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 2fbdb3f42..87738a0e8 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 @@ -23,6 +23,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -249,7 +250,24 @@ public class MappersTest { final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); + assertEquals(d.getId(), r1.getSource()); + assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget()); + assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType()); + assertEquals(ModelConstants.OUTCOME, r1.getSubRelType()); + assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass()); + assertTrue(r1.getValidated()); + assertEquals("2020-01-01", r1.getValidationDate()); + + assertEquals(d.getId(), r2.getTarget()); + assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource()); + assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType()); + assertEquals(ModelConstants.OUTCOME, r2.getSubRelType()); + assertEquals(ModelConstants.PRODUCES, r2.getRelClass()); + assertTrue(r2.getValidated()); + assertEquals("2020-01-01", r2.getValidationDate()); + assertValidId(d.getId()); + assertEquals("50|doi_________::000374d100a9db469bd42b69dbb40b36", d.getId()); assertEquals(2, d.getOriginalId().size()); assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); @@ -303,10 +321,12 @@ public class MappersTest { }); assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid()); assertNotNull(d.getInstance().get(0).getPid()); - assertTrue(d.getInstance().get(0).getPid().isEmpty()); + assertFalse(d.getInstance().get(0).getPid().isEmpty()); - assertEquals("doi", d.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid()); - assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getAlternateIdentifier().get(0).getValue()); + assertEquals("doi", d.getInstance().get(0).getPid().get(0).getQualifier().getClassid()); + assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getPid().get(0).getValue()); + + assertTrue(d.getInstance().get(0).getAlternateIdentifier().isEmpty()); assertValidId(r1.getSource()); assertValidId(r1.getTarget()); @@ -736,12 +756,11 @@ public class MappersTest { } private void assertValidId(final String id) { - System.out.println(id); + // System.out.println(id); assertEquals(49, id.length()); - assertEquals('|', id.charAt(2)); - assertEquals(':', id.charAt(15)); - assertEquals(':', id.charAt(16)); + assertEquals(IdentifierFactory.ID_PREFIX_SEPARATOR, id.substring(2, 3)); + assertEquals(IdentifierFactory.ID_SEPARATOR, id.substring(15, 17)); } private List vocs() throws IOException { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary index 4d581044a..e1fd758b4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/oaf_to_summary @@ -1,20 +1,10 @@ -{"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":null,"relType":"resultResult","subRelType":"relationship","relClass":"References","source":"50|doi_________::0f2129f0a8ddfb099b9fabba3105245f","target":"50|doi_________::4af011e641e0ba286660fd24a3f603b7","validated":false,"validationDate":null,"properties":[{"key":"RelationDate","value":"2018-01-01","dataInfo":null}]} -{"id":"50|doi_________::0f2129f0a8ddfb099b9fabba3105245f","localIdentifier":[{"identifier":"10.1111/1346-8138.14162","schema":"doi","url":"http://onlinelibrary.wiley.com/wol1/doi/10.1111/1346-8138.14162/fullpdf"}],"typology":"publication","subType":"Article","title":["Guideline of SSc","Diagnostic criteria, severity classification and guidelines of systemic sclerosis"],"author":["Yoshihide Asano","Masatoshi Jinnin","Yasushi Kawaguchi","Masataka Kuwana","Daisuke Goto","Shinichi Sato","Kazuhiko Takehara","Masaru Hatano","Manabu Fujimoto","Naoki Mugii","Hironobu Ihn"],"date":["2018-04-23","2018-01-01"],"subject":null,"publisher":["Wiley"],"relatedPublications":0,"relatedDatasets":0,"relatedUnknown":0,"datasources":[{"datasourceName":"Crossref","datasourceId":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","completionStatus":"complete"},{"datasourceName":"Datacite","datasourceId":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","completionStatus":"complete"}],"abstract":null} -{"collectedfrom":[{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":null,"relType":"resultResult","subRelType":"relationship","relClass":"References","source":"50|doi_________::1b57d5ebe71734c1fa98624d9609971e","target":"50|doi_________::7e79063f205480e61ee7fdcf7ab03bad","validated":false,"validationDate":null,"properties":[{"key":"RelationDate","value":"2004-11-01","dataInfo":null}]} -{"id":"50|doi_________::1b57d5ebe71734c1fa98624d9609971e","localIdentifier":[{"identifier":"10.1002/ajmg.a.30270","schema":"doi","url":"https://onlinelibrary.wiley.com/doi/full/10.1002/ajmg.a.30270"}],"typology":"publication","subType":"Article","title":["Clinical variability in a Noonan syndrome family with a newPTPN11 gene mutation"],"author":["D�bora Romeo Bertola","Alexandre C. 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Unfortunately, conventional wave theories based on Stokes-type expansions do not consider fluid motions at levels above the unperturbed fluid level. The usual practice of extrapolating the fluid kinematics from the unperturbed free surface to higher points in the fluid is generally reasonable for narrowband waves, but for broadband ocean waves this results in dramatic (and nonphysical) overestimation of surface velocities. Consequently, practical approximations for random waves are at best empirical and are often only loosely constrained by physical principles. In the present work, the authors formulate the governing equations for water waves in an incompressible and inviscid fluid, using a boundary-fitted coordinate system (i.e., sigma or s coordinates) to derive expressions for near-surface kinematics in nonlinear random waves from first principles. Comparison to a numerical model valid for highly nonlinear waves shows that the new results 1) are consistent with second-order Stokes theory, 2) are similar to extrapolation methods in narrowband waves, and 3) greatly improve estimates of surface kinematics in random seas.","dataInfo":null}],"dateofacceptance":{"value":"2017-05-09T19:33:59Z","dataInfo":null},"publisher":{"value":"American Meteorological 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SOURCER.organization o on o.id=ro.organization + join organization o on o.id=ro.organization where cast(year as int)>=2003 and cast(year as int)<=2021 group by year, country) tmp; diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_bipFinderScores.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_bipFinderScores.xml new file mode 100644 index 000000000..e4680a0cf --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_bipFinderScores.xml @@ -0,0 +1,100 @@ + +
+ + + + + +
+ + Import bipFinder scores + Import bipFinder scores + 30 + + + declares the path holding the BIP SCORE data + + bipScorePath + /data/bip/20201206 + + + + + + + declares the path holding the LATEST GRAPH dump + + latestGraphPath + /tmp/stable_ids/graph/14_graph_blacklisted + + + + + + + prepare action sets + + + [ + { + 'set' : 'bipfinder-scores', + 'jobProperty' : 'export_action_set_bipfinder-scores', + 'enablingProperty' : 'active_bipfinder-scores', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + prepare AS for the bipFinder scores integration + + executeOozieJob + IIS + + { + 'bipScorePath':'bipScorePath', + 'inputPath':'latestGraphPath', + 'outputPath': 'outputPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/bipfinder/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/bipfinder' + } + + build-report + + + + + + + update action sets + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_datacite.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_datacite.xml new file mode 100644 index 000000000..d2ea9d35f --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_datacite.xml @@ -0,0 +1,144 @@ + +
+ + + + + +
+ + Import Datacite ActionSet + Import InfoSpace + 30 + + + set the resume from + + resumeFrom + TransformDatacite + + + + + + + shall the datacite mapping produce the links? + + exportLinks + false + + + + + + + set the path storing the OAF Datacite records + + oafTargetPath + /data/datacite/production/datacite_oaf + + + + + + + set the input path for Datacite content + + datacitePath + /data/datacite + + + + + + + prepare action sets + + + [ + { + 'set' : 'datacite', + 'jobProperty' : 'export_action_set_datacite', + 'enablingProperty' : 'active_datacite', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + prepare a new version of Datacite ActionSet + + executeOozieJob + IIS + + { + 'mainPath' : 'datacitePath', + 'oafTargetPath' : 'oafTargetPath', + 'exportLinks' : 'exportLinks', + 'resumeFrom' : 'resumeFrom' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/datacite_import/oozie_app', + 'sparkExecutorMemory' : '7G' + } + + build-report + + + + + + + prepare a new version of Datacite ActionSet + + executeOozieJob + IIS + + { + 'sourcePath' : 'oafTargetPath', + 'outputPath' : 'outputPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/datacite_actionset/oozie_app', + 'sparkExecutorMemory' : '7G' + } + + build-report + + + + + + + update action sets + + + + + + + + wf_20210723_163342_752 + 2021-07-23T16:44:05+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_doiboost.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_doiboost.xml new file mode 100644 index 000000000..ce9eb8f4c --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_doiboost.xml @@ -0,0 +1,200 @@ + +
+ + + + + +
+ + Import DOIboost + Import InfoSpace + 30 + + + set the input path for MAG + + MAGDumpPath + /data/doiboost/mag-2021-02-15 + + + + + + + set the input path for CROSSREF dump + + crossrefDumpPath + /data/doiboost/crossref/ + + + + + + + set the intermediate path used to process MAG + + intermediatePathMAG + /data/doiboost/input/mag + + + + + + + set the input path for Crossref + + inputPathCrossref + /data/doiboost/input/crossref + + + + + + + set the timestamp for the Crossref incremental harvesting + + crossrefTimestamp + 1607614921429 + + + + + + + set the input path for UnpayWall + + inputPathUnpayWall + /data/doiboost/input/unpayWall + + + + + + + set the input path for ORCID + + inputPathOrcid + /data/orcid_activities_2020/last_orcid_dataset + + + + + + + set the working path for ORCID + + workingPathOrcid + /data/doiboost/input/orcid + + + + + + + set the hostedBy map path + + hostedByMapPath + /data/doiboost/input/hostedBy/hbMap.gz + + + + + + + set the oozie workflow name from which the execution will be resumed + + resumeFrom + ConvertCrossrefToOAF + + + + + + + wait configurations + + + + + + + prepare action sets + + + [ + { + 'set' : 'doiboost', + 'jobProperty' : 'export_action_set_doiboost', + 'enablingProperty' : 'active_doiboost', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + prepare a new version of DOIBoost + + executeOozieJob + IIS + + { + 'crossrefTimestamp' : 'crossrefTimestamp', + 'hostedByMapPath' : 'hostedByMapPath', + 'MAGDumpPath' :'MAGDumpPath', + 'inputPathMAG' : 'intermediatePathMAG', + 'inputPathCrossref' : 'inputPathCrossref', + 'crossrefDumpPath':'crossrefDumpPath', + 'inputPathUnpayWall' : 'inputPathUnpayWall', + 'inputPathOrcid' : 'inputPathOrcid', + 'outputPath' : 'outputPath', + 'workingPathOrcid':'workingPathOrcid', + 'resumeFrom' : 'resumeFrom' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/doiboost_process/oozie_app', + 'workingPath' : '/data/doiboost/process_p', + 'sparkExecutorCores' : '2', + 'sparkExecutorIntersectionMemory' : '12G', + 'sparkExecutorMemory' : '8G', + 'esServer' : '[es_server]', + 'esIndex' : 'crossref' + } + + build-report + + + + + + + update action sets + + + + + + + + wf_20210714_075237_381 + 2021-07-14T09:51:46+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_h2020_classification.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_h2020_classification.xml new file mode 100644 index 000000000..6d29e25a1 --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_h2020_classification.xml @@ -0,0 +1,132 @@ + +
+ + + + + +
+ + Import H2020classification + Import H2020classification + 30 + + + sets the URL to download the project file + + projectFileURL + https://cordis.europa.eu/data/cordis-h2020projects.csv + + + + + + + sets the URL to download the programme file + + programmeFileURL + https://cordis.europa.eu/data/reference/cordisref-h2020programmes.csv + + + + + + + sets the URL to download the topics file + + topicFileURL + https://cordis.europa.eu/data/reference/cordisref-h2020topics.xlsx + + + + + + + sets the name of the sheet in the topic file to be read + + sheetName + Topics + + + + + + + wait configurations + + + + + + + prepare action sets + + + [ + { + 'set' : 'h2020classification', + 'jobProperty' : 'export_action_set_h2020classification', + 'enablingProperty' : 'active_h2020classification', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + prepare updates for the H2020 Classification + + executeOozieJob + IIS + + { + 'outputPath': 'outputPath', + 'sheetName':'sheetName', + 'projectFileURL' : 'projectFileURL', + 'programmeFileURL' : 'programmeFileURL', + 'topicFileURL':'topicFileURL' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/project/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/h2020classification', + 'postgresURL':'', + 'postgresUser':'', + 'postgresPassword':'' + } + + build-report + + + + + + + update action sets + + + + + + + + wf_20210524_084803_740 + 2021-05-24T09:05:50+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_orcidworks-no-doi.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_orcidworks-no-doi.xml new file mode 100644 index 000000000..c5642dadc --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_orcidworks-no-doi.xml @@ -0,0 +1,101 @@ + +
+ + + + + +
+ + Import Orcid + Import InfoSpace + 30 + + + set the hdfs input path + + inputPath + /data/orcid_activities_2020 + + + + + + + set the temporary path where to store the action set + + processOutputPath + /tmp/prod_provision/working_path_orcid_activities + + + + + + + prepare action sets + + + [ + { + 'set' : 'orcidworks-no-doi', + 'jobProperty' : 'export_action_set_orcidworks_no_doi', + 'enablingProperty' : 'active_orcidworks_no_doi', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + prepare updates for the Orcid No Doi + + executeOozieJob + IIS + + { + 'workingPath' : 'inputPath', + 'processOutputPath' : 'processOutputPath', + 'outputPath': 'outputPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/orcidnodoi_actionset/oozie_app', + 'spark2GenNoDoiDatasetMaxExecutors' : '200', + 'spark2GenNoDoiDatasetExecutorMemory' : '2G' + } + + build-report + + + + + + + update action sets + + + + + + + + wf_20210713_170819_470 + 2021-07-13T17:28:26+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_ror.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_ror.xml new file mode 100644 index 000000000..4810fda3b --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/actionmanager/actionset_ror.xml @@ -0,0 +1,89 @@ + +
+ + + + + +
+ + Update ROR actionset + Import Infospace + 30 + + + Set the base path containing the no_doi_dataset folder + + inputPath + /data/ror/ror-data-2021-04-06.json + + + + + + + prepare action sets + + + [ + { + 'set' : 'ror', + 'jobProperty' : 'export_action_set_ror', + 'enablingProperty' : 'active_ror', + 'enabled' : 'true' + } + ] + + + + + + + + extract the hdfs output path generated in the previous node + + outputPath + + + + + + + update the ROR actionset + + executeOozieJob + IIS + + { + 'rorJsonInputPath' : 'inputPath', + 'rorActionSetPath': 'outputPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/ror/oozie_app', + 'workingDir': '/tmp/import_ror_actionset_prod' + } + + build-report + + + + + + + update action sets + + + + + + + + wf_20210518_143542_478 + 2021-05-18T14:37:13+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_beta_graph_for_IIS.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_beta_graph_for_IIS.xml new file mode 100644 index 000000000..ef2205e32 --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_beta_graph_for_IIS.xml @@ -0,0 +1,628 @@ + +
+ + + + + +
+ + Graph construction for IIS [BETA] + IIS + 30 + + + set blacklist of funder nsPrefixes + + nsPrefixBlacklist + gsrt________,rcuk________ + + + + + + + set the path of the map defining the relations id mappings + + idMappingPath + /data/maps/fct_map.json + + + + + + + Set the target path to store the MERGED graph + + mergedGraphPath + /tmp/beta_inference/graph/01_graph_merged + + + + + + + Set the target path to store the RAW graph + + rawGraphPath + /tmp/beta_inference/graph/02_graph_raw + + + + + + + Set the target path to store the CLEANED graph + + cleanedFirstGraphPath + /tmp/beta_inference/graph/03_graph_clean_first + + + + + + + Set the target path to store the DEDUPED graph + + dedupGraphPath + /tmp/beta_inference/graph/04_graph_dedup + + + + + + + Set the target path to store the CONSISTENCY graph + + consistentGraphPath + /tmp/beta_inference/graph/05_graph_consistent + + + + + + + Set the target path to store the CLEANED graph + + cleanedGraphPath + /tmp/beta_inference/graph/06_graph_cleaned + + + + + + + Set the dedup orchestrator name + + dedupConfig + dedup-similarity-result-decisiontree-v2 + + + + + + + declares the ActionSet ids to promote in the RAW graph + + actionSetIdsRawGraph + scholexplorer-dump,doiboost,orcidworks-no-doi,datacite + + + + + + + Set the IS lookup service address + + isLookUpUrl + http://beta.services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + wait configurations + + + + + + + + reuse cached ODF claims from the PROD aggregation system + + reuseODFClaims_PROD + true + + + + + + + reuse cached ODF records on HDFS from the PROD aggregation system + + reuseODFhdfs_PROD + true + + + + + + + reuse cached OAF claims from the PROD aggregation system + + reuseOAFClaims_PROD + true + + + + + + + reuse cached OAF records on HDFS from the PROD aggregation system + + reuseOAFhdfs_PROD + true + + + + + + + reuse cached DB content from the PROD aggregation system + + reuseDB_PROD + true + + + + + + + reuse cached OpenOrgs content from the PROD aggregation system + + reuseDBOpenorgs_PROD + true + + + + + + + reuse cached ODF content from the PROD aggregation system + + reuseODF_PROD + true + + + + + + + reuse cached OAF content from the PROD aggregation system + + reuseOAF_PROD + true + + + + + + + should apply the relations id patching based on the provided idMapping on PROD? + + shouldPatchRelations_PROD + false + + + + + + + set the PROD aggregator content path + + prodContentPath + /tmp/prod_aggregator_for_beta + + + + + + + Set the path containing the PROD AGGREGATOR graph + + prodAggregatorGraphPath + /tmp/beta_inference/graph/00_prod_graph_aggregator + + + + + + + reuse cached ODF claims from the BETA aggregation system + + reuseODFClaims_BETA + true + + + + + + + reuse cached ODF records on HDFS from the BETA aggregation system + + reuseODFhdfs_BETA + true + + + + + + + reuse cached OAF claims from the BETA aggregation system + + reuseOAFClaims_BETA + true + + + + + + + reuse cached OAF records on HDFS from the BETA aggregation system + + reuseOAFhdfs_BETA + true + + + + + + + reuse cached DB content from the BETA aggregation system + + reuseDB_BETA + true + + + + + + + reuse cached OpenOrgs content from the BETA aggregation system + + reuseDBOpenorgs_BETA + true + + + + + + + reuse cached ODF content from the BETA aggregation system + + reuseODF_BETA + true + + + + + + + reuse cached OAF content from the BETA aggregation system + + reuseOAF_BETA + true + + + + + + + should apply the relations id patching based on the provided idMapping on BETA? + + shouldPatchRelations_BETA + false + + + + + + + set the BETA aggregator content path + + betaContentPath + /tmp/beta_aggregator + + + + + + + Set the path containing the BETA AGGREGATOR graph + + betaAggregatorGraphPath + /tmp/beta_inference/graph/00_beta_graph_aggregator + + + + + + + wait configurations + + + + + + + + create the BETA AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'betaAggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims_BETA', + 'reuseOAFClaims' : 'reuseOAFClaims_BETA', + 'reuseDB' : 'reuseDB_BETA', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs_BETA', + 'reuseODF' : 'reuseODF_BETA', + 'reuseODF_hdfs' : 'reuseODFhdfs_BETA', + 'reuseOAF' : 'reuseOAF_BETA', + 'reuseOAF_hdfs' : 'reuseOAFhdfs_BETA', + 'contentPath' : 'betaContentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist', + 'shouldPatchRelations' : 'shouldPatchRelations_BETA', + 'idMappingPath' : 'idMappingPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/beta_inference/working_dir/beta_aggregator' + } + + build-report + + + + + + + create the PROD AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'prodAggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims_PROD', + 'reuseOAFClaims' : 'reuseOAFClaims_PROD', + 'reuseDB' : 'reuseDB_PROD', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs_PROD', + 'reuseODF' : 'reuseODF_PROD', + 'reuseODF_hdfs' : 'reuseODFhdfs_PROD', + 'reuseOAF' : 'reuseOAF_PROD', + 'reuseOAF_hdfs' : 'reuseOAFhdfs_PROD', + 'contentPath' : 'prodContentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist', + 'shouldPatchRelations' : 'shouldPatchRelations_PROD', + 'idMappingPath' : 'idMappingPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/beta_inference/working_dir/prod_aggregator' + } + + build-report + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'betaInputGraphPath' : 'betaAggregatorGraphPath', + 'prodInputGraphPath' : 'prodAggregatorGraphPath', + 'graphOutputPath' : 'mergedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/merge/oozie_app', + 'workingDir' : '/tmp/beta_inference/working_dir/merge_graph', + 'priority' : 'BETA' + } + + build-report + + + + + + + create the RAW graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsRawGraph', + 'inputGraphRootPath' : 'mergedGraphPath', + 'outputGraphRootPath' : 'rawGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/beta_inference/working_dir/promoteActionsRaw' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'rawGraphPath', + 'graphOutputPath': 'cleanedFirstGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/beta_inference/working_dir/clean_first' + } + + build-report + + + + + + + search for duplicates in the raw graph + + executeOozieJob + IIS + + { + 'actionSetId' : 'dedupConfig', + 'graphBasePath' : 'cleanedFirstGraphPath', + 'dedupGraphPath': 'dedupGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/dedup/scan/oozie_app', + 'actionSetIdOpenorgs' : 'dedup-similarity-organization-simple', + 'workingPath' : '/tmp/beta_inference/working_dir/dedup', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G' + } + + build-report + + + + + + + mark duplicates as deleted and redistribute the relationships + + executeOozieJob + IIS + + { + 'graphBasePath' : 'dedupGraphPath', + 'graphOutputPath': 'consistentGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/dedup/consistency/oozie_app', + 'workingPath' : '/tmp/beta_inference/working_dir/dedup' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'consistentGraphPath', + 'graphOutputPath': 'cleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/beta_inference/working_dir/clean' + } + + build-report + + + + + + + + wf_20210730_094240_462 + 2021-07-30T15:04:19+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_prod_graph_for_IIS.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_prod_graph_for_IIS.xml new file mode 100644 index 000000000..e5ce3d710 --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/00_prod_graph_for_IIS.xml @@ -0,0 +1,437 @@ + +
+ + + + + +
+ + Graph construction for IIS [PROD NEW] + IIS + 30 + + + set blacklist of funder nsPrefixes + + nsPrefixBlacklist + conicytf____,dfgf________,gsrt________,innoviris___,miur________,rif_________,rsf_________,sgov________,sfrs________ + + + + + + + set the path of the map defining the relations id mappings + + idMappingPath + /data/maps/fct_map.json + + + + + + + Set the path containing the PROD AGGREGATOR graph + + aggregatorGraphPath + /tmp/prod_inference/graph/00_graph_aggregator + + + + + + + Set the target path to store the RAW graph + + rawGraphPath + /tmp/prod_inference/graph/01_graph_raw + + + + + + + Set the target path to store the CLEANED graph + + cleanedFirstGraphPath + /tmp/prod_inference/graph/02_graph_clean_first + + + + + + + Set the target path to store the DEDUPED graph + + dedupGraphPath + /tmp/prod_inference/graph/03_graph_dedup + + + + + + + Set the target path to store the CONSISTENCY graph + + consistentGraphPath + /tmp/prod_inference/graph/04_graph_consistent + + + + + + + Set the target path to store the CLEANED graph + + cleanedGraphPath + /tmp/prod_inference/graph/05_graph_cleaned + + + + + + + Set the dedup orchestrator name + + dedupConfig + dedup-similarity-result-decisiontree-v2 + + + + + + + declares the ActionSet ids to promote in the RAW graph + + actionSetIdsRawGraph + scholexplorer-dump,doiboost,orcidworks-no-doi,datacite + + + + + + + Set the IS lookup service address + + isLookUpUrl + http://services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + wait configurations + + + + + + + + + + + + + + + + reuse cached ODF claims from the PROD aggregation system + + reuseODFClaims + true + + + + + + + reuse cached OAF claims from the PROD aggregation system + + reuseOAFClaims + true + + + + + + + reuse cached ODF records on HDFS from the PROD aggregation system + + reuseODFhdfs + true + + + + + + + reuse cached OAF records on HDFS from the PROD aggregation system + + reuseOAFhdfs + true + + + + + + + reuse cached ODF content from the PROD aggregation system + + reuseODF + true + + + + + + + reuse cached OAF content from the PROD aggregation system + + reuseOAF + true + + + + + + + reuse cached DB content from the PROD aggregation system + + reuseDB + true + + + + + + + reuse cached OpenOrgs content from the PROD aggregation system + + reuseDBOpenorgs + true + + + + + + + should apply the relations id patching based on the provided idMapping? + + shouldPatchRelations + false + + + + + + + set the PROD aggregator content path + + contentPath + /tmp/prod_aggregator + + + + + + + wait configurations + + + + + + + create the PROD AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'aggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims', + 'reuseOAFClaims' : 'reuseOAFClaims', + 'reuseDB' : 'reuseDB', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs', + 'reuseODF' : 'reuseODF', + 'reuseODF_hdfs' : 'reuseODFhdfs', + 'reuseOAF' : 'reuseOAF', + 'reuseOAF_hdfs' : 'reuseOAFhdfs', + 'contentPath' : 'contentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist', + 'shouldPatchRelations' : 'shouldPatchRelations', + 'idMappingPath' : 'idMappingPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/prod_inference/working_dir/prod_aggregator' + } + + build-report + + + + + + + create the RAW graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsRawGraph', + 'inputGraphRootPath' : 'aggregatorGraphPath', + 'outputGraphRootPath' : 'rawGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/prod_inference/working_dir/promoteActionsRaw' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'rawGraphPath', + 'graphOutputPath': 'cleanedFirstGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/prod_inference/working_dir/clean_first' + } + + build-report + + + + + + + search for duplicates in the raw graph + + executeOozieJob + IIS + + { + 'actionSetId' : 'dedupConfig', + 'graphBasePath' : 'cleanedFirstGraphPath', + 'dedupGraphPath': 'dedupGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/dedup/scan/oozie_app', + 'actionSetIdOpenorgs' : 'dedup-similarity-organization-simple', + 'workingPath' : '/tmp/prod_inference/working_dir/dedup', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G' + } + + build-report + + + + + + + mark duplicates as deleted and redistribute the relationships + + executeOozieJob + IIS + + { + 'graphBasePath' : 'dedupGraphPath', + 'graphOutputPath': 'consistentGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/dedup/consistency/oozie_app', + 'workingPath' : '/tmp/prod_inference/working_dir/dedup' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'consistentGraphPath', + 'graphOutputPath': 'cleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/prod_inference/working_dir/clean' + } + + build-report + + + + + + + + wf_20210719_165159_86 + 2021-07-19T20:45:09+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/01_IIS.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/01_IIS.xml new file mode 100644 index 000000000..126d5f58d --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/01_IIS.xml @@ -0,0 +1,225 @@ + +
+ + + + + +
+ + IIS main workflow V3 [PROD] + IIS + 30 + + + start + + + + + + + Set a regex of funder shortnames to exclude from the project reference processing + + referenceextraction_project_fundingclass_blacklist_regex + ^DFG::.*$|^CONICYT::.*$|^RSF::.*$|^SGOV::.*$|^GSRT::.*$|^MIUR::.*$|^INNOVIRIS::.*$|^RIF::.*$|^SFRS::.*$ + + + + + + + prepare action sets + + + [ + { + 'set' : 'iis-document-affiliation', + 'jobProperty' : 'export_action_set_id_matched_doc_organizations', + 'enablingProperty' : 'active_document_affiliation', + 'enabled' : 'true' + }, + { + 'set' : 'iis-referenced-projects-main', + 'jobProperty' : 'export_action_set_id_document_referencedProjects', + 'enablingProperty' : 'active_referenceextraction_project', + 'enabled' : 'true' + }, + { + 'set' : 'iis-referenced-datasets-main', + 'jobProperty' : 'export_action_set_id_document_referencedDatasets', + 'enablingProperty' : 'active_referenceextraction_dataset', + 'enabled' : 'true' + }, + { + 'set' : 'iis-researchinitiative', + 'jobProperty' : 'export_action_set_id_document_research_initiative', + 'enablingProperty' : 'active_referenceextraction_researchinitiative', + 'enabled' : 'true' + }, + { + 'set' : 'iis-document-similarities', + 'jobProperty' : 'export_action_set_id_document_similarities_standard', + 'enablingProperty' : 'active_documentssimilarity', + 'enabled' : 'true' + }, + { + 'set' : 'iis-document-classes', + 'jobProperty' : 'export_action_set_id_document_classes', + 'enablingProperty' : 'active_documentsclassification', + 'enabled' : 'true' + }, + { + 'set' : 'iis-document-citations', + 'jobProperty' : 'export_action_set_id_document_referencedDocuments', + 'enablingProperty' : 'active_citationmatching', + 'enabled' : 'true' + }, + { + 'set' : 'iis-document-citations-relations', + 'jobProperty' : 'export_action_set_id_citation_relations', + 'enablingProperty' : 'active_citationmatching_relations', + 'enabled' : 'true' + }, + { + 'set' : 'iis-referenceextraction-pdb', + 'jobProperty' : 'export_action_set_id_document_pdb', + 'enablingProperty' : 'active_referenceextraction_pdb', + 'enabled' : 'true' + }, + { + 'set' : 'document_software_url', + 'jobProperty' : 'export_action_set_id_document_software_url', + 'enablingProperty' : 'active_referenceextraction_software_url', + 'enabled' : 'true' + }, + { + 'set' : 'iis-entities-software', + 'jobProperty' : 'export_action_set_id_entity_software', + 'enablingProperty' : 'active_referenceextraction_software_url', + 'enabled' : 'true' + }, + { + 'set' : 'iis-communities', + 'jobProperty' : 'export_action_set_id_document_community', + 'enablingProperty' : 'active_referenceextraction_community', + 'enabled' : 'true' + }, + { + 'set' : 'iis-referenced-patents', + 'jobProperty' : 'export_action_set_id_document_patent', + 'enablingProperty' : 'active_referenceextraction_patent', + 'enabled' : 'true' + }, + { + 'set' : 'iis-entities-patent', + 'jobProperty' : 'export_action_set_id_entity_patent', + 'enablingProperty' : 'active_referenceextraction_patent', + 'enabled' : 'true' + }, + { + 'set' : 'iis-covid-19', + 'jobProperty' : 'export_action_set_id_document_covid19', + 'enablingProperty' : 'active_referenceextraction_covid19', + 'enabled' : 'true' + } + ] + + + + + + + + prepare parameters + + import_islookup_service_location + import_content_objectstores_csv + import_content_object_store_location + import_mdstore_service_location + import_dataset_mdstore_ids_csv + oozie.wf.application.path + /lib/iis/primary/snapshots/2021-06-23 + IIS + /tmp/prod_inference/graph/05_graph_cleaned + import_infospace_graph_location + + import_project_concepts_context_ids_csv + aginfra,beopen,clarin,covid-19,dariah,dh-ch,oa-pg,egi,elixir-gr,enermaps,epos,fam,fet-fp7,fet-h2020,gotriple,instruct,mes,ni,rda,science-innovation-policy,risis,rural-digital-europe,sdsn-gr,sobigdata + + + + + + + IIS main + + iisMainJobV3 + + { + 'cluster' : 'cluster', + 'oozie.wf.application.path' : 'oozie.wf.application.path', + 'referenceextraction_project_fundingclass_blacklist_regex' : 'referenceextraction_project_fundingclass_blacklist_regex', + + 'active_document_affiliation' : 'active_document_affiliation', + 'active_referenceextraction_project' : 'active_referenceextraction_project', + 'active_referenceextraction_dataset' : 'active_referenceextraction_dataset', + 'active_referenceextraction_researchinitiative' : 'active_referenceextraction_researchinitiative', + 'active_documentsclassification' : 'active_documentsclassification', + 'active_documentssimilarity' : 'active_documentssimilarity', + 'active_citationmatching' : 'active_citationmatching', + 'active_citationmatching_relations' : 'active_citationmatching_relations', + 'active_referenceextraction_pdb' : 'active_referenceextraction_pdb', + 'active_referenceextraction_software_url' : 'active_referenceextraction_software_url', + 'active_referenceextraction_community' : 'active_referenceextraction_community', + 'active_referenceextraction_patent' : 'active_referenceextraction_patent', + 'active_referenceextraction_covid19' : 'active_referenceextraction_covid19', + + 'import_content_objectstores_csv' : 'import_content_objectstores_csv', + 'import_content_object_store_location' : 'import_content_object_store_location', + 'import_mdstore_service_location' : 'import_mdstore_service_location', + 'import_islookup_service_location' : 'import_islookup_service_location', + 'import_project_concepts_context_ids_csv' : 'import_project_concepts_context_ids_csv', + 'import_dataset_mdstore_ids_csv' : 'import_dataset_mdstore_ids_csv', + 'import_infospace_graph_location' : 'import_infospace_graph_location', + + 'export_action_set_id_matched_doc_organizations' : 'export_action_set_id_matched_doc_organizations', + 'export_action_set_id_document_referencedDatasets' : 'export_action_set_id_document_referencedDatasets', + 'export_action_set_id_document_referencedProjects' : 'export_action_set_id_document_referencedProjects', + 'export_action_set_id_document_research_initiative' : 'export_action_set_id_document_research_initiative', + 'export_action_set_id_document_similarities_standard' : 'export_action_set_id_document_similarities_standard', + + 'export_action_set_id_document_referencedDocuments' : 'export_action_set_id_document_referencedDocuments', + 'export_action_set_id_document_pdb' : 'export_action_set_id_document_pdb', + 'export_action_set_id_document_software_url' : 'export_action_set_id_document_software_url', + 'export_action_set_id_entity_software' : 'export_action_set_id_entity_software', + 'export_action_set_id_document_community' : 'export_action_set_id_document_community', + 'export_action_set_id_document_patent' : 'export_action_set_id_document_patent', + 'export_action_set_id_entity_patent' : 'export_action_set_id_entity_patent', + 'export_action_set_id_document_covid19' : 'export_action_set_id_document_covid19', + 'export_action_set_id_document_classes' : 'export_action_set_id_document_classes' + } + + false + build-report + + + + + + + update action sets + + + + + + + + wf_20210719_221139_780 + 2021-07-21T01:23:13+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_beta_graph.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_beta_graph.xml new file mode 100644 index 000000000..766783f8b --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_beta_graph.xml @@ -0,0 +1,995 @@ + +
+ + + + + +
+ + Graph Construction [BETA] + Data Provision + 30 + + + set blacklist of funder nsPrefixes + + nsPrefixBlacklist + gsrt________,rcuk________ + + + + + + + set the path of the map defining the relations id mappings + + idMappingPath + /data/maps/fct_map.json + + + + + + + Set the target path to store the MERGED graph + + mergedGraphPath + /tmp/beta_provision/graph/01_graph_merged + + + + + + + Set the target path to store the RAW graph + + rawGraphPath + /tmp/beta_provision/graph/02_graph_raw + + + + + + + Set the target path to store the the consistent graph cleaned + + cleanedFirstGraphPath + /tmp/beta_provision/graph/03_graph_cleaned + + + + + + + Set the target path to store the DEDUPED graph + + dedupGraphPath + /tmp/beta_provision/graph/04_graph_dedup + + + + + + + Set the target path to store the INFERRED graph + + inferredGraphPath + /tmp/beta_provision/graph/05_graph_inferred + + + + + + + Set the target path to store the CONSISTENCY graph + + consistentGraphPath + /tmp/beta_provision/graph/06_graph_consistent + + + + + + + Set the target path to store the ORCID enriched graph + + orcidGraphPath + /tmp/beta_provision/graph/07_graph_orcid + + + + + + + Set the target path to store the BULK TAGGED graph + + bulkTaggingGraphPath + /tmp/beta_provision/graph/08_graph_bulktagging + + + + + + + Set the target path to store the AFFILIATION from INSTITUTIONAL REPOS graph + + affiliationGraphPath + /tmp/beta_provision/graph/09_graph_affiliation + + + + + + + Set the target path to store the COMMUNITY from SELECTED SOURCES graph + + communityOrganizationGraphPath + /tmp/beta_provision/graph/10_graph_comunity_organization + + + + + + + Set the target path to store the FUNDING from SEMANTIC RELATION graph + + fundingGraphPath + /tmp/beta_provision/graph/11_graph_funding + + + + + + + Set the target path to store the COMMUNITY from SEMANTIC RELATION graph + + communitySemRelGraphPath + /tmp/beta_provision/graph/12_graph_comunity_sem_rel + + + + + + + Set the target path to store the COUNTRY enriched graph + + countryGraphPath + /tmp/beta_provision/graph/13_graph_country + + + + + + + Set the target path to store the CLEANED graph + + cleanedGraphPath + /tmp/beta_provision/graph/14_graph_cleaned + + + + + + + Set the target path to store the blacklisted graph + + blacklistedGraphPath + /tmp/beta_provision/graph/15_graph_blacklisted + + + + + + + Set the map of paths for the Bulk Tagging + + bulkTaggingPathMap + {"author" : "$['author'][*]['fullname']", "title" : "$['title'][*]['value']", "orcid" : "$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']", "contributor" : "$['contributor'][*]['value']", "description" : "$['description'][*]['value']"} + + + + + + + Set the map of associations organization, community list for the propagation of community to result through organization + + propagationOrganizationCommunityMap + {"20|corda__h2020::3fb05a9524c3f790391261347852f638":["mes","euromarine"], "20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8":["mes","euromarine"], "20|snsf________::9b253f265e3bef5cae6d881fdf61aceb":["mes","euromarine"],"20|rcuk________::e054eea0a47665af8c3656b5785ccf76":["mes","euromarine"],"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151":["mes","euromarine"],"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a":["mes","euromarine"],"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27":["mes","euromarine"],"20|snsf________::8fa091f8f25a846779acb4ea97b50aef":["mes","euromarine"],"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|corda_______::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78":["mes","euromarine"],"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db":["mes","euromarine"],"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70":["mes","euromarine"],"20|rcuk________::e16010089551a1a9182a94604fc0ea59":["mes","euromarine"],"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7":["mes","euromarine"],"20|snsf________::74730ef1439d7f7636a8be58a6b471b8":["mes","euromarine"],"20|nsf_________::ad72e19043a5a467e35f9b444d11563e":["mes","euromarine"],"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3":["mes","euromarine"],"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea":["mes","euromarine"],"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860":["mes","euromarine"],"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317":["mes","euromarine"], "20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f":["mes","euromarine"], "20|corda__h2020::65531bd11be9935948c7f2f4db1c1832":["mes","euromarine"], "20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946":["mes","euromarine"], "20|snsf________::3eb43582ac27601459a8d8b3e195724b":["mes","euromarine"], "20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6":["mes","euromarine"], "20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929":["mes","euromarine"], "20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0":["mes","euromarine"], "20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0":["beopen"], + "20|grid________::a867f78acdc5041b34acfe4f9a349157":["beopen"], "20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff":["beopen"], "20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad":["beopen"], "20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda_______::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda__h2020::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::15911e01e9744d57205825d77c218737":["beopen"], "20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab":["beopen"], "20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3":["beopen"], "20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3":["beopen"], "20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9":["beopen"], "20|corda_______::3ff558e30c2e434d688539548300b050":["beopen"], "20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39":["beopen"], "20|corda__h2020::5187217e2e806a6df3579c46f82401bc":["beopen"], "20|grid________::5fa7e2709bcd945e26bfa18689adeec1":["beopen"], "20|corda_______::d8696683c53027438031a96ad27c3c07":["beopen"], "20|corda__h2020::d8696683c53027438031a96ad27c3c07":["beopen"], "20|rcuk________::23a79ebdfa59790864e4a485881568c1":["beopen"], "20|corda__h2020::b76cf8fe49590a966953c37e18608af9":["beopen"], "20|grid________::d2f0204126ee709244a488a4cd3b91c2":["beopen"], "20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6":["beopen"], "20|grid________::802401579481dc32062bdee69f5e6a34":["beopen"], "20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d":["beopen"]} + + + + + + + + Set the dedup orchestrator name + + dedupConfig + dedup-similarity-result-decisiontree-v2 + + + + + + + declares the ActionSet ids to promote in the RAW graph + + actionSetIdsRawGraph + scholexplorer-dump,doiboost,orcidworks-no-doi,iis-entities-software,iis-entities-patent,datacite + + + + + + + declares the ActionSet ids to promote in the INFERRED graph + + actionSetIdsIISGraph + iis-researchinitiative,iis-document-citations,iis-document-citations-relations,iis-document-affiliation,iis-document-classes,iis-document-similarities,iis-referenced-datasets-main,iis-referenced-projects-main,iis-referenceextraction-pdb,document_software_url,iis-extracted-metadata,iis-communities,iis-referenced-patents,iis-covid-19,h2020classification,bipfinder-scores + + + + + + + Set the IS lookup service address + + isLookUpUrl + http://beta.services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + wait configurations + + + + + + + + reuse cached ODF claims from the PROD aggregation system + + reuseODFClaims_PROD + true + + + + + + + reuse cached ODF records on HDFS from the PROD aggregation system + + reuseODFhdfs_PROD + true + + + + + + + reuse cached OAF claims from the PROD aggregation system + + reuseOAFClaims_PROD + true + + + + + + + reuse cached OAF records on HDFS from the PROD aggregation system + + reuseOAFhdfs_PROD + true + + + + + + + reuse cached DB content from the PROD aggregation system + + reuseDB_PROD + true + + + + + + + reuse cached OpenOrgs content from the PROD aggregation system + + reuseDBOpenorgs_PROD + true + + + + + + + reuse cached ODF content from the PROD aggregation system + + reuseODF_PROD + true + + + + + + + reuse cached OAF content from the PROD aggregation system + + reuseOAF_PROD + true + + + + + + + should apply the relations id patching based on the provided idMapping on PROD? + + shouldPatchRelations_PROD + true + + + + + + + set the PROD aggregator content path + + prodContentPath + /tmp/prod_aggregator_for_beta + + + + + + + Set the path containing the PROD AGGREGATOR graph + + prodAggregatorGraphPath + /tmp/beta_provision/graph/00_prod_graph_aggregator + + + + + + + reuse cached ODF claims from the BETA aggregation system + + reuseODFClaims_BETA + true + + + + + + + reuse cached ODF records on HDFS from the BETA aggregation system + + reuseODFhdfs_BETA + true + + + + + + + reuse cached OAF claims from the BETA aggregation system + + reuseOAFClaims_BETA + true + + + + + + + reuse cached OAF records on HDFS from the BETA aggregation system + + reuseOAFhdfs_BETA + true + + + + + + + reuse cached DB content from the BETA aggregation system + + reuseDB_BETA + true + + + + + + + reuse cached OpenOrgs content from the BETA aggregation system + + reuseDBOpenorgs_BETA + true + + + + + + + reuse cached ODF content from the BETA aggregation system + + reuseODF_BETA + true + + + + + + + reuse cached OAF content from the BETA aggregation system + + reuseOAF_BETA + true + + + + + + + should apply the relations id patching based on the provided idMapping on BETA? + + shouldPatchRelations_BETA + true + + + + + + + set the BETA aggregator content path + + betaContentPath + /tmp/beta_aggregator + + + + + + + Set the path containing the BETA AGGREGATOR graph + + betaAggregatorGraphPath + /tmp/beta_provision/graph/00_beta_graph_aggregator + + + + + + + wait configurations + + + + + + + + create the BETA AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'betaAggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims_BETA', + 'reuseOAFClaims' : 'reuseOAFClaims_BETA', + 'reuseDB' : 'reuseDB_BETA', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs_BETA', + 'reuseODF' : 'reuseODF_BETA', + 'reuseODF_hdfs' : 'reuseODFhdfs_BETA', + 'reuseOAF' : 'reuseOAF_BETA', + 'reuseOAF_hdfs' : 'reuseOAFhdfs_BETA', + 'contentPath' : 'betaContentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist', + 'shouldPatchRelations' : 'shouldPatchRelations_BETA', + 'idMappingPath' : 'idMappingPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/beta_provision/working_dir/beta_aggregator' + } + + build-report + + + + + + + create the PROD AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'prodAggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims_PROD', + 'reuseOAFClaims' : 'reuseOAFClaims_PROD', + 'reuseDB' : 'reuseDB_PROD', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs_PROD', + 'reuseODF' : 'reuseODF_PROD', + 'reuseODF_hdfs' : 'reuseODFhdfs_PROD', + 'reuseOAF' : 'reuseOAF_PROD', + 'reuseOAF_hdfs' : 'reuseOAFhdfs_PROD', + 'contentPath' : 'prodContentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist', + 'shouldPatchRelations' : 'shouldPatchRelations_PROD', + 'idMappingPath' : 'idMappingPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/beta_provision/working_dir/prod_aggregator' + } + + build-report + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'betaInputGraphPath' : 'betaAggregatorGraphPath', + 'prodInputGraphPath' : 'prodAggregatorGraphPath', + 'graphOutputPath' : 'mergedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/merge/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/merge_graph', + 'priority' : 'BETA' + } + + build-report + + + + + + + create the RAW graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsRawGraph', + 'inputGraphRootPath' : 'mergedGraphPath', + 'outputGraphRootPath' : 'rawGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/beta_provision/working_dir/promoteActionsRaw' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'rawGraphPath', + 'graphOutputPath': 'cleanedFirstGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/clean' + } + + build-report + + + + + + + search for duplicates in the raw graph + + executeOozieJob + IIS + + { + 'actionSetId' : 'dedupConfig', + 'graphBasePath' : 'cleanedFirstGraphPath', + 'dedupGraphPath': 'dedupGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/dedup/scan/oozie_app', + 'actionSetIdOpenorgs' : 'dedup-similarity-organization-simple', + 'workingPath' : '/tmp/beta_provision/working_dir/dedup', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G' + } + + build-report + + + + + + + create the INFERRED graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsIISGraph', + 'inputGraphRootPath' : 'dedupGraphPath', + 'outputGraphRootPath' : 'inferredGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/beta_provision/working_dir/promoteActionsIIS' + } + + build-report + + + + + + + mark duplicates as deleted and redistribute the relationships + + executeOozieJob + IIS + + { + 'graphBasePath' : 'inferredGraphPath', + 'graphOutputPath': 'consistentGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/dedup/consistency/oozie_app', + 'workingPath' : '/tmp/beta_provision/working_dir/dedup' + } + + build-report + + + + + + + + propagates ORCID among results linked by allowedsemrels semantic relationships + + executeOozieJob + IIS + + { + 'sourcePath' : 'consistentGraphPath', + 'outputPath': 'orcidGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/orcidtoresultfromsemrel/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/orcid', + 'allowedsemrels' : 'IsSupplementedBy;IsSupplementTo;isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G' + } + + build-report + + + + + + + mark results respecting some rules as belonging to communities + + executeOozieJob + IIS + + { + 'sourcePath' : 'orcidGraphPath', + 'outputPath': 'bulkTaggingGraphPath', + 'isLookUpUrl' : 'isLookUpUrl', + 'pathMap' : 'bulkTaggingPathMap' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/bulktag/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/bulktag' + } + + build-report + + + + + + + creates relashionships between results and organizations when the organizations are associated to institutional repositories + + executeOozieJob + IIS + + { + 'sourcePath' : 'bulkTaggingGraphPath', + 'outputPath': 'affiliationGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/affiliation/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/affiliation', + 'saveGraph' : 'true', + 'blacklist' : 'empty' + } + + build-report + + + + + + + marks as belonging to communities the result collected from datasources related to the organizations specified in the organizationCommunityMap + + executeOozieJob + IIS + + { + 'sourcePath' : 'affiliationGraphPath', + 'outputPath': 'communityOrganizationGraphPath', + 'organizationtoresultcommunitymap': 'propagationOrganizationCommunityMap' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/community_organization/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/community_organization', + 'saveGraph' : 'true' + } + + build-report + + + + + + + created relation between projects and results linked to other results trough allowedsemrel semantic relations linked to projects + + executeOozieJob + IIS + + { + 'sourcePath' : 'communityOrganizationGraphPath', + 'outputPath': 'fundingGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/funding/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/funding', + 'allowedsemrels' : 'IsSupplementedBy;IsSupplementTo', + 'saveGraph' : 'true' + } + + build-report + + + + + + + tag as belonging to communitites result in in allowedsemrels relation with other result already linked to communities + + executeOozieJob + IIS + + { + 'sourcePath' : 'fundingGraphPath', + 'outputPath': 'communitySemRelGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/community_semrel/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/community_semrel', + 'allowedsemrels' : 'IsSupplementedBy;IsSupplementTo', + 'saveGraph' : 'true' + } + + build-report + + + + + + + associated to results colleced from allowedtypes and those in the whithelist the country of the organization(s) handling the datasource it is collected from + + executeOozieJob + IIS + + { + 'sourcePath' : 'communitySemRelGraphPath', + 'outputPath': 'countryGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/country/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'workingDir' : '/tmp/beta_provision/working_dir/country', + 'allowedtypes' : 'pubsrepository::institutional', + 'whitelist' : '10|openaire____::e783372970a1dc066ce99c673090ff88;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0', + 'saveGraph' : 'true' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'countryGraphPath', + 'graphOutputPath': 'cleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/clean' + } + + build-report + + + + + + + removes blacklisted relations + + executeOozieJob + IIS + + { + 'sourcePath' : 'cleanedGraphPath', + 'outputPath': 'blacklistedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/BETA/oa/enrichment/blacklist/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/blacklist', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '' + } + + build-report + + + + + + + + wf_20210803_134357_367 + 2021-08-03T17:08:11+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_prod_graph.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_prod_graph.xml new file mode 100644 index 000000000..be6155f2f --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/02_prod_graph.xml @@ -0,0 +1,778 @@ + +
+ + + + + +
+ + Graph construction [PROD NEW] + Data Provision + 30 + + + set blacklist of funder nsPrefixes + + nsPrefixBlacklist + conicytf____,dfgf________,gsrt________,innoviris___,miur________,rif_________,rsf_________,sgov________,sfrs________ + + + + + + + Set the path containing the PROD AGGREGATOR graph + + aggregatorGraphPath + /tmp/prod_provision/graph/00_prod_graph_aggregator + + + + + + + Set the target path to store the RAW graph + + rawGraphPath + /tmp/prod_provision/graph/01_graph_raw + + + + + + + Set the target path to store the the consistent graph cleaned + + cleanedFirstGraphPath + /tmp/prod_provision/graph/02_graph_cleaned + + + + + + + Set the target path to store the DEDUPED graph + + dedupGraphPath + /tmp/prod_provision/graph/03_graph_dedup + + + + + + + Set the target path to store the INFERRED graph + + inferredGraphPath + /tmp/prod_provision/graph/04_graph_inferred + + + + + + + Set the target path to store the CONSISTENCY graph + + consistentGraphPath + /tmp/prod_provision/graph/05_graph_consistent + + + + + + + Set the target path to store the ORCID enriched graph + + orcidGraphPath + /tmp/prod_provision/graph/06_graph_orcid + + + + + + + Set the target path to store the BULK TAGGED graph + + bulkTaggingGraphPath + /tmp/prod_provision/graph/07_graph_bulktagging + + + + + + + Set the target path to store the AFFILIATION from INSTITUTIONAL REPOS graph + + affiliationGraphPath + /tmp/prod_provision/graph/08_graph_affiliation + + + + + + + Set the target path to store the COMMUNITY from SELECTED SOURCES graph + + communityOrganizationGraphPath + /tmp/prod_provision/graph/09_graph_comunity_organization + + + + + + + Set the target path to store the FUNDING from SEMANTIC RELATION graph + + fundingGraphPath + /tmp/prod_provision/graph/10_graph_funding + + + + + + + Set the target path to store the COMMUNITY from SEMANTIC RELATION graph + + communitySemRelGraphPath + /tmp/prod_provision/graph/11_graph_comunity_sem_rel + + + + + + + Set the target path to store the COUNTRY enriched graph + + countryGraphPath + /tmp/prod_provision/graph/12_graph_country + + + + + + + Set the target path to store the CLEANED graph + + cleanedGraphPath + /tmp/prod_provision/graph/13_graph_cleaned + + + + + + + Set the target path to store the blacklisted graph + + blacklistedGraphPath + /tmp/prod_provision/graph/14_graph_blacklisted + + + + + + + Set the map of paths for the Bulk Tagging + + bulkTaggingPathMap + {"author" : "$['author'][*]['fullname']", "title" : "$['title'][*]['value']", "orcid" : "$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']", "contributor" : "$['contributor'][*]['value']", "description" : "$['description'][*]['value']"} + + + + + + + Set the map of associations organization, community list for the propagation of community to result through organization + + propagationOrganizationCommunityMap + {"20|corda__h2020::3fb05a9524c3f790391261347852f638":["mes","euromarine"], "20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8":["mes","euromarine"], "20|snsf________::9b253f265e3bef5cae6d881fdf61aceb":["mes","euromarine"],"20|rcuk________::e054eea0a47665af8c3656b5785ccf76":["mes","euromarine"],"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151":["mes","euromarine"],"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a":["mes","euromarine"],"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27":["mes","euromarine"],"20|snsf________::8fa091f8f25a846779acb4ea97b50aef":["mes","euromarine"],"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|corda_______::81e020977211c2c40fae2e1a50bffd71":["mes","euromarine"],"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78":["mes","euromarine"],"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db":["mes","euromarine"],"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70":["mes","euromarine"],"20|rcuk________::e16010089551a1a9182a94604fc0ea59":["mes","euromarine"],"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b":["mes","euromarine"],"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7":["mes","euromarine"],"20|snsf________::74730ef1439d7f7636a8be58a6b471b8":["mes","euromarine"],"20|nsf_________::ad72e19043a5a467e35f9b444d11563e":["mes","euromarine"],"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3":["mes","euromarine"],"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea":["mes","euromarine"],"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860":["mes","euromarine"],"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317":["mes","euromarine"], "20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f":["mes","euromarine"], "20|corda__h2020::65531bd11be9935948c7f2f4db1c1832":["mes","euromarine"], "20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946":["mes","euromarine"], "20|snsf________::3eb43582ac27601459a8d8b3e195724b":["mes","euromarine"], "20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6":["mes","euromarine"], "20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929":["mes","euromarine"], "20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0":["mes","euromarine"], "20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0":["beopen"], + "20|grid________::a867f78acdc5041b34acfe4f9a349157":["beopen"], "20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff":["beopen"], "20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad":["beopen"], "20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda_______::8ba50792bc5f4d51d79fca47d860c602":["beopen"], "20|corda__h2020::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::e70e9114979e963eef24666657b807c3":["beopen"], "20|corda_______::15911e01e9744d57205825d77c218737":["beopen"], "20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab":["beopen"], "20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3":["beopen"], "20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3":["beopen"], "20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9":["beopen"], "20|corda_______::3ff558e30c2e434d688539548300b050":["beopen"], "20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39":["beopen"], "20|corda__h2020::5187217e2e806a6df3579c46f82401bc":["beopen"], "20|grid________::5fa7e2709bcd945e26bfa18689adeec1":["beopen"], "20|corda_______::d8696683c53027438031a96ad27c3c07":["beopen"], "20|corda__h2020::d8696683c53027438031a96ad27c3c07":["beopen"], "20|rcuk________::23a79ebdfa59790864e4a485881568c1":["beopen"], "20|corda__h2020::b76cf8fe49590a966953c37e18608af9":["beopen"], "20|grid________::d2f0204126ee709244a488a4cd3b91c2":["beopen"], "20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6":["beopen"], "20|grid________::802401579481dc32062bdee69f5e6a34":["beopen"], "20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d":["beopen"]} + + + + + + + + Set the dedup orchestrator name + + dedupConfig + dedup-similarity-result-decisiontree-v2 + + + + + + + declares the ActionSet ids to promote in the RAW graph + + actionSetIdsRawGraph + scholexplorer-dump,doiboost,orcidworks-no-doi,iis-entities-software,iis-entities-patent,datacite + + + + + + + declares the ActionSet ids to promote in the INFERRED graph + + actionSetIdsIISGraph + iis-researchinitiative,iis-document-citations,iis-document-citations-relations,iis-document-affiliation,iis-document-classes,iis-document-similarities,iis-referenced-datasets-main,iis-referenced-projects-main,iis-referenceextraction-pdb,document_software_url,iis-extracted-metadata,iis-communities,iis-referenced-patents,iis-covid-19,h2020classification,bipfinder-scores + + + + + + + Set the IS lookup service address + + isLookUpUrl + http://services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + wait configurations + + + + + + + + + + + + + + + reuse cached ODF claims from the PROD aggregation system + + reuseODFClaims + true + + + + + + + reuse cached ODF records on HDFS from the PROD aggregation system + + reuseODFhdfs + true + + + + + + + reuse cached OAF claims from the PROD aggregation system + + reuseOAFClaims + true + + + + + + + reuse cached OAF records on HDFS from the PROD aggregation system + + reuseOAFhdfs + true + + + + + + + reuse cached DB content from the PROD aggregation system + + reuseDB + true + + + + + + + reuse cached OpenOrgs content from the PROD aggregation system + + reuseDBOpenorgs + true + + + + + + + reuse cached ODF content from the PROD aggregation system + + reuseODF + true + + + + + + + reuse cached OAF content from the PROD aggregation system + + reuseOAF + true + + + + + + + set the PROD aggregator content path + + contentPath + /tmp/prod_aggregator + + + + + + + wait configurations + + + + + + + create the PROD AGGREGATOR graph + + executeOozieJob + IIS + + { + 'graphOutputPath' : 'aggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl', + 'reuseODFClaims' : 'reuseODFClaims', + 'reuseOAFClaims' : 'reuseOAFClaims', + 'reuseDB' : 'reuseDB', + 'reuseDBOpenorgs' : 'reuseDBOpenorgs', + 'reuseODF' : 'reuseODF', + 'reuseODF_hdfs' : 'reuseODFhdfs', + 'reuseOAF' : 'reuseOAF', + 'reuseOAF_hdfs' : 'reuseOAFhdfs', + 'contentPath' : 'contentPath', + 'nsPrefixBlacklist' : 'nsPrefixBlacklist' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/raw_all/oozie_app', + 'mongoURL' : '', + 'mongoDb' : '', + 'mdstoreManagerUrl' : '', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '', + 'postgresOpenOrgsURL' : '', + 'postgresOpenOrgsUser' : '', + 'postgresOpenOrgsPassword' : '', + 'shouldHashId' : 'true', + 'importOpenorgs' : 'true', + 'workingDir' : '/tmp/prod_provision/working_dir/prod_aggregator' + } + + build-report + + + + + + + create the RAW graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsRawGraph', + 'inputGraphRootPath' : 'aggregatorGraphPath', + 'outputGraphRootPath' : 'rawGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/prod_provision/working_dir/promoteActionsRaw' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'rawGraphPath', + 'graphOutputPath': 'cleanedFirstGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/clean' + } + + build-report + + + + + + + search for duplicates in the raw graph + + executeOozieJob + IIS + + { + 'actionSetId' : 'dedupConfig', + 'graphBasePath' : 'cleanedFirstGraphPath', + 'dedupGraphPath': 'dedupGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/dedup/scan/oozie_app', + 'actionSetIdOpenorgs' : 'dedup-similarity-organization-simple', + 'workingPath' : '/tmp/prod_provision/working_dir/dedup', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G' + } + + build-report + + + + + + + create the INFERRED graph + + executeOozieJob + IIS + + { + 'inputActionSetIds' : 'actionSetIdsIISGraph', + 'inputGraphRootPath' : 'dedupGraphPath', + 'outputGraphRootPath' : 'inferredGraphPath', + 'isLookupUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'activePromoteDatasetActionPayload' : 'true', + 'activePromoteDatasourceActionPayload' : 'true', + 'activePromoteOrganizationActionPayload' : 'true', + 'activePromoteOtherResearchProductActionPayload' : 'true', + 'activePromoteProjectActionPayload' : 'true', + 'activePromotePublicationActionPayload' : 'true', + 'activePromoteRelationActionPayload' : 'true', + 'activePromoteResultActionPayload' : 'true', + 'activePromoteSoftwareActionPayload' : 'true', + 'mergeAndGetStrategy' : 'MERGE_FROM_AND_GET', + 'workingDir' : '/tmp/prod_provision/working_dir/promoteActionsIIS' + } + + build-report + + + + + + + mark duplicates as deleted and redistribute the relationships + + executeOozieJob + IIS + + { + 'graphBasePath' : 'inferredGraphPath', + 'graphOutputPath': 'consistentGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/dedup/consistency/oozie_app', + 'workingPath' : '/tmp/prod_provision/working_dir/dedup' + } + + build-report + + + + + + + propagates ORCID among results linked by allowedsemrels semantic relationships + + executeOozieJob + IIS + + { + 'sourcePath' : 'consistentGraphPath', + 'outputPath': 'orcidGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/orcidtoresultfromsemrel/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/orcid', + 'allowedsemrels' : 'isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true' + } + + build-report + + + + + + + mark results respecting some rules as belonging to communities + + executeOozieJob + IIS + + { + 'sourcePath' : 'orcidGraphPath', + 'outputPath': 'bulkTaggingGraphPath', + 'isLookUpUrl' : 'isLookUpUrl', + 'pathMap' : 'bulkTaggingPathMap' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/bulktag/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/bulktag' + } + + build-report + + + + + + + creates relashionships between results and organizations when the organizations are associated to institutional repositories + + executeOozieJob + IIS + + { + 'sourcePath' : 'bulkTaggingGraphPath', + 'outputPath': 'affiliationGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/affiliation/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/affiliation', + 'saveGraph' : 'true', + 'blacklist' : 'empty' + } + + build-report + + + + + + + marks as belonging to communities the result collected from datasources related to the organizations specified in the organizationCommunityMap + + executeOozieJob + IIS + + { + 'sourcePath' : 'affiliationGraphPath', + 'outputPath': 'communityOrganizationGraphPath', + 'organizationtoresultcommunitymap': 'propagationOrganizationCommunityMap' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/community_organization/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/community_organization', + 'saveGraph' : 'true' + } + + build-report + + + + + + + created relation between projects and results linked to other results trough allowedsemrel semantic relations linked to projects + + executeOozieJob + IIS + + { + 'sourcePath' : 'communityOrganizationGraphPath', + 'outputPath': 'fundingGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/funding/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/funding', + 'allowedsemrels' : 'isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true' + } + + build-report + + + + + + + tag as belonging to communitites result in in allowedsemrels relation with other result already linked to communities + + executeOozieJob + IIS + + { + 'sourcePath' : 'fundingGraphPath', + 'outputPath': 'communitySemRelGraphPath', + 'isLookUpUrl' : 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/community_semrel/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/community_semrel', + 'allowedsemrels' : 'isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true' + } + + build-report + + + + + + + associated to results colleced from allowedtypes and those in the whithelist the country of the organization(s) handling the datasource it is collected from + + executeOozieJob + IIS + + { + 'sourcePath' : 'communitySemRelGraphPath', + 'outputPath': 'countryGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/country/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', + 'workingDir' : '/tmp/prod_provision/working_dir/country', + 'allowedtypes' : 'pubsrepository::institutional', + 'whitelist' : '10|openaire____::e783372970a1dc066ce99c673090ff88;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0', + 'saveGraph' : 'true' + } + + build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'countryGraphPath', + 'graphOutputPath': 'cleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/clean/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/clean' + } + + build-report + + + + + + + removes blacklisted relations + + executeOozieJob + IIS + + { + 'sourcePath' : 'cleanedGraphPath', + 'outputPath': 'blacklistedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/enrichment/blacklist/oozie_app', + 'workingDir' : '/tmp/prod_provision/working_dir/blacklist', + 'postgresURL' : '', + 'postgresUser' : '', + 'postgresPassword' : '' + } + + build-report + + + + + + + + wf_20210723_171026_279 + 2021-07-24T00:00:39+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/03_graph2hive.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/03_graph2hive.xml new file mode 100644 index 000000000..836e69d6f --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/03_graph2hive.xml @@ -0,0 +1,74 @@ + +
+ + + + + +
+ + Graph to HiveDB [PROD] + Data Provision + 30 + + + Set the path containing the AGGREGATOR graph + + inputPath + + + + + + + + Set the target path to store the RAW graph + + hiveDbName + + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'inputPath' : 'inputPath', + 'hiveDbName' : 'hiveDbName' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/hive/oozie_app', + 'sparkDriverMemory' : '4G', + 'sparkExecutorMemory' : '10G', + 'sparkExecutorCores' : '3' + } + + build-report + + + + + + + + wf_20210728_075001_400 + 2021-07-28T08:04:00+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/04_graph2solr.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/04_graph2solr.xml new file mode 100644 index 000000000..6cdf41bb6 --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/04_graph2solr.xml @@ -0,0 +1,99 @@ + +
+ + + + + +
+ + Update Solr [PROD] + Data Provision + 30 + + + Set the path containing the GRAPH to index + + inputGraphRootPath + /tmp/prod_provision/graph/14_graph_blacklisted + + + + + + + Set the target path to store the RAW graph + + format + DMF + + + + + + + Set the lookup address + + isLookupUrl + http://services.openaire.eu:8280/is/services/isLookUp?wsdl + + + + + + + wait configurations + + + + + + + create the AGGREGATOR graph + + executeOozieJob + IIS + + { + 'inputGraphRootPath' : 'inputGraphRootPath', + 'isLookupUrl' : 'isLookupUrl', + 'format' : 'format' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/provision/oozie_app', + 'sourceMaxRelations' : '1000', + 'targetMaxRelations' : '10000000', + 'relPartitions' : '3000', + 'batchSize' : '2000', + 'relationFilter' : 'isAuthorInstitutionOf,produces,hasAmongTopNSimilarDocuments,cites,isCitedBy', + 'otherDsTypeId' : 'scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource', + 'resumeFrom' : 'prepare_relations', + 'shouldIndex' : 'true', + 'outputFormat' : 'SOLR', + 'sparkDriverMemoryForJoining' : '3G', + 'sparkExecutorMemoryForJoining' : '7G', + 'sparkExecutorCoresForJoining' : '4', + 'sparkDriverMemoryForIndexing' : '2G', + 'sparkExecutorMemoryForIndexing' : '2G', + 'sparkExecutorCoresForIndexing' : '64', + 'sparkNetworkTimeout' : '600', + 'workingDir' : '/tmp/prod_provision/working_dir/update_solr' + } + + build-report + + + + + + + + wf_20210724_062705_620 + 2021-07-25T13:25:37+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/05_graph2stats.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/05_graph2stats.xml new file mode 100644 index 000000000..4dfae3c7d --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/05_graph2stats.xml @@ -0,0 +1,100 @@ + +
+ + + + + +
+ + Update Stats [PROD] + Data Provision + 30 + + + Set the OpenAIRE graph DB name + + openaire_db_name + openaire_prod_yyyyMMdd + + + + + + + Set the STATS DB name + + stats_db_name + openaire_prod_stats_yyyyMMdd + + + + + + + Set the STATS MONITOR DB name + + monitor_db_name + openaire_prod_stats_monitor_yyyyMMdd + + + + + + + Set the STATS OBSERVATORY DB name + + observatory_db_name + openaire_prod_stats_observatory_yyyyMMdd + + + + + + + wait configurations + + + + + + + update the content in the stats DB + + executeOozieJob + IIS + + { + 'openaire_db_name' : 'openaire_db_name', + 'stats_db_name' : 'stats_db_name', + 'monitor_db_name' : 'monitor_db_name', + 'observatory_db_name' : 'observatory_db_name' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/stats_update/oozie_app', + 'hive_timeout' : '15000', + 'stats_tool_api_url' : 'https://services.openaire.eu/stats-tool', + 'stats_db_shadow_name' : 'openaire_prod_stats_shadow', + 'external_stats_db_name' : 'stats_ext', + 'monitor_db_shadow_name' : 'openaire_prod_stats_monitor_shadow', + 'observatory_db_shadow_name' : 'openaire_prod_stats_observatory_shadow', + 'context_api_url' : 'https://services.openaire.eu/openaire' + } + + build-report + + + + + + + + wf_20210725_065608_71 + 2021-07-26T07:35:55+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/06_publish_stats.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/06_publish_stats.xml new file mode 100644 index 000000000..d8def071f --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/06_publish_stats.xml @@ -0,0 +1,87 @@ + +
+ + + + + +
+ + Publish Stats [PROD] + Content Publishing + 35 + + + Set the STATS DB name + + stats_db_name + openaire_prod_stats_yyyyMMdd + + + + + + + Set the STATS MONITOR DB name + + monitor_db_name + openaire_prod_stats_monitor_yyyyMMdd + + + + + + + Set the STATS OBSERVATORY DB name + + observatory_db_name + openaire_prod_stats_observatory_yyyyMMdd + + + + + + + wait configurations + + + + + + + publishes the stats DB to the public schema + + executeOozieJob + IIS + + { + 'stats_db_name' : 'stats_db_name', + 'monitor_db_name' : 'monitor_db_name', + 'observatory_db_name' : 'observatory_db_name' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/graph/stats_promote/oozie_app', + 'hive_timeout' : '150000', + 'stats_tool_api_url' : 'https://services.openaire.eu/stats-tool', + 'stats_db_production_name' : 'openaire_prod_stats', + 'monitor_db_production_name' : 'openaire_prod_stats_monitor', + 'observatory_db_production_name' : 'openaire_prod_stats_observatory' + } + + build-report + + + + + + + + wf_20210727_160728_625 + 2021-07-27T16:53:01+00:00 + SUCCESS + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/07_broker.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/07_broker.xml new file mode 100644 index 000000000..cf337fd7e --- /dev/null +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/provision/07_broker.xml @@ -0,0 +1,131 @@ + +
+ + + + + +
+ + Update Broker events [PROD OCEAN] + Data Provision + 30 + + + Set the path containing the GRAPH to scan + + graphInputPath + + + + + + + + Set the datasource Ids Whitelist + + datasourceIdWhitelist + openaire____::9ecafa3655143cbc4bc75853035cd432,opendoar____::dc6e224a8d74ce03bf301152d6e33e97,openaire____::09da65eaaa6deac2f785df1e0ae95a06,openaire____::3db634fc5446f389d0b826ea400a5da6,openaire____::5a38cb462ac487bf26bdb86009fe3e74,openaire____::3c29379cc184f66861e858bc7aa9615b,openaire____::4657147e48a1f32637bfe3743bce76c6,openaire____::c3267ea1c3f378c456209b6df241624e,opendoar____::358aee4cc897452c00244351e4d91f69,re3data_____::7b0ad08687b2c960d5aeef06f811d5e6,opendoar____::798ed7d4ee7138d49b8828958048130a,opendoar____::6f4922f45568161a8cdf4ad2299f6d23,opendoar____::4aa0e93b918848be0b7728b4b1568d8a,openaire____::02b55e4f52388520bfe11f959f836e68 + + + + + + + Set the datasource type Whitelist + + datasourceTypeWhitelist + pubsrepository::unknown,pubsrepository::institutional,pubsrepository::thematic,datarepository::unknown,orprepository,softwarerepository + + + + + + + Set the datasource Id Blacklist + + datasourceIdBlacklist + - + + + + + + + Set the TOPIC whitelist (* = all topics) + + topicWhitelist + ENRICH/MISSING/SUBJECT/DDC,ENRICH/MISSING/SUBJECT/JEL,ENRICH/MISSING/SUBJECT/MESHEUROPMC,ENRICH/MISSING/PUBLICATION_DATE,ENRICH/MISSING/PID,ENRICH/MISSING/PROJECT,ENRICH/MISSING/SUBJECT/ACM,ENRICH/MISSING/SUBJECT/ARXIV,ENRICH/MISSING/OPENACCESS_VERSION,ENRICH/MISSING/AUTHOR/ORCID,ENRICH/MISSING/ABSTRACT,ENRICH/MORE/SUBJECT/ACM,ENRICH/MORE/SUBJECT/ARXIV,ENRICH/MORE/SUBJECT/DDC,ENRICH/MORE/SUBJECT/JEL,ENRICH/MORE/OPENACCESS_VERSION,ENRICH/MORE/SUBJECT/MESHEUROPMC,ENRICH/MORE/PID + + + + + + + Set the output path to store the Event records + + outputDir + /var/lib/dnet/broker_PROD/events + + + + + + + wait configurations + + + + + + + update the BROKER events + + executeOozieJob + IIS + + { + 'graphInputPath' : 'graphInputPath', + 'datasourceIdWhitelist' : 'datasourceIdWhitelist', + 'datasourceTypeWhitelist' : 'datasourceTypeWhitelist', + 'datasourceIdBlacklist' : 'datasourceIdBlacklist', + 'topicWhitelist' : 'topicWhitelist', + 'outputDir' : 'outputDir' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/PROD/oa/broker/generate_events/oozie_app', + 'esEventIndexName' : '', + 'esNotificationsIndexName' : '', + 'esIndexHost' : '', + 'maxIndexedEventsForDsAndTopic' : '100', + 'esBatchWriteRetryCount' : '8', + 'esBatchWriteRetryWait' : '60s', + 'esBatchSizeEntries' : '200', + 'esNodesWanOnly' : 'true', + 'brokerApiBaseUrl' : '', + 'brokerDbUrl' : '', + 'brokerDbUser' : '', + 'brokerDbPassword' : '', + 'sparkDriverMemory' : '3G', + 'sparkExecutorMemory' : '7G', + 'sparkExecutorCores' : '6', + 'workingDir' : '/tmp/prod_provision/working_dir/broker_events' + } + + build-report + + + + + + + + wf_20210709_073839_206 + 2021-07-09T11:01:01+00:00 + FAILURE + + + + \ No newline at end of file diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index cfdf36573..22ee77619 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -24,8 +24,6 @@ dhp-dedup-openaire dhp-enrichment dhp-graph-provision - - dhp-blacklist dhp-stats-update dhp-stats-promote