [PATCH 102/106] resolved conflict --- .../java/eu/dnetlib/dhp/utils/DHPUtils.java | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 66e4cb780..5a59bc0df 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -1,12 +1,12 @@ package eu.dnetlib.dhp.utils; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.Maps; -import com.jayway.jsonpath.JsonPath; -import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; -import net.minidev.json.JSONArray; +import java.io.*; +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.util.*; +import java.util.stream.Collectors; + import org.apache.commons.codec.binary.Hex; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -21,15 +21,17 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Maps; +import com.jayway.jsonpath.JsonPath; + +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import net.minidev.json.JSONArray; import scala.collection.JavaConverters; import scala.collection.Seq; -import java.io.*; -import java.nio.charset.StandardCharsets; -import java.security.MessageDigest; -import java.util.*; -import java.util.stream.Collectors; - public class DHPUtils { private static final Logger log = LoggerFactory.getLogger(DHPUtils.class); From 4acfa8fa2e317874caabe209f1d6c685b36d9a66 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Oct 2021 17:51:20 +0200 Subject: [PATCH 103/106] Scholexplorer Datasource Aggregation: - Added collectedfrom in the inverse relation generated Relation resolution: - increased number of partitions in workflow.xml - using classid instead of classname to build the pid-dnetId mapping --- .../java/eu/dnetlib/dhp/collection/CollectionUtils.scala | 6 ++++++ .../dhp/oa/graph/resolution/SparkResolveRelation.scala | 4 ++-- .../dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml | 2 +- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala index e212d7e2a..11ecfd6cb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -34,6 +34,12 @@ object CollectionUtils { inverse.setRelType(currentRel.getRelType) inverse.setSubRelType(currentRel.getSubReltype) inverse.setRelClass(currentRel.getInverseRelClass) + inverse.setCollectedfrom(r.getCollectedfrom) + inverse.setDataInfo(r.getDataInfo) + inverse.setProperties(r.getProperties) + inverse.setLastupdatetimestamp(r.getLastupdatetimestamp) + inverse.setValidated(r.getValidated) + inverse.setValidationDate(r.getValidationDate) return List(r, inverse) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala index e87f46b00..5ca7d9782 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala @@ -104,14 +104,14 @@ object SparkResolveRelation { JObject(pids) <- json \\ "instance" \ "pid" JField("value", JString(pidValue)) <- pids JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier + JField("classid", JString(pidType)) <- qualifier } yield (pidValue, pidType) val alternateIds: List[(String, String)] = for { JObject(pids) <- json \\ "alternateIdentifier" JField("value", JString(pidValue)) <- pids JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier + JField("classid", JString(pidType)) <- qualifier } yield (pidValue, pidType) (id, result ::: alternateIds) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml index e9e1a8ede..31cc53ae3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml @@ -24,7 +24,7 @@ --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.shuffle.partitions=8000 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} From 1be9aa0a5f2d747ad7eb41191956d14a4f3c0943 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Oct 2021 17:52:20 +0200 Subject: [PATCH 104/106] Removed filter of datacite items from the raw graph merging phase, Datacite is not an actionset anymore in beta --- .../dhp/oa/graph/merge/MergeGraphTableSparkJob.java | 7 ------- 1 file changed, 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java index ef419a042..474944260 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java @@ -127,13 +127,6 @@ public class MergeGraphTableSparkJob { } }, Encoders.bean(p_clazz)) .filter((FilterFunction

) Objects::nonNull) - .filter((FilterFunction

) o -> { - HashSet collectedFromNames = Optional - .ofNullable(o.getCollectedfrom()) - .map(c -> c.stream().map(KeyValue::getValue).collect(Collectors.toCollection(HashSet::new))) - .orElse(new HashSet<>()); - return !collectedFromNames.contains("Datacite"); - }) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") From d9cbca83f7911b53190a9f999f5e02a7f00382ac Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 28 Oct 2021 16:13:24 +0200 Subject: [PATCH 105/106] moved filter on next phase --- .../dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala index 5ca7d9782..db93bc43f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala @@ -75,7 +75,7 @@ object SparkResolveRelation { if (targetResolved != null && targetResolved._1.nonEmpty) currentRelation.setTarget(targetResolved._1) currentRelation - }.filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")) + } .write .mode(SaveMode.Overwrite) .save(s"$workingPath/relation_resolved") @@ -88,6 +88,7 @@ object SparkResolveRelation { fs.rename(new Path(s"$graphBasePath/relation"), new Path(s"$workingPath/relation")) spark.read.load(s"$workingPath/relation_resolved").as[Relation] + .filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")) .map(r => mapper.writeValueAsString(r)) .write .option("compression", "gzip") From 1225ba0b9223ae6049ea5c80772dcf72407a01b8 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 28 Oct 2021 16:18:17 +0200 Subject: [PATCH 106/106] [resolution] increasing number of partitions to avoid OOM --- .../eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml index 31cc53ae3..52f0e6e9d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml @@ -24,7 +24,7 @@ --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=8000 + --conf spark.sql.shuffle.partitions=15000 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}