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/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/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-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-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..d5b106c81b 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 @@ -1,6 +1,16 @@ package eu.dnetlib.dhp.oa.dedup; +import java.util.*; +import java.util.stream.Stream; + +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; @@ -8,180 +18,195 @@ 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 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 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; + public static final class DedupRecordReduceState { + public final String dedupId; - public final ArrayList aliases = new ArrayList<>(); + public final ArrayList aliases = new ArrayList<>(); - public final HashSet acceptanceDate = new HashSet<>(); + public final HashSet acceptanceDate = new HashSet<>(); - public OafEntity entity; + public OafEntity entity; - public DedupRecordReduceState(String dedupId, String id, OafEntity entity) { - this.dedupId = dedupId; - this.entity = entity; - if (entity == null) { - aliases.add(id); - } else { - if (Result.class.isAssignableFrom(entity.getClass())) { - Result result = (Result) entity; - if (result.getDateofacceptance() != null && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { - acceptanceDate.add(result.getDateofacceptance().getValue()); - } - } - } - } + public DedupRecordReduceState(String dedupId, String id, OafEntity entity) { + this.dedupId = dedupId; + this.entity = entity; + if (entity == null) { + aliases.add(id); + } else { + if (Result.class.isAssignableFrom(entity.getClass())) { + Result result = (Result) entity; + if (result.getDateofacceptance() != null + && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { + acceptanceDate.add(result.getDateofacceptance().getValue()); + } + } + } + } - public String getDedupId() { - return dedupId; - } - } - private static final int MAX_ACCEPTANCE_DATE = 20; + public String getDedupId() { + return dedupId; + } + } - private DedupRecordFactory() { - } + private static final int MAX_ACCEPTANCE_DATE = 20; - public static Dataset createDedupRecord( - final SparkSession spark, - final DataInfo dataInfo, - final String mergeRelsInputPath, - final String entitiesInputPath, - final Class clazz) { + private DedupRecordFactory() { + } - final long ts = System.currentTimeMillis(); - final Encoder beanEncoder = Encoders.bean(clazz); - final Encoder kryoEncoder = Encoders.kryo(clazz); + public static Dataset createDedupRecord( + final SparkSession spark, + final DataInfo dataInfo, + final String mergeRelsInputPath, + final String entitiesInputPath, + final Class clazz) { - // - Dataset entities = spark - .read() - .schema(Encoders.bean(clazz).schema()) - .json(entitiesInputPath) - .as(beanEncoder) - .map( - (MapFunction>) entity -> { - return new Tuple2<>(entity.getId(), entity); - }, - Encoders.tuple(Encoders.STRING(), kryoEncoder)) - .selectExpr("_1 AS id", "_2 AS kryoObject"); + final long ts = System.currentTimeMillis(); + final Encoder beanEncoder = Encoders.bean(clazz); + final Encoder kryoEncoder = Encoders.kryo(clazz); - // : source is the dedup_id, target is the id of the mergedIn - Dataset mergeRels = spark - .read() - .load(mergeRelsInputPath) - .where("relClass == 'merges'") - .selectExpr("source as dedupId", "target as id"); + // + Dataset entities = spark + .read() + .schema(Encoders.bean(clazz).schema()) + .json(entitiesInputPath) + .as(beanEncoder) + .map( + (MapFunction>) entity -> { + return new Tuple2<>(entity.getId(), entity); + }, + Encoders.tuple(Encoders.STRING(), kryoEncoder)) + .selectExpr("_1 AS id", "_2 AS kryoObject"); - return mergeRels - .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()) - .reduceGroups( - (ReduceFunction) (t1, t2) -> { - if (t1.entity == null) { - t2.aliases.addAll(t1.aliases); - return t2; - } - if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) { - t1.acceptanceDate.addAll(t2.acceptanceDate); - } - t1.aliases.addAll(t2.aliases); - t1.entity = reduceEntity(t1.entity, t2.entity); + // : source is the dedup_id, target is the id of the mergedIn + Dataset mergeRels = spark + .read() + .load(mergeRelsInputPath) + .where("relClass == 'merges'") + .selectExpr("source as dedupId", "target as id"); - return t1; - } - ) - .flatMap - ((FlatMapFunction, OafEntity>) t -> { - String dedupId = t._1(); - DedupRecordReduceState agg = t._2(); + return mergeRels + .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()) + .reduceGroups( + (ReduceFunction) (t1, t2) -> { + if (t1.entity == null) { + t2.aliases.addAll(t1.aliases); + return t2; + } + if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) { + t1.acceptanceDate.addAll(t2.acceptanceDate); + } + t1.aliases.addAll(t2.aliases); + t1.entity = reduceEntity(t1.entity, t2.entity); - if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { - return Collections.emptyIterator(); - } + return t1; + }) + .flatMap((FlatMapFunction, OafEntity>) t -> { + String dedupId = t._1(); + DedupRecordReduceState agg = t._2(); - 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); - } + if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { + return Collections.emptyIterator(); + } - private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) { + 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; } + int compare = new IdentifierComparator<>() + .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); - int compare = new IdentifierComparator<>() - .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); - - if (compare > 0) { + if (compare > 0) { OafEntity swap = duplicate; - duplicate = entity; - entity = swap; - } + duplicate = entity; + entity = swap; + } - entity.mergeFrom(duplicate); + entity.mergeFrom(duplicate); - if (ModelSupport.isSubClass(duplicate, Result.class)) { - Result re = (Result) entity; - Result rd = (Result) duplicate; + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result re = (Result) entity; + Result rd = (Result) duplicate; - List> authors = new ArrayList<>(); - if (re.getAuthor() != null) { - authors.add(re.getAuthor()); - } - if (rd.getAuthor() != null) { - authors.add(rd.getAuthor()); - } + List> authors = new ArrayList<>(); + if (re.getAuthor() != null) { + authors.add(re.getAuthor()); + } + if (rd.getAuthor() != null) { + authors.add(rd.getAuthor()); + } - re.setAuthor(AuthorMerger.merge(authors)); - } + re.setAuthor(AuthorMerger.merge(authors)); + } - return entity; - } + return entity; + } - public static T entityMerger( - String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { - T base = entities.next()._2(); + public static T entityMerger( + String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { + T base = entities.next()._2(); - while (entities.hasNext()) { - T duplicate = entities.next()._2(); - if (duplicate != null) - base = (T) reduceEntity(base, duplicate); - } + while (entities.hasNext()) { + T duplicate = entities.next()._2(); + if (duplicate != null) + base = (T) reduceEntity(base, duplicate); + } - base.setId(id); - base.setDataInfo(dataInfo); - base.setLastupdatetimestamp(ts); + base.setId(id); + base.setDataInfo(dataInfo); + base.setLastupdatetimestamp(ts); - return base; - } + return base; + } } 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/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/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/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. Phys."],"DOI":"10.1038\/s41567-022-01757-y","type":"journal-article","created":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T15:32:19Z","timestamp":1676043139000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Observation of electroweak production of two jets and a Z-boson pair"],"prefix":"10.1038","author":[{"name":"ATLAS Collaboration","sequence":"first","affiliation":[]},{"given":"G.","family":"Aad","sequence":"additional","affiliation":[]},{"given":"B.","family":"Abbott","sequence":"additional","affiliation":[]},{"given":"D. C.","family":"Abbott","sequence":"additional","affiliation":[]},{"given":"A.","family":"Abed Abud","sequence":"additional","affiliation":[]},{"given":"K.","family":"Abeling","sequence":"additional","affiliation":[]},{"given":"D. K.","family":"Abhayasinghe","sequence":"additional","affiliation":[]},{"given":"S. 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--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-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 ce117b5e9a..3493ecb2fa 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 @@ -43,6 +43,17 @@ --graphPath${graphPath} --masteryarn + + + + + + + + + + + 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..a6bbd30cff 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 +1278,21 @@ 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-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-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..ef6370bf3a 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. Sutherland","name":"W. J.","surname":"Sutherland","rank":1,"pid":[],"affiliation":[]},{"fullname":"S.T. Alvarez-Castaneda","name":"S. T.","surname":"Alvarez-Castaneda","rank":2,"pid":[],"affiliation":[]},{"fullname":"T. Amano","name":"T.","surname":"Amano","rank":3,"pid":[],"affiliation":[]},{"fullname":"R. Ambrosini","name":"R.","surname":"Ambrosini","rank":4,"pid":[],"affiliation":[]},{"fullname":"P. Atkinson","name":"P.","surname":"Atkinson","rank":5,"pid":[],"affiliation":[]},{"fullname":"J.M. Baxter","name":"J. M.","surname":"Baxter","rank":6,"pid":[],"affiliation":[]},{"fullname":"A.L. Bond","name":"A. L.","surname":"Bond","rank":7,"pid":[],"affiliation":[]},{"fullname":"P.J. Boon","name":"P. J.","surname":"Boon","rank":8,"pid":[],"affiliation":[]},{"fullname":"K.L. Buchanan","name":"K. L.","surname":"Buchanan","rank":9,"pid":[],"affiliation":[]},{"fullname":"J. Barlow","name":"J.","surname":"Barlow","rank":10,"pid":[],"affiliation":[]},{"fullname":"G. Bogliani","name":"G.","surname":"Bogliani","rank":11,"pid":[],"affiliation":[]},{"fullname":"O.M. Bragg","name":"O. M.","surname":"Bragg","rank":12,"pid":[],"affiliation":[]},{"fullname":"M. Burgman","name":"M.","surname":"Burgman","rank":13,"pid":[],"affiliation":[]},{"fullname":"M.W. Cadotte","name":"M. W.","surname":"Cadotte","rank":14,"pid":[],"affiliation":[]},{"fullname":"M. Calver","name":"M.","surname":"Calver","rank":15,"pid":[],"affiliation":[]},{"fullname":"S.J. Cooke","name":"S. J.","surname":"Cooke","rank":16,"pid":[],"affiliation":[]},{"fullname":"R.T. Corlett","name":"R. T.","surname":"Corlett","rank":17,"pid":[],"affiliation":[]},{"fullname":"V. Devictor","name":"V.","surname":"Devictor","rank":18,"pid":[],"affiliation":[]},{"fullname":"J.G. Ewen","name":"J. G.","surname":"Ewen","rank":19,"pid":[],"affiliation":[]},{"fullname":"M. Fisher","name":"M.","surname":"Fisher","rank":20,"pid":[],"affiliation":[]},{"fullname":"G. Freeman","name":"G.","surname":"Freeman","rank":21,"pid":[],"affiliation":[]},{"fullname":"E. Game","name":"E.","surname":"Game","rank":22,"pid":[],"affiliation":[]},{"fullname":"B.J. Godley","name":"B. J.","surname":"Godley","rank":23,"pid":[],"affiliation":[]},{"fullname":"C. Gortazar","name":"C.","surname":"Gortazar","rank":24,"pid":[],"affiliation":[]},{"fullname":"I.R. Hartley","name":"I. R.","surname":"Hartley","rank":25,"pid":[],"affiliation":[]},{"fullname":"D.L. Hawksworth","name":"D. L.","surname":"Hawksworth","rank":26,"pid":[],"affiliation":[]},{"fullname":"K.A. Hobson","name":"K. A.","surname":"Hobson","rank":27,"pid":[],"affiliation":[]},{"fullname":"M.-. Lu","name":"M. -.","surname":"Lu","rank":28,"pid":[],"affiliation":[]},{"fullname":"B. Martin-Lopez","name":"B.","surname":"Martin-Lopez","rank":29,"pid":[],"affiliation":[]},{"fullname":"K. Ma","name":"K.","surname":"Ma","rank":30,"pid":[],"affiliation":[]},{"fullname":"A. 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Power","name":"J.","surname":"Power","rank":41,"pid":[],"affiliation":[]},{"fullname":"E.C. Ree","name":"E. C.","surname":"Ree","rank":42,"pid":[],"affiliation":[]},{"fullname":"M.W. Schwartz","name":"M. W.","surname":"Schwartz","rank":43,"pid":[],"affiliation":[]},{"fullname":"I. Storch","name":"I.","surname":"Storch","rank":44,"pid":[],"affiliation":[]},{"fullname":"C. 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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