From 6a3b081263b67876b37d4fb6e59732b8b1c7d58a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 11 May 2020 16:09:20 +0200 Subject: [PATCH 01/70] added the last step of blacklisteing --- .../eu/dnetlib/dhp/wf/profiles/provision.xml | 128 +++++++----------- 1 file changed, 51 insertions(+), 77 deletions(-) diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml index 0467e618f6..7c918a0d70 100644 --- a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml @@ -4,7 +4,7 @@ - + Data Provision [OCEAN] @@ -131,6 +131,16 @@ + + Set the target path to store the blacklisted graph + + blacklistedGraphPath + /tmp/beta_provision/graph/12_graph_blacklisted + + + + + Set the lookup address @@ -155,64 +165,8 @@ 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"] - } + {"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"]} @@ -273,8 +227,8 @@ 'mongoDb' : 'mdstore', 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', 'postgresUser' : 'dnet', - 'postgresPassword' : '*****', - 'reuseContent' : 'false', + 'postgresPassword' : 'dnetPwd', + 'reuseContent' : 'true', 'contentPath' : '/tmp/beta_provision/aggregator', 'workingDir' : '/tmp/beta_provision/working_dir/aggregator' } @@ -403,7 +357,6 @@ - propagates ORCID among results linked by allowedsemrels semantic relationships @@ -429,7 +382,6 @@ - mark results respecting some rules as belonging to communities @@ -440,7 +392,7 @@ 'sourcePath' : 'orcidGraphPath', 'outputPath': 'bulkTaggingGraphPath', 'isLookUpUrl' : 'isLookUpUrl', - 'pathMap' : 'bulkTaggingPathMap', + 'pathMap' : 'bulkTaggingPathMap' } @@ -455,7 +407,6 @@ - creates relashionships between results and organizations when the organizations are associated to institutional repositories @@ -464,14 +415,14 @@ { 'sourcePath' : 'bulkTaggingGraphPath', - 'outputPath': 'affiliationGraphPath', - 'saveGraph' : 'true' + 'outputPath': 'affiliationGraphPath' } { 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/affiliation/oozie_app', - 'workingDir' : '/tmp/beta_provision/working_dir/affiliation' + 'workingDir' : '/tmp/beta_provision/working_dir/affiliation', + 'saveGraph' : 'true' } build-report @@ -480,7 +431,6 @@ - marks as belonging to communities the result collected from datasources related to the organizations specified in the organizationCommunityMap @@ -506,7 +456,6 @@ - created relation between projects and results linked to other results trough allowedsemrel semantic relations linked to projects @@ -532,7 +481,6 @@ - tag as belonging to communitites result in in allowedsemrels relation with other result already linked to communities @@ -542,14 +490,15 @@ { 'sourcePath' : 'fundingGraphPath', 'outputPath': 'communitySemRelGraphPath', - 'isLookupUrl' : 'isLookUpUrl' + 'isLookUpUrl' : 'isLookUpUrl' } { 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/community_semrel/oozie_app', 'workingDir' : '/tmp/beta_provision/working_dir/community_semrel', - 'allowedsemrels' : 'isSupplementedBy;isSupplementTo' + 'allowedsemrels' : 'isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true' } build-report @@ -558,7 +507,6 @@ - associated to results colleced from allowedtypes and those in the whithelist the country of the organization(s) handling the datasource it is collected from @@ -581,16 +529,42 @@ build-report + + + + + + removes blacklisted relations + + executeOozieJob + IIS + + { + 'sourcePath' : 'countryGraphPath', + 'outputPath': 'blacklistedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/blacklist/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/blacklist', + 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', + 'postgresUser' : 'dnet', + 'postgresPassword' : 'dnetPwd' + } + + build-report + - wf_20200428_155848_495 - 2020-04-28T16:53:23+00:00 + wf_20200509_100941_857 + 2020-05-09T13:26:09+00:00 FAILURE - + eu.dnetlib.data.hadoop.rmi.HadoopServiceException: hadoop job: 0002933-200403132837156-oozie-oozi-W failed with status: KILLED, oozie log: 2020-05-09 13:23:31,194 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No results found 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] Start action [0002933-200403132837156-oozie-oozi-W@:start:] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action status=DONE 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action updated in DB! 2020-05-09 13:23:31,257 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No results found 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@:start: 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:23:31,314 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] Start action [0002933-200403132837156-oozie-oozi-W@reset-outputpath] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action status=DONE 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action updated in DB! 2020-05-09 13:23:33,947 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No results found 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] Start action [0002933-200403132837156-oozie-oozi-W@copy_entities] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action status=DONE 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action updated in DB! 2020-05-09 13:23:34,012 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,018 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,023 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,029 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,124 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Start action [0002933-200403132837156-oozie-oozi-W@copy_relation] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Start action [0002933-200403132837156-oozie-oozi-W@copy_projects] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Start action [0002933-200403132837156-oozie-oozi-W@copy_datasources] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,140 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Start action [0002933-200403132837156-oozie-oozi-W@copy_organization] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:35,010 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action status=RUNNING 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action updated in DB! 2020-05-09 13:23:35,022 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:23:35,027 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action status=RUNNING 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action updated in DB! 2020-05-09 13:23:35,031 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action status=RUNNING 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action updated in DB! 2020-05-09 13:23:35,037 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:23:35,048 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:23:35,072 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action status=RUNNING 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action updated in DB! 2020-05-09 13:23:35,084 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_entities 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@reset-outputpath 2020-05-09 13:23:58,926 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:23:59,085 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:59,242 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:23:59,386 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:24:01,343 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Hadoop Jobs launched : [job_1585920557248_14573] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] action completed, external ID [job_1585920557248_14570] 2020-05-09 13:24:01,493 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:24:01,935 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Hadoop Jobs launched : [job_1585920557248_14572] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] action completed, external ID [job_1585920557248_14569] 2020-05-09 13:24:02,076 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:25:03,172 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:03,336 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:25:05,598 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:05,688 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Hadoop Jobs launched : [job_1585920557248_14574] 2020-05-09 13:25:05,691 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] action completed, external ID [job_1585920557248_14571] 2020-05-09 13:25:05,748 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:25:23,274 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:23,409 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:25:25,419 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:25,510 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Hadoop Jobs launched : [job_1585920557248_14575] 2020-05-09 13:25:25,511 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] action completed, external ID [job_1585920557248_14568] 2020-05-09 13:25:25,565 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No results found 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] Start action [0002933-200403132837156-oozie-oozi-W@copy_wait] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action status=DONE 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action updated in DB! 2020-05-09 13:25:25,627 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No results found 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] Start action [0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action status=DONE 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action updated in DB! 2020-05-09 13:25:25,694 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,700 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,706 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,711 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,801 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,828 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:27,165 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] checking action, hadoop job ID [job_1585920557248_14578] status [RUNNING] 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action status=RUNNING 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action updated in DB! 2020-05-09 13:25:27,179 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] checking action, hadoop job ID [job_1585920557248_14577] status [RUNNING] 2020-05-09 13:25:27,181 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action status=RUNNING 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action updated in DB! 2020-05-09 13:25:27,188 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:27,617 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] checking action, hadoop job ID [job_1585920557248_14576] status [RUNNING] 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action status=RUNNING 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action updated in DB! 2020-05-09 13:25:27,625 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] checking action, hadoop job ID [job_1585920557248_14579] status [RUNNING] 2020-05-09 13:25:27,628 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action status=RUNNING 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action updated in DB! 2020-05-09 13:25:27,634 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_wait 2020-05-09 13:25:27,640 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:25:41,416 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] 2020-05-09 13:25:41,490 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] action completed, external ID [job_1585920557248_14577] 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher ERROR, reason: Main class [org.apache.oozie.action.hadoop.SparkMain], main() threw exception, File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher exception: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist java.io.FileNotFoundException: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:598) at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:811) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:588) at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:432) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:340) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:292) at org.apache.spark.deploy.yarn.Client.copyFileToRemote(Client.scala:404) at org.apache.spark.deploy.yarn.Client.org$apache$spark$deploy$yarn$Client$$distribute$1(Client.scala:496) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:595) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:594) at scala.Option.foreach(Option.scala:257) at org.apache.spark.deploy.yarn.Client.prepareLocalResources(Client.scala:594) at org.apache.spark.deploy.yarn.Client.createContainerLaunchContext(Client.scala:886) at org.apache.spark.deploy.yarn.Client.submitApplication(Client.scala:180) at org.apache.spark.deploy.yarn.Client.run(Client.scala:1156) at org.apache.spark.deploy.yarn.YarnClusterApplication.start(Client.scala:1608) at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:849) at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:167) at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:195) at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86) at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:924) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:933) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) at org.apache.oozie.action.hadoop.SparkMain.runSpark(SparkMain.java:178) at org.apache.oozie.action.hadoop.SparkMain.run(SparkMain.java:90) at org.apache.oozie.action.hadoop.LauncherMain.run(LauncherMain.java:81) at org.apache.oozie.action.hadoop.SparkMain.main(SparkMain.java:57) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.oozie.action.hadoop.LauncherMapper.map(LauncherMapper.java:235) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:54) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:459) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343) at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:422) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1924) at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158) 2020-05-09 13:25:41,514 INFO org.apache.oozie.command.wf.ActionEndXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] ERROR is considered as FAILED for SLA 2020-05-09 13:25:41,541 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No results found 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Start action [0002933-200403132837156-oozie-oozi-W@Kill] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action status=DONE 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action updated in DB! 2020-05-09 13:25:41,692 WARN org.apache.oozie.workflow.lite.LiteWorkflowInstance: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Workflow completed [KILLED], killing [3] running nodes 2020-05-09 13:25:41,760 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@Kill 2020-05-09 13:25:41,766 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:41,852 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:41,914 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] 2020-05-09 13:25:41,920 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:41,938 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:42,005 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] 2020-05-09 13:25:42,010 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:42,113 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] 2020-05-09 13:25:42,116 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) \ No newline at end of file From 5ab3424c77ca90b06055a055f2f98baefcb919b7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 11 May 2020 16:09:37 +0200 Subject: [PATCH 02/70] removed unused dependencies --- dhp-workflows/dhp-bulktag/pom.xml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/dhp-workflows/dhp-bulktag/pom.xml b/dhp-workflows/dhp-bulktag/pom.xml index 7c2afa0cca..98922c1939 100644 --- a/dhp-workflows/dhp-bulktag/pom.xml +++ b/dhp-workflows/dhp-bulktag/pom.xml @@ -43,17 +43,6 @@ com.jayway.jsonpath json-path - - org.reflections - reflections - 0.9.11 - compile - - - com.google.guava - guava - 23.3-jre - io.github.classgraph classgraph From e883daf87e79daad9cca2d88ed4b55eafab7b7ad Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 11 May 2020 16:10:24 +0200 Subject: [PATCH 03/70] added the outputPath parameter and the reset path to remove the outputath directory --- .../eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml index 855cac65eb..b980016628 100644 --- a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml @@ -16,6 +16,10 @@ sourcePath the source path + + outputPath + the path were to store the graph without the blacklisted relations + @@ -25,7 +29,8 @@ - + + @@ -87,7 +92,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${sourcePath}/relation - --outputPath${workingDir}/relation + --outputPath${outputPath}/relation --hdfsPath${workingDir}/blacklist --mergesPath${workingDir}/mergesRelation From 50659011ebe7719eb7ede6558a32a5878efdb8f3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 11 May 2020 16:14:26 +0200 Subject: [PATCH 04/70] refactoring --- .../test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java index 2d6b1061b3..0487a5844d 100644 --- a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java +++ b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java @@ -19,6 +19,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.schema.oaf.Relation; public class BlackListTest { @@ -60,12 +61,7 @@ public class BlackListTest { spark.stop(); } - /* - * String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath = - * parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String blacklistPath = - * parser.get("hdfsPath"); log.info("blacklistPath {}: ", blacklistPath); final String mergesPath = - * parser.get("mergesPath"); log.info("mergesPath {}: ", mergesPath); - */ + @Test public void noRemoveTest() throws Exception { SparkRemoveBlacklistedRelationJob From 1547ca7e15a7353476b794ec51e3d53791f2d66c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 12 May 2020 12:17:27 +0200 Subject: [PATCH 05/70] added blacklist step to the end of the provision wf --- .../eu/dnetlib/dhp/wf/profiles/provision.xml | 130 +++++++----------- 1 file changed, 52 insertions(+), 78 deletions(-) diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml index f99ea7aed9..7c918a0d70 100644 --- a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml @@ -4,7 +4,7 @@ - + Data Provision [OCEAN] @@ -131,6 +131,16 @@ + + Set the target path to store the blacklisted graph + + blacklistedGraphPath + /tmp/beta_provision/graph/12_graph_blacklisted + + + + + Set the lookup address @@ -155,64 +165,8 @@ 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"] - } + {"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"]} @@ -273,8 +227,8 @@ 'mongoDb' : 'mdstore', 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', 'postgresUser' : 'dnet', - 'postgresPassword' : '*****', - 'reuseContent' : 'false', + 'postgresPassword' : 'dnetPwd', + 'reuseContent' : 'true', 'contentPath' : '/tmp/beta_provision/aggregator', 'workingDir' : '/tmp/beta_provision/working_dir/aggregator' } @@ -403,7 +357,6 @@ - propagates ORCID among results linked by allowedsemrels semantic relationships @@ -429,7 +382,6 @@ - mark results respecting some rules as belonging to communities @@ -440,7 +392,7 @@ 'sourcePath' : 'orcidGraphPath', 'outputPath': 'bulkTaggingGraphPath', 'isLookUpUrl' : 'isLookUpUrl', - 'pathMap' : 'bulkTaggingPathMap', + 'pathMap' : 'bulkTaggingPathMap' } @@ -455,7 +407,6 @@ - creates relashionships between results and organizations when the organizations are associated to institutional repositories @@ -464,14 +415,14 @@ { 'sourcePath' : 'bulkTaggingGraphPath', - 'outputPath': 'affiliationGraphPath', - 'saveGraph' : 'true' + 'outputPath': 'affiliationGraphPath' } { 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/affiliation/oozie_app', - 'workingDir' : '/tmp/beta_provision/working_dir/affiliation' + 'workingDir' : '/tmp/beta_provision/working_dir/affiliation', + 'saveGraph' : 'true' } build-report @@ -480,9 +431,8 @@ - - marks as belonging to communities the result collected from providers related to the organizations specified in the organizationCommunityMap + marks as belonging to communities the result collected from datasources related to the organizations specified in the organizationCommunityMap executeOozieJob IIS @@ -506,7 +456,6 @@ - created relation between projects and results linked to other results trough allowedsemrel semantic relations linked to projects @@ -532,7 +481,6 @@ - tag as belonging to communitites result in in allowedsemrels relation with other result already linked to communities @@ -542,14 +490,15 @@ { 'sourcePath' : 'fundingGraphPath', 'outputPath': 'communitySemRelGraphPath', - 'isLookupUrl' : 'isLookUpUrl' + 'isLookUpUrl' : 'isLookUpUrl' } { 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/community_semrel/oozie_app', 'workingDir' : '/tmp/beta_provision/working_dir/community_semrel', - 'allowedsemrels' : 'isSupplementedBy;isSupplementTo' + 'allowedsemrels' : 'isSupplementedBy;isSupplementTo', + 'saveGraph' : 'true' } build-report @@ -558,7 +507,6 @@ - associated to results colleced from allowedtypes and those in the whithelist the country of the organization(s) handling the datasource it is collected from @@ -581,16 +529,42 @@ build-report + + + + + + removes blacklisted relations + + executeOozieJob + IIS + + { + 'sourcePath' : 'countryGraphPath', + 'outputPath': 'blacklistedGraphPath' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/blacklist/oozie_app', + 'workingDir' : '/tmp/beta_provision/working_dir/blacklist', + 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', + 'postgresUser' : 'dnet', + 'postgresPassword' : 'dnetPwd' + } + + build-report + - wf_20200428_155848_495 - 2020-04-28T16:53:23+00:00 + wf_20200509_100941_857 + 2020-05-09T13:26:09+00:00 FAILURE - + eu.dnetlib.data.hadoop.rmi.HadoopServiceException: hadoop job: 0002933-200403132837156-oozie-oozi-W failed with status: KILLED, oozie log: 2020-05-09 13:23:31,194 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No results found 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] Start action [0002933-200403132837156-oozie-oozi-W@:start:] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action status=DONE 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action updated in DB! 2020-05-09 13:23:31,257 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No results found 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@:start: 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:23:31,314 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] Start action [0002933-200403132837156-oozie-oozi-W@reset-outputpath] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action status=DONE 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action updated in DB! 2020-05-09 13:23:33,947 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No results found 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] Start action [0002933-200403132837156-oozie-oozi-W@copy_entities] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action status=DONE 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action updated in DB! 2020-05-09 13:23:34,012 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,018 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,023 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,029 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,124 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Start action [0002933-200403132837156-oozie-oozi-W@copy_relation] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Start action [0002933-200403132837156-oozie-oozi-W@copy_projects] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Start action [0002933-200403132837156-oozie-oozi-W@copy_datasources] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,140 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Start action [0002933-200403132837156-oozie-oozi-W@copy_organization] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:35,010 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action status=RUNNING 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action updated in DB! 2020-05-09 13:23:35,022 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:23:35,027 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action status=RUNNING 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action updated in DB! 2020-05-09 13:23:35,031 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action status=RUNNING 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action updated in DB! 2020-05-09 13:23:35,037 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:23:35,048 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:23:35,072 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action status=RUNNING 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action updated in DB! 2020-05-09 13:23:35,084 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_entities 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@reset-outputpath 2020-05-09 13:23:58,926 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:23:59,085 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:59,242 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:23:59,386 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:24:01,343 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Hadoop Jobs launched : [job_1585920557248_14573] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] action completed, external ID [job_1585920557248_14570] 2020-05-09 13:24:01,493 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:24:01,935 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Hadoop Jobs launched : [job_1585920557248_14572] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] action completed, external ID [job_1585920557248_14569] 2020-05-09 13:24:02,076 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:25:03,172 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:03,336 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:25:05,598 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:05,688 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Hadoop Jobs launched : [job_1585920557248_14574] 2020-05-09 13:25:05,691 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] action completed, external ID [job_1585920557248_14571] 2020-05-09 13:25:05,748 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:25:23,274 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:23,409 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:25:25,419 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:25,510 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Hadoop Jobs launched : [job_1585920557248_14575] 2020-05-09 13:25:25,511 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] action completed, external ID [job_1585920557248_14568] 2020-05-09 13:25:25,565 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No results found 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] Start action [0002933-200403132837156-oozie-oozi-W@copy_wait] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action status=DONE 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action updated in DB! 2020-05-09 13:25:25,627 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No results found 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] Start action [0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action status=DONE 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action updated in DB! 2020-05-09 13:25:25,694 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,700 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,706 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,711 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,801 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,828 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:27,165 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] checking action, hadoop job ID [job_1585920557248_14578] status [RUNNING] 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action status=RUNNING 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action updated in DB! 2020-05-09 13:25:27,179 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] checking action, hadoop job ID [job_1585920557248_14577] status [RUNNING] 2020-05-09 13:25:27,181 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action status=RUNNING 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action updated in DB! 2020-05-09 13:25:27,188 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:27,617 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] checking action, hadoop job ID [job_1585920557248_14576] status [RUNNING] 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action status=RUNNING 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action updated in DB! 2020-05-09 13:25:27,625 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] checking action, hadoop job ID [job_1585920557248_14579] status [RUNNING] 2020-05-09 13:25:27,628 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action status=RUNNING 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action updated in DB! 2020-05-09 13:25:27,634 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_wait 2020-05-09 13:25:27,640 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:25:41,416 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] 2020-05-09 13:25:41,490 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] action completed, external ID [job_1585920557248_14577] 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher ERROR, reason: Main class [org.apache.oozie.action.hadoop.SparkMain], main() threw exception, File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher exception: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist java.io.FileNotFoundException: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:598) at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:811) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:588) at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:432) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:340) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:292) at org.apache.spark.deploy.yarn.Client.copyFileToRemote(Client.scala:404) at org.apache.spark.deploy.yarn.Client.org$apache$spark$deploy$yarn$Client$$distribute$1(Client.scala:496) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:595) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:594) at scala.Option.foreach(Option.scala:257) at org.apache.spark.deploy.yarn.Client.prepareLocalResources(Client.scala:594) at org.apache.spark.deploy.yarn.Client.createContainerLaunchContext(Client.scala:886) at org.apache.spark.deploy.yarn.Client.submitApplication(Client.scala:180) at org.apache.spark.deploy.yarn.Client.run(Client.scala:1156) at org.apache.spark.deploy.yarn.YarnClusterApplication.start(Client.scala:1608) at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:849) at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:167) at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:195) at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86) at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:924) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:933) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) at org.apache.oozie.action.hadoop.SparkMain.runSpark(SparkMain.java:178) at org.apache.oozie.action.hadoop.SparkMain.run(SparkMain.java:90) at org.apache.oozie.action.hadoop.LauncherMain.run(LauncherMain.java:81) at org.apache.oozie.action.hadoop.SparkMain.main(SparkMain.java:57) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.oozie.action.hadoop.LauncherMapper.map(LauncherMapper.java:235) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:54) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:459) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343) at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:422) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1924) at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158) 2020-05-09 13:25:41,514 INFO org.apache.oozie.command.wf.ActionEndXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] ERROR is considered as FAILED for SLA 2020-05-09 13:25:41,541 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No results found 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Start action [0002933-200403132837156-oozie-oozi-W@Kill] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action status=DONE 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action updated in DB! 2020-05-09 13:25:41,692 WARN org.apache.oozie.workflow.lite.LiteWorkflowInstance: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Workflow completed [KILLED], killing [3] running nodes 2020-05-09 13:25:41,760 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@Kill 2020-05-09 13:25:41,766 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:41,852 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:41,914 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] 2020-05-09 13:25:41,920 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:41,938 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:42,005 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] 2020-05-09 13:25:42,010 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:42,113 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] 2020-05-09 13:25:42,116 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) \ No newline at end of file From ec0782e582961bea41f8fa30ac43a3d4a3a366fa Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 12 May 2020 15:49:28 +0200 Subject: [PATCH 06/70] renamed jar containing the bulktagging and propagation workflows from dhp-[bulktagging|propagation] to dhp-enrichment; adjusted xml formatting --- .../dhp/bulktag/oozie_app/workflow.xml | 8 +- .../countrypropagation/oozie_app/workflow.xml | 18 +- .../oozie_app/workflow.xml | 160 +++++++----------- .../projecttoresult/oozie_app/workflow.xml | 107 ++++++------ .../oozie_app/workflow.xml | 10 +- .../oozie_app/workflow.xml | 21 ++- .../oozie_app/workflow.xml | 10 +- 7 files changed, 144 insertions(+), 190 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 524281bc91..754aba4f29 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -101,7 +101,7 @@ cluster bulkTagging-publication eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-bulktag-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} --executor-memory=${sparkExecutorMemory} @@ -130,7 +130,7 @@ cluster bulkTagging-dataset eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-bulktag-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} --executor-memory=${sparkExecutorMemory} @@ -159,7 +159,7 @@ cluster bulkTagging-orp eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-bulktag-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} --executor-memory=${sparkExecutorMemory} @@ -188,7 +188,7 @@ cluster bulkTagging-software eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-bulktag-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index f269c54421..fc877071df 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -92,7 +92,7 @@ cluster PrepareDatasourceCountryAssociation eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -126,7 +126,7 @@ cluster prepareResultCountry-Publication eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -156,7 +156,7 @@ cluster prepareResultCountry-Dataset eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -186,7 +186,7 @@ cluster prepareResultCountry-ORP eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -216,7 +216,7 @@ cluster prepareResultCountry-Software eu.dnetlib.dhp.countrypropagation.PrepareResultCountrySet - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -255,7 +255,7 @@ cluster countryPropagationForPublications eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -285,7 +285,7 @@ cluster countryPropagationForDataset eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -315,7 +315,7 @@ cluster countryPropagationForORP eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -345,7 +345,7 @@ cluster countryPropagationForSoftware eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml index 7b06b65040..e4429b710c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml @@ -95,7 +95,7 @@ cluster ORCIDPropagation-PreparePhase1-Publications eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -111,16 +111,11 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --sourcePath - ${sourcePath} - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Publication - --outputPath - ${workingDir}/preparedInfo/targetOrcidAssoc - --allowedsemrels - ${allowedsemrels} + --sourcePath${sourcePath} + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/preparedInfo/targetOrcidAssoc + --allowedsemrels${allowedsemrels} @@ -132,7 +127,7 @@ cluster ORCIDPropagation-PreparePhase1-Dataset eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -144,16 +139,11 @@ --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - --sourcePath - ${sourcePath} - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Dataset - --outputPath - ${workingDir}/preparedInfo/targetOrcidAssoc - --allowedsemrels - ${allowedsemrels} + --sourcePath${sourcePath} + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/preparedInfo/targetOrcidAssoc + --allowedsemrels${allowedsemrels} @@ -165,7 +155,7 @@ cluster ORCIDPropagation-PreparePhase1-ORP eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -177,16 +167,11 @@ --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - --sourcePath - ${sourcePath} - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath - ${workingDir}/preparedInfo/targetOrcidAssoc - --allowedsemrels - ${allowedsemrels} + --sourcePath${sourcePath} + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/preparedInfo/targetOrcidAssoc + --allowedsemrels${allowedsemrels} @@ -198,7 +183,7 @@ cluster ORCIDPropagation-PreparePhase1-Software eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -210,16 +195,11 @@ --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - --sourcePath - ${sourcePath} - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Software - --outputPath - ${workingDir}/preparedInfo/targetOrcidAssoc - --allowedsemrels - ${allowedsemrels} + --sourcePath${sourcePath} + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/preparedInfo/targetOrcidAssoc + --allowedsemrels${allowedsemrels} @@ -233,7 +213,7 @@ cluster ORCIDPropagation-PreparePhase2 eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep2 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -245,13 +225,10 @@ --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - --sourcePath - ${workingDir}/preparedInfo/targetOrcidAssoc - --outputPath - ${workingDir}/preparedInfo/mergedOrcidAssoc + --sourcePath${workingDir}/preparedInfo/targetOrcidAssoc + --outputPath${workingDir}/preparedInfo/mergedOrcidAssoc - @@ -268,7 +245,7 @@ cluster ORCIDPropagation-Publication eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -284,18 +261,12 @@ --conf spark.hadoop.mapreduce.reduce.speculative=false --conf spark.sql.shuffle.partitions=3840 - --possibleUpdatesPath - ${workingDir}/preparedInfo/mergedOrcidAssoc - --sourcePath - ${sourcePath}/publication - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Publication - --outputPath - ${outputPath}/publication - --saveGraph - ${saveGraph} + --possibleUpdatesPath${workingDir}/preparedInfo/mergedOrcidAssoc + --sourcePath${sourcePath}/publication + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${outputPath}/publication + --saveGraph${saveGraph} @@ -306,7 +277,7 @@ cluster ORCIDPropagation-Dataset eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -321,18 +292,12 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath - ${workingDir}/preparedInfo/mergedOrcidAssoc - --sourcePath - ${sourcePath}/dataset - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Dataset - --outputPath - ${outputPath}/dataset - --saveGraph - ${saveGraph} + --possibleUpdatesPath${workingDir}/preparedInfo/mergedOrcidAssoc + --sourcePath${sourcePath}/dataset + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${outputPath}/dataset + --saveGraph${saveGraph} @@ -343,7 +308,7 @@ cluster ORCIDPropagation-ORP eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -358,18 +323,12 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath - ${workingDir}/preparedInfo/mergedOrcidAssoc - --sourcePath - ${sourcePath}/otherresearchproduct - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath - ${outputPath}/otherresearchproduct - --saveGraph - ${saveGraph} + --possibleUpdatesPath${workingDir}/preparedInfo/mergedOrcidAssoc + --sourcePath${sourcePath}/otherresearchproduct + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${outputPath}/otherresearchproduct + --saveGraph${saveGraph} @@ -380,7 +339,7 @@ cluster ORCIDPropagation-Software eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -395,22 +354,19 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --possibleUpdatesPath - ${workingDir}/preparedInfo/mergedOrcidAssoc - --sourcePath - ${sourcePath}/software - --hive_metastore_uris - ${hive_metastore_uris} - --resultTableName - eu.dnetlib.dhp.schema.oaf.Software - --outputPath - ${outputPath}/software - --saveGraph - ${saveGraph} + --possibleUpdatesPath${workingDir}/preparedInfo/mergedOrcidAssoc + --sourcePath${sourcePath}/software + --hive_metastore_uris${hive_metastore_uris} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${outputPath}/software + --saveGraph${saveGraph} + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml index dd7f258463..687d668698 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml @@ -127,61 +127,60 @@ + + + + yarn + cluster + PrepareProjectResultsAssociation + eu.dnetlib.dhp.projecttoresult.PrepareProjectResultsAssociation + dhp-propagation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${sourcePath}/relation + --allowedsemrels${allowedsemrels} + --hive_metastore_uris${hive_metastore_uris} + --potentialUpdatePath${workingDir}/preparedInfo/potentialUpdates + --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + + + + - - - - yarn - cluster - PrepareProjectResultsAssociation - eu.dnetlib.dhp.projecttoresult.PrepareProjectResultsAssociation - dhp-propagation-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath}/relation - --allowedsemrels${allowedsemrels} - --hive_metastore_uris${hive_metastore_uris} - --potentialUpdatePath${workingDir}/preparedInfo/potentialUpdates - --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked - - - - - - - - yarn - cluster - ProjectToResultPropagation - eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob - dhp-propagation-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --saveGraph${saveGraph} - --hive_metastore_uris${hive_metastore_uris} - --outputPath${outputPath}/relation - --potentialUpdatePath${workingDir}/preparedInfo/potentialUpdates - --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked - - - - + + + yarn + cluster + ProjectToResultPropagation + eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob + dhp-enrichment-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.dynamicAllocation.enabled=true + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + + --saveGraph${saveGraph} + --hive_metastore_uris${hive_metastore_uris} + --outputPath${outputPath}/relation + --potentialUpdatePath${workingDir}/preparedInfo/potentialUpdates + --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + + + + diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index 3be69bde66..d481cad052 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -88,7 +88,7 @@ cluster Prepare-Community-Result-Organization eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -122,7 +122,7 @@ cluster community2resultfromorganization-Publication eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -151,7 +151,7 @@ cluster community2resultfromorganization-Dataset eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -180,7 +180,7 @@ cluster community2resultfromorganization-ORP eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -209,7 +209,7 @@ cluster community2resultfromorganization-Software eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml index b75b2d31eb..81b51443c6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml @@ -99,7 +99,7 @@ cluster ResultToCommunitySemRel-PreparePhase1-Publications eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -128,7 +128,7 @@ cluster ResultToCommunitySemRel-PreparePhase1-Dataset eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -150,13 +150,14 @@ + yarn cluster ResultToCommunitySemRel-PreparePhase1-ORP eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -185,7 +186,7 @@ cluster ResultToCommunitySemRel-PreparePhase1-Software eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep1 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -216,7 +217,7 @@ cluster ResultToCommunityEmRelPropagation-PreparePhase2 eu.dnetlib.dhp.resulttocommunityfromsemrel.PrepareResultCommunitySetStep2 - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -232,9 +233,7 @@ --outputPath${workingDir}/preparedInfo/mergedCommunityAssoc - - @@ -250,7 +249,7 @@ cluster Result2CommunitySemRelPropagation-Publication eu.dnetlib.dhp.resulttocommunityfromsemrel.SparkResultToCommunityThroughSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -279,7 +278,7 @@ cluster Result2CommunitySemRelPropagation-Dataset eu.dnetlib.dhp.resulttocommunityfromsemrel.SparkResultToCommunityThroughSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -308,7 +307,7 @@ cluster Result2CommunitySemRelPropagation-ORP eu.dnetlib.dhp.resulttocommunityfromsemrel.SparkResultToCommunityThroughSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -337,7 +336,7 @@ cluster Result2CommunitySemRelPropagation-Software eu.dnetlib.dhp.resulttocommunityfromsemrel.SparkResultToCommunityThroughSemRelJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml index 73268fcc76..a1b7f4ad79 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml @@ -131,7 +131,7 @@ cluster PrepareResultOrganizationAssociation eu.dnetlib.dhp.resulttoorganizationfrominstrepo.PrepareResultInstRepoAssociation - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -163,7 +163,7 @@ cluster resultToOrganizationFromInstRepoPropagationForPublications eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -193,7 +193,7 @@ cluster resultToOrganizationFromInstRepoPropagationForDataset eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -223,7 +223,7 @@ cluster resultToOrganizationFromInstRepoPropagationForORP eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} @@ -253,7 +253,7 @@ cluster resultToOrganizationFromInstRepoPropagationForSoftware eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} From 43f127448ddf38d2a2328585ff4d2b1562bd0ff5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 12 May 2020 18:24:26 +0200 Subject: [PATCH 07/70] changed the package name from dhp-propagation to dhp-enrichment for the preparation phase of funding propagation --- .../eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml index 687d668698..24e1d3b7fa 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml @@ -134,7 +134,7 @@ cluster PrepareProjectResultsAssociation eu.dnetlib.dhp.projecttoresult.PrepareProjectResultsAssociation - dhp-propagation-${projectVersion}.jar + dhp-enrichment-${projectVersion}.jar --executor-cores=${sparkExecutorCores} --executor-memory=${sparkExecutorMemory} From 85f3c55992b9d9b526020aa096e9867774b92270 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 May 2020 09:04:33 +0200 Subject: [PATCH 08/70] fixed node names in blacklist workflow --- .../eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml index 59fd30fead..1538318c14 100644 --- a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + postgresURL @@ -102,7 +102,7 @@ - + ${jobTracker} ${nameNode} @@ -113,7 +113,7 @@ - + ${jobTracker} ${nameNode} From c0265213a0b2119a30f00ec0013c6c88de3b826a Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 13 May 2020 12:00:27 +0200 Subject: [PATCH 09/70] partial implementation --- .../dhp/broker/model/EventFactory.java | 31 ++++----- .../eu/dnetlib/dhp/broker/model/Topic.java | 52 +++++++++++++++ .../broker/oa/GenerateEventsApplication.java | 55 +++++++--------- .../broker/oa/util/EnrichMissingAbstract.java | 30 +++++---- .../oa/util/EnrichMissingAuthorOrcid.java | 32 +++++----- .../oa/util/EnrichMissingOpenAccess.java | 31 ++++----- .../dhp/broker/oa/util/EnrichMissingPid.java | 28 ++++----- .../broker/oa/util/EnrichMissingProject.java | 30 ++++----- .../oa/util/EnrichMissingPublicationDate.java | 29 ++++----- .../broker/oa/util/EnrichMissingSubject.java | 30 +++++---- .../broker/oa/util/EnrichMoreOpenAccess.java | 29 ++++----- .../dhp/broker/oa/util/EnrichMorePid.java | 28 ++++----- .../dhp/broker/oa/util/EnrichMoreSubject.java | 30 +++++---- .../dhp/broker/oa/util/UpdateInfo.java | 59 ++++++++++++++--- .../dhp/broker/oa/util/UpdateMatcher.java | 63 +++++++++++++++++++ 15 files changed, 363 insertions(+), 194 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java index 0694556b2e..9e5d986448 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -29,31 +29,32 @@ public class EventFactory { "yyyy-MM-dd" }; - public static Event newBrokerEvent(final Result source, final Result target, final UpdateInfo updateInfo) { + public static Event newBrokerEvent(final UpdateInfo updateInfo) { final long now = new Date().getTime(); final Event res = new Event(); - final Map map = createMapFromResult(target, source, updateInfo); + final Map map = createMapFromResult(updateInfo); - final String payload = createPayload(target, updateInfo); + final String payload = createPayload(updateInfo); final String eventId = calculateEventId( - updateInfo.getTopic(), target.getOriginalId().get(0), updateInfo.getHighlightValueAsString()); + updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0), + updateInfo.getHighlightValueAsString()); res.setEventId(eventId); res.setProducerId(PRODUCER_ID); res.setPayload(payload); res.setMap(map); - res.setTopic(updateInfo.getTopic()); + res.setTopic(updateInfo.getTopicPath()); res.setCreationDate(now); res.setExpiryDate(calculateExpiryDate(now)); res.setInstantMessage(false); return res; } - private static String createPayload(final Result result, final UpdateInfo updateInfo) { + private static String createPayload(final UpdateInfo updateInfo) { final OpenAireEventPayload payload = new OpenAireEventPayload(); // TODO @@ -62,32 +63,34 @@ public class EventFactory { return payload.toJSON(); } - private static Map createMapFromResult(final Result oaf, final Result source, - final UpdateInfo updateInfo) { + private static Map createMapFromResult(final UpdateInfo updateInfo) { final Map map = new HashMap<>(); - final List collectedFrom = oaf.getCollectedfrom(); + final Result source = updateInfo.getSource(); + final Result target = updateInfo.getTarget(); + + final List collectedFrom = target.getCollectedfrom(); if (collectedFrom.size() == 1) { map.put("target_datasource_id", collectedFrom.get(0).getKey()); map.put("target_datasource_name", collectedFrom.get(0).getValue()); } - final List ids = oaf.getOriginalId(); + final List ids = target.getOriginalId(); if (ids.size() > 0) { map.put("target_publication_id", ids.get(0)); } - final List titles = oaf.getTitle(); + final List titles = target.getTitle(); if (titles.size() > 0) { map.put("target_publication_title", titles.get(0)); } - final long date = parseDateTolong(oaf.getDateofacceptance().getValue()); + final long date = parseDateTolong(target.getDateofacceptance().getValue()); if (date > 0) { map.put("target_dateofacceptance", date); } - final List subjects = oaf.getSubject(); + final List subjects = target.getSubject(); if (subjects.size() > 0) { map .put( @@ -95,7 +98,7 @@ public class EventFactory { subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList())); } - final List authors = oaf.getAuthor(); + final List authors = target.getAuthor(); if (authors.size() > 0) { map .put( diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java new file mode 100644 index 0000000000..29f6cbe3af --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.broker.model; + +public enum Topic { + + // ENRICHMENT MISSING + ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT( + "ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE( + "ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID( + "ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE( + "ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC( + "ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV( + "ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL( + "ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC( + "ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM( + "ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK( + "ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID( + "ENRICH/MISSING/AUTHOR/ORCID"), + + // ENRICHMENT MORE + ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT( + "ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT( + "ENRICH/MORE/PROJECT"), ENRICH_MORE_SUBJECT_MESHEUROPMC( + "ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV( + "ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL( + "ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC( + "ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM( + "ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), + + // ADDITION + ADD_BY_PROJECT("ADD/BY_PROJECT"); + + Topic(final String path) { + this.path = path; + } + + protected String path; + + public String getPath() { + return this.path; + } + + public static Topic fromPath(final String path) { + for (final Topic t : Topic.values()) { + if (t.getPath().equals(path)) { + return t; + } + } + return null; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 54d4ef36aa..c4c167c13f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -14,8 +14,6 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; @@ -30,6 +28,7 @@ import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess; import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid; import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.broker.oa.util.UpdateMatcher; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.Result; @@ -37,7 +36,16 @@ public class GenerateEventsApplication { private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final UpdateMatcher enrichMissingAbstract = new EnrichMissingAbstract(); + private static final UpdateMatcher enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid(); + private static final UpdateMatcher enrichMissingOpenAccess = new EnrichMissingOpenAccess(); + private static final UpdateMatcher enrichMissingPid = new EnrichMissingPid(); + private static final UpdateMatcher enrichMissingProject = new EnrichMissingProject(); + private static final UpdateMatcher enrichMissingPublicationDate = new EnrichMissingPublicationDate(); + private static final UpdateMatcher enrichMissingSubject = new EnrichMissingSubject(); + private static final UpdateMatcher enrichMoreOpenAccess = new EnrichMoreOpenAccess(); + private static final UpdateMatcher enrichMorePid = new EnrichMorePid(); + private static final UpdateMatcher enrichMoreSubject = new EnrichMoreSubject(); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -76,37 +84,22 @@ public class GenerateEventsApplication { } private List generateEvents(final Result... children) { - final List list = new ArrayList<>(); + final List> list = new ArrayList<>(); - for (final Result source : children) { - for (final Result target : children) { - if (source != target) { - list - .addAll( - findUpdates(source, target) - .stream() - .map(info -> EventFactory.newBrokerEvent(source, target, info)) - .collect(Collectors.toList())); - } - } + for (final Result target : children) { + list.addAll(enrichMissingAbstract.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingPid.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingProject.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, children)); + list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, children)); + list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, children)); + list.addAll(enrichMorePid.searchUpdatesForRecord(target, children)); + list.addAll(enrichMoreSubject.searchUpdatesForRecord(target, children)); } - return list; - } - - private List> findUpdates(final Result source, final Result target) { - final List> list = new ArrayList<>(); - list.addAll(EnrichMissingAbstract.findUpdates(source, target)); - list.addAll(EnrichMissingAuthorOrcid.findUpdates(source, target)); - list.addAll(EnrichMissingOpenAccess.findUpdates(source, target)); - list.addAll(EnrichMissingPid.findUpdates(source, target)); - list.addAll(EnrichMissingProject.findUpdates(source, target)); - list.addAll(EnrichMissingPublicationDate.findUpdates(source, target)); - list.addAll(EnrichMissingSubject.findUpdates(source, target)); - list.addAll(EnrichMoreOpenAccess.findUpdates(source, target)); - list.addAll(EnrichMorePid.findUpdates(source, target)); - list.addAll(EnrichMoreSubject.findUpdates(source, target)); - return list; + return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java index 493d1f97c7..6b6e35d1d6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java @@ -1,31 +1,35 @@ package eu.dnetlib.dhp.broker.oa.util; +import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingAbstract extends UpdateInfo { +public class EnrichMissingAbstract extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); - } - - private EnrichMissingAbstract(final String highlightValue, final float trust) { - super("ENRICH/MISSING/ABSTRACT", highlightValue, trust); + public EnrichMissingAbstract() { + super(false); } @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getAbstracts().add(getHighlightValue()); + protected List> findUpdates(final Result source, final Result target) { + if (isMissing(target.getDescription()) && !isMissing(source.getDescription())) { + return Arrays.asList(generateUpdateInfo(source.getDescription().get(0).getValue(), source, target)); + } + return new ArrayList<>(); } @Override - public String getHighlightValueAsString() { - return getHighlightValue(); + public UpdateInfo generateUpdateInfo(final String highlightValue, final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_ABSTRACT, + highlightValue, source, target, + (p, s) -> p.getAbstracts().add(s), + s -> s); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java index 6899c62a37..d81427e05c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java @@ -4,28 +4,30 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingAuthorOrcid extends UpdateInfo { +public class EnrichMissingAuthorOrcid extends UpdateMatcher> { - public static List findUpdates(final Result source, final Result target) { + public EnrichMissingAuthorOrcid() { + super(true); + } + + @Override + protected List>> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMissingAuthorOrcid(final String highlightValue, final float trust) { - super("ENRICH/MISSING/AUTHOR/ORCID", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - // TODO + public UpdateInfo> generateUpdateInfo(final Pair highlightValue, + final Result source, final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_AUTHOR_ORCID, + highlightValue, source, target, + (p, pair) -> p.getCreators().add(pair.getLeft() + " - ORCID: " + pair.getRight()), + pair -> pair.getLeft() + "::" + pair.getRight()); } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue(); - } - } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java index 9464130f31..9079ee24b0 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java @@ -5,28 +5,29 @@ import java.util.Arrays; import java.util.List; import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingOpenAccess extends UpdateInfo { +public class EnrichMissingOpenAccess extends UpdateMatcher { + + public EnrichMissingOpenAccess() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { - public static List findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMissingOpenAccess(final Instance highlightValue, final float trust) { - super("ENRICH/MISSING/OPENACCESS_VERSION", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getInstances().add(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue().getUrl(); + public UpdateInfo generateUpdateInfo(final Instance highlightValue, final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_OA_VERSION, + highlightValue, source, target, + (p, i) -> p.getInstances().add(i), + Instance::getUrl); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java index 293d4993f3..0b4045a0e4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java @@ -4,29 +4,29 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingPid extends UpdateInfo { +public class EnrichMissingPid extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { + public EnrichMissingPid() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMissingPid(final Pid highlightValue, final float trust) { - super("ENRICH/MISSING/PID", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getPids().add(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue().getType() + "::" + getHighlightValue().getValue(); + public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PID, + highlightValue, source, target, + (p, pid) -> p.getPids().add(pid), + pid -> pid.getType() + "::" + pid.getValue()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java index a22c179a20..45b16801c2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java @@ -4,30 +4,30 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingProject extends UpdateInfo { +public class EnrichMissingProject extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { + public EnrichMissingProject() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMissingProject(final Project highlightValue, final float trust) { - super("ENRICH/MISSING/PROJECT", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getProjects().add(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue().getFunder() + "::" + getHighlightValue().getFundingProgram() - + getHighlightValue().getCode(); + public UpdateInfo generateUpdateInfo(final Project highlightValue, final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PROJECT, + highlightValue, source, target, + (p, prj) -> p.getProjects().add(prj), + prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java index 869dca2645..7fcd2a66f9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java @@ -4,28 +4,29 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingPublicationDate extends UpdateInfo { +public class EnrichMissingPublicationDate extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { + public EnrichMissingPublicationDate() { + super(false); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMissingPublicationDate(final String highlightValue, final float trust) { - super("ENRICH/MISSING/PUBLICATION_DATE", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().setPublicationdate(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue(); + public UpdateInfo generateUpdateInfo(final String highlightValue, final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_DATE, + highlightValue, source, target, + (p, date) -> p.setPublicationdate(date), + s -> s); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java index a2ed5d0439..4470bd9d98 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java @@ -4,12 +4,19 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingSubject extends UpdateInfo { +public class EnrichMissingSubject extends UpdateMatcher> { - public static List findUpdates(final Result source, final Result target) { + public EnrichMissingSubject() { + super(true); + } + + @Override + protected List>> findUpdates(final Result source, final Result target) { // MESHEUROPMC // ARXIV // JEL @@ -19,18 +26,15 @@ public class EnrichMissingSubject extends UpdateInfo { return Arrays.asList(); } - private EnrichMissingSubject(final String subjectClassification, final String highlightValue, final float trust) { - super("ENRICH/MISSING/SUBJECT/" + subjectClassification, highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getSubjects().add(getHighlightValue()); - } + public UpdateInfo> generateUpdateInfo(final Pair highlightValue, + final Result source, final Result target) { - @Override - public String getHighlightValueAsString() { - return getHighlightValue(); + return new UpdateInfo<>( + Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()), + highlightValue, source, target, + (p, pair) -> p.getSubjects().add(pair.getRight()), + pair -> pair.getLeft() + "::" + pair.getRight()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java index 4f1e88d3d5..bc37ce659a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java @@ -5,28 +5,29 @@ import java.util.Arrays; import java.util.List; import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMoreOpenAccess extends UpdateInfo { +public class EnrichMoreOpenAccess extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { + public EnrichMoreOpenAccess() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMoreOpenAccess(final Instance highlightValue, final float trust) { - super("ENRICH/MORE/OPENACCESS_VERSION", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getInstances().add(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue().getUrl(); + public UpdateInfo generateUpdateInfo(final Instance highlightValue, final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MORE_OA_VERSION, + highlightValue, source, target, + (p, i) -> p.getInstances().add(i), + Instance::getUrl); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java index ecf2cf3107..8cd67f5536 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java @@ -4,29 +4,29 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMorePid extends UpdateInfo { +public class EnrichMorePid extends UpdateMatcher { - public static List findUpdates(final Result source, final Result target) { + public EnrichMorePid() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); } - private EnrichMorePid(final Pid highlightValue, final float trust) { - super("ENRICH/MORE/PID", highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getPids().add(getHighlightValue()); - } - - @Override - public String getHighlightValueAsString() { - return getHighlightValue().getType() + "::" + getHighlightValue().getValue(); + public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MORE_PID, + highlightValue, source, target, + (p, pid) -> p.getPids().add(pid), + pid -> pid.getType() + "::" + pid.getValue()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java index f29b86292d..9e0d8e6939 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java @@ -4,12 +4,19 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.OpenAireEventPayload; +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMoreSubject extends UpdateInfo { +public class EnrichMoreSubject extends UpdateMatcher> { - public static List findUpdates(final Result source, final Result target) { + public EnrichMoreSubject() { + super(true); + } + + @Override + protected List>> findUpdates(final Result source, final Result target) { // MESHEUROPMC // ARXIV // JEL @@ -19,18 +26,15 @@ public class EnrichMoreSubject extends UpdateInfo { return Arrays.asList(); } - private EnrichMoreSubject(final String subjectClassification, final String highlightValue, final float trust) { - super("ENRICH/MORE/SUBJECT/" + subjectClassification, highlightValue, trust); - } - @Override - public void compileHighlight(final OpenAireEventPayload payload) { - payload.getHighlight().getSubjects().add(getHighlightValue()); - } + public UpdateInfo> generateUpdateInfo(final Pair highlightValue, + final Result source, final Result target) { - @Override - public String getHighlightValueAsString() { - return getHighlightValue(); + return new UpdateInfo<>( + Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()), + highlightValue, source, target, + (p, pair) -> p.getSubjects().add(pair.getRight()), + pair -> pair.getLeft() + "::" + pair.getRight()); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index f7b6b69e9e..1dfc14e5eb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -1,36 +1,77 @@ package eu.dnetlib.dhp.broker.oa.util; +import java.util.function.BiConsumer; +import java.util.function.Function; + import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.Publication; +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.schema.oaf.Result; -public abstract class UpdateInfo { +public final class UpdateInfo { - private final String topic; + private final Topic topic; private final T highlightValue; + private final Result source; + + private final Result target; + + private final BiConsumer compileHighlight; + + private final Function highlightToString; + private final float trust; - protected UpdateInfo(final String topic, final T highlightValue, final float trust) { + protected UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target, + final BiConsumer compileHighlight, + final Function highlightToString) { this.topic = topic; this.highlightValue = highlightValue; - this.trust = trust; + this.source = source; + this.target = target; + this.compileHighlight = compileHighlight; + this.highlightToString = highlightToString; + this.trust = calculateTrust(source, target); } public T getHighlightValue() { return highlightValue; } + public Result getSource() { + return source; + } + + public Result getTarget() { + return target; + } + + private float calculateTrust(final Result source, final Result target) { + // TODO + return 0.9f; + } + + protected Topic getTopic() { + return topic; + } + + public String getTopicPath() { + return topic.getPath(); + } + public float getTrust() { return trust; } - public String getTopic() { - return topic; + public void compileHighlight(final OpenAireEventPayload payload) { + compileHighlight.accept(payload.getHighlight(), getHighlightValue()); } - abstract public void compileHighlight(OpenAireEventPayload payload); - - abstract public String getHighlightValueAsString(); + public String getHighlightValueAsString() { + return highlightToString.apply(getHighlightValue()); + } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java new file mode 100644 index 0000000000..3fd6d40276 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java @@ -0,0 +1,63 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.Arrays; +import java.util.Collection; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import org.apache.commons.codec.digest.DigestUtils; +import org.apache.commons.lang3.StringUtils; + +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Result; + +public abstract class UpdateMatcher { + + private final boolean multipleUpdate; + + public UpdateMatcher(final boolean multipleUpdate) { + this.multipleUpdate = multipleUpdate; + } + + public Collection> searchUpdatesForRecord(final Result res, final Result... others) { + + final Map> infoMap = new HashMap<>(); + + for (final Result source : others) { + if (source != res) { + for (final UpdateInfo info : findUpdates(source, res)) { + final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); + if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { + } else { + infoMap.put(s, info); + } + } + } + } + + final Collection> values = infoMap.values(); + + if (values.isEmpty() || multipleUpdate) { + return values; + } else { + final UpdateInfo v = values + .stream() + .sorted((o1, o2) -> Float.compare(o1.getTrust(), o2.getTrust())) + .findFirst() + .get(); + return Arrays.asList(v); + } + } + + protected abstract List> findUpdates(Result source, Result target); + + protected abstract UpdateInfo generateUpdateInfo(final T highlightValue, final Result source, + final Result target); + + protected static boolean isMissing(final List> list) { + return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue()); + } + +} From 5ecacad70a0539bd94e336ad604cc32ac8e0ce1a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 May 2020 17:01:11 +0200 Subject: [PATCH 10/70] fixed default resource typing in Oaf/Odf mapping --- .../raw/AbstractMdRecordToOafMapper.java | 168 +++++++++--------- 1 file changed, 84 insertions(+), 84 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index fd12716b42..be0b910226 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -64,7 +64,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( - "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -75,20 +75,20 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText( - xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); + .parseText( + xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); if (collectedFrom == null) { return null; } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + ? collectedFrom + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); if (hostedBy == null) { return null; @@ -112,22 +112,21 @@ public abstract class AbstractMdRecordToOafMapper { } return keyValue( - createOpenaireId(10, dsId, true), - dsName); + createOpenaireId(10, dsId, true), + dsName); } protected List createOafs( - final Document doc, - final String type, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { + final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "": case "publication": final Publication p = new Publication(); populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); @@ -138,7 +137,7 @@ public abstract class AbstractMdRecordToOafMapper { case "dataset": final Dataset d = new Dataset(); populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -158,6 +157,7 @@ public abstract class AbstractMdRecordToOafMapper { s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); oafs.add(s); break; + case "": case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); @@ -179,10 +179,10 @@ public abstract class AbstractMdRecordToOafMapper { } private List addProjectRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { final List res = new ArrayList<>(); @@ -196,15 +196,15 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add( + getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp)); res - .add( - getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + .add( + getRelation( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp)); } } @@ -212,7 +212,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected Relation getRelation(String source, String target, String relType, String subRelType, String relClass, - KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { + KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { final Relation rel = new Relation(); rel.setRelType(relType); rel.setSubRelType(subRelType); @@ -226,27 +226,27 @@ public abstract class AbstractMdRecordToOafMapper { } protected abstract List addOtherResultRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); private void populateResultFields( - final Result r, - final Document doc, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { + final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setCollectedfrom(Arrays.asList(collectedFrom)); r - .setPid( - prepareListStructProps( - doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + .setPid( + prepareListStructProps( + doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES @@ -289,7 +289,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract List prepareInstances( - Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); protected abstract List> prepareSources(Document doc, DataInfo info); @@ -314,13 +314,13 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareAuthors(Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductTools( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); @@ -329,7 +329,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); @@ -359,37 +359,37 @@ public abstract class AbstractMdRecordToOafMapper { final String edition = n.valueOf("@edition"); if (StringUtils.isNotBlank(name)) { return journal( - name, - issnPrinted, - issnOnline, - issnLinking, - ep, - iss, - sp, - vol, - edition, - null, - null, - info); + name, + issnPrinted, + issnOnline, + issnLinking, + ep, + iss, + sp, + vol, + edition, + null, + null, + info); } } return null; } protected Qualifier prepareQualifier( - final Node node, final String xpath, final String schemeId, final String schemeName) { + final Node node, final String xpath, final String schemeId, final String schemeName) { final String classId = node.valueOf(xpath); final String className = code2name.get(classId); return qualifier(classId, className, schemeId, schemeName); } protected List prepareListStructProps( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final String schemeName, - final DataInfo info) { + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; @@ -401,7 +401,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; @@ -411,19 +411,19 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final DataInfo info) { + final Node node, final String xpath, final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add( - structuredProperty( - n.getText(), - n.valueOf("@classid"), - n.valueOf("@classname"), - n.valueOf("@schemeid"), - n.valueOf("@schemename"), - info)); + .add( + structuredProperty( + n.getText(), + n.valueOf("@classid"), + n.valueOf("@classname"), + n.valueOf("@schemeid"), + n.valueOf("@schemename"), + info)); } return res; } @@ -450,7 +450,7 @@ public abstract class AbstractMdRecordToOafMapper { if (n == null) { return dataInfo( - false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); @@ -464,12 +464,12 @@ public abstract class AbstractMdRecordToOafMapper { final String trust = n.valueOf("./oaf:trust"); return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), - trust); + deletedbyinference, + inferenceprovenance, + inferred, + false, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), + trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { @@ -477,7 +477,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected List> prepareListFields( - final Node node, final String xpath, final DataInfo info) { + final Node node, final String xpath, final DataInfo info) { return listFields(info, prepareListString(node, xpath)); } From ab37953332755ed53ebf95655547a4736d8f7395 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 14 May 2020 10:25:41 +0200 Subject: [PATCH 11/70] added global properties in wf definitions to avoid repeating name-node and job-tracker in the (many) distcp actions; reintroduced output directory removal at the beginning of each spark action --- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 2 + .../SparkCountryPropagationJob.java | 17 +- .../PrepareResultOrcidAssociationStep1.java | 4 +- .../PrepareResultOrcidAssociationStep2.java | 4 +- .../SparkOrcidToResultFromSemRelJob.java | 7 +- .../PrepareProjectResultsAssociation.java | 2 + .../PrepareResultCommunitySet.java | 4 +- ...kResultToCommunityFromOrganizationJob.java | 7 +- .../PrepareResultInstRepoAssociation.java | 43 +++-- ...arkResultToOrganizationFromIstRepoJob.java | 7 +- .../dhp/bulktag/oozie_app/workflow.xml | 27 ++- .../countrypropagation/oozie_app/workflow.xml | 20 ++- .../oozie_app/workflow.xml | 7 +- .../projecttoresult/oozie_app/workflow.xml | 29 ++-- .../oozie_app/workflow.xml | 29 ++-- .../oozie_app/workflow.xml | 52 +++--- .../raw/AbstractMdRecordToOafMapper.java | 164 +++++++++--------- 17 files changed, 213 insertions(+), 212 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 75d85e2bad..1c65e8adec 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.bulktag; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Optional; @@ -84,6 +85,7 @@ public class SparkBulkTagJob { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc); }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 9dc17701bc..974b3a3b11 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -69,13 +69,16 @@ public class SparkCountryPropagationJob { runWithSparkSession( conf, isSparkSessionManaged, - spark -> execPropagation( - spark, - sourcePath, - preparedInfoPath, - outputPath, - resultClazz, - saveGraph)); + spark -> { + removeOutputDir(spark, outputPath); + execPropagation( + spark, + sourcePath, + preparedInfoPath, + outputPath, + resultClazz, + saveGraph); + }); } private static void execPropagation( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index 3e16b4b4b3..400c8d8efa 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -74,9 +74,7 @@ public class PrepareResultOrcidAssociationStep1 { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } + removeOutputDir(spark, outputPath); prepareInfo( spark, inputRelationPath, inputResultPath, outputResultPath, resultClazz, allowedsemrel); }); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java index 65d8811bc7..2cea32e58f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java @@ -50,9 +50,7 @@ public class PrepareResultOrcidAssociationStep2 { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } + removeOutputDir(spark, outputPath); mergeInfo(spark, inputPath, outputPath); }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index ebb75a5a67..b34b29c481 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -70,11 +70,10 @@ public class SparkOrcidToResultFromSemRelJob { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } - if (saveGraph) + removeOutputDir(spark, outputPath); + if (saveGraph) { execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz); + } }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java index 05dcdc6928..c27da42583 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java @@ -60,6 +60,8 @@ public class PrepareProjectResultsAssociation { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, potentialUpdatePath); + removeOutputDir(spark, alreadyLinkedPath); prepareResultProjProjectResults( spark, inputPath, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index e2d4d56878..90eb54e5fa 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -55,9 +55,7 @@ public class PrepareResultCommunitySet { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } + removeOutputDir(spark, outputPath); prepareInfo(spark, inputPath, outputPath, organizationMap); }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 71275cc7f0..66297e1779 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -68,11 +68,10 @@ public class SparkResultToCommunityFromOrganizationJob { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } - if (saveGraph) + removeOutputDir(spark, outputPath); + if (saveGraph) { execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath); + } }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java index f8fe1668fd..5f549be531 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java @@ -58,30 +58,15 @@ public class PrepareResultInstRepoAssociation { isSparkSessionManaged, spark -> { readNeededResources(spark, inputPath); + + removeOutputDir(spark, datasourceOrganizationPath); prepareDatasourceOrganization(spark, datasourceOrganizationPath); + + removeOutputDir(spark, alreadyLinkedPath); prepareAlreadyLinkedAssociation(spark, alreadyLinkedPath); }); } - private static void prepareAlreadyLinkedAssociation( - SparkSession spark, String alreadyLinkedPath) { - String query = "Select source resultId, collect_set(target) organizationSet " - + "from relation " - + "where datainfo.deletedbyinference = false " - + "and relClass = '" - + RELATION_RESULT_ORGANIZATION_REL_CLASS - + "' " - + "group by source"; - - spark - .sql(query) - .as(Encoders.bean(ResultOrganizationSet.class)) - // TODO retry to stick with datasets - .toJavaRDD() - .map(r -> OBJECT_MAPPER.writeValueAsString(r)) - .saveAsTextFile(alreadyLinkedPath, GzipCodec.class); - } - private static void readNeededResources(SparkSession spark, String inputPath) { Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class); datasource.createOrReplaceTempView("datasource"); @@ -119,4 +104,24 @@ public class PrepareResultInstRepoAssociation { .option("compression", "gzip") .json(datasourceOrganizationPath); } + + private static void prepareAlreadyLinkedAssociation( + SparkSession spark, String alreadyLinkedPath) { + String query = "Select source resultId, collect_set(target) organizationSet " + + "from relation " + + "where datainfo.deletedbyinference = false " + + "and relClass = '" + + RELATION_RESULT_ORGANIZATION_REL_CLASS + + "' " + + "group by source"; + + spark + .sql(query) + .as(Encoders.bean(ResultOrganizationSet.class)) + // TODO retry to stick with datasets + .toJavaRDD() + .map(r -> OBJECT_MAPPER.writeValueAsString(r)) + .saveAsTextFile(alreadyLinkedPath, GzipCodec.class); + } + } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index 86634d43fc..13577fa7c1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -83,10 +83,8 @@ public class SparkResultToOrganizationFromIstRepoJob { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } - if (saveGraph) + removeOutputDir(spark, outputPath); + if (saveGraph) { execPropagation( spark, datasourceorganization, @@ -94,6 +92,7 @@ public class SparkResultToOrganizationFromIstRepoJob { inputPath, outputPath, resultClazz); + } }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 754aba4f29..f019f8413d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -18,6 +18,17 @@ + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -42,8 +53,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/relation ${nameNode}/${outputPath}/relation @@ -53,8 +62,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization @@ -64,8 +71,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -75,8 +80,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource @@ -95,8 +98,6 @@ - ${jobTracker} - ${nameNode} yarn-cluster cluster bulkTagging-publication @@ -124,8 +125,6 @@ - ${jobTracker} - ${nameNode} yarn-cluster cluster bulkTagging-dataset @@ -153,8 +152,6 @@ - ${jobTracker} - ${nameNode} yarn-cluster cluster bulkTagging-orp @@ -182,8 +179,6 @@ - ${jobTracker} - ${nameNode} yarn-cluster cluster bulkTagging-software diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index fc877071df..85116e4cc9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -19,6 +19,17 @@ + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -43,8 +54,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/relation ${nameNode}/${outputPath}/relation @@ -54,18 +63,15 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization + - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -75,8 +81,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml index e4429b710c..5ddc5fedf4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml @@ -57,6 +57,7 @@ + ${jobTracker} @@ -81,7 +82,6 @@ - @@ -230,8 +230,8 @@ - + @@ -271,6 +271,7 @@ + yarn @@ -302,6 +303,7 @@ + yarn @@ -333,6 +335,7 @@ + yarn diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml index 24e1d3b7fa..9e91c06fb3 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml @@ -14,6 +14,17 @@ + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -42,8 +53,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/relation ${nameNode}/${outputPath}/relation @@ -53,8 +62,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/publication ${nameNode}/${outputPath}/publication @@ -64,8 +71,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/dataset ${nameNode}/${outputPath}/dataset @@ -75,8 +80,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/otherresearchproduct ${nameNode}/${outputPath}/otherresearchproduct @@ -86,28 +89,24 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/software ${nameNode}/${outputPath}/software + - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization + - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -117,8 +116,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index d481cad052..6a329fdc46 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -14,6 +14,17 @@ + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -38,8 +49,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/relation ${nameNode}/${outputPath}/relation @@ -49,8 +58,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization @@ -60,8 +67,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -71,8 +76,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource @@ -101,8 +104,8 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/relation - --hive_metastore_uris${hive_metastore_uris} --outputPath${workingDir}/preparedInfo/resultCommunityList + --hive_metastore_uris${hive_metastore_uris} --organizationtoresultcommunitymap${organizationtoresultcommunitymap} @@ -136,9 +139,9 @@ --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList --sourcePath${sourcePath}/publication + --outputPath${outputPath}/publication --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${outputPath}/publication --saveGraph${saveGraph} @@ -165,9 +168,9 @@ --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList --sourcePath${sourcePath}/dataset + --outputPath${outputPath}/dataset --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${outputPath}/dataset --saveGraph${saveGraph} @@ -194,9 +197,9 @@ --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList --sourcePath${sourcePath}/otherresearchproduct + --outputPath${outputPath}/otherresearchproduct --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${outputPath}/otherresearchproduct --saveGraph${saveGraph} @@ -223,9 +226,9 @@ --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList --sourcePath${sourcePath}/software + --outputPath${outputPath}/software --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${outputPath}/software --saveGraph${saveGraph} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml index a1b7f4ad79..e0563abae8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml @@ -10,6 +10,17 @@ + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -38,8 +49,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/relation ${nameNode}/${outputPath}/relation @@ -49,8 +58,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/publication ${nameNode}/${outputPath}/publication @@ -60,8 +67,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/dataset ${nameNode}/${outputPath}/dataset @@ -71,8 +76,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/otherresearchproduct ${nameNode}/${outputPath}/otherresearchproduct @@ -82,8 +85,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/software ${nameNode}/${outputPath}/software @@ -93,8 +94,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization @@ -104,8 +103,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -115,8 +112,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource @@ -125,6 +120,7 @@ + yarn @@ -176,12 +172,12 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/publication - --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/relation --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + --hive_metastore_uris${hive_metastore_uris} + --saveGraph${saveGraph} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication @@ -206,12 +202,12 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/dataset - --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/relation --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + --hive_metastore_uris${hive_metastore_uris} + --saveGraph${saveGraph} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset @@ -236,12 +232,12 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/otherresearchproduct - --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/relation --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + --hive_metastore_uris${hive_metastore_uris} + --saveGraph${saveGraph} + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct @@ -266,12 +262,12 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/software - --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/relation --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked + --hive_metastore_uris${hive_metastore_uris} + --saveGraph${saveGraph} + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index be0b910226..b9c4e6c804 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -64,7 +64,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( - "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -75,20 +75,20 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText( - xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); + .parseText( + xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); final String type = doc.valueOf("//dr:CobjCategory/@type"); final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); if (collectedFrom == null) { return null; } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + ? collectedFrom + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); if (hostedBy == null) { return null; @@ -112,17 +112,17 @@ public abstract class AbstractMdRecordToOafMapper { } return keyValue( - createOpenaireId(10, dsId, true), - dsName); + createOpenaireId(10, dsId, true), + dsName); } protected List createOafs( - final Document doc, - final String type, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { + final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { final List oafs = new ArrayList<>(); @@ -179,10 +179,10 @@ public abstract class AbstractMdRecordToOafMapper { } private List addProjectRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { final List res = new ArrayList<>(); @@ -196,15 +196,15 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add( + getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp)); res - .add( - getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + .add( + getRelation( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp)); } } @@ -212,7 +212,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected Relation getRelation(String source, String target, String relType, String subRelType, String relClass, - KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { + KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { final Relation rel = new Relation(); rel.setRelType(relType); rel.setSubRelType(subRelType); @@ -226,27 +226,27 @@ public abstract class AbstractMdRecordToOafMapper { } protected abstract List addOtherResultRels( - final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); + final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); private void populateResultFields( - final Result r, - final Document doc, - final KeyValue collectedFrom, - final KeyValue hostedBy, - final DataInfo info, - final long lastUpdateTimestamp) { + final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setCollectedfrom(Arrays.asList(collectedFrom)); r - .setPid( - prepareListStructProps( - doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + .setPid( + prepareListStructProps( + doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES @@ -289,7 +289,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract List prepareInstances( - Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); protected abstract List> prepareSources(Document doc, DataInfo info); @@ -314,13 +314,13 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareAuthors(Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductTools( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); @@ -329,7 +329,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, DataInfo info); + Document doc, DataInfo info); protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); @@ -359,37 +359,37 @@ public abstract class AbstractMdRecordToOafMapper { final String edition = n.valueOf("@edition"); if (StringUtils.isNotBlank(name)) { return journal( - name, - issnPrinted, - issnOnline, - issnLinking, - ep, - iss, - sp, - vol, - edition, - null, - null, - info); + name, + issnPrinted, + issnOnline, + issnLinking, + ep, + iss, + sp, + vol, + edition, + null, + null, + info); } } return null; } protected Qualifier prepareQualifier( - final Node node, final String xpath, final String schemeId, final String schemeName) { + final Node node, final String xpath, final String schemeId, final String schemeName) { final String classId = node.valueOf(xpath); final String className = code2name.get(classId); return qualifier(classId, className, schemeId, schemeName); } protected List prepareListStructProps( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final String schemeName, - final DataInfo info) { + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; @@ -401,7 +401,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; @@ -411,19 +411,19 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final DataInfo info) { + final Node node, final String xpath, final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add( - structuredProperty( - n.getText(), - n.valueOf("@classid"), - n.valueOf("@classname"), - n.valueOf("@schemeid"), - n.valueOf("@schemename"), - info)); + .add( + structuredProperty( + n.getText(), + n.valueOf("@classid"), + n.valueOf("@classname"), + n.valueOf("@schemeid"), + n.valueOf("@schemename"), + info)); } return res; } @@ -450,7 +450,7 @@ public abstract class AbstractMdRecordToOafMapper { if (n == null) { return dataInfo( - false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); @@ -464,12 +464,12 @@ public abstract class AbstractMdRecordToOafMapper { final String trust = n.valueOf("./oaf:trust"); return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), - trust); + deletedbyinference, + inferenceprovenance, + inferred, + false, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), + trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { @@ -477,7 +477,7 @@ public abstract class AbstractMdRecordToOafMapper { } protected List> prepareListFields( - final Node node, final String xpath, final DataInfo info) { + final Node node, final String xpath, final DataInfo info) { return listFields(info, prepareListString(node, xpath)); } From 8828458acfd38e47b03c1a88335b4b5bc69c9eab Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 May 2020 10:34:12 +0200 Subject: [PATCH 12/70] minor changes --- .../PrepareResultOrcidAssociationStep1.java | 33 ++++++++++--------- .../SparkOrcidToResultFromSemRelJob.java | 22 +++++++------ 2 files changed, 29 insertions(+), 26 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index 3e16b4b4b3..7cd057cf39 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -97,22 +97,23 @@ public class PrepareResultOrcidAssociationStep1 { Dataset result = readPath(spark, inputResultPath, resultClazz); result.createOrReplaceTempView("result"); - String query = " select target resultId, author authorList" - + " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " - + " from ( " - + " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " - + " from result " - + " lateral view explode (author) a as MyT " - + " lateral view explode (MyT.pid) p as MyP " - + " where MyP.qualifier.classid = 'ORCID') tmp " - + " group by id) r_t " - + " join (" - + " select source, target " - + " from relation " - + " where datainfo.deletedbyinference = false " - + getConstraintList(" relclass = '", allowedsemrel) - + ") rel_rel " - + " on source = id"; + String query = + "SELECT target resultId, author authorList" + + " FROM (SELECT id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " + + " FROM ( " + + " SELECT DISTINCT id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " + + " FROM result " + + " LATERAL VIEW EXPLODE (author) a AS MyT " + + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " + + " WHERE MyP.qualifier.classid = 'ORCID') tmp " + + " GROUP BY id) r_t " + + " JOIN (" + + " SELECT source, target " + + " FROM relation " + + " WHERE datainfo.deletedbyinference = false " + + getConstraintList(" relclass = '", allowedsemrel) + + " ) rel_rel " + + " ON source = id"; spark .sql(query) .as(Encoders.bean(ResultOrcidList.class)) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index ebb75a5a67..b93b66d9f9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -132,16 +132,16 @@ public class SparkOrcidToResultFromSemRelJob { private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) { boolean toaddpid = false; - if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) { - if (StringUtils.isNoneEmpty(author.getSurname())) { + if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { + if (StringUtils.isNotEmpty(author.getSurname())) { if (autoritative_author .getSurname() .trim() .equalsIgnoreCase(author.getSurname().trim())) { // have the same surname. Check the name - if (StringUtils.isNoneEmpty(autoritative_author.getName())) { - if (StringUtils.isNoneEmpty(author.getName())) { + if (StringUtils.isNotEmpty(autoritative_author.getName())) { + if (StringUtils.isNotEmpty(author.getName())) { if (autoritative_author .getName() .trim() @@ -150,12 +150,14 @@ public class SparkOrcidToResultFromSemRelJob { } // they could be differently written (i.e. only the initials of the name // in one of the two - if (autoritative_author - .getName() - .trim() - .substring(0, 0) - .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { - toaddpid = true; + else { + if (autoritative_author + .getName() + .trim() + .substring(0, 0) + .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { + toaddpid = true; + } } } } From f044d093156c3c29cf00a4a9b498459885ebcdd0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 14 May 2020 15:07:24 +0200 Subject: [PATCH 13/70] revised mapping: more accurate mapping for name/surname from datacite format; improved mapping of null values --- .../migration/ProtoConverter.java | 27 ++++++++++++----- .../raw/MigrateDbEntitiesApplication.java | 20 +++++-------- .../dhp/oa/graph/raw/OdfToOafMapper.java | 30 +++++++++++++++---- .../dhp/oa/graph/raw/common/PacePerson.java | 1 - 4 files changed, 51 insertions(+), 27 deletions(-) diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index 90d573ac07..e55c0eb7b6 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -523,7 +523,9 @@ public class ProtoConverter implements Serializable { } private static Context mapContext(ResultProtos.Result.Context context) { - + if (context == null || StringUtils.isBlank(context.getId())) { + return null; + } final Context entity = new Context(); entity.setId(context.getId()); entity @@ -537,6 +539,10 @@ public class ProtoConverter implements Serializable { } public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) { + if (kv == null || StringUtils.isBlank(kv.getKey()) & StringUtils.isBlank(kv.getValue())) { + return null; + } + final KeyValue keyValue = new KeyValue(); keyValue.setKey(kv.getKey()); keyValue.setValue(kv.getValue()); @@ -575,6 +581,10 @@ public class ProtoConverter implements Serializable { } public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) { + if (sp == null | StringUtils.isBlank(sp.getValue())) { + return null; + } + final StructuredProperty structuredProperty = new StructuredProperty(); structuredProperty.setValue(sp.getValue()); structuredProperty.setQualifier(mapQualifier(sp.getQualifier())); @@ -611,6 +621,10 @@ public class ProtoConverter implements Serializable { } public static Field mapStringField(FieldTypeProtos.StringField s) { + if (s == null || StringUtils.isBlank(s.getValue())) { + return null; + } + final Field stringField = new Field<>(); stringField.setValue(s.getValue()); stringField.setDataInfo(mapDataInfo(s.getDataInfo())); @@ -618,19 +632,16 @@ public class ProtoConverter implements Serializable { } public static Field mapBoolField(FieldTypeProtos.BoolField b) { + if (b == null) { + return null; + } + final Field booleanField = new Field<>(); booleanField.setValue(b.getValue()); booleanField.setDataInfo(mapDataInfo(b.getDataInfo())); return booleanField; } - public static Field mapIntField(FieldTypeProtos.IntField b) { - final Field entity = new Field<>(); - entity.setValue(b.getValue()); - entity.setDataInfo(mapDataInfo(b.getDataInfo())); - return entity; - } - public static Journal mapJournal(FieldTypeProtos.Journal j) { final Journal journal = new Journal(); journal.setConferencedate(j.getConferencedate()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index e5e348642c..ebe2b703ba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -50,8 +50,7 @@ import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -public class MigrateDbEntitiesApplication extends AbstractMigrationApplication - implements Closeable { +public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); @@ -128,9 +127,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication } public List processDatasource(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); final Datasource ds = new Datasource(); @@ -194,7 +191,6 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication public List processProject(final ResultSet rs) { try { - final DataInfo info = prepareDataInfo(rs); final Project p = new Project(); @@ -249,9 +245,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication } public List processOrganization(final ResultSet rs) { - try { - final DataInfo info = prepareDataInfo(rs); final Organization o = new Organization(); @@ -370,14 +364,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final DataInfo info = dataInfo( false, null, false, false, - qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9"); final List collectedFrom = listKeyValues( createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); try { - if (rs.getString(SOURCE_TYPE).equals("context")) { final Result r; @@ -461,9 +453,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication final Boolean inferred = rs.getBoolean("inferred"); final String trust = rs.getString("trust"); return dataInfo( - - deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); - + deletedbyinference, + inferenceprovenance, + inferred, + false, + ENTITYREGISTRY_PROVENANCE_ACTION, + trust); } private Qualifier prepareQualifierSplitting(final String s) { @@ -535,4 +530,5 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication super.close(); dbClient.close(); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 04984d0086..5baac12fd0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -12,6 +12,7 @@ import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; +import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -44,9 +45,24 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//datacite:creator")) { final Node n = (Node) o; final Author author = new Author(); - author.setFullname(n.valueOf("./datacite:creatorName")); - author.setName(n.valueOf("./datacite:givenName")); - author.setSurname(n.valueOf("./datacite:familyName")); + final String fullname = n.valueOf("./datacite:creatorName"); + author.setFullname(fullname); + + PacePerson pp = new PacePerson(fullname, false); + final String name = n.valueOf("./datacite:givenName"); + if (StringUtils.isBlank(name) & pp.isAccurate()) { + author.setName(pp.getNormalisedFirstName()); + } else { + author.setName(name); + } + + final String surname = n.valueOf("./datacite:familyName"); + if (StringUtils.isBlank(surname) & pp.isAccurate()) { + author.setSurname(pp.getNormalisedSurname()); + } else { + author.setSurname(surname); + } + author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info)); author.setPid(preparePids(doc, info)); author.setRank(pos++); @@ -77,8 +93,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final KeyValue hostedby) { final Instance instance = new Instance(); - final Set url = new HashSet<>(); - instance.setUrl(new ArrayList<>()); instance .setInstancetype( prepareQualifier( @@ -97,6 +111,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { .setProcessingchargecurrency( field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + final Set url = new HashSet<>(); for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { url.add(((Node) o).getText().trim()); } @@ -109,7 +124,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) { url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); } - instance.getUrl().addAll(url); + if (!url.isEmpty()) { + instance.setUrl(new ArrayList<>()); + instance.getUrl().addAll(url); + } return Arrays.asList(instance); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java index d1c615dcdd..6e474f2f38 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.oa.graph.raw.common; -import java.nio.charset.Charset; import java.nio.charset.StandardCharsets; import java.text.Normalizer; import java.util.HashSet; From 42085e8d99220ccdf1f4c9cc38d26db24b9544a2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 May 2020 18:22:28 +0200 Subject: [PATCH 14/70] added some constants --- .../java/eu/dnetlib/dhp/schema/common/ModelConstants.java | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index accc06d122..e32dd10fa9 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -13,6 +13,7 @@ public class ModelConstants { public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date"; public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource"; public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; + public static final String DNET_COUNTRY_TYPE = "dnet:countries"; public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository"; public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry"; @@ -49,6 +50,13 @@ public class ModelConstants { public static final String HAS_PARTICIPANT = "hasParticipant"; public static final String IS_PARTICIPANT = "isParticipant"; + public static final String RESULT_ORGANIZATION = "resultOrganization"; + public static final String AFFILIATION = "affiliation"; + public static final String IS_AUTHOR_INSTITUTION_OF = "isAuthorInstitutionOf"; + public static final String HAS_AUTHOR_INSTITUTION = "hasAuthorInstitution"; + + public static final String MERGES = "merges"; + public static final String UNKNOWN = "UNKNOWN"; public static final String NOT_AVAILABLE = "not available"; From d05630d9795f1a26a9ea9ce33d2337c9156217ff Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 May 2020 18:22:50 +0200 Subject: [PATCH 15/70] removed the constants added in ModelConstants --- .../eu/dnetlib/dhp/PropagationConstant.java | 30 ++++--------------- 1 file changed, 6 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 8d2fede82e..13ed46508a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -4,6 +4,8 @@ package eu.dnetlib.dhp; import java.util.List; import java.util.Optional; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -24,10 +26,6 @@ public class PropagationConstant { public static final String TRUE = "true"; - public static final String DNET_COUNTRY_SCHEMA = "dnet:countries"; - public static final String DNET_SCHEMA_NAME = "dnet:provenanceActions"; - public static final String DNET_SCHEMA_ID = "dnet:provenanceActions"; - public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_ID = "country:instrepos"; public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME = "Propagation of country to result collected from datasources of type institutional repositories"; @@ -46,22 +44,6 @@ public class PropagationConstant { public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result"; public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations"; - public static final String RELATION_DATASOURCE_ORGANIZATION_REL_CLASS = "isProvidedBy"; - - public static final String RELATION_RESULTORGANIZATION_REL_TYPE = "resultOrganization"; - public static final String RELATION_RESULTORGANIZATION_SUBREL_TYPE = "affiliation"; - public static final String RELATION_ORGANIZATION_RESULT_REL_CLASS = "isAuthorInstitutionOf"; - public static final String RELATION_RESULT_ORGANIZATION_REL_CLASS = "hasAuthorInstitution"; - - public static final String RELATION_RESULTRESULT_REL_TYPE = "resultResult"; - - public static final String RELATION_RESULTPROJECT_REL_TYPE = "resultProject"; - public static final String RELATION_RESULTPROJECT_SUBREL_TYPE = "outcome"; - public static final String RELATION_RESULT_PROJECT_REL_CLASS = "isProducedBy"; - public static final String RELATION_PROJECT_RESULT_REL_CLASS = "produces"; - - public static final String RELATION_REPRESENTATIVERESULT_RESULT_CLASS = "merges"; - public static final String PROPAGATION_AUTHOR_PID = "ORCID"; public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -76,8 +58,8 @@ public class PropagationConstant { Country nc = new Country(); nc.setClassid(classid); nc.setClassname(classname); - nc.setSchemename(DNET_COUNTRY_SCHEMA); - nc.setSchemeid(DNET_COUNTRY_SCHEMA); + nc.setSchemename(ModelConstants.DNET_COUNTRY_TYPE); + nc.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE); nc .setDataInfo( getDataInfo( @@ -102,8 +84,8 @@ public class PropagationConstant { Qualifier pa = new Qualifier(); pa.setClassid(inference_class_id); pa.setClassname(inference_class_name); - pa.setSchemeid(DNET_SCHEMA_ID); - pa.setSchemename(DNET_SCHEMA_NAME); + pa.setSchemeid(ModelConstants.DNET_PID_TYPES); + pa.setSchemename(ModelConstants.DNET_PID_TYPES); return pa; } From f25db01664eb56d2250d00e95822b4aaacaf52bf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 May 2020 18:29:24 +0200 Subject: [PATCH 16/70] changed in the constant from propagationconstants to modelconstants --- .../PrepareDatasourceCountryAssociation.java | 3 ++- .../PrepareProjectResultsAssociation.java | 3 ++- .../SparkResultToProjectThroughSemRelJob.java | 13 +++++++------ .../PrepareResultCommunitySet.java | 5 +++-- .../PrepareResultInstRepoAssociation.java | 5 +++-- .../SparkResultToOrganizationFromIstRepoJob.java | 13 +++++++------ 6 files changed, 24 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index e91a1e48a7..1d01d35e5f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Arrays; import java.util.List; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -100,7 +101,7 @@ public class PrepareDatasourceCountryAssociation { + "JOIN ( SELECT source, target " + " FROM relation " + " WHERE relclass = '" - + RELATION_DATASOURCE_ORGANIZATION_REL_CLASS + + ModelConstants.IS_PROVIDED_BY + "' " + " AND datainfo.deletedbyinference = false ) rel " + "ON d.id = rel.source " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java index c27da42583..920ef1f06d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java @@ -8,6 +8,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Arrays; import java.util.List; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -85,7 +86,7 @@ public class PrepareProjectResultsAssociation { + " FROM relation " + " WHERE datainfo.deletedbyinference = false " + " AND relClass = '" - + RELATION_RESULT_PROJECT_REL_CLASS + + ModelConstants.IS_PRODUCED_BY + "'"; Dataset resproj_relation = spark.sql(resproj_relation_query); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index 36694b3dd5..44a439ab78 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -9,6 +9,7 @@ import java.util.Iterator; import java.util.List; import java.util.Optional; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; @@ -122,9 +123,9 @@ public class SparkResultToProjectThroughSemRelJob { getRelation( resId, projectId, - RELATION_RESULT_PROJECT_REL_CLASS, - RELATION_RESULTPROJECT_REL_TYPE, - RELATION_RESULTPROJECT_SUBREL_TYPE, + ModelConstants.IS_PRODUCED_BY, + ModelConstants.RESULT_PROJECT , + ModelConstants.OUTCOME, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME)); @@ -133,9 +134,9 @@ public class SparkResultToProjectThroughSemRelJob { getRelation( projectId, resId, - RELATION_PROJECT_RESULT_REL_CLASS, - RELATION_RESULTPROJECT_REL_TYPE, - RELATION_RESULTPROJECT_SUBREL_TYPE, + ModelConstants.PRODUCES, + ModelConstants.RESULT_PROJECT, + ModelConstants.OUTCOME, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME)); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 90eb54e5fa..fc9f395d1b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -74,13 +75,13 @@ public class PrepareResultCommunitySet { + " FROM relation " + " WHERE datainfo.deletedbyinference = false " + " AND relClass = '" - + RELATION_RESULT_ORGANIZATION_REL_CLASS + + ModelConstants.HAS_AUTHOR_INSTITUTION + "') result_organization " + "LEFT JOIN (SELECT source, collect_set(target) org_set " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " + " AND relClass = '" - + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + + ModelConstants.MERGES + "' " + " GROUP BY source) organization_organization " + "ON result_organization.target = organization_organization.source "; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java index 5f549be531..0a83e4195c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -91,7 +92,7 @@ public class PrepareResultInstRepoAssociation { + "JOIN ( SELECT source, target " + "FROM relation " + "WHERE relclass = '" - + RELATION_DATASOURCE_ORGANIZATION_REL_CLASS + + ModelConstants.IS_PROVIDED_BY + "' " + "AND datainfo.deletedbyinference = false ) rel " + "ON d.id = rel.source "; @@ -111,7 +112,7 @@ public class PrepareResultInstRepoAssociation { + "from relation " + "where datainfo.deletedbyinference = false " + "and relClass = '" - + RELATION_RESULT_ORGANIZATION_REL_CLASS + + ModelConstants.HAS_AUTHOR_INSTITUTION + "' " + "group by source"; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index 13577fa7c1..fc9a46d725 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; @@ -150,9 +151,9 @@ public class SparkResultToOrganizationFromIstRepoJob { getRelation( orgId, resultId, - RELATION_ORGANIZATION_RESULT_REL_CLASS, - RELATION_RESULTORGANIZATION_REL_TYPE, - RELATION_RESULTORGANIZATION_SUBREL_TYPE, + ModelConstants.IS_AUTHOR_INSTITUTION_OF, + ModelConstants.RESULT_ORGANIZATION, + ModelConstants.AFFILIATION, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME)); @@ -161,9 +162,9 @@ public class SparkResultToOrganizationFromIstRepoJob { getRelation( resultId, orgId, - RELATION_RESULT_ORGANIZATION_REL_CLASS, - RELATION_RESULTORGANIZATION_REL_TYPE, - RELATION_RESULTORGANIZATION_SUBREL_TYPE, + ModelConstants.HAS_AUTHOR_INSTITUTION, + ModelConstants.RESULT_ORGANIZATION, + ModelConstants.AFFILIATION, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME)); From eb64335a547c1a8b9e708f50b6f33b362fa1e54e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 09:05:26 +0200 Subject: [PATCH 17/70] parallel implementation for graph Hive importer --- .../graph/hive/GraphHiveTableImporterJob.java | 79 +++++++ .../hive/oozie_app/lib/scripts/reset_db.sql | 2 + .../dhp/oa/graph/hive/oozie_app/workflow.xml | 200 +++++++++++++++++- .../oa/graph/hive_db_importer_parameters.json | 26 +++ .../graph/hive_table_importer_parameters.json | 32 +++ 5 files changed, 331 insertions(+), 8 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/reset_db.sql create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_db_importer_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java new file mode 100644 index 0000000000..f88f7457f0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java @@ -0,0 +1,79 @@ + +package eu.dnetlib.dhp.oa.graph.hive; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.schema.common.ModelSupport.tableIdentifier; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Oaf; + +public class GraphHiveTableImporterJob { + + private static final Logger log = LoggerFactory.getLogger(GraphHiveTableImporterJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GraphHiveTableImporterJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json"))); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String hiveDbName = parser.get("hiveDbName"); + log.info("hiveDbName: {}", hiveDbName); + + final String className = parser.get("className"); + log.info("className: {}", className); + + Class clazz = (Class) Class.forName(className); + + String hiveMetastoreUris = parser.get("hiveMetastoreUris"); + log.info("hiveMetastoreUris: {}", hiveMetastoreUris); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", hiveMetastoreUris); + + runWithSparkHiveSession( + conf, isSparkSessionManaged, spark -> loadGraphTable(spark, inputPath, hiveDbName, clazz)); + } + + // protected for testing + private static void loadGraphTable(SparkSession spark, String inputPath, String hiveDbName, + Class clazz) { + + spark + .read() + .textFile(inputPath) + .map((MapFunction) s -> OBJECT_MAPPER.readValue(s, clazz), Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .saveAsTable(tableIdentifier(hiveDbName, clazz)); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/reset_db.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/reset_db.sql new file mode 100644 index 0000000000..484afde804 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/reset_db.sql @@ -0,0 +1,2 @@ +DROP DATABASE IF EXISTS ${hiveDbName} CASCADE; +CREATE DATABASE ${hiveDbName}; \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index e837ac6b31..2bcbbba5eb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -72,18 +72,44 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + + + + + hive.metastore.uris + ${hiveMetastoreUris} + + + ${hiveJdbcUrl}/${hiveDbName} + + hiveDbName=${hiveDbName} + + + + + + + + + + + + + + + + yarn cluster - MapGraphAsHiveDB - eu.dnetlib.dhp.oa.graph.hive.GraphHiveImporterJob + Import table publication + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -95,18 +121,175 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --inputPath${inputPath} + --inputPath${inputPath}/publication --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Publication --hiveMetastoreUris${hiveMetastoreUris} - + + + + yarn + cluster + Import table dataset + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/dataset + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Dataset + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + + yarn + cluster + Import table otherresearchproduct + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/otherresearchproduct + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + + yarn + cluster + Import table software + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/software + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Software + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + + yarn + cluster + Import table datasource + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/datasource + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Datasource + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + + yarn + cluster + Import table organization + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/organization + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Organization + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + + yarn + cluster + Import table project + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/project + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Project + --hiveMetastoreUris${hiveMetastoreUris} + + + + + + + - ${jobTracker} - ${nameNode} hive.metastore.uris @@ -122,4 +305,5 @@ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_db_importer_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_db_importer_parameters.json new file mode 100644 index 0000000000..d6c13773ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_db_importer_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "hmu", + "paramLongName": "hiveMetastoreUris", + "paramDescription": "the hive metastore uris", + "paramRequired": true + }, + { + "paramName": "db", + "paramLongName": "hiveDbName", + "paramDescription": "the target hive database name", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json new file mode 100644 index 0000000000..5b5b0743c7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "hmu", + "paramLongName": "hiveMetastoreUris", + "paramDescription": "the hive metastore uris", + "paramRequired": true + }, + { + "paramName": "db", + "paramLongName": "hiveDbName", + "paramDescription": "the target hive database name", + "paramRequired": true + }, + { + "paramName": "tn", + "paramLongName": "className", + "paramDescription": "the class modelling the target table", + "paramRequired": true + } +] \ No newline at end of file From fd62359538d397cfd9e73a3602e38638a5a0ff1d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 09:28:15 +0200 Subject: [PATCH 18/70] cleanup --- .../graph/migrate_actionsets_parameters.json | 10 ---------- .../eu/dnetlib/dhp/oa/graph/scriptFile.scala | 0 .../transform_actionsets_parameters.json | 20 ------------------- 3 files changed, 30 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json deleted file mode 100644 index c4910ec61b..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json +++ /dev/null @@ -1,10 +0,0 @@ -[ - {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, - {"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true}, - {"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true}, - {"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true}, - {"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true}, - {"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true}, - {"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true} -] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json deleted file mode 100644 index 6fa10f7399..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, - { - "paramName": "is", - "paramLongName": "isLookupUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, - { - "paramName": "i", - "paramLongName": "inputPaths", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - } -] From 9d028ffe1c91c270482c75d5860e9f0222c01341 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 09:28:55 +0200 Subject: [PATCH 19/70] cleanup --- .../src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/scriptFile.scala deleted file mode 100644 index e69de29bb2..0000000000 From 18f46e47b915a3770e584765bce4e4d281f3668f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 09:34:48 +0200 Subject: [PATCH 20/70] added relations to the graph2hive import workflow --- .../dhp/oa/graph/hive/oozie_app/workflow.xml | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index 2bcbbba5eb..8566d76670 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -102,6 +102,7 @@ + @@ -286,6 +287,32 @@ + + + yarn + cluster + Import table project + eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${inputPath}/relation + --hiveDbName${hiveDbName} + --classNameeu.dnetlib.dhp.schema.oaf.Relation + --hiveMetastoreUris${hiveMetastoreUris} + + + + + From 50d6a2ad3c2f6fe19a52ff279749bd5633917fd6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 09:53:37 +0200 Subject: [PATCH 21/70] added output directory removal in the blacklist spark actions; included common global properties in blacklist's workflow.xml --- .../blacklist/PrepareMergedRelationJob.java | 7 ++++ .../SparkRemoveBlacklistedRelationJob.java | 7 +++- .../dhp/blacklist/oozie_app/workflow.xml | 37 +++++++++++-------- 3 files changed, 34 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java index 0ef59e8c2b..2a46043e20 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Optional; +import eu.dnetlib.dhp.common.HdfsSupport; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -56,6 +57,7 @@ public class PrepareMergedRelationJob { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); selectMergesRelations( spark, inputPath, @@ -84,4 +86,9 @@ public class PrepareMergedRelationJob { (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), Encoders.bean(Relation.class)); } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + } diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java index 86587bfc90..fe4310217c 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Objects; import java.util.Optional; +import eu.dnetlib.dhp.common.HdfsSupport; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -62,6 +63,7 @@ public class SparkRemoveBlacklistedRelationJob { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); removeBlacklistedRelations( spark, blacklistPath, @@ -69,7 +71,6 @@ public class SparkRemoveBlacklistedRelationJob { outputPath, mergesPath); }); - } private static void removeBlacklistedRelations(SparkSession spark, String blacklistPath, String inputPath, @@ -144,4 +145,8 @@ public class SparkRemoveBlacklistedRelationJob { Encoders.bean(Relation.class)); } + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + } diff --git a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml index 1538318c14..dd7827da4e 100644 --- a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml @@ -22,6 +22,25 @@ + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -49,8 +68,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/publication ${nameNode}/${outputPath}/publication @@ -60,8 +77,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/dataset ${nameNode}/${outputPath}/dataset @@ -71,8 +86,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/otherresearchproduct ${nameNode}/${outputPath}/otherresearchproduct @@ -82,8 +95,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/software ${nameNode}/${outputPath}/software @@ -93,8 +104,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/organization ${nameNode}/${outputPath}/organization @@ -104,8 +113,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/project ${nameNode}/${outputPath}/project @@ -115,8 +122,6 @@ - ${jobTracker} - ${nameNode} ${nameNode}/${sourcePath}/datasource ${nameNode}/${outputPath}/datasource @@ -128,8 +133,6 @@ - ${jobTracker} - ${nameNode} eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB --hdfsPath${workingDir}/blacklist --hdfsNameNode${nameNode} @@ -156,6 +159,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath}/relation --outputPath${workingDir}/mergesRelation @@ -180,6 +184,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath}/relation --outputPath${outputPath}/relation From b7e198475a7fdfacf5cdc3ea39d35f58af657d0c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 10:20:07 +0200 Subject: [PATCH 22/70] added common methods to create HiveDB table identifiers --- .../dhp/schema/common/ModelSupport.java | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java index fc85b1ac14..9ee7c2debc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java @@ -1,10 +1,15 @@ package eu.dnetlib.dhp.schema.common; +import static com.google.common.base.Preconditions.checkArgument; + import java.util.Map; +import java.util.Objects; import java.util.Optional; import java.util.function.Function; +import org.apache.commons.lang3.StringUtils; + import com.google.common.collect.Maps; import eu.dnetlib.dhp.schema.oaf.*; @@ -379,6 +384,21 @@ public class ModelSupport { entityMapping.get(EntityType.valueOf(targetType)).name()); } + public static String tableIdentifier(String dbName, String tableName) { + + checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty"); + checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty"); + + return String.format("%s.%s", dbName, tableName); + } + + public static String tableIdentifier(String dbName, Class clazz) { + + checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null"); + + return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase()); + } + public static Function idFn() { return x -> { if (isSubClass(x, Relation.class)) { From a83265829608c6a318e0a35cbdc7abc95dd9d1b6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 10:21:09 +0200 Subject: [PATCH 23/70] code formatting --- .../dhp/blacklist/PrepareMergedRelationJob.java | 2 +- .../blacklist/SparkRemoveBlacklistedRelationJob.java | 2 +- .../java/eu/dnetlib/dhp/PropagationConstant.java | 4 ++-- .../PrepareDatasourceCountryAssociation.java | 2 +- .../PrepareResultOrcidAssociationStep1.java | 5 ++--- .../SparkOrcidToResultFromSemRelJob.java | 8 ++++---- .../PrepareProjectResultsAssociation.java | 2 +- .../SparkResultToProjectThroughSemRelJob.java | 6 +++--- .../PrepareResultCommunitySet.java | 2 +- .../PrepareResultInstRepoAssociation.java | 2 +- .../SparkResultToOrganizationFromIstRepoJob.java | 8 ++++---- .../oa/graph/raw/MigrateDbEntitiesApplication.java | 12 ++++++------ 12 files changed, 27 insertions(+), 28 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java index 2a46043e20..b4bcc509ee 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java @@ -5,7 +5,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Optional; -import eu.dnetlib.dhp.common.HdfsSupport; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -19,6 +18,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.Relation; public class PrepareMergedRelationJob { diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java index fe4310217c..92289ec2d3 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Objects; import java.util.Optional; -import eu.dnetlib.dhp.common.HdfsSupport; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -19,6 +18,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 13ed46508a..c8eb017c71 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -4,8 +4,6 @@ package eu.dnetlib.dhp; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -17,6 +15,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; public class PropagationConstant { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 1d01d35e5f..98b573102a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Arrays; import java.util.List; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -22,6 +21,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; /** diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index 6549d1ed29..b15f813acd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -95,8 +95,7 @@ public class PrepareResultOrcidAssociationStep1 { Dataset result = readPath(spark, inputResultPath, resultClazz); result.createOrReplaceTempView("result"); - String query = - "SELECT target resultId, author authorList" + String query = "SELECT target resultId, author authorList" + " FROM (SELECT id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " + " FROM ( " + " SELECT DISTINCT id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " @@ -109,7 +108,7 @@ public class PrepareResultOrcidAssociationStep1 { + " SELECT source, target " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + getConstraintList(" relclass = '", allowedsemrel) + + getConstraintList(" relclass = '", allowedsemrel) + " ) rel_rel " + " ON source = id"; spark diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index fd1de3282d..bea847ca76 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -151,10 +151,10 @@ public class SparkOrcidToResultFromSemRelJob { // in one of the two else { if (autoritative_author - .getName() - .trim() - .substring(0, 0) - .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { + .getName() + .trim() + .substring(0, 0) + .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { toaddpid = true; } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java index 920ef1f06d..4cd7f88dff 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java @@ -8,7 +8,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.Arrays; import java.util.List; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -22,6 +21,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; public class PrepareProjectResultsAssociation { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index 44a439ab78..1f6264c186 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -9,7 +9,6 @@ import java.util.Iterator; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; @@ -21,6 +20,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -124,7 +124,7 @@ public class SparkResultToProjectThroughSemRelJob { resId, projectId, ModelConstants.IS_PRODUCED_BY, - ModelConstants.RESULT_PROJECT , + ModelConstants.RESULT_PROJECT, ModelConstants.OUTCOME, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, @@ -135,7 +135,7 @@ public class SparkResultToProjectThroughSemRelJob { projectId, resId, ModelConstants.PRODUCES, - ModelConstants.RESULT_PROJECT, + ModelConstants.RESULT_PROJECT, ModelConstants.OUTCOME, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index fc9f395d1b..5574aad753 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -18,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; public class PrepareResultCommunitySet { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java index 0a83e4195c..84e40fa88b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java @@ -4,7 +4,6 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -18,6 +17,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Relation; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index fc9a46d725..0ce741b873 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; @@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; @@ -151,7 +151,7 @@ public class SparkResultToOrganizationFromIstRepoJob { getRelation( orgId, resultId, - ModelConstants.IS_AUTHOR_INSTITUTION_OF, + ModelConstants.IS_AUTHOR_INSTITUTION_OF, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, PROPAGATION_DATA_INFO_TYPE, @@ -163,8 +163,8 @@ public class SparkResultToOrganizationFromIstRepoJob { resultId, orgId, ModelConstants.HAS_AUTHOR_INSTITUTION, - ModelConstants.RESULT_ORGANIZATION, - ModelConstants.AFFILIATION, + ModelConstants.RESULT_ORGANIZATION, + ModelConstants.AFFILIATION, PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index ebe2b703ba..5b8296c19b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -453,12 +453,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Boolean inferred = rs.getBoolean("inferred"); final String trust = rs.getString("trust"); return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - ENTITYREGISTRY_PROVENANCE_ACTION, - trust); + deletedbyinference, + inferenceprovenance, + inferred, + false, + ENTITYREGISTRY_PROVENANCE_ACTION, + trust); } private Qualifier prepareQualifierSplitting(final String s) { From 2a4e68a292d98e261527ab267c054cec9ae3aad9 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 15 May 2020 12:25:37 +0200 Subject: [PATCH 24/70] events recognition --- .../broker/oa/GenerateEventsApplication.java | 22 ++++---- .../EnrichMissingAbstract.java | 3 +- .../EnrichMissingAuthorOrcid.java | 3 +- .../oa/matchers/EnrichMissingOpenAccess.java | 55 +++++++++++++++++++ .../{util => matchers}/EnrichMissingPid.java | 19 ++++++- .../EnrichMissingProject.java | 6 +- .../EnrichMissingPublicationDate.java | 3 +- .../oa/matchers/EnrichMissingSubject.java | 53 ++++++++++++++++++ .../oa/matchers/EnrichMoreOpenAccess.java | 53 ++++++++++++++++++ .../oa/{util => matchers}/EnrichMorePid.java | 22 ++++++-- .../{util => matchers}/EnrichMoreSubject.java | 28 +++++++--- .../oa/{util => matchers}/UpdateMatcher.java | 3 +- .../dhp/broker/oa/util/BrokerConstants.java | 7 +++ .../dhp/broker/oa/util/ConversionUtils.java | 36 ++++++++++++ .../oa/util/EnrichMissingOpenAccess.java | 33 ----------- .../broker/oa/util/EnrichMissingSubject.java | 40 -------------- .../broker/oa/util/EnrichMoreOpenAccess.java | 33 ----------- .../dhp/broker/oa/util/UpdateInfo.java | 2 +- 18 files changed, 281 insertions(+), 140 deletions(-) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMissingAbstract.java (90%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMissingAuthorOrcid.java (91%) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMissingPid.java (60%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMissingProject.java (86%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMissingPublicationDate.java (89%) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMorePid.java (50%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/EnrichMoreSubject.java (51%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{util => matchers}/UpdateMatcher.java (94%) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index c4c167c13f..43ebd6dd84 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -17,18 +17,18 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAbstract; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAuthorOrcid; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingOpenAccess; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPid; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingProject; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPublicationDate; -import eu.dnetlib.dhp.broker.oa.util.EnrichMissingSubject; -import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess; -import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid; -import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.broker.oa.util.UpdateMatcher; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java index 6b6e35d1d6..43cf738f8c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMissingAbstract extends UpdateMatcher { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java index d81427e05c..beeccdbe84 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMissingAuthorOrcid extends UpdateMatcher> { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java new file mode 100644 index 0000000000..a4a2ea0c6c --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java @@ -0,0 +1,55 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; + +import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingOpenAccess extends UpdateMatcher { + + public EnrichMissingOpenAccess() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { + final long count = target + .getInstance() + .stream() + .map(i -> i.getAccessright().getClassid()) + .filter(right -> right.equals(BrokerConstants.OPEN_ACCESS)) + .count(); + + if (count > 0) { + return Arrays.asList(); + } + + return source + .getInstance() + .stream() + .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(s -> s) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + } + + @Override + public UpdateInfo generateUpdateInfo(final Instance highlightValue, + final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_OA_VERSION, + highlightValue, source, target, + (p, i) -> p.getInstances().add(i), + Instance::getUrl); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java similarity index 60% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java index 0b4045a0e4..a8df62541e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java @@ -1,11 +1,14 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.List; +import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMissingPid extends UpdateMatcher { @@ -16,8 +19,18 @@ public class EnrichMissingPid extends UpdateMatcher { @Override protected List> findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); + final long count = target.getPid().size(); + + if (count > 0) { + return Arrays.asList(); + } + + return source + .getPid() + .stream() + .map(ConversionUtils::oafPidToBrokerPid) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java similarity index 86% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java index 45b16801c2..b6e5b3b574 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.List; import eu.dnetlib.broker.objects.Project; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMissingProject extends UpdateMatcher { @@ -21,7 +22,8 @@ public class EnrichMissingProject extends UpdateMatcher { } @Override - public UpdateInfo generateUpdateInfo(final Project highlightValue, final Result source, + public UpdateInfo generateUpdateInfo(final Project highlightValue, + final Result source, final Result target) { return new UpdateInfo<>( Topic.ENRICH_MISSING_PROJECT, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java similarity index 89% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java index 7fcd2a66f9..e9ec082c46 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java @@ -1,10 +1,11 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMissingPublicationDate extends UpdateMatcher { diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java new file mode 100644 index 0000000000..79e9d469be --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class EnrichMissingSubject extends UpdateMatcher> { + + public EnrichMissingSubject() { + super(true); + } + + @Override + protected List>> findUpdates(final Result source, final Result target) { + final Set existingTypes = target + .getSubject() + .stream() + .map(StructuredProperty::getQualifier) + .map(Qualifier::getClassid) + .collect(Collectors.toSet()); + + return source + .getPid() + .stream() + .filter(pid -> !existingTypes.contains(pid.getQualifier().getClassid())) + .map(ConversionUtils::oafSubjectToPair) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + } + + @Override + public UpdateInfo> generateUpdateInfo(final Pair highlightValue, + final Result source, + final Result target) { + + return new UpdateInfo<>( + Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()), + highlightValue, source, target, + (p, pair) -> p.getSubjects().add(pair.getRight()), + pair -> pair.getLeft() + "::" + pair.getRight()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java new file mode 100644 index 0000000000..40c9b0500a --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMoreOpenAccess extends UpdateMatcher { + + public EnrichMoreOpenAccess() { + super(true); + } + + @Override + protected List> findUpdates(final Result source, final Result target) { + final Set urls = target + .getInstance() + .stream() + .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) + .map(i -> i.getUrl()) + .flatMap(List::stream) + .collect(Collectors.toSet()); + + return source + .getInstance() + .stream() + .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(s -> s) + .filter(i -> !urls.contains(i.getUrl())) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + } + + @Override + public UpdateInfo generateUpdateInfo(final Instance highlightValue, + final Result source, + final Result target) { + return new UpdateInfo<>( + Topic.ENRICH_MORE_OA_VERSION, + highlightValue, source, target, + (p, i) -> p.getInstances().add(i), + Instance::getUrl); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java similarity index 50% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java index 8cd67f5536..0e7b7766ab 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java @@ -1,11 +1,14 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; -import java.util.Arrays; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMorePid extends UpdateMatcher { @@ -16,8 +19,19 @@ public class EnrichMorePid extends UpdateMatcher { @Override protected List> findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); + final Set existingPids = target + .getPid() + .stream() + .map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue()) + .collect(Collectors.toSet()); + + return source + .getPid() + .stream() + .filter(pid -> !existingPids.contains(pid.getQualifier().getClassid() + "::" + pid.getValue())) + .map(ConversionUtils::oafPidToBrokerPid) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); } @Override diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java similarity index 51% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java index 9e0d8e6939..e6374479bf 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java @@ -1,12 +1,15 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; -import java.util.Arrays; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; public class EnrichMoreSubject extends UpdateMatcher> { @@ -17,18 +20,25 @@ public class EnrichMoreSubject extends UpdateMatcher> { @Override protected List>> findUpdates(final Result source, final Result target) { - // MESHEUROPMC - // ARXIV - // JEL - // DDC - // ACM + final Set existingSubjects = target + .getSubject() + .stream() + .map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue()) + .collect(Collectors.toSet()); - return Arrays.asList(); + return source + .getPid() + .stream() + .filter(pid -> !existingSubjects.contains(pid.getQualifier().getClassid() + "::" + pid.getValue())) + .map(ConversionUtils::oafSubjectToPair) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); } @Override public UpdateInfo> generateUpdateInfo(final Pair highlightValue, - final Result source, final Result target) { + final Result source, + final Result target) { return new UpdateInfo<>( Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()), diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java similarity index 94% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index 3fd6d40276..b8b6132cd1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.util; +package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.Collection; @@ -10,6 +10,7 @@ import java.util.Map; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.lang3.StringUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java new file mode 100644 index 0000000000..d61d5bfb7d --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java @@ -0,0 +1,7 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +public class BrokerConstants { + + public final static String OPEN_ACCESS = "OPEN"; +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java new file mode 100644 index 0000000000..2e2ce202ad --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.util.stream.Stream; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class ConversionUtils { + + public static Stream oafInstanceToBrokerInstances(final eu.dnetlib.dhp.schema.oaf.Instance i) { + return i.getUrl().stream().map(url -> { + final Instance r = new Instance(); + r.setUrl(url); + r.setInstancetype(i.getInstancetype().getClassid()); + r.setLicense(BrokerConstants.OPEN_ACCESS); + r.setHostedby(i.getHostedby().getValue()); + return r; + }); + } + + public static Pid oafPidToBrokerPid(final StructuredProperty sp) { + final Pid pid = new Pid(); + pid.setValue(sp.getValue()); + pid.setType(sp.getQualifier().getClassid()); + return pid; + } + + public static final Pair oafSubjectToPair(final StructuredProperty sp) { + return Pair.of(sp.getQualifier().getClassid(), sp.getValue()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java deleted file mode 100644 index 9079ee24b0..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingOpenAccess.java +++ /dev/null @@ -1,33 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util; - -import java.util.Arrays; -import java.util.List; - -import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingOpenAccess extends UpdateMatcher { - - public EnrichMissingOpenAccess() { - super(true); - } - - @Override - protected List> findUpdates(final Result source, final Result target) { - - return Arrays.asList(); - } - - @Override - public UpdateInfo generateUpdateInfo(final Instance highlightValue, final Result source, - final Result target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_OA_VERSION, - highlightValue, source, target, - (p, i) -> p.getInstances().add(i), - Instance::getUrl); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java deleted file mode 100644 index 4470bd9d98..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMissingSubject.java +++ /dev/null @@ -1,40 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingSubject extends UpdateMatcher> { - - public EnrichMissingSubject() { - super(true); - } - - @Override - protected List>> findUpdates(final Result source, final Result target) { - // MESHEUROPMC - // ARXIV - // JEL - // DDC - // ACM - - return Arrays.asList(); - } - - @Override - public UpdateInfo> generateUpdateInfo(final Pair highlightValue, - final Result source, final Result target) { - - return new UpdateInfo<>( - Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()), - highlightValue, source, target, - (p, pair) -> p.getSubjects().add(pair.getRight()), - pair -> pair.getLeft() + "::" + pair.getRight()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java deleted file mode 100644 index bc37ce659a..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EnrichMoreOpenAccess.java +++ /dev/null @@ -1,33 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util; - -import java.util.Arrays; -import java.util.List; - -import eu.dnetlib.broker.objects.Instance; -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMoreOpenAccess extends UpdateMatcher { - - public EnrichMoreOpenAccess() { - super(true); - } - - @Override - protected List> findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); - } - - @Override - public UpdateInfo generateUpdateInfo(final Instance highlightValue, final Result source, - final Result target) { - return new UpdateInfo<>( - Topic.ENRICH_MORE_OA_VERSION, - highlightValue, source, target, - (p, i) -> p.getInstances().add(i), - Instance::getUrl); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index 1dfc14e5eb..5cc0d371db 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -25,7 +25,7 @@ public final class UpdateInfo { private final float trust; - protected UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target, + public UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target, final BiConsumer compileHighlight, final Function highlightToString) { this.topic = topic; From cfc8948717b4f5da506af7fc3c0a3d230ecb4c69 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 12:26:16 +0200 Subject: [PATCH 25/70] fixed mapping OdfToGraph: pick the correct element to map author pids and author affiliations; extended mapping Oaf2Graph: added support for author pids --- .../dhp/oa/graph/raw/OafToOafMapper.java | 20 +++++-- .../dhp/oa/graph/raw/OdfToOafMapper.java | 8 +-- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 55 +++++++++++++++++-- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 2 +- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 3 +- 5 files changed, 71 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 891fee57e8..6b6aa15e88 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,15 +1,16 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; +import org.dom4j.Element; import org.dom4j.Node; import com.google.common.collect.Lists; @@ -28,15 +29,24 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List res = new ArrayList<>(); int pos = 1; for (final Object o : doc.selectNodes("//dc:creator")) { - final Node n = (Node) o; + final Element e = (Element) o; final Author author = new Author(); - author.setFullname(n.getText()); + author.setFullname(e.getText()); author.setRank(pos++); - final PacePerson p = new PacePerson(n.getText(), false); + final PacePerson p = new PacePerson(e.getText(), false); if (p.isAccurate()) { author.setName(p.getNormalisedFirstName()); author.setSurname(p.getNormalisedSurname()); } + + final String pid = e.attributeValue("nameIdentifier"); + final String pidType = e.attributeValue("nameIdentifierScheme"); + + if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) { + author.setPid(new ArrayList<>()); + author.getPid().add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); + } + res.add(author); } return res; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 5baac12fd0..30b980c422 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -63,17 +63,17 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { author.setSurname(surname); } - author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info)); - author.setPid(preparePids(doc, info)); + author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); + author.setPid(preparePids(n, info)); author.setRank(pos++); res.add(author); } return res; } - private List preparePids(final Document doc, final DataInfo info) { + private List preparePids(final Node n, final DataInfo info) { final List res = new ArrayList<>(); - for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) { + for (final Object o : n.selectNodes("./datacite:nameIdentifier")) { res .add( structuredProperty( 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 951c97d9de..d7635c9ea3 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 @@ -10,7 +10,10 @@ import static org.mockito.Mockito.when; import java.io.IOException; import java.util.List; import java.util.Map; +import java.util.Optional; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -19,12 +22,6 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; - @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -54,7 +51,26 @@ public class MappersTest { assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertTrue(p.getAuthor().size() > 0); + Optional author = p.getAuthor() + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .findFirst(); + assertTrue(author.isPresent()); + StructuredProperty pid = author.get().getPid() + .stream() + .findFirst() + .get(); + assertEquals("0000-0001-6651-1178", pid.getValue()); + assertEquals("ORCID", pid.getQualifier().getClassid()); + assertEquals("ORCID", pid.getQualifier().getClassname()); + assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid()); + assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename()); + assertEquals("Votsi,Nefta", author.get().getFullname()); + assertEquals("Votsi", author.get().getSurname()); + assertEquals("Nefta", author.get().getName()); + assertTrue(p.getSubject().size() > 0); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); @@ -100,6 +116,33 @@ public class MappersTest { assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); + + Optional author = d.getAuthor() + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .findFirst(); + assertTrue(author.isPresent()); + StructuredProperty pid = author.get().getPid() + .stream() + .findFirst() + .get(); + assertEquals("0000-0001-9074-1619", pid.getValue()); + assertEquals("ORCID", pid.getQualifier().getClassid()); + assertEquals("ORCID", pid.getQualifier().getClassname()); + assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid()); + assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename()); + assertEquals("Baracchini, Theo", author.get().getFullname()); + assertEquals("Baracchini", author.get().getSurname()); + assertEquals("Theo", author.get().getName()); + + assertEquals(1, author.get().getAffiliation().size()); + Optional> opAff = author.get().getAffiliation() + .stream() + .findFirst(); + assertTrue(opAff.isPresent()); + Field affiliation = opAff.get(); + assertEquals("ISTI-CNR", affiliation.getValue()); + assertTrue(d.getSubject().size() > 0); assertTrue(d.getInstance().size() > 0); assertTrue(d.getContext().size() > 0); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index e898d4434f..2cb0ba1c78 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -19,7 +19,7 @@ Ecosystem Service capacity is higher in areas of multiple designation types Nikolaidou,Charitini - Votsi,Nefta + Votsi,Nefta Sgardelis,Steanos Halley,John Pantis,John diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 94dc802fac..88ae9d1063 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -35,9 +35,10 @@ Baracchini, Theo + 0000-0001-9074-1619 Theo Baracchini - Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland + ISTI-CNR Wüest, Alfred From 5ec8c49ad5144d056512ac25ea3a8444e71ca4f1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 15 May 2020 12:49:58 +0200 Subject: [PATCH 26/70] removed serialization points --- .../dhp/blacklist/SparkRemoveBlacklistedRelationJob.java | 7 ------- 1 file changed, 7 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java index 92289ec2d3..91bcb9d1c7 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java @@ -79,8 +79,6 @@ public class SparkRemoveBlacklistedRelationJob { Dataset inputRelation = readRelations(spark, inputPath); Dataset mergesRelation = readRelations(spark, mergesPath); - log.info("InputRelationCount: {}", inputRelation.count()); - Dataset dedupSource = blackListed .joinWith( mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")), @@ -103,11 +101,6 @@ public class SparkRemoveBlacklistedRelationJob { return c._1(); }, Encoders.bean(Relation.class)); - dedupBL - .write() - .mode(SaveMode.Overwrite) - .json(blacklistPath + "/deduped"); - inputRelation .joinWith( dedupBL, (inputRelation From 7a89507ab1b1f347cdcfb46ffa8a908072aed057 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 15:16:54 +0200 Subject: [PATCH 27/70] code formatting --- .../dhp/oa/graph/raw/OafToOafMapper.java | 6 ++- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 51 +++++++++++-------- 2 files changed, 34 insertions(+), 23 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 6b6aa15e88..54594cb803 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -16,6 +15,7 @@ import org.dom4j.Node; import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -44,7 +44,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) { author.setPid(new ArrayList<>()); - author.getPid().add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); + author + .getPid() + .add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); } res.add(author); 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 d7635c9ea3..5a006e3513 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 @@ -12,8 +12,6 @@ import java.util.List; import java.util.Map; import java.util.Optional; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -22,6 +20,9 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; + @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -53,15 +54,18 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(p.getAuthor().size() > 0); - Optional author = p.getAuthor() - .stream() - .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) - .findFirst(); + Optional author = p + .getAuthor() + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .findFirst(); assertTrue(author.isPresent()); - StructuredProperty pid = author.get().getPid() - .stream() - .findFirst() - .get(); + StructuredProperty pid = author + .get() + .getPid() + .stream() + .findFirst() + .get(); assertEquals("0000-0001-6651-1178", pid.getValue()); assertEquals("ORCID", pid.getQualifier().getClassid()); assertEquals("ORCID", pid.getQualifier().getClassname()); @@ -117,15 +121,18 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); - Optional author = d.getAuthor() - .stream() - .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) - .findFirst(); + Optional author = d + .getAuthor() + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .findFirst(); assertTrue(author.isPresent()); - StructuredProperty pid = author.get().getPid() - .stream() - .findFirst() - .get(); + StructuredProperty pid = author + .get() + .getPid() + .stream() + .findFirst() + .get(); assertEquals("0000-0001-9074-1619", pid.getValue()); assertEquals("ORCID", pid.getQualifier().getClassid()); assertEquals("ORCID", pid.getQualifier().getClassname()); @@ -136,9 +143,11 @@ public class MappersTest { assertEquals("Theo", author.get().getName()); assertEquals(1, author.get().getAffiliation().size()); - Optional> opAff = author.get().getAffiliation() - .stream() - .findFirst(); + Optional> opAff = author + .get() + .getAffiliation() + .stream() + .findFirst(); assertTrue(opAff.isPresent()); Field affiliation = opAff.get(); assertEquals("ISTI-CNR", affiliation.getValue()); From 82b615ab33be893b8527c0629b6a1e228fd80393 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 16:04:46 +0200 Subject: [PATCH 28/70] NPE check --- .../src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java index d3ae8ee4f9..a6ec364c4b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java @@ -129,6 +129,9 @@ public class DedupUtility { .max(Comparator.comparing(Tuple2::_1)); if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { Author r = simAuhtor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } r.getPid().add(a._1()); } }); From 7838f2c63fb99e956aaf4bed024363b0c3f54178 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 17:06:01 +0200 Subject: [PATCH 29/70] init the empty list for author pids mapped from OAF --- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 54594cb803..ed09016da8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -42,8 +42,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final String pid = e.attributeValue("nameIdentifier"); final String pidType = e.attributeValue("nameIdentifierScheme"); + author.setPid(new ArrayList<>()); if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) { - author.setPid(new ArrayList<>()); author .getPid() .add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); From ef9a9a9f1af74f49fe0d4dda802d33790a84c4a6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 May 2020 22:34:19 +0200 Subject: [PATCH 30/70] remove the outout path when starting --- .../PrepareResultCommunitySetStep2.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java index 723aa89606..09340369d3 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java @@ -53,9 +53,7 @@ public class PrepareResultCommunitySetStep2 { conf, isSparkSessionManaged, spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } + removeOutputDir(spark, outputPath); mergeInfo(spark, inputPath, outputPath); }); } From b71fbb68b16cb1515614f16237d8fa8196871d29 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 May 2020 13:57:20 +0200 Subject: [PATCH 31/70] removed the removeOutputDir command from code. Reltions are written in Append. The erase of the output dir ment to remove all the relations computed in the prevoius steps --- .../SparkResultToOrganizationFromIstRepoJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index 0ce741b873..0c5e1d8be6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -84,7 +84,7 @@ public class SparkResultToOrganizationFromIstRepoJob { conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, outputPath); + // removeOutputDir(spark, outputPath); if (saveGraph) { execPropagation( spark, From f3bc8aed31f8e865fbb54d9afc4d5d6130baedfc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 18 May 2020 15:29:10 +0200 Subject: [PATCH 32/70] lifted memory requirements for country propagation wf --- .../src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml index 7c918a0d70..487afee4fa 100644 --- a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml @@ -521,6 +521,8 @@ { 'oozie.wf.application.path' : '/lib/dnet/oa/enrichment/country/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', 'workingDir' : '/tmp/beta_provision/working_dir/country', 'allowedtypes' : 'pubsrepository::institutional', 'whitelist' : '10|opendoar____::300891a62162b960cf02ce3827bb363c', From 0bdfbb0a5794125b4bcbd761a0490d708997bbdd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 May 2020 15:02:21 +0200 Subject: [PATCH 33/70] reintroduced RDD based relation cut off procedure --- .../dhp/oa/provision/PrepareRelationsJob.java | 48 ++++++++++++++----- .../oa/provision/model/SortableRelation.java | 6 +-- .../input_params_prepare_relations.json | 14 +++++- .../dhp/oa/provision/oozie_app/workflow.xml | 4 +- 4 files changed, 56 insertions(+), 16 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index dbdc54fc04..32a20d62c4 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -3,7 +3,9 @@ package eu.dnetlib.dhp.oa.provision; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.HashSet; import java.util.Optional; +import java.util.Set; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -15,17 +17,21 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.sources.In; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.base.Splitter; import com.google.common.collect.Iterables; import com.google.common.collect.Iterators; +import com.google.common.collect.Sets; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner; +import scala.Int; import scala.Tuple2; /** @@ -58,6 +64,8 @@ public class PrepareRelationsJob { public static final int MAX_RELS = 100; + public static final int DEFAULT_NUM_PARTITIONS = 3000; + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -79,6 +87,24 @@ public class PrepareRelationsJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); + int relPartitions = Optional + .ofNullable(parser.get("relPartitions")) + .map(Integer::valueOf) + .orElse(DEFAULT_NUM_PARTITIONS); + log.info("relPartitions: {}", relPartitions); + + Set relationFilter = Optional + .ofNullable(parser.get("relationFilter")) + .map(s -> Sets.newHashSet(Splitter.on(",").split(s))) + .orElse(new HashSet<>()); + log.info("relationFilter: {}", relationFilter); + + int maxRelations = Optional + .ofNullable(parser.get("maxRelations")) + .map(Integer::valueOf) + .orElse(MAX_RELS); + log.info("maxRelations: {}", maxRelations); + SparkConf conf = new SparkConf(); runWithSparkSession( @@ -86,12 +112,13 @@ public class PrepareRelationsJob { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareRelationsFromPaths(spark, inputRelationsPath, outputPath); + prepareRelationsRDDFromPaths( + spark, inputRelationsPath, outputPath, relationFilter, relPartitions, maxRelations); }); } private static void prepareRelationsFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath) { + SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter) { readPathRelation(spark, inputRelationsPath) .filter("dataInfo.deletedbyinference == false") .groupByKey( @@ -125,20 +152,19 @@ public class PrepareRelationsJob { // TODO work in progress private static void prepareRelationsRDDFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { - JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath).repartition(numPartitions); + SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter, int relPartitions, + int maxRelations) { + JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath).repartition(relPartitions); + // only consider those that are not virtually deleted RDD d = rels - .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) // only - // consider - // those - // that are not virtually - // deleted + .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) + .filter(rel -> !relationFilter.contains(rel.getRelClass())) .mapToPair( (PairFunction) rel -> new Tuple2<>(rel, rel)) .groupByKey(new RelationPartitioner(rels.getNumPartitions())) - .map(p -> Iterables.limit(p._2(), MAX_RELS)) - .flatMap(p -> p.iterator()) + .map(group -> Iterables.limit(group._2(), maxRelations)) + .flatMap(group -> group.iterator()) .rdd(); spark diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java index 7c866001be..b6571b9bf9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java @@ -16,10 +16,10 @@ public class SortableRelation extends Relation implements Comparable, static { weights.put("outcome", 0); weights.put("supplement", 1); - weights.put("publicationDataset", 2); + weights.put("affiliation", 2); weights.put("relationship", 3); - weights.put("similarity", 4); - weights.put("affiliation", 5); + weights.put("publicationDataset", 4); + weights.put("similarity", 5); weights.put("provision", 6); weights.put("participation", 7); diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json index bfb248d012..5ce37aa7be 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json @@ -21,6 +21,18 @@ "paramName": "rp", "paramLongName": "relPartitions", "paramDescription": "number or partitions for the relations Dataset", - "paramRequired": true + "paramRequired": false + }, + { + "paramName": "rf", + "paramLongName": "relationFilter", + "paramDescription": "filter applied reading relations (by relClass)", + "paramRequired": false + }, + { + "paramName": "mr", + "paramLongName": "maxRelations", + "paramDescription": "maximum number of relations applied reading relations (by relClass)", + "paramRequired": false } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 298ac75892..a84db86880 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -102,7 +102,9 @@ --inputRelationsPath${inputGraphRootPath}/relation --outputPath${workingDir}/relation - --relPartitions3000 + --relPartitions${relPartitions} + --relationFilter${relationFilter} + --maxRelations${maxRelations} From 85ca5622d45569683191713e0d0e06dfcd3f3fbf Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 19 May 2020 16:17:35 +0200 Subject: [PATCH 34/70] partial implementation of generation of simple events --- .../eu/dnetlib/dhp/broker/model/Topic.java | 63 ++++++++++------ .../broker/oa/GenerateEventsApplication.java | 74 +++++++++++++++++-- .../EnrichMissingPublicationDate.java | 10 ++- .../dhp/broker/oa/matchers/UpdateMatcher.java | 10 ++- 4 files changed, 120 insertions(+), 37 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java index 29f6cbe3af..98088dd0aa 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java @@ -4,31 +4,48 @@ package eu.dnetlib.dhp.broker.model; public enum Topic { // ENRICHMENT MISSING - ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT( - "ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE( - "ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID( - "ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE( - "ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC( - "ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV( - "ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL( - "ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC( - "ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM( - "ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK( - "ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID( - "ENRICH/MISSING/AUTHOR/ORCID"), + ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), + ENRICH_MISSING_ABSTRACT("ENRICH/MISSING/ABSTRACT"), + ENRICH_MISSING_PUBLICATION_DATE("ENRICH/MISSING/PUBLICATION_DATE"), + ENRICH_MISSING_PID("ENRICH/MISSING/PID"), + ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), + ENRICH_MISSING_SOFTWARE("ENRICH/MISSING/SOFTWARE"), + ENRICH_MISSING_SUBJECT_MESHEUROPMC("ENRICH/MISSING/SUBJECT/MESHEUROPMC"), + ENRICH_MISSING_SUBJECT_ARXIV("ENRICH/MISSING/SUBJECT/ARXIV"), + ENRICH_MISSING_SUBJECT_JEL("ENRICH/MISSING/SUBJECT/JEL"), + ENRICH_MISSING_SUBJECT_DDC("ENRICH/MISSING/SUBJECT/DDC"), + ENRICH_MISSING_SUBJECT_ACM("ENRICH/MISSING/SUBJECT/ACM"), + ENRICH_MISSING_SUBJECT_RVK("ENRICH/MISSING/SUBJECT/RVK"), + ENRICH_MISSING_AUTHOR_ORCID("ENRICH/MISSING/AUTHOR/ORCID"), // ENRICHMENT MORE - ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT( - "ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT( - "ENRICH/MORE/PROJECT"), ENRICH_MORE_SUBJECT_MESHEUROPMC( - "ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV( - "ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL( - "ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC( - "ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM( - "ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), + ENRICH_MORE_PID("ENRICH/MORE/PID"), + ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), + ENRICH_MORE_ABSTRACT("ENRICH/MORE/ABSTRACT"), + ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), + ENRICH_MORE_PROJECT("ENRICH/MORE/PROJECT"), + ENRICH_MORE_SUBJECT_MESHEUROPMC("ENRICH/MORE/SUBJECT/MESHEUROPMC"), + ENRICH_MORE_SUBJECT_ARXIV("ENRICH/MORE/SUBJECT/ARXIV"), + ENRICH_MORE_SUBJECT_JEL("ENRICH/MORE/SUBJECT/JEL"), + ENRICH_MORE_SUBJECT_DDC("ENRICH/MORE/SUBJECT/DDC"), + ENRICH_MORE_SUBJECT_ACM("ENRICH/MORE/SUBJECT/ACM"), + ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), // ADDITION - ADD_BY_PROJECT("ADD/BY_PROJECT"); + ADD_BY_PROJECT("ADD/BY_PROJECT"), + + // OTHER RELS + ENRICH_MISSING_PUBLICATION_IS_RELATED_TO("ENRICH/MISSING/PUBLICATION/IS_RELATED_TO"), + ENRICH_MISSING_PUBLICATION_REFERENCES("ENRICH/MISSING/PUBLICATION/REFERENCES"), + ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY("ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY"), + ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO"), + ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY"), + + ENRICH_MISSING_DATASET_IS_RELATED_TO("ENRICH/MISSING/DATASET/IS_RELATED_TO"), + ENRICH_MISSING_DATASET_REFERENCES("ENRICH/MISSING/DATASET/REFERENCES"), + ENRICH_MISSING_DATASET_IS_REFERENCED_BY("ENRICH/MISSING/DATASET/IS_REFERENCED_BY"), + ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO"), + ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY"); Topic(final String path) { this.path = path; @@ -42,9 +59,7 @@ public enum Topic { public static Topic fromPath(final String path) { for (final Topic t : Topic.values()) { - if (t.getPath().equals(path)) { - return t; - } + if (t.getPath().equals(path)) { return t; } } return null; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 43ebd6dd84..5fdd109252 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -9,11 +9,21 @@ import java.util.Optional; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Column; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; @@ -30,7 +40,11 @@ import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; public class GenerateEventsApplication { @@ -47,12 +61,13 @@ public class GenerateEventsApplication { private static final UpdateMatcher enrichMorePid = new EnrichMorePid(); private static final UpdateMatcher enrichMoreSubject = new EnrichMoreSubject(); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + .toString(GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -67,10 +82,23 @@ public class GenerateEventsApplication { final String eventsPath = parser.get("eventsPath"); log.info("eventsPath: {}", eventsPath); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); removeOutputDir(spark, eventsPath); - generateEvents(spark, graphPath, eventsPath); + + final JavaRDD eventsRdd = sc.emptyRDD(); + + eventsRdd.union(generateSimpleEvents(spark, graphPath, Publication.class)); + eventsRdd.union(generateSimpleEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class)); + eventsRdd.union(generateSimpleEvents(spark, graphPath, Software.class)); + eventsRdd.union(generateSimpleEvents(spark, graphPath, OtherResearchProduct.class)); + + eventsRdd.saveAsTextFile(eventsPath, GzipCodec.class); }); } @@ -79,11 +107,34 @@ public class GenerateEventsApplication { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void generateEvents(final SparkSession spark, final String graphPath, final String eventsPath) { - // TODO + private static JavaRDD generateSimpleEvents(final SparkSession spark, + final String graphPath, + final Class resultClazz) { + + final Dataset results = + readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz) + .filter(r -> r.getDataInfo().getDeletedbyinference()); + + final Dataset rels = + readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelClass().equals("TODO")); // TODO mergedIN + + final Column c = null; // TODO + + final Dataset aa = results.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner") + .groupBy(rels.col("target")) + .agg(c) + .filter(x -> x.size() > 1) + // generateSimpleEvents(...) + // flatMap() + // toRdd() + ; + + return null; + } - private List generateEvents(final Result... children) { + private List generateSimpleEvents(final Result... children) { final List> list = new ArrayList<>(); for (final Result target : children) { @@ -102,4 +153,13 @@ public class GenerateEventsApplication { return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); } + public static Dataset readPath( + final SparkSession spark, + final String inputPath, + final Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java index e9ec082c46..372a4e4c9d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.broker.oa.matchers; +import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -16,12 +17,15 @@ public class EnrichMissingPublicationDate extends UpdateMatcher { @Override protected List> findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); + if (isMissing(target.getDateofacceptance()) && !isMissing(source.getDateofacceptance())) { + return Arrays.asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target)); + } + return new ArrayList<>(); } @Override - public UpdateInfo generateUpdateInfo(final String highlightValue, final Result source, + public UpdateInfo generateUpdateInfo(final String highlightValue, + final Result source, final Result target) { return new UpdateInfo<>( Topic.ENRICH_MISSING_PUBLICATION_DATE, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index b8b6132cd1..d91b03200e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -30,8 +30,7 @@ public abstract class UpdateMatcher { if (source != res) { for (final UpdateInfo info : findUpdates(source, res)) { final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); - if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { - } else { + if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {} else { infoMap.put(s, info); } } @@ -54,11 +53,16 @@ public abstract class UpdateMatcher { protected abstract List> findUpdates(Result source, Result target); - protected abstract UpdateInfo generateUpdateInfo(final T highlightValue, final Result source, + protected abstract UpdateInfo generateUpdateInfo(final T highlightValue, + final Result source, final Result target); protected static boolean isMissing(final List> list) { return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue()); } + protected boolean isMissing(final Field field) { + return field == null || StringUtils.isBlank(field.getValue()); + } + } From d7d2a0637f262f3e51c519db78744ef8c713de0f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 20 May 2020 14:55:38 +0200 Subject: [PATCH 35/70] added extra parameters to the provision indexing workflow --- .../input_params_prepare_relations.json | 2 +- .../dhp/oa/provision/oozie_app/workflow.xml | 25 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json index 5ce37aa7be..71b2becc4d 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json @@ -32,7 +32,7 @@ { "paramName": "mr", "paramLongName": "maxRelations", - "paramDescription": "maximum number of relations applied reading relations (by relClass)", + "paramDescription": "maximum number of relations allowed for a each entity", "paramRequired": false } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index a84db86880..9600ccbaa4 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -9,6 +9,30 @@ isLookupUrl URL for the isLookup service + + relPartitions + number or partitions for the relations Dataset + + + relationFilter + filter applied reading relations (by relClass) + + + maxRelations + maximum number of relations allowed for a each entity + + + otherDsTypeId + mapping used to populate datasourceTypeUi field + + + format + metadata format name (DMF|TMF) + + + batchSize + number of records to be included in each indexing request + sparkDriverMemoryForJoining @@ -421,4 +445,5 @@ + \ No newline at end of file From b3bcbb3129fb26b3222e85cbfc7c421ab6fbeaa3 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 21 May 2020 08:41:32 +0200 Subject: [PATCH 36/70] resolve name of organization countries --- .../eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index aeb04aff91..4dbd1c4298 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -22,12 +22,13 @@ SELECT '' AS inferenceprovenance, d.id AS collectedfromid, d.officialname AS collectedfromname, - o.country || '@@@' || o.country || '@@@dnet:countries@@@dnet:countries' AS country, + o.country || '@@@' || cntr.name || '@@@dnet:countries@@@dnet:countries' AS country, 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, - ARRAY[]::text[] AS pid + FROM dsm_organizations o LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) + LEFT OUTER JOIN class cntr ON (cntr.code = o.country) From dbfb9c19fe12181c61ef0435937b298a863ed555 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 May 2020 10:00:14 +0200 Subject: [PATCH 37/70] minor changes --- .../dhp/oa/provision/PrepareRelationsJob.java | 82 ++++++++++++------- .../dhp/oa/provision/oozie_app/workflow.xml | 9 +- 2 files changed, 59 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java index 32a20d62c4..72d68a389e 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -17,7 +17,6 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.apache.spark.sql.sources.In; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -31,7 +30,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner; -import scala.Int; import scala.Tuple2; /** @@ -112,26 +110,74 @@ public class PrepareRelationsJob { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareRelationsRDDFromPaths( + prepareRelationsRDD( spark, inputRelationsPath, outputPath, relationFilter, relPartitions, maxRelations); }); } - private static void prepareRelationsFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter) { + /** + * Dataset based implementation that prepares the graph relations by limiting the number of outgoing links and + * filtering the relation types according to the given criteria. + * + * @param spark the spark session + * @param inputRelationsPath source path for the graph relations + * @param outputPath output path for the processed relations + * @param relationFilter set of relation filters applied to the `relClass` field + * @param maxRelations maximum number of allowed outgoing edges + */ + private static void prepareRelations( + SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter, + int maxRelations) { readPathRelation(spark, inputRelationsPath) .filter("dataInfo.deletedbyinference == false") + .filter((FilterFunction) rel -> !relationFilter.contains(rel.getRelClass())) .groupByKey( (MapFunction) value -> value.getSource(), Encoders.STRING()) .flatMapGroups( (FlatMapGroupsFunction) (key, values) -> Iterators - .limit(values, MAX_RELS), + .limit(values, maxRelations), Encoders.bean(SortableRelation.class)) .write() .mode(SaveMode.Overwrite) .parquet(outputPath); } + /** + * RDD based implementation that prepares the graph relations by limiting the number of outgoing links and filtering + * the relation types according to the given criteria. Moreover, outgoing links kept within the given limit are + * prioritized according to the weights indicated in eu.dnetlib.dhp.oa.provision.model.SortableRelation. + * + * @param spark the spark session + * @param inputRelationsPath source path for the graph relations + * @param outputPath output path for the processed relations + * @param relationFilter set of relation filters applied to the `relClass` field + * @param maxRelations maximum number of allowed outgoing edges + */ + // TODO work in progress + private static void prepareRelationsRDD( + SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter, int relPartitions, + int maxRelations) { + JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath).repartition(relPartitions); + RelationPartitioner partitioner = new RelationPartitioner(rels.getNumPartitions()); + + // only consider those that are not virtually deleted + RDD d = rels + .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) + .filter(rel -> !relationFilter.contains(rel.getRelClass())) + .mapToPair( + (PairFunction) rel -> new Tuple2<>(rel, rel)) + .groupByKey(partitioner) + .map(group -> Iterables.limit(group._2(), maxRelations)) + .flatMap(group -> group.iterator()) + .rdd(); + + spark + .createDataset(d, Encoders.bean(SortableRelation.class)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + /** * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text * file, @@ -150,30 +196,6 @@ public class PrepareRelationsJob { Encoders.bean(SortableRelation.class)); } - // TODO work in progress - private static void prepareRelationsRDDFromPaths( - SparkSession spark, String inputRelationsPath, String outputPath, Set relationFilter, int relPartitions, - int maxRelations) { - JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath).repartition(relPartitions); - - // only consider those that are not virtually deleted - RDD d = rels - .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) - .filter(rel -> !relationFilter.contains(rel.getRelClass())) - .mapToPair( - (PairFunction) rel -> new Tuple2<>(rel, rel)) - .groupByKey(new RelationPartitioner(rels.getNumPartitions())) - .map(group -> Iterables.limit(group._2(), maxRelations)) - .flatMap(group -> group.iterator()) - .rdd(); - - spark - .createDataset(d, Encoders.bean(SortableRelation.class)) - .write() - .mode(SaveMode.Overwrite) - .parquet(outputPath); - } - private static JavaRDD readPathRelationRDD( SparkSession spark, final String inputPath) { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 9600ccbaa4..fd8f5ba89a 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -80,6 +80,11 @@ spark2EventLogDir spark 2.* event log dir location + + sparkNetworkTimeout + configures spark.network.timeout + + @@ -357,7 +362,7 @@ --inputGraphRootPath${inputGraphRootPath} --inputRelatedEntitiesPath${workingDir}/join_partial --outputPath${workingDir}/join_entities - --numPartitions12000 + --numPartitions24000 @@ -381,7 +386,7 @@ --conf spark.sql.shuffle.partitions=7680 --conf spark.network.timeout=${sparkNetworkTimeout} - --inputPath ${workingDir}/join_entities + --inputPath${workingDir}/join_entities --outputPath${workingDir}/joined From e43d4d7778851846bb0f4f361996682d2c3056f4 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 21 May 2020 11:08:07 +0200 Subject: [PATCH 38/70] added a coalesce in sql query --- .../eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index 4dbd1c4298..d13bd43425 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -22,7 +22,7 @@ SELECT '' AS inferenceprovenance, d.id AS collectedfromid, d.officialname AS collectedfromname, - o.country || '@@@' || cntr.name || '@@@dnet:countries@@@dnet:countries' AS country, + o.country || '@@@' || COALESCE(cntr.name,o.country) || '@@@dnet:countries@@@dnet:countries' AS country, 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, ARRAY[]::text[] AS pid From 8bbd1d0501ada82c6a037e0379c71006723544ab Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 21 May 2020 11:52:14 +0200 Subject: [PATCH 39/70] reimplementation of the author merging in deduprecord creation. implementation of the test class. --- .../eu/dnetlib/dhp/oa/dedup/AuthorMerger.java | 159 ++++++++++++++++++ .../dhp/oa/dedup/DedupRecordFactory.java | 23 +-- .../eu/dnetlib/dhp/oa/dedup/DedupUtility.java | 112 ------------ .../dhp/oa/dedup/EntityMergerTest.java | 138 +++++++++++++++ .../dnetlib/dhp/oa/dedup/MergeAuthorTest.java | 54 ------ .../dhp/dedup/json/publication_merge.json | 3 + 6 files changed, 313 insertions(+), 176 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java new file mode 100644 index 0000000000..108f4a4bec --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -0,0 +1,159 @@ +package eu.dnetlib.dhp.oa.dedup; + +import com.wcohen.ss.JaroWinkler; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.model.Person; +import org.apache.commons.lang3.StringUtils; +import scala.Tuple2; + +import java.text.Normalizer; +import java.util.*; +import java.util.stream.Collectors; + +public class AuthorMerger { + + private static final Double THRESHOLD = 0.95; + + public static List merge(List> authors){ + + authors.sort(new Comparator>() { + @Override + public int compare(List o1, List o2) { + return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); + } + }); + + List author = new ArrayList<>(); + + for(List a : authors){ + author = mergeAuthor(author, a); + } + + return author; + + } + + public static List mergeAuthor(final List a, final List b) { + int pa = countAuthorsPids(a); + int pb = countAuthorsPids(b); + List base, enrich; + int sa = authorsSize(a); + int sb = authorsSize(b); + + if (pa == pb) { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; + } else { + base = pa > pb ? a : b; + enrich = pa > pb ? b : a; + } + enrichPidFromList(base, enrich); + return base; + } + + private static void enrichPidFromList(List base, List enrich) { + if (base == null || enrich == null) + return; + final Map basePidAuthorMap = base + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> a + .getPid() + .stream() + .map(p -> new Tuple2<>(pidToComparableString(p), a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + + final List> pidToEnrich = enrich + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> a + .getPid() + .stream() + .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) + .map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); + + pidToEnrich + .forEach( + a -> { + Optional> simAuthor = base + .stream() + .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) + .max(Comparator.comparing(Tuple2::_1)); + if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { + Author r = simAuthor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } + r.getPid().add(a._1()); + } + }); + } + + public static String pidToComparableString(StructuredProperty pid){ + return (pid.getQualifier()!=null? pid.getQualifier().getClassid()!=null?pid.getQualifier().getClassid().toLowerCase():"":"") + (pid.getValue()!=null? pid.getValue().toLowerCase():""); + } + + public static int countAuthorsPids(List authors) { + if (authors == null) + return 0; + + return (int) authors.stream().filter(AuthorMerger::hasPid).count(); + } + + private static int authorsSize(List authors) { + if (authors == null) + return 0; + return authors.size(); + } + + private static Double sim(Author a, Author b) { + + final Person pa = parse(a); + final Person pb = parse(b); + + if (pa.isAccurate() & pb.isAccurate()) { + return new JaroWinkler() + .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); + } else { + return new JaroWinkler() + .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); + } + } + + private static boolean hasPid(Author a) { + if (a == null || a.getPid() == null || a.getPid().size() == 0) + return false; + return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); + } + + private static Person parse(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return new Person(author.getSurname() + ", " + author.getName(), false); + } else { + return new Person(author.getFullname(), false); + } + } + + private static String normalize(final String s) { + return nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index fa06424d7a..eed783e536 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,8 +1,9 @@ - package eu.dnetlib.dhp.oa.dedup; +import java.io.Serializable; import java.util.Collection; import java.util.Iterator; +import java.util.List; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; @@ -67,16 +68,18 @@ public class DedupRecordFactory { (MapFunction, String>) entity -> entity._1(), Encoders.STRING()) .mapGroups( (MapGroupsFunction, T>) (key, - values) -> entityMerger(key, values, ts, dataInfo), + values) -> entityMerger(key, values, ts, dataInfo, clazz), Encoders.bean(clazz)); } - private static T entityMerger( - String id, Iterator> entities, long ts, DataInfo dataInfo) { + public static T entityMerger( + String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) throws IllegalAccessException, InstantiationException { - T entity = entities.next()._2(); + T entity = clazz.newInstance(); final Collection dates = Lists.newArrayList(); + final List> authors = Lists.newArrayList(); + entities .forEachRemaining( t -> { @@ -84,17 +87,17 @@ public class DedupRecordFactory { entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; - Result er = (Result) entity; - er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor())); - - if (r1.getDateofacceptance() != null) { + if (r1.getAuthor() != null && r1.getAuthor().size()>0) + authors.add(r1.getAuthor()); + if (r1.getDateofacceptance() != null) dates.add(r1.getDateofacceptance().getValue()); - } } }); + //set authors and date if (ModelSupport.isSubClass(entity, Result.class)) { ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); + ((Result) entity).setAuthor(AuthorMerger.merge(authors)); } entity.setId(id); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java index d3ae8ee4f9..222794d64d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java @@ -32,7 +32,6 @@ import eu.dnetlib.pace.model.Person; import scala.Tuple2; public class DedupUtility { - private static final Double THRESHOLD = 0.95; public static Map constructAccumulator( final DedupConfig dedupConf, final SparkContext context) { @@ -82,58 +81,6 @@ public class DedupUtility { } } - public static List mergeAuthor(final List a, final List b) { - int pa = countAuthorsPids(a); - int pb = countAuthorsPids(b); - List base, enrich; - int sa = authorsSize(a); - int sb = authorsSize(b); - - if (pa == pb) { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } else { - base = pa > pb ? a : b; - enrich = pa > pb ? b : a; - } - enrichPidFromList(base, enrich); - return base; - } - - private static void enrichPidFromList(List base, List enrich) { - if (base == null || enrich == null) - return; - final Map basePidAuthorMap = base - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap(a -> a.getPid().stream().map(p -> new Tuple2<>(p.toComparableString(), a))) - .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - - final List> pidToEnrich = enrich - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap( - a -> a - .getPid() - .stream() - .filter(p -> !basePidAuthorMap.containsKey(p.toComparableString())) - .map(p -> new Tuple2<>(p, a))) - .collect(Collectors.toList()); - - pidToEnrich - .forEach( - a -> { - Optional> simAuhtor = base - .stream() - .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) - .max(Comparator.comparing(Tuple2::_1)); - if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { - Author r = simAuhtor.get()._2(); - r.getPid().add(a._1()); - } - }); - } - public static String createDedupRecordPath( final String basePath, final String actionSetId, final String entityType) { return String.format("%s/%s/%s_deduprecord", basePath, actionSetId, entityType); @@ -153,65 +100,6 @@ public class DedupUtility { return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType); } - private static Double sim(Author a, Author b) { - - final Person pa = parse(a); - final Person pb = parse(b); - - if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler() - .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); - } else { - return new JaroWinkler() - .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); - } - } - - private static String normalize(final String s) { - return nfd(s) - .toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError - // in case - // of large input strings - .replaceAll("(\\W)+", " ") - .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") - .replaceAll("(\\p{Punct})+", " ") - .replaceAll("(\\d)+", " ") - .replaceAll("(\\n)+", " ") - .trim(); - } - - private static String nfd(final String s) { - return Normalizer.normalize(s, Normalizer.Form.NFD); - } - - private static Person parse(Author author) { - if (StringUtils.isNotBlank(author.getSurname())) { - return new Person(author.getSurname() + ", " + author.getName(), false); - } else { - return new Person(author.getFullname(), false); - } - } - - private static int countAuthorsPids(List authors) { - if (authors == null) - return 0; - - return (int) authors.stream().filter(DedupUtility::hasPid).count(); - } - - private static int authorsSize(List authors) { - if (authors == null) - return 0; - return authors.size(); - } - - private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().size() == 0) - return false; - return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); - } - public static List getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java new file mode 100644 index 0000000000..526dd73bb0 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -0,0 +1,138 @@ +package eu.dnetlib.dhp.oa.dedup; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.io.Serializable; +import java.nio.file.Paths; +import java.util.*; + +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.jupiter.api.BeforeEach; + +import org.junit.jupiter.api.Test; +import scala.Tuple2; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +public class EntityMergerTest implements Serializable { + + List> publications; + + String testEntityBasePath; + DataInfo dataInfo; + String dedupId = "dedup_id"; + Publication pub_top; + + @BeforeEach + public void setUp() throws Exception { + + testEntityBasePath = Paths + .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) + .toFile() + .getAbsolutePath(); + + publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); + + pub_top = getTopPub(publications); + + dataInfo = setDI(); + + } + + @Test + public void publicationMergerTest() throws InstantiationException, IllegalAccessException { + + Publication pub_merged = DedupRecordFactory.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); + + assertEquals(dedupId, pub_merged.getId()); + + assertEquals(pub_merged.getJournal(), pub_top.getJournal()); + assertEquals(pub_merged.getBestaccessright(), pub_top.getBestaccessright()); + assertEquals(pub_merged.getResulttype(), pub_top.getResulttype()); + assertEquals(pub_merged.getLanguage(), pub_merged.getLanguage()); + assertEquals(pub_merged.getPublisher(), pub_top.getPublisher()); + assertEquals(pub_merged.getEmbargoenddate(), pub_top.getEmbargoenddate()); + assertEquals(pub_merged.getResourcetype().getClassid(), "0004"); + assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation()); + assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance()); + assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection()); + assertEquals(pub_merged.getInstance().size(),3); + assertEquals(pub_merged.getCountry().size(), 2); + assertEquals(pub_merged.getSubject().size(), 0); + assertEquals(pub_merged.getTitle().size(), 2); + assertEquals(pub_merged.getRelevantdate().size(),0); + assertEquals(pub_merged.getDescription().size(),0); + assertEquals(pub_merged.getSource().size(),0); + assertEquals(pub_merged.getFulltext().size(),0); + assertEquals(pub_merged.getFormat().size(),0); + assertEquals(pub_merged.getContributor().size(),0); + assertEquals(pub_merged.getCoverage().size(),0); + assertEquals(pub_merged.getContext().size(),0); + assertEquals(pub_merged.getExternalReference().size(),0); + assertEquals(pub_merged.getOriginalId().size(),3); + assertEquals(pub_merged.getCollectedfrom().size(),3); + assertEquals(pub_merged.getPid().size(),1); + assertEquals(pub_merged.getExtraInfo().size(),0); + + //verify datainfo + assertEquals(pub_merged.getDataInfo(), dataInfo); + + //verify datepicker + assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); + + //verify authors + assertEquals(pub_merged.getAuthor().size(), 9); + assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + } + + public DataInfo setDI(){ + DataInfo dataInfo = new DataInfo(); + dataInfo.setTrust("0.9"); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferenceprovenance("testing"); + dataInfo.setInferred(true); + return dataInfo; + } + + public Publication getTopPub(List> publications){ + + Double maxTrust = 0.0; + Publication maxPub = new Publication(); + for (Tuple2 publication : publications) { + Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust()); + if(pubTrust > maxTrust){ + maxTrust = pubTrust; + maxPub = publication._2(); + } + } + return maxPub; + } + + public List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res.add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz)) + ); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } + + return res; + } + + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java deleted file mode 100644 index a217a2657f..0000000000 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.dedup; - -import java.io.IOException; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.jupiter.api.BeforeEach; - -import eu.dnetlib.dhp.schema.oaf.Publication; - -public class MergeAuthorTest { - - private List publicationsToMerge; - private final ObjectMapper mapper = new ObjectMapper(); - - @BeforeEach - public void setUp() throws Exception { - final String json = IOUtils - .toString( - this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json")); - - publicationsToMerge = Arrays - .asList(json.split("\n")) - .stream() - .map( - s -> { - try { - return mapper.readValue(s, Publication.class); - } catch (IOException e) { - throw new RuntimeException(e); - } - }) - .collect(Collectors.toList()); - } - - // FIX ME Michele DB this tests doesn't work - // @Test - public void test() throws Exception { - Publication dedup = new Publication(); - - publicationsToMerge - .forEach( - p -> { - dedup.mergeFrom(p); - dedup.setAuthor(DedupUtility.mergeAuthor(dedup.getAuthor(), p.getAuthor())); - }); - - System.out.println(mapper.writeValueAsString(dedup)); - } -} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json new file mode 100644 index 0000000000..015f9294a3 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json @@ -0,0 +1,3 @@ +{"context": [], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.95"}, "resourcetype": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", 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"", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Antichains of copies of ultrahomogeneous structures"}]} \ No newline at end of file From 3e345174790135695590409284747c42d6c9cbf3 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 21 May 2020 16:47:53 +0200 Subject: [PATCH 40/70] partial implementation of events with rels --- .../eu/dnetlib/dhp/broker/model/Topic.java | 69 ++++---- .../broker/oa/GenerateEventsApplication.java | 161 +++++++++++++++--- .../oa/matchers/EnrichMissingAbstract.java | 5 +- .../oa/matchers/EnrichMissingAuthorOrcid.java | 5 +- .../EnrichMissingDatasetIsReferencedBy.java | 38 +++++ .../EnrichMissingDatasetIsRelatedTo.java | 38 +++++ .../EnrichMissingDatasetIsSupplementedBy.java | 38 +++++ .../EnrichMissingDatasetIsSupplementedTo.java | 38 +++++ .../EnrichMissingDatasetReferences.java | 38 +++++ .../oa/matchers/EnrichMissingOpenAccess.java | 2 +- .../broker/oa/matchers/EnrichMissingPid.java | 2 +- .../oa/matchers/EnrichMissingProject.java | 21 ++- .../EnrichMissingPublicationDate.java | 2 +- ...nrichMissingPublicationIsReferencedBy.java | 42 +++++ .../EnrichMissingPublicationIsRelatedTo.java | 42 +++++ ...ichMissingPublicationIsSupplementedBy.java | 42 +++++ ...ichMissingPublicationIsSupplementedTo.java | 42 +++++ .../EnrichMissingPublicationReferences.java | 42 +++++ .../oa/matchers/EnrichMissingSoftware.java | 41 +++++ .../oa/matchers/EnrichMissingSubject.java | 2 +- .../oa/matchers/EnrichMoreOpenAccess.java | 2 +- .../dhp/broker/oa/matchers/EnrichMorePid.java | 2 +- .../broker/oa/matchers/EnrichMoreProject.java | 39 +++++ .../oa/matchers/EnrichMoreSoftware.java | 41 +++++ .../broker/oa/matchers/EnrichMoreSubject.java | 2 +- .../dhp/broker/oa/matchers/UpdateMatcher.java | 16 +- .../dhp/broker/oa/util/BrokerConstants.java | 2 + 27 files changed, 729 insertions(+), 85 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java index 98088dd0aa..0716bd98de 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java @@ -4,48 +4,45 @@ package eu.dnetlib.dhp.broker.model; public enum Topic { // ENRICHMENT MISSING - ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), - ENRICH_MISSING_ABSTRACT("ENRICH/MISSING/ABSTRACT"), - ENRICH_MISSING_PUBLICATION_DATE("ENRICH/MISSING/PUBLICATION_DATE"), - ENRICH_MISSING_PID("ENRICH/MISSING/PID"), - ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), - ENRICH_MISSING_SOFTWARE("ENRICH/MISSING/SOFTWARE"), - ENRICH_MISSING_SUBJECT_MESHEUROPMC("ENRICH/MISSING/SUBJECT/MESHEUROPMC"), - ENRICH_MISSING_SUBJECT_ARXIV("ENRICH/MISSING/SUBJECT/ARXIV"), - ENRICH_MISSING_SUBJECT_JEL("ENRICH/MISSING/SUBJECT/JEL"), - ENRICH_MISSING_SUBJECT_DDC("ENRICH/MISSING/SUBJECT/DDC"), - ENRICH_MISSING_SUBJECT_ACM("ENRICH/MISSING/SUBJECT/ACM"), - ENRICH_MISSING_SUBJECT_RVK("ENRICH/MISSING/SUBJECT/RVK"), - ENRICH_MISSING_AUTHOR_ORCID("ENRICH/MISSING/AUTHOR/ORCID"), + ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT( + "ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE( + "ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID( + "ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE( + "ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC( + "ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV( + "ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL( + "ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC( + "ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM( + "ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK( + "ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID( + "ENRICH/MISSING/AUTHOR/ORCID"), // ENRICHMENT MORE - ENRICH_MORE_PID("ENRICH/MORE/PID"), - ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), - ENRICH_MORE_ABSTRACT("ENRICH/MORE/ABSTRACT"), - ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), - ENRICH_MORE_PROJECT("ENRICH/MORE/PROJECT"), - ENRICH_MORE_SUBJECT_MESHEUROPMC("ENRICH/MORE/SUBJECT/MESHEUROPMC"), - ENRICH_MORE_SUBJECT_ARXIV("ENRICH/MORE/SUBJECT/ARXIV"), - ENRICH_MORE_SUBJECT_JEL("ENRICH/MORE/SUBJECT/JEL"), - ENRICH_MORE_SUBJECT_DDC("ENRICH/MORE/SUBJECT/DDC"), - ENRICH_MORE_SUBJECT_ACM("ENRICH/MORE/SUBJECT/ACM"), - ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), + ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT( + "ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT( + "ENRICH/MORE/PROJECT"), ENRICH_MORE_SOFTWARE("ENRICH/MORE/SOFTWARE"), ENRICH_MORE_SUBJECT_MESHEUROPMC( + "ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV( + "ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL( + "ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC( + "ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM( + "ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), // ADDITION ADD_BY_PROJECT("ADD/BY_PROJECT"), // OTHER RELS - ENRICH_MISSING_PUBLICATION_IS_RELATED_TO("ENRICH/MISSING/PUBLICATION/IS_RELATED_TO"), - ENRICH_MISSING_PUBLICATION_REFERENCES("ENRICH/MISSING/PUBLICATION/REFERENCES"), - ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY("ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY"), - ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO"), - ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY"), + ENRICH_MISSING_PUBLICATION_IS_RELATED_TO( + "ENRICH/MISSING/PUBLICATION/IS_RELATED_TO"), ENRICH_MISSING_PUBLICATION_REFERENCES( + "ENRICH/MISSING/PUBLICATION/REFERENCES"), ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY( + "ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY"), ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO( + "ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO"), ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY( + "ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY"), - ENRICH_MISSING_DATASET_IS_RELATED_TO("ENRICH/MISSING/DATASET/IS_RELATED_TO"), - ENRICH_MISSING_DATASET_REFERENCES("ENRICH/MISSING/DATASET/REFERENCES"), - ENRICH_MISSING_DATASET_IS_REFERENCED_BY("ENRICH/MISSING/DATASET/IS_REFERENCED_BY"), - ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO"), - ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY"); + ENRICH_MISSING_DATASET_IS_RELATED_TO("ENRICH/MISSING/DATASET/IS_RELATED_TO"), ENRICH_MISSING_DATASET_REFERENCES( + "ENRICH/MISSING/DATASET/REFERENCES"), ENRICH_MISSING_DATASET_IS_REFERENCED_BY( + "ENRICH/MISSING/DATASET/IS_REFERENCED_BY"), ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO( + "ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO"), ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY( + "ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY"),; Topic(final String path) { this.path = path; @@ -59,7 +56,9 @@ public enum Topic { public static Topic fromPath(final String path) { for (final Topic t : Topic.values()) { - if (t.getPath().equals(path)) { return t; } + if (t.getPath().equals(path)) { + return t; + } } return null; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 5fdd109252..fa425a1819 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -4,11 +4,14 @@ package eu.dnetlib.dhp.broker.oa; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Collection; import java.util.List; +import java.util.Map; import java.util.Optional; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.tuple.Pair; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -29,18 +32,33 @@ import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetReferences; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationReferences; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSoftware; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreProject; +import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSoftware; import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; @@ -50,24 +68,44 @@ public class GenerateEventsApplication { private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class); - private static final UpdateMatcher enrichMissingAbstract = new EnrichMissingAbstract(); - private static final UpdateMatcher enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid(); - private static final UpdateMatcher enrichMissingOpenAccess = new EnrichMissingOpenAccess(); - private static final UpdateMatcher enrichMissingPid = new EnrichMissingPid(); - private static final UpdateMatcher enrichMissingProject = new EnrichMissingProject(); - private static final UpdateMatcher enrichMissingPublicationDate = new EnrichMissingPublicationDate(); - private static final UpdateMatcher enrichMissingSubject = new EnrichMissingSubject(); - private static final UpdateMatcher enrichMoreOpenAccess = new EnrichMoreOpenAccess(); - private static final UpdateMatcher enrichMorePid = new EnrichMorePid(); - private static final UpdateMatcher enrichMoreSubject = new EnrichMoreSubject(); + // Simple Matchers + private static final UpdateMatcher enrichMissingAbstract = new EnrichMissingAbstract(); + private static final UpdateMatcher enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid(); + private static final UpdateMatcher enrichMissingOpenAccess = new EnrichMissingOpenAccess(); + private static final UpdateMatcher enrichMissingPid = new EnrichMissingPid(); + private static final UpdateMatcher enrichMissingPublicationDate = new EnrichMissingPublicationDate(); + private static final UpdateMatcher enrichMissingSubject = new EnrichMissingSubject(); + private static final UpdateMatcher enrichMoreOpenAccess = new EnrichMoreOpenAccess(); + private static final UpdateMatcher enrichMorePid = new EnrichMorePid(); + private static final UpdateMatcher enrichMoreSubject = new EnrichMoreSubject(); + + // Advanced matchers + private static final UpdateMatcher>, ?> enrichMissingProject = new EnrichMissingProject(); + private static final UpdateMatcher>, ?> enrichMoreProject = new EnrichMoreProject(); + + private static final UpdateMatcher>, ?> enrichMissingSoftware = new EnrichMissingSoftware(); + private static final UpdateMatcher>, ?> enrichMoreSoftware = new EnrichMoreSoftware(); + + private static final UpdateMatcher>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsReferencedBy = new EnrichMissingPublicationIsReferencedBy(); + private static final UpdateMatcher>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedTo = new EnrichMissingPublicationIsSupplementedTo(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedBy = new EnrichMissingPublicationIsSupplementedBy(); + + private static final UpdateMatcher>, ?> enrichMisissingDatasetIsRelatedTo = new EnrichMissingDatasetIsRelatedTo(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsReferencedBy = new EnrichMissingDatasetIsReferencedBy(); + private static final UpdateMatcher>, ?> enrichMissingDatasetReferences = new EnrichMissingDatasetReferences(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedTo = new EnrichMissingDatasetIsSupplementedTo(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedBy = new EnrichMissingDatasetIsSupplementedBy(); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + .toString( + GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -82,9 +120,6 @@ public class GenerateEventsApplication { final String eventsPath = parser.get("eventsPath"); log.info("eventsPath: {}", eventsPath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { @@ -111,17 +146,17 @@ public class GenerateEventsApplication { final String graphPath, final Class resultClazz) { - final Dataset results = - readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz) + final Dataset results = readPath( + spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz) .filter(r -> r.getDataInfo().getDeletedbyinference()); - final Dataset rels = - readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> r.getRelClass().equals("TODO")); // TODO mergedIN + final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) + .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); final Column c = null; // TODO - final Dataset aa = results.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner") + final Dataset aa = results + .joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner") .groupBy(rels.col("target")) .agg(c) .filter(x -> x.size() > 1) @@ -134,7 +169,7 @@ public class GenerateEventsApplication { } - private List generateSimpleEvents(final Result... children) { + private List generateSimpleEvents(final Collection children) { final List> list = new ArrayList<>(); for (final Result target : children) { @@ -142,7 +177,6 @@ public class GenerateEventsApplication { list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, children)); list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, children)); list.addAll(enrichMissingPid.searchUpdatesForRecord(target, children)); - list.addAll(enrichMissingProject.searchUpdatesForRecord(target, children)); list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, children)); list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, children)); list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, children)); @@ -153,6 +187,87 @@ public class GenerateEventsApplication { return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); } + private List generateProjectsEvents(final Collection>> childrenWithProjects) { + final List> list = new ArrayList<>(); + + for (final Pair> target : childrenWithProjects) { + list.addAll(enrichMissingProject.searchUpdatesForRecord(target, childrenWithProjects)); + list.addAll(enrichMoreProject.searchUpdatesForRecord(target, childrenWithProjects)); + } + + return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); + } + + private List generateSoftwareEvents(final Collection>> childrenWithSoftwares) { + final List> list = new ArrayList<>(); + + for (final Pair> target : childrenWithSoftwares) { + list.addAll(enrichMissingSoftware.searchUpdatesForRecord(target, childrenWithSoftwares)); + list.addAll(enrichMoreSoftware.searchUpdatesForRecord(target, childrenWithSoftwares)); + } + return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); + } + + private List generatePublicationRelatedEvents(final String relType, + final Collection>>> childrenWithRels) { + + final List> list = new ArrayList<>(); + + final List>> cleanedChildrens = childrenWithRels + .stream() + .filter(p -> p.getRight().containsKey(relType)) + .map(p -> Pair.of(p.getLeft(), p.getRight().get(relType))) + .filter(p -> p.getRight().size() > 0) + .collect(Collectors.toList()); + + for (final Pair> target : cleanedChildrens) { + if (relType.equals("isRelatedTo")) { + list.addAll(enrichMisissingPublicationIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("references")) { + list.addAll(enrichMissingPublicationReferences.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isReferencedBy")) { + list.addAll(enrichMissingPublicationIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isSupplementedTo")) { + list.addAll(enrichMissingPublicationIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isSupplementedBy")) { + list.addAll(enrichMissingPublicationIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens)); + } + } + + return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); + + } + + private List generateDatasetRelatedEvents(final String relType, + final Collection>>> childrenWithRels) { + + final List> list = new ArrayList<>(); + + final List>> cleanedChildrens = childrenWithRels + .stream() + .filter(p -> p.getRight().containsKey(relType)) + .map(p -> Pair.of(p.getLeft(), p.getRight().get(relType))) + .filter(p -> p.getRight().size() > 0) + .collect(Collectors.toList()); + + for (final Pair> target : cleanedChildrens) { + if (relType.equals("isRelatedTo")) { + list.addAll(enrichMisissingDatasetIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("references")) { + list.addAll(enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isReferencedBy")) { + list.addAll(enrichMissingDatasetIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isSupplementedTo")) { + list.addAll(enrichMissingDatasetIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens)); + } else if (relType.equals("isSupplementedBy")) { + list.addAll(enrichMissingDatasetIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens)); + } + } + + return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); + + } + public static Dataset readPath( final SparkSession spark, final String inputPath, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java index 43cf738f8c..6dab6355fd 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java @@ -9,7 +9,7 @@ import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingAbstract extends UpdateMatcher { +public class EnrichMissingAbstract extends UpdateMatcher { public EnrichMissingAbstract() { super(false); @@ -24,7 +24,8 @@ public class EnrichMissingAbstract extends UpdateMatcher { } @Override - public UpdateInfo generateUpdateInfo(final String highlightValue, final Result source, + public UpdateInfo generateUpdateInfo(final String highlightValue, + final Result source, final Result target) { return new UpdateInfo<>( Topic.ENRICH_MISSING_ABSTRACT, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java index beeccdbe84..c7146ad79a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingAuthorOrcid extends UpdateMatcher> { +public class EnrichMissingAuthorOrcid extends UpdateMatcher> { public EnrichMissingAuthorOrcid() { super(true); @@ -24,7 +24,8 @@ public class EnrichMissingAuthorOrcid extends UpdateMatcher @Override public UpdateInfo> generateUpdateInfo(final Pair highlightValue, - final Result source, final Result target) { + final Result source, + final Result target) { return new UpdateInfo<>( Topic.ENRICH_MISSING_AUTHOR_ORCID, highlightValue, source, target, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java new file mode 100644 index 0000000000..3b9326fef2 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingDatasetIsReferencedBy + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + public EnrichMissingDatasetIsReferencedBy() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return null; + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java new file mode 100644 index 0000000000..35f7c52b42 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingDatasetIsRelatedTo + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + public EnrichMissingDatasetIsRelatedTo() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return null; + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java new file mode 100644 index 0000000000..1faa305b52 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingDatasetIsSupplementedBy + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + public EnrichMissingDatasetIsSupplementedBy() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return null; + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java new file mode 100644 index 0000000000..d1b067272d --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingDatasetIsSupplementedTo + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + public EnrichMissingDatasetIsSupplementedTo() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return null; + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java new file mode 100644 index 0000000000..ce6adeba27 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingDatasetReferences + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + public EnrichMissingDatasetReferences() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return null; + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_DATASET_REFERENCES, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java index a4a2ea0c6c..81263c6c3f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java @@ -12,7 +12,7 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingOpenAccess extends UpdateMatcher { +public class EnrichMissingOpenAccess extends UpdateMatcher { public EnrichMissingOpenAccess() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java index a8df62541e..5f10bb4d9e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java @@ -11,7 +11,7 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingPid extends UpdateMatcher { +public class EnrichMissingPid extends UpdateMatcher { public EnrichMissingPid() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java index b6e5b3b574..0197c99b1b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java @@ -4,30 +4,35 @@ package eu.dnetlib.dhp.broker.oa.matchers; import java.util.Arrays; import java.util.List; -import eu.dnetlib.broker.objects.Project; +import org.apache.commons.lang3.tuple.Pair; + import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingProject extends UpdateMatcher { +public class EnrichMissingProject + extends UpdateMatcher>, eu.dnetlib.broker.objects.Project> { public EnrichMissingProject() { super(true); } @Override - protected List> findUpdates(final Result source, final Result target) { - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO return Arrays.asList(); } @Override - public UpdateInfo generateUpdateInfo(final Project highlightValue, - final Result source, - final Result target) { + public UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Project highlightValue, + final Pair> source, + final Pair> target) { return new UpdateInfo<>( Topic.ENRICH_MISSING_PROJECT, - highlightValue, source, target, + highlightValue, source.getLeft(), target.getLeft(), (p, prj) -> p.getProjects().add(prj), prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java index 372a4e4c9d..19ef2bab7e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java @@ -9,7 +9,7 @@ import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMissingPublicationDate extends UpdateMatcher { +public class EnrichMissingPublicationDate extends UpdateMatcher { public EnrichMissingPublicationDate() { super(false); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java new file mode 100644 index 0000000000..8bcee5a1fc --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationIsReferencedBy + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + public EnrichMissingPublicationIsReferencedBy() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return Arrays.asList(); + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getOriginalId()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java new file mode 100644 index 0000000000..0c16f9f564 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationIsRelatedTo + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + public EnrichMissingPublicationIsRelatedTo() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return Arrays.asList(); + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getOriginalId()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java new file mode 100644 index 0000000000..0b3c332708 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationIsSupplementedBy + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + public EnrichMissingPublicationIsSupplementedBy() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return Arrays.asList(); + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getOriginalId()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java new file mode 100644 index 0000000000..0e72a84239 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationIsSupplementedTo + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + public EnrichMissingPublicationIsSupplementedTo() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return Arrays.asList(); + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getOriginalId()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java new file mode 100644 index 0000000000..6d1124974e --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMissingPublicationReferences + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + public EnrichMissingPublicationReferences() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO Auto-generated method stub + return Arrays.asList(); + } + + @Override + protected UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_PUBLICATION_REFERENCES, + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getOriginalId()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java new file mode 100644 index 0000000000..954ee48be7 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java @@ -0,0 +1,41 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; + +public class EnrichMissingSoftware + extends UpdateMatcher>, eu.dnetlib.broker.objects.Software> { + + public EnrichMissingSoftware() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO + return Arrays.asList(); + } + + @Override + public UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Software highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MISSING_SOFTWARE, + highlightValue, source.getLeft(), target.getLeft(), + (p, s) -> p.getSoftwares().add(s), + s -> s.getName()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java index 79e9d469be..a7c72f6ea3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java @@ -14,7 +14,7 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -public class EnrichMissingSubject extends UpdateMatcher> { +public class EnrichMissingSubject extends UpdateMatcher> { public EnrichMissingSubject() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java index 40c9b0500a..2cd2775c9e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java @@ -12,7 +12,7 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMoreOpenAccess extends UpdateMatcher { +public class EnrichMoreOpenAccess extends UpdateMatcher { public EnrichMoreOpenAccess() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java index 0e7b7766ab..048d19747d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java @@ -11,7 +11,7 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMorePid extends UpdateMatcher { +public class EnrichMorePid extends UpdateMatcher { public EnrichMorePid() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java new file mode 100644 index 0000000000..4bf45d9437 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java @@ -0,0 +1,39 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class EnrichMoreProject extends UpdateMatcher>, eu.dnetlib.broker.objects.Project> { + + public EnrichMoreProject() { + super(true); + } + + @Override + protected List> findUpdates(final Pair> source, + final Pair> target) { + // TODO + return Arrays.asList(); + } + + @Override + public UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Project highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MORE_PROJECT, + highlightValue, source.getLeft(), target.getLeft(), + (p, prj) -> p.getProjects().add(prj), + prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java new file mode 100644 index 0000000000..9760504f64 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java @@ -0,0 +1,41 @@ + +package eu.dnetlib.dhp.broker.oa.matchers; + +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; + +public class EnrichMoreSoftware + extends UpdateMatcher>, eu.dnetlib.broker.objects.Software> { + + public EnrichMoreSoftware() { + super(true); + } + + @Override + protected List> findUpdates( + final Pair> source, + final Pair> target) { + // TODO + return Arrays.asList(); + } + + @Override + public UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Software highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + Topic.ENRICH_MORE_SOFTWARE, + highlightValue, source.getLeft(), target.getLeft(), + (p, s) -> p.getSoftwares().add(s), + s -> s.getName()); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java index e6374479bf..67c2f01161 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java @@ -12,7 +12,7 @@ import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; -public class EnrichMoreSubject extends UpdateMatcher> { +public class EnrichMoreSubject extends UpdateMatcher> { public EnrichMoreSubject() { super(true); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index d91b03200e..5bfe108a56 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -12,9 +12,8 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Result; -public abstract class UpdateMatcher { +public abstract class UpdateMatcher { private final boolean multipleUpdate; @@ -22,15 +21,16 @@ public abstract class UpdateMatcher { this.multipleUpdate = multipleUpdate; } - public Collection> searchUpdatesForRecord(final Result res, final Result... others) { + public Collection> searchUpdatesForRecord(final K res, final Collection others) { final Map> infoMap = new HashMap<>(); - for (final Result source : others) { + for (final K source : others) { if (source != res) { for (final UpdateInfo info : findUpdates(source, res)) { final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); - if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {} else { + if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { + } else { infoMap.put(s, info); } } @@ -51,11 +51,11 @@ public abstract class UpdateMatcher { } } - protected abstract List> findUpdates(Result source, Result target); + protected abstract List> findUpdates(K source, K target); protected abstract UpdateInfo generateUpdateInfo(final T highlightValue, - final Result source, - final Result target); + final K source, + final K target); protected static boolean isMissing(final List> list) { return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue()); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java index d61d5bfb7d..8e97192bfb 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java @@ -4,4 +4,6 @@ package eu.dnetlib.dhp.broker.oa.util; public class BrokerConstants { public final static String OPEN_ACCESS = "OPEN"; + public final static String IS_MERGED_IN_CLASS = "isMergedIn"; + } From b33dd58be4dbaeb841363c61d95f3f9bab890d25 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 22 May 2020 08:50:06 +0200 Subject: [PATCH 41/70] replaced parameter 'reuseRecords' with 'resumeFrom', allowing to restart the provision workflow execution from any step, useful for manual submissions or debugging --- .../dhp/oa/provision/oozie_app/workflow.xml | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index fd8f5ba89a..6983ecf53c 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -84,7 +84,6 @@ sparkNetworkTimeout configures spark.network.timeout - @@ -98,12 +97,16 @@ - + - + - ${wf:conf('reuseRecords') eq false} - ${wf:conf('reuseRecords') eq true} + ${wf:conf('resumeFrom') eq 'prepare_relations'} + ${wf:conf('resumeFrom') eq 'fork_join_related_entities'} + ${wf:conf('resumeFrom') eq 'join_all_entities'} + ${wf:conf('resumeFrom') eq 'adjancency_lists'} + ${wf:conf('resumeFrom') eq 'convert_to_xml'} + ${wf:conf('resumeFrom') eq 'to_solr_index'} @@ -131,9 +134,7 @@ --inputRelationsPath${inputGraphRootPath}/relation --outputPath${workingDir}/relation - --relPartitions${relPartitions} - --relationFilter${relationFilter} - --maxRelations${maxRelations} + --relPartitions3000 @@ -340,7 +341,6 @@ - yarn @@ -362,7 +362,7 @@ --inputGraphRootPath${inputGraphRootPath} --inputRelatedEntitiesPath${workingDir}/join_partial --outputPath${workingDir}/join_entities - --numPartitions24000 + --numPartitions12000 @@ -386,7 +386,7 @@ --conf spark.sql.shuffle.partitions=7680 --conf spark.network.timeout=${sparkNetworkTimeout} - --inputPath${workingDir}/join_entities + --inputPath ${workingDir}/join_entities --outputPath${workingDir}/joined From 925d933204529190205d67c0f580ef58975575e1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 22 May 2020 08:50:44 +0200 Subject: [PATCH 42/70] making XmlRecordFactory immune to graph encoding changes (mostly to avoid NPEs) --- .../oa/provision/utils/TemplateFactory.java | 3 +- .../oa/provision/utils/XmlRecordFactory.java | 77 +++++++++++++++---- 2 files changed, 62 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java index 6cb025b4fd..21b526ab1b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix; import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml; import java.io.IOException; +import java.util.ArrayList; import java.util.Collection; import java.util.List; import java.util.stream.Collectors; @@ -95,7 +96,7 @@ public class TemplateFactory { .add("metadata", instancemetadata) .add( "webresources", - webresources + (webresources != null ? webresources : new ArrayList()) .stream() .filter(StringUtils::isNotBlank) .map(w -> getWebResource(w)) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index ce1c71312e..6f042b45cf 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -174,6 +174,7 @@ public class XmlRecordFactory implements Serializable { entity .getCollectedfrom() .stream() + .filter(XmlRecordFactory::kvNotBlank) .map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv)) .collect(Collectors.toList())); } @@ -183,6 +184,7 @@ public class XmlRecordFactory implements Serializable { entity .getOriginalId() .stream() + .filter(Objects::nonNull) .map(s -> XmlSerializationUtils.asXmlElement("originalId", s)) .collect(Collectors.toList())); } @@ -192,6 +194,7 @@ public class XmlRecordFactory implements Serializable { entity .getPid() .stream() + .filter(Objects::nonNull) .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) .collect(Collectors.toList())); } @@ -213,6 +216,7 @@ public class XmlRecordFactory implements Serializable { r .getTitle() .stream() + .filter(Objects::nonNull) .map(t -> XmlSerializationUtils.mapStructuredProperty("title", t)) .collect(Collectors.toList())); } @@ -225,6 +229,7 @@ public class XmlRecordFactory implements Serializable { r .getAuthor() .stream() + .filter(Objects::nonNull) .map( a -> { final StringBuilder sb = new StringBuilder(" isNotBlank(sp.getQualifier().getClassid()) && isNotBlank(sp.getValue())) + .collect( + Collectors + .toMap( + p -> getAuthorPidType(p.getQualifier().getClassid()), + p -> p, + (p1, p2) -> p1)) + .values() .forEach( sp -> { - String pidType = XmlSerializationUtils - .escapeXml( - sp.getQualifier().getClassid()) - .replaceAll("\\W", ""); + String pidType = getAuthorPidType(sp.getQualifier().getClassid()); String pidValue = XmlSerializationUtils.escapeXml(sp.getValue()); - // ugly hack: some records - // provide swapped pidtype and - // pidvalue + // ugly hack: some records provide swapped pidtype and pidvalue if (authorPidTypes.contains(pidValue.toLowerCase().trim())) { sb.append(String.format(" %s=\"%s\"", pidValue, pidType)); } else { - pidType = pidType.replaceAll("\\W", "").replaceAll("\\d", ""); if (isNotBlank(pidType)) { sb .append( @@ -285,6 +292,7 @@ public class XmlRecordFactory implements Serializable { r .getContributor() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("contributor", c.getValue())) .collect(Collectors.toList())); } @@ -294,6 +302,7 @@ public class XmlRecordFactory implements Serializable { r .getCountry() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.mapQualifier("country", c)) .collect(Collectors.toList())); } @@ -303,6 +312,7 @@ public class XmlRecordFactory implements Serializable { r .getCoverage() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("coverage", c.getValue())) .collect(Collectors.toList())); } @@ -319,6 +329,7 @@ public class XmlRecordFactory implements Serializable { r .getDescription() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("description", c.getValue())) .collect(Collectors.toList())); } @@ -333,6 +344,7 @@ public class XmlRecordFactory implements Serializable { r .getSubject() .stream() + .filter(Objects::nonNull) .map(s -> XmlSerializationUtils.mapStructuredProperty("subject", s)) .collect(Collectors.toList())); } @@ -345,6 +357,7 @@ public class XmlRecordFactory implements Serializable { r .getRelevantdate() .stream() + .filter(Objects::nonNull) .map(s -> XmlSerializationUtils.mapStructuredProperty("relevantdate", s)) .collect(Collectors.toList())); } @@ -357,6 +370,7 @@ public class XmlRecordFactory implements Serializable { r .getSource() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("source", c.getValue())) .collect(Collectors.toList())); } @@ -366,6 +380,7 @@ public class XmlRecordFactory implements Serializable { r .getFormat() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("format", c.getValue())) .collect(Collectors.toList())); } @@ -429,6 +444,7 @@ public class XmlRecordFactory implements Serializable { orp .getContactperson() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("contactperson", c.getValue())) .collect(Collectors.toList())); } @@ -439,6 +455,7 @@ public class XmlRecordFactory implements Serializable { orp .getContactgroup() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("contactgroup", c.getValue())) .collect(Collectors.toList())); } @@ -448,6 +465,7 @@ public class XmlRecordFactory implements Serializable { orp .getTool() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("tool", c.getValue())) .collect(Collectors.toList())); } @@ -461,6 +479,7 @@ public class XmlRecordFactory implements Serializable { s .getDocumentationUrl() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("documentationUrl", c.getValue())) .collect(Collectors.toList())); } @@ -470,6 +489,7 @@ public class XmlRecordFactory implements Serializable { s .getLicense() .stream() + .filter(Objects::nonNull) .map(l -> XmlSerializationUtils.mapStructuredProperty("license", l)) .collect(Collectors.toList())); } @@ -576,6 +596,7 @@ public class XmlRecordFactory implements Serializable { ds .getOdlanguages() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) .collect(Collectors.toList())); } @@ -585,6 +606,7 @@ public class XmlRecordFactory implements Serializable { ds .getOdcontenttypes() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("odcontenttypes", c.getValue())) .collect(Collectors.toList())); } @@ -697,6 +719,7 @@ public class XmlRecordFactory implements Serializable { ds .getPolicies() .stream() + .filter(XmlRecordFactory::kvNotBlank) .map(kv -> XmlSerializationUtils.mapKeyValue("policies", kv)) .collect(Collectors.toList())); } @@ -709,6 +732,7 @@ public class XmlRecordFactory implements Serializable { ds .getSubjects() .stream() + .filter(Objects::nonNull) .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) .collect(Collectors.toList())); } @@ -735,6 +759,7 @@ public class XmlRecordFactory implements Serializable { o .getAlternativeNames() .stream() + .filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("alternativeNames", c.getValue())) .collect(Collectors.toList())); } @@ -862,6 +887,7 @@ public class XmlRecordFactory implements Serializable { p .getSubjects() .stream() + .filter(Objects::nonNull) .map(sp -> XmlSerializationUtils.mapStructuredProperty("subject", sp)) .collect(Collectors.toList())); } @@ -912,7 +938,12 @@ public class XmlRecordFactory implements Serializable { if (p.getFundingtree() != null) { metadata .addAll( - p.getFundingtree().stream().map(ft -> ft.getValue()).collect(Collectors.toList())); + p + .getFundingtree() + .stream() + .filter(Objects::nonNull) + .map(ft -> ft.getValue()) + .collect(Collectors.toList())); } break; @@ -923,6 +954,17 @@ public class XmlRecordFactory implements Serializable { return metadata; } + private String getAuthorPidType(String s) { + return XmlSerializationUtils + .escapeXml(s) + .replaceAll("\\W", "") + .replaceAll("\\d", ""); + } + + private static boolean kvNotBlank(KeyValue kv) { + return kv != null && StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue()); + } + private void mapDatasourceType(List metadata, final Qualifier dsType) { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetype", dsType)); @@ -960,7 +1002,7 @@ public class XmlRecordFactory implements Serializable { .add( XmlSerializationUtils.asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl())); } - if (re.getResulttype() != null & re.getResulttype().isBlank()) { + if (re.getResulttype() != null && re.getResulttype().isBlank()) { metadata.add(XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); } if (re.getCollectedfrom() != null) { @@ -969,6 +1011,7 @@ public class XmlRecordFactory implements Serializable { re .getCollectedfrom() .stream() + .filter(XmlRecordFactory::kvNotBlank) .map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv)) .collect(Collectors.toList())); } @@ -986,10 +1029,10 @@ public class XmlRecordFactory implements Serializable { if (isNotBlank(re.getOfficialname())) { metadata.add(XmlSerializationUtils.asXmlElement("officialname", re.getOfficialname())); } - if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { + if (re.getDatasourcetype() != null && !re.getDatasourcetype().isBlank()) { mapDatasourceType(metadata, re.getDatasourcetype()); } - if (re.getOpenairecompatibility() != null & !re.getOpenairecompatibility().isBlank()) { + if (re.getOpenairecompatibility() != null && !re.getOpenairecompatibility().isBlank()) { metadata .add( XmlSerializationUtils @@ -1006,7 +1049,7 @@ public class XmlRecordFactory implements Serializable { .add( XmlSerializationUtils.asXmlElement("legalshortname", re.getLegalshortname())); } - if (re.getCountry() != null & !re.getCountry().isBlank()) { + if (re.getCountry() != null && !re.getCountry().isBlank()) { metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); } break; @@ -1020,10 +1063,10 @@ public class XmlRecordFactory implements Serializable { if (isNotBlank(re.getAcronym())) { metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym())); } - if (re.getContracttype() != null & !re.getContracttype().isBlank()) { + if (re.getContracttype() != null && !re.getContracttype().isBlank()) { metadata.add(XmlSerializationUtils.mapQualifier("contracttype", re.getContracttype())); } - if (re.getFundingtree() != null & contexts != null) { + if (re.getFundingtree() != null && contexts != null) { metadata .addAll( re @@ -1091,12 +1134,12 @@ public class XmlRecordFactory implements Serializable { .add( XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright())); } - if (instance.getCollectedfrom() != null) { + if (instance.getCollectedfrom() != null && kvNotBlank(instance.getCollectedfrom())) { fields .add( XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom())); } - if (instance.getHostedby() != null) { + if (instance.getHostedby() != null && kvNotBlank(instance.getHostedby())) { fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby())); } if (instance.getDateofacceptance() != null From c5f7e173481f7b761a56742067454f58ff0b4ace Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 May 2020 10:08:02 +0200 Subject: [PATCH 43/70] author fullnames --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 126 ++++++++---------- 1 file changed, 55 insertions(+), 71 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 30b980c422..3a56aa8e0e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -4,16 +4,32 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENTED_BY; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENT_TO; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PART; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.SUPPLEMENT; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; @@ -22,7 +38,6 @@ import eu.dnetlib.dhp.schema.oaf.Instance; import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @@ -48,7 +63,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String fullname = n.valueOf("./datacite:creatorName"); author.setFullname(fullname); - PacePerson pp = new PacePerson(fullname, false); + final PacePerson pp = new PacePerson(fullname, false); final String name = n.valueOf("./datacite:givenName"); if (StringUtils.isBlank(name) & pp.isAccurate()) { author.setName(pp.getNormalisedFirstName()); @@ -63,6 +78,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { author.setSurname(surname); } + if (StringUtils.isBlank(author.getFullname())) { + author.setFullname(String.format("%s, %s", author.getSurname(), author.getName())); + } + author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info)); author.setPid(preparePids(n, info)); author.setRank(pos++); @@ -75,12 +94,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List res = new ArrayList<>(); for (final Object o : n.selectNodes("./datacite:nameIdentifier")) { res - .add( - structuredProperty( - ((Node) o).getText(), - prepareQualifier( - (Node) o, "./@nameIdentifierScheme", DNET_PID_TYPES, DNET_PID_TYPES), - info)); + .add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", DNET_PID_TYPES, DNET_PID_TYPES), info)); } return res; } @@ -94,22 +108,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final Instance instance = new Instance(); instance - .setInstancetype( - prepareQualifier( - doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); + .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); instance.setCollectedfrom(collectedfrom); instance.setHostedby(hostedby); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); instance - .setAccessright( - prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); + .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); instance.setLicense(field(doc.valueOf("//oaf:license"), info)); instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); instance - .setProcessingchargecurrency( - field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); final Set url = new HashSet<>(); for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { @@ -147,14 +157,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { && !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) { res - .add( - structuredProperty( - ((Node) o).getText(), - "UNKNOWN", - "UNKNOWN", - DNET_DATA_CITE_DATE, - DNET_DATA_CITE_DATE, - info)); + .add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info)); } } return res; @@ -197,53 +200,49 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List> prepareOtherResearchProductTools( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // Not present in ODF ??? } @Override protected List> prepareOtherResearchProductContactGroups( - final Document doc, final DataInfo info) { - return prepareListFields( - doc, - "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", - info); + final Document doc, + final DataInfo info) { + return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info); } @Override protected List> prepareOtherResearchProductContactPersons( - final Document doc, final DataInfo info) { - return prepareListFields( - doc, - "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", - info); + final Document doc, + final DataInfo info) { + return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info); } @Override protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { - return prepareQualifier( - doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages"); + return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages"); } @Override protected Field prepareSoftwareCodeRepositoryUrl( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return null; // Not present in ODF ??? } @Override protected List prepareSoftwareLicenses( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // Not present in ODF ??? } @Override protected List> prepareSoftwareDocumentationUrls( - final Document doc, final DataInfo info) { - return prepareListFields( - doc, - "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", - info); + final Document doc, + final DataInfo info) { + return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); } // DATASETS @@ -264,13 +263,15 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Field prepareDatasetMetadataVersionNumber( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return null; // Not present in ODF ??? } @Override protected Field prepareDatasetLastMetadataUpdate( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return prepareField(doc, "//datacite:date[@dateType='Updated']", info); } @@ -315,29 +316,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { if (type.equalsIgnoreCase("IsSupplementTo")) { res - .add( - getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp)); res - .add( - getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp)); } else if (type.equals("IsPartOf")) { res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp)); res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, - lastUpdateTimestamp)); - } else { - } + .add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp)); + } else {} } } return res; @@ -345,10 +333,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { - return prepareQualifier( - doc, - "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", - DNET_DATA_CITE_RESOURCE, - DNET_DATA_CITE_RESOURCE); + return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE); } } From 9de71e54a8ae4f8bab8c78b5da4d790be711918e Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 May 2020 10:47:39 +0200 Subject: [PATCH 44/70] filter ORCID e MAG identifiers --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 3a56aa8e0e..1d4f80894e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE; @@ -44,6 +45,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; + public static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + public static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + public OdfToOafMapper(final Map code2name) { super(code2name); } @@ -93,8 +97,19 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { private List preparePids(final Node n, final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : n.selectNodes("./datacite:nameIdentifier")) { - res - .add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", DNET_PID_TYPES, DNET_PID_TYPES), info)); + + final String id = ((Node) o).getText(); + final String type = ((Node) o).valueOf("./@nameIdentifierScheme") + .trim() + .toUpperCase() + .replaceAll(" ", ""); + + if (type.startsWith("ORCID")) { + final String cleanedId = id.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", ""); + res.add(structuredProperty(cleanedId, ORCID_PID_TYPE, info)); + } else if (type.startsWith("MAGID")) { + res.add(structuredProperty(id, MAG_PID_TYPE, info)); + } } return res; } From 9f2d0f1b0893ba8fdba8ceef27f631a83c2aaa15 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 May 2020 11:00:27 +0200 Subject: [PATCH 45/70] filter ORCID e MAG identifiers --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 3 ++- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 23 ++++++++++++------- 2 files changed, 17 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 1d4f80894e..d51433a182 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -102,7 +102,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String type = ((Node) o).valueOf("./@nameIdentifierScheme") .trim() .toUpperCase() - .replaceAll(" ", ""); + .replaceAll(" ", "") + .replaceAll("_", ""); if (type.startsWith("ORCID")) { final String cleanedId = id.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", ""); 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 5a006e3513..6ff76e839a 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 @@ -21,7 +21,14 @@ import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -54,13 +61,13 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertTrue(p.getAuthor().size() > 0); - Optional author = p + final Optional author = p .getAuthor() .stream() .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) .findFirst(); assertTrue(author.isPresent()); - StructuredProperty pid = author + final StructuredProperty pid = author .get() .getPid() .stream() @@ -121,13 +128,13 @@ public class MappersTest { assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(d.getAuthor().size() > 0); - Optional author = d + final Optional author = d .getAuthor() .stream() .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) .findFirst(); assertTrue(author.isPresent()); - StructuredProperty pid = author + final StructuredProperty pid = author .get() .getPid() .stream() @@ -135,7 +142,7 @@ public class MappersTest { .get(); assertEquals("0000-0001-9074-1619", pid.getValue()); assertEquals("ORCID", pid.getQualifier().getClassid()); - assertEquals("ORCID", pid.getQualifier().getClassname()); + assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname()); assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid()); assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename()); assertEquals("Baracchini, Theo", author.get().getFullname()); @@ -143,13 +150,13 @@ public class MappersTest { assertEquals("Theo", author.get().getName()); assertEquals(1, author.get().getAffiliation().size()); - Optional> opAff = author + final Optional> opAff = author .get() .getAffiliation() .stream() .findFirst(); assertTrue(opAff.isPresent()); - Field affiliation = opAff.get(); + final Field affiliation = opAff.get(); assertEquals("ISTI-CNR", affiliation.getValue()); assertTrue(d.getSubject().size() > 0); From dc4621b3cb98ab01185e350e99f35091b628d0c5 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 May 2020 12:25:01 +0200 Subject: [PATCH 46/70] filter ORCID e MAG identifiers --- .../raw/AbstractMdRecordToOafMapper.java | 223 ++++++++---------- .../dhp/oa/graph/raw/OafToOafMapper.java | 113 +++++---- .../dhp/oa/graph/raw/OdfToOafMapper.java | 5 - .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- 4 files changed, 169 insertions(+), 174 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index b9c4e6c804..84b200c076 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -10,7 +10,16 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; +import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import java.util.ArrayList; import java.util.Arrays; @@ -50,6 +59,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; + protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -63,8 +74,7 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( - "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -75,24 +85,18 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText( - xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); + .parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { - return null; - } + if (collectedFrom == null) { return null; } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { - return null; - } + if (hostedBy == null) { return null; } final DataInfo info = prepareDataInfo(doc); final long lastUpdateTimestamp = new Date().getTime(); @@ -103,17 +107,13 @@ public abstract class AbstractMdRecordToOafMapper { } } - private KeyValue getProvenanceDatasource(Document doc, String xpathId, String xpathName) { + private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { - return null; - } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } - return keyValue( - createOpenaireId(10, dsId, true), - dsName); + return keyValue(createOpenaireId(10, dsId, true), dsName); } protected List createOafs( @@ -127,47 +127,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -196,23 +196,23 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp)); res - .add( - getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp)); } } return res; } - protected Relation getRelation(String source, String target, String relType, String subRelType, String relClass, - KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) { + protected Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { final Relation rel = new Relation(); rel.setRelType(relType); rel.setSubRelType(subRelType); @@ -244,9 +244,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setCollectedfrom(Arrays.asList(collectedFrom)); r - .setPid( - prepareListStructProps( - doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + .setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES @@ -289,7 +287,10 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract List prepareInstances( - Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + Document doc, + DataInfo info, + KeyValue collectedfrom, + KeyValue hostedby); protected abstract List> prepareSources(Document doc, DataInfo info); @@ -314,13 +315,16 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareAuthors(Document doc, DataInfo info); protected abstract List> prepareOtherResearchProductTools( - Document doc, DataInfo info); + Document doc, + DataInfo info); protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, DataInfo info); + Document doc, + DataInfo info); protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, DataInfo info); + Document doc, + DataInfo info); protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); @@ -329,7 +333,8 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, DataInfo info); + Document doc, + DataInfo info); protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); @@ -357,27 +362,16 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal( - name, - issnPrinted, - issnOnline, - issnLinking, - ep, - iss, - sp, - vol, - edition, - null, - null, - info); - } + if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } } return null; } protected Qualifier prepareQualifier( - final Node node, final String xpath, final String schemeId, final String schemeName) { + final Node node, + final String xpath, + final String schemeId, + final String schemeName) { final String classId = node.valueOf(xpath); final String className = code2name.get(classId); return qualifier(classId, className, schemeId, schemeName); @@ -401,7 +395,10 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final Node node, + final String xpath, + final Qualifier qualifier, + final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; @@ -411,19 +408,14 @@ public abstract class AbstractMdRecordToOafMapper { } protected List prepareListStructProps( - final Node node, final String xpath, final DataInfo info) { + final Node node, + final String xpath, + final DataInfo info) { final List res = new ArrayList<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add( - structuredProperty( - n.getText(), - n.valueOf("@classid"), - n.valueOf("@classname"), - n.valueOf("@schemeid"), - n.valueOf("@schemename"), - info)); + .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); } return res; } @@ -431,9 +423,7 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { - return null; - } + if (n == null) { return null; } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -448,10 +438,7 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { - return dataInfo( - false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); - } + if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -463,13 +450,7 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo( - deletedbyinference, - inferenceprovenance, - inferred, - false, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), - trust); + return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { @@ -477,7 +458,9 @@ public abstract class AbstractMdRecordToOafMapper { } protected List> prepareListFields( - final Node node, final String xpath, final DataInfo info) { + final Node node, + final String xpath, + final DataInfo info) { return listFields(info, prepareListString(node, xpath)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index ed09016da8..24a8b45270 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,10 +1,19 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; +import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET; +import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; -import java.util.*; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; @@ -15,8 +24,15 @@ import org.dom4j.Node; import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -39,14 +55,22 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { author.setSurname(p.getNormalisedSurname()); } - final String pid = e.attributeValue("nameIdentifier"); - final String pidType = e.attributeValue("nameIdentifierScheme"); + final String pid = e.valueOf("./@nameIdentifier"); + final String type = e.valueOf("./@nameIdentifierScheme") + .trim() + .toUpperCase() + .replaceAll(" ", "") + .replaceAll("_", ""); author.setPid(new ArrayList<>()); - if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) { - author - .getPid() - .add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); + + if (StringUtils.isNotBlank(pid)) { + if (type.startsWith("ORCID")) { + final String cleanedId = pid.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", ""); + author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info)); + } else if (type.startsWith("MAGID")) { + author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info)); + } } res.add(author); @@ -103,38 +127,29 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final Instance instance = new Instance(); instance - .setInstancetype( - prepareQualifier( - doc, - "//dr:CobjCategory", - DNET_PUBLICATION_RESOURCE, - DNET_PUBLICATION_RESOURCE)); + .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); instance.setCollectedfrom(collectedfrom); instance.setHostedby(hostedby); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); instance - .setAccessright( - prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); + .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES)); instance.setLicense(field(doc.valueOf("//oaf:license"), info)); instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); instance - .setProcessingchargeamount( - field(doc.valueOf("//oaf:processingchargeamount"), info)); + .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); instance - .setProcessingchargecurrency( - field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); + final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); instance - .setUrl( - nodes - .stream() - .filter(n -> StringUtils.isNotBlank(n.getText())) - .map(n -> n.getText().trim()) - .filter(u -> u.startsWith("http")) - .distinct() - .collect(Collectors.toCollection(ArrayList::new))); + .setUrl(nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .distinct() + .collect(Collectors.toCollection(ArrayList::new))); return Lists.newArrayList(instance); } @@ -158,19 +173,22 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Field prepareSoftwareCodeRepositoryUrl( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return null; // NOT PRESENT IN OAF } @Override protected List prepareSoftwareLicenses( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // NOT PRESENT IN OAF } @Override protected List> prepareSoftwareDocumentationUrls( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // NOT PRESENT IN OAF } @@ -182,13 +200,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Field prepareDatasetMetadataVersionNumber( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return null; // NOT PRESENT IN OAF } @Override protected Field prepareDatasetLastMetadataUpdate( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return null; // NOT PRESENT IN OAF } @@ -216,19 +236,22 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List> prepareOtherResearchProductTools( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // NOT PRESENT IN OAF } @Override protected List> prepareOtherResearchProductContactGroups( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // NOT PRESENT IN OAF } @Override protected List> prepareOtherResearchProductContactPersons( - final Document doc, final DataInfo info) { + final Document doc, + final DataInfo info) { return new ArrayList<>(); // NOT PRESENT IN OAF } @@ -251,15 +274,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final String otherId = createOpenaireId(50, originalId, false); res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, - lastUpdateTimestamp)); + .add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); } } return res; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index d51433a182..e7edfb2487 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -3,13 +3,11 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF; @@ -45,9 +43,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; - public static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - public static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); - public OdfToOafMapper(final Map code2name) { super(code2name); } 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 6ff76e839a..631e7235ec 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 @@ -75,7 +75,7 @@ public class MappersTest { .get(); assertEquals("0000-0001-6651-1178", pid.getValue()); assertEquals("ORCID", pid.getQualifier().getClassid()); - assertEquals("ORCID", pid.getQualifier().getClassname()); + assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname()); assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid()); assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename()); assertEquals("Votsi,Nefta", author.get().getFullname()); From 3cf2796ac6a945fe63377b3b5c062bed5af21014 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 22 May 2020 12:34:00 +0200 Subject: [PATCH 47/70] code formatting --- .../eu/dnetlib/dhp/oa/dedup/AuthorMerger.java | 259 +++++++++--------- .../dhp/oa/dedup/DedupRecordFactory.java | 8 +- .../dhp/oa/dedup/EntityMergerTest.java | 69 ++--- .../raw/AbstractMdRecordToOafMapper.java | 141 ++++++---- .../dhp/oa/graph/raw/OafToOafMapper.java | 35 ++- .../dhp/oa/graph/raw/OdfToOafMapper.java | 47 +++- 6 files changed, 315 insertions(+), 244 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java index 108f4a4bec..43df19f8a4 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -1,159 +1,164 @@ -package eu.dnetlib.dhp.oa.dedup; -import com.wcohen.ss.JaroWinkler; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.pace.model.Person; -import org.apache.commons.lang3.StringUtils; -import scala.Tuple2; +package eu.dnetlib.dhp.oa.dedup; import java.text.Normalizer; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; + +import com.wcohen.ss.JaroWinkler; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.model.Person; +import scala.Tuple2; + public class AuthorMerger { - private static final Double THRESHOLD = 0.95; + private static final Double THRESHOLD = 0.95; - public static List merge(List> authors){ + public static List merge(List> authors) { - authors.sort(new Comparator>() { - @Override - public int compare(List o1, List o2) { - return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); - } - }); + authors.sort(new Comparator>() { + @Override + public int compare(List o1, List o2) { + return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); + } + }); - List author = new ArrayList<>(); + List author = new ArrayList<>(); - for(List a : authors){ - author = mergeAuthor(author, a); - } + for (List a : authors) { + author = mergeAuthor(author, a); + } - return author; + return author; - } + } - public static List mergeAuthor(final List a, final List b) { - int pa = countAuthorsPids(a); - int pb = countAuthorsPids(b); - List base, enrich; - int sa = authorsSize(a); - int sb = authorsSize(b); + public static List mergeAuthor(final List a, final List b) { + int pa = countAuthorsPids(a); + int pb = countAuthorsPids(b); + List base, enrich; + int sa = authorsSize(a); + int sb = authorsSize(b); - if (pa == pb) { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } else { - base = pa > pb ? a : b; - enrich = pa > pb ? b : a; - } - enrichPidFromList(base, enrich); - return base; - } + if (pa == pb) { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; + } else { + base = pa > pb ? a : b; + enrich = pa > pb ? b : a; + } + enrichPidFromList(base, enrich); + return base; + } - private static void enrichPidFromList(List base, List enrich) { - if (base == null || enrich == null) - return; - final Map basePidAuthorMap = base - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap( - a -> a - .getPid() - .stream() - .map(p -> new Tuple2<>(pidToComparableString(p), a))) - .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + private static void enrichPidFromList(List base, List enrich) { + if (base == null || enrich == null) + return; + final Map basePidAuthorMap = base + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> a + .getPid() + .stream() + .map(p -> new Tuple2<>(pidToComparableString(p), a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - final List> pidToEnrich = enrich - .stream() - .filter(a -> a.getPid() != null && a.getPid().size() > 0) - .flatMap( - a -> a - .getPid() - .stream() - .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) - .map(p -> new Tuple2<>(p, a))) - .collect(Collectors.toList()); + final List> pidToEnrich = enrich + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap( + a -> a + .getPid() + .stream() + .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) + .map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); - pidToEnrich - .forEach( - a -> { - Optional> simAuthor = base - .stream() - .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) - .max(Comparator.comparing(Tuple2::_1)); - if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { - Author r = simAuthor.get()._2(); - if (r.getPid() == null) { - r.setPid(new ArrayList<>()); - } - r.getPid().add(a._1()); - } - }); - } + pidToEnrich + .forEach( + a -> { + Optional> simAuthor = base + .stream() + .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) + .max(Comparator.comparing(Tuple2::_1)); + if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { + Author r = simAuthor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } + r.getPid().add(a._1()); + } + }); + } - public static String pidToComparableString(StructuredProperty pid){ - return (pid.getQualifier()!=null? pid.getQualifier().getClassid()!=null?pid.getQualifier().getClassid().toLowerCase():"":"") + (pid.getValue()!=null? pid.getValue().toLowerCase():""); - } + public static String pidToComparableString(StructuredProperty pid) { + return (pid.getQualifier() != null + ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" + : "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + } - public static int countAuthorsPids(List authors) { - if (authors == null) - return 0; + public static int countAuthorsPids(List authors) { + if (authors == null) + return 0; - return (int) authors.stream().filter(AuthorMerger::hasPid).count(); - } + return (int) authors.stream().filter(AuthorMerger::hasPid).count(); + } - private static int authorsSize(List authors) { - if (authors == null) - return 0; - return authors.size(); - } + private static int authorsSize(List authors) { + if (authors == null) + return 0; + return authors.size(); + } - private static Double sim(Author a, Author b) { + private static Double sim(Author a, Author b) { - final Person pa = parse(a); - final Person pb = parse(b); + final Person pa = parse(a); + final Person pb = parse(b); - if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler() - .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); - } else { - return new JaroWinkler() - .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); - } - } + if (pa.isAccurate() & pb.isAccurate()) { + return new JaroWinkler() + .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); + } else { + return new JaroWinkler() + .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); + } + } - private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().size() == 0) - return false; - return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); - } + private static boolean hasPid(Author a) { + if (a == null || a.getPid() == null || a.getPid().size() == 0) + return false; + return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); + } - private static Person parse(Author author) { - if (StringUtils.isNotBlank(author.getSurname())) { - return new Person(author.getSurname() + ", " + author.getName(), false); - } else { - return new Person(author.getFullname(), false); - } - } + private static Person parse(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return new Person(author.getSurname() + ", " + author.getName(), false); + } else { + return new Person(author.getFullname(), false); + } + } - private static String normalize(final String s) { - return nfd(s) - .toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError - // in case - // of large input strings - .replaceAll("(\\W)+", " ") - .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") - .replaceAll("(\\p{Punct})+", " ") - .replaceAll("(\\d)+", " ") - .replaceAll("(\\n)+", " ") - .trim(); - } + private static String normalize(final String s) { + return nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } - private static String nfd(final String s) { - return Normalizer.normalize(s, Normalizer.Form.NFD); - } + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index eed783e536..8028d5a94f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.oa.dedup; import java.io.Serializable; @@ -73,7 +74,8 @@ public class DedupRecordFactory { } public static T entityMerger( - String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) throws IllegalAccessException, InstantiationException { + String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) + throws IllegalAccessException, InstantiationException { T entity = clazz.newInstance(); @@ -87,14 +89,14 @@ public class DedupRecordFactory { entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; - if (r1.getAuthor() != null && r1.getAuthor().size()>0) + if (r1.getAuthor() != null && r1.getAuthor().size() > 0) authors.add(r1.getAuthor()); if (r1.getDateofacceptance() != null) dates.add(r1.getDateofacceptance().getValue()); } }); - //set authors and date + // set authors and date if (ModelSupport.isSubClass(entity, Result.class)) { ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setAuthor(AuthorMerger.merge(authors)); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 526dd73bb0..0a3bf62ea8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -1,5 +1,8 @@ + package eu.dnetlib.dhp.oa.dedup; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; @@ -7,15 +10,13 @@ import java.io.Serializable; import java.nio.file.Paths; import java.util.*; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.pace.util.MapDocumentUtil; import org.codehaus.jackson.map.ObjectMapper; import org.junit.jupiter.api.BeforeEach; - import org.junit.jupiter.api.Test; -import scala.Tuple2; -import static org.junit.jupiter.api.Assertions.assertEquals; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.pace.util.MapDocumentUtil; +import scala.Tuple2; public class EntityMergerTest implements Serializable { @@ -30,9 +31,9 @@ public class EntityMergerTest implements Serializable { public void setUp() throws Exception { testEntityBasePath = Paths - .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) - .toFile() - .getAbsolutePath(); + .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) + .toFile() + .getAbsolutePath(); publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); @@ -45,7 +46,8 @@ public class EntityMergerTest implements Serializable { @Test public void publicationMergerTest() throws InstantiationException, IllegalAccessException { - Publication pub_merged = DedupRecordFactory.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); + Publication pub_merged = DedupRecordFactory + .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); assertEquals(dedupId, pub_merged.getId()); @@ -59,36 +61,36 @@ public class EntityMergerTest implements Serializable { assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation()); assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance()); assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection()); - assertEquals(pub_merged.getInstance().size(),3); + assertEquals(pub_merged.getInstance().size(), 3); assertEquals(pub_merged.getCountry().size(), 2); assertEquals(pub_merged.getSubject().size(), 0); assertEquals(pub_merged.getTitle().size(), 2); - assertEquals(pub_merged.getRelevantdate().size(),0); - assertEquals(pub_merged.getDescription().size(),0); - assertEquals(pub_merged.getSource().size(),0); - assertEquals(pub_merged.getFulltext().size(),0); - assertEquals(pub_merged.getFormat().size(),0); - assertEquals(pub_merged.getContributor().size(),0); - assertEquals(pub_merged.getCoverage().size(),0); - assertEquals(pub_merged.getContext().size(),0); - assertEquals(pub_merged.getExternalReference().size(),0); - assertEquals(pub_merged.getOriginalId().size(),3); - assertEquals(pub_merged.getCollectedfrom().size(),3); - assertEquals(pub_merged.getPid().size(),1); - assertEquals(pub_merged.getExtraInfo().size(),0); + assertEquals(pub_merged.getRelevantdate().size(), 0); + assertEquals(pub_merged.getDescription().size(), 0); + assertEquals(pub_merged.getSource().size(), 0); + assertEquals(pub_merged.getFulltext().size(), 0); + assertEquals(pub_merged.getFormat().size(), 0); + assertEquals(pub_merged.getContributor().size(), 0); + assertEquals(pub_merged.getCoverage().size(), 0); + assertEquals(pub_merged.getContext().size(), 0); + assertEquals(pub_merged.getExternalReference().size(), 0); + assertEquals(pub_merged.getOriginalId().size(), 3); + assertEquals(pub_merged.getCollectedfrom().size(), 3); + assertEquals(pub_merged.getPid().size(), 1); + assertEquals(pub_merged.getExtraInfo().size(), 0); - //verify datainfo + // verify datainfo assertEquals(pub_merged.getDataInfo(), dataInfo); - //verify datepicker + // verify datepicker assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); - //verify authors + // verify authors assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); } - public DataInfo setDI(){ + public DataInfo setDI() { DataInfo dataInfo = new DataInfo(); dataInfo.setTrust("0.9"); dataInfo.setDeletedbyinference(false); @@ -97,13 +99,13 @@ public class EntityMergerTest implements Serializable { return dataInfo; } - public Publication getTopPub(List> publications){ + public Publication getTopPub(List> publications) { Double maxTrust = 0.0; Publication maxPub = new Publication(); for (Tuple2 publication : publications) { Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust()); - if(pubTrust > maxTrust){ + if (pubTrust > maxTrust) { maxTrust = pubTrust; maxPub = publication._2(); } @@ -118,11 +120,11 @@ public class EntityMergerTest implements Serializable { reader = new BufferedReader(new FileReader(path)); String line = reader.readLine(); while (line != null) { - res.add( + res + .add( new Tuple2<>( - MapDocumentUtil.getJPathString("$.id", line), - new ObjectMapper().readValue(line, clazz)) - ); + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); // read next line line = reader.readLine(); } @@ -134,5 +136,4 @@ public class EntityMergerTest implements Serializable { return res; } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 84b200c076..c4639eb44a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -59,8 +59,10 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; - protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier ORCID_PID_TYPE = qualifier( + "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier( + "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Map nsContext = new HashMap<>(); @@ -74,7 +76,8 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier( + "main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); protected AbstractMdRecordToOafMapper(final Map code2name) { this.code2name = code2name; @@ -88,15 +91,20 @@ public abstract class AbstractMdRecordToOafMapper { .parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); final String type = doc.valueOf("//dr:CobjCategory/@type"); - final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - if (collectedFrom == null) { return null; } + if (collectedFrom == null) { + return null; + } final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - if (hostedBy == null) { return null; } + if (hostedBy == null) { + return null; + } final DataInfo info = prepareDataInfo(doc); final long lastUpdateTimestamp = new Date().getTime(); @@ -111,7 +119,9 @@ public abstract class AbstractMdRecordToOafMapper { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); - if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; } + if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { + return null; + } return keyValue(createOpenaireId(10, dsId, true), dsName); } @@ -127,47 +137,47 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = new ArrayList<>(); switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); - p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_DEFAULT_RESULTTYPE); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(ORP_DEFAULT_RESULTTYPE); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; } if (!oafs.isEmpty()) { @@ -196,9 +206,15 @@ public abstract class AbstractMdRecordToOafMapper { final String projectId = createOpenaireId(40, originalId, true); res - .add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, + lastUpdateTimestamp)); res - .add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, + lastUpdateTimestamp)); } } @@ -244,7 +260,9 @@ public abstract class AbstractMdRecordToOafMapper { r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); r.setCollectedfrom(Arrays.asList(collectedFrom)); r - .setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + .setPid( + prepareListStructProps( + doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES @@ -362,7 +380,9 @@ public abstract class AbstractMdRecordToOafMapper { final String sp = n.valueOf("@sp"); final String vol = n.valueOf("@vol"); final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } + if (StringUtils.isNotBlank(name)) { + return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); + } } return null; } @@ -415,7 +435,10 @@ public abstract class AbstractMdRecordToOafMapper { for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; res - .add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info)); + .add( + structuredProperty( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); } return res; } @@ -423,7 +446,9 @@ public abstract class AbstractMdRecordToOafMapper { protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n == null) { return null; } + if (n == null) { + return null; + } final String identifier = n.valueOf("./*[local-name()='identifier']"); final String baseURL = n.valueOf("./*[local-name()='baseURL']"); @@ -438,7 +463,9 @@ public abstract class AbstractMdRecordToOafMapper { protected DataInfo prepareDataInfo(final Document doc) { final Node n = doc.selectSingleNode("//oaf:datainfo"); - if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); } + if (n == null) { + return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + } final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); @@ -450,7 +477,9 @@ public abstract class AbstractMdRecordToOafMapper { final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); final String trust = n.valueOf("./oaf:trust"); - return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + return dataInfo( + deletedbyinference, inferenceprovenance, inferred, false, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } protected Field prepareField(final Node node, final String xpath, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 24a8b45270..af9fe7197e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -56,7 +56,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { } final String pid = e.valueOf("./@nameIdentifier"); - final String type = e.valueOf("./@nameIdentifierScheme") + final String type = e + .valueOf("./@nameIdentifierScheme") .trim() .toUpperCase() .replaceAll(" ", "") @@ -66,7 +67,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { if (StringUtils.isNotBlank(pid)) { if (type.startsWith("ORCID")) { - final String cleanedId = pid.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", ""); + final String cleanedId = pid + .replaceAll("http://orcid.org/", "") + .replaceAll("https://orcid.org/", ""); author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info)); } else if (type.startsWith("MAGID")) { author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info)); @@ -127,7 +130,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final Instance instance = new Instance(); instance - .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); + .setInstancetype( + prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); instance.setCollectedfrom(collectedfrom); instance.setHostedby(hostedby); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); @@ -143,13 +147,14 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); instance - .setUrl(nodes - .stream() - .filter(n -> StringUtils.isNotBlank(n.getText())) - .map(n -> n.getText().trim()) - .filter(u -> u.startsWith("http")) - .distinct() - .collect(Collectors.toCollection(ArrayList::new))); + .setUrl( + nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .distinct() + .collect(Collectors.toCollection(ArrayList::new))); return Lists.newArrayList(instance); } @@ -274,9 +279,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final String otherId = createOpenaireId(50, originalId, false); res - .add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, + lastUpdateTimestamp)); res - .add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, + lastUpdateTimestamp)); } } return res; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index e7edfb2487..9c74c4a938 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -94,7 +94,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : n.selectNodes("./datacite:nameIdentifier")) { final String id = ((Node) o).getText(); - final String type = ((Node) o).valueOf("./@nameIdentifierScheme") + final String type = ((Node) o) + .valueOf("./@nameIdentifierScheme") .trim() .toUpperCase() .replaceAll(" ", "") @@ -119,7 +120,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final Instance instance = new Instance(); instance - .setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); + .setInstancetype( + prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE)); instance.setCollectedfrom(collectedfrom); instance.setHostedby(hostedby); instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); @@ -168,7 +170,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { && !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) { res - .add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info)); + .add( + structuredProperty( + ((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, + info)); } } return res; @@ -220,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected List> prepareOtherResearchProductContactGroups( final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info); + return prepareListFields( + doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info); } @Override protected List> prepareOtherResearchProductContactPersons( final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info); + return prepareListFields( + doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info); } @Override @@ -253,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected List> prepareSoftwareDocumentationUrls( final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); + return prepareListFields( + doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); } // DATASETS @@ -327,16 +335,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { if (type.equalsIgnoreCase("IsSupplementTo")) { res - .add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, + lastUpdateTimestamp)); res - .add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, + lastUpdateTimestamp)); } else if (type.equals("IsPartOf")) { res - .add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp)); + .add( + getRelation( + docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, + lastUpdateTimestamp)); res - .add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp)); - } else {} + .add( + getRelation( + otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, + lastUpdateTimestamp)); + } else { + } } } return res; @@ -344,6 +365,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { - return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE); + return prepareQualifier( + doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, + DNET_DATA_CITE_RESOURCE); } } From 4308f311650bca96eab1ad5d3e09c87f56d97901 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 13:13:01 +0200 Subject: [PATCH 48/70] added fix to make test run --- .../ResultToOrganizationJobTest.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java index 435b766052..cfcccc5f0d 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/ResultToOrganizationJobTest.java @@ -99,6 +99,7 @@ public class ResultToOrganizationJobTest { .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); Assertions.assertEquals(0, tmp.count()); + FileUtils.deleteDirectory(workingDir.toFile()); } /** @@ -171,6 +172,7 @@ public class ResultToOrganizationJobTest { + "(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' " + "or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')") .count()); + FileUtils.deleteDirectory(workingDir.toFile()); } @Test @@ -266,5 +268,6 @@ public class ResultToOrganizationJobTest { "relclass = 'isAuthorInstitutionOf' and " + "substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'") .count()); + FileUtils.deleteDirectory(workingDir.toFile()); } } From 8610ad5142c932a8eddb2deb09475fd7bce1f0d4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 15:32:55 +0200 Subject: [PATCH 49/70] added groupby id to fix multiple result with same id at join step --- .../PrepareResultCommunitySet.java | 24 +++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 5574aad753..5d0b75a8e0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; @@ -19,6 +20,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; public class PrepareResultCommunitySet { @@ -93,10 +95,24 @@ public class PrepareResultCommunitySet { result_organizationset .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class)) .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .toJavaRDD() + .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) + .reduceByKey((a, b) -> { + ArrayList cl = a.getCommunityList(); + b.getCommunityList().stream().forEach(s -> { + if (!cl.contains(s)) { + cl.add(s); + } + }); + a.setCommunityList(cl); + return a; + }) + .map(value -> OBJECT_MAPPER.writeValueAsString(value._2())) + .saveAsTextFile(outputPath, GzipCodec.class); +// .write() +// .mode(SaveMode.Overwrite) +// .option("compression", "gzip") +// .json(outputPath); } private static MapFunction mapResultCommunityFn( From 29066a6b46f94903bdbb709c5bf32552a5be5343 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 15:38:50 +0200 Subject: [PATCH 50/70] applied code cleanup --- .../dhp/bulktag/community/CommunityConfiguration.java | 2 +- .../java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java | 2 +- .../SparkResultToProjectThroughSemRelJob.java | 6 +----- .../SparkResultToOrganizationFromIstRepoJob.java | 4 +--- 4 files changed, 4 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 29ddde15f8..844fe29621 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -131,7 +131,7 @@ public class CommunityConfiguration implements Serializable { p -> { if (p.getSnd() == null) return p.getFst(); - if (((SelectionConstraints) p.getSnd()).verifyCriteria(param)) + if (p.getSnd().verifyCriteria(param)) return p.getFst(); else return null; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java index 3d0db20632..f54a1cebab 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/VerbResolver.java @@ -34,7 +34,7 @@ public class VerbResolver implements Serializable { .collect( Collectors .toMap( - value -> (String) ((ClassInfo) value) + value -> (String) value .getAnnotationInfo() .get(0) .getParameterValues() diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index 1f6264c186..17f6a057d8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -105,11 +105,7 @@ public class SparkResultToProjectThroughSemRelJob { .stream() .forEach( (p -> { - if (potential_update - .getProjectSet() - .contains(p)) { - potential_update.getProjectSet().remove(p); - } + potential_update.getProjectSet().remove(p); })); } String resId = potential_update.getResultId(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index 0c5e1d8be6..ff34bd42a7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -136,9 +136,7 @@ public class SparkResultToOrganizationFromIstRepoJob { .stream() .forEach( rId -> { - if (organization_list.contains(rId)) { - organization_list.remove(rId); - } + organization_list.remove(rId); }); } String resultId = potential_update.getResultId(); From eb606dc1e298f397b69464eb98b96fb5c9374aea Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 May 2020 17:17:41 +0200 Subject: [PATCH 51/70] partial implementation of events with rels --- .../broker/oa/GenerateEventsApplication.java | 46 ++++++------- .../EnrichMissingDatasetIsReferencedBy.java | 38 ----------- .../EnrichMissingDatasetIsRelatedTo.java | 38 ----------- .../EnrichMissingDatasetIsSupplementedBy.java | 38 ----------- .../EnrichMissingDatasetIsSupplementedTo.java | 38 ----------- .../EnrichMissingDatasetReferences.java | 38 ----------- ...nrichMissingPublicationIsReferencedBy.java | 42 ------------ .../EnrichMissingPublicationIsRelatedTo.java | 42 ------------ ...ichMissingPublicationIsSupplementedBy.java | 42 ------------ ...ichMissingPublicationIsSupplementedTo.java | 42 ------------ .../EnrichMissingPublicationReferences.java | 42 ------------ .../AbstractEnrichMissingDataset.java | 63 ++++++++++++++++++ .../EnrichMissingDatasetIsReferencedBy.java | 12 ++++ .../EnrichMissingDatasetIsRelatedTo.java | 12 ++++ .../EnrichMissingDatasetIsSupplementedBy.java | 12 ++++ .../EnrichMissingDatasetIsSupplementedTo.java | 12 ++++ .../EnrichMissingDatasetReferences.java | 12 ++++ .../EnrichMissingProject.java | 3 +- .../EnrichMoreProject.java | 3 +- .../AbstractEnrichMissingPublication.java | 64 +++++++++++++++++++ ...nrichMissingPublicationIsReferencedBy.java | 12 ++++ .../EnrichMissingPublicationIsRelatedTo.java | 12 ++++ ...ichMissingPublicationIsSupplementedBy.java | 12 ++++ ...ichMissingPublicationIsSupplementedTo.java | 12 ++++ .../EnrichMissingPublicationReferences.java | 12 ++++ .../{ => simple}/EnrichMissingAbstract.java | 3 +- .../EnrichMissingAuthorOrcid.java | 3 +- .../{ => simple}/EnrichMissingOpenAccess.java | 3 +- .../{ => simple}/EnrichMissingPid.java | 3 +- .../EnrichMissingPublicationDate.java | 3 +- .../{ => simple}/EnrichMissingSoftware.java | 3 +- .../{ => simple}/EnrichMissingSubject.java | 3 +- .../{ => simple}/EnrichMoreOpenAccess.java | 3 +- .../matchers/{ => simple}/EnrichMorePid.java | 3 +- .../{ => simple}/EnrichMoreSoftware.java | 3 +- .../{ => simple}/EnrichMoreSubject.java | 3 +- .../dhp/broker/oa/util/ConversionUtils.java | 13 ++++ 37 files changed, 309 insertions(+), 436 deletions(-) delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => relatedProjects}/EnrichMissingProject.java (90%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => relatedProjects}/EnrichMoreProject.java (90%) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingAbstract.java (90%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingAuthorOrcid.java (90%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingOpenAccess.java (93%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingPid.java (91%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingPublicationDate.java (90%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingSoftware.java (91%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMissingSubject.java (93%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMoreOpenAccess.java (93%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMorePid.java (92%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMoreSoftware.java (91%) rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/{ => simple}/EnrichMoreSubject.java (93%) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index fa425a1819..d5e577972d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -30,30 +30,30 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.EventFactory; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsReferencedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsRelatedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetIsSupplementedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingDatasetReferences; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsReferencedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsRelatedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedBy; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationIsSupplementedTo; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationReferences; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSoftware; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreProject; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSoftware; -import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetReferences; +import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMissingProject; +import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMoreProject; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsReferencedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsRelatedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedBy; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedTo; +import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationReferences; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAbstract; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAuthorOrcid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSoftware; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSubject; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSoftware; +import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.common.HdfsSupport; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java deleted file mode 100644 index 3b9326fef2..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsReferencedBy.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsReferencedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsReferencedBy() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java deleted file mode 100644 index 35f7c52b42..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsRelatedTo.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsRelatedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsRelatedTo() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java deleted file mode 100644 index 1faa305b52..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedBy.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsSupplementedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsSupplementedBy() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java deleted file mode 100644 index d1b067272d..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetIsSupplementedTo.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetIsSupplementedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetIsSupplementedTo() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java deleted file mode 100644 index ce6adeba27..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingDatasetReferences.java +++ /dev/null @@ -1,38 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingDatasetReferences - extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { - - public EnrichMissingDatasetReferences() { - super(true); - } - - @Override - protected List> findUpdates(final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return null; - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Dataset highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_DATASET_REFERENCES, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); - } -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java deleted file mode 100644 index 8bcee5a1fc..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsReferencedBy.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsReferencedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsReferencedBy() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java deleted file mode 100644 index 0c16f9f564..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsRelatedTo.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsRelatedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsRelatedTo() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java deleted file mode 100644 index 0b3c332708..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedBy.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsSupplementedBy - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsSupplementedBy() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java deleted file mode 100644 index 0e72a84239..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationIsSupplementedTo.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationIsSupplementedTo - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationIsSupplementedTo() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java deleted file mode 100644 index 6d1124974e..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationReferences.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.matchers; - -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; - -import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class EnrichMissingPublicationReferences - extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { - - public EnrichMissingPublicationReferences() { - super(true); - } - - @Override - protected List> findUpdates( - final Pair> source, - final Pair> target) { - // TODO Auto-generated method stub - return Arrays.asList(); - } - - @Override - protected UpdateInfo generateUpdateInfo( - final eu.dnetlib.broker.objects.Publication highlightValue, - final Pair> source, - final Pair> target) { - return new UpdateInfo<>( - Topic.ENRICH_MISSING_PUBLICATION_REFERENCES, - highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common - rel -> rel.getOriginalId()); - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java new file mode 100644 index 0000000000..321fd43184 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java @@ -0,0 +1,63 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Result; + +public abstract class AbstractEnrichMissingDataset + extends UpdateMatcher>, eu.dnetlib.broker.objects.Dataset> { + + private final Topic topic; + + public AbstractEnrichMissingDataset(final Topic topic) { + super(true); + this.topic = topic; + } + + @Override + protected final List> findUpdates( + final Pair> source, + final Pair> target) { + + final Set existingDatasets = target + .getRight() + .stream() + .map(Dataset::getId) + .collect(Collectors.toSet()); + + return source + .getRight() + .stream() + .filter(d -> !existingDatasets.contains(d.getId())) + .map(ConversionUtils::oafDatasetToBrokerDataset) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + + } + + @Override + protected final UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Dataset highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + getTopic(), + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> p.getDatasets().add(rel), + rel -> rel.getInstances().get(0).getUrl()); + } + + public Topic getTopic() { + return topic; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java new file mode 100644 index 0000000000..74ce761f48 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsReferencedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsReferencedBy() { + super(Topic.ENRICH_MISSING_DATASET_IS_REFERENCED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java new file mode 100644 index 0000000000..05a8910591 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsRelatedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsRelatedTo() { + super(Topic.ENRICH_MISSING_DATASET_IS_RELATED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java new file mode 100644 index 0000000000..23bd68fa1b --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsSupplementedBy() { + super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java new file mode 100644 index 0000000000..03160b6f00 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetIsSupplementedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetIsSupplementedTo() { + super(Topic.ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java new file mode 100644 index 0000000000..bf1df053d6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/EnrichMissingDatasetReferences.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset { + + public EnrichMissingDatasetReferences() { + super(Topic.ENRICH_MISSING_DATASET_REFERENCES); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java index 0197c99b1b..461266d567 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java index 4bf45d9437..d9bfb62d59 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java new file mode 100644 index 0000000000..405b06ca6a --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -0,0 +1,64 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; + +import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public abstract class AbstractEnrichMissingPublication + extends UpdateMatcher>, eu.dnetlib.broker.objects.Publication> { + + private final Topic topic; + + public AbstractEnrichMissingPublication(final Topic topic) { + super(true); + this.topic = topic; + } + + @Override + protected final List> findUpdates( + final Pair> source, + final Pair> target) { + + final Set existingPublications = target + .getRight() + .stream() + .map(Publication::getId) + .collect(Collectors.toSet()); + + return source + .getRight() + .stream() + .filter(d -> !existingPublications.contains(d.getId())) + .map(ConversionUtils::oafPublicationToBrokerPublication) + .map(i -> generateUpdateInfo(i, source, target)) + .collect(Collectors.toList()); + + } + + @Override + protected final UpdateInfo generateUpdateInfo( + final eu.dnetlib.broker.objects.Publication highlightValue, + final Pair> source, + final Pair> target) { + return new UpdateInfo<>( + getTopic(), + highlightValue, source.getLeft(), target.getLeft(), + (p, rel) -> { + }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + rel -> rel.getInstances().get(0).getUrl()); + } + + public Topic getTopic() { + return topic; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java new file mode 100644 index 0000000000..73fa8a45f6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsReferencedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsReferencedBy() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java new file mode 100644 index 0000000000..361ea3b342 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsRelatedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsRelatedTo() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_RELATED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java new file mode 100644 index 0000000000..7e8863b1ed --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedBy.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsSupplementedBy() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java new file mode 100644 index 0000000000..dc4e513777 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationIsSupplementedTo.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationIsSupplementedTo() { + super(Topic.ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java new file mode 100644 index 0000000000..5198098bcf --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/EnrichMissingPublicationReferences.java @@ -0,0 +1,12 @@ + +package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications; + +import eu.dnetlib.dhp.broker.model.Topic; + +public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication { + + public EnrichMissingPublicationReferences() { + super(Topic.ENRICH_MISSING_PUBLICATION_REFERENCES); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java index 6dab6355fd..a418b633ed 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index c7146ad79a..b5c2f7e723 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index 81263c6c3f..c7e9dcbc11 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java index 5f10bb4d9e..522d46d402 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java similarity index 90% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java index 19ef2bab7e..197ace97c8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java @@ -1,11 +1,12 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java index 954ee48be7..4fcba43a40 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSoftware.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index a7c72f6ea3..290bad48b3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -8,6 +8,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Qualifier; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index 2cd2775c9e..c376da44d2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java similarity index 92% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java index 048d19747d..2ee327c831 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Pid; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java similarity index 91% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java index 9760504f64..a1affff623 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSoftware.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.Arrays; import java.util.List; @@ -7,6 +7,7 @@ import java.util.List; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java similarity index 93% rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index 67c2f01161..b38445e885 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.broker.oa.matchers; +package eu.dnetlib.dhp.broker.oa.matchers.simple; import java.util.List; import java.util.Set; @@ -8,6 +8,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; +import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.schema.oaf.Result; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 2e2ce202ad..2f87d0ee76 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -7,6 +7,8 @@ import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class ConversionUtils { @@ -33,4 +35,15 @@ public class ConversionUtils { return Pair.of(sp.getQualifier().getClassid(), sp.getValue()); } + public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) { + final eu.dnetlib.broker.objects.Dataset res = new eu.dnetlib.broker.objects.Dataset(); + // TODO + return res; + } + + public static final eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication d) { + final eu.dnetlib.broker.objects.Publication res = new eu.dnetlib.broker.objects.Publication(); + // TODO + return res; + } } From 0fd0c7d72520f97322504f405496358a3778ecdd Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 22 May 2020 17:24:57 +0200 Subject: [PATCH 52/70] reimplementation of the sim between two authors. now it takes into account both name and surname. threshold incremented to 1.0 if the name is too short --- .../eu/dnetlib/dhp/oa/dedup/AuthorMerger.java | 41 +++++++++++-------- .../dhp/oa/dedup/EntityMergerTest.java | 13 ++++++ .../dhp/dedup/json/publication_merge2.json | 4 ++ 3 files changed, 40 insertions(+), 18 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge2.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java index 43df19f8a4..5e63c4b656 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -20,12 +20,7 @@ public class AuthorMerger { public static List merge(List> authors) { - authors.sort(new Comparator>() { - @Override - public int compare(List o1, List o2) { - return -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)); - } - }); + authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2))); List author = new ArrayList<>(); @@ -86,20 +81,28 @@ public class AuthorMerger { .stream() .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) .max(Comparator.comparing(Tuple2::_1)); - if (simAuthor.isPresent() && simAuthor.get()._1() > THRESHOLD) { - Author r = simAuthor.get()._2(); - if (r.getPid() == null) { - r.setPid(new ArrayList<>()); + + if(simAuthor.isPresent()) { + double th = THRESHOLD; + //increase the threshold if the surname is too short + if (simAuthor.get()._2().getSurname() != null && simAuthor.get()._2().getSurname().length()<=3) + th = 0.99; + + if (simAuthor.get()._1() > th) { + Author r = simAuthor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } + r.getPid().add(a._1()); } - r.getPid().add(a._1()); } }); } public static String pidToComparableString(StructuredProperty pid) { - return (pid.getQualifier() != null - ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" - : "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + return (pid.getQualifier() != null ? + pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); } public static int countAuthorsPids(List authors) { @@ -120,12 +123,14 @@ public class AuthorMerger { final Person pa = parse(a); final Person pb = parse(b); + //if both are accurate (e.g. they have name and surname) if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler() - .score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())); + return + new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString()))*0.5 + + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString()))*0.5; } else { - return new JaroWinkler() - .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); + return + new JaroWinkler().score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 0a3bf62ea8..55879030be 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -21,6 +21,7 @@ import scala.Tuple2; public class EntityMergerTest implements Serializable { List> publications; + List> publications2; String testEntityBasePath; DataInfo dataInfo; @@ -36,6 +37,7 @@ public class EntityMergerTest implements Serializable { .getAbsolutePath(); publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); + publications2 = readSample(testEntityBasePath + "/publication_merge2.json", Publication.class); pub_top = getTopPub(publications); @@ -90,6 +92,17 @@ public class EntityMergerTest implements Serializable { assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); } + @Test + public void publicationMergerTest2() throws InstantiationException, IllegalAccessException, IOException { + + Publication pub_merged = DedupRecordFactory + .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); + + assertEquals(pub_merged.getAuthor().size(), 27); + // insert assertions here + + } + public DataInfo setDI() { DataInfo dataInfo = new DataInfo(); dataInfo.setTrust("0.9"); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge2.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge2.json new file mode 100644 index 0000000000..a7937c2873 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge2.json @@ -0,0 +1,4 @@ +{"id":"50|doajarticles::842fa3b99fcdccafb4d5c8a815f56efa","dateofcollection":"2020-04-06T12:22:31.216Z","title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Increased Expression of Herpes Virus-Encoded hsv1-miR-H18 and hsv2-miR-H9-5p in Cancer-Containing Prostate Tissue Compared to That in Benign Prostate 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Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Diseases of the genitourinary system. Urology"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"RC870-923"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open 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In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"dataInfo":null,"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed 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In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue.","dateofcollection":"false\u0004\u0004false\u0004false\u0004\u0005\u0005\u0005\u0004\u00032016-6-30","title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":null,"inferred":null,"invisible":null,"provenanceaction":null,"trust":null},"qualifier":{"classid":"","classname":null,"schemeid":null,"schemename":null},"value":"false"},{"dataInfo":{"deletedbyinference":null,"inferenceprovenance":null,"inferred":null,"invisible":null,"provenanceaction":null,"trust":null},"qualifier":null,"value":null}],"publisher":{"dataInfo":{"deletedbyinference":null,"inferenceprovenance":null,"inferred":null,"invisible":null,"provenanceaction":null,"trust":null},"value":""},"bestaccessright":{"classid":"","classname":null,"schemeid":null,"schemename":null},"dataInfo":{"deletedbyinference":null,"inferenceprovenance":"UNKNOWN\u0005not available\u0005dnet:access_modes\u0005dnet:access_modes\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u000510|openaire____::081b82f96300b6a6e3d282bad31cb6e2\u0005Crossref\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u000510|openaire____::55045bd2a65019fd8e6741a755395c8c\u0005Unknown Repository\u00040001\u0005Article\u0005dnet:publication_resource\u0005dnet:publication_resource\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004http://einj.org/upload/pdf/inj-1632552-276.pdf","inferred":null,"invisible":null,"provenanceaction":{"classid":"UNKNOWN\u0005not available\u0005dnet:access_modes\u0005dnet:access_modes","classname":"false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u000510|openaire____::5f532a3fc4f1ea403f37070f59a7a53a\u0005Microsoft Academic Graph","schemeid":"false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005","schemename":""},"trust":"RESTRICTED\u0005Restricted\u0005dnet:access_modes\u0005dnet:access_modes\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u000510|openaire____::081b82f96300b6a6e3d282bad31cb6e2\u0005Crossref\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u000510|doajarticles::52db9a4f8e176f6e8e1d9f0c1e0a2de0\u0005International Neurourology Journal\u00040001\u0005Article\u0005dnet:publication_resource\u0005dnet:publication_resource\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004false\u0006\u0006false\u0006false\u0006\u0007\u0007\u0007\u0006\u0005\u0004http://dx.doi.org/10.5213/inj.1632552.276"},"collectedfrom":null,"pid":null,"author":null,"resulttype":null,"language":null,"country":null,"subject":null,"description":null,"dateofacceptance":null,"embargoenddate":null,"resourcetype":null,"context":null,"instance":null} \ No newline at end of file From 0d1ec1913f40827b5e3fbda2575082072c9123ba Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 18:42:25 +0200 Subject: [PATCH 53/70] added fix to avoid duplication of results --- .../PrepareResultCommunitySet.java | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 5d0b75a8e0..750d333e53 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -95,20 +95,20 @@ public class PrepareResultCommunitySet { result_organizationset .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class)) .filter(Objects::nonNull) - .toJavaRDD() - .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) - .reduceByKey((a, b) -> { - ArrayList cl = a.getCommunityList(); - b.getCommunityList().stream().forEach(s -> { - if (!cl.contains(s)) { - cl.add(s); - } - }); - a.setCommunityList(cl); - return a; - }) - .map(value -> OBJECT_MAPPER.writeValueAsString(value._2())) - .saveAsTextFile(outputPath, GzipCodec.class); + .toJavaRDD() + .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) + .reduceByKey((a, b) -> { + ArrayList cl = a.getCommunityList(); + b.getCommunityList().stream().forEach(s -> { + if (!cl.contains(s)) { + cl.add(s); + } + }); + a.setCommunityList(cl); + return a; + }) + .map(value -> OBJECT_MAPPER.writeValueAsString(value._2())) + .saveAsTextFile(outputPath, GzipCodec.class); // .write() // .mode(SaveMode.Overwrite) // .option("compression", "gzip") From 7181807e644ed8db9765aa45a7b4b3ff65d49a60 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 23 May 2020 09:51:48 +0200 Subject: [PATCH 54/70] code formatting --- .../eu/dnetlib/dhp/oa/dedup/AuthorMerger.java | 25 ++++++++++--------- .../dhp/oa/dedup/EntityMergerTest.java | 2 +- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java index 5e63c4b656..ee5fd51656 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -82,10 +82,11 @@ public class AuthorMerger { .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) .max(Comparator.comparing(Tuple2::_1)); - if(simAuthor.isPresent()) { + if (simAuthor.isPresent()) { double th = THRESHOLD; - //increase the threshold if the surname is too short - if (simAuthor.get()._2().getSurname() != null && simAuthor.get()._2().getSurname().length()<=3) + // increase the threshold if the surname is too short + if (simAuthor.get()._2().getSurname() != null + && simAuthor.get()._2().getSurname().length() <= 3) th = 0.99; if (simAuthor.get()._1() > th) { @@ -100,9 +101,10 @@ public class AuthorMerger { } public static String pidToComparableString(StructuredProperty pid) { - return (pid.getQualifier() != null ? - pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" : "") - + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + return (pid.getQualifier() != null + ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" + : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); } public static int countAuthorsPids(List authors) { @@ -123,14 +125,13 @@ public class AuthorMerger { final Person pa = parse(a); final Person pb = parse(b); - //if both are accurate (e.g. they have name and surname) + // if both are accurate (e.g. they have name and surname) if (pa.isAccurate() & pb.isAccurate()) { - return - new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString()))*0.5 - + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString()))*0.5; + return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5 + + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5; } else { - return - new JaroWinkler().score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); + return new JaroWinkler() + .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 55879030be..144d5d49a0 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -96,7 +96,7 @@ public class EntityMergerTest implements Serializable { public void publicationMergerTest2() throws InstantiationException, IllegalAccessException, IOException { Publication pub_merged = DedupRecordFactory - .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); + .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); assertEquals(pub_merged.getAuthor().size(), 27); // insert assertions here From 6b56cae57db666e79866c627fa1d95cf080c30fe Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 23 May 2020 09:57:39 +0200 Subject: [PATCH 55/70] added mapping for bestaccessrights --- .../dhp/schema/common/LicenseComparator.java | 69 +++++++++++++++++++ .../raw/AbstractMdRecordToOafMapper.java | 52 +++++++++----- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 21 +++++- 3 files changed, 124 insertions(+), 18 deletions(-) create mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java new file mode 100644 index 0000000000..1fb8421804 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.dhp.schema.common; + +import eu.dnetlib.dhp.schema.oaf.Qualifier; + +import java.util.Comparator; + +public class LicenseComparator implements Comparator { + + @Override + public int compare(Qualifier left, Qualifier right) { + + if (left == null && right == null) + return 0; + if (left == null) + return 1; + if (right == null) + return -1; + + String lClass = left.getClassid(); + String rClass = right.getClassid(); + + if (lClass.equals(rClass)) + return 0; + + if (lClass.equals("OPEN SOURCE")) + return -1; + if (rClass.equals("OPEN SOURCE")) + return 1; + + if (lClass.equals("OPEN")) + return -1; + if (rClass.equals("OPEN")) + return 1; + + if (lClass.equals("6MONTHS")) + return -1; + if (rClass.equals("6MONTHS")) + return 1; + + if (lClass.equals("12MONTHS")) + return -1; + if (rClass.equals("12MONTHS")) + return 1; + + if (lClass.equals("EMBARGO")) + return -1; + if (rClass.equals("EMBARGO")) + return 1; + + if (lClass.equals("RESTRICTED")) + return -1; + if (rClass.equals("RESTRICTED")) + return 1; + + if (lClass.equals("CLOSED")) + return -1; + if (rClass.equals("CLOSED")) + return 1; + + if (lClass.equals("UNKNOWN")) + return -1; + if (rClass.equals("UNKNOWN")) + return 1; + + // Else (but unlikely), lexicographical ordering will do. + return lClass.compareTo(rClass); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index c4639eb44a..46fff2f425 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -10,24 +10,12 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import java.util.*; +import eu.dnetlib.dhp.schema.common.LicenseComparator; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; @@ -285,7 +273,9 @@ public abstract class AbstractMdRecordToOafMapper { r.setCoverage(prepareCoverages(doc, info)); r.setContext(prepareContexts(doc, info)); r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + r.setInstance(instances); + r.setBestaccessright(getBestAccessRights(instances)); } private List prepareContexts(final Document doc, final DataInfo info) { @@ -368,6 +358,34 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + protected static Qualifier getBestAccessRights(List instanceList) { + if (instanceList != null) { + final Optional min = instanceList + .stream() + .map(i -> i.getAccessright()) + .min(new LicenseComparator()); + + final Qualifier rights = min.isPresent() ? min.get() : new Qualifier(); + + if (StringUtils.isBlank(rights.getClassid())) { + rights.setClassid(UNKNOWN); + } + if (StringUtils.isBlank(rights.getClassname()) + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + rights.setClassname(NOT_AVAILABLE); + } + if (StringUtils.isBlank(rights.getSchemeid())) { + rights.setSchemeid(DNET_ACCESS_MODES); + } + if (StringUtils.isBlank(rights.getSchemename())) { + rights.setSchemename(DNET_ACCESS_MODES); + } + + return rights; + } + return null; + } + private Journal prepareJournal(final Document doc, final DataInfo info) { final Node n = doc.selectSingleNode("//oaf:journal"); if (n != null) { 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 631e7235ec..e9ee2dabe9 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 @@ -85,8 +85,18 @@ public class MappersTest { assertTrue(p.getSubject().size() > 0); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); - assertTrue(p.getInstance().size() > 0); + assertNotNull(p.getInstance()); + assertTrue(p.getInstance().size() > 0); + p.getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); + + assertNotNull(p.getBestaccessright()); + assertEquals("OPEN", p.getBestaccessright().getClassid()); assertValidId(r1.getSource()); assertValidId(r1.getTarget()); assertValidId(r2.getSource()); @@ -164,6 +174,15 @@ public class MappersTest { assertTrue(d.getContext().size() > 0); assertTrue(d.getContext().get(0).getId().length() > 0); + assertNotNull(d.getInstance()); + assertTrue(d.getInstance().size() > 0); + d.getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); + assertValidId(r1.getSource()); assertValidId(r1.getTarget()); assertValidId(r2.getSource()); From de108f54d6f3ac33a57db8d5737d10557d9637d2 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Sat, 23 May 2020 10:21:19 +0200 Subject: [PATCH 56/70] code formatting --- .../dhp/schema/common/LicenseComparator.java | 4 +-- .../raw/AbstractMdRecordToOafMapper.java | 10 +++---- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 26 ++++++++++--------- 3 files changed, 21 insertions(+), 19 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java index 1fb8421804..db523ad1ac 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.schema.common; -import eu.dnetlib.dhp.schema.oaf.Qualifier; - import java.util.Comparator; +import eu.dnetlib.dhp.schema.oaf.Qualifier; + public class LicenseComparator implements Comparator { @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 46fff2f425..5c89d5096f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -15,13 +15,13 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; import java.util.*; -import eu.dnetlib.dhp.schema.common.LicenseComparator; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; +import eu.dnetlib.dhp.schema.common.LicenseComparator; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -361,9 +361,9 @@ public abstract class AbstractMdRecordToOafMapper { protected static Qualifier getBestAccessRights(List instanceList) { if (instanceList != null) { final Optional min = instanceList - .stream() - .map(i -> i.getAccessright()) - .min(new LicenseComparator()); + .stream() + .map(i -> i.getAccessright()) + .min(new LicenseComparator()); final Qualifier rights = min.isPresent() ? min.get() : new Qualifier(); @@ -371,7 +371,7 @@ public abstract class AbstractMdRecordToOafMapper { rights.setClassid(UNKNOWN); } if (StringUtils.isBlank(rights.getClassname()) - || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { rights.setClassname(NOT_AVAILABLE); } if (StringUtils.isBlank(rights.getSchemeid())) { 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 e9ee2dabe9..b9da9fb297 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 @@ -88,12 +88,13 @@ public class MappersTest { assertNotNull(p.getInstance()); assertTrue(p.getInstance().size() > 0); - p.getInstance() - .stream() - .forEach(i -> { - assertNotNull(i.getAccessright()); - assertEquals("OPEN", i.getAccessright().getClassid()); - }); + p + .getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); @@ -176,12 +177,13 @@ public class MappersTest { assertNotNull(d.getInstance()); assertTrue(d.getInstance().size() > 0); - d.getInstance() - .stream() - .forEach(i -> { - assertNotNull(i.getAccessright()); - assertEquals("OPEN", i.getAccessright().getClassid()); - }); + d + .getInstance() + .stream() + .forEach(i -> { + assertNotNull(i.getAccessright()); + assertEquals("OPEN", i.getAccessright().getClassid()); + }); assertValidId(r1.getSource()); assertValidId(r1.getTarget()); From 0ab0206b4d42452a99625043ddecdc75f474d4df Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 May 2020 10:11:41 +0200 Subject: [PATCH 57/70] removed null objects from flattened Field in mergeLists --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 09742748d7..2823ee49dd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -106,6 +106,7 @@ public abstract class OafEntity extends Oaf implements Serializable { .stream(lists) .filter(Objects::nonNull) .flatMap(List::stream) + .filter(Objects::nonNull) .distinct() .collect(Collectors.toList()); } From 4b34872b44701581d5378c13765483e6d42fd77f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 May 2020 10:14:15 +0200 Subject: [PATCH 58/70] using Objects.equals to check Field equivalence --- dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java index 1a85c6842d..8358bc4b37 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class Field implements Serializable { @@ -39,6 +40,6 @@ public class Field implements Serializable { if (getClass() != obj.getClass()) return false; Field other = (Field) obj; - return getValue().equals(other.getValue()); + return Objects.equals(getValue(), other.getValue()); } } From 8f6ce970f9e527d30f30cf69882cfc67505d70bf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:25:55 +0200 Subject: [PATCH 59/70] moved PacePerson to dhp-common to avoid conflict in dependency with graph-mapper --- .../src/main/java/eu/dnetlib/dhp}/common/PacePerson.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename {dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw => dhp-common/src/main/java/eu/dnetlib/dhp}/common/PacePerson.java (99%) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java similarity index 99% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java index 6e474f2f38..1909ddcca6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.oa.graph.raw.common; +package eu.dnetlib.dhp.common; import java.nio.charset.StandardCharsets; import java.text.Normalizer; From b258f99ece5ab9ff2ffce961dc91d18383690947 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:26:48 +0200 Subject: [PATCH 60/70] fix for issue that duplicated result --- .../PrepareDatasourceCountryAssociation.java | 65 ++++++++++++------- .../PrepareResultCountrySet.java | 38 +++++++++-- 2 files changed, 76 insertions(+), 27 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 98b573102a..f28c5aa06d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -77,9 +77,15 @@ public class PrepareDatasourceCountryAssociation { List allowedtypes, String inputPath, String outputPath) { - String whitelisted = ""; - for (String i : whitelist) { - whitelisted += " OR id = '" + i + "'"; + String whitelisted = " d.id = '" + whitelist.get(0) + "'"; + for (int i = 1; i < whitelist.size(); i++) { + whitelisted += " OR d.id = '" + whitelist.get(i) + "'"; + } + + String allowed = "d.datasourcetype.classid = '" + allowedtypes.get(0) + "'"; + + for (int i = 1; i < allowedtypes.size(); i++) { + allowed += " OR d.datasourcetype.classid = '" + allowedtypes.get(i) + "'"; } Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class); @@ -90,26 +96,39 @@ public class PrepareDatasourceCountryAssociation { relation.createOrReplaceTempView("relation"); organization.createOrReplaceTempView("organization"); - String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " - + "FROM ( SELECT id " - + " FROM datasource " - + " WHERE (datainfo.deletedbyinference = false " - + whitelisted - + ") " - + getConstraintList("datasourcetype.classid = '", allowedtypes) - + ") d " - + "JOIN ( SELECT source, target " - + " FROM relation " - + " WHERE relclass = '" - + ModelConstants.IS_PROVIDED_BY - + "' " - + " AND datainfo.deletedbyinference = false ) rel " - + "ON d.id = rel.source " - + "JOIN (SELECT id, country " - + " FROM organization " - + " WHERE datainfo.deletedbyinference = false " - + " AND length(country.classid) > 0) o " - + "ON o.id = rel.target"; +// String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " +// + "FROM ( SELECT id " +// + " FROM datasource " +// + " WHERE (datainfo.deletedbyinference = false " +// + whitelisted +// + ") " +// + getConstraintList("datasourcetype.classid = '", allowedtypes) +// + ") d " +// + "JOIN ( SELECT source, target " +// + " FROM relation " +// + " WHERE relclass = '" +// + ModelConstants.IS_PROVIDED_BY +// + "' " +// + " AND datainfo.deletedbyinference = false ) rel " +// + "ON d.id = rel.source " +// + "JOIN (SELECT id, country " +// + " FROM organization " +// + " WHERE datainfo.deletedbyinference = false " +// + " AND length(country.classid) > 0) o " +// + "ON o.id = rel.target"; + + String query = "SELECT source dataSourceId, " + + "named_struct('classid', country.classid, 'classname', country.classname) country " + + "FROM datasource d " + + "JOIN relation rel " + + "ON d.id = rel.source " + + "JOIN organization o " + + "ON o.id = rel.target " + + "WHERE rel.datainfo.deletedbyinference = false " + + "and rel.relclass = '" + ModelConstants.IS_PROVIDED_BY + "'" + + "and o.datainfo.deletedbyinference = false " + + "and length(o.country.classid) > 0 " + + "and (" + allowed + " or " + whitelisted + ")"; spark .sql(query) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java index 34b3764131..8d0d6c48b9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java @@ -4,7 +4,12 @@ package eu.dnetlib.dhp.countrypropagation; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import java.util.ArrayList; +import java.util.Set; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; @@ -13,6 +18,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.*; +import scala.Tuple2; public class PrepareResultCountrySet { private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); @@ -60,6 +66,7 @@ public class PrepareResultCountrySet { conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); getPotentialResultToUpdate( spark, inputPath, @@ -89,10 +96,33 @@ public class PrepareResultCountrySet { spark .sql(RESULT_COUNTRYSET_QUERY) .as(Encoders.bean(ResultCountrySet.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); + .toJavaRDD() + .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) + .reduceByKey((a, b) -> { + ArrayList countryList = a.getCountrySet(); + Set countryCodes = countryList + .stream() + .map(country -> country.getClassid()) + .collect(Collectors.toSet()); + b + .getCountrySet() + .stream() + .forEach(c -> { + if (!countryCodes.contains(c.getClassid())) { + countryList.add(c); + countryCodes.add(c.getClassid()); + } + + }); + a.setCountrySet(countryList); + return a; + }) + .map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2())) + .saveAsTextFile(outputPath, GzipCodec.class); +// .write() +// .option("compression", "gzip") +// .mode(SaveMode.Append) +// .json(outputPath); } } From 8f51af4e9bb965af3994b607d0288d0ba7bb31d4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:34:30 +0200 Subject: [PATCH 61/70] added PacePerson to get name surname for authors having only fullname set --- .../SparkOrcidToResultFromSemRelJob.java | 98 +++++++++++-------- 1 file changed, 56 insertions(+), 42 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index bea847ca76..e4ffc56982 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.List; import java.util.Optional; +import eu.dnetlib.dhp.common.PacePerson; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -129,61 +130,74 @@ public class SparkOrcidToResultFromSemRelJob { } private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) { - boolean toaddpid = false; + boolean toaddpid = false; - if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { - if (StringUtils.isNotEmpty(author.getSurname())) { - if (autoritative_author - .getSurname() - .trim() - .equalsIgnoreCase(author.getSurname().trim())) { + String author_name = author.getName(); + String author_surname = author.getSurname(); - // have the same surname. Check the name - if (StringUtils.isNotEmpty(autoritative_author.getName())) { - if (StringUtils.isNotEmpty(author.getName())) { - if (autoritative_author - .getName() - .trim() - .equalsIgnoreCase(author.getName().trim())) { - toaddpid = true; - } - // they could be differently written (i.e. only the initials of the name - // in one of the two - else { + if(StringUtils.isEmpty(author_name) || StringUtils.isEmpty(author_surname)){ + PacePerson pp = new PacePerson(author.getFullname(), false); + if (pp.isAccurate()){ + author_name = pp.getNormalisedFirstName(); + author_surname = pp.getNormalisedSurname(); + + } + } + + if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { + if (StringUtils.isNotEmpty(author_surname)) { + if (autoritative_author + .getSurname() + .trim() + .equalsIgnoreCase(author_surname.trim())) { + + // have the same surname. Check the name + if (StringUtils.isNotEmpty(autoritative_author.getName())) { + if (StringUtils.isNotEmpty(author_name)) { if (autoritative_author - .getName() - .trim() - .substring(0, 0) - .equalsIgnoreCase(author.getName().trim().substring(0, 0))) { + .getName() + .trim() + .equalsIgnoreCase(author_name.trim())) { toaddpid = true; } + // they could be differently written (i.e. only the initials of the name + // in one of the two + else { + if (autoritative_author + .getName() + .trim() + .substring(0, 0) + .equalsIgnoreCase(author_name.trim().substring(0, 0))) { + toaddpid = true; + } + } } } } } } - } - if (toaddpid) { - StructuredProperty p = new StructuredProperty(); - p.setValue(autoritative_author.getOrcid()); - p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID)); - p - .setDataInfo( - getDataInfo( - PROPAGATION_DATA_INFO_TYPE, - PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, - PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME)); + if (toaddpid) { + StructuredProperty p = new StructuredProperty(); + p.setValue(autoritative_author.getOrcid()); + p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID)); + p + .setDataInfo( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, + PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME)); + + Optional> authorPid = Optional.ofNullable(author.getPid()); + if (authorPid.isPresent()) { + authorPid.get().add(p); + } else { + author.setPid(Lists.newArrayList(p)); + } - Optional> authorPid = Optional.ofNullable(author.getPid()); - if (authorPid.isPresent()) { - authorPid.get().add(p); - } else { - author.setPid(Lists.newArrayList(p)); } - + return toaddpid; } - return toaddpid; - } + private static boolean containsAllowedPid(Author a) { Optional> pids = Optional.ofNullable(a.getPid()); From f754c424bd87aaf6d403e3734a281288b584de83 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:35:02 +0200 Subject: [PATCH 62/70] changed logic to compute only onece PacePerson for each Author to be enriched --- .../SparkOrcidToResultFromSemRelJob.java | 24 +++++++++---------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index e4ffc56982..34882b5872 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -122,29 +122,24 @@ public class SparkOrcidToResultFromSemRelJob { } private static void enrichAuthor(Author a, List au) { + PacePerson pp = new PacePerson(a.getFullname(), false); for (AutoritativeAuthor aa : au) { - if (enrichAuthor(aa, a)) { + if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname() )) { return; } } } - private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) { + private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author, + String author_name, + String author_surname) { boolean toaddpid = false; - String author_name = author.getName(); - String author_surname = author.getSurname(); - - if(StringUtils.isEmpty(author_name) || StringUtils.isEmpty(author_surname)){ - PacePerson pp = new PacePerson(author.getFullname(), false); - if (pp.isAccurate()){ - author_name = pp.getNormalisedFirstName(); - author_surname = pp.getNormalisedSurname(); - - } - } if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { + if (StringUtils.isNotEmpty(author.getSurname())){ + author_surname = author.getSurname(); + } if (StringUtils.isNotEmpty(author_surname)) { if (autoritative_author .getSurname() @@ -153,6 +148,9 @@ public class SparkOrcidToResultFromSemRelJob { // have the same surname. Check the name if (StringUtils.isNotEmpty(autoritative_author.getName())) { + if(StringUtils.isNotEmpty(author.getName())){ + author_name = author.getName(); + } if (StringUtils.isNotEmpty(author_name)) { if (autoritative_author .getName() From dbde2d243a21c218a22a315af785236f9d56658f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:35:39 +0200 Subject: [PATCH 63/70] changed due to move of PacePerson from dhp-graph-mapper to dhp-common --- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java | 2 +- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index af9fe7197e..53c0913c23 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -23,7 +23,7 @@ import org.dom4j.Node; import com.google.common.collect.Lists; -import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 9c74c4a938..b9a1599174 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -28,7 +28,7 @@ import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; -import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; From 74215f6d9f2ae3ea9a06f7e66b10be25a2f08568 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 May 2020 10:38:16 +0200 Subject: [PATCH 64/70] refactoring --- .../projecttoresult/SparkResultToProjectThroughSemRelJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java index 17f6a057d8..0791fd68ce 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java @@ -105,7 +105,7 @@ public class SparkResultToProjectThroughSemRelJob { .stream() .forEach( (p -> { - potential_update.getProjectSet().remove(p); + potential_update.getProjectSet().remove(p); })); } String resId = potential_update.getResultId(); From da1e5cf55703dd318f33cae1b780111a3179f67d Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 25 May 2020 18:02:57 +0200 Subject: [PATCH 65/70] implementation of the result title merge. main title with higher trust, distinct between the others --- .../eu/dnetlib/dhp/schema/oaf/Result.java | 28 +++++++++++++++++++ .../dhp/oa/dedup/EntityMergerTest.java | 10 ++++++- .../dhp/dedup/json/publication_merge.json | 2 +- 3 files changed, 38 insertions(+), 2 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 711b1ca681..213a585a8c 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -244,7 +244,25 @@ public class Result extends OafEntity implements Serializable { subject = mergeLists(subject, r.getSubject()); + //merge title lists: main title with higher trust and distinct between the others + StructuredProperty baseMainTitle = null; + if(title != null) { + baseMainTitle = getMainTitle(title); + title.remove(baseMainTitle); + } + + StructuredProperty newMainTitle = null; + if(r.getTitle() != null) { + newMainTitle = getMainTitle(r.getTitle()); + r.getTitle().remove(newMainTitle); + } + + if (newMainTitle != null && compareTrust(this, r) < 0 ) + baseMainTitle = newMainTitle; + title = mergeLists(title, r.getTitle()); + if (title != null && baseMainTitle != null) + title.add(baseMainTitle); relevantdate = mergeLists(relevantdate, r.getRelevantdate()); @@ -294,4 +312,14 @@ public class Result extends OafEntity implements Serializable { } return a.size() > b.size() ? a : b; } + + private StructuredProperty getMainTitle(List titles) { + //need to check if the list of titles contains more than 1 main title? (in that case, we should chose which main title select in the list) + for (StructuredProperty title: titles) { + if (title.getQualifier() != null && title.getQualifier().getClassid() != null) + if (title.getQualifier().getClassid().equals("main title")) + return title; + } + return null; + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 144d5d49a0..f4b2c22522 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -90,10 +90,18 @@ public class EntityMergerTest implements Serializable { // verify authors assertEquals(pub_merged.getAuthor().size(), 9); assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + + //verify title + int count = 0; + for (StructuredProperty title: pub_merged.getTitle()){ + if (title.getQualifier().getClassid().equals("main title")) + count++; + } + assertEquals(count, 1); } @Test - public void publicationMergerTest2() throws InstantiationException, IllegalAccessException, IOException { + public void publicationMergerTest2() throws InstantiationException, IllegalAccessException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json index 015f9294a3..28548c5322 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json @@ -1,3 +1,3 @@ {"context": [], 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false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "coverage": [], "publisher": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "en", "classname": "en", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "country": [{"classid": "FI", "classname": "Finland", "schemeid": "dnet:countries", "schemename": "dnet:countries"}], "extraInfo": [], "originalId": ["(BISIS)113444", "https://www.cris.uns.ac.rs/record.jsf?recordId=113444&source=OpenAIRE&language=en"], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "test title", "classname": "test title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Antichains of copies of ultrahomogeneous structures"}]} \ No newline at end of file From ae04234472661b4c0b2e99a710b015ba6295023f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 May 2020 19:32:48 +0200 Subject: [PATCH 66/70] DataInfo.deletedbyinference is false by default --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java index cc77e1ea0c..9d572ee30a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java @@ -8,7 +8,7 @@ public class DataInfo implements Serializable { private Boolean invisible = false; private Boolean inferred; - private Boolean deletedbyinference; + private Boolean deletedbyinference = false; private String trust; private String inferenceprovenance; private Qualifier provenanceaction; From 01c2e933958a17d6a23b150d5d8fdccf371baf09 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 May 2020 19:48:14 +0200 Subject: [PATCH 67/70] [maven-release-plugin] prepare release dhp-1.2.1 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-schemas/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 6 ++---- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-dedup-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 6 ++---- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-worfklow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 21 files changed, 24 insertions(+), 28 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 327c33d6f2..0b05a71de4 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1-SNAPSHOT + 1.2.1 dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 873046e080..0dab4bf361 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1-SNAPSHOT + 1.2.1 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 8099a72e4e..3e94ba7975 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.1-SNAPSHOT + 1.2.1 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a700a29187..6e1751ec5d 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.1 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c7cb11b085..0fc78c9116 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.1 ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index fe5d0c431a..1f72251fa3 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.1 ../ diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 22a81f7da8..0c0bbb1342 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1-SNAPSHOT + 1.2.1 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 1c5465c14a..ae64a1cb85 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1-SNAPSHOT + 1.2.1 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 37abc22f61..89d7ec6a75 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 8b7ec38511..c851fbd2a7 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index fcc356ac08..05a373507b 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml index dff376c2d2..21069f42d2 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index c13bec8e6d..7f15601aec 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index fe9833e3ea..ecf00a7bc4 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 62968c4107..066aea97ac 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index e0ee03660b..533093598d 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 39699b3b67..a78eab8ec9 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 06408937bc..a15f3efe15 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index 5f99cdc8d3..b1c5da730d 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1-SNAPSHOT + 1.2.1 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 271c669397..fe7adf79b8 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.1 ../ diff --git a/pom.xml b/pom.xml index 419de3540d..77675b576d 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.1-SNAPSHOT + 1.2.1 pom @@ -38,7 +38,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD + dhp-1.2.1 This module is the root descriptor for the dnet-hadoop project From 7582532e737d3d6e29febe3374607ce42ff13c8d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 May 2020 19:48:18 +0200 Subject: [PATCH 68/70] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-schemas/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-dedup-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 2 +- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-worfklow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 21 files changed, 22 insertions(+), 22 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 0b05a71de4..8bae191d38 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1 + 1.2.2-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 0dab4bf361..ad8cd57b4a 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.1 + 1.2.2-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 3e94ba7975..08f5de9ee8 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.1 + 1.2.2-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 6e1751ec5d..369e25b24b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.1 + 1.2.2-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 0fc78c9116..60e66f45a2 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1 + 1.2.2-SNAPSHOT ../ diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index 1f72251fa3..5e864cf940 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.1 + 1.2.2-SNAPSHOT ../ diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 0c0bbb1342..ec6247102e 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1 + 1.2.2-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index ae64a1cb85..9f082df70a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.1 + 1.2.2-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 89d7ec6a75..a3cc15b744 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index c851fbd2a7..fa1a14b4a0 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 05a373507b..44cf9e67cc 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml index 21069f42d2..429c8a6486 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 7f15601aec..8454c29a4d 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index ecf00a7bc4..2dc0f24366 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 066aea97ac..aee3d27c1d 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index 533093598d..e0ce739cfb 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index a78eab8ec9..62bf7186ce 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index a15f3efe15..d6ec4e6ab2 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-worfklow-profiles/pom.xml index b1c5da730d..cb20db57eb 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-worfklow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.1 + 1.2.2-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index fe7adf79b8..cf9753da40 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.1 + 1.2.2-SNAPSHOT ../ diff --git a/pom.xml b/pom.xml index 77675b576d..e0ee189001 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.1 + 1.2.2-SNAPSHOT pom @@ -38,7 +38,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - dhp-1.2.1 + HEAD This module is the root descriptor for the dnet-hadoop project From b1546605e3a9a566167af7d7e795b320a4d21ea2 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 26 May 2020 08:44:15 +0200 Subject: [PATCH 69/70] updated version of a dependency --- dhp-workflows/dhp-broker-events/pom.xml | 2 +- .../relatedPublications/AbstractEnrichMissingPublication.java | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 8b7ec38511..51ea4247b2 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -57,7 +57,7 @@ eu.dnetlib dnet-openaire-broker-common - [1.0.0,2.0.0) + [2.0.0,3.0.0) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java index 405b06ca6a..75e77b3c6f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -53,8 +53,7 @@ public abstract class AbstractEnrichMissingPublication return new UpdateInfo<>( getTopic(), highlightValue, source.getLeft(), target.getLeft(), - (p, rel) -> { - }, // p.getPublications().add(rel), //TODO available in the future release of dnet-openaire-broker-common + (p, rel) -> p.getPublications().add(rel), rel -> rel.getInstances().get(0).getUrl()); } From eea07f4c4208ad1eef36efea397308dc32f7bd54 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 26 May 2020 09:21:49 +0200 Subject: [PATCH 70/70] refactoring --- .../dnetlib/dhp/blacklist/BlackListTest.java | 1 - .../SparkOrcidToResultFromSemRelJob.java | 106 +++++++++--------- 2 files changed, 52 insertions(+), 55 deletions(-) diff --git a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java index 0487a5844d..585848589c 100644 --- a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java +++ b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlackListTest.java @@ -61,7 +61,6 @@ public class BlackListTest { spark.stop(); } - @Test public void noRemoveTest() throws Exception { SparkRemoveBlacklistedRelationJob diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 34882b5872..3fc1270645 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.common.PacePerson; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; @@ -23,6 +22,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; @@ -124,78 +124,76 @@ public class SparkOrcidToResultFromSemRelJob { private static void enrichAuthor(Author a, List au) { PacePerson pp = new PacePerson(a.getFullname(), false); for (AutoritativeAuthor aa : au) { - if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname() )) { + if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname())) { return; } } } private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author, - String author_name, - String author_surname) { - boolean toaddpid = false; + String author_name, + String author_surname) { + boolean toaddpid = false; + if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { + if (StringUtils.isNotEmpty(author.getSurname())) { + author_surname = author.getSurname(); + } + if (StringUtils.isNotEmpty(author_surname)) { + if (autoritative_author + .getSurname() + .trim() + .equalsIgnoreCase(author_surname.trim())) { - if (StringUtils.isNotEmpty(autoritative_author.getSurname())) { - if (StringUtils.isNotEmpty(author.getSurname())){ - author_surname = author.getSurname(); - } - if (StringUtils.isNotEmpty(author_surname)) { - if (autoritative_author - .getSurname() - .trim() - .equalsIgnoreCase(author_surname.trim())) { - - // have the same surname. Check the name - if (StringUtils.isNotEmpty(autoritative_author.getName())) { - if(StringUtils.isNotEmpty(author.getName())){ - author_name = author.getName(); + // have the same surname. Check the name + if (StringUtils.isNotEmpty(autoritative_author.getName())) { + if (StringUtils.isNotEmpty(author.getName())) { + author_name = author.getName(); + } + if (StringUtils.isNotEmpty(author_name)) { + if (autoritative_author + .getName() + .trim() + .equalsIgnoreCase(author_name.trim())) { + toaddpid = true; } - if (StringUtils.isNotEmpty(author_name)) { + // they could be differently written (i.e. only the initials of the name + // in one of the two + else { if (autoritative_author - .getName() - .trim() - .equalsIgnoreCase(author_name.trim())) { + .getName() + .trim() + .substring(0, 0) + .equalsIgnoreCase(author_name.trim().substring(0, 0))) { toaddpid = true; } - // they could be differently written (i.e. only the initials of the name - // in one of the two - else { - if (autoritative_author - .getName() - .trim() - .substring(0, 0) - .equalsIgnoreCase(author_name.trim().substring(0, 0))) { - toaddpid = true; - } - } } } } } } - if (toaddpid) { - StructuredProperty p = new StructuredProperty(); - p.setValue(autoritative_author.getOrcid()); - p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID)); - p - .setDataInfo( - getDataInfo( - PROPAGATION_DATA_INFO_TYPE, - PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, - PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME)); - - Optional> authorPid = Optional.ofNullable(author.getPid()); - if (authorPid.isPresent()) { - authorPid.get().add(p); - } else { - author.setPid(Lists.newArrayList(p)); - } - - } - return toaddpid; } + if (toaddpid) { + StructuredProperty p = new StructuredProperty(); + p.setValue(autoritative_author.getOrcid()); + p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID)); + p + .setDataInfo( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, + PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME)); + Optional> authorPid = Optional.ofNullable(author.getPid()); + if (authorPid.isPresent()) { + authorPid.get().add(p); + } else { + author.setPid(Lists.newArrayList(p)); + } + + } + return toaddpid; + } private static boolean containsAllowedPid(Author a) { Optional> pids = Optional.ofNullable(a.getPid());