diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000000..aff151f945 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,43 @@ +# Contributor Code of Conduct + +Openness, transparency and our community-driven participatory approach guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share. + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +- Using welcoming and inclusive language +- Being respectful of differing viewpoints and experiences +- Gracefully accepting constructive criticism +- Attempting collaboration before conflict +- Focusing on what is best for the community +- Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +- Violence, threats of violence, or inciting others to commit self-harm +- The use of sexualized language or imagery and unwelcome sexual attention or advances +- Trolling, intentionally spreading misinformation, insulting/derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or electronic address, without explicit permission +- Abuse of the reporting process to intentionally harass or exclude others +- Advocating for, or encouraging, any of the above behavior +- Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/), [version 1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html). \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000000..13a359c865 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,10 @@ +# Contributing to D-Net Hadoop + +:+1::tada: First off, thanks for taking the time to contribute! :tada::+1: + +This project and everyone participating in it is governed by our [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it). + +The following is a set of guidelines for contributing to this project and its packages. These are mostly guidelines, not rules, which applies to this project as a while, including all its sub-modules. +Use your best judgment, and feel free to propose changes to this document in a pull request. + +All contributions are welcome, all contributions will be considered to be contributed under the [project license](LICENSE.md). diff --git a/LICENSE b/LICENSE.md similarity index 100% rename from LICENSE rename to LICENSE.md diff --git a/README.md b/README.md index 2c1440f44e..b6575814d5 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,11 @@ Dnet-hadoop is the project that defined all the [OOZIE workflows](https://oozie.apache.org/) for the OpenAIRE Graph construction, processing, provisioning. +This project adheres to the Contributor Covenant [code of conduct](CODE_OF_CONDUCT.md). +By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it). + +This project is licensed under the [AGPL v3 or later version](#LICENSE.md). + How to build, package and run oozie workflows ==================== diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java new file mode 100644 index 0000000000..fff28dbdfd --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.common.api.context; + +public class CategorySummary { + + private String id; + + private String label; + + private boolean hasConcept; + + public String getId() { + return id; + } + + public String getLabel() { + return label; + } + + public boolean isHasConcept() { + return hasConcept; + } + + public CategorySummary setId(final String id) { + this.id = id; + return this; + } + + public CategorySummary setLabel(final String label) { + this.label = label; + return this; + } + + public CategorySummary setHasConcept(final boolean hasConcept) { + this.hasConcept = hasConcept; + return this; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java new file mode 100644 index 0000000000..7213a945a6 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java @@ -0,0 +1,7 @@ + +package eu.dnetlib.dhp.common.api.context; + +import java.util.ArrayList; + +public class CategorySummaryList extends ArrayList { +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java new file mode 100644 index 0000000000..a576f9a1e1 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.common.api.context; + +import java.util.List; + +public class ConceptSummary { + + private String id; + + private String label; + + public boolean hasSubConcept; + + private List concepts; + + public String getId() { + return id; + } + + public String getLabel() { + return label; + } + + public List getConcepts() { + return concepts; + } + + public ConceptSummary setId(final String id) { + this.id = id; + return this; + } + + public ConceptSummary setLabel(final String label) { + this.label = label; + return this; + } + + public boolean isHasSubConcept() { + return hasSubConcept; + } + + public ConceptSummary setHasSubConcept(final boolean hasSubConcept) { + this.hasSubConcept = hasSubConcept; + return this; + } + + public ConceptSummary setConcept(final List concepts) { + this.concepts = concepts; + return this; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java new file mode 100644 index 0000000000..45ccd28109 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java @@ -0,0 +1,7 @@ + +package eu.dnetlib.dhp.common.api.context; + +import java.util.ArrayList; + +public class ConceptSummaryList extends ArrayList { +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java new file mode 100644 index 0000000000..46a0d0d5ad --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java @@ -0,0 +1,50 @@ + +package eu.dnetlib.dhp.common.api.context; + +public class ContextSummary { + + private String id; + + private String label; + + private String type; + + private String status; + + public String getId() { + return id; + } + + public String getLabel() { + return label; + } + + public String getType() { + return type; + } + + public String getStatus() { + return status; + } + + public ContextSummary setId(final String id) { + this.id = id; + return this; + } + + public ContextSummary setLabel(final String label) { + this.label = label; + return this; + } + + public ContextSummary setType(final String type) { + this.type = type; + return this; + } + + public ContextSummary setStatus(final String status) { + this.status = status; + return this; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java new file mode 100644 index 0000000000..6186000077 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java @@ -0,0 +1,7 @@ + +package eu.dnetlib.dhp.common.api.context; + +import java.util.ArrayList; + +public class ContextSummaryList extends ArrayList { +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java index 905457bcd0..342d73cdc2 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java @@ -8,10 +8,13 @@ import java.io.InputStream; import java.net.*; import java.util.List; import java.util.Map; +import java.util.concurrent.TimeUnit; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.math.NumberUtils; +import org.apache.commons.lang3.time.DateUtils; import org.apache.http.HttpHeaders; +import org.joda.time.Instant; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -94,14 +97,16 @@ public class HttpConnector2 { throw new CollectorException(msg); } - log.info("Request attempt {} [{}]", retryNumber, requestUrl); - InputStream input = null; + long start = System.currentTimeMillis(); try { if (getClientParams().getRequestDelay() > 0) { backoffAndSleep(getClientParams().getRequestDelay()); } + + log.info("Request attempt {} [{}]", retryNumber, requestUrl); + final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection(); urlConn.setInstanceFollowRedirects(false); urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000); @@ -115,9 +120,8 @@ public class HttpConnector2 { urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue()); } } - if (log.isDebugEnabled()) { - logHeaderFields(urlConn); - } + + logHeaderFields(urlConn); int retryAfter = obtainRetryAfter(urlConn.getHeaderFields()); String rateLimit = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT); @@ -132,9 +136,7 @@ public class HttpConnector2 { } if (is2xx(urlConn.getResponseCode())) { - input = urlConn.getInputStream(); - responseType = urlConn.getContentType(); - return input; + return getInputStream(urlConn, start); } if (is3xx(urlConn.getResponseCode())) { // REDIRECTS @@ -144,6 +146,7 @@ public class HttpConnector2 { .put( REPORT_PREFIX + urlConn.getResponseCode(), String.format("Moved to: %s", newUrl)); + logRequestTime(start); urlConn.disconnect(); if (retryAfter > 0) { backoffAndSleep(retryAfter); @@ -159,26 +162,50 @@ public class HttpConnector2 { if (retryAfter > 0) { log .warn( - "{} - waiting and repeating request after suggested retry-after {} sec.", - requestUrl, retryAfter); + "waiting and repeating request after suggested retry-after {} sec for URL {}", + retryAfter, requestUrl); backoffAndSleep(retryAfter * 1000); } else { log .warn( - "{} - waiting and repeating request after default delay of {} sec.", - requestUrl, getClientParams().getRetryDelay()); - backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000); + "waiting and repeating request after default delay of {} sec for URL {}", + getClientParams().getRetryDelay(), requestUrl); + backoffAndSleep(retryNumber * getClientParams().getRetryDelay()); } report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl); + + logRequestTime(start); + urlConn.disconnect(); + return attemptDownload(requestUrl, retryNumber + 1, report); + case 422: // UNPROCESSABLE ENTITY + report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl); + log.warn("waiting and repeating request after 10 sec for URL {}", requestUrl); + backoffAndSleep(10000); + urlConn.disconnect(); + logRequestTime(start); + try { + return getInputStream(urlConn, start); + } catch (IOException e) { + log + .error( + "server returned 422 and got IOException accessing the response body from URL {}", + requestUrl); + log.error("IOException:", e); + return attemptDownload(requestUrl, retryNumber + 1, report); + } default: + log.error("gor error {} from URL: {}", urlConn.getResponseCode(), urlConn.getURL()); + log.error("response message: {}", urlConn.getResponseMessage()); report .put( REPORT_PREFIX + urlConn.getResponseCode(), String .format( "%s Error: %s", requestUrl, urlConn.getResponseMessage())); + logRequestTime(start); + urlConn.disconnect(); throw new CollectorException(urlConn.getResponseCode() + " error " + report); } } @@ -199,13 +226,27 @@ public class HttpConnector2 { } } + private InputStream getInputStream(HttpURLConnection urlConn, long start) throws IOException { + InputStream input = urlConn.getInputStream(); + responseType = urlConn.getContentType(); + logRequestTime(start); + return input; + } + + private static void logRequestTime(long start) { + log + .info( + "request time elapsed: {}sec", + TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - start)); + } + private void logHeaderFields(final HttpURLConnection urlConn) throws IOException { - log.debug("StatusCode: {}", urlConn.getResponseMessage()); + log.info("Response: {} - {}", urlConn.getResponseCode(), urlConn.getResponseMessage()); for (Map.Entry> e : urlConn.getHeaderFields().entrySet()) { if (e.getKey() != null) { for (String v : e.getValue()) { - log.debug(" key: {} - value: {}", e.getKey(), v); + log.info(" key: {} - value: {}", e.getKey(), v); } } } @@ -225,7 +266,7 @@ public class HttpConnector2 { for (String key : headerMap.keySet()) { if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (!headerMap.get(key).isEmpty()) && NumberUtils.isCreatable(headerMap.get(key).get(0))) { - return Integer.parseInt(headerMap.get(key).get(0)) + 10; + return Integer.parseInt(headerMap.get(key).get(0)); } } return -1; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 0461c9353c..b413a0bb94 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -145,105 +145,6 @@ public class AuthorMerger { return null; } - /** - * This method tries to figure out when two author are the same in the contest - * of ORCID enrichment - * - * @param left Author in the OAF entity - * @param right Author ORCID - * @return based on a heuristic on the names of the authors if they are the same. - */ - public static boolean checkORCIDSimilarity(final Author left, final Author right) { - final Person pl = parse(left); - final Person pr = parse(right); - - // If one of them didn't have a surname we verify if they have the fullName not empty - // and verify if the normalized version is equal - if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && - pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) { - - if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null - && !pr.getFullname().isEmpty()) { - return pl - .getFullname() - .stream() - .anyMatch( - fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr)))); - } else { - return false; - } - } - // The Authors have one surname in common - if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { - - // If one of them has only a surname and is the same we can say that they are the same author - if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) || - (pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank))) - return true; - // The authors have the same initials of Name in common - if (pl - .getName() - .stream() - .anyMatch( - nl -> pr - .getName() - .stream() - .anyMatch(nr -> nr.equalsIgnoreCase(nl)))) - return true; - } - - // Sometimes we noticed that publication have author wrote in inverse order Surname, Name - // We verify if we have an exact match between name and surname - if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) && - pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl)))) - return true; - else - return false; - } - // - - /** - * Method to enrich ORCID information in one list of authors based on another list - * - * @param baseAuthor the Author List in the OAF Entity - * @param orcidAuthor The list of ORCID Author intersected - * @return The Author List of the OAF Entity enriched with the orcid Author - */ - public static List enrichOrcid(List baseAuthor, List orcidAuthor) { - - if (baseAuthor == null || baseAuthor.isEmpty()) - return orcidAuthor; - - if (orcidAuthor == null || orcidAuthor.isEmpty()) - return baseAuthor; - - if (baseAuthor.size() == 1 && orcidAuthor.size() > 10) - return baseAuthor; - - final List oAuthor = new ArrayList<>(); - oAuthor.addAll(orcidAuthor); - - baseAuthor.forEach(ba -> { - Optional aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst(); - if (aMatch.isPresent()) { - final Author sameAuthor = aMatch.get(); - addPid(ba, sameAuthor.getPid()); - oAuthor.remove(sameAuthor); - } - }); - return baseAuthor; - } - - private static void addPid(final Author a, final List pids) { - - if (a.getPid() == null) { - a.setPid(new ArrayList<>()); - } - - a.getPid().addAll(pids); - - } - public static String pidToComparableString(StructuredProperty pid) { final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index 0225a50635..eadca231ef 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -1,24 +1,6 @@ package eu.dnetlib.dhp.oa.merge; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.spark.sql.functions.col; -import static org.apache.spark.sql.functions.when; - -import java.util.Map; -import java.util.Optional; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ForkJoinPool; -import java.util.stream.Collectors; - -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.ReduceFunction; -import org.apache.spark.sql.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -26,169 +8,186 @@ import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; 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.function.MapFunction; +import org.apache.spark.api.java.function.ReduceFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; +import java.util.Map; +import java.util.Optional; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.ForkJoinPool; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.col; +import static org.apache.spark.sql.functions.when; + /** * Groups the graph content by entity identifier to ensure ID uniqueness */ public class GroupEntitiesSparkJob { - private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); - private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); - private ArgumentApplicationParser parser; + private ArgumentApplicationParser parser; - public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { - this.parser = parser; - } + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - GroupEntitiesSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + GroupEntitiesSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_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); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); - final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); - new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); - } + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } - public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) - throws ISLookUpException { + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { - String graphInputPath = parser.get("graphInputPath"); - log.info("graphInputPath: {}", graphInputPath); + String graphInputPath = parser.get("graphInputPath"); + log.info("graphInputPath: {}", graphInputPath); - String checkpointPath = parser.get("checkpointPath"); - log.info("checkpointPath: {}", checkpointPath); + String checkpointPath = parser.get("checkpointPath"); + log.info("checkpointPath: {}", checkpointPath); - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); - log.info("filterInvisible: {}", filterInvisible); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); + log.info("filterInvisible: {}", filterInvisible); - SparkConf conf = new SparkConf(); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); + }); + } - private static void groupEntities( - SparkSession spark, - String inputPath, - String checkpointPath, - String outputPath, - boolean filterInvisible, VocabularyGroup vocs) { + private static void groupEntities( + SparkSession spark, + String inputPath, + String checkpointPath, + String outputPath, + boolean filterInvisible, VocabularyGroup vocs) { - Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); + Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); - String entityInputPath = inputPath + "/" + entity; + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); + String entityInputPath = inputPath + "/" + entity; - if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { - continue; - } + if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { + continue; + } - allEntities = allEntities - .union( - ((Dataset) spark - .read() - .schema(Encoders.bean(entityClass).schema()) - .json(entityInputPath) - .filter("length(id) > 0") - .as(Encoders.bean(entityClass))) - .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); - } + allEntities = allEntities + .union( + ((Dataset) spark + .read() + .schema(Encoders.bean(entityClass).schema()) + .json(entityInputPath) + .filter("length(id) > 0") + .as(Encoders.bean(entityClass))) + .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); + } - Dataset groupedEntities = allEntities - .map( - (MapFunction) entity -> GraphCleaningFunctions - .applyCoarVocabularies(entity, vocs), - OAFENTITY_KRYO_ENC) - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) - .map( - (MapFunction, Tuple2>) t -> new Tuple2<>( - t._2().getClass().getName(), t._2()), - Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); + Dataset groupedEntities = allEntities + .map( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) MergeUtils::checkedMerge) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( + t._2().getClass().getName(), t._2()), + Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); - // pivot on "_1" (classname of the entity) - // created columns containing only entities of the same class - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + // pivot on "_1" (classname of the entity) + // created columns containing only entities of the same class + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - groupedEntities = groupedEntities - .withColumn( - entity, - when(col("_1").equalTo(entityClass.getName()), col("_2"))); - } + groupedEntities = groupedEntities + .withColumn( + entity, + when(col("_1").equalTo(entityClass.getName()), col("_2"))); + } - groupedEntities - .drop("_1", "_2") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .save(checkpointPath); + groupedEntities + .drop("_1", "_2") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .save(checkpointPath); - ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); + ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); - ModelSupport.entityTypes - .entrySet() - .stream() - .map(e -> parPool.submit(() -> { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + ModelSupport.entityTypes + .entrySet() + .stream() + .map(e -> parPool.submit(() -> { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - spark - .read() - .load(checkpointPath) - .select(col(entity).as("value")) - .filter("value IS NOT NULL") - .as(OAFENTITY_KRYO_ENC) - .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) - .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + entity); - })) - .collect(Collectors.toList()) - .forEach(t -> { - try { - t.get(); - } catch (InterruptedException | ExecutionException e) { - throw new RuntimeException(e); - } - }); - } + spark + .read() + .load(checkpointPath) + .select(col(entity).as("value")) + .filter("value IS NOT NULL") + .as(OAFENTITY_KRYO_ENC) + .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) + .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + entity); + })) + .collect(Collectors.toList()) + .forEach(t -> { + try { + t.get(); + } catch (InterruptedException | ExecutionException e) { + throw new RuntimeException(e); + } + }); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java new file mode 100644 index 0000000000..027bf0735d --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java @@ -0,0 +1,77 @@ + +package eu.dnetlib.dhp.oozie; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + +import java.net.URL; +import java.nio.charset.StandardCharsets; +import java.util.HashMap; +import java.util.Map; +import java.util.Optional; + +import org.apache.commons.lang3.time.DurationFormatUtils; +import org.apache.commons.text.StringSubstitutor; +import org.apache.spark.SparkConf; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.io.Resources; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class RunSQLSparkJob { + private static final Logger log = LoggerFactory.getLogger(RunSQLSparkJob.class); + + private final ArgumentApplicationParser parser; + + public RunSQLSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + + public static void main(String[] args) throws Exception { + + Map params = new HashMap<>(); + for (int i = 0; i < args.length - 1; i++) { + if (args[i].startsWith("--")) { + params.put(args[i].substring(2), args[++i]); + } + } + + /* + * String jsonConfiguration = IOUtils .toString( Objects .requireNonNull( RunSQLSparkJob.class + * .getResourceAsStream( "/eu/dnetlib/dhp/oozie/run_sql_parameters.json"))); final ArgumentApplicationParser + * parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); + */ + + Boolean isSparkSessionManaged = Optional + .ofNullable(params.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + URL url = com.google.common.io.Resources.getResource(params.get("sql")); + String raw_sql = Resources.toString(url, StandardCharsets.UTF_8); + + String sql = StringSubstitutor.replace(raw_sql, params); + log.info("sql: {}", sql); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", params.get("hiveMetastoreUris")); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + for (String statement : sql.split(";\\s*/\\*\\s*EOS\\s*\\*/\\s*")) { + log.info("executing: {}", statement); + long startTime = System.currentTimeMillis(); + spark.sql(statement).show(); + log + .info( + "executed in {}", + DurationFormatUtils.formatDuration(System.currentTimeMillis() - startTime, "HH:mm:ss.S")); + } + }); + } + +} 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 0124e96fc1..f01f90fe4f 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 @@ -312,7 +312,8 @@ public class GraphCleaningFunctions extends CleaningFunctions { } if (value instanceof Datasource) { - // nothing to evaluate here + final Datasource d = (Datasource) value; + return Objects.nonNull(d.getOfficialname()) && StringUtils.isNotBlank(d.getOfficialname().getValue()); } else if (value instanceof Project) { final Project p = (Project) value; return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue()); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java new file mode 100644 index 0000000000..ffb0e600ab --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java @@ -0,0 +1,79 @@ +package eu.dnetlib.dhp.schema.oaf.utils; + +// +// Source code recreated from a .class file by IntelliJ IDEA +// (powered by FernFlower decompiler) +// + + +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; + +import java.util.Comparator; +import java.util.HashSet; +import java.util.Optional; +import java.util.stream.Collectors; + +public class MergeComparator implements Comparator { + public MergeComparator() { + } + + public int compare(Oaf left, Oaf right) { + // nulls at the end + if (left == null && right == null) { + return 0; + } else if (left == null) { + return -1; + } else if (right == null) { + return 1; + } + + // invisible + if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) { + if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) { + return -1; + } + } + + // collectedfrom + HashSet lCf = getCollectedFromIds(left); + HashSet rCf = getCollectedFromIds(right); + if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return -1; + } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return 1; + } + + + + SubEntityType lClass = SubEntityType.fromClass(left.getClass()); + SubEntityType rClass = SubEntityType.fromClass(right.getClass()); + return lClass.ordinal() - rClass.ordinal(); + + } + + protected HashSet getCollectedFromIds(Oaf left) { + return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> { + return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); + }).orElse(new HashSet()); + } + + enum SubEntityType { + publication, dataset, software, otherresearchproduct, datasource, organization, project; + + /** + * Resolves the EntityType, given the relative class name + * + * @param clazz the given class name + * @param actual OafEntity subclass + * @return the EntityType associated to the given class + */ + public static SubEntityType fromClass(Class clazz) { + return valueOf(clazz.getSimpleName().toLowerCase()); + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java new file mode 100644 index 0000000000..072a86bf1b --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -0,0 +1,707 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import eu.dnetlib.dhp.schema.common.AccessRightComparator; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.tuple.ImmutablePair; +import org.apache.commons.lang3.tuple.Pair; + +import java.text.ParseException; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static com.google.common.base.Objects.firstNonNull; +import static com.google.common.base.Preconditions.checkArgument; + +public class MergeUtils { + + public static T checkedMerge(final T left, final T right) { + return (T) merge(left, right, false); + } + + public static Oaf merge(final Oaf left, final Oaf right) { + return merge(left, right, false); + } + + public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) { + if (sameClass(left, right, OafEntity.class)) { + return mergeEntities(left, right, checkDelegatedAuthority); + } else if (sameClass(left, right, Relation.class)) { + return mergeRelation((Relation) left, (Relation) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } + + private static boolean sameClass(Object left, Object right, Class cls) { + return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass()); + } + + private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) { + + if (sameClass(left, right, Result.class)) { + if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) { + return mergeResultsOfDifferentTypes((Result)left, (Result) right); + } + + if (sameClass(left, right, Publication.class)) { + return mergePublication((Publication) left, (Publication) right); + } + if (sameClass(left, right, Dataset.class)) { + return mergeDataset((Dataset) left, (Dataset) right); + } + if (sameClass(left, right, OtherResearchProduct.class)) { + return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right); + } + if (sameClass(left, right, Software.class)) { + return mergeSoftware((Software) left, (Software) right); + } + + return mergeResult((Result) left, (Result) right); + } else if (sameClass(left, right, Datasource.class)) { + // TODO + final int trust = compareTrust(left, right); + return mergeOafEntityFields((Datasource) left, (Datasource) right, trust); + } else if (sameClass(left, right, Organization.class)) { + return mergeOrganization((Organization) left, (Organization) right); + } else if (sameClass(left, right, Project.class)) { + return mergeProject((Project) left, (Project) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } + + /** + * This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority + * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers + * such version. + *

+ * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator} + * and proceeds with the canonical property merging. + * + * @param left + * @param right + * @return + */ + private static T mergeResultsOfDifferentTypes(T left, T right) { + + final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); + final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); + + if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { + return left; + } + if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { + return right; + } + //TODO: raise trust to have preferred fields from one or the other?? + if (new ResultTypeComparator().compare(left, right) < 0) { + return mergeResult(left, right); + } else { + return mergeResult(right, left); + } + } + + private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) { + return right; + } else { + return left; + } + } else { + return right; + } + } + + private static String chooseString(String left, String right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return StringUtils.isNotBlank(left) ? left : right; + } else { + return right; + } + } + + private static T chooseReference(T left, T right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return left != null ? left : right; + } else { + return right; + } + } + + private static Long max(Long left, Long right) { + if (left == null) + return right; + if (right == null) + return left; + + return Math.max(left, right); + } + + // trust ?? + private static Boolean booleanOR(Boolean a, Boolean b) { + if (a == null) { + return b; + } else if (b == null) { + return a; + } + + return a || b; + } + + + private static List unionDistinctLists(final List left, final List right, int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream.concat(h.stream(), l.stream()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + + private static List unionDistinctListOfString(final List l, final List r) { + if (l == null) { + return r; + } else if (r == null) { + return l; + } + + return Stream.concat(l.stream(), r.stream()) + .filter(StringUtils::isNotBlank) + .distinct() + .collect(Collectors.toList()); + } + + //TODO review + private static List mergeKeyValue(List left, List right, int trust) { + if (trust < 0) { + List s = left; + left = right; + right = s; + } + + HashMap values = new HashMap<>(); + left.forEach(kv -> values.put(kv.getKey(), kv)); + right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv)); + + return new ArrayList<>(values.values()); + } + + private static List unionTitle(List left, List right, int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream.concat(h.stream(), l.stream()) + .filter(Objects::isNull) + .distinct() + .collect(Collectors.toList()); + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param merged + * @param enrich + * @param + * @return + */ + private static T mergeOafFields(T merged, T enrich, int trust) { + + //TODO: union of all values, but what does it mean with KeyValue pairs??? + merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust)); + merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust)); + merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp())); + + return merged; + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param original + * @param enrich + * @param + * @return + */ + private static T mergeOafEntityFields(T original, T enrich, int trust) { + final T merged = mergeOafFields(original, enrich, trust); + + merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId())); + merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust)); + // dateofcollection mettere today quando si fa merge + merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust)); + // setDateoftransformation mettere vuota in dedup, nota per Claudio + merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust)); + // TODO: was missing in OafEntity.merge + merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust)); + //oaiprovenanze da mettere a null quando si genera merge + merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust)); + merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust)); + + return merged; + } + + + public static T mergeRelation(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeOafFields(original, enrich, trust); + + checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal"); + checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal"); + checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal"); + checkArgument( + Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal"); + checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal"); + + //merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance())); + + //TODO: trust ?? + merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated())); + try { + merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate())); + } catch (ParseException e) { + throw new IllegalArgumentException(String + .format( + "invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(), + merge.getTarget(), + merge.getValidationDate())); + } + + // TODO keyvalue merge + merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust)); + + return merge; + } + + public static T mergeResult(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merge = mergeOafEntityFields(original, enrich, trust); + + if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) { + merge.setProcessingchargeamount(enrich.getProcessingchargeamount()); + merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency()); + } + + // author = usare la stessa logica che in dedup + merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust)); + // il primo che mi arriva secondo l'ordinamento per priorita' + merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust)); + // gestito come il resulttype perche' e' un subtype + merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust)); + // spostiamo nell'instance e qui prendo il primo che arriva + merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust)); + // country lasicamo,o cosi' -> parentesi sul datainfo + merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust)); + //ok + merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust)); + // union per priority quindi vanno in append + merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust)); + //ok + merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust)); + // prima trust e poi longest list + merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription())); + // trust piu' alto e poi piu' vecchia + merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust)); + // ok, ma publisher va messo ripetibile + merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust)); + // ok + merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust)); + // ok + merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust)); + // ok + merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust)); + // ok + merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust)); + // ok + merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust)); + + // prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO + // trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario) + // vedi note + merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype())); + + // ok + merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust)); + + // most open ok + if (enrich.getBestaccessright() != null + && new AccessRightComparator<>() + .compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) { + merge.setBestaccessright(enrich.getBestaccessright()); + } + + // TODO merge of datainfo given same id + merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust)); + + //ok + merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust)); + + //instance enrichment or union + // review instance equals => add pid to comparision + if (!isAnEnrichment(merge) && !isAnEnrichment(enrich)) + merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust)); + else { + final List enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance() + : enrich.getInstance(); + final List enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance() + : merge.getInstance(); + if (isAnEnrichment(merge)) + merge.setDataInfo(enrich.getDataInfo()); + merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances)); + } + + merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust)); + merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen())); + // OK but should be list of values + merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust)); + merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal())); + merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded())); + + return merge; + } + + private static T mergeORP(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust)); + merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust)); + merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust)); + + return merge; + } + + private static T mergeSoftware(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust)); + merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust)); + merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust)); + merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust)); + + return merge; + } + + private static T mergeDataset(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeResult(original, enrich); + + merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust)); + merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust)); + merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust)); + merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust)); + merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust)); + merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust)); + merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust)); + + return merge; + } + + public static T mergePublication(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merged = mergeResult(original, enrich); + + merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust)); + + return merged; + } + + private static T mergeOrganization(T left, T enrich) { + int trust = compareTrust(left, enrich); + T merged = mergeOafEntityFields(left, enrich, trust); + + merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust)); + merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust)); + merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust)); + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust)); + merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust)); + merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust)); + merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust)); + merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust)); + merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust)); + merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust)); + merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust)); + merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust)); + merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust)); + merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust)); + merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust)); + + return merged; + } + + public static T mergeProject(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merged = mergeOafEntityFields(original, enrich, trust); + + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust)); + merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust)); + merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust)); + merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust)); + merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust)); + merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust)); + merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust)); + merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust)); + merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust)); + merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust)); + merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust)); + merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust)); + merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust)); + merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust)); + merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust)); + merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust)); + merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust)); + merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust)); + merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust)); + merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust)); + merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust)); + merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust)); + merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust)); + + //missin in Project.merge + merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust)); + merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust)); + + // trust ?? + if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) { + merged.setH2020topiccode(enrich.getH2020topiccode()); + merged.setH2020topicdescription(enrich.getH2020topicdescription()); + } + + merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust)); + + return merged; + } + + + /** + * Longest lists list. + * + * @param a the a + * @param b the b + * @return the list + */ + public static List> longestLists(List> a, List> b) { + if (a == null || b == null) + return a == null ? b : a; + + return a.size() >= b.size() ? a : b; + } + + /** + * This main method apply the enrichment of the instances + * + * @param toEnrichInstances the instances that could be enriched + * @param enrichmentInstances the enrichment instances + * @return list of instances possibly enriched + */ + private static List enrichInstances(final List toEnrichInstances, + final List enrichmentInstances) { + final List enrichmentResult = new ArrayList<>(); + + if (toEnrichInstances == null) { + return enrichmentResult; + } + if (enrichmentInstances == null) { + return enrichmentResult; + } + Map ri = toInstanceMap(enrichmentInstances); + + toEnrichInstances.forEach(i -> { + final List e = findEnrichmentsByPID(i.getPid(), ri); + if (e != null && e.size() > 0) { + e.forEach(enr -> applyEnrichment(i, enr)); + } else { + final List a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri); + if (a != null && a.size() > 0) { + a.forEach(enr -> applyEnrichment(i, enr)); + } + } + enrichmentResult.add(i); + }); + return enrichmentResult; + } + + /** + * This method converts the list of instance enrichments + * into a Map where the key is the normalized identifier + * and the value is the instance itself + * + * @param ri the list of enrichment instances + * @return the result map + */ + private static Map toInstanceMap(final List ri) { + return ri + .stream() + .filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null) + .flatMap(i -> { + final List> result = new ArrayList<>(); + if (i.getPid() != null) + i + .getPid() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + if (i.getAlternateIdentifier() != null) + i + .getAlternateIdentifier() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + return result.stream(); + }) + .collect( + Collectors + .toMap( + Pair::getLeft, + Pair::getRight, + (a, b) -> a)); + } + + private static boolean isFromDelegatedAuthority(Result r) { + return Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .filter(i -> Objects.nonNull(i.getCollectedfrom())) + .map(i -> i.getCollectedfrom().getKey()) + .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) + .orElse(false); + } + + /** + * Valid pid boolean. + * + * @param p the p + * @return the boolean + */ + private static boolean validPid(final StructuredProperty p) { + return p.getValue() != null && p.getQualifier() != null && p.getQualifier().getClassid() != null; + } + + /** + * Normalize pid string. + * + * @param pid the pid + * @return the string + */ + private static String extractKeyFromPid(final StructuredProperty pid) { + if (pid == null) + return null; + final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid); + + return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue()); + } + + /** + * This utility method finds the list of enrichment instances + * that match one or more PIDs in the input list + * + * @param pids the list of PIDs + * @param enrichments the List of enrichment instances having the same pid + * @return the list + */ + private static List findEnrichmentsByPID(final List pids, + final Map enrichments) { + if (pids == null || enrichments == null) + return null; + return pids + .stream() + .map(MergeUtils::extractKeyFromPid) + .map(enrichments::get) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } + + /** + * Is an enrichment boolean. + * + * @param e the e + * @return the boolean + */ + private static boolean isAnEnrichment(OafEntity e) { + return e.getDataInfo() != null && + e.getDataInfo().getProvenanceaction() != null + && ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid()); + } + + /** + * This method apply enrichment on a single instance + * The enrichment consists of replacing values on + * single attribute only if in the current instance is missing + * The only repeatable field enriched is measures + * + * @param merge the current instance + * @param enrichment the enrichment instance + */ + private static void applyEnrichment(final Instance merge, final Instance enrichment) { + if (merge == null || enrichment == null) + return; + + merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense())); + merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright())); + merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype())); + merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping())); + merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby())); + merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0)); + merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation())); + merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom())); + // pid and alternateId are used for matching + merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance())); + merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount())); + merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency())); + merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed())); + merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0)); + merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext())); + } + + private static int compareTrust(Oaf a, Oaf b) { + String left = Optional + .ofNullable(a.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + String right = Optional + .ofNullable(b.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + return left.compareTo(right); + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 4cecd08954..417516b0f6 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -14,7 +14,6 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; -import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; public class OafMapperUtils { @@ -22,65 +21,6 @@ public class OafMapperUtils { private OafMapperUtils() { } - public static Oaf merge(final Oaf left, final Oaf right) { - if (ModelSupport.isSubClass(left, OafEntity.class)) { - return mergeEntities((OafEntity) left, (OafEntity) right); - } else if (ModelSupport.isSubClass(left, Relation.class)) { - ((Relation) left).mergeFrom((Relation) right); - } else { - throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName()); - } - return left; - } - - public static OafEntity mergeEntities(OafEntity left, OafEntity right) { - if (ModelSupport.isSubClass(left, Result.class)) { - return mergeResults((Result) left, (Result) right); - } else if (ModelSupport.isSubClass(left, Datasource.class)) { - left.mergeFrom(right); - } else if (ModelSupport.isSubClass(left, Organization.class)) { - left.mergeFrom(right); - } else if (ModelSupport.isSubClass(left, Project.class)) { - left.mergeFrom(right); - } else { - throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName()); - } - return left; - } - - public static Result mergeResults(Result left, Result right) { - - final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); - final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); - - if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { - return left; - } - if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { - return right; - } - - if (new ResultTypeComparator().compare(left, right) < 0) { - left.mergeFrom(right); - return left; - } else { - right.mergeFrom(left); - return right; - } - } - - private static boolean isFromDelegatedAuthority(Result r) { - return Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .filter(i -> Objects.nonNull(i.getCollectedfrom())) - .map(i -> i.getCollectedfrom().getKey()) - .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) - .orElse(false); - } - public static KeyValue keyValue(final String k, final String v) { final KeyValue kv = new KeyValue(); kv.setKey(k); diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/oozie/run_sql_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oozie/run_sql_parameters.json new file mode 100644 index 0000000000..355f38e2fc --- /dev/null +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/oozie/run_sql_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "hmu", + "paramLongName": "hiveMetastoreUris", + "paramDescription": "the hive metastore uris", + "paramRequired": true + }, + { + "paramName": "sql", + "paramLongName": "sql", + "paramDescription": "sql script to execute", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java new file mode 100644 index 0000000000..ef35b50fb2 --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java @@ -0,0 +1,111 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.util.HashSet; +import java.util.List; +import java.util.stream.Collectors; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +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.Dataset; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class MergeUtilsTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Test + void testMergePubs() throws IOException { + Publication p1 = read("publication_1.json", Publication.class); + Publication p2 = read("publication_2.json", Publication.class); + Dataset d1 = read("dataset_1.json", Dataset.class); + Dataset d2 = read("dataset_2.json", Dataset.class); + + assertEquals(1, p1.getCollectedfrom().size()); + assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey()); + assertEquals(1, d2.getCollectedfrom().size()); + assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + + assertEquals(1, p2.getCollectedfrom().size()); + assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + assertEquals(1, d1.getCollectedfrom().size()); + assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + + final Result p1d2 = MergeUtils.checkedMerge(p1, d2); + assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid()); + assertTrue(p1d2 instanceof Publication); + assertEquals(p1.getId(), p1d2.getId()); + } + + @Test + void testMergePubs_1() throws IOException { + Publication p2 = read("publication_2.json", Publication.class); + Dataset d1 = read("dataset_1.json", Dataset.class); + + final Result p2d1 = MergeUtils.checkedMerge(p2, d1); + assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid()); + assertTrue(p2d1 instanceof Dataset); + assertEquals(d1.getId(), p2d1.getId()); + assertEquals(2, p2d1.getCollectedfrom().size()); + } + + @Test + void testMergePubs_2() throws IOException { + Publication p1 = read("publication_1.json", Publication.class); + Publication p2 = read("publication_2.json", Publication.class); + + Result p1p2 = MergeUtils.checkedMerge(p1, p2); + assertTrue(p1p2 instanceof Publication); + assertEquals(p1.getId(), p1p2.getId()); + assertEquals(2, p1p2.getCollectedfrom().size()); + } + + @Test + void testDelegatedAuthority_1() throws IOException { + Dataset d1 = read("dataset_2.json", Dataset.class); + Dataset d2 = read("dataset_delegated.json", Dataset.class); + + assertEquals(1, d2.getCollectedfrom().size()); + assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); + + Result res = (Result) MergeUtils.merge(d1, d2, true); + + assertEquals(d2, res); + } + + @Test + void testDelegatedAuthority_2() throws IOException { + Dataset p1 = read("publication_1.json", Dataset.class); + Dataset d2 = read("dataset_delegated.json", Dataset.class); + + assertEquals(1, d2.getCollectedfrom().size()); + assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); + + Result res = (Result) MergeUtils.merge(p1, d2, true); + + assertEquals(d2, res); + } + + protected HashSet cfId(List collectedfrom) { + return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); + } + + protected T read(String filename, Class clazz) throws IOException { + final String json = IOUtils.toString(getClass().getResourceAsStream(filename)); + return OBJECT_MAPPER.readValue(json, clazz); + } + +} 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 9111ac2df4..2bbc3bc3ea 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 @@ -149,7 +149,7 @@ class OafMapperUtilsTest { void testDate() { final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998"); assertNotNull(date); - System.out.println(date); + assertEquals("1998-02-23", date); } @Test @@ -166,8 +166,8 @@ class OafMapperUtilsTest { assertEquals( ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, - OafMapperUtils - .mergeResults(p1, d2) + MergeUtils + .mergeResult(p1, d2) .getResulttype() .getClassid()); @@ -178,8 +178,8 @@ class OafMapperUtilsTest { assertEquals( ModelConstants.DATASET_RESULTTYPE_CLASSID, - OafMapperUtils - .mergeResults(p2, d1) + MergeUtils + .mergeResult(p2, d1) .getResulttype() .getClassid()); } @@ -192,7 +192,7 @@ class OafMapperUtilsTest { assertEquals(1, d2.getCollectedfrom().size()); assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); - Result res = OafMapperUtils.mergeResults(d1, d2); + Result res = MergeUtils.mergeResult(d1, d2); assertEquals(d2, res); diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java index 34ebcf7a7d..42459ef00e 100644 --- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java @@ -23,15 +23,18 @@ public class InstanceTypeMatch extends AbstractListComparator { // jolly types translationMap.put("Conference object", "*"); + translationMap.put("Research", "*"); translationMap.put("Other literature type", "*"); translationMap.put("Unknown", "*"); translationMap.put("UNKNOWN", "*"); // article types translationMap.put("Article", "Article"); + translationMap.put("Journal", "Article"); translationMap.put("Data Paper", "Article"); translationMap.put("Software Paper", "Article"); translationMap.put("Preprint", "Article"); + translationMap.put("Part of book or chapter of book", "Article"); // thesis types translationMap.put("Thesis", "Thesis"); diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java index eccfa445cc..6de6311739 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java @@ -1,14 +1,13 @@ package eu.dnetlib.dhp.actionmanager.promote; -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import java.util.function.BiFunction; -import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Relation; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; /** OAF model merging support. */ public class MergeAndGet { @@ -46,20 +45,7 @@ public class MergeAndGet { } private static G mergeFromAndGet(G x, A y) { - if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { - ((Relation) x).mergeFrom((Relation) y); - return x; - } else if (isSubClass(x, OafEntity.class) - && isSubClass(y, OafEntity.class) - && isSubClass(x, y)) { - ((OafEntity) x).mergeFrom((OafEntity) y); - return x; - } - throw new RuntimeException( - String - .format( - "MERGE_FROM_AND_GET incompatible types: %s, %s", - x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + return (G) MergeUtils.merge(x, y); } @SuppressWarnings("unchecked") diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteAction.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteAction.java new file mode 100644 index 0000000000..8fb9c8c953 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteAction.java @@ -0,0 +1,39 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.actionmanager.promote; + +/** Encodes the Actionset promotion strategies */ +public class PromoteAction { + + /** The supported actionset promotion strategies + * + * ENRICH: promotes only records in the actionset matching another record in the + * graph and enriches them applying the given MergeAndGet strategy + * UPSERT: promotes all the records in an actionset, matching records are updated + * using the given MergeAndGet strategy, the non-matching record as inserted as they are. + */ + public enum Strategy { + ENRICH, UPSERT + } + + /** + * Returns the string representation of the join type implementing the given PromoteAction. + * + * @param strategy the strategy to be used to promote the Actionset contents + * @return the join type used to implement the promotion strategy + */ + public static String joinTypeForStrategy(PromoteAction.Strategy strategy) { + switch (strategy) { + case ENRICH: + return "left_outer"; + case UPSERT: + return "full_outer"; + default: + throw new IllegalStateException("unsupported PromoteAction: " + strategy.toString()); + } + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java index 7b024bea8b..56cbda4d67 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java @@ -67,8 +67,9 @@ public class PromoteActionPayloadForGraphTableJob { String outputGraphTablePath = parser.get("outputGraphTablePath"); logger.info("outputGraphTablePath: {}", outputGraphTablePath); - MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); - logger.info("strategy: {}", strategy); + MergeAndGet.Strategy mergeAndGetStrategy = MergeAndGet.Strategy + .valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); + logger.info("mergeAndGetStrategy: {}", mergeAndGetStrategy); Boolean shouldGroupById = Optional .ofNullable(parser.get("shouldGroupById")) @@ -76,6 +77,12 @@ public class PromoteActionPayloadForGraphTableJob { .orElse(true); logger.info("shouldGroupById: {}", shouldGroupById); + PromoteAction.Strategy promoteActionStrategy = Optional + .ofNullable(parser.get("promoteActionStrategy")) + .map(PromoteAction.Strategy::valueOf) + .orElse(PromoteAction.Strategy.UPSERT); + logger.info("promoteActionStrategy: {}", promoteActionStrategy); + @SuppressWarnings("unchecked") Class rowClazz = (Class) Class.forName(graphTableClassName); @SuppressWarnings("unchecked") @@ -97,7 +104,8 @@ public class PromoteActionPayloadForGraphTableJob { inputGraphTablePath, inputActionPayloadPath, outputGraphTablePath, - strategy, + mergeAndGetStrategy, + promoteActionStrategy, rowClazz, actionPayloadClazz, shouldGroupById); @@ -124,14 +132,16 @@ public class PromoteActionPayloadForGraphTableJob { String inputGraphTablePath, String inputActionPayloadPath, String outputGraphTablePath, - MergeAndGet.Strategy strategy, + MergeAndGet.Strategy mergeAndGetStrategy, + PromoteAction.Strategy promoteActionStrategy, Class rowClazz, Class actionPayloadClazz, Boolean shouldGroupById) { Dataset rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz); Dataset actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); Dataset result = promoteActionPayloadForGraphTable( - rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz, shouldGroupById) + rowDS, actionPayloadDS, mergeAndGetStrategy, promoteActionStrategy, rowClazz, actionPayloadClazz, + shouldGroupById) .map((MapFunction) value -> value, Encoders.bean(rowClazz)); saveGraphTable(result, outputGraphTablePath); @@ -183,7 +193,8 @@ public class PromoteActionPayloadForGraphTableJob { private static Dataset promoteActionPayloadForGraphTable( Dataset rowDS, Dataset actionPayloadDS, - MergeAndGet.Strategy strategy, + MergeAndGet.Strategy mergeAndGetStrategy, + PromoteAction.Strategy promoteActionStrategy, Class rowClazz, Class actionPayloadClazz, Boolean shouldGroupById) { @@ -195,8 +206,9 @@ public class PromoteActionPayloadForGraphTableJob { SerializableSupplier> rowIdFn = ModelSupport::idFn; SerializableSupplier> actionPayloadIdFn = ModelSupport::idFn; - SerializableSupplier> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy); - SerializableSupplier> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier> mergeRowWithActionPayloadAndGetFn = MergeAndGet + .functionFor(mergeAndGetStrategy); + SerializableSupplier> mergeRowsAndGetFn = MergeAndGet.functionFor(mergeAndGetStrategy); SerializableSupplier zeroFn = zeroFn(rowClazz); SerializableSupplier> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSourceAndTarget; @@ -207,6 +219,7 @@ public class PromoteActionPayloadForGraphTableJob { rowIdFn, actionPayloadIdFn, mergeRowWithActionPayloadAndGetFn, + promoteActionStrategy, rowClazz, actionPayloadClazz); diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java index d799c646bc..f0b094240e 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java @@ -34,6 +34,7 @@ public class PromoteActionPayloadFunctions { * @param rowIdFn Function used to get the id of graph table row * @param actionPayloadIdFn Function used to get id of action payload instance * @param mergeAndGetFn Function used to merge graph table row and action payload instance + * @param promoteActionStrategy the Actionset promotion strategy * @param rowClazz Class of graph table * @param actionPayloadClazz Class of action payload * @param Type of graph table row @@ -46,6 +47,7 @@ public class PromoteActionPayloadFunctions { SerializableSupplier> rowIdFn, SerializableSupplier> actionPayloadIdFn, SerializableSupplier> mergeAndGetFn, + PromoteAction.Strategy promoteActionStrategy, Class rowClazz, Class actionPayloadClazz) { if (!isSubClass(rowClazz, actionPayloadClazz)) { @@ -61,7 +63,7 @@ public class PromoteActionPayloadFunctions { .joinWith( actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), - "full_outer") + PromoteAction.joinTypeForStrategy(promoteActionStrategy)) .map( (MapFunction, Tuple2>, G>) value -> { Optional rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2); diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json index 00c9404ef0..81a7c77d7b 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json @@ -41,6 +41,12 @@ "paramDescription": "strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET", "paramRequired": true }, + { + "paramName": "pas", + "paramLongName": "promoteActionStrategy", + "paramDescription": "strategy for promoting the actionset contents into the graph tables, ENRICH or UPSERT (default)", + "paramRequired": false + }, { "paramName": "sgid", "paramLongName": "shouldGroupById", diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml index 4f374a75a0..5401b45cac 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml @@ -115,6 +115,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Dataset --outputGraphTablePath${workingDir}/dataset --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} @@ -167,6 +168,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result --outputGraphTablePath${outputGraphRootPath}/dataset --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml index c85ba4ac1c..f9bd66ae3a 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml @@ -106,6 +106,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Datasource --outputGraphTablePath${outputGraphRootPath}/datasource --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml index 412cad70bc..ebfdeee312 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml @@ -106,6 +106,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Organization --outputGraphTablePath${outputGraphRootPath}/organization --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml index 7bac760e2c..02399ed9b9 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml @@ -114,6 +114,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputGraphTablePath${workingDir}/otherresearchproduct --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} @@ -166,6 +167,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result --outputGraphTablePath${outputGraphRootPath}/otherresearchproduct --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml index daf48e9d78..57c2357b4a 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml @@ -106,6 +106,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Project --outputGraphTablePath${outputGraphRootPath}/project --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml index b76dc82f14..92b114776a 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml @@ -115,6 +115,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Publication --outputGraphTablePath${workingDir}/publication --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} @@ -167,6 +168,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result --outputGraphTablePath${outputGraphRootPath}/publication --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml index d3086dbdc0..e9e5f0b454 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml @@ -107,6 +107,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Relation --outputGraphTablePath${outputGraphRootPath}/relation --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml index b5673b18f4..1d36ddf94b 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml @@ -114,6 +114,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Software --outputGraphTablePath${workingDir}/software --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} @@ -166,6 +167,7 @@ --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result --outputGraphTablePath${outputGraphRootPath}/software --mergeAndGetStrategy${mergeAndGetStrategy} + --promoteActionStrategy${promoteActionStrategy} --shouldGroupById${shouldGroupById} diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java index cbc1bfaba7..777e2fa1ce 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java @@ -54,7 +54,7 @@ public class PromoteActionPayloadFunctionsTest { RuntimeException.class, () -> PromoteActionPayloadFunctions .joinGraphTableWithActionPayloadAndMerge( - null, null, null, null, null, OafImplSubSub.class, OafImpl.class)); + null, null, null, null, null, null, OafImplSubSub.class, OafImpl.class)); } @Test @@ -104,6 +104,7 @@ public class PromoteActionPayloadFunctionsTest { rowIdFn, actionPayloadIdFn, mergeAndGetFn, + PromoteAction.Strategy.UPSERT, OafImplSubSub.class, OafImplSubSub.class) .collectAsList(); @@ -183,6 +184,7 @@ public class PromoteActionPayloadFunctionsTest { rowIdFn, actionPayloadIdFn, mergeAndGetFn, + PromoteAction.Strategy.UPSERT, OafImplSubSub.class, OafImplSub.class) .collectAsList(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 1bdb06ecc0..f9a5c539f5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -64,6 +64,9 @@ public class PrepareAffiliationRelations implements Serializable { final String pubmedInputPath = parser.get("pubmedInputPath"); log.info("pubmedInputPath: {}", pubmedInputPath); + final String openapcInputPath = parser.get("openapcInputPath"); + log.info("openapcInputPath: {}", openapcInputPath); + final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); @@ -85,8 +88,14 @@ public class PrepareAffiliationRelations implements Serializable { JavaPairRDD pubmedRelations = prepareAffiliationRelations( spark, pubmedInputPath, collectedFromPubmed); + List collectedFromOpenAPC = OafMapperUtils + .listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC"); + JavaPairRDD openAPCRelations = prepareAffiliationRelations( + spark, openapcInputPath, collectedFromOpenAPC); + crossrefRelations .union(pubmedRelations) + .union(openAPCRelations) .saveAsHadoopFile( outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c897829..76c8ec7fae 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + //project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java index 680e12504f..a415405647 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java @@ -34,6 +34,11 @@ public class BipProjectModel { String totalCitationCount; + public String getProjectId() { + return projectId; + } + + // each project bip measure has exactly one value, hence one key-value pair private Measure createMeasure(String measureId, String measureValue) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index a32d04e1f2..21f3044a5a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -1,12 +1,20 @@ package eu.dnetlib.dhp.actionmanager.project; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Arrays; -import java.util.Objects; -import java.util.Optional; - +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject; +import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.H2020Classification; +import eu.dnetlib.dhp.schema.oaf.H2020Programme; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -18,24 +26,14 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme; -import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject; -import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic; -import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.H2020Classification; -import eu.dnetlib.dhp.schema.oaf.H2020Programme; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; +import java.util.Arrays; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + /** * Class that makes the ActionSet. To prepare the AS two joins are needed * @@ -160,9 +158,11 @@ public class SparkAtomicActionJob { (MapFunction) OafEntity::getId, Encoders.STRING()) .mapGroups((MapGroupsFunction) (s, it) -> { - Project first = it.next(); - it.forEachRemaining(first::mergeFrom); - return first; + Project merge = it.next(); + while (it.hasNext()) { + merge = MergeUtils.mergeProject(merge, it.next()); + } + return merge; }, Encoders.bean(Project.class)) .toJavaRDD() .map(p -> new AtomicAction(Project.class, p)) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java new file mode 100644 index 0000000000..e1c3226cd6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java @@ -0,0 +1,195 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.IOUtils; +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.api.java.JavaRDD; +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.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Country; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.*; +import scala.Tuple2; + +public class CreateActionSetSparkJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63"; + private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement"; + + public static void main(final String[] args) throws IOException, ParseException { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + CreateActionSetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json")))); + + 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("inputPath"); + log.info("inputPath {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> createActionSet(spark, inputPath, outputPath)); + + } + + private static void createActionSet(SparkSession spark, String inputPath, String outputPath) { + JavaRDD relations = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, TransformativeAgreementModel.class), + Encoders.bean(TransformativeAgreementModel.class)) + .flatMap( + (FlatMapFunction) value -> createRelation( + value) + .iterator(), + Encoders.bean(Relation.class)) + .filter((FilterFunction) Objects::nonNull) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)); +//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file + spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, TransformativeAgreementModel.class), + Encoders.bean(TransformativeAgreementModel.class)) + .map( + (MapFunction) value -> createResult( + value), + Encoders.bean(Result.class)) + .filter((FilterFunction) r -> r != null) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile( + outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + } + + private static Result createResult(TransformativeAgreementModel value) { + Result r = new Result(); + r + .setId( + "50|doi_________::" + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()))); + r.setTransformativeAgreement(value.getAgreement()); + Country country = new Country(); + country.setClassid(value.getCountry()); + country.setClassname(value.getCountry()); + country + .setDataInfo( + OafMapperUtils + .dataInfo( + false, ModelConstants.SYSIMPORT_ACTIONSET, false, false, + OafMapperUtils + .qualifier( + "openapc::transformativeagreement", + "Harvested from Trnasformative Agreement file from OpenAPC", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9")); + country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE); + country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE); + r.setCountry(Arrays.asList(country)); + return r; + } + + private static List createRelation(TransformativeAgreementModel value) { + + List relationList = new ArrayList<>(); + + if (value.getAgreement().startsWith("IReL")) { + String paper; + + paper = "50|doi_________::" + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())); + + relationList + .add( + getRelation( + paper, + IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); + + relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES)); + } + return relationList; + } + + public static Relation getRelation( + String source, + String target, + String relClass) { + + return OafMapperUtils + .getRelation( + source, + target, + ModelConstants.RESULT_PROJECT, + ModelConstants.OUTCOME, + relClass, + Arrays + .asList( + OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + TRANSFORMATIVE_AGREEMENT, "Transformative Agreement", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java new file mode 100644 index 0000000000..3a53fec0a4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java @@ -0,0 +1,51 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement.model; + +import java.io.Serializable; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +/** + * @author miriam.baglioni + * @Date 18/12/23 + */ +@JsonIgnoreProperties(ignoreUnknown = true) + +public class TransformativeAgreementModel implements Serializable { + private String institution; + private String doi; + private String agreement; + private String country; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getInstitution() { + return institution; + } + + public void setInstitution(String institution) { + this.institution = institution; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getAgreement() { + return agreement; + } + + public void setAgreement(String agreement) { + this.agreement = agreement; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index c35fbb497f..98caa17416 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.aggregation.common.ReporterCallback; import eu.dnetlib.dhp.aggregation.common.ReportingJob; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin; @@ -120,6 +121,8 @@ public class CollectorWorker extends ReportingJob { return new FileCollectorPlugin(fileSystem); case fileGzip: return new FileGZipCollectorPlugin(fileSystem); + case baseDump: + return new BaseCollectorPlugin(this.fileSystem); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(api.getParams().get("other_plugin_type")) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java new file mode 100644 index 0000000000..2767a3e41d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -0,0 +1,244 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.IOException; +import java.io.InputStream; +import java.net.HttpURLConnection; +import java.net.URL; +import java.util.concurrent.BlockingQueue; + +import javax.swing.*; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.http.HttpHeaders; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.common.collection.HttpClientParams; + +public class ORCIDWorker extends Thread { + + final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class); + + public static String JOB_COMPLETE = "JOB_COMPLETE"; + + private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; + + private final BlockingQueue queue; + + private boolean hasComplete = false; + + private final SequenceFile.Writer employments; + + private final SequenceFile.Writer summary; + private final SequenceFile.Writer works; + + private final String token; + + private final String id; + + public static ORCIDWorkerBuilder builder() { + return new ORCIDWorkerBuilder(); + } + + public ORCIDWorker(String id, BlockingQueue myqueue, SequenceFile.Writer employments, + SequenceFile.Writer summary, SequenceFile.Writer works, String token) { + this.id = id; + this.queue = myqueue; + this.employments = employments; + this.summary = summary; + this.works = works; + this.token = token; + } + + public static String retrieveURL(final String id, final String apiUrl, String token) { + try { + final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token); + if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) { + InputStream input = urlConn.getInputStream(); + return IOUtils.toString(input); + } else { + log + .error( + "Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}", id, apiUrl, + urlConn.getResponseCode()); + } + } catch (Exception e) { + log.error("Thread {} Error on retrieving URL {} {}", id, apiUrl, e); + } + return null; + } + + @NotNull + private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection(); + final HttpClientParams clientParams = new HttpClientParams(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); + urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); + urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent); + urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token)); + return urlConn; + } + + private static String generateSummaryURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/record"; + } + + private static String generateWorksURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/works"; + } + + private static String generateEmploymentsURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/employments"; + } + + private static void writeResultToSequenceFile(String id, String url, String token, String orcidId, + SequenceFile.Writer file) throws IOException { + final String response = retrieveURL(id, url, token); + if (response != null) { + if (orcidId == null) { + log.error("Thread {} {} {}", id, orcidId, response); + throw new RuntimeException("null items "); + } + + if (file == null) { + log.error("Thread {} file is null for {} URL:{}", id, url, orcidId); + } else { + file.append(new Text(orcidId), new Text(response)); + file.hflush(); + } + + } else + log.error("Thread {} response is null for {} URL:{}", id, url, orcidId); + + } + + @Override + public void run() { + final Text key = new Text(); + final Text value = new Text(); + long start; + long total_time; + String orcidId = ""; + int requests = 0; + if (summary == null || employments == null || works == null) + throw new RuntimeException("Null files"); + + while (!hasComplete) { + try { + + orcidId = queue.take(); + + if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) { + hasComplete = true; + } else { + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateSummaryURL(orcidId), token, orcidId, summary); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateWorksURL(orcidId), token, orcidId, works); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateEmploymentsURL(orcidId), token, orcidId, employments); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + if (requests % 30 == 0) { + log.info("Thread {} Downloaded {}", id, requests); + } + } + + } catch (Throwable e) { + + log.error("Thread {} Unable to save ORICD: {} item error", id, orcidId, e); + + } + + } + try { + works.close(); + summary.close(); + employments.close(); + } catch (Throwable e) { + throw new RuntimeException(e); + } + + log.info("Thread {} COMPLETE ", id); + log.info("Thread {} Downloaded {}", id, requests); + + } + + public static class ORCIDWorkerBuilder { + + private String id; + private SequenceFile.Writer employments; + private SequenceFile.Writer summary; + private SequenceFile.Writer works; + private BlockingQueue queue; + + private String token; + + public ORCIDWorkerBuilder withId(final String id) { + this.id = id; + return this; + } + + public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) { + this.employments = sequenceFile; + return this; + } + + public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) { + this.summary = sequenceFile; + return this; + } + + public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) { + this.works = sequenceFile; + return this; + } + + public ORCIDWorkerBuilder withAccessToken(final String accessToken) { + this.token = accessToken; + return this; + } + + public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue queue) { + this.queue = queue; + return this; + } + + public ORCIDWorker build() { + if (this.summary == null || this.works == null || this.employments == null || StringUtils.isEmpty(token) + || queue == null) + throw new RuntimeException("Unable to build missing required params"); + return new ORCIDWorker(id, queue, employments, summary, works, token); + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java new file mode 100644 index 0000000000..d9afd0796f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -0,0 +1,171 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.*; +import java.net.HttpURLConnection; +import java.net.URL; +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.ArrayBlockingQueue; +import java.util.concurrent.BlockingQueue; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.collection.HttpClientParams; + +public class OrcidGetUpdatesFile { + + private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class); + + public static void main(String[] args) throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + OrcidGetUpdatesFile.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json"))) + + ); + parser.parseArgument(args); + + final String namenode = parser.get("namenode"); + log.info("got variable namenode: {}", namenode); + + final String master = parser.get("master"); + log.info("got variable master: {}", master); + + final String targetPath = parser.get("targetPath"); + log.info("got variable targetPath: {}", targetPath); + + final String apiURL = parser.get("apiURL"); + log.info("got variable apiURL: {}", apiURL); + + final String accessToken = parser.get("accessToken"); + log.info("got variable accessToken: {}", accessToken); + + final String graphPath = parser.get("graphPath"); + log.info("got variable graphPath: {}", graphPath); + + final SparkSession spark = SparkSession + .builder() + .appName(OrcidGetUpdatesFile.class.getName()) + .master(master) + .getOrCreate(); + + final String latestDate = spark + .read() + .load(graphPath + "/Authors") + .selectExpr("max(lastModifiedDate)") + .first() + .getString(0); + + log.info("latest date is {}", latestDate); + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode)); + + new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, latestDate); + + } + + private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException { + return SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(aPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + } + + private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue queue, + final String accessToken, FileSystem fileSystem) throws Exception { + return ORCIDWorker + .builder() + .withId(id) + .withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem)) + .withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem)) + .withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem)) + .withAccessToken(accessToken) + .withBlockingQueue(queue) + .build(); + } + + public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath, + final String startDate) throws Exception { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection(); + final HttpClientParams clientParams = new HttpClientParams(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); + urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); + if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) { + InputStream input = urlConn.getInputStream(); + + Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz"); + final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); + IOUtils.copy(input, fsDataOutputStream); + fsDataOutputStream.flush(); + fsDataOutputStream.close(); + FSDataInputStream updateFile = fileSystem.open(hdfsWritePath); + TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream( + new BufferedInputStream( + updateFile.getWrappedStream()))); + TarArchiveEntry entry; + + BlockingQueue queue = new ArrayBlockingQueue(3000); + final List workers = new ArrayList<>(); + for (int i = 0; i < 22; i++) { + workers.add(createWorker("" + i, targetPath, queue, accessToken, fileSystem)); + } + workers.forEach(Thread::start); + + while ((entry = tais.getNextTarEntry()) != null) { + + if (entry.isFile()) { + + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + System.out.println(br.readLine()); + br + .lines() + .map(l -> l.split(",")) + .filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0) + .map(s -> s[0]) + .forEach(s -> { + try { + queue.put(s); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + }); + + } + } + + for (int i = 0; i < 22; i++) { + queue.put(ORCIDWorker.JOB_COMPLETE); + } + for (ORCIDWorker worker : workers) { + worker.join(); + } + } + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java index 159b8a5fca..ea108821ef 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java @@ -1,11 +1,15 @@ package eu.dnetlib.dhp.collection.orcid; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.DocumentFactory; +import org.dom4j.DocumentHelper; +import org.dom4j.Node; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -40,8 +44,8 @@ public class OrcidParser { private static final String NS_ERROR = "error"; private static final String NS_HISTORY = "history"; private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; - private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk"; - private static final String NS_BULK = "bulk"; + private static final String NS_EMPLOYMENT = "employment"; + private static final String NS_EMPLOYMENT_URL = "http://www.orcid.org/ns/employment"; private static final String NS_EXTERNAL = "external-identifier"; private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier"; @@ -61,6 +65,7 @@ public class OrcidParser { ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL); ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL); + ap.declareXPathNameSpace(NS_EMPLOYMENT, NS_EMPLOYMENT_URL); } public Author parseSummary(final String xml) { @@ -70,13 +75,15 @@ public class OrcidParser { generateParsedDocument(xml); List recordNodes = VtdUtilityParser .getTextValuesWithAttributes( - ap, vn, "//record:record", Arrays.asList("path")); + ap, vn, "//record:record", Collections.singletonList("path")); if (!recordNodes.isEmpty()) { final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); author.setOrcid(oid); } else { return null; } + final String ltm = VtdUtilityParser.getSingleValue(ap, vn, "//common:last-modified-date"); + author.setLastModifiedDate(ltm); List personNodes = VtdUtilityParser .getTextValuesWithAttributes( ap, vn, "//person:name", Arrays.asList("visibility")); @@ -129,6 +136,64 @@ public class OrcidParser { } } + public List parseWorks(final String xml) { + + try { + String oid; + + generateParsedDocument(xml); + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//activities:works", Arrays.asList("path", "visibility")); + if (!workNodes.isEmpty()) { + oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + + } else { + return null; + } + final List works = new ArrayList<>(); + ap.selectXPath("//work:work-summary"); + + while (ap.evalXPath() != -1) { + final Work work = new Work(); + work.setOrcid(oid); + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + ap1.selectXPath("./work:title/common:title"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + work.setTitle(vn.toNormalizedString(it)); + } + ap1.selectXPath(".//common:external-id"); + while (ap1.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap2 = new AutoPilot(ap1.getNav()); + + ap2.selectXPath("./common:external-id-type"); + while (ap2.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap2.selectXPath("./common:external-id-value"); + while (ap2.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + work.addPid(pid); + } + + works.add(work); + } + return works; + + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + public Work parseWork(final String xml) { try { @@ -176,11 +241,15 @@ public class OrcidParser { } private String extractEmploymentDate(final String xpath) throws Exception { + return extractEmploymentDate(xpath, ap); + } - ap.selectXPath(xpath); + private String extractEmploymentDate(final String xpath, AutoPilot pp) throws Exception { + + pp.selectXPath(xpath); StringBuilder sb = new StringBuilder(); - while (ap.evalXPath() != -1) { - final AutoPilot ap1 = new AutoPilot(ap.getNav()); + while (pp.evalXPath() != -1) { + final AutoPilot ap1 = new AutoPilot(pp.getNav()); ap1.selectXPath("./common:year"); while (ap1.evalXPath() != -1) { int it = vn.getText(); @@ -203,6 +272,104 @@ public class OrcidParser { } + public List parseEmployments(final String xml) { + try { + String oid; + Map nsContext = getNameSpaceMap(); + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + Document doc = DocumentHelper.parseText(xml); + oid = doc.valueOf("//activities:employments/@path"); + if (oid == null || StringUtils.isEmpty(oid)) + return null; + final String orcid = oid.split("/")[1]; + + List nodes = doc.selectNodes("//employment:employment-summary"); + return nodes.stream().map(n -> { + final Employment e = new Employment(); + e.setOrcid(orcid); + + final String depName = n.valueOf(".//common:department-name"); + if (StringUtils.isNotBlank(depName)) + e.setDepartmentName(depName); + final String roleTitle = n.valueOf(".//common:role-title"); + e.setRoleTitle(roleTitle); + final String organizationName = n.valueOf(".//common:organization/common:name"); + if (StringUtils.isEmpty(e.getDepartmentName())) + e.setDepartmentName(organizationName); + final Pid p = new Pid(); + final String pid = n + .valueOf( + "./common:organization/common:disambiguated-organization/common:disambiguated-organization-identifier"); + p.setValue(pid); + final String pidType = n + .valueOf("./common:organization/common:disambiguated-organization/common:disambiguation-source"); + p.setSchema(pidType); + e.setAffiliationId(p); + + final StringBuilder aDate = new StringBuilder(); + final String sy = n.valueOf("./common:start-date/common:year"); + if (StringUtils.isNotBlank(sy)) { + aDate.append(sy); + final String sm = n.valueOf("./common:start-date/common:month"); + final String sd = n.valueOf("./common:start-date/common:day"); + aDate.append("-"); + if (StringUtils.isNotBlank(sm)) + aDate.append(sm); + else + aDate.append("01"); + aDate.append("-"); + if (StringUtils.isNotBlank(sd)) + aDate.append(sd); + else + aDate.append("01"); + e.setEndDate(aDate.toString()); + } + + final String ey = n.valueOf("./common:end-date/common:year"); + if (StringUtils.isNotBlank(ey)) { + aDate.append(ey); + final String em = n.valueOf("./common:end-date/common:month"); + final String ed = n.valueOf("./common:end-date/common:day"); + aDate.append("-"); + if (StringUtils.isNotBlank(em)) + aDate.append(em); + else + aDate.append("01"); + aDate.append("-"); + if (StringUtils.isNotBlank(ed)) + aDate.append(ed); + else + aDate.append("01"); + e.setEndDate(aDate.toString()); + } + + return e; + + }).collect(Collectors.toList()); + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + } + + @NotNull + private static Map getNameSpaceMap() { + Map nsContext = new HashMap<>(); + nsContext.put(NS_COMMON, NS_COMMON_URL); + nsContext.put(NS_PERSON, NS_PERSON_URL); + nsContext.put(NS_DETAILS, NS_DETAILS_URL); + nsContext.put(NS_OTHER, NS_OTHER_URL); + nsContext.put(NS_RECORD, NS_RECORD_URL); + nsContext.put(NS_ERROR, NS_ERROR_URL); + nsContext.put(NS_HISTORY, NS_HISTORY_URL); + nsContext.put(NS_WORK, NS_WORK_URL); + nsContext.put(NS_EXTERNAL, NS_EXTERNAL_URL); + nsContext.put(NS_ACTIVITIES, NS_ACTIVITIES_URL); + nsContext.put(NS_EMPLOYMENT, NS_EMPLOYMENT_URL); + return nsContext; + } + public Employment parseEmployment(final String xml) { try { final Employment employment = new Employment(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java index 32c321b41c..df87e43331 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java @@ -18,6 +18,8 @@ public class Author extends ORCIDItem { private String biography; + private String lastModifiedDate; + public String getBiography() { return biography; } @@ -74,6 +76,14 @@ public class Author extends ORCIDItem { this.otherPids = otherPids; } + public String getLastModifiedDate() { + return lastModifiedDate; + } + + public void setLastModifiedDate(String lastModifiedDate) { + this.lastModifiedDate = lastModifiedDate; + } + public void addOtherPid(final Pid pid) { if (otherPids == null) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index a19ca5c685..97d2d25854 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,8 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, file, fileGzip; + + oai, other, rest_json2xml, file, fileGzip, baseDump; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIterator.java new file mode 100644 index 0000000000..c41cc8f0f6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIterator.java @@ -0,0 +1,171 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import java.io.BufferedInputStream; +import java.io.ByteArrayInputStream; +import java.io.InputStream; +import java.io.StringWriter; +import java.util.Iterator; +import java.util.concurrent.BlockingQueue; +import java.util.concurrent.LinkedBlockingQueue; + +import javax.xml.stream.XMLEventReader; +import javax.xml.stream.XMLEventWriter; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLOutputFactory; +import javax.xml.stream.events.EndElement; +import javax.xml.stream.events.StartElement; +import javax.xml.stream.events.XMLEvent; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.CompressorInputStream; +import org.apache.commons.compress.compressors.CompressorStreamFactory; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; + +public class BaseCollectorIterator implements Iterator { + + private String nextElement; + + private final BlockingQueue queue = new LinkedBlockingQueue<>(100); + + private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class); + + private static final String END_ELEM = "__END__"; + + public BaseCollectorIterator(final FileSystem fs, final Path filePath, final AggregatorReport report) { + new Thread(() -> importHadoopFile(fs, filePath, report)).start(); + try { + this.nextElement = this.queue.take(); + } catch (final InterruptedException e) { + throw new RuntimeException(e); + } + } + + protected BaseCollectorIterator(final String resourcePath, final AggregatorReport report) { + new Thread(() -> importTestFile(resourcePath, report)).start(); + try { + this.nextElement = this.queue.take(); + } catch (final InterruptedException e) { + throw new RuntimeException(e); + } + } + + @Override + public synchronized boolean hasNext() { + return (this.nextElement != null) & !END_ELEM.equals(this.nextElement); + } + + @Override + public synchronized String next() { + try { + return END_ELEM.equals(this.nextElement) ? null : this.nextElement; + } finally { + try { + this.nextElement = this.queue.take(); + } catch (final InterruptedException e) { + throw new RuntimeException(e); + } + } + + } + + private void importHadoopFile(final FileSystem fs, final Path filePath, final AggregatorReport report) { + log.info("I start to read the TAR stream"); + + try (InputStream origInputStream = fs.open(filePath); + final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) { + importTarStream(tarInputStream, report); + } catch (final Throwable e) { + throw new RuntimeException("Error processing BASE records", e); + } + } + + private void importTestFile(final String resourcePath, final AggregatorReport report) { + try (final InputStream origInputStream = BaseCollectorIterator.class.getResourceAsStream(resourcePath); + final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) { + importTarStream(tarInputStream, report); + } catch (final Throwable e) { + throw new RuntimeException("Error processing BASE records", e); + } + } + + private void importTarStream(final TarArchiveInputStream tarInputStream, final AggregatorReport report) { + long count = 0; + + final XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance(); + final XMLOutputFactory xmlOutputFactory = XMLOutputFactory.newInstance(); + + try { + TarArchiveEntry entry; + while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) { + final String name = entry.getName(); + + if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) { + + log.info("Processing file (BZIP): " + name); + + final byte[] bzipData = new byte[(int) entry.getSize()]; + IOUtils.readFully(tarInputStream, bzipData); + + try (InputStream bzipIs = new ByteArrayInputStream(bzipData); + final BufferedInputStream bzipBis = new BufferedInputStream(bzipIs); + final CompressorInputStream bzipInput = new CompressorStreamFactory() + .createCompressorInputStream(bzipBis)) { + + final XMLEventReader reader = xmlInputFactory.createXMLEventReader(bzipInput); + + XMLEventWriter eventWriter = null; + StringWriter xmlWriter = null; + + while (reader.hasNext()) { + final XMLEvent nextEvent = reader.nextEvent(); + + if (nextEvent.isStartElement()) { + final StartElement startElement = nextEvent.asStartElement(); + if ("record".equals(startElement.getName().getLocalPart())) { + xmlWriter = new StringWriter(); + eventWriter = xmlOutputFactory.createXMLEventWriter(xmlWriter); + } + } + + if (eventWriter != null) { + eventWriter.add(nextEvent); + } + + if (nextEvent.isEndElement()) { + final EndElement endElement = nextEvent.asEndElement(); + if ("record".equals(endElement.getName().getLocalPart())) { + eventWriter.flush(); + eventWriter.close(); + + this.queue.put(xmlWriter.toString()); + + eventWriter = null; + xmlWriter = null; + count++; + } + } + + } + } + } + } + + this.queue.put(END_ELEM); // TO INDICATE THE END OF THE QUEUE + } catch (final Throwable e) { + log.error("Error processing BASE records", e); + report.put(e.getClass().getName(), e.getMessage()); + throw new RuntimeException("Error processing BASE records", e); + } finally { + log.info("Total records (written in queue): " + count); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java new file mode 100644 index 0000000000..42341b4064 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java @@ -0,0 +1,159 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import java.io.IOException; +import java.sql.SQLException; +import java.util.HashSet; +import java.util.Iterator; +import java.util.Optional; +import java.util.Set; +import java.util.Spliterator; +import java.util.Spliterators; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.DocumentHelper; +import org.dom4j.Node; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.AbstractSplittedRecordPlugin; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class BaseCollectorPlugin implements CollectorPlugin { + + private final FileSystem fs; + + private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class); + + // MAPPING AND FILTERING ARE DEFINED HERE: + // https://docs.google.com/document/d/1Aj-ZAV11b44MCrAAUCPiS2TUlXb6PnJEu1utCMAcCOU/edit + + public BaseCollectorPlugin(final FileSystem fs) { + this.fs = fs; + } + + @Override + public Stream collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException { + // the path of the dump file on HDFS + // http://oai.base-search.net/initial_load/base_oaipmh_dump-current.tar + // it could be downloaded from iis-cdh5-test-gw.ocean.icm.edu.pl and then copied on HDFS + final Path filePath = Optional + .ofNullable(api.getBaseUrl()) + .map(Path::new) + .orElseThrow(() -> new CollectorException("missing baseUrl")); + + // get the parameters for the connection to the OpenAIRE database. + // the database is used to obtain the list of the datasources that the plugin will collect + final String dbUrl = api.getParams().get("dbUrl"); + final String dbUser = api.getParams().get("dbUser"); + final String dbPassword = api.getParams().get("dbPassword"); + + // the types(comma separated, empty value for all) that the plugin will collect, + // the types should be expressed in the format of the normalized types of BASE (for example 1,121,...) + final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes"); + + log.info("baseUrl: {}", filePath); + log.info("dbUrl: {}", dbUrl); + log.info("dbUser: {}", dbUser); + log.info("dbPassword: {}", "***"); + log.info("acceptedNormTypes: {}", acceptedNormTypesString); + + try { + if (!this.fs.exists(filePath)) { + throw new CollectorException("path does not exist: " + filePath); + } + } catch (final Throwable e) { + throw new CollectorException(e); + } + + final Set acceptedOpendoarIds = findAcceptedOpendoarIds(dbUrl, dbUser, dbPassword); + + final Set acceptedNormTypes = new HashSet<>(); + if (StringUtils.isNotBlank(acceptedNormTypesString)) { + for (final String s : StringUtils.split(acceptedNormTypesString, ",")) { + if (StringUtils.isNotBlank(s)) { + acceptedNormTypes.add(s.trim()); + } + } + } + + final Iterator iterator = new BaseCollectorIterator(this.fs, filePath, report); + final Spliterator spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED); + return StreamSupport + .stream(spliterator, false) + .filter(doc -> filterXml(doc, acceptedOpendoarIds, acceptedNormTypes)); + } + + private Set findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword) + throws CollectorException { + final Set accepted = new HashSet<>(); + + try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { + + final String sql = IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql")); + + dbClient.processResults(sql, row -> { + try { + final String dsId = row.getString("id"); + log.info("Accepted Datasource: " + dsId); + accepted.add(dsId); + } catch (final SQLException e) { + log.error("Error in SQL", e); + throw new RuntimeException("Error in SQL", e); + } + }); + + } catch (final IOException e) { + log.error("Error accessong SQL", e); + throw new CollectorException("Error accessong SQL", e); + } + + log.info("Accepted Datasources (TOTAL): " + accepted.size()); + + return accepted; + } + + protected static boolean filterXml(final String xml, + final Set acceptedOpendoarIds, + final Set acceptedNormTypes) { + try { + + final Document doc = DocumentHelper.parseText(xml); + + final String id = doc.valueOf("//*[local-name()='collection']/@opendoar_id").trim(); + + if (StringUtils.isBlank(id) || !acceptedOpendoarIds.contains("opendoar____::" + id)) { + return false; + } + + if (acceptedNormTypes.isEmpty()) { + return true; + } + + for (final Object s : doc.selectNodes("//*[local-name()='typenorm']")) { + if (acceptedNormTypes.contains(((Node) s).getText().trim())) { + return true; + } + } + + return false; + } catch (final DocumentException e) { + log.error("Error parsing document", e); + throw new RuntimeException("Error parsing document", e); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java index e4bad2f8d6..1107bcf46e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java @@ -52,8 +52,6 @@ public class RestIterator implements Iterator { private final String BASIC = "basic"; - private final JsonUtils jsonUtils; - private final String baseUrl; private final String resumptionType; private final String resumptionParam; @@ -106,7 +104,6 @@ public class RestIterator implements Iterator { final String resultOutputFormat) { this.clientParams = clientParams; - this.jsonUtils = new JsonUtils(); this.baseUrl = baseUrl; this.resumptionType = resumptionType; this.resumptionParam = resumptionParam; @@ -126,6 +123,7 @@ public class RestIterator implements Iterator { } catch (Exception e) { throw new IllegalStateException("xml transformation init failed: " + e.getMessage()); } + initQueue(); } @@ -190,7 +188,7 @@ public class RestIterator implements Iterator { String resultJson; String resultXml = ""; String nextQuery = ""; - String emptyXml = resultXml + "<" + JsonUtils.wrapName + ">"; + String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + ">"; Node resultNode = null; NodeList nodeList = null; String qUrlArgument = ""; @@ -231,7 +229,7 @@ public class RestIterator implements Iterator { resultStream = theHttpInputStream; if ("json".equals(resultOutputFormat)) { resultJson = IOUtils.toString(resultStream, StandardCharsets.UTF_8); - resultXml = jsonUtils.convertToXML(resultJson); + resultXml = JsonUtils.convertToXML(resultJson); resultStream = IOUtils.toInputStream(resultXml, UTF_8); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java index 15401e2230..1bdc8b1384 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java @@ -3,82 +3,142 @@ package eu.dnetlib.dhp.collection.plugin.utils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import org.json.JSONArray; +import org.json.JSONObject; public class JsonUtils { + public static final String XML_WRAP_TAG = "recordWrap"; + private static final String XML_HEADER = ""; + private static final String INVALID_XMLTAG_CHARS = "!\"#$%&'()*+,/;<=>?@[\\]^`{|}~,"; private static final Log log = LogFactory.getLog(JsonUtils.class); - public static final String wrapName = "recordWrap"; - /** - * convert in JSON-KeyName 'whitespace(s)' to '_' and '/' to '_', '(' and ')' to '' + * cleanup in JSON-KeyName * check W3C XML syntax: https://www.w3.org/TR/2006/REC-xml11-20060816/#sec-starttags for valid tag names * and work-around for the JSON to XML converting of org.json.XML-package. * - * known bugs: doesn't prevent "key name":" ["sexy name",": penari","erotic dance"], - * - * @param jsonInput - * @return convertedJsonKeynameOutput + * @param input + * @return converted json object */ - public String syntaxConvertJsonKeyNames(String jsonInput) { - - log.trace("before convertJsonKeyNames: " + jsonInput); - // pre-clean json - rid spaces of element names (misinterpreted as elements with attributes in xml) - // replace ' 's in JSON Namens with '_' - while (jsonInput.matches(".*\"([^\"]*)\\s+([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*)\\s+([^\"]*)\":", "\"$1_$2\":"); + public static JSONObject cleanJsonObject(final JSONObject input) { + if (null == input) { + return null; } - // replace forward-slash (sign '/' ) in JSON Names with '_' - while (jsonInput.matches(".*\"([^\"]*)/([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*)/([^\"]*)\":", "\"$1_$2\":"); + JSONObject result = new JSONObject(); + + for (String key : input.keySet()) { + Object value = input.opt(key); + if (value != null) { + result.put(cleanKey(key), cleanValue(value)); + } } - // replace '(' in JSON Names with '' - while (jsonInput.matches(".*\"([^\"]*)[(]([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*)[(]([^\"]*)\":", "\"$1$2\":"); - } - - // replace ')' in JSON Names with '' - while (jsonInput.matches(".*\"([^\"]*)[)]([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*)[)]([^\"]*)\":", "\"$1$2\":"); - } - - // add prefix of startNumbers in JSON Keynames with 'n_' - while (jsonInput.matches(".*\"([^\"][0-9])([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"][0-9])([^\"]*)\":", "\"n_$1$2\":"); - } - // add prefix of only numbers in JSON Keynames with 'm_' - while (jsonInput.matches(".*\"([0-9]+)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([0-9]+)\":", "\"m_$1\":"); - } - - // replace ':' between number like '2018-08-28T11:05:00Z' in JSON keynames with '' - while (jsonInput.matches(".*\"([^\"]*[0-9]):([0-9][^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*[0-9]):([0-9][^\"]*)\":", "\"$1$2\":"); - } - - // replace ',' in JSON Keynames with '.' to prevent , in xml tagnames. - // while (jsonInput.matches(".*\"([^\"]*),([^\"]*)\":.*")) { - // jsonInput = jsonInput.replaceAll("\"([^\"]*),([^\"]*)\":", "\"$1.$2\":"); - // } - - // replace '=' in JSON Keynames with '-' - while (jsonInput.matches(".*\"([^\"]*)=([^\"]*)\":.*")) { - jsonInput = jsonInput.replaceAll("\"([^\"]*)=([^\"]*)\":", "\"$1-$2\":"); - } - - log.trace("after syntaxConvertJsonKeyNames: " + jsonInput); - return jsonInput; + return result; } - public String convertToXML(final String jsonRecord) { - String resultXml = ""; - org.json.JSONObject jsonObject = new org.json.JSONObject(syntaxConvertJsonKeyNames(jsonRecord)); - resultXml += org.json.XML.toString(jsonObject, wrapName); // wrap xml in single root element - log.trace("before inputStream: " + resultXml); - resultXml = XmlCleaner.cleanAllEntities(resultXml); - log.trace("after cleaning: " + resultXml); - return resultXml; + private static Object cleanValue(Object object) { + if (object instanceof JSONObject) { + return cleanJsonObject((JSONObject) object); + } else if (object instanceof JSONArray) { + JSONArray array = (JSONArray) object; + JSONArray res = new JSONArray(); + + for (int i = array.length() - 1; i >= 0; i--) { + res.put(i, cleanValue(array.opt(i))); + } + return res; + } else if (object instanceof String) { + String value = (String) object; + + // XML 1.0 Allowed characters + // Char ::= #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF] + + return value + .codePoints() + .filter( + cp -> cp == 0x9 || cp == 0xA || cp == 0xD || (cp >= 0x20 && cp <= 0xD7FF) + || (cp >= 0xE000 && cp <= 0xFFFD) + || (cp >= 0x10000 && cp <= 0x10FFFF)) + .collect( + StringBuilder::new, + StringBuilder::appendCodePoint, + StringBuilder::append) + .toString(); + } + + return object; + } + + private static String cleanKey(String key) { + if (key == null || key.isEmpty()) { + return key; + } + + // xml tag cannot begin with "-", ".", or a numeric digit. + switch (key.charAt(0)) { + case '-': + case '.': + key = "_" + key.substring(1); + break; + } + + if (Character.isDigit(key.charAt(0))) { + if (key.matches("^[0-9]+$")) { + // add prefix of only numbers in JSON Keynames with 'm_' + key = "m_" + key; + } else { + // add prefix of startNumbers in JSON Keynames with 'n_' + key = "n_" + key; + } + } + + StringBuilder res = new StringBuilder(key.length()); + for (int i = 0; i < key.length(); i++) { + char c = key.charAt(i); + + // sequence of whitespaces are rendered as a single '_' + if (Character.isWhitespace(c)) { + while (i + 1 < key.length() && Character.isWhitespace(key.charAt(i + 1))) { + i++; + } + res.append('_'); + } + // remove invalid chars for xml tags with the expception of '=' and '/' + else if (INVALID_XMLTAG_CHARS.indexOf(c) >= 0) { + switch (c) { + case '=': + res.append('-'); + break; + case '/': + res.append('_'); + break; + default: + break; + } + // nothing + } + // all other chars are kept + else { + res.append(c); + } + } + + return res.toString(); + } + + static public String convertToXML(final String jsonRecord) { + if (log.isTraceEnabled()) { + log.trace("input json: " + jsonRecord); + } + + JSONObject jsonObject = cleanJsonObject(new org.json.JSONObject(jsonRecord)); + String res = XML_HEADER + org.json.XML.toString(jsonObject, XML_WRAP_TAG); // wrap xml in single root element + + if (log.isTraceEnabled()) { + log.trace("outout xml: " + res); + } + return res; } } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json index c6f9051996..5a91ace75d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json @@ -17,6 +17,12 @@ "paramDescription": "the path to get the input data from Pubmed", "paramRequired": true }, + { + "paramName": "oip", + "paramLongName": "openapcInputPath", + "paramDescription": "the path to get the input data from OpenAPC", + "paramRequired": true + }, { "paramName": "o", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties index a3d55ff0c1..69c667732e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties @@ -31,6 +31,7 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen # The following is needed as a property of a workflow oozie.wf.application.path=${oozieTopWfApplicationPath} -crossrefInputPath=/data/bip-affiliations/data.json +crossrefInputPath=/data/bip-affiliations/crossref-data.json pubmedInputPath=/data/bip-affiliations/pubmed-data.json +openapcInputPath=/data/bip-affiliations/openapc-data.json outputPath=/tmp/crossref-affiliations-output-v5 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml index c5ac6f8843..e424373960 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml @@ -9,6 +9,10 @@ pubmedInputPath the path where to find the inferred affiliation relations from Pubmed + + openapcInputPath + the path where to find the inferred affiliation relations from OpenAPC + outputPath the path where to store the actionset @@ -102,6 +106,7 @@ --crossrefInputPath${crossrefInputPath} --pubmedInputPath${pubmedInputPath} + --openapcInputPath${openapcInputPath} --outputPath${outputPath} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json new file mode 100644 index 0000000000..5c55bbabeb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json new file mode 100644 index 0000000000..5986abd550 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json @@ -0,0 +1,30 @@ +[ + + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, + { + "paramName": "d", + "paramLongName": "delimiter", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the hdfs name node", + "paramRequired": true + }, + { + "paramName": "if", + "paramLongName": "inputFile", + "paramDescription": "the hdfs name node", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml new file mode 100644 index 0000000000..a1755f329b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + 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 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh new file mode 100644 index 0000000000..66b1a1bf68 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh @@ -0,0 +1,2 @@ +#!/bin/bash +curl -L $1 | hdfs dfs -put - $2 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml new file mode 100644 index 0000000000..0c5b1c119b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml @@ -0,0 +1,82 @@ + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + ${wf:conf('resumeFrom') eq 'DownloadDump'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${inputFile} + ${workingDir}/transformativeagreement/transformativeAgreement.json + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + + + yarn + cluster + Produces the AS for the Transformative Agreement + eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob + 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}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${workingDir}/transformativeagreement/ + --outputPath${outputPath} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json new file mode 100644 index 0000000000..3d3374c743 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH of the DF tables", + "paramRequired": true + }, + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the PATH of the current graph path", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "updatePath", + "paramDescription": "the PATH of the current graph update path", + "paramRequired": true + } + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json new file mode 100644 index 0000000000..48b37f85df --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json @@ -0,0 +1,37 @@ +[ { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the URL to download the tar file", + "paramRequired": true + }, + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the path of the input graph", + "paramRequired": true + }, + { + "paramName": "at", + "paramLongName": "accessToken", + "paramDescription": "the accessToken to contact API", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json index 01d81ea974..d088e8c778 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json @@ -16,6 +16,12 @@ "paramLongName": "sourcePath", "paramDescription": "the PATH of the ORCID sequence file", "paramRequired": true + }, + { + "paramName": "fu", + "paramLongName": "fromUpdate", + "paramDescription": "whether we have to generate table from dump or from update", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml new file mode 100644 index 0000000000..dd3c32c620 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/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/collection/orcid/update/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml new file mode 100644 index 0000000000..e46e303a95 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml @@ -0,0 +1,114 @@ + + + + graphPath + the path to store the original ORCID dump + + + targetPath + the path to store the original ORCID dump + + + apiURL + http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar + The URL of the update CSV list + + + accessToken + The access token + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Check Latest Orcid and Download updates + eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --namenode${nameNode} + --graphPath${graphPath} + --targetPath${targetPath} + --apiURL${apiURL} + --accessToken${accessToken} + + + + + + + + + yarn + cluster + Generate ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${targetPath} + --targetPath${targetPath}/updateTable + --fromUpdatetrue + --masteryarn + + + + + + + + yarn + cluster + Update ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkApplyUpdate + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --graphPath${graphPath} + --updatePath${targetPath}/updateTable + --targetPath${targetPath}/newTable + --masteryarn + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql new file mode 100644 index 0000000000..9a3012949c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql @@ -0,0 +1,114 @@ +BEGIN; + +INSERT INTO dsm_services( + _dnet_resource_identifier_, + id, + officialname, + englishname, + namespaceprefix, + websiteurl, + logourl, + platform, + contactemail, + collectedfrom, + provenanceaction, + _typology_to_remove_, + eosc_type, + eosc_datasource_type, + research_entity_types, + thematic +) VALUES ( + 'openaire____::base_search', + 'openaire____::base_search', + 'Bielefeld Academic Search Engine (BASE)', + 'Bielefeld Academic Search Engine (BASE)', + 'base_search_', + 'https://www.base-search.net', + 'https://www.base-search.net/about/download/logo_224x57_white.gif', + 'BASE', + 'openaire-helpdesk@uni-bielefeld.de', + 'infrastruct_::openaire', + 'user:insert', + 'aggregator::pubsrepository::unknown', + 'Data Source', + 'Aggregator', + ARRAY['Research Products'], + false +); + +INSERT INTO dsm_service_organization( + _dnet_resource_identifier_, + organization, + service +) VALUES ( + 'fairsharing_::org::214@@openaire____::base_search', + 'fairsharing_::org::214', + 'openaire____::base_search' +); + +INSERT INTO dsm_api( + _dnet_resource_identifier_, + id, + service, + protocol, + baseurl, + metadata_identifier_path +) VALUES ( + 'api_________::openaire____::base_search::dump', + 'api_________::openaire____::base_search::dump', + 'openaire____::base_search', + 'baseDump', + '/user/michele.artini/base-import/base_oaipmh_dump-current.tar', + '//*[local-name()=''header'']/*[local-name()=''identifier'']' +); + + +INSERT INTO dsm_apiparams( + _dnet_resource_identifier_, + api, + param, + value +) VALUES ( + 'api_________::openaire____::base_search::dump@@dbUrl', + 'api_________::openaire____::base_search::dump', + 'dbUrl', + 'jdbc:postgresql://postgresql.services.openaire.eu:5432/dnet_openaireplus' +); + +INSERT INTO dsm_apiparams( + _dnet_resource_identifier_, + api, + param, + value +) VALUES ( + 'api_________::openaire____::base_search::dump@@dbUser', + 'api_________::openaire____::base_search::dump', + 'dbUser', + 'dnet' +); + +INSERT INTO dsm_apiparams( + _dnet_resource_identifier_, + api, + param, + value +) VALUES ( + 'api_________::openaire____::base_search::dump@@dbPassword', + 'api_________::openaire____::base_search::dump', + 'dbPassword', + '***' +); + +INSERT INTO dsm_apiparams( + _dnet_resource_identifier_, + api, + param, + value +) VALUES ( + 'api_________::openaire____::base_search::dump@@acceptedNormTypes', + 'api_________::openaire____::base_search::dump', + 'acceptedNormTypes', + '1,11,111,121,14,15,18,181,182,183,1A,6,7' +); + +COMMIT; \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql new file mode 100644 index 0000000000..7b3cb96108 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql @@ -0,0 +1,9 @@ +select s.id as id +from dsm_services s +where collectedfrom = 'openaire____::opendoar' +and jurisdiction = 'Institutional' +and s.id in ( + select service from dsm_api where coalesce(compatibility_override, compatibility) = 'driver' or coalesce(compatibility_override, compatibility) = 'UNKNOWN' +) and s.id not in ( + select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%' +); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql new file mode 100644 index 0000000000..7aeead8f33 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql @@ -0,0 +1,11 @@ +select + s.id as id, + s.jurisdiction as jurisdiction, + array_remove(array_agg(a.id || ' (compliance: ' || coalesce(a.compatibility_override, a.compatibility, 'UNKNOWN') || ')@@@' || coalesce(a.last_collection_total, 0)), NULL) as aggregations +from + dsm_services s + join dsm_api a on (s.id = a.service) +where + collectedfrom = 'openaire____::opendoar' +group by + s.id; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base-types.vocabulary.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base-types.vocabulary.xml new file mode 100644 index 0000000000..51f4ee6ca9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base-types.vocabulary.xml @@ -0,0 +1,180 @@ + +

+ + + + + +
+ + + base:normalized_types + base:normalized_types + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + String + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml new file mode 100644 index 0000000000..a49687e3ad --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml @@ -0,0 +1,432 @@ + +
+ + + + + +
+ + + + + + + + + + +
\ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml new file mode 100644 index 0000000000..0e0e41f129 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml @@ -0,0 +1,461 @@ + +
+ + + + + +
+ + + + + + + + + + +
\ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala new file mode 100644 index 0000000000..57cb0e2e45 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala @@ -0,0 +1,120 @@ +package eu.dnetlib.dhp.collection.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import org.apache.spark.sql.{DataFrame, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + + val graphPath: String = parser.get("graphPath") + log.info("found parameters graphPath: {}", graphPath) + val updatePath: String = parser.get("updatePath") + log.info("found parameters updatePath: {}", updatePath) + val targetPath: String = parser.get("targetPath") + log.info("found parameters targetPath: {}", targetPath) + applyTableUpdate(spark, graphPath, updatePath, targetPath) + checkUpdate(spark, graphPath, targetPath) + moveTable(spark, graphPath, targetPath) + + } + + private def moveTable(spark: SparkSession, graphPath: String, updatePath: String): Unit = { + spark.read + .load(s"$updatePath/Authors") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Authors") + spark.read + .load(s"$updatePath/Works") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Works") + spark.read + .load(s"$updatePath/Employments") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Employments") + + } + + private def updateDataset( + inputDataset: DataFrame, + idUpdate: DataFrame, + updateDataframe: DataFrame, + targetPath: String + ): Unit = { + inputDataset + .join(idUpdate, inputDataset("orcid").equalTo(idUpdate("orcid")), "leftanti") + .select(inputDataset("*")) + .unionByName(updateDataframe) + .write + .mode(SaveMode.Overwrite) + .save(targetPath) + } + + private def checkUpdate(spark: SparkSession, graphPath: String, updatePath: String): Unit = { + val totalOriginalAuthors = spark.read.load(s"$graphPath/Authors").count + val totalOriginalWorks = spark.read.load(s"$graphPath/Works").count + val totalOriginalEmployments = spark.read.load(s"$graphPath/Employments").count + val totalUpdateAuthors = spark.read.load(s"$updatePath/Authors").count + val totalUpdateWorks = spark.read.load(s"$updatePath/Works").count + val totalUpdateEmployments = spark.read.load(s"$updatePath/Employments").count + + log.info("totalOriginalAuthors: {}", totalOriginalAuthors) + log.info("totalOriginalWorks: {}", totalOriginalWorks) + log.info("totalOriginalEmployments: {}", totalOriginalEmployments) + log.info("totalUpdateAuthors: {}", totalUpdateAuthors) + log.info("totalUpdateWorks: {}", totalUpdateWorks) + log.info("totalUpdateEmployments: {}", totalUpdateEmployments) + if ( + totalUpdateAuthors < totalOriginalAuthors || totalUpdateEmployments < totalOriginalEmployments || totalUpdateWorks < totalOriginalWorks + ) + throw new RuntimeException("The updated Graph contains less elements of the original one") + + } + + private def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String): Unit = { + val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid") + updateDataset( + spark.read.load(s"$graphPath/Authors"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Authors"), + s"$targetPath/Authors" + ) + updateDataset( + spark.read.load(s"$graphPath/Employments"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Employments"), + s"$targetPath/Employments" + ) + updateDataset( + spark.read.load(s"$graphPath/Works"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Works"), + s"$targetPath/Works" + ) + } + +} + +object SparkApplyUpdate { + + val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass) + + def main(args: Array[String]): Unit = { + + new SparkApplyUpdate("/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json", args, log) + .initialize() + .run() + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala index f0c4cd2140..4f617f15cd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala @@ -6,6 +6,7 @@ import org.apache.hadoop.io.Text import org.apache.spark.SparkContext import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger) extends AbstractScalaApplication(propertyPath, args, log: Logger) { @@ -18,12 +19,16 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo log.info("found parameters sourcePath: {}", sourcePath) val targetPath: String = parser.get("targetPath") log.info("found parameters targetPath: {}", targetPath) - extractORCIDTable(spark, sourcePath, targetPath) - extractORCIDEmploymentsTable(spark, sourcePath, targetPath) - extractORCIDWorksTable(spark, sourcePath, targetPath) + val fromUpdate = "true".equals(parser.get("fromUpdate")) + val sourceSummaryPath = if (fromUpdate) s"$sourcePath/summary*" else sourcePath + val sourceEmploymentsPath = if (fromUpdate) s"$sourcePath/employments*" else sourcePath + val sourceWorksPath = if (fromUpdate) s"$sourcePath/works*" else sourcePath + extractORCIDTable(spark, sourceSummaryPath, targetPath, fromUpdate) + extractORCIDEmploymentsTable(spark, sourceEmploymentsPath, targetPath, fromUpdate) + extractORCIDWorksTable(spark, sourceWorksPath, targetPath, fromUpdate) } - def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String, skipFilterByKey: Boolean): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -32,8 +37,8 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author]) -// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("summaries")) + val newDf = if (!skipFilterByKey) df.filter(r => r._1.contains("summaries")) else df + newDf .map { r => val p = new OrcidParser p.parseSummary(r._2) @@ -44,7 +49,12 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .save(s"$targetPath/Authors") } - def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDWorksTable( + spark: SparkSession, + sourcePath: String, + targetPath: String, + skipFilterByKey: Boolean + ): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -53,19 +63,37 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work]) - implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("works")) - .map { r => + + //We are in the case of parsing ORCID UPDATE + if (skipFilterByKey) { + df.flatMap { r => val p = new OrcidParser - p.parseWork(r._2) - } - .filter(p => p != null) - .write - .mode(SaveMode.Overwrite) - .save(s"$targetPath/Works") + p.parseWorks(r._2).asScala + }.filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } + //We are in the case of parsing ORCID DUMP + else { + df.filter(r => r._1.contains("works")) + .map { r => + val p = new OrcidParser + p.parseWork(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } } - def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDEmploymentsTable( + spark: SparkSession, + sourcePath: String, + targetPath: String, + skipFilterByKey: Boolean + ): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -74,16 +102,27 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment]) - implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("employments")) - .map { r => + if (skipFilterByKey) { + df.flatMap { r => val p = new OrcidParser - p.parseEmployment(r._2) - } - .filter(p => p != null) - .write - .mode(SaveMode.Overwrite) - .save(s"$targetPath/Employments") + p.parseEmployments(r._2).asScala + }.filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } + //We are in the case of parsing ORCID DUMP + else { + df.filter(r => r._1.contains("employments")) + .map { r => + val p = new OrcidParser + p.parseEmployment(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java index b877388791..c164aad8b1 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java @@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest { .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getPath(); - String pubmedAffiliationRelationsPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") - .getPath(); - String outputPath = workingDir.toString() + "/actionSet"; PrepareAffiliationRelations @@ -89,7 +85,8 @@ public class PrepareAffiliationRelationsTest { new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-crossrefInputPath", crossrefAffiliationRelationPath, - "-pubmedInputPath", pubmedAffiliationRelationsPath, + "-pubmedInputPath", crossrefAffiliationRelationPath, + "-openapcInputPath", crossrefAffiliationRelationPath, "-outputPath", outputPath }); @@ -106,7 +103,7 @@ public class PrepareAffiliationRelationsTest { // ); // } // count the number of relations - assertEquals(40, tmp.count()); + assertEquals(60, tmp.count()); Dataset dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); dataset.createOrReplaceTempView("result"); @@ -117,7 +114,7 @@ public class PrepareAffiliationRelationsTest { // verify that we have equal number of bi-directional relations Assertions .assertEquals( - 20, execVerification + 30, execVerification .filter( "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") .collectAsList() @@ -125,7 +122,7 @@ public class PrepareAffiliationRelationsTest { Assertions .assertEquals( - 20, execVerification + 30, execVerification .filter( "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") .collectAsList() diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java new file mode 100644 index 0000000000..0ec34311fd --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java @@ -0,0 +1,324 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +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.actionmanager.opencitations.CreateActionSetSparkJob; +import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; + +/** + * @author miriam.baglioni + * @Date 13/02/24 + */ +public class CreateTAActionSetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateOpenCitationsASTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateTAActionSetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateTAActionSetTest.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(CreateTAActionSetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void createActionSet() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json") + .getPath(); + + eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + } + + @Test + void testNumberofRelations2() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet2" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + assertEquals(23, tmp.count()); + + // tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + + } + + @Test + void testRelationsCollectedFrom() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet3" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue()); + assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey()); + }); + + } + + @Test + void testRelationsDataInfo() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet4" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(false, r.getDataInfo().getInferred()); + assertEquals(false, r.getDataInfo().getDeletedbyinference()); + assertEquals("0.91", r.getDataInfo().getTrust()); + assertEquals( + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSID, + r.getDataInfo().getProvenanceaction().getClassid()); + assertEquals( + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, + r.getDataInfo().getProvenanceaction().getClassname()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename()); + }); + + } + + @Test + void testRelationsSemantics() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet5" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("citation", r.getSubRelType()); + assertEquals("resultResult", r.getRelType()); + }); + assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count()); + assertEquals(0, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count()); + + } + + @Test + void testRelationsSourceTargetPrefix() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet6" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("50|doi_________::", r.getSource().substring(0, 17)); + assertEquals("50|doi_________::", r.getTarget().substring(0, 17)); + }); + + } + + @Test + void testRelationsSourceTargetCouple() throws Exception { + final String doi1 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); + final String doi2 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); + final String doi3 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); + final String doi4 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); + final String doi5 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); + final String doi6 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet7" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + JavaRDD check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1)); + + assertEquals(5, check.count()); + +// check.foreach(r -> { +// if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) || +// r.getSource().equals(doi5) || r.getSource().equals(doi6)) { +// assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass()); +// assertEquals(doi1, r.getTarget()); +// } +// }); + + assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count()); + check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass())); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java index 868f4e92d0..f42d1d8752 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.collection.orcid; import java.io.IOException; +import java.net.URI; import java.util.Arrays; import java.util.List; import java.util.Objects; @@ -9,7 +10,12 @@ import java.util.Objects; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.spark.SparkContext; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.Encoders; @@ -27,6 +33,7 @@ import com.ximpleware.XPathParseException; import eu.dnetlib.dhp.collection.orcid.model.Author; import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem; +import eu.dnetlib.dhp.collection.orcid.model.Work; import eu.dnetlib.dhp.parser.utility.VtdException; public class DownloadORCIDTest { @@ -82,6 +89,34 @@ public class DownloadORCIDTest { }); } + @Test + public void testParsingOrcidUpdateEmployments() throws Exception { + final String xml = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_employments.xml"))); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(parser.parseEmployments(xml))); + } + + @Test + public void testParsingOrcidUpdateWorks() throws Exception { + final String xml = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_work.xml"))); + + final OrcidParser parser = new OrcidParser(); + final List works = parser.parseWorks(xml); + + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(works)); + } + @Test public void testParsingEmployments() throws Exception { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectionInfo.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectionInfo.java new file mode 100644 index 0000000000..06dfe45e23 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectionInfo.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import java.io.Serializable; + +public class BaseCollectionInfo implements Serializable { + + private static final long serialVersionUID = 5766333937429419647L; + + private String id; + private String opendoarId; + private String rorId; + + public String getId() { + return this.id; + } + + public void setId(final String id) { + this.id = id; + } + + public String getOpendoarId() { + return this.opendoarId; + } + + public void setOpendoarId(final String opendoarId) { + this.opendoarId = opendoarId; + } + + public String getRorId() { + return this.rorId; + } + + public void setRorId(final String rorId) { + this.rorId = rorId; + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIteratorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIteratorTest.java new file mode 100644 index 0000000000..7ffe4bb871 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIteratorTest.java @@ -0,0 +1,184 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +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.SparkSession; +import org.dom4j.Attribute; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.DocumentHelper; +import org.dom4j.Element; +import org.dom4j.Node; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; + +@Disabled +public class BaseCollectorIteratorTest { + + @Test + void testImportFile() throws Exception { + + long count = 0; + + final BaseCollectorIterator iterator = new BaseCollectorIterator("base-sample.tar", new AggregatorReport()); + + final Map> collections = new HashMap<>(); + final Map fields = new HashMap<>(); + final Set types = new HashSet<>(); + + while (iterator.hasNext()) { + + final Document record = DocumentHelper.parseText(iterator.next()); + + count++; + + if ((count % 1000) == 0) { + System.out.println("# Read records: " + count); + } + + // System.out.println(record.asXML()); + + for (final Object o : record.selectNodes("//*|//@*")) { + final String path = ((Node) o).getPath(); + + if (fields.containsKey(path)) { + fields.get(path).incrementAndGet(); + } else { + fields.put(path, new AtomicInteger(1)); + } + + if (o instanceof Element) { + final Element n = (Element) o; + + if ("collection".equals(n.getName())) { + final String collName = n.getText().trim(); + if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) { + final Map collAttrs = new HashMap<>(); + for (final Object ao : n.attributes()) { + collAttrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue()); + } + collections.put(collName, collAttrs); + } + } else if ("type".equals(n.getName())) { + types.add(n.getText().trim()); + } + + } + } + + } + + final ObjectMapper mapper = new ObjectMapper(); + for (final Entry> e : collections.entrySet()) { + System.out.println(e.getKey() + ": " + mapper.writeValueAsString(e.getValue())); + + } + + for (final Entry e : fields.entrySet()) { + System.out.println(e.getKey() + ": " + e.getValue().get()); + + } + + System.out.println("TYPES: "); + for (final String s : types) { + System.out.println(s); + + } + + assertEquals(30000, count); + } + + @Test + public void testParquet() throws Exception { + + final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml")); + + final SparkSession spark = SparkSession.builder().master("local[*]").getOrCreate(); + + final List ls = new ArrayList<>(); + + for (int i = 0; i < 10; i++) { + ls.add(extractInfo(xml)); + } + + final JavaRDD rdd = JavaSparkContext + .fromSparkContext(spark.sparkContext()) + .parallelize(ls); + + final Dataset df = spark + .createDataset(rdd.rdd(), Encoders.bean(BaseRecordInfo.class)); + + df.printSchema(); + + df.show(false); + } + + private BaseRecordInfo extractInfo(final String s) { + try { + final Document record = DocumentHelper.parseText(s); + + final BaseRecordInfo info = new BaseRecordInfo(); + + final Set paths = new LinkedHashSet<>(); + final Set types = new LinkedHashSet<>(); + final List colls = new ArrayList<>(); + + for (final Object o : record.selectNodes("//*|//@*")) { + paths.add(((Node) o).getPath()); + + if (o instanceof Element) { + final Element n = (Element) o; + + final String nodeName = n.getName(); + + if ("collection".equals(nodeName)) { + final String collName = n.getText().trim(); + + if (StringUtils.isNotBlank(collName)) { + final BaseCollectionInfo coll = new BaseCollectionInfo(); + coll.setId(collName); + coll.setOpendoarId(n.valueOf("@opendoar_id").trim()); + coll.setRorId(n.valueOf("@ror_id").trim()); + colls.add(coll); + } + } else if ("type".equals(nodeName)) { + types.add("TYPE: " + n.getText().trim()); + } else if ("typenorm".equals(nodeName)) { + types.add("TYPE_NORM: " + n.getText().trim()); + } + } + } + + info.setId(record.valueOf("//*[local-name() = 'header']/*[local-name() = 'identifier']").trim()); + info.getTypes().addAll(types); + info.getPaths().addAll(paths); + info.setCollections(colls); + + return info; + } catch (final DocumentException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPluginTest.java new file mode 100644 index 0000000000..d3b08f212f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPluginTest.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.util.Arrays; +import java.util.HashSet; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +class BaseCollectorPluginTest { + + @Test + void testFilterXml() throws Exception { + final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml")); + + final Set validIds = new HashSet<>(Arrays.asList("opendoar____::1234", "opendoar____::4567")); + final Set validTypes = new HashSet<>(Arrays.asList("1", "121")); + final Set validTypes2 = new HashSet<>(Arrays.asList("1", "11")); + + assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, validTypes)); + assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, new HashSet<>())); + + assertFalse(BaseCollectorPlugin.filterXml(xml, new HashSet<>(), validTypes)); + assertFalse(BaseCollectorPlugin.filterXml(xml, validIds, validTypes2)); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseRecordInfo.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseRecordInfo.java new file mode 100644 index 0000000000..0fe6175a74 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseRecordInfo.java @@ -0,0 +1,49 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +public class BaseRecordInfo implements Serializable { + + private static final long serialVersionUID = -8848232018350074593L; + + private String id; + private List collections = new ArrayList<>(); + private List paths = new ArrayList<>(); + private List types = new ArrayList<>(); + + public String getId() { + return this.id; + } + + public void setId(final String id) { + this.id = id; + } + + public List getPaths() { + return this.paths; + } + + public void setPaths(final List paths) { + this.paths = paths; + } + + public List getTypes() { + return this.types; + } + + public void setTypes(final List types) { + this.types = types; + } + + public List getCollections() { + return this.collections; + } + + public void setCollections(final List collections) { + this.collections = collections; + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java new file mode 100644 index 0000000000..6c0c23922f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java @@ -0,0 +1,94 @@ + +package eu.dnetlib.dhp.collection.plugin.base; + +import static org.junit.jupiter.api.Assertions.assertThrows; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.util.LongAccumulator; +import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest; +import eu.dnetlib.dhp.aggregation.common.AggregationCounter; +import eu.dnetlib.dhp.schema.mdstore.MetadataRecord; +import eu.dnetlib.dhp.schema.mdstore.Provenance; +import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; + +// @Disabled +@ExtendWith(MockitoExtension.class) +public class BaseTransfomationTest extends AbstractVocabularyTest { + + private SparkConf sparkConf; + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + setUpVocabulary(); + + this.sparkConf = new SparkConf(); + this.sparkConf.setMaster("local[*]"); + this.sparkConf.set("spark.driver.host", "localhost"); + this.sparkConf.set("spark.ui.enabled", "false"); + } + + @Test + void testBase2ODF() throws Exception { + + final MetadataRecord mr = new MetadataRecord(); + mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml"))); + + final XSLTTransformationFunction tr = loadTransformationRule("xml/base2odf.transformationRule.xml"); + + final MetadataRecord result = tr.call(mr); + + System.out.println(result.getBody()); + } + + @Test + void testBase2OAF() throws Exception { + + final MetadataRecord mr = new MetadataRecord(); + mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml"))); + + final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml"); + + final MetadataRecord result = tr.call(mr); + + System.out.println(result.getBody()); + } + + @Test + void testBase2ODF_wrong_date() throws Exception { + + final MetadataRecord mr = new MetadataRecord(); + mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record_wrong_1.xml"))); + + final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml"); + + assertThrows(NullPointerException.class, () -> { + final MetadataRecord result = tr.call(mr); + System.out.println(result.getBody()); + }); + } + + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { + final String xslt = new SAXReader() + .read(this.getClass().getResourceAsStream(path)) + .selectSingleNode("//CODE/*") + .asXML(); + + final LongAccumulator la = new LongAccumulator(); + + return new XSLTTransformationFunction(new AggregationCounter(la, la, la), xslt, 0, this.vocabularies); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java index 906f69dc9e..e2d6ad3e7f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java @@ -9,6 +9,7 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpClientParams; /** @@ -37,7 +38,7 @@ public class RestIteratorTest { @Disabled @Test - public void test() { + public void test() throws CollectorException { HttpClientParams clientParams = new HttpClientParams(); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtilsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtilsTest.java new file mode 100644 index 0000000000..59d24fdc2d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtilsTest.java @@ -0,0 +1,48 @@ + +package eu.dnetlib.dhp.collection.plugin.utils; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.junit.jupiter.api.Test; + +class JsonUtilsTest { + + static private String wrapped(String xml) { + return "" + xml + ""; + } + + @Test + void keyStartWithDigit() { + assertEquals( + wrapped("null"), + JsonUtils.convertToXML("{\"100\" : {\"200v\" : null}}")); + } + + @Test + void keyStartWithSpecialchars() { + assertEquals( + wrapped("<_parent><_nest1><_nest2>null"), + JsonUtils.convertToXML("{\" parent\" : {\"-nest1\" : {\".nest2\" : null}}}")); + } + + @Test + void encodeArray() { + assertEquals( + wrapped("<_parent.child>1<_parent.child>2"), + JsonUtils.convertToXML("{\" parent.child\":[1, 2]}")); + } + + @Test + void arrayOfObjects() { + assertEquals( + wrapped("12"), + JsonUtils.convertToXML("{\"parent\": [{\"id\": 1}, {\"id\": 2}]}")); + } + + @Test + void removeControlCharacters() { + assertEquals( + wrapped("Test"), + JsonUtils.convertToXML("{\"100\" : {\"200v\" : \"\\u0000\\u000cTest\"}}")); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json new file mode 100644 index 0000000000..e2801ddf37 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json @@ -0,0 +1,96499 @@ +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Soft Computing", "issn": "1432-7643", "doi": "10.1007/s00500-015-1923-y", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Geoheritage", "issn": "1867-2477", "doi": "10.1007/s12371-015-0172-x", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Studies in Philosophy and Education", "issn": "0039-3746", "doi": "10.1007/s11217-016-9515-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Language Policy", "issn": "1568-4555", "doi": "10.1007/s10993-016-9402-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Conservation Genetics Resources", "issn": "1877-7252", "doi": "10.1007/s12686-016-0537-8", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Sports Medicine", "issn": "0112-1642", "doi": "10.1007/s40279-016-0559-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Journal of Autism and Developmental Disorders", "issn": "0162-3257", "doi": "10.1007/s10803-015-2693-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Experimental Brain Research", "issn": "0014-4819", "doi": "10.1007/s00221-016-4567-y", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Morphology", "issn": "1871-5621", "doi": "10.1007/s11525-016-9286-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "The International Sports Law Journal", "issn": "1567-7559", "doi": "10.1007/s40318-016-0091-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aston University", "institution": "Aston University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "International Journal of Clinical Pharmacy", "issn": "2210-7703", "doi": "10.1007/s11096-015-0236-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aston University", "institution": "Aston University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Small Business Economics", "issn": "0921-898X", "doi": "10.1007/s11187-015-9698-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "European Journal of Ageing", "issn": "1613-9372", "doi": "10.1007/s10433-015-0359-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Plant and Soil", "issn": "0032-079X", "doi": "10.1007/s11104-015-2747-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Biology and Fertility of Soils", "issn": "0178-2762", "doi": "10.1007/s00374-016-1092-x", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Facies", "issn": "0172-9179", "doi": "10.1007/s10347-016-0468-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Agroforestry Systems", "issn": "0167-4366", "doi": "10.1007/s10457-016-9912-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Polar Biology", "issn": "0722-4060", "doi": "10.1007/s00300-016-1914-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Small-scale Forestry", "issn": "1873-7617", "doi": "10.1007/s11842-016-9331-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Environmental Management", "issn": "0364-152X", "doi": "10.1007/s00267-016-0696-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Estuaries and Coasts", "issn": "1559-2723", "doi": "10.1007/s12237-016-0103-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Regional Environmental Change", "issn": "1436-3798", "doi": "10.1007/s10113-016-0978-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Biodiversity and Conservation", "issn": "0960-3115", "doi": "10.1007/s10531-016-1131-9", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Organisms Diversity & Evolution", "issn": "1439-6092", "doi": "10.1007/s13127-016-0289-z", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Psychonomic Bulletin & Review", "issn": "1069-9384", "doi": "10.3758/s13423-015-0995-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "European Journal of Nutrition", "issn": "1436-6207", "doi": "10.1007/s00394-015-1130-8", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Hydrobiologia", "issn": "0018-8158", "doi": "10.1007/s10750-016-2641-x", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Marine Biology", "issn": "0025-3162", "doi": "10.1007/s00227-015-2805-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Sports Medicine", "issn": "0112-1642", "doi": "10.1007/s40279-016-0476-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "The Computer Games Journal", "issn": "2052-773X", "doi": "10.1007/s40869-016-0017-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Annals of Behavioral Medicine", "issn": "0883-6612", "doi": "10.1007/s12160-016-9784-x", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Journal of Ocean Engineering and Marine Energy", "issn": "2198-6444", "doi": "10.1007/s40722-016-0044-8", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Sports Engineering", "issn": "1369-7072", "doi": "10.1007/s12283-016-0202-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Criminal Law Forum", "issn": "1046-8374", "doi": "10.1007/s10609-015-9271-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Higher Education", "issn": "0018-1560", "doi": "10.1007/s10734-015-9976-5", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Chromosoma", "issn": "0009-5915", "doi": "10.1007/s00412-015-0561-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Computational Economics", "issn": "0927-7099", "doi": "10.1007/s10614-016-9567-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Scientometrics", "issn": "0138-9130", "doi": "10.1007/s11192-016-1895-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Current Genetics", "issn": "0172-8083", "doi": "10.1007/s00294-016-0589-z", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "JOM", "issn": "1047-4838", "doi": "10.1007/s11837-016-1855-8", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Empirical Economics", "issn": "0377-7332", "doi": "10.1007/s00181-016-1075-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Software & Systems Modeling", "issn": "1619-1366", "doi": "10.1007/s10270-016-0521-5", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Brunel University", "institution": "Brunel University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Journal of Materials Engineering and Performance", "issn": "1059-9495", "doi": "10.1007/s11665-016-2070-z", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff Metropolitan University", "institution": "Cardiff Metropolitan University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Sports Medicine", "issn": "0112-1642", "doi": "10.1007/s40279-016-0474-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Advances in Health Sciences Education", "issn": "1382-4996", "doi": "10.1007/s10459-015-9652-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Journal of Business Ethics", "issn": "0167-4544", "doi": "10.1007/s10551-015-2940-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Journal of Electronic Materials", "issn": "0361-5235", "doi": "10.1007/s11664-015-4180-z", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Journal of Neurology", "issn": "0340-5354", "doi": "10.1007/s00415-015-7974-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "International Review of Education", "issn": "0020-8566", "doi": "10.1007/s11159-015-9516-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Motivation and Emotion", "issn": "0146-7239", "doi": "10.1007/s11031-015-9526-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Ethical Theory and Moral Practice", "issn": "1386-2820", "doi": "10.1007/s10677-015-9665-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Quality of Life Research", "issn": "0962-9343", "doi": "10.1007/s11136-015-1194-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Public Organization Review", "issn": "1566-7170", "doi": "10.1007/s11115-015-0340-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Brain Structure and Function", "issn": "1863-2653", "doi": "10.1007/s00429-016-1183-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Cardiff University", "institution": "Cardiff University", "period": "2016", 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https://orcid.org/client/APP-N0TAO4G9BBK9PWHT + APP-N0TAO4G9BBK9PWHT + orcid.org + + Tampere University + + + Hermosolun solunsisäisten toimintojen matemaattinen mallinnus ja simulointi + + + + source-work-id + ca0966d2-a83d-42f5-9905-b6e84115ac54 + ca0966d2-a83d-42f5-9905-b6e84115ac54 + self + + + https://researchportal.tuni.fi/en/publications/ca0966d2-a83d-42f5-9905-b6e84115ac54 + other + + 2003 + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/base-sample.tar b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/base-sample.tar new file mode 100644 index 0000000000..c575fe1471 Binary files /dev/null and b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/base-sample.tar differ diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record.xml 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+ ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1 + 2022-12-31T11:48:55Z +
+ + + ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1 + cww + org + ftdoajarticles + TEST REPO + Assessment of cultural heritage: the legislative and methodological framework of Russian Federation + ALBU, Svetlana + LEȘAN, Anna + architectural heritage + evaluation of architectural heritage + types of values + experience of russian federation + Social Sciences + H + Architectural heritage is the real estate inheritance by population of a country becoming an extremely valuable and specific category, preserving and capitalizing on those assets requires considerable effort. The state does not have sufficient means to maintain and preserve cultural heritage, as a result it is included in the civil circuit. The transfer of property right or of some partial rights over the architectural patrimony is accompanied by the necessity to estimate the value of goods. In this article, the authors examine the experience of Russian Federation (one of the largest countries with a huge architectural heritage) on the legislative framework of architectural and methodological heritage of architectural heritage assessment. The particularities of cultural assets valuation compared to other categories of real estate are examined, as well as the methodological aspects (types of values, methods applied in valuation, approaches according to the purpose of valuation) regarding the valuation of real estate with architectural value in Russian Federation. + Technical University of Moldova + 2020-09-01T00:00:00Z + 2020 + article + 121 + https://doi.org/10.5281/zenodo.3971988 + https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1 + https://doi.org/10.5281/zenodo.3971988 + Journal of Social Sciences, Vol 3, Iss 3, Pp 134-143 (2020) + EN + FR + RO + http://ibn.idsi.md/sites/default/files/imag_file/JSS-3-2020_134-143.pdf + https://doaj.org/toc/2587-3490 + https://doaj.org/toc/2587-3504 + doi:10.5281/zenodo.3971988 + 2587-3490 + 2587-3504 + https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1 + 720 + + ALBU, Svetlana + https://orcid.org/0000-0002-8648-950X + + + LEȘAN, Anna + https://orcid.org/0000-0003-3284-0525 + + https://doi.org/10.5281/zenodo.3971988 + 1 + eng + fre + rum + + +
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+ ftunivminnesdc:oai:conservancy.umn.edu:11299/109914 + 2023-07-18T20:05:40Z +
+ + + ftunivminnesdc:oai:conservancy.umn.edu:11299/109914 + cna + us + ftunivminnesdc + University of Minnesota Digital Conservancy + An Experimental Investigation of the influence of an air bubble layer on radiated noise and surface pressure fluctuations in a turbulent boundary layer + Killen, John M. + Boundary layer noise + Kinetic energy dissipation + Air bubble layer + Maximum stable bubble size + bubble noise spectra + between the noise spectra of a layer of air bubbles in a turbulent flow and' a maximum stable bubble size which can exist in the same flow. An air bubbie layer with individual bubble sizes greater than a maximum stable size was introduced into the boundary layer of water flowing along a smooth flat plate. It was found that the maximum stable bubble size was related to the turbulent kinetic energy dissipation as had been previously shown by other investigators ; Office of Naval Research Arlington, Virginia 22217 + 1981-09-31T21:42:52Z + 1981 + Report + 14 + http://purl.umn.edu/109914 + http://purl.umn.edu/109914 + en_US + Project Reports + 202 + http://purl.umn.edu/109914 + 2 + eng + + +
\ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt index 74a75e46a7..6b7979a6b4 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -1496,4 +1496,30 @@ cnr:institutes @=@ __CDS131__ @=@ IBE - Istituto per la BioEconomia cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132 cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\" cnr:institutes @=@ __CDS133__ @=@ CDS133 -cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili \ No newline at end of file +cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili +base:normalized_types @=@ Text @=@ 1 +base:normalized_types @=@ Book @=@ 11 +base:normalized_types @=@ Book part @=@ 111 +base:normalized_types @=@ Journal/Newspaper @=@ 12 +base:normalized_types @=@ Article contribution @=@ 121 +base:normalized_types @=@ Other non-article @=@ 122 +base:normalized_types @=@ Conference object @=@ 13 +base:normalized_types @=@ Report @=@ 14 +base:normalized_types @=@ Review @=@ 15 +base:normalized_types @=@ Course material @=@ 16 +base:normalized_types @=@ Lecture @=@ 17 +base:normalized_types @=@ Thesis @=@ 18 +base:normalized_types @=@ Bachelor's thesis @=@ 181 +base:normalized_types @=@ Master's thesis @=@ 182 +base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ 183 +base:normalized_types @=@ Manuscript @=@ 19 +base:normalized_types @=@ Patent @=@ 1A +base:normalized_types @=@ Musical notation @=@ 2 +base:normalized_types @=@ Map @=@ 3 +base:normalized_types @=@ Audio @=@ 4 +base:normalized_types @=@ Image/Video @=@ 5 +base:normalized_types @=@ Still image @=@ 51 +base:normalized_types @=@ Moving image/Video @=@ 52 +base:normalized_types @=@ Software @=@ 6 +base:normalized_types @=@ Dataset @=@ 7 +base:normalized_types @=@ Unknown @=@ F diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 0f0ebaad42..29e42ffd9a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1210,4 +1210,29 @@ cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__ cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__ cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895 cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__ - +base:normalized_types @=@ base:normalized_types @=@ Text @=@ Text +base:normalized_types @=@ base:normalized_types @=@ Book @=@ Book +base:normalized_types @=@ base:normalized_types @=@ Book part @=@ Book part +base:normalized_types @=@ base:normalized_types @=@ Journal/Newspaper @=@ Journal/Newspaper +base:normalized_types @=@ base:normalized_types @=@ Article contribution @=@ Article contribution +base:normalized_types @=@ base:normalized_types @=@ Other non-article @=@ Other non-article +base:normalized_types @=@ base:normalized_types @=@ Conference object @=@ Conference object +base:normalized_types @=@ base:normalized_types @=@ Report @=@ Report +base:normalized_types @=@ base:normalized_types @=@ Review @=@ Review +base:normalized_types @=@ base:normalized_types @=@ Course material @=@ Course material +base:normalized_types @=@ base:normalized_types @=@ Lecture @=@ Lecture +base:normalized_types @=@ base:normalized_types @=@ Thesis @=@ Thesis +base:normalized_types @=@ base:normalized_types @=@ Bachelor's thesis @=@ Bachelor's thesis +base:normalized_types @=@ base:normalized_types @=@ Master's thesis @=@ Master's thesis +base:normalized_types @=@ base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ Doctoral and postdoctoral thesis +base:normalized_types @=@ base:normalized_types @=@ Manuscript @=@ Manuscript +base:normalized_types @=@ base:normalized_types @=@ Patent @=@ Patent +base:normalized_types @=@ base:normalized_types @=@ Musical notation @=@ Musical notation +base:normalized_types @=@ base:normalized_types @=@ Map @=@ Map +base:normalized_types @=@ base:normalized_types @=@ Audio @=@ Audio +base:normalized_types @=@ base:normalized_types @=@ Image/Video @=@ Image/Video +base:normalized_types @=@ base:normalized_types @=@ Still image @=@ Still image +base:normalized_types @=@ base:normalized_types @=@ Moving image/Video @=@ Moving image/Video +base:normalized_types @=@ base:normalized_types @=@ Software @=@ Software +base:normalized_types @=@ base:normalized_types @=@ Dataset @=@ Dataset +base:normalized_types @=@ base:normalized_types @=@ Unknown @=@ Unknown \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 4c12d1dc65..35fa61b947 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,26 +1,29 @@ package eu.dnetlib.dhp.oa.dedup; -import eu.dnetlib.dhp.oa.dedup.model.Identifier; -import eu.dnetlib.dhp.oa.merge.AuthorMerger; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; +import java.util.*; +import java.util.stream.Stream; + +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.ReduceFunction; import org.apache.spark.sql.*; + +import eu.dnetlib.dhp.oa.dedup.model.Identifier; +import eu.dnetlib.dhp.oa.merge.AuthorMerger; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; import scala.Tuple3; import scala.collection.JavaConversions; -import java.util.*; -import java.util.stream.Stream; - public class DedupRecordFactory { public static final class DedupRecordReduceState { public final String dedupId; @@ -39,7 +42,8 @@ public class DedupRecordFactory { } else { if (Result.class.isAssignableFrom(entity.getClass())) { Result result = (Result) entity; - if (result.getDateofacceptance() != null && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { + if (result.getDateofacceptance() != null + && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { acceptanceDate.add(result.getDateofacceptance().getValue()); } } @@ -50,6 +54,7 @@ public class DedupRecordFactory { return dedupId; } } + private static final int MAX_ACCEPTANCE_DATE = 20; private DedupRecordFactory() { @@ -90,8 +95,12 @@ public class DedupRecordFactory { .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left") .select("dedupId", "id", "kryoObject") .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder)) - .map((MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState(t._1(), t._2(), t._3()), Encoders.kryo(DedupRecordReduceState.class)) - .groupByKey((MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) + .map( + (MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState( + t._1(), t._2(), t._3()), + Encoders.kryo(DedupRecordReduceState.class)) + .groupByKey( + (MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) .reduceGroups( (ReduceFunction) (t1, t2) -> { if (t1.entity == null) { @@ -105,49 +114,67 @@ public class DedupRecordFactory { t1.entity = reduceEntity(t1.entity, t2.entity); return t1; - } - ) - .flatMap - ((FlatMapFunction, OafEntity>) t -> { - String dedupId = t._1(); - DedupRecordReduceState agg = t._2(); + }) + .flatMap((FlatMapFunction, OafEntity>) t -> { + String dedupId = t._1(); + DedupRecordReduceState agg = t._2(); - if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { - return Collections.emptyIterator(); - } + if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { + return Collections.emptyIterator(); + } - return Stream.concat(Stream.of(agg.getDedupId()), agg.aliases.stream()) - .map(id -> { - try { - OafEntity res = (OafEntity) BeanUtils.cloneBean(agg.entity); - res.setId(id); - res.setDataInfo(dataInfo); - res.setLastupdatetimestamp(ts); - return res; - } catch (Exception e) { - throw new RuntimeException(e); - } - }).iterator(); - }, beanEncoder); + return Stream + .concat( + Stream + .of(agg.getDedupId()) + .map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)), + agg.aliases + .stream() + .map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts))) + .iterator(); + }, beanEncoder); + } + + private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { + try { + OafEntity res = (OafEntity) BeanUtils.cloneBean(base); + res.setId(id); + res.setDataInfo(dataInfo); + res.setLastupdatetimestamp(ts); + return res; + } catch (Exception e) { + throw new RuntimeException(e); + } + } + + private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { + try { + OafEntity res = createDedupOafEntity(id, base, dataInfo, ts); + DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo); + ds.setDeletedbyinference(true); + res.setDataInfo(ds); + return res; + } catch (Exception e) { + throw new RuntimeException(e); + } } private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) { - if (duplicate == null) { - return entity; - } - + if (duplicate == null) { + return entity; + } int compare = new IdentifierComparator<>() .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); if (compare > 0) { - OafEntity swap = duplicate; + OafEntity swap = duplicate; duplicate = entity; entity = swap; } - entity.mergeFrom(duplicate); + entity = MergeUtils.checkedMerge(entity, duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result re = (Result) entity; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index 191870d3b0..59626c1414 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -242,13 +242,14 @@ public class SparkCreateMergeRels extends AbstractSparkAction { // this was a pivot in a previous graph but it has been merged into a new group with different // pivot - if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id) && !dedupId.equals(pivotDedupId)) { + if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id) + && !dedupId.equals(pivotDedupId)) { // materialize the previous dedup record as a merge relation with the new one res.add(new Tuple3<>(dedupId, pivotDedupId, null)); } // add merge relations - if (cut <=0 || r.getAs("position") <= cut) { + if (cut <= 0 || r. getAs("position") <= cut) { res.add(new Tuple3<>(id, pivotDedupId, pivot)); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index cb1c700599..77e6965019 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup; import static org.apache.spark.sql.functions.col; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -127,10 +128,8 @@ public class SparkPropagateRelation extends AbstractSparkAction { (MapFunction) r -> String .join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()), Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> { - b.mergeFrom(a); - return b; - }) + .reduceGroups((ReduceFunction) MergeUtils::mergeRelation + ) .map((MapFunction, Relation>) Tuple2::_2, REL_BEAN_ENC); final String outputRelationPath = graphOutputPath + "/relation"; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/config-default.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/config-default.xml new file mode 100644 index 0000000000..17bb706477 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/config-default.xml @@ -0,0 +1,26 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + sparkSqlWarehouseDir + /user/hive/warehouse + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql new file mode 100644 index 0000000000..86dbda1c97 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql @@ -0,0 +1,62 @@ + +CREATE TABLE `${pivot_history_db}`.`dataset_new` STORED AS PARQUET AS +WITH pivots ( + SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation` + LEFT SEMI JOIN `${new_graph_db}`.`dataset` ON relation.source = dataset.id + LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot' +UNION + SELECT id, usedIn FROM `${pivot_history_db}`.`dataset` LATERAL VIEW EXPLODE(usages) AS usedIn +) +SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages + FROM pivots + GROUP BY id; /*EOS*/ +CREATE TABLE `${pivot_history_db}`.`publication_new` STORED AS PARQUET AS +WITH pivots ( + SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation` + LEFT SEMI JOIN `${new_graph_db}`.`publication` ON relation.source = publication.id + LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot' +UNION + SELECT id, usedIn FROM `${pivot_history_db}`.`publication` LATERAL VIEW EXPLODE(usages) AS usedIn +) +SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages + FROM pivots + GROUP BY id; /*EOS*/ +CREATE TABLE `${pivot_history_db}`.`software_new` STORED AS PARQUET AS +WITH pivots ( + SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation` + LEFT SEMI JOIN `${new_graph_db}`.`software` ON relation.source = software.id + LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot' +UNION + SELECT id, usedIn FROM `${pivot_history_db}`.`software` LATERAL VIEW EXPLODE(usages) AS usedIn +) +SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages + FROM pivots + GROUP BY id; /*EOS*/ +CREATE TABLE `${pivot_history_db}`.`otherresearchproduct_new` STORED AS PARQUET AS +WITH pivots ( + SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation` + LEFT SEMI JOIN `${new_graph_db}`.`otherresearchproduct` ON relation.source = otherresearchproduct.id + LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot' +UNION + SELECT id, usedIn FROM `${pivot_history_db}`.`otherresearchproduct` LATERAL VIEW EXPLODE(usages) AS usedIn +) +SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages + FROM pivots + GROUP BY id; /*EOS*/ + + +DROP TABLE IF EXISTS `${pivot_history_db}`.`dataset_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`dataset` RENAME TO `${pivot_history_db}`.`dataset_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`dataset_new` RENAME TO `${pivot_history_db}`.`dataset`; /*EOS*/ + +DROP TABLE IF EXISTS `${pivot_history_db}`.`publication_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`publication` RENAME TO `${pivot_history_db}`.`publication_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`publication_new` RENAME TO `${pivot_history_db}`.`publication`; /*EOS*/ + +DROP TABLE IF EXISTS `${pivot_history_db}`.`software_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`software` RENAME TO `${pivot_history_db}`.`software_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`software_new` RENAME TO `${pivot_history_db}`.`software`; /*EOS*/ + +DROP TABLE IF EXISTS `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`otherresearchproduct` RENAME TO `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/ +ALTER TABLE `${pivot_history_db}`.`otherresearchproduct_new` RENAME TO `${pivot_history_db}`.`otherresearchproduct`; /*EOS*/ diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/workflow.xml new file mode 100644 index 0000000000..d562f088e9 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/workflow.xml @@ -0,0 +1,95 @@ + + + + + pivot_history_db + + Pivot history DB on hive + + + new_graph_db + + New graph DB on hive + + + new_graph_date + + Creation date of new graph db + + + + + hiveMetastoreUris + hive server metastore URIs + + + sparkSqlWarehouseDir + + + + sparkClusterOpts + --conf spark.network.timeout=600 --conf spark.extraListeners= --conf spark.sql.queryExecutionListeners= --conf spark.yarn.historyServer.address=http://iis-cdh5-test-m3.ocean.icm.edu.pl:18088 --conf spark.eventLog.dir=hdfs://nameservice1/user/spark/applicationHistory + spark cluster-wide options + + + sparkResourceOpts + --executor-memory=3G --conf spark.executor.memoryOverhead=3G --executor-cores=6 --driver-memory=8G --driver-cores=4 + spark resource options + + + sparkApplicationOpts + --conf spark.sql.shuffle.partitions=3840 + spark resource options + + + + + ${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 + Upgrade Pivot History + eu.dnetlib.dhp.oozie.RunSQLSparkJob + dhp-dedup-openaire-${projectVersion}.jar + + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + ${sparkClusterOpts} + ${sparkResourceOpts} + ${sparkApplicationOpts} + + --hiveMetastoreUris${hiveMetastoreUris} + --sqleu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql + --pivot_history_db${pivot_history_db} + --new_graph_db${new_graph_db} + --new_graph_date${new_graph_date} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9ffaeeeef7..42332b02ed 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -3,17 +3,18 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.functions.col import org.apache.spark.sql._ 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 SparkGenerateDoiBoost { @@ -78,8 +79,10 @@ object SparkGenerateDoiBoost { if (item._2 != null) { val otherPub = item._2._2 if (otherPub != null) { - crossrefPub.mergeFrom(otherPub) - crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)) + val mergedAuthor = AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor) + val res = MergeUtils.mergePublication(crossrefPub, otherPub) + res.setAuthor(mergedAuthor); + return res } } crossrefPub @@ -130,14 +133,13 @@ object SparkGenerateDoiBoost { // So we have to merge val b1 = left._2 val b2 = right._2 - b1.mergeFrom(b2) - b1.mergeOAFDataInfo(b2) val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) + val merged = MergeUtils.mergePublication(b1, b2); + merged.setAuthor(authors) if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) + merged.setId(b2.getId) //Return publication Merged - (b1.getId, b1) + (merged.getId, merged) } } else { // Left is Null so we return right diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index ee857e2c4c..64090733d7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -25,7 +25,7 @@ case class mappingAffiliation(name: String) {} case class mappingAuthor( given: Option[String], - family: String, + family: Option[String], sequence: Option[String], ORCID: Option[String], affiliation: Option[mappingAffiliation] @@ -226,14 +226,14 @@ case object Crossref2Oaf { //Mapping Author val authorList: List[mappingAuthor] = - (json \ "author").extractOrElse[List[mappingAuthor]](List()) + (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined) val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) => a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first") ) result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) => - generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull, index) + generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index) }.asJava) // Mapping instance diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala index 9a0b0d8455..185381f8f7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -1,8 +1,8 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory -import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject} +import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, MergeUtils} +import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, Subject} import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import org.json4s @@ -142,8 +142,7 @@ case object ConversionUtil { def mergePublication(a: Publication, b: Publication): Publication = { if ((a != null) && (b != null)) { - a.mergeFrom(b) - a + MergeUtils.mergePublication(a, b) } else { if (a == null) b else a } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json new file mode 100644 index 0000000000..8e75f35866 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json @@ -0,0 +1 @@ +{"indexed":{"date-parts":[[2023,12,29]],"date-time":"2023-12-29T10:40:34Z","timestamp":1703846434800},"reference-count":65,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2023,2,9]],"date-time":"2023-02-09T00:00:00Z","timestamp":1675900800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,2,9]],"date-time":"2023-02-09T00:00:00Z","timestamp":1675900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat. 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diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java new file mode 100644 index 0000000000..987e7afef4 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Action implements Serializable { + private String clazz; + private String method; + private List params; + + public String getClazz() { + return clazz; + } + + public void setClazz(String clazz) { + this.clazz = clazz; + } + + public String getMethod() { + return method; + } + + public void setMethod(String method) { + this.method = method; + } + + public List getParams() { + return params; + } + + public void setParams(List params) { + this.params = params; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java new file mode 100644 index 0000000000..444e8b82dd --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 19/01/24 + */ +public class ExecSubstringAction implements Serializable { + + private String value; + private String from; + private String to; + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getFrom() { + return from; + } + + public void setFrom(String from) { + this.from = from; + } + + public String getTo() { + return to; + } + + public void setTo(String to) { + this.to = to; + } + + public String execSubstring() { + + return this.value.substring(Integer.valueOf(this.from), Integer.valueOf(this.to)); + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java new file mode 100644 index 0000000000..6a0d20b579 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class MapModel implements Serializable { + + private String path; + private Action action; + + public String getPath() { + return path; + } + + public void setPath(String path) { + this.path = path; + } + + public Action getAction() { + return action; + } + + public void setAction(Action action) { + this.action = action; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java new file mode 100644 index 0000000000..973b00b770 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Parameters implements Serializable { + private String paramName; + private String paramValue; + + public String getParamName() { + return paramName; + } + + public void setParamName(String paramName) { + this.paramName = paramName; + } + + public String getParamValue() { + return paramValue; + } + + public void setParamValue(String paramValue) { + this.paramValue = paramValue; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java index fd74817199..dc75aec37e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java @@ -4,7 +4,9 @@ package eu.dnetlib.dhp.bulktag.community; import java.io.Serializable; import java.util.HashMap; -public class ProtoMap extends HashMap implements Serializable { +import eu.dnetlib.dhp.bulktag.actions.MapModel; + +public class ProtoMap extends HashMap implements Serializable { public ProtoMap() { super(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 98c46cf003..2ea229e3e1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -5,6 +5,8 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.lang.reflect.Method; import java.util.*; import java.util.stream.Collectors; @@ -15,7 +17,10 @@ import org.slf4j.LoggerFactory; import com.google.gson.Gson; import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.JsonPath; +import com.jayway.jsonpath.PathNotFoundException; +import eu.dnetlib.dhp.bulktag.actions.MapModel; +import eu.dnetlib.dhp.bulktag.actions.Parameters; import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @@ -35,27 +40,59 @@ public class ResultTagger implements Serializable { return (tmp != clist.size()); } - private Map> getParamMap(final Result result, Map params) { + private Map> getParamMap(final Result result, Map params) + throws NoSuchMethodException, InvocationTargetException { Map> param = new HashMap<>(); String json = new Gson().toJson(result, Result.class); DocumentContext jsonContext = JsonPath.parse(json); + if (params == null) { params = new HashMap<>(); } for (String key : params.keySet()) { + MapModel mapModel = params.get(key); + try { - param.put(key, jsonContext.read(params.get(key))); - } catch (com.jayway.jsonpath.PathNotFoundException e) { + String path = mapModel.getPath(); + Object obj = jsonContext.read(path); + List pathValue; + if (obj instanceof java.lang.String) + pathValue = Arrays.asList((String) obj); + else + pathValue = (List) obj; + if (Optional.ofNullable(mapModel.getAction()).isPresent()) { + Class c = Class.forName(mapModel.getAction().getClazz()); + Object class_instance = c.newInstance(); + Method setField = c.getMethod("setValue", String.class); + setField.invoke(class_instance, pathValue.get(0)); + for (Parameters p : mapModel.getAction().getParams()) { + setField = c.getMethod("set" + p.getParamName(), String.class); + setField.invoke(class_instance, p.getParamValue()); + } + + param + .put( + key, Arrays + .asList((String) c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance))); + + } + + else { + param.put(key, pathValue); + } + + } catch (PathNotFoundException | ClassNotFoundException | InstantiationException + | IllegalAccessException e) { param.put(key, new ArrayList<>()); } } return param; + } public R enrichContextCriteria( - final R result, final CommunityConfiguration conf, final Map criteria) { - - final Map> param = getParamMap(result, criteria); + final R result, final CommunityConfiguration conf, final Map criteria) + throws InvocationTargetException, NoSuchMethodException { // Verify if the entity is deletedbyinference. In case verify if to clean the context list // from all the zenodo communities @@ -64,6 +101,8 @@ public class ResultTagger implements Serializable { return result; } + final Map> param = getParamMap(result, criteria); + // Execute the EOSCTag for the services switch (result.getResulttype().getClassid()) { case PUBLICATION_RESULTTYPE_CLASSID: diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java new file mode 100644 index 0000000000..f771208007 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("greater_than") +public class GreatThanVerb implements Selection, Serializable { + + private String param; + + public GreatThanVerb() { + } + + public GreatThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) > 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java new file mode 100644 index 0000000000..4aa52bfae1 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("lesser_than") +public class LessThanVerb implements Selection, Serializable { + + private String param; + + public LessThanVerb() { + } + + public LessThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) < 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} 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 4f755266a1..f84a10d1c0 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 @@ -149,7 +149,7 @@ public class SparkResultToCommunityFromOrganizationJob { } } // res.setContext(propagatedContexts); - // ret.mergeFrom(res); + // return MergeUtils.mergeResult(ret, res); } return ret; }; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index f9c36d7ca3..f791825a76 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -13,6 +13,7 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -24,8 +25,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; -import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Context; @@ -162,7 +161,7 @@ public class SparkResultToCommunityFromProject implements Serializable { } } res.setContext(propagatedContexts); - ret.mergeFrom(res); + return MergeUtils.checkedMerge(ret, res); } return ret; }; 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 3cf2f73c3e..d2bfd75c11 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 @@ -25,118 +25,118 @@ import scala.Tuple2; public class SparkResultToCommunityThroughSemRelJob { - private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class); + private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkResultToCommunityThroughSemRelJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")); + String jsonConfiguration = IOUtils + .toString( + SparkResultToCommunityThroughSemRelJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + parser.parseArgument(args); - Boolean isSparkSessionManaged = isSparkSessionManaged(parser); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + 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); - final String preparedInfoPath = parser.get("preparedInfoPath"); - log.info("preparedInfoPath: {}", preparedInfoPath); + final String preparedInfoPath = parser.get("preparedInfoPath"); + log.info("preparedInfoPath: {}", preparedInfoPath); - SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); + final Boolean saveGraph = Optional + .ofNullable(parser.get("saveGraph")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("saveGraph: {}", saveGraph); - @SuppressWarnings("unchecked") - Class resultClazz = (Class) Class.forName(resultClassName); + @SuppressWarnings("unchecked") + Class resultClazz = (Class) Class.forName(resultClassName); - runWithSparkHiveSession( - conf, - isSparkSessionManaged, - spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } - if (saveGraph) { - execPropagation( - spark, inputPath, outputPath, preparedInfoPath, resultClazz); - } - }); - } + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + if (isTest(parser)) { + removeOutputDir(spark, outputPath); + } + if (saveGraph) { + execPropagation( + spark, inputPath, outputPath, preparedInfoPath, resultClazz); + } + }); + } - private static void execPropagation( - SparkSession spark, - String inputPath, - String outputPath, - String preparedInfoPath, - Class resultClazz) { + private static void execPropagation( + SparkSession spark, + String inputPath, + String outputPath, + String preparedInfoPath, + Class resultClazz) { - Dataset possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class); - Dataset result = readPath(spark, inputPath, resultClazz); + Dataset possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class); + Dataset result = readPath(spark, inputPath, resultClazz); - result - .joinWith( - possibleUpdates, - result.col("id").equalTo(possibleUpdates.col("resultId")), - "left_outer") - .map(contextUpdaterFn(), Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + result + .joinWith( + possibleUpdates, + result.col("id").equalTo(possibleUpdates.col("resultId")), + "left_outer") + .map(contextUpdaterFn(), Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); - } + } - private static MapFunction, R> contextUpdaterFn() { - return value -> { - R ret = value._1(); - Optional rcl = Optional.ofNullable(value._2()); - if (rcl.isPresent()) { - Set contexts = new HashSet<>(); - ret.getContext().forEach(c -> contexts.add(c.getId())); - rcl - .get() - .getCommunityList() - .stream() - .forEach( - c -> { - if (!contexts.contains(c)) { - Context newContext = new Context(); - newContext.setId(c); - newContext - .setDataInfo( - Arrays - .asList( - getDataInfo( - PROPAGATION_DATA_INFO_TYPE, - PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, - PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); - ret.getContext().add(newContext); - } + private static MapFunction, R> contextUpdaterFn() { + return value -> { + R ret = value._1(); + Optional rcl = Optional.ofNullable(value._2()); + if (rcl.isPresent()) { + Set contexts = new HashSet<>(); + ret.getContext().forEach(c -> contexts.add(c.getId())); + rcl + .get() + .getCommunityList() + .stream() + .forEach( + c -> { + if (!contexts.contains(c)) { + Context newContext = new Context(); + newContext.setId(c); + newContext + .setDataInfo( + Arrays + .asList( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, + PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS))); + ret.getContext().add(newContext); + } - }); + }); - } + } - return ret; - }; - } + return ret; + }; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml index bab1e55dfa..a9642d6379 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml @@ -114,7 +114,7 @@ --sourcePath${sourcePath} --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/orcid/preparedInfo/targetOrcidAssoc + --outputPath${workingDir}/orcid/targetOrcidAssoc --allowedsemrels${allowedsemrels} @@ -142,7 +142,7 @@ --sourcePath${sourcePath} --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/orcid/preparedInfo/targetOrcidAssoc + --outputPath${workingDir}/orcid/targetOrcidAssoc --allowedsemrels${allowedsemrels} @@ -170,7 +170,7 @@ --sourcePath${sourcePath} --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/orcid/preparedInfo/targetOrcidAssoc + --outputPath${workingDir}/orcid/targetOrcidAssoc --allowedsemrels${allowedsemrels} @@ -198,7 +198,7 @@ --sourcePath${sourcePath} --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/orcid/preparedInfo/targetOrcidAssoc + --outputPath${workingDir}/orcid/targetOrcidAssoc --allowedsemrels${allowedsemrels} @@ -225,8 +225,8 @@ --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - --sourcePath${workingDir}/orcid/orcidprop - --outputPath${workingDir}/orcid/orcidprop/mergedOrcidAssoc + --sourcePath${workingDir}/orcid/targetOrcidAssoc + --outputPath${workingDir}/orcid/mergedOrcidAssoc @@ -247,9 +247,10 @@ eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob dhp-enrichment-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} + --executor-cores=4 + --executor-memory=4G --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=5G --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} @@ -259,9 +260,9 @@ --conf spark.speculation=false --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=15000 - --possibleUpdatesPath${workingDir}/orcid/orcidprop/mergedOrcidAssoc + --possibleUpdatesPath${workingDir}/orcid/mergedOrcidAssoc --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -291,7 +292,7 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath${workingDir}/orcid/orcidprop/mergedOrcidAssoc + --possibleUpdatesPath${workingDir}/orcid/mergedOrcidAssoc --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -321,7 +322,7 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath${workingDir}/orcid/orcidprop/mergedOrcidAssoc + --possibleUpdatesPath${workingDir}/orcid/mergedOrcidAssoc --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -351,7 +352,7 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath${workingDir}/orcid/orcidprop/mergedOrcidAssoc + --possibleUpdatesPath${workingDir}/orcid/mergedOrcidAssoc --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 743e62b5f9..433e046cc8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -13,6 +13,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -31,18 +32,26 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," - + " \"title\" : \"$['title'][*]['value']\"," - + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," - + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\", " - + " \"subject\" :\"$['subject'][*]['value']\" , " + - "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + - "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + - "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + - "\"publisher\":\"$['publisher'].value\"," + - "\"publicationyear\":\"$['dateofacceptance'].value\"} "; + public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," + + " \"title\":{\"path\":\"$['title'][*]['value']\"}, " + + " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " + + " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ," + + + "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," + + " \"description\" : {\"path\":\"$['description'][*]['value']\"}," + + " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " + + " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " + + "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," + + "\"journal\":{\"path\":\"$['journal'].name\"}," + + "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," + + "\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," + + "\"publisher\":{\"path\":\"$['publisher'].value\"}," + + "\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " + + " \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," + + "\"method\":\"execSubstring\"," + + "\"params\":[" + + "{\"paramName\":\"From\", \"paramValue\":0}, " + + "{\"paramName\":\"To\",\"paramValue\":4}]}}}"; private static SparkSession spark; @@ -1600,4 +1609,94 @@ public class BulkTagJobTest { Assertions.assertEquals(0, spark.sql(query).count()); } + @Test + void pubdateTest() throws Exception { + + final String pathMap = BulkTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(), + "-taggingConf", + IOUtils + .toString( + BulkTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")), + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset queryResult = spark.sql(query); + queryResult.show(false); + Assertions.assertEquals(5, queryResult.count()); + + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")) + .count()); + + } + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml new file mode 100644 index 0000000000..26f1ca8221 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml @@ -0,0 +1,1431 @@ + + + + + + + zenodo + + + + + + + + + + + + + + + + + + + + + + 10|re3data_____::a507cdacc5bbcc08761c92185dee5cab + + + + + + + + + + + + rda + + + + + + + + SDG13 - Climate action + SDG8 - Decent work and economic growth + SDG15 - Life on land + SDG2 - Zero hunger + SDG17 - Partnerships for the goals + SDG10 - Reduced inequalities + SDG5 - Gender equality + SDG12 - Responsible consumption and production + SDG14 - Life below water + SDG6 - Clean water and sanitation + SDG11 - Sustainable cities and communities + SDG1 - No poverty + SDG3 - Good health and well being + SDG7 - Affordable and clean energy + SDG4 - Quality education + SDG9 - Industry innovation and infrastructure + SDG16 - Peace justice and strong institutions + + + + + + + + modern art + monuments + europeana data model + sites + field walking + frescoes + LIDO metadata schema + art history + excavation + Arts and Humanities General + cities + coins + temples + numismatics + lithics + roads + environmental archaeology + digital cultural heritage + archaeological reports + history + CRMba + churches + cultural heritage + archaeological stratigraphy + religious art + buidings + digital humanities + survey + archaeological sites + linguistic studies + bioarchaeology + architectural orders + palaeoanthropology + fine arts + europeana + CIDOC CRM + decorations + classic art + stratigraphy + digital archaeology + intangible cultural heritage + walls + humanities + chapels + CRMtex + Language and Literature + paintings + archaeology + fair data + mosaics + burials + architecture + medieval art + castles + CARARE metadata schema + statues + natural language processing + inscriptions + CRMsci + vaults + contemporary art + Arts and Humanities + CRMarchaeo + pottery + site + architectural + vessels + + + + 10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + 10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + 10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + 10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + + 10|doajarticles::0da84e9dfdc8419576169e027baa8028 + + + + 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 + + + + 10|openaire____::c5502a43e76feab55dd00cf50f519125 + + + + 10|re3data_____::a48f09c562b247a9919acfe195549b47 + + + + 10|opendoar____::97275a23ca44226c9964043c8462be96 + + + + + + storm + + + + crosscult + + + + wholodance_eu + + + + digcur2013 + + + + gravitate + + + + dipp2014 + + + + digitalhumanities + + + + dimpo + + + + adho + + + + chc + + + + wahr + + + + ibe + + + + ariadne + + + + parthenos-hub + + + + parthenos-training + + + + gandhara + + + + cmsouthasia + + + + nilgirihills + + + + shamsa_mustecio + + + + bodhgaya + + + + oac_dh-ch + + + + + + + Stock Assessment + pelagic + Acoustic + Fish farming + Fisheries + Fishermen + maximum sustainable yield + trawler + Fishing vessel + Fisherman + Fishing gear + mackerel + RFMO + Fish Aggregating Device + Bycatch + Fishery + common fisheries policy + Fishing fleet + Aquaculture + + + + 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Transport + transport vulnerability + Pipeline transport + European Association of Aviation Training and Education Organisations + Defrosting of railway infrastructure + Inclusive and affordable transport + River Information Services + jel:L92 + Increased use of public transport + Seamless mobility + STRIA + trolleybus transport + Intelligent Transport System + Low-emission alternative energy for transport + Shared mobility for people and goods + Business model for urban mobility + Interoperability of transport systems + Cross-border train slot booking + Air transport + Transport pricing + Sustainable transport + European Rail Transport Research Advisory Council + Alternative aircraft configurations + Transport and Mobility + Railways applications + urban transport + Environmental impact of transport + urban freight delivery systems + Automated Road Transport + Alternative fuels in public transport + Active LIDAR-sensor for GHG-measurements + Autonomous logistics operations + Rational 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Europea","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":"Desinformación","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":"Política","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":"Periodismo","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":"Ciudadanos europeos","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":"Democracias","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":"Estado de derecho","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":"Derechos humanos","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":"5910.02 Medios de Comunicación de Masas","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":"Ramón Luis Varcárcel - La Unión Europea ante el reto de la desinformación","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":"Conferencia de Ramón Luis Valcárcel, vicepresidente del Parlamento Europeo, en el Campus de Almagro de la Universidad Camilo José Cela (UCJC) bajo el título \"La Unión Europea ante el reto de la desinformación\", en la que ha alertado sobre el alcance de la desinformación en las democracias y sobre cómo pone en peligro los derechos de los ciudadanos europeos. También ha participado el rector de la UCJC, Samuel Martín-Barbero.","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":"2018-10-11","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":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":{"value":"http://creativecommons.org/licenses/by-nc-nd/4.0/","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"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0024","classname":"Film","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::3989","value":"Depósito Digital e-UCJC","dataInfo":null},"url":["http://hdl.handle.net/20.500.12020/795"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::3989","value":"Depósito Digital e-UCJC","dataInfo":null},"dateofacceptance":{"value":"2018-10-11","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":null}],"storagedate":null,"device":null,"size":null,"version":null,"lastmetadataupdate":null,"metadataversionnumber":null,"geolocation":[]} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/datasource b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/datasource new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/otherresearchproduct b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/otherresearchproduct new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/publication b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/publication new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/software b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/software new file mode 100644 index 0000000000..e69de29bb2 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 d4f1d9f55e..66a178c700 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 @@ -7,6 +7,7 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -24,7 +25,6 @@ import eu.dnetlib.dhp.common.HdfsSupport; 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.utils.OafMapperUtils; import scala.Tuple2; /** @@ -248,11 +248,11 @@ public class MergeGraphTableSparkJob { private T mergeAndGet(T b, T a) { if (Objects.nonNull(a) && Objects.nonNull(b)) { if (ModelSupport.isSubClass(a, OafEntity.class) && ModelSupport.isSubClass(b, OafEntity.class)) { - return (T) OafMapperUtils.mergeEntities((OafEntity) b, (OafEntity) a); + return (T) MergeUtils.merge(b, a); } if (a instanceof Relation && b instanceof Relation) { ((Relation) a).mergeFrom(b); - return a; + return (T) MergeUtils.mergeRelation((Relation)a, (Relation) b); } } return Objects.isNull(a) ? b : a; 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 79ee5c5b65..9e1f3c78c4 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 @@ -1,14 +1,16 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Arrays; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; - +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.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.Text; @@ -16,27 +18,18 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.rdd.RDD; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.dom4j.DocumentException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -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.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + public class GenerateEntitiesApplication extends AbstractMigrationApplication { private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); @@ -137,7 +130,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication { save( inputRdd .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf)) - .reduceByKey(OafMapperUtils::merge) + .reduceByKey(MergeUtils::merge) .map(Tuple2::_2), targetPath); break; 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 c69a7a6ffa..da6885db38 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 @@ -317,7 +317,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"))); - p.setPid(new ArrayList<>()); + p.setPid(prepareListOfStructProps(rs.getArray("pid"), info)); p.setDateofcollection(asString(rs.getDate("dateofcollection"))); p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); p.setExtraInfo(new ArrayList<>()); // Values not present in the DB 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 08529125c8..57e0d29555 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 @@ -238,11 +238,23 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { (Element) doc .selectSingleNode( "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) - .map(element -> { - final String resourceTypeURI = element.attributeValue("uri"); - final String resourceTypeAnyURI = element.attributeValue("anyURI"); - final String resourceTypeTxt = element.getText(); - final String resourceTypeGeneral = element.attributeValue("resourceTypeGeneral"); + .map(e -> { + final String resourceTypeURI = Optional + .ofNullable(e.attributeValue("uri")) + .filter(StringUtils::isNotBlank) + .orElse(null); + final String resourceTypeAnyURI = Optional + .ofNullable(e.attributeValue("anyURI")) + .filter(StringUtils::isNotBlank) + .orElse(null); + final String resourceTypeTxt = Optional + .ofNullable(e.getText()) + .filter(StringUtils::isNotBlank) + .orElse(null); + final String resourceTypeGeneral = Optional + .ofNullable(e.attributeValue("resourceTypeGeneral")) + .filter(StringUtils::isNotBlank) + .orElse(null); return ObjectUtils .firstNonNull(resourceTypeURI, resourceTypeAnyURI, resourceTypeTxt, resourceTypeGeneral); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml index bbd3581c57..72fc9e3387 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml @@ -12,6 +12,16 @@ targetPath the output path of the graph enriched + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + @@ -31,8 +41,8 @@ --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.executor.memoryOverhead=2g - --conf spark.sql.shuffle.partitions=3000 + --conf spark.executor.memoryOverhead=${sparkExecutorMemory} + --conf spark.sql.shuffle.partitions=5000 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} @@ -49,10 +59,10 @@ - - - - + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql index af5913e75f..fb584943f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql @@ -33,7 +33,7 @@ SELECT dc.officialname AS collectedfromname, p.contracttype || '@@@' || p.contracttypescheme AS contracttype, p.provenanceactionclass || '@@@' || p.provenanceactionscheme AS provenanceaction, - array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, + array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid,, array_agg(DISTINCT s.name || '###' || s.semanticclass || '@@@' || s.semanticscheme) AS subjects, array_agg(DISTINCT fp.path) AS fundingtree diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql index 80cbda4b7b..76a7fce234 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql @@ -33,7 +33,7 @@ SELECT dc.officialname AS collectedfromname, p.contracttypeclass || '@@@' || p.contracttypescheme AS contracttype, p.provenanceactionclass || '@@@' || p.provenanceactionscheme AS provenanceaction, - array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, + array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid, array_agg(DISTINCT s.name || '###' || s.semanticclass || '@@@' || s.semanticscheme) AS subjects, array_agg(DISTINCT fp.path) AS fundingtree FROM projects p diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala deleted file mode 100644 index 15513c8af7..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala +++ /dev/null @@ -1,40 +0,0 @@ -package eu.dnetlib.dhp.enrich.orcid - -import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.{Author, Publication} -import eu.dnetlib.dhp.schema.sx.OafUtils -import org.apache.spark.sql.Row - -import scala.collection.JavaConverters._ - -object AuthorEnricher extends Serializable { - - def createAuthor(givenName: String, familyName: String, orcid: String): Author = { - val a = new Author - a.setName(givenName) - a.setSurname(familyName) - a.setFullname(s"$givenName $familyName") - val pid = OafUtils.createSP(orcid, ModelConstants.ORCID, ModelConstants.ORCID) - pid.setDataInfo(OafUtils.generateDataInfo()) - pid.getDataInfo.setProvenanceaction(OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT")) - a.setPid(List(pid).asJava) - a - } - - def toOAFAuthor(r: Row): java.util.List[Author] = { - r.getList[Row](1) - .asScala - .map(s => createAuthor(s.getAs[String]("givenName"), s.getAs[String]("familyName"), s.getAs[String]("orcid"))) - .toList - .asJava - } - -// def enrichAuthor(p:Publication,r:Row): Unit = { -// val k:Map[String, OAuthor] =r.getList[Row](1).asScala.map(s => (s.getAs[String]("orcid"), OAuthor(s.getAs[String]("givenName") ,s.getAs[String]("familyName") ))).groupBy(_._1).mapValues(_.map(_._2).head) -// println(k) -// -// -// -// } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala new file mode 100644 index 0000000000..e2e7fada6e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala @@ -0,0 +1,128 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Author, StructuredProperty} +import eu.dnetlib.dhp.schema.sx.OafUtils + +import java.util +import scala.beans.BeanProperty +import scala.collection.JavaConverters._ +import scala.util.control.Breaks.{break, breakable} + +case class ORCIDAuthorEnricherResult( + @BeanProperty var id: String, + @BeanProperty var enriched_author: java.util.List[Author], + @BeanProperty var author_matched: java.util.List[MatchedAuthors], + @BeanProperty var author_unmatched: java.util.List[Author], + @BeanProperty var orcid_unmatched: java.util.List[OrcidAutor] +) + +object ORCIDAuthorEnricher extends Serializable { + + def enrichOrcid( + id: String, + graph_authors: java.util.List[Author], + orcid_authors: java.util.List[OrcidAutor] + ): ORCIDAuthorEnricherResult = { + // Author enriching strategy: + // 1) create a copy of graph author list in unmatched_authors + // 2) find best match in unmatched_authors, remove it from unmatched_authors and enrich it so + // that the enrichment is reflected in graph_authors (they share author instances) + // 3) repeat (2) till the end of the list and then with different matching algorithms that have decreasing + // trust in their output + // At the end unmatched_authors will contain authors not matched with any of the matching algos + val unmatched_authors = new util.ArrayList[Author](graph_authors) + + val matches = { + // Look after exact fullname match, reconstruct ORCID fullname as givenName + familyName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.givenName + " " + orcid.familyName), + "fullName" + ) ++ + // Look after exact reversed fullname match, reconstruct ORCID fullname as familyName + givenName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.familyName + " " + orcid.givenName), + "reversedFullName" + ) ++ + // split author names in tokens, order the tokens, then check for matches of full tokens or abbreviations + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers + .matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName), + "orderedTokens" + ) ++ + // look after exact matches of ORCID creditName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.creditName), + "creditName" + ) ++ + // look after exact matches in ORCID otherNames + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + orcid.otherNames != null && ORCIDAuthorMatchers.matchOtherNames(author.getFullname, orcid.otherNames.asScala), + "otherNames" + ) + } + + ORCIDAuthorEnricherResult(id, graph_authors, matches.asJava, unmatched_authors, orcid_authors) + } + + private def extractAndEnrichMatches( + graph_authors: java.util.List[Author], + orcid_authors: java.util.List[OrcidAutor], + matchingFunc: (Author, OrcidAutor) => Boolean, + matchName: String + ) = { + val matched = scala.collection.mutable.ArrayBuffer.empty[MatchedAuthors] + + if (graph_authors != null && !graph_authors.isEmpty) { + val ait = graph_authors.iterator + + while (ait.hasNext) { + val author = ait.next() + val oit = orcid_authors.iterator + + breakable { + while (oit.hasNext) { + val orcid = oit.next() + + if (matchingFunc(author, orcid)) { + ait.remove() + oit.remove() + matched += MatchedAuthors(author, orcid, matchName) + + if (author.getPid == null) { + author.setPid(new util.ArrayList[StructuredProperty]()) + } + + val orcidPID = OafUtils.createSP(orcid.orcid, ModelConstants.ORCID, ModelConstants.ORCID) + orcidPID.setDataInfo(OafUtils.generateDataInfo()) + orcidPID.getDataInfo.setProvenanceaction( + OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT") + ) + + author.getPid.add(orcidPID) + + break() + } + } + } + } + } + + matched + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala new file mode 100644 index 0000000000..49574fe2d4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala @@ -0,0 +1,65 @@ +package eu.dnetlib.dhp.enrich.orcid + +import java.util.Locale +import java.util.regex.Pattern + +object ORCIDAuthorMatchers { + val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+") + + val WORD_DIFF = 2 + + def matchEqualsIgnoreCase(a1: String, a2: String): Boolean = { + if (a1 == null || a2 == null) + false + else + a1 == a2 || a1.toLowerCase(Locale.ROOT).equals(a2.toLowerCase(Locale.ROOT)) + } + + def matchOtherNames(fullName: String, otherNames: Seq[String]): Boolean = { + if (otherNames != null) { + otherNames.exists(matchEqualsIgnoreCase(fullName, _)) + } else { + false + } + } + + def matchOrderedTokenAndAbbreviations(a1: String, a2: String): Boolean = { + val p1: Array[String] = SPLIT_REGEX.split(a1.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted + val p2: Array[String] = SPLIT_REGEX.split(a2.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted + + if (p1.length < 2 || p2.length < 2) return false + if (Math.abs(p1.length - p2.length) > WORD_DIFF) return false // use alternative comparison algo + + var p1Idx: Int = 0 + var p2Idx: Int = 0 + var shortMatches: Int = 0 + var longMatches: Int = 0 + while (p1Idx < p1.length && p2Idx < p2.length) { + val e1: String = p1(p1Idx) + val c1: Char = e1.charAt(0) + val e2: String = p2(p2Idx) + val c2: Char = e2.charAt(0) + if (c1 < c2) p1Idx += 1 + else if (c1 > c2) p2Idx += 1 + else { + var res: Boolean = false + if (e1.length != 1 && e2.length != 1) { + res = e1 == e2 + longMatches += 1 + } else { + res = true + shortMatches += 1 + } + if (res) { + p1Idx += 1 + p2Idx += 1 + } else { + val diff: Int = e1.compareTo(e2) + if (diff < 0) p1Idx += 1 + else if (diff > 0) p2Idx += 1 + } + } + } + longMatches > 0 && (shortMatches + longMatches) == Math.min(p1.length, p2.length) + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala index 4822059c65..0824c2a71e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -1,14 +1,39 @@ package eu.dnetlib.dhp.enrich.orcid import eu.dnetlib.dhp.application.AbstractScalaApplication -import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.common.ModelSupport -import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software} -import org.apache.spark.sql.functions._ +import eu.dnetlib.dhp.schema.oaf._ import org.apache.spark.sql._ +import org.apache.spark.sql.functions._ import org.slf4j.{Logger, LoggerFactory} + +import scala.beans.BeanProperty import scala.collection.JavaConverters._ +case class OrcidAutor( + @BeanProperty var orcid: String, + @BeanProperty var familyName: String, + @BeanProperty var givenName: String, + @BeanProperty var creditName: String, + @BeanProperty var otherNames: java.util.List[String] +) { + def this() = this("null", "null", "null", "null", null) +} + +case class MatchData( + @BeanProperty var id: String, + @BeanProperty var graph_authors: java.util.List[Author], + @BeanProperty var orcid_authors: java.util.List[OrcidAutor] +) { + def this() = this("null", null, null) +} + +case class MatchedAuthors( + @BeanProperty var author: Author, + @BeanProperty var orcid: OrcidAutor, + @BeanProperty var `type`: String +) + class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) extends AbstractScalaApplication(propertyPath, args, log: Logger) { @@ -22,107 +47,132 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] log.info(s"orcidPath is '$orcidPath'") val targetPath = parser.get("targetPath") log.info(s"targetPath is '$targetPath'") - val orcidPublication: Dataset[Row] = generateOrcidTable(spark, orcidPath) -// ModelSupport.entityTypes.entrySet().asScala.filter(k => k.getKey.getClass isInstance(Result)) - enrichResult( - spark, - s"$graphPath/publication", - orcidPublication, - s"$targetPath/publication", - Encoders.bean(classOf[Publication]) - ) - enrichResult( - spark, - s"$graphPath/dataset", - orcidPublication, - s"$targetPath/dataset", - Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset]) - ) - enrichResult( - spark, - s"$graphPath/software", - orcidPublication, - s"$targetPath/software", - Encoders.bean(classOf[Software]) - ) - enrichResult( - spark, - s"$graphPath/otherresearchproduct", - orcidPublication, - s"$targetPath/otherresearchproduct", - Encoders.bean(classOf[OtherResearchProduct]) - ) + createTemporaryData(graphPath, orcidPath, targetPath) + analisys(targetPath) + generateGraph(graphPath, targetPath) } - private def enrichResult[T <: Result]( - spark: SparkSession, - graphPath: String, - orcidPublication: Dataset[Row], - outputPath: String, - enc: Encoder[T] - ): Unit = { + private def generateGraph(graphPath: String, targetPath: String): Unit = { - val entities = spark.read - .schema(enc.schema) - .json(graphPath) - .select(col("id"), col("datainfo"), col("instance")) - .where("datainfo.deletedbyinference != true") - .drop("datainfo") - .withColumn("instances", explode(col("instance"))) - .withColumn("pids", explode(col("instances.pid"))) - .select( - col("pids.qualifier.classid").alias("pid_schema"), - col("pids.value").alias("pid_value"), - col("id").alias("dnet_id") - ) + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + val enc = Encoders.bean(e._2) - val orcidDnet = orcidPublication - .join( - entities, - lower(col("schema")).equalTo(lower(col("pid_schema"))) && - lower(col("value")).equalTo(lower(col("pid_value"))), - "inner" - ) - .groupBy(col("dnet_id")) - .agg(collect_set(orcidPublication("author")).alias("orcid_authors")) - .select("dnet_id", "orcid_authors") - .cache() - orcidDnet.count() - val result = spark.read.schema(enc.schema).json(graphPath).as[T](enc) + val matched = spark.read + .schema(Encoders.bean(classOf[ORCIDAuthorEnricherResult]).schema) + .parquet(s"${targetPath}/${resultType}_matched") + .selectExpr("id", "enriched_author") + + spark.read + .schema(enc.schema) + .json(s"$graphPath/$resultType") + .join(matched, Seq("id"), "left") + .withColumn( + "author", + when(size(col("enriched_author")).gt(0), col("enriched_author")) + .otherwise(col("author")) + ) + .drop("enriched_author") + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(s"${targetPath}/${resultType}") + + }) - result - .joinWith(orcidDnet, result("id").equalTo(orcidDnet("dnet_id")), "left") - .map { - case (r: T, null) => - r - case (p: T, r: Row) => - p.setAuthor(AuthorMerger.enrichOrcid(p.getAuthor, AuthorEnricher.toOAFAuthor(r))) - p - }(enc) - .write - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath) } - private def generateOrcidTable(spark: SparkSession, inputPath: String): Dataset[Row] = { + private def createTemporaryData(graphPath: String, orcidPath: String, targetPath: String): Unit = { val orcidAuthors = - spark.read.load(s"$inputPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + spark.read.load(s"$orcidPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + val orcidWorks = spark.read - .load(s"$inputPath/Works") + .load(s"$orcidPath/Works") .select(col("orcid"), explode(col("pids")).alias("identifier")) .where( - "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" + "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" // scopus eid ? ) - val orcidPublication = orcidAuthors - .join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) + + val orcidWorksWithAuthors = orcidAuthors + .join(orcidWorks, Seq("orcid")) .select( - col("identifier.schema").alias("schema"), - col("identifier.value").alias("value"), - struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") + lower(col("identifier.schema")).alias("pid_schema"), + lower(col("identifier.value")).alias("pid_value"), + struct( + col("orcid"), + col("givenName"), + col("familyName"), + col("creditName"), + col("otherNames") + ).alias("author") ) - orcidPublication.cache() + .cache() + + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + val enc = Encoders.bean(e._2) + + val oaEntities = spark.read + .schema(enc.schema) + .json(s"$graphPath/$resultType") + .select(col("id"), col("datainfo"), col("instance")) + .where("datainfo.deletedbyinference != true") + .drop("datainfo") + .withColumn("instances", explode(col("instance"))) + .withColumn("pids", explode(col("instances.pid"))) + .select( + lower(col("pids.qualifier.classid")).alias("pid_schema"), + lower(col("pids.value")).alias("pid_value"), + col("id") + ) + + val orcidDnet = orcidWorksWithAuthors + .join( + oaEntities, + Seq("pid_schema", "pid_value"), + "inner" + ) + .groupBy(col("id")) + .agg(collect_set(col("author")).alias("orcid_authors")) + .select("id", "orcid_authors") + + val result = + spark.read.schema(enc.schema).json(s"$graphPath/$resultType").selectExpr("id", "author as graph_authors") + + result + .join(orcidDnet, Seq("id")) + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .parquet(s"$targetPath/${resultType}_unmatched") + }) + + orcidWorksWithAuthors.unpersist() + } + + private def analisys(targetPath: String): Unit = { + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + + spark.read + .parquet(s"$targetPath/${resultType}_unmatched") + .where("size(graph_authors) > 0") + .as[MatchData](Encoders.bean(classOf[MatchData])) + .map(md => { + ORCIDAuthorEnricher.enrichOrcid(md.id, md.graph_authors, md.orcid_authors) + })(Encoders.bean(classOf[ORCIDAuthorEnricherResult])) + .write + .option("compression", "gzip") + .mode("overwrite") + .parquet(s"$targetPath/${resultType}_matched") + }) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala index 5339482896..9d7cca7dd2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala @@ -93,8 +93,8 @@ object CopyHdfsOafSparkApplication { hasSource != null && hasTarget != null } else { val hasId = (json \ "id").extractOrElse[String](null) - val resultType = (json \ "resulttype" \ "classid").extractOrElse[String](null) - hasId != null && oafType.equalsIgnoreCase(resultType) + val resultType = (json \ "resulttype" \ "classid").extractOrElse[String]("") + hasId != null && oafType.startsWith(resultType) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala index f5a13e72bf..0c9f0d7bad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.IOUtils import org.apache.hadoop.fs.{FileSystem, Path} @@ -118,15 +119,12 @@ object SparkResolveEntities { currentEntityDataset .joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left") .map(k => { - val a = k._1 val b = k._2 if (b == null) a._2 - else { - a._2.mergeFrom(b._2) - a._2 - } + else + MergeUtils.mergeResult(a._2, b._2) }) .map(r => mapper.writeValueAsString(r))(Encoders.STRING) .write diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala index 704c9ab5c5..ecf612cc74 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.sx.graph import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf @@ -130,10 +131,7 @@ object SparkCreateInputGraph { val ds: Dataset[T] = spark.read.load(sourcePath).as[T] ds.groupByKey(_.getId) - .reduceGroups { (x: T, y: T) => - x.mergeFrom(y) - x - } + .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] } .map(_._2) .write .mode(SaveMode.Overwrite) diff --git a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java similarity index 71% rename from dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java rename to dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java index c0a8d69279..0b50312a59 100644 --- a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java @@ -1,10 +1,9 @@ -package eu.dnetlib.oa.merge; - -import static org.junit.jupiter.api.Assertions.*; +package eu.dnetlib.dhp.enrich.orcid; import java.io.BufferedReader; import java.io.InputStreamReader; +import java.util.Collections; import java.util.List; import java.util.Objects; @@ -14,10 +13,9 @@ import org.junit.platform.commons.util.StringUtils; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.oaf.Author; -public class AuthorMergerTest { +public class ORCIDAuthorEnricherTest { @Test public void testEnrcichAuthor() throws Exception { @@ -26,12 +24,13 @@ public class AuthorMergerTest { BufferedReader pr = new BufferedReader(new InputStreamReader( Objects .requireNonNull( - AuthorMergerTest.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); + ORCIDAuthorEnricherTest.class + .getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json")))); BufferedReader or = new BufferedReader(new InputStreamReader( Objects .requireNonNull( - AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); + ORCIDAuthorEnricherTest.class + .getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json")))); TypeReference> aclass = new TypeReference>() { }; @@ -67,7 +66,8 @@ public class AuthorMergerTest { long start = System.currentTimeMillis(); // final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); - final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + final List enrichedList = Collections.emptyList(); // SparkEnrichGraphWithOrcidAuthors.enrichOrcid(publicationAuthors, + // orcidAuthors); long enrichedAuthorWithPid = enrichedList .stream() @@ -91,24 +91,4 @@ public class AuthorMergerTest { } } - @Test - public void checkSimilarityTest() { - final Author left = new Author(); - left.setName("Anand"); - left.setSurname("Rachna"); - left.setFullname("Anand, Rachna"); - - System.out.println(AuthorMerger.normalizeFullName(left.getFullname())); - - final Author right = new Author(); - right.setName("Rachna"); - right.setSurname("Anand"); - right.setFullname("Rachna, Anand"); -// System.out.println(AuthorMerger.normalize(right.getFullname())); - boolean same = AuthorMerger.checkORCIDSimilarity(left, right); - - assertTrue(same); - - } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java index 85cb551bc3..3c6fc9c7fc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java @@ -59,7 +59,19 @@ public class CopyHdfsOafSparkApplicationTest { .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/raw/publication_2_unknownProperty.json")), "publication")); + } + @Test + void isOafType_Datacite_ORP() throws IOException { + assertTrue( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/raw/datacite_orp.json")), + "otherresearchproduct")); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 6d6b2ffbdf..bf275814c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -1,13 +1,12 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.Mockito.lenient; - -import java.io.IOException; -import java.util.List; - +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.dom4j.DocumentException; import org.junit.jupiter.api.BeforeEach; @@ -16,13 +15,12 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -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.OafMapperUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.util.List; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; @ExtendWith(MockitoExtension.class) class GenerateEntitiesApplicationTest { @@ -72,7 +70,7 @@ class GenerateEntitiesApplicationTest { protected void verifyMerge(Result publication, Result dataset, Class clazz, String resultType) { - final Result merge = OafMapperUtils.mergeResults(publication, dataset); + final Result merge = MergeUtils.mergeResult(publication, dataset); assertTrue(clazz.isAssignableFrom(merge.getClass())); assertEquals(resultType, merge.getResulttype().getClassid()); } 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 ac0435ce21..405f91b9f1 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 @@ -1171,6 +1171,34 @@ class MappersTest { } + @Test + void test_Zenodo2() throws IOException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo2.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + assertEquals(3, list.size()); + Publication p = cleanup((Publication) list.get(0), vocs); + + assertNotNull(p.getInstance()); + assertEquals(1, p.getInstance().size()); + + final Instance instance = p.getInstance().get(0); + + assertNotNull(instance.getInstanceTypeMapping()); + assertEquals(1, instance.getInstanceTypeMapping().size()); + + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertNotNull(coarType.get().getOriginalType()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); + } + @Test void testROHub2() throws IOException { final String xml = IOUtils @@ -1229,7 +1257,7 @@ class MappersTest { } @Test - public void testD4ScienceTraining() throws IOException { + void testD4ScienceTraining() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-1-training.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -1240,7 +1268,7 @@ class MappersTest { } @Test - public void testD4ScienceDataset() throws IOException { + void testD4ScienceDataset() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-2-dataset.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -1250,6 +1278,22 @@ class MappersTest { System.out.println("***************"); } + @Test + void testIRISPub() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("iris-odf.xml"))); + final List list = new OdfToOafMapper(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); + assertNotNull(p.getInstance().get(0).getUrl().get(0)); + assertValidId(p.getId()); + System.out.println(p.getInstance().get(0).getUrl()); + p.getPid().forEach(x -> System.out.println(x.getValue())); + p.getInstance().get(0).getAlternateIdentifier().forEach(x -> System.out.println(x.getValue())); + + } + @Test void testNotWellFormed() throws IOException { final String xml = IOUtils diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json similarity index 100% rename from dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json similarity index 100% rename from dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datacite_orp.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datacite_orp.json new file mode 100644 index 0000000000..abf44b49cc --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datacite_orp.json @@ -0,0 +1 @@ +{"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":null,"id":"50|doi_________::0a2763977bb76876aff2d3b33a874552","originalId":["50|datacite____::0a2763977bb76876aff2d3b33a874552","10.25935/nhb2-wy29"],"pid":[{"value":"10.25935/nhb2-wy29","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofcollection":"2024-01-15T18:00:35+0000","dateoftransformation":"2024-01-15T18:00:35+0000","extraInfo":null,"oaiprovenance":null,"measures":null,"processingchargeamount":null,"processingchargecurrency":null,"author":[{"fullname":"Louis, Corentin","name":"Corentin","surname":"Louis","rank":1,"pid":[{"value":"https://orcid.org/0000-0002-9552-8822","qualifier":{"classid":"orcid","classname":"Open Researcher and Contributor ID","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"affiliation":[{"value":"Dublin Institute For Advanced Studies","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"fullname":"Zarka, 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William","name":"William","surname":"Kurth","rank":4,"pid":[{"value":"https://orcid.org/0000-0002-5471-6202","qualifier":{"classid":"orcid","classname":"Open Researcher and Contributor ID","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"affiliation":[{"value":"University of Iowa","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"metaResourceType":null,"language":null,"country":null,"subject":[],"title":[{"value":"Catalogue of Jupiter radio emissions identified in the Juno/Waves observations","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":null}],"relevantdate":[{"value":"2021-01-01","qualifier":{"classid":"issued","classname":"issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"dataInfo":null}],"description":[],"dateofacceptance":{"value":"2021-01-01","dataInfo":null},"publisher":{"value":"PADC/MASER","dataInfo":null},"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"context":null,"externalReference":null,"instance":[{"license":{"value":"https://creativecommons.org/licenses/by/4.0/legalcode","dataInfo":null},"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes","openAccessRoute":null},"instancetype":{"classid":"0022","classname":"Collection","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"instanceTypeMapping":[{"originalType":"Collection","typeCode":null,"typeLabel":null,"vocabularyName":"openaire::coar_resource_types_3_1"}],"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository","dataInfo":null},"url":["https://dx.doi.org/10.25935/nhb2-wy29"],"distributionlocation":null,"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite","dataInfo":null},"pid":[{"value":"10.25935/nhb2-wy29","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"alternateIdentifier":null,"dateofacceptance":{"value":"2021-01-01","dataInfo":null},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null,"measures":null,"fulltext":null}],"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"contactperson":null,"contactgroup":null,"tool":null,"isGreen":null,"isInDiamondJournal":null} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/iris-odf.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/iris-odf.xml new file mode 100644 index 0000000000..1b875ec361 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/iris-odf.xml @@ -0,0 +1,215 @@ + + + + oai:air.unimi.it:2434/907506 + 2024-01-04T12:42:51Z + com_2434_73555 + col_2434_73557 + openaire + 2024-01-29T16:56:50.632Z + + od______1261::ff2d9e058e7bea90a27f41c31078e601 + oai:air.unimi.it:2434/907506 + + + + + od______1261 + + + + + Ensuring tests of conservation interventions build on existing literature + + + + W.J. Sutherland + + + S.T. Alvarez-Castaneda + + + T. Amano + + + R. Ambrosini + + + P. Atkinson + + + J.M. Baxter + + + A.L. Bond + + + P.J. Boon + + + K.L. Buchanan + + + J. Barlow + + + G. Bogliani + + + O.M. Bragg + + + M. Burgman + + + M.W. Cadotte + + + M. Calver + + + S.J. Cooke + + + R.T. Corlett + + + V. Devictor + + + J.G. Ewen + + + M. Fisher + + + G. Freeman + + + E. Game + + + B.J. Godley + + + C. Gortazar + + + I.R. Hartley + + + D.L. Hawksworth + + + K.A. Hobson + + + M.-. Lu + + + B. Martin-Lopez + + + K. Ma + + + A. Machado + + + D. Mae + + + M. Mangiacotti + + + D.J. Mccafferty + + + V. Melfi + + + S. Molur + + + A.J. Moore + + + S.D. Murphy + + + D. Norri + + + A.P.E. van Oudenhoven + + + J. Power + + + E.C. Ree + + + M.W. Schwartz + + + I. Storch + + + C. Wordley + + + + + + 2020 + 2020 + 2022-06-20 + + eng + Wiley Blackwell Publishing + journal article + application/pdf + 2434/907506 + open access + + Conservation of Natural Resources + + + + + 191802 bytes + + https://air.unimi.it/bitstream/2434/907506/4/Full%20manuscript%20resubmitted.pdf + + 10.1111/cobi.13555 + 32779884 + https://air.unimi.it/bitstream/2434/907506/4/Full%20manuscript%20resubmitted.pdf + 0001 + 2020-01-01 + OPEN + eng + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo2.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo2.xml new file mode 100644 index 0000000000..ebe105de86 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo2.xml @@ -0,0 +1,59 @@ + + +
+ oai:zenodo.org:1596086 + 2020-01-20T13:50:28Z + openaire + 2024-02-08T11:03:10.994Z + od______2659::036d5555a6688ed00c8d0da97bdece3b + 2024-02-08T11:03:10.994Z + 2024-02-08T11:03:10.994Z +
+ + + https://zenodo.org/record/1596086 + + + + Bonney, T. G. + T. G. + Bonney + + + + Ice Blocks on a Moraine + + Zenodo + 1889 + + 1889-08-22 + + + + 10.1038/040391a0 + + + Creative Commons Zero v1.0 Universal + Open Access + + + n/a + + + 0001 + 1889-08-22 + OPEN + http://creativecommons.org/publicdomain/zero/1.0/legalcode + + + + +
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala new file mode 100644 index 0000000000..f109ebe245 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala @@ -0,0 +1,35 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.enrich.orcid.ORCIDAuthorMatchers.matchOrderedTokenAndAbbreviations +import org.junit.jupiter.api.Assertions.{assertFalse, assertTrue} +import org.junit.jupiter.api.Test + +class ORCIDAuthorMatchersTest { + + @Test def testShortNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Lasagni Mariozzi Federico", "Lasagni F. Mariozzi")) + } + + @Test def testInvertedNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Andrea, Paolo Marcello", "Marcello Paolo, Andrea")) + } + + @Test def testHomonymy(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Jang Myung Lee", "J Lee")) + } + + @Test def testAmbiguousShortNames(): Unit = { + assertFalse(matchOrderedTokenAndAbbreviations("P. Mariozzi", "M. Paolozzi")) + } + + @Test def testNonMatches(): Unit = { + assertFalse(matchOrderedTokenAndAbbreviations("Giovanni Paolozzi", "Francesco Paolozzi")) + assertFalse(matchOrderedTokenAndAbbreviations("G. Paolozzi", "F. Paolozzi")) + } + + @Test def testChineseNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin")) + // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java index 518f411204..6f43ca3f72 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java @@ -62,8 +62,8 @@ public class XmlConverterJob { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); + final String contextApiBaseUrl = parser.get("contextApiBaseUrl"); + log.info("contextApiBaseUrl: {}", contextApiBaseUrl); final SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); @@ -71,7 +71,7 @@ public class XmlConverterJob { runWithSparkSession(conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - convertToXml(spark, inputPath, outputPath, ContextMapper.fromIS(isLookupUrl)); + convertToXml(spark, inputPath, outputPath, ContextMapper.fromAPI(contextApiBaseUrl)); }); } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java index bcaf406039..083dbe988f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java @@ -1,18 +1,22 @@ package eu.dnetlib.dhp.oa.provision.utils; -import java.io.Serializable; -import java.io.StringReader; +import java.io.*; +import java.net.HttpURLConnection; +import java.net.URL; import java.util.HashMap; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; import com.google.common.base.Joiner; +import eu.dnetlib.dhp.common.api.context.*; +import eu.dnetlib.dhp.common.rest.DNetRestClient; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -23,6 +27,45 @@ public class ContextMapper extends HashMap implements Serial private static final String XQUERY = "for $x in //RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ContextDSResourceType']//*[name()='context' or name()='category' or name()='concept'] return "; + public static ContextMapper fromAPI(final String baseURL) throws Exception { + + final ContextMapper contextMapper = new ContextMapper(); + + for (ContextSummary ctx : DNetRestClient + .doGET(String.format("%s/contexts", baseURL), ContextSummaryList.class)) { + + contextMapper.put(ctx.getId(), new ContextDef(ctx.getId(), ctx.getLabel(), "context", ctx.getType())); + + for (CategorySummary cat : DNetRestClient + .doGET(String.format("%s/context/%s?all=true", baseURL, ctx.getId()), CategorySummaryList.class)) { + contextMapper.put(cat.getId(), new ContextDef(cat.getId(), cat.getLabel(), "category", "")); + if (cat.isHasConcept()) { + for (ConceptSummary c : DNetRestClient + .doGET( + String.format("%s/context/category/%s?all=true", baseURL, cat.getId()), + ConceptSummaryList.class)) { + contextMapper.put(c.getId(), new ContextDef(c.getId(), c.getLabel(), "concept", "")); + if (c.isHasSubConcept()) { + for (ConceptSummary cs : c.getConcepts()) { + contextMapper.put(cs.getId(), new ContextDef(cs.getId(), cs.getLabel(), "concept", "")); + if (cs.isHasSubConcept()) { + for (ConceptSummary css : cs.getConcepts()) { + contextMapper + .put( + css.getId(), + new ContextDef(css.getId(), css.getLabel(), "concept", "")); + } + } + } + } + } + } + } + } + return contextMapper; + } + + @Deprecated public static ContextMapper fromIS(final String isLookupUrl) throws DocumentException, ISLookUpException, SAXException { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); @@ -32,6 +75,7 @@ public class ContextMapper extends HashMap implements Serial return fromXml(sb.toString()); } + @Deprecated public static ContextMapper fromXml(final String xml) throws DocumentException, SAXException { final ContextMapper contextMapper = new ContextMapper(); diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json index eda6154d7e..653a69ed11 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json @@ -12,9 +12,9 @@ "paramRequired": true }, { - "paramName": "ilu", - "paramLongName": "isLookupUrl", - "paramDescription": "URL of the isLookUp Service", + "paramName": "cau", + "paramLongName": "contextApiBaseUrl", + "paramDescription": "URL of the context API", "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 2e7b11ddee..9eab960f07 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -9,6 +9,10 @@ isLookupUrl URL for the isLookup service + + contextApiBaseUrl + context API URL + relPartitions number or partitions for the relations Dataset @@ -589,7 +593,7 @@ --inputPath${workingDir}/join_entities --outputPath${workingDir}/xml - --isLookupUrl${isLookupUrl} + --contextApiBaseUrl${contextApiBaseUrl} 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 de69795f88..ba9572b173 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 @@ -244,4 +244,27 @@ public class XmlRecordFactoryTest { } + @Test + public void testIrisGuidelines4() throws DocumentException, IOException { + final ContextMapper contextMapper = new ContextMapper(); + + final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, + XmlConverterJob.schemaLocation); + + final Publication p = OBJECT_MAPPER + .readValue( + IOUtils.toString(getClass().getResourceAsStream("iris-odf-4.json")), + Publication.class); + + final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + + assertNotNull(xml); + + final Document doc = new SAXReader().read(new StringReader(xml)); + + assertNotNull(doc); + System.out.println(doc.asXML()); + + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/iris-odf-4.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/iris-odf-4.json new file mode 100644 index 0000000000..4c5ec97081 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/iris-odf-4.json @@ -0,0 +1 @@ +{"collectedfrom":[{"key":"10|opendoar____::17326d10d511828f6b34fa6d751739e2","value":"Archivio Istituzionale della Ricerca dell'Università degli Studi di Milano","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1706638577436,"id":"50|od______1261::ff2d9e058e7bea90a27f41c31078e601","originalId":["oai:air.unimi.it:2434/907506","50|od______1261::ff2d9e058e7bea90a27f41c31078e601"],"pid":[{"value":"2434/907506","qualifier":{"classid":"handle","classname":"Handle","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofcollection":"","dateoftransformation":"2024-01-29T16:56:50.632Z","extraInfo":[],"oaiprovenance":null,"measures":null,"processingchargeamount":null,"processingchargecurrency":null,"author":[{"fullname":"W.J. 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diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index f491b58689..cc15b8a15b 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -8,6 +8,11 @@ 4.0.0 dhp-stats-update + + eu.dnetlib.dhp + dhp-common + ${project.version} + org.apache.spark spark-core_${scala.binary.version} diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 5aa14e2c26..f13b2500cb 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -1,5 +1,5 @@ -- Sprint 1 ---- -drop table if exists ${stats_db_name}.indi_pub_green_oa purge; +drop table if exists ${stats_db_name}.indi_pub_green_oa purge; /*EOS*/ --create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as --select distinct p.id, coalesce(green_oa, 0) as green_oa @@ -24,9 +24,9 @@ from ${stats_db_name}.publication p where datasource.type like '%Repository%' and (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and datasource.name!='Other') tmp - on p.id= tmp.id; + on p.id= tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_grey_lit purge; +drop table if exists ${stats_db_name}.indi_pub_grey_lit purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit @@ -37,9 +37,9 @@ from ${stats_db_name}.publication p join ${stats_db_name}.result_classifications rt on rt.id = p.id where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from ${stats_db_name}.result_classifications rc where type ='Other literature type' - and rc.id=p.id)) tmp on p.id=tmp.id; + and rc.id=p.id)) tmp on p.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_doi_from_crossref purge; +drop table if exists ${stats_db_name}.indi_pub_doi_from_crossref purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref @@ -48,10 +48,10 @@ from ${stats_db_name}.publication p (select ri.id, 1 as doi_from_crossref from ${stats_db_name}.result_instance ri join ${stats_db_name}.datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp - on tmp.id=p.id; + on tmp.id=p.id; /*EOS*/ -- Sprint 2 ---- -drop table if exists ${stats_db_name}.indi_result_has_cc_licence purge; +drop table if exists ${stats_db_name}.indi_result_has_cc_licence purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -59,9 +59,9 @@ from ${stats_db_name}.result r left outer join (select r.id, license.type as lic from ${stats_db_name}.result r join ${stats_db_name}.result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp - on r.id= tmp.id; + on r.id= tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_has_cc_licence_url purge; +drop table if exists ${stats_db_name}.indi_result_has_cc_licence_url purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url @@ -70,32 +70,32 @@ from ${stats_db_name}.result r from ${stats_db_name}.result r join ${stats_db_name}.result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp - on r.id= tmp.id; + on r.id= tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_has_abstract purge; +drop table if exists ${stats_db_name}.indi_pub_has_abstract purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_has_abstract stored as parquet as select distinct publication.id, cast(coalesce(abstract, true) as int) has_abstract -from ${stats_db_name}.publication; +from ${stats_db_name}.publication; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_with_orcid purge; +drop table if exists ${stats_db_name}.indi_result_with_orcid purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from ${stats_db_name}.result r left outer join (select id, 1 as has_orcid from ${stats_db_name}.result_orcid) tmp - on r.id= tmp.id; + on r.id= tmp.id; /*EOS*/ ---- Sprint 3 ---- -drop table if exists ${stats_db_name}.indi_funded_result_with_fundref purge; +drop table if exists ${stats_db_name}.indi_funded_result_with_fundref purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_funded_result_with_fundref stored as parquet as select distinct r.result as id, coalesce(fundref, 0) as fundref from ${stats_db_name}.project_results r left outer join (select distinct result, 1 as fundref from ${stats_db_name}.project_results where provenance='Harvested') tmp - on r.result= tmp.result; + on r.result= tmp.result; /*EOS*/ -- create table indi_result_org_collab stored as parquet as -- select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations @@ -105,65 +105,65 @@ from ${stats_db_name}.project_results r -- -- compute stats indi_result_org_collab; -- -create TEMPORARY TABLE ${stats_db_name}.tmp AS SELECT ro.organization organization, ro.id, o.name from ${stats_db_name}.result_organization ro -join ${stats_db_name}.organization o on o.id=ro.organization where o.name is not null; +create TEMPORARY VIEW tmp AS SELECT ro.organization organization, ro.id, o.name from ${stats_db_name}.result_organization ro +join ${stats_db_name}.organization o on o.id=ro.organization where o.name is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_org_collab purge; +drop table if exists ${stats_db_name}.indi_result_org_collab purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_org_collab stored as parquet as select o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations -from ${stats_db_name}.tmp as o1 -join ${stats_db_name}.tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name -group by o1.organization, o2.organization, o1.name, o2.name; +from tmp as o1 +join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name +group by o1.organization, o2.organization, o1.name, o2.name; /*EOS*/ -drop table if exists ${stats_db_name}.tmp purge; +DROP VIEW if exists tmp; /*EOS*/ -create TEMPORARY TABLE ${stats_db_name}.tmp AS +create TEMPORARY VIEW tmp AS select distinct ro.organization organization, ro.id, o.name, o.country from ${stats_db_name}.result_organization ro -join ${stats_db_name}.organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null; +join ${stats_db_name}.organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_org_country_collab purge; +drop table if exists ${stats_db_name}.indi_result_org_country_collab purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_org_country_collab stored as parquet as select o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations -from ${stats_db_name}.tmp as o1 join ${stats_db_name}.tmp as o2 on o1.id=o2.id +from tmp as o1 join tmp as o2 on o1.id=o2.id where o1.id=o2.id and o1.country!=o2.country -group by o1.organization, o1.id, o1.name, o2.country; +group by o1.organization, o1.id, o1.name, o2.country; /*EOS*/ -drop table if exists ${stats_db_name}.tmp purge; +drop table if exists tmp purge; /*EOS*/ -create TEMPORARY TABLE ${stats_db_name}.tmp AS +create TEMPORARY VIEW tmp AS select o.id organization, o.name, ro.project as project from ${stats_db_name}.organization o - join ${stats_db_name}.organization_projects ro on o.id=ro.id where o.name is not null; + join ${stats_db_name}.organization_projects ro on o.id=ro.id where o.name is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_project_collab_org purge; +drop table if exists ${stats_db_name}.indi_project_collab_org purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_project_collab_org stored as parquet as select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations -from ${stats_db_name}.tmp as o1 - join ${stats_db_name}.tmp as o2 on o1.project=o2.project +from tmp as o1 + join tmp as o2 on o1.project=o2.project where o1.organization<>o2.organization and o1.name<>o2.name -group by o1.name,o2.name, o1.organization, o2.organization; +group by o1.name,o2.name, o1.organization, o2.organization; /*EOS*/ -drop table if exists ${stats_db_name}.tmp purge; +DROP VIEW if exists tmp; /*EOS*/ -create TEMPORARY TABLE ${stats_db_name}.tmp AS +create TEMPORARY VIEW tmp AS select o.id organization, o.name, o.country , ro.project as project from ${stats_db_name}.organization o join ${stats_db_name}.organization_projects ro on o.id=ro.id - and o.country <> 'UNKNOWN' and o.name is not null; + and o.country <> 'UNKNOWN' and o.name is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_project_collab_org_country purge; +drop table if exists ${stats_db_name}.indi_project_collab_org_country purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_project_collab_org_country stored as parquet as select o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations -from ${stats_db_name}.tmp as o1 - join ${stats_db_name}.tmp as o2 on o1.project=o2.project +from tmp as o1 + join tmp as o2 on o1.project=o2.project where o1.organization<>o2.organization and o1.country<>o2.country -group by o1.organization, o2.country, o1.name; +group by o1.organization, o2.country, o1.name; /*EOS*/ -drop table if exists ${stats_db_name}.tmp purge; +DROP VIEW if exists tmp; /*EOS*/ -drop table if exists ${stats_db_name}.indi_funder_country_collab purge; +drop table if exists ${stats_db_name}.indi_funder_country_collab purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from ${stats_db_name}.organization_projects op @@ -174,26 +174,26 @@ select f1.funder, f1.country as country1, f2.country as country2, count(distinct from tmp as f1 join tmp as f2 on f1.project=f2.project where f1.country<>f2.country -group by f1.funder, f2.country, f1.country; +group by f1.funder, f2.country, f1.country; /*EOS*/ -create TEMPORARY TABLE ${stats_db_name}.tmp AS +create TEMPORARY VIEW tmp AS select distinct country, ro.id as result from ${stats_db_name}.organization o join ${stats_db_name}.result_organization ro on o.id=ro.organization - where country <> 'UNKNOWN' and o.name is not null; + where country <> 'UNKNOWN' and o.name is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_country_collab purge; +drop table if exists ${stats_db_name}.indi_result_country_collab purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_country_collab stored as parquet as select o1.country country1, o2.country country2, count(o1.result) as collaborations -from ${stats_db_name}.tmp as o1 - join ${stats_db_name}.tmp as o2 on o1.result=o2.result +from tmp as o1 + join tmp as o2 on o1.result=o2.result where o1.country<>o2.country -group by o1.country, o2.country; +group by o1.country, o2.country; /*EOS*/ -drop table if exists ${stats_db_name}.tmp purge; +DROP VIEW if exists tmp; /*EOS*/ ---- Sprint 4 ---- -drop table if exists ${stats_db_name}.indi_pub_diamond purge; +drop table if exists ${stats_db_name}.indi_pub_diamond purge; /*EOS*/ --create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as --select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal @@ -212,9 +212,9 @@ left outer join (select pd.id, 1 as in_diamond_journal from ${stats_db_name}.pub join ${stats_db_name}.datasource d on d.id=pd.datasource join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id; +on pd.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_in_transformative purge; +drop table if exists ${stats_db_name}.indi_pub_in_transformative purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative @@ -224,9 +224,9 @@ from ${stats_db_name}.publication pd join ${stats_db_name}.datasource d on d.id=pd.datasource join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and ps.is_transformative_journal=true) tmp - on pd.id=tmp.id; + on pd.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_closed_other_open purge; +drop table if exists ${stats_db_name}.indi_pub_closed_other_open purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from ${stats_db_name}.result_instance ri @@ -236,53 +236,53 @@ select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_op join ${stats_db_name}.datasource d on ri.hostedby=d.id where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp - on tmp.id=ri.id; + on tmp.id=ri.id; /*EOS*/ ---- Sprint 5 ---- -drop table if exists ${stats_db_name}.indi_result_no_of_copies purge; +drop table if exists ${stats_db_name}.indi_result_no_of_copies purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_no_of_copies stored as parquet as -select id, count(id) as number_of_copies from ${stats_db_name}.result_instance group by id; +select id, count(id) as number_of_copies from ${stats_db_name}.result_instance group by id; /*EOS*/ ---- Sprint 6 ---- -drop table if exists ${stats_db_name}.indi_pub_downloads purge; +drop table if exists ${stats_db_name}.indi_pub_downloads purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join ${stats_db_name}.publication on result_id=id where downloads>0 GROUP BY result_id -order by no_downloads desc; +order by no_downloads desc; /*EOS*/ --ANALYZE TABLE ${stats_db_name}.indi_pub_downloads COMPUTE STATISTICS; -drop table if exists ${stats_db_name}.indi_pub_downloads_datasource purge; +drop table if exists ${stats_db_name}.indi_pub_downloads_datasource purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join ${stats_db_name}.publication on result_id=id where downloads>0 GROUP BY result_id, repository_id -order by result_id; +order by result_id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_downloads_year purge; +drop table if exists ${stats_db_name}.indi_pub_downloads_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_downloads_year stored as parquet as SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats us join ${stats_db_name}.publication on result_id=id where downloads>0 -GROUP BY result_id, substring(us.`date`, 1,4); +GROUP BY result_id, substring(us.`date`, 1,4); /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_downloads_datasource_year purge; +drop table if exists ${stats_db_name}.indi_pub_downloads_datasource_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats us join ${stats_db_name}.publication on result_id=id where downloads>0 -GROUP BY result_id, repository_id, substring(us.`date`, 1,4); +GROUP BY result_id, repository_id, substring(us.`date`, 1,4); /*EOS*/ ---- Sprint 7 ---- -drop table if exists ${stats_db_name}.indi_pub_gold_oa purge; +drop table if exists ${stats_db_name}.indi_pub_gold_oa purge; /*EOS*/ --create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as -- WITH gold_oa AS ( SELECT @@ -381,9 +381,9 @@ left outer join ( select pd.id, 1 as is_gold FROM ${stats_db_name}.publication_datasources pd join dd on dd.id=pd.datasource - left outer join ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; + left outer join ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc purge; +drop table if exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as parquet as WITH hybrid_oa AS ( @@ -414,9 +414,9 @@ FROM ${stats_db_name}.publication_datasources pd JOIN hybrid_oa ON issn.issn = hybrid_oa.issn JOIN ${stats_db_name}.indi_result_has_cc_licence cc on pd.id=cc.id JOIN ${stats_db_name}.indi_pub_gold_oa ga on pd.id=ga.id - where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; + where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_hybrid purge; +drop table if exists ${stats_db_name}.indi_pub_hybrid purge; /*EOS*/ --create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as -- WITH gold_oa AS ( SELECT @@ -489,9 +489,9 @@ join ${stats_db_name}.result_accessroute ra on ra.id=pd.id join ${stats_db_name}.datasource d on d.id=ri.hostedby where indi_gold.is_gold=0 and ((d.type like '%Journal%' and ri.accessright!='Closed Access' and ri.accessright!='Restricted' and ri.license is not null) or ra.accessroute='hybrid'))tmp -on pd.id=tmp.id; +on pd.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_fairness purge; +drop table if exists ${stats_db_name}.indi_org_fairness purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_fairness stored as parquet as --return results with PIDs, and rich metadata group by organization @@ -509,9 +509,9 @@ create table if not exists ${stats_db_name}.indi_org_fairness stored as parquet --return results_fair/all_results select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness from allresults - join result_fair on result_fair.organization=allresults.organization; + join result_fair on result_fair.organization=allresults.organization; /*EOS*/ -CREATE TEMPORARY table ${stats_db_name}.result_fair as +CREATE TEMPORARY VIEW result_fair as select ro.organization organization, count(distinct ro.id) no_result_fair from ${stats_db_name}.result_organization ro join ${stats_db_name}.publication p on p.id=ro.id @@ -519,296 +519,296 @@ select ro.organization organization, count(distinct ro.id) no_result_fair join ${stats_db_name}.indi_pub_grey_lit gl on gl.id=p.id where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003 and dc.doi_from_crossref=1 and gl.grey_lit=0 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as +CREATE TEMPORARY VIEW allresults as select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.publication p on p.id=ro.id where cast(year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_fairness_pub_pr purge; +drop table if exists ${stats_db_name}.indi_org_fairness_pub_pr purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_fairness_pub_pr stored as parquet as select ar.organization, rf.no_result_fair/ar.no_allresults org_fairness -from ${stats_db_name}.allresults ar - join ${stats_db_name}.result_fair rf on rf.organization=ar.organization; +from allresults ar + join result_fair rf on rf.organization=ar.organization; /*EOS*/ -DROP table ${stats_db_name}.result_fair purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_fair; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY table ${stats_db_name}.result_fair as +CREATE TEMPORARY VIEW result_fair as select year, ro.organization organization, count(distinct ro.id) no_result_fair from ${stats_db_name}.result_organization ro join ${stats_db_name}.result p on p.id=ro.id where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as select year, ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro +CREATE TEMPORARY VIEW allresults as select year, ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.result p on p.id=ro.id where cast(year as int)>2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_fairness_pub_year purge; +drop table if exists ${stats_db_name}.indi_org_fairness_pub_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_fairness_pub_year stored as parquet as select cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness -from ${stats_db_name}.allresults - join ${stats_db_name}.result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; +from allresults + join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; /*EOS*/ -DROP table ${stats_db_name}.result_fair purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_fair; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.result_fair as +CREATE TEMPORARY VIEW result_fair as select ro.organization organization, count(distinct ro.id) no_result_fair from ${stats_db_name}.result_organization ro join ${stats_db_name}.result p on p.id=ro.id where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as +CREATE TEMPORARY VIEW allresults as select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.result p on p.id=ro.id where cast(year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_fairness_pub purge; +drop table if exists ${stats_db_name}.indi_org_fairness_pub purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_fairness_pub as select ar.organization, rf.no_result_fair/ar.no_allresults org_fairness -from ${stats_db_name}.allresults ar join ${stats_db_name}.result_fair rf -on rf.organization=ar.organization; +from allresults ar join result_fair rf +on rf.organization=ar.organization; /*EOS*/ -DROP table ${stats_db_name}.result_fair purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_fair; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.result_fair as +CREATE TEMPORARY VIEW result_fair as select year, ro.organization organization, count(distinct ro.id) no_result_fair from ${stats_db_name}.result_organization ro join ${stats_db_name}.result r on r.id=ro.id join ${stats_db_name}.result_pids rp on r.id=rp.id where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as +CREATE TEMPORARY VIEW allresults as select year, ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.result r on r.id=ro.id where cast(year as int)>2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_fairness_year purge; +drop table if exists ${stats_db_name}.indi_org_fairness_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_fairness_year stored as parquet as select cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness - from ${stats_db_name}.allresults - join ${stats_db_name}.result_fair on result_fair.organization=allresults.organization and cast(result_fair.year as int)=cast(allresults.year as int); + from allresults + join result_fair on result_fair.organization=allresults.organization and cast(result_fair.year as int)=cast(allresults.year as int); /*EOS*/ -DROP table ${stats_db_name}.result_fair purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_fair; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.result_with_pid as +CREATE TEMPORARY VIEW result_with_pid as select year, ro.organization, count(distinct rp.id) no_result_with_pid from ${stats_db_name}.result_organization ro join ${stats_db_name}.result_pids rp on rp.id=ro.id join ${stats_db_name}.result r on r.id=rp.id where cast(year as int) >2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as +CREATE TEMPORARY VIEW allresults as select year, ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.result r on r.id=ro.id where cast(year as int) >2003 - group by ro.organization, year; + group by ro.organization, year; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_findable_year purge; +drop table if exists ${stats_db_name}.indi_org_findable_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_findable_year stored as parquet as select cast(allresults.year as int) year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable -from ${stats_db_name}.allresults - join ${stats_db_name}.result_with_pid on result_with_pid.organization=allresults.organization and cast(result_with_pid.year as int)=cast(allresults.year as int); +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization and cast(result_with_pid.year as int)=cast(allresults.year as int); /*EOS*/ -DROP table ${stats_db_name}.result_with_pid purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_with_pid; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.result_with_pid as +CREATE TEMPORARY VIEW result_with_pid as select ro.organization, count(distinct rp.id) no_result_with_pid from ${stats_db_name}.result_organization ro join ${stats_db_name}.result_pids rp on rp.id=ro.id join ${stats_db_name}.result r on r.id=rp.id where cast(year as int) >2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allresults as +CREATE TEMPORARY VIEW allresults as select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro join ${stats_db_name}.result r on r.id=ro.id where cast(year as int) >2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_findable purge; +drop table if exists ${stats_db_name}.indi_org_findable purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_findable stored as parquet as select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable -from ${stats_db_name}.allresults - join ${stats_db_name}.result_with_pid on result_with_pid.organization=allresults.organization; +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization; /*EOS*/ -DROP table ${stats_db_name}.result_with_pid purge; -DROP table ${stats_db_name}.allresults purge; +DROP VIEW result_with_pid; /*EOS*/ +DROP VIEW allresults; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.pubs_oa as +CREATE TEMPORARY VIEW pubs_oa as SELECT ro.organization, count(distinct r.id) no_oapubs FROM ${stats_db_name}.publication r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.datasets_oa as +CREATE TEMPORARY VIEW datasets_oa as SELECT ro.organization, count(distinct r.id) no_oadatasets FROM ${stats_db_name}.dataset r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.software_oa as +CREATE TEMPORARY VIEW software_oa as SELECT ro.organization, count(distinct r.id) no_oasoftware FROM ${stats_db_name}.software r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubs as +CREATE TEMPORARY VIEW allpubs as SELECT ro.organization, count(ro.id) no_allpubs FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.publication ps on ps.id=ro.id where cast(ps.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasets as +CREATE TEMPORARY VIEW alldatasets as SELECT ro.organization, count(ro.id) no_alldatasets FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.dataset ps on ps.id=ro.id where cast(ps.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftware as +CREATE TEMPORARY VIEW allsoftware as SELECT ro.organization, count(ro.id) no_allsoftware FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.software ps on ps.id=ro.id where cast(ps.year as int)>2003 - group by ro.organization; + group by ro.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubsshare as -select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from ${stats_db_name}.allpubs - join ${stats_db_name}.pubs_oa on allpubs.organization=pubs_oa.organization; +CREATE TEMPORARY VIEW allpubsshare as +select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasetssshare as +CREATE TEMPORARY VIEW alldatasetssshare as select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d - from ${stats_db_name}.alldatasets - join ${stats_db_name}.datasets_oa on alldatasets.organization=datasets_oa.organization; + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftwaresshare as +CREATE TEMPORARY VIEW allsoftwaresshare as select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from ${stats_db_name}.allsoftware - join ${stats_db_name}.software_oa on allsoftware.organization=software_oa.organization; + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization; /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_openess purge; +drop table if exists ${stats_db_name}.indi_org_openess purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_openess stored as parquet as select allpubsshare.organization, (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end) +(case when d is null then 0 else 1 end)) - org_openess FROM ${stats_db_name}.allpubsshare + org_openess FROM allpubsshare left outer join (select organization,d from - ${stats_db_name}.alldatasetssshare) tmp1 + alldatasetssshare) tmp1 on tmp1.organization=allpubsshare.organization left outer join (select organization,s from - ${stats_db_name}.allsoftwaresshare) tmp2 - on tmp2.organization=allpubsshare.organization; + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization; /*EOS*/ -DROP TABLE ${stats_db_name}.pubs_oa purge; -DROP TABLE ${stats_db_name}.datasets_oa purge; -DROP TABLE ${stats_db_name}.software_oa purge; -DROP TABLE ${stats_db_name}.allpubs purge; -DROP TABLE ${stats_db_name}.alldatasets purge; -DROP TABLE ${stats_db_name}.allsoftware purge; -DROP TABLE ${stats_db_name}.allpubsshare purge; -DROP TABLE ${stats_db_name}.alldatasetssshare purge; -DROP TABLE ${stats_db_name}.allsoftwaresshare purge; +DROP VIEW pubs_oa; /*EOS*/ +DROP VIEW datasets_oa; /*EOS*/ +DROP VIEW software_oa; /*EOS*/ +DROP VIEW allpubs; /*EOS*/ +DROP VIEW alldatasets; /*EOS*/ +DROP VIEW allsoftware; /*EOS*/ +DROP VIEW allpubsshare; /*EOS*/ +DROP VIEW alldatasetssshare; /*EOS*/ +DROP VIEW allsoftwaresshare; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.pubs_oa AS +CREATE TEMPORARY VIEW pubs_oa AS SELECT r.year, ro.organization, count(distinct r.id) no_oapubs FROM ${stats_db_name}.publication r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization,r.year; + group by ro.organization,r.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.datasets_oa AS +CREATE TEMPORARY VIEW datasets_oa AS SELECT r.year,ro.organization, count(distinct r.id) no_oadatasets FROM ${stats_db_name}.dataset r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization, r.year; + group by ro.organization, r.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.software_oa AS +CREATE TEMPORARY VIEW software_oa AS SELECT r.year,ro.organization, count(distinct r.id) no_oasoftware FROM ${stats_db_name}.software r join ${stats_db_name}.result_organization ro on ro.id=r.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 - group by ro.organization, r.year; + group by ro.organization, r.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubs as +CREATE TEMPORARY VIEW allpubs as SELECT p.year,ro.organization organization, count(ro.id) no_allpubs FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.publication p on p.id=ro.id where cast(p.year as int)>2003 - group by ro.organization, p.year; + group by ro.organization, p.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasets as +CREATE TEMPORARY VIEW alldatasets as SELECT d.year, ro.organization organization, count(ro.id) no_alldatasets FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.dataset d on d.id=ro.id where cast(d.year as int)>2003 - group by ro.organization, d.year; + group by ro.organization, d.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftware as +CREATE TEMPORARY VIEW allsoftware as SELECT s.year,ro.organization organization, count(ro.id) no_allsoftware FROM ${stats_db_name}.result_organization ro join ${stats_db_name}.software s on s.id=ro.id where cast(s.year as int)>2003 - group by ro.organization, s.year; + group by ro.organization, s.year; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubsshare as -select allpubs.year, pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from ${stats_db_name}.allpubs - join ${stats_db_name}.pubs_oa on allpubs.organization=pubs_oa.organization where cast(allpubs.year as INT)=cast(pubs_oa.year as int); +CREATE TEMPORARY VIEW allpubsshare as +select allpubs.year, pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization where cast(allpubs.year as INT)=cast(pubs_oa.year as int); /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasetssshare as +CREATE TEMPORARY VIEW alldatasetssshare as select alldatasets.year, datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d - from ${stats_db_name}.alldatasets - join ${stats_db_name}.datasets_oa on alldatasets.organization=datasets_oa.organization where cast(alldatasets.year as INT)=cast(datasets_oa.year as int); + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization where cast(alldatasets.year as INT)=cast(datasets_oa.year as int); /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftwaresshare as +CREATE TEMPORARY VIEW allsoftwaresshare as select allsoftware.year, software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from ${stats_db_name}.allsoftware - join ${stats_db_name}.software_oa on allsoftware.organization=software_oa.organization where cast(allsoftware.year as INT)=cast(software_oa.year as int); + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization where cast(allsoftware.year as INT)=cast(software_oa.year as int); /*EOS*/ -drop table if exists ${stats_db_name}.indi_org_openess_year purge; +drop table if exists ${stats_db_name}.indi_org_openess_year purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_org_openess_year stored as parquet as select cast(allpubsshare.year as int) year, allpubsshare.organization, (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end) +(case when d is null then 0 else 1 end)) - org_openess FROM ${stats_db_name}.allpubsshare + org_openess FROM allpubsshare left outer join (select cast(year as int), organization,d from - ${stats_db_name}.alldatasetssshare) tmp1 + alldatasetssshare) tmp1 on tmp1.organization=allpubsshare.organization and tmp1.year=allpubsshare.year left outer join (select cast(year as int), organization,s from - ${stats_db_name}.allsoftwaresshare) tmp2 - on tmp2.organization=allpubsshare.organization and cast(tmp2.year as int)=cast(allpubsshare.year as int); + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization and cast(tmp2.year as int)=cast(allpubsshare.year as int); /*EOS*/ -DROP TABLE ${stats_db_name}.pubs_oa purge; -DROP TABLE ${stats_db_name}.datasets_oa purge; -DROP TABLE ${stats_db_name}.software_oa purge; -DROP TABLE ${stats_db_name}.allpubs purge; -DROP TABLE ${stats_db_name}.alldatasets purge; -DROP TABLE ${stats_db_name}.allsoftware purge; -DROP TABLE ${stats_db_name}.allpubsshare purge; -DROP TABLE ${stats_db_name}.alldatasetssshare purge; -DROP TABLE ${stats_db_name}.allsoftwaresshare purge; +DROP VIEW pubs_oa; /*EOS*/ +DROP VIEW datasets_oa; /*EOS*/ +DROP VIEW software_oa; /*EOS*/ +DROP VIEW allpubs; /*EOS*/ +DROP VIEW alldatasets; /*EOS*/ +DROP VIEW allsoftware; /*EOS*/ +DROP VIEW allpubsshare; /*EOS*/ +DROP VIEW alldatasetssshare; /*EOS*/ +DROP VIEW allsoftwaresshare; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_has_preprint purge; +drop table if exists ${stats_db_name}.indi_pub_has_preprint purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_has_preprint stored as parquet as select distinct p.id, coalesce(has_preprint, 0) as has_preprint @@ -817,8 +817,8 @@ from ${stats_db_name}.publication_classifications p select p.id, 1 as has_preprint from ${stats_db_name}.publication_classifications p where p.type='Preprint') tmp - on p.id= tmp.id; -drop table if exists ${stats_db_name}.indi_pub_in_subscribed purge; + on p.id= tmp.id; /*EOS*/ +drop table if exists ${stats_db_name}.indi_pub_in_subscribed purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_in_subscribed stored as parquet as select distinct p.id, coalesce(is_subscription, 0) as is_subscription @@ -829,9 +829,9 @@ from ${stats_db_name}.publication p join ${stats_db_name}.indi_pub_hybrid h on p.id=h.id join ${stats_db_name}.indi_pub_in_transformative t on p.id=t.id where g.is_gold=0 and h.is_hybrid=0 and t.is_transformative=0) tmp - on p.id=tmp.id; + on p.id=tmp.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_result_with_pid purge; +drop table if exists ${stats_db_name}.indi_result_with_pid purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_result_with_pid as select distinct p.id, coalesce(result_with_pid, 0) as result_with_pid @@ -839,25 +839,25 @@ from ${stats_db_name}.result p left outer join ( select p.id, 1 as result_with_pid from ${stats_db_name}.result_pids p) tmp - on p.id= tmp.id; + on p.id= tmp.id; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.pub_fos_totals as +CREATE TEMPORARY VIEW pub_fos_totals as select rf.id, count(distinct lvl3) totals from ${stats_db_name}.result_fos rf -group by rf.id; +group by rf.id; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_interdisciplinarity purge; +drop table if exists ${stats_db_name}.indi_pub_interdisciplinarity purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_interdisciplinarity as select distinct p.id as id, coalesce(is_interdisciplinary, 0) as is_interdisciplinary -from ${stats_db_name}.pub_fos_totals p +from pub_fos_totals p left outer join ( -select pub_fos_totals.id, 1 as is_interdisciplinary from ${stats_db_name}.pub_fos_totals -where totals>1) tmp on p.id=tmp.id; +select pub_fos_totals.id, 1 as is_interdisciplinary from pub_fos_totals +where totals>1) tmp on p.id=tmp.id; /*EOS*/ -drop table ${stats_db_name}.pub_fos_totals purge; +drop view pub_fos_totals; /*EOS*/ -drop table if exists ${stats_db_name}.indi_pub_bronze_oa purge; +drop table if exists ${stats_db_name}.indi_pub_bronze_oa purge; /*EOS*/ --create table if not exists ${stats_db_name}.indi_pub_bronze_oa stored as parquet as --select distinct p.id, coalesce(is_bronze_oa,0) as is_bronze_oa @@ -883,38 +883,38 @@ join ${stats_db_name}.datasource d on d.id=ri.hostedby where indi_gold.is_gold=0 and indi_hybrid.is_hybrid=0 and ((d.type like '%Journal%' and ri.accessright!='Closed Access' and ri.accessright!='Restricted' and ri.license is null) or ra.accessroute='bronze')) tmp -on pd.id=tmp.id; +on pd.id=tmp.id; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.project_year_result_year as +CREATE TEMPORARY VIEW project_year_result_year as select p.id project_id, acronym, r.id result_id, r.year, p.end_year from ${stats_db_name}.project p join ${stats_db_name}.result_projects rp on p.id=rp.project join ${stats_db_name}.result r on r.id=rp.id -where p.end_year is NOT NULL and r.year is not null; +where p.end_year is NOT NULL and r.year is not null; /*EOS*/ -drop table if exists ${stats_db_name}.indi_is_project_result_after purge; +drop table if exists ${stats_db_name}.indi_is_project_result_after purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_is_project_result_after stored as parquet as select pry.project_id, pry.acronym, pry.result_id, coalesce(is_project_result_after, 0) as is_project_result_after -from ${stats_db_name}.project_year_result_year pry +from project_year_result_year pry left outer join (select pry.project_id, pry.acronym, pry.result_id, 1 as is_project_result_after -from ${stats_db_name}.project_year_result_year pry -where pry.year>pry.end_year) tmp on pry.result_id=tmp.result_id; +from project_year_result_year pry +where pry.year>pry.end_year) tmp on pry.result_id=tmp.result_id; /*EOS*/ -drop table ${stats_db_name}.project_year_result_year purge; +drop view project_year_result_year; /*EOS*/ -drop table ${stats_db_name}.indi_is_funder_plan_s purge; +drop table if exists ${stats_db_name}.indi_is_funder_plan_s purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_is_funder_plan_s stored as parquet as select distinct f.id, f.name, coalesce(is_funder_plan_s, 0) as is_funder_plan_s from ${stats_db_name}.funder f left outer join (select id, name, 1 as is_funder_plan_s from ${stats_db_name}.funder join stats_ext.plan_s_short on c_o_alition_s_organisation_funder=name) tmp - on f.name= tmp.name; + on f.name= tmp.name; /*EOS*/ --Funder Fairness -drop table ${stats_db_name}.indi_funder_fairness purge; +drop table if exists ${stats_db_name}.indi_funder_fairness purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_funder_fairness stored as parquet as with result_fair as @@ -930,10 +930,10 @@ create table if not exists ${stats_db_name}.indi_funder_fairness stored as parqu group by p.funder) select allresults.funder, result_fair.no_result_fair/allresults.no_allresults funder_fairness from allresults - join result_fair on result_fair.funder=allresults.funder; + join result_fair on result_fair.funder=allresults.funder; /*EOS*/ --RIs Fairness -drop table ${stats_db_name}.indi_ris_fairness purge; +drop table if exists ${stats_db_name}.indi_ris_fairness purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_ris_fairness stored as parquet as with result_contexts as @@ -953,188 +953,188 @@ allresults as group by rc.ri_initiative) select allresults.ri_initiative, result_fair.no_result_fair/allresults.no_allresults ris_fairness from allresults - join result_fair on result_fair.ri_initiative=allresults.ri_initiative; + join result_fair on result_fair.ri_initiative=allresults.ri_initiative; /*EOS*/ --Funder Openess -CREATE TEMPORARY TABLE ${stats_db_name}.pubs_oa as +CREATE TEMPORARY VIEW pubs_oa as select p.funder funder, count(distinct rp.id) no_oapubs from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.publication r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.datasets_oa as +CREATE TEMPORARY VIEW datasets_oa as select p.funder funder, count(distinct rp.id) no_oadatasets from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.dataset r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.software_oa as +CREATE TEMPORARY VIEW software_oa as select p.funder funder, count(distinct rp.id) no_oasoftware from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.software r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubs as +CREATE TEMPORARY VIEW allpubs as select p.funder funder, count(distinct rp.id) no_allpubs from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.publication r on r.id=rp.id where cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasets as +CREATE TEMPORARY VIEW alldatasets as select p.funder funder, count(distinct rp.id) no_alldatasets from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.dataset r on r.id=rp.id where cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftware as +CREATE TEMPORARY VIEW allsoftware as select p.funder funder, count(distinct rp.id) no_allsoftware from ${stats_db_name}.result_projects rp join ${stats_db_name}.project p on p.id=rp.project join ${stats_db_name}.software r on r.id=rp.id where cast(r.year as int)>2003 -group by p.funder; +group by p.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubsshare as -select pubs_oa.funder, pubs_oa.no_oapubs/allpubs.no_allpubs p from ${stats_db_name}.allpubs - join ${stats_db_name}.pubs_oa on allpubs.funder=pubs_oa.funder; +CREATE TEMPORARY VIEW allpubsshare as +select pubs_oa.funder, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.funder=pubs_oa.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasetssshare as +CREATE TEMPORARY VIEW alldatasetssshare as select datasets_oa.funder, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d - from ${stats_db_name}.alldatasets - join ${stats_db_name}.datasets_oa on alldatasets.funder=datasets_oa.funder; + from alldatasets + join datasets_oa on alldatasets.funder=datasets_oa.funder; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftwaresshare as +CREATE TEMPORARY VIEW allsoftwaresshare as select software_oa.funder, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from ${stats_db_name}.allsoftware - join ${stats_db_name}.software_oa on allsoftware.funder=software_oa.funder; + from allsoftware + join software_oa on allsoftware.funder=software_oa.funder; /*EOS*/ -drop table ${stats_db_name}.indi_funder_openess purge; +drop table if exists ${stats_db_name}.indi_funder_openess purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_funder_openess stored as parquet as select allpubsshare.funder, (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end) +(case when d is null then 0 else 1 end)) - funder_openess FROM ${stats_db_name}.allpubsshare + funder_openess FROM allpubsshare left outer join (select funder,d from - ${stats_db_name}.alldatasetssshare) tmp1 + alldatasetssshare) tmp1 on tmp1.funder=allpubsshare.funder left outer join (select funder,s from - ${stats_db_name}.allsoftwaresshare) tmp2 - on tmp2.funder=allpubsshare.funder; + allsoftwaresshare) tmp2 + on tmp2.funder=allpubsshare.funder; /*EOS*/ -DROP TABLE ${stats_db_name}.pubs_oa purge; -DROP TABLE ${stats_db_name}.datasets_oa purge; -DROP TABLE ${stats_db_name}.software_oa purge; -DROP TABLE ${stats_db_name}.allpubs purge; -DROP TABLE ${stats_db_name}.alldatasets purge; -DROP TABLE ${stats_db_name}.allsoftware purge; -DROP TABLE ${stats_db_name}.allpubsshare purge; -DROP TABLE ${stats_db_name}.alldatasetssshare purge; -DROP TABLE ${stats_db_name}.allsoftwaresshare purge; +DROP VIEW pubs_oa; /*EOS*/ +DROP VIEW datasets_oa; /*EOS*/ +DROP VIEW software_oa; /*EOS*/ +DROP VIEW allpubs; /*EOS*/ +DROP VIEW alldatasets; /*EOS*/ +DROP VIEW allsoftware; /*EOS*/ +DROP VIEW allpubsshare; /*EOS*/ +DROP VIEW alldatasetssshare; /*EOS*/ +DROP VIEW allsoftwaresshare; /*EOS*/ --RIs Openess -CREATE TEMPORARY TABLE ${stats_db_name}.result_contexts as +CREATE TEMPORARY VIEW result_contexts as select distinct rc.id, context.name ri_initiative from ${stats_db_name}.result_concepts rc join ${stats_db_name}.concept on concept.id=rc.concept join ${stats_db_name}.category on category.id=concept.category -join ${stats_db_name}.context on context.id=category.context; +join ${stats_db_name}.context on context.id=category.context; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.pubs_oa as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oapubs from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW pubs_oa as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oapubs from result_contexts rp join ${stats_db_name}.publication r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.datasets_oa as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oadatasets from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW datasets_oa as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oadatasets from result_contexts rp join ${stats_db_name}.dataset r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.software_oa as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oasoftware from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW software_oa as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_oasoftware from result_contexts rp join ${stats_db_name}.software r on r.id=rp.id join ${stats_db_name}.result_instance ri on ri.id=r.id where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubs as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_allpubs from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW allpubs as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_allpubs from result_contexts rp join ${stats_db_name}.publication r on r.id=rp.id where cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasets as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_alldatasets from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW alldatasets as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_alldatasets from result_contexts rp join ${stats_db_name}.dataset r on r.id=rp.id where cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftware as -select rp.ri_initiative ri_initiative, count(distinct rp.id) no_allsoftware from ${stats_db_name}.result_contexts rp +CREATE TEMPORARY VIEW allsoftware as +select rp.ri_initiative ri_initiative, count(distinct rp.id) no_allsoftware from result_contexts rp join ${stats_db_name}.software r on r.id=rp.id where cast(r.year as int)>2003 -group by rp.ri_initiative; +group by rp.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allpubsshare as -select pubs_oa.ri_initiative, pubs_oa.no_oapubs/allpubs.no_allpubs p from ${stats_db_name}.allpubs - join ${stats_db_name}.pubs_oa on allpubs.ri_initiative=pubs_oa.ri_initiative; +CREATE TEMPORARY VIEW allpubsshare as +select pubs_oa.ri_initiative, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.ri_initiative=pubs_oa.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.alldatasetssshare as +CREATE TEMPORARY VIEW alldatasetssshare as select datasets_oa.ri_initiative, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d - from ${stats_db_name}.alldatasets - join ${stats_db_name}.datasets_oa on alldatasets.ri_initiative=datasets_oa.ri_initiative; + from alldatasets + join datasets_oa on alldatasets.ri_initiative=datasets_oa.ri_initiative; /*EOS*/ -CREATE TEMPORARY TABLE ${stats_db_name}.allsoftwaresshare as +CREATE TEMPORARY VIEW allsoftwaresshare as select software_oa.ri_initiative, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from ${stats_db_name}.allsoftware - join ${stats_db_name}.software_oa on allsoftware.ri_initiative=software_oa.ri_initiative; + from allsoftware + join software_oa on allsoftware.ri_initiative=software_oa.ri_initiative; /*EOS*/ -drop table ${stats_db_name}.indi_ris_openess purge; +drop table if exists ${stats_db_name}.indi_ris_openess purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_ris_openess stored as parquet as select allpubsshare.ri_initiative, (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end) +(case when d is null then 0 else 1 end)) - ris_openess FROM ${stats_db_name}.allpubsshare + ris_openess FROM allpubsshare left outer join (select ri_initiative,d from - ${stats_db_name}.alldatasetssshare) tmp1 + alldatasetssshare) tmp1 on tmp1.ri_initiative=allpubsshare.ri_initiative left outer join (select ri_initiative,s from - ${stats_db_name}.allsoftwaresshare) tmp2 - on tmp2.ri_initiative=allpubsshare.ri_initiative; + allsoftwaresshare) tmp2 + on tmp2.ri_initiative=allpubsshare.ri_initiative; /*EOS*/ -DROP TABLE ${stats_db_name}.result_contexts purge; -DROP TABLE ${stats_db_name}.pubs_oa purge; -DROP TABLE ${stats_db_name}.datasets_oa purge; -DROP TABLE ${stats_db_name}.software_oa purge; -DROP TABLE ${stats_db_name}.allpubs purge; -DROP TABLE ${stats_db_name}.alldatasets purge; -DROP TABLE ${stats_db_name}.allsoftware purge; -DROP TABLE ${stats_db_name}.allpubsshare purge; -DROP TABLE ${stats_db_name}.alldatasetssshare purge; -DROP TABLE ${stats_db_name}.allsoftwaresshare purge; +DROP VIEW result_contexts; /*EOS*/ +DROP VIEW pubs_oa; /*EOS*/ +DROP VIEW datasets_oa; /*EOS*/ +DROP VIEW software_oa; /*EOS*/ +DROP VIEW allpubs; /*EOS*/ +DROP VIEW alldatasets; /*EOS*/ +DROP VIEW allsoftware; /*EOS*/ +DROP VIEW allpubsshare; /*EOS*/ +DROP VIEW alldatasetssshare; /*EOS*/ +DROP VIEW allsoftwaresshare; /*EOS*/ --Funder Findability -drop table ${stats_db_name}.indi_funder_findable purge; +drop table if exists ${stats_db_name}.indi_funder_findable purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_funder_findable stored as parquet as with result_findable as @@ -1151,10 +1151,10 @@ with result_findable as group by p.funder) select allresults.funder, result_findable.no_result_findable/allresults.no_allresults funder_findable from allresults - join result_findable on result_findable.funder=allresults.funder; + join result_findable on result_findable.funder=allresults.funder; /*EOS*/ --RIs Findability -drop table ${stats_db_name}.indi_ris_findable purge; +drop table if exists ${stats_db_name}.indi_ris_findable purge; /*EOS*/ create table if not exists ${stats_db_name}.indi_ris_findable stored as parquet as with result_contexts as @@ -1175,7 +1175,7 @@ allresults as group by rc.ri_initiative) select allresults.ri_initiative, result_findable.no_result_findable/allresults.no_allresults ris_findable from allresults - join result_findable on result_findable.ri_initiative=allresults.ri_initiative; + join result_findable on result_findable.ri_initiative=allresults.ri_initiative; /*EOS*/ create table if not exists ${stats_db_name}.indi_pub_publicly_funded stored as parquet as with org_names_pids as @@ -1195,6 +1195,7 @@ and pf.publicly_funded='yes') foo) select distinct p.id, coalesce(publicly_funded, 0) as publicly_funded from ${stats_db_name}.publication p left outer join ( -select distinct ro.id, 1 as publicly_funded from result_organization ro +select distinct ro.id, 1 as publicly_funded from ${stats_db_name}.result_organization ro join ${stats_db_name}.organization o on o.id=ro.organization -join publicly_funded_orgs pfo on o.name=pfo.name) tmp on p.id=tmp.id; \ No newline at end of file +join publicly_funded_orgs pfo on o.name=pfo.name) tmp on p.id=tmp.id; /*EOS*/ + diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index cbf97944dc..709de65959 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -64,6 +64,26 @@ hadoop_user_name user name of the wf owner + + + sparkSqlWarehouseDir + + + + sparkClusterOpts + --conf spark.network.timeout=600 --conf spark.extraListeners= --conf spark.sql.queryExecutionListeners= --conf spark.yarn.historyServer.address=http://iis-cdh5-test-m3.ocean.icm.edu.pl:18088 --conf spark.eventLog.dir=hdfs://nameservice1/user/spark/applicationHistory + spark cluster-wide options + + + sparkResourceOpts + --executor-memory=6G --conf spark.executor.memoryOverhead=4G --executor-cores=6 --driver-memory=8G --driver-cores=4 + spark resource options + + + sparkApplicationOpts + --conf spark.sql.shuffle.partitions=3840 + spark resource options +
@@ -75,13 +95,21 @@ ${hive_metastore_uris} - hive.txn.timeout - ${hive_timeout} + hive.txn.timeout + ${hive_timeout} + + + hive.mapjoin.followby.gby.localtask.max.memory.usage + 0.80 + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + mapred.job.queue.name + analytics - - mapred.job.queue.name - analytics - @@ -129,164 +157,164 @@ ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} - external_stats_db_name=${external_stats_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} + external_stats_db_name=${external_stats_db_name} - + - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} - external_stats_db_name=${external_stats_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} + external_stats_db_name=${external_stats_db_name} - - + + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} - + ${hive_jdbc_url} - stats_db_name=${stats_db_name} - openaire_db_name=${openaire_db_name} + stats_db_name=${stats_db_name} + openaire_db_name=${openaire_db_name} @@ -318,12 +346,23 @@ - - ${hive_jdbc_url} - - stats_db_name=${stats_db_name} - external_stats_db_name=${external_stats_db_name} - + + yarn + cluster + Step16-createIndicatorsTables + eu.dnetlib.dhp.oozie.RunSQLSparkJob + dhp-stats-update-${projectVersion}.jar + + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + ${sparkClusterOpts} + ${sparkResourceOpts} + ${sparkApplicationOpts} + + --hiveMetastoreUris${hive_metastore_uris} + --sqleu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql + --stats_db_name${stats_db_name} + --external_stats_db_name${external_stats_db_name} + @@ -383,18 +422,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -439,8 +478,8 @@ ${jobTracker} ${nameNode} copyDataToImpalaCluster.sh - - + + ${stats_db_name} ${monitor_db_name} ${observatory_db_name} @@ -501,4 +540,4 @@ - + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 6ef320253e..c8514a3cb5 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.2] + [5.17.3] [4.0.3] [6.0.5] [3.1.6]