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Author SHA1 Message Date
Claudio Atzori 741bc99c47 Merge branch 'beta' into datasource_pdf_consent 2022-03-28 09:20:48 +02:00
Claudio Atzori 61319b2e83 updated dhp-schema version; set entity-level dataInfo before & after merging the fields from the group of duplicates 2022-03-25 16:38:33 +01:00
Antonis Lempesis d8503cd191 added moooar organizations 2022-03-24 14:02:36 +02:00
Miriam Baglioni 7b8f85692e [Enrichment country] fixed issues with parameters and workflow args 2022-03-23 17:20:23 +01:00
Claudio Atzori 48d32466e4 instances grouped by URL expose only one refereed 2022-03-23 14:52:03 +01:00
Claudio Atzori f10066547b increased spark.sql.shuffle.partitions in affiliation_from_semrel_propagation 2022-03-23 12:22:26 +01:00
Claudio Atzori 43733c1a18 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2022-03-23 12:14:27 +01:00
Enrico Ottonello f11dfc51f7 fix resolved url format, added alternate identifier from original pid 2022-03-22 16:39:21 +01:00
Antonis Lempesis 62f91b0869 cleanup 2022-03-22 16:17:49 +02:00
Antonis Lempesis 2e8394ecf8 creating aaall tables as parquet 2022-03-22 16:16:08 +02:00
Antonis Lempesis dcfbeb8142 yet more typos 2022-03-21 12:36:03 +02:00
Miriam Baglioni 89fd275480 [HostedByMap] added left over from PR and fixed issue on workflow 2022-03-21 09:54:45 +01:00
Enrico Ottonello afe84c4244 added subjects to oaf generation 2022-03-18 18:10:39 +01:00
Enrico Ottonello db831e6f43 removed dynamic allocation on wf 2022-03-18 17:43:53 +01:00
Enrico Ottonello 861f2a3306 added titles merging title page and protein identifier 2022-03-18 14:51:57 +01:00
Enrico Ottonello f43bfdb594 added subjects 2022-03-17 19:24:07 +01:00
miconis c763aded70 dependency updated to the new pace-core version 2022-03-16 16:41:50 +01:00
Enrico Ottonello 3ef5eec3a6 added bmuse and rdfconverter modules - added repository for bmuse jars 2022-03-16 12:07:36 +01:00
Enrico Ottonello 41284ec2f9 retrieving vocabulary terms from nquads 2022-03-16 11:26:50 +01:00
Enrico Ottonello e53a606afc added date of collection, resource type as workflow parameter 2022-03-15 17:36:48 +01:00
miconis c959639bd5 dependency updated to the new pace-core version 2022-03-15 16:33:03 +01:00
Miriam Baglioni 0f7d8ca2e0 [HostedByMap] change on master to align to PR 201 on beta merged as 9f3036c847 2022-03-11 15:16:02 +01:00
Claudio Atzori f430029596 cleanup 2022-03-11 14:28:28 +01:00
Miriam Baglioni 12de9acb0d [Country Propagation] left out from previous commit 2022-03-11 14:17:02 +01:00
Miriam Baglioni 2fbb35ade5 mergin with branch beta 2022-03-11 13:58:10 +01:00
Miriam Baglioni 4437f9345d [Country Propagation] left out from previous commit 2022-03-11 13:57:47 +01:00
Miriam Baglioni 2b643059fa [Country Propagation] changed the logic to get the collectedfrom at the result level. To fix issue when no instance is created for a result that should have the country associated. Change the code to use spark instead of hive to prepare the data needed for the propagation step. Added new tests for the intermediate steps and new verification for the propagation itself 2022-03-11 13:56:48 +01:00
Claudio Atzori f25407bbe2 added mapping for datasource consent fields to integrate them in the graph 2022-03-11 09:32:42 +01:00
Miriam Baglioni 2c5087d55a [HostedByMap] download of doaj from json, modification of test resources, deletion of class no more needed for the CSV download 2022-03-04 15:18:21 +01:00
Miriam Baglioni 5d608d6291 [HostedByMap] changed the model to include also oaStart date and review process that could be possibly used in the future 2022-03-04 11:06:09 +01:00
Miriam Baglioni b7c2340952 [HostedByMap - DOIBoost] changed to use code moved to common since used also from hostedbymap now 2022-03-04 11:05:23 +01:00
Miriam Baglioni 8a41f63348 [HostedByMap] update to download the json instead of the csv 2022-03-04 10:38:43 +01:00
Miriam Baglioni 44b0c03080 [HostedByMap] update to download the json instead of the csv 2022-03-04 10:37:59 +01:00
Enrico Ottonello bd37f14941 added working ocean configuration 2022-03-03 14:38:21 +01:00
Enrico Ottonello 29ee1b9d82 added datasource key to workflow parameter to properly choose collected from and id values 2022-03-03 12:31:29 +01:00
Antonis Lempesis ad78e505da yet another fix 2022-03-03 12:28:12 +02:00
Enrico Ottonello e57216a1fa added oozie workflow to generate bioschema dataset on hdfs 2022-03-02 16:58:10 +01:00
Miriam Baglioni 3be8737c32 [graph-stats] fixed query after the change in the indicator table related to PR#200 2022-03-02 14:09:05 +01:00
Miriam Baglioni 3970651ee1 Merge pull request 'fixed query after the change in the indicator table' (#200) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#200
 2022-03-02 14:05:58 +01:00
Antonis Lempesis efeeebfee1 fixed query after the change in the indicator table 2022-03-02 13:29:25 +02:00
Enrico Ottonello f28d7e3b9d added spark dataset creation 2022-03-02 12:12:37 +01:00
Enrico Ottonello 8f281846a4 update test file 2022-02-28 13:37:53 +01:00
Enrico Ottonello f833de8a75 added relatedIdentifierType, fix IsCitedBy value 2022-02-28 13:37:28 +01:00
Enrico Ottonello 7f9636ef00 added alternateIdentifiers to oaf 2022-02-25 14:42:08 +01:00
Claudio Atzori 580d904aae manually merging PR#199 D-Net/dnet-hadoop#199 2022-02-25 12:22:50 +01:00
Claudio Atzori 1932a65d1c Merge pull request '[Stats wf] sprint 6 indicators' (#198) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#198
 2022-02-25 12:09:18 +01:00
Miriam Baglioni f5b0a6f89c [master to beta] fixed issues in test files 2022-02-25 10:21:57 +01:00
miconis 8991d097b4 bug fix in the DedupRecordFactory, DataInfo set before merge 2022-02-24 17:13:12 +01:00
miconis fe1c966cbf Merge branch 'master_202203' of code-repo.d4science.org:D-Net/dnet-hadoop into master_202203 2022-02-24 17:08:38 +01:00
miconis b0f369dc78 bug fix in the DedupRecordFactory, DataInfo set before merge 2022-02-24 17:08:24 +01:00
Enrico Ottonello 2f5caef77b resolution of generated relations url to uniprot and pubmed datasources 2022-02-24 16:59:50 +01:00
Miriam Baglioni 859cb7ac9d [DoiBoost AR] changed test resource to be sure the result will always have EMBARGO as value for AccessRight 2022-02-24 16:55:32 +01:00
Miriam Baglioni a40b59b7d5 [ResultToOrgFromInstRepoTest] fixed issue in model of the input resources 2022-02-24 16:05:57 +01:00
Claudio Atzori 66c09b1bc7 code formatting 2022-02-24 12:58:07 +01:00
Claudio Atzori a87c070447 conflicts resolved, merged from beta 2022-02-24 12:51:31 +01:00
Claudio Atzori 86cdb7a38f [provision] serialize measures defined on the result level 2022-02-23 15:54:18 +01:00
Alessia Bardi 9d6203f79b test mapping datasource 2022-02-23 15:00:53 +01:00
Antonis Lempesis 3b92a2ab9c added the rest of spring 6 in monitor db 2022-02-23 12:05:57 +02:00
Antonis Lempesis 87c91f70a2 added sprint 6 indicators to monitor db 2022-02-22 14:41:48 +02:00
Enrico Ottonello 4975278558 added modules for downloading data with bmuse and converting to datacite json format 2022-02-22 12:53:19 +01:00
Enrico Ottonello 2bc79c50f8 mapping bioschema to oaf 2022-02-22 11:46:29 +01:00
Enrico Ottonello 446f81ee60 wf to generate oaf from bioschema json datacite 2022-02-22 11:42:57 +01:00
Claudio Atzori 5226d0a100 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2022-02-18 15:21:07 +01:00
Claudio Atzori 99f5b14469 [graph raw] invisible records stored among the raw graph rather than the claimed subgraph 2022-02-18 15:20:57 +01:00
Claudio Atzori 401dd38074 code formatting 2022-02-18 15:19:15 +01:00
Claudio Atzori cf8443780e added processingchargeamount to the result view 2022-02-18 15:17:48 +01:00
Sandro La Bruzzo 891781ee3f Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2022-02-18 11:11:32 +01:00
Sandro La Bruzzo d3f03abd51 fixed wrong json path 2022-02-18 11:11:17 +01:00
Claudio Atzori 89c7313fc5 Merge branch 'beta' into hierarchical_orgs_relations 2022-02-17 10:30:04 +01:00
dimitrispie 58c59f46eb Added Sprint 6 2022-02-17 10:21:09 +02:00
Antonis Lempesis 393a4ee956 fixed yet another typo... 2022-02-15 12:56:50 +02:00
Sandro La Bruzzo 3aa2020b24 added script to regenerate hostedBy Map following instruction defined on ticket #7539 
updated hosted By Map
 2022-02-15 11:05:27 +01:00
Miriam Baglioni be64055cfe [OpenCitation] changed the name of destination folders 2022-02-14 15:49:44 +01:00
Miriam Baglioni 1490867cc7 [OpenCitation] cleaning of the COCI model 2022-02-14 14:52:12 +01:00
Miriam Baglioni c191080965 mergin with branch beta 2022-02-14 14:49:39 +01:00
Alessia Bardi 600ede1798 serialisation of APCs int he XML records 2022-02-11 11:00:20 +01:00
Miriam Baglioni 5c4043dba8 [OpenCitation] refactoring 2022-02-08 16:23:05 +01:00
Miriam Baglioni 759ed519f2 [OpenCitation] added logic to avoid the genration of self citations relations 2022-02-08 16:15:34 +01:00
Miriam Baglioni b071f8e415 [OpenCitation] change to extract in json format each folder just onece 2022-02-08 15:37:28 +01:00
Miriam Baglioni fbc28ee8c3 [OpenCitation] change the integration logic to consider dois with commas inside 2022-02-07 18:32:08 +01:00
Miriam Baglioni 78be2975f0 [stats-wf]fixed another typo related to PR#193 2022-02-07 11:22:08 +01:00
Miriam Baglioni 1f8302dc37 Merge pull request '[stats-wf]fixed yet another typo' (#193) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#193
 2022-02-07 11:19:26 +01:00
Antonis Lempesis 5f762cbd09 fixed yet another typo 2022-02-07 12:09:12 +02:00
Alessia Bardi ac8b8f224f Merge branch 'beta' into extendResult 2022-02-04 16:43:27 +01:00
Miriam Baglioni 493caef358 [stats-wf]fixed the result_result table related to PR#191 2022-02-04 14:51:25 +01:00
Miriam Baglioni 0547fd6ee7 Merge pull request '[stats-wf]fixed the result_result table' (#191) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#191
 2022-02-04 14:47:31 +01:00
Antonis Lempesis ae633c566b fixed the result_result table 2022-02-04 15:04:19 +02:00
Miriam Baglioni aae667e6b6 [APC at the result level] added the APC at the level of the result and modified test class 2022-02-04 12:34:25 +01:00
Sandro La Bruzzo bcfdf9a0d7 iis repository with https 2022-02-03 16:49:31 +01:00
Miriam Baglioni 3c60e53a96 [stats-wf]fixed the result_result creation for monitor PR#190 on beta 2022-02-03 14:47:08 +01:00
Miriam Baglioni 89922156c9 Merge pull request '[stats-wf]fixed the result_result creation for monitor' (#190) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#190
 2022-02-03 13:00:56 +01:00
Antonis Lempesis c2b44530a3 typo... 2022-02-03 13:44:07 +02:00
Antonis Lempesis dbd2646d59 fixed the result_result creation for monitor 2022-02-03 12:37:10 +02:00
Alessia Bardi 2e215abfa8 test for instances with URLs for OpenAPC 2022-02-02 17:27:44 +01:00
Miriam Baglioni 37784209c9 [dhp-schemas-] updated the version of dhp-schema to 2.10.27 for APC name and id modification 2022-02-02 12:46:31 +01:00
Miriam Baglioni 73eba34d42 [UnresolvedEntities] Changed the way to merge the unresolved because the new merge removed the dataInfo from the merged result. Added also data info for subjects 2022-02-01 08:38:41 +01:00
Miriam Baglioni dce7f5fea8 [BULK TAGGING] changed to fix issue that should have been fixed already 2022-01-31 08:20:28 +01:00
Claudio Atzori 8eb75ca169 adapted GenerateEntitiesApplicationTest behaviour 2022-01-27 16:24:37 +01:00
Claudio Atzori af61e44acc ported changes to the GraphCleaningFunctionsTest from 8de9788308 2022-01-27 16:19:14 +01:00
Claudio Atzori 1322379741 Merge branch 'beta' into delegated_authorities 2022-01-25 14:28:25 +01:00
Claudio Atzori 59a250337c [graph resolution] drop output path at the beginning 2022-01-24 18:02:39 +01:00
Claudio Atzori 97ad94d7d9 [graph resolution] drop output path at the beginning 2022-01-24 18:02:07 +01:00
Claudio Atzori 8de9788308 applied fix for avoiding ruling out the invisible (APC) records during the graph cleaning 2022-01-24 11:29:22 +01:00
Claudio Atzori 2f385b3ac6 updated dnet workflow profile definitions 2022-01-21 13:59:46 +01:00
Claudio Atzori dd52bf1bb8 copy relations to the graphOutputPath 2022-01-21 13:59:29 +01:00
Claudio Atzori 4983d6536d Merge branch 'beta' into delegated_authorities 2022-01-21 13:02:48 +01:00
Claudio Atzori f0ea2410e5 improved mapping titles from datacite records to consider title types 2022-01-21 10:50:34 +01:00
Claudio Atzori b37bc277c4 reintroduced the hostedby patching to the datacite records 2022-01-21 09:15:13 +01:00
Claudio Atzori f2fde5566b using helper method from ModelSupport to find the inverse relation descriptor 2022-01-20 09:19:07 +01:00
Claudio Atzori 3b9020c1b7 added unit test for the DispatchEntitiesJob 2022-01-19 18:15:55 +01:00
Claudio Atzori abfa9c6045 code formatting 2022-01-19 17:17:11 +01:00
Claudio Atzori 391aa1373b added unit test 2022-01-19 17:13:21 +01:00
Claudio Atzori 44a937f4ed factored out entity grouping implementation, extended to consider results from delegated authorities rather than identical records from other sources 2022-01-19 12:24:52 +01:00
Miriam Baglioni a7c4d0d16d [DoiBoost Organizations] added parameter to specify the action in the wf raw_organizations to be able to load the openorgs organization as in the loading step for the construction of the graph 2022-01-13 13:52:00 +01:00
Miriam Baglioni a75fb8c47a [BipFinderInstanceLevel] change pom to align to the dhp-schema release 2.10.24 and refactoring 2022-01-12 18:06:26 +01:00
Miriam Baglioni e7d5a39c03 [BipFinderInstanceLevel] added tests in test class 2022-01-12 17:25:04 +01:00
Miriam Baglioni 4993666d73 [BipFinderInstanceLevel] changed creation of the instance to allow to enrich existing instances with same pid 2022-01-12 16:53:47 +01:00
Claudio Atzori 9acc32faa6 [stats wf] final touches for the integration of PRs #166, #179 in the master branch 2022-01-12 12:04:31 +01:00
dimitrispie b053b0178e Sprint 5 and other changes 2022-01-12 11:23:37 +01:00
Antonis Lempesis b6b4bc0df9 added first indicator of sprint 5 2022-01-12 11:20:28 +01:00
Antonis Lempesis e91f06f39b fixed typos in indicators. Added extra views in monitor 2022-01-12 11:18:28 +01:00
Antonis Lempesis 3ce1976627 fixed column names 2022-01-12 11:14:41 +01:00
Antonis Lempesis 4878d7485c added usage stats 2022-01-12 11:13:25 +01:00
Antonis Lempesis a4316bafed fixed a typo 2022-01-12 11:12:53 +01:00
Antonis Lempesis bb17e070d8 added result_result relations 2022-01-12 11:09:38 +01:00
Claudio Atzori a30a98a716 Applying PR#166 in the master branch (Added sprint 3&4 of indicators). Merge commit '0df9574a6f5d9d75bc840decb023561ae941f9d6' 2022-01-12 10:57:19 +01:00
Sandro La Bruzzo 57e2c4b749 formatted code 2022-01-12 09:40:28 +01:00
Claudio Atzori 0f2144b5e0 scalafmt: code formatting 2022-01-11 17:03:44 +01:00
Claudio Atzori dcd282977c pulled from beta 2022-01-11 16:59:41 +01:00
Claudio Atzori 4f212652ca scalafmt: code formatting 2022-01-11 16:57:48 +01:00
Sandro La Bruzzo 0163dadb7f [doiboost] 
- update MAG schema, new filed added on version dec-2021
 2022-01-11 11:05:44 +01:00
Miriam Baglioni 904e1c2667 Merge pull request 'Affiliation Propagation through semantic relation' (#183) from enrichment into beta 
Reviewed-on: D-Net/dnet-hadoop#183
 2022-01-07 19:18:16 +01:00
Miriam Baglioni 064f9bbd87 [AFFPropSR] added new paprameter for the number of iterations and new code for just one iteration 2022-01-07 18:58:51 +01:00
Miriam Baglioni b7e450070b [SDG-FOS] to import SDG file not considering the header 2022-01-07 12:13:26 +01:00
Miriam Baglioni 639190370a mergin with branch beta 2022-01-07 11:29:25 +01:00
Miriam Baglioni adccc2346a [SDG-FOS] to lower case for the doi 2022-01-07 11:28:50 +01:00
Claudio Atzori 8ae46ca789 OAF-store-graph mdstores: firther fix for PR#180 2022-01-05 15:52:15 +01:00
Claudio Atzori 908294d86e OAF-store-graph mdstores: firther fix for PR#180 2022-01-05 15:49:05 +01:00
Claudio Atzori 3bd3653be9 OAF-store-graph mdstores: save them in text format 2022-01-04 16:39:39 +01:00
Claudio Atzori 3dc48c7ab5 OAF-store-graph mdstores: save them in text format 2022-01-04 16:39:27 +01:00
Claudio Atzori f82db765db OAF-store-graph mdstores: save them in text format 2022-01-04 16:39:15 +01:00
Claudio Atzori 8d13effa31 test for the tolerant deserialisation utility method 2022-01-04 16:38:26 +01:00
Claudio Atzori 9458ee7938 serialise records in the OAF-store-graph mdstores in json format. Read them again in the graph construction phase using a tolerant parser to support backward compatible changes in the evolution of the schema 2022-01-04 16:38:09 +01:00
Claudio Atzori 58f8998e3d OAF-store-graph mdstores: save them in text format 2022-01-04 15:02:09 +01:00
Claudio Atzori 174c3037e1 OAF-store-graph mdstores: save them in text format 2022-01-04 14:40:16 +01:00
Claudio Atzori 045d767013 OAF-store-graph mdstores: save them in text format 2022-01-04 14:23:01 +01:00
Claudio Atzori bd59b58efb test for the tolerant deserialisation utility method 2022-01-04 11:26:56 +01:00
Claudio Atzori a6977197b3 serialise records in the OAF-store-graph mdstores in json format. Read them again in the graph construction phase using a tolerant parser to support backward compatible changes in the evolution of the schema 2022-01-03 17:25:26 +01:00
Miriam Baglioni 4c60ee1718 mergin with branch beta 2022-01-03 15:24:02 +01:00
Miriam Baglioni 92fd69e25d [SDG-FOS] alternative way to get input data to avoid OOM error while getting csv 2022-01-03 15:23:06 +01:00