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4114 Commits

Author SHA1 Message Date
Giambattista Bloisi 21a14fcd80 Reusable RunSQLSparkJob for executing SQL in Spark through Oozie Spark Actions 
Implements pivots table update oozie workflow
 2024-01-15 10:18:14 +01:00
Sandro La Bruzzo e0753f19da Fixed error of connection timeout 2024-01-13 09:27:08 +01:00
sandro.labruzzo e328bc0ade fixed missing parameter on download update 2024-01-12 16:18:20 +01:00
Miriam Baglioni f612125939 fix issue on FoS integration. Removing the null values from FoS 2024-01-12 10:20:28 +01:00
Claudio Atzori cb9e739484 Merge branch 'beta' into resource_types 2024-01-11 16:29:41 +01:00
Claudio Atzori 2753044d13 refined mapping for the extraction of the original resource type 2024-01-11 16:28:26 +01:00
Giambattista Bloisi 3c66e3bd7b Create dedup record for "merged" pivots 
Do not create dedup records for group that have more than 20 different acceptance date
 2024-01-10 22:59:52 +01:00
Giambattista Bloisi 10e135db1e Use dedup_wf_002 in place of dedup_wf_001 to make explicit a different algorithm has been used to generate those kind of ids 2024-01-10 22:59:52 +01:00
Giambattista Bloisi 831cc1fdde Generate "merged" dedup id relations also for records that are filtered out by the cut parameters 2024-01-10 22:59:52 +01:00
Giambattista Bloisi 1287315ffb Do no longer use dedupId information from pivotHistory Database 2024-01-10 22:59:52 +01:00
Giambattista Bloisi 02636e802c SparkCreateSimRels: 
- Create dedup blocks from the complete queue of records matching cluster key instead of truncating the results
- Clean titles once before clustering and similarity comparisons
- Added support for filtered fields in model
- Added support for sorting List fields in model
- Added new JSONListClustering and numAuthorsTitleSuffixPrefixChain clustering functions
- Added new maxLengthMatch comparator function
- Use reduced complexity Levenshtein with threshold in levensteinTitle
- Use reduced complexity AuthorsMatch with threshold early-quit
- Use incremental Connected Component to decrease comparisons in similarity match in BlockProcessor
- Use new clusterings configuration in Dedup tests

SparkWhitelistSimRels: use left semi join for clarity and performance

SparkCreateMergeRels:
- Use new connected component algorithm that converge faster than Spark GraphX provided algorithm
- Refactored to use Windowing sorting rather than groupBy to reduce memory pressure
- Use historical pivot table to generate singleton rels, merged rels and keep continuity with dedupIds used in the past
- Comparator for pivot record selection now uses "tomorrow" as filler for missing or incorrect date instead of "2000-01-01"
- Changed generation of ids of type dedup_wf_001 to avoid collisions

DedupRecordFactory: use reduceGroups instead of mapGroups to decrease memory pressure
 2024-01-10 22:59:52 +01:00
Sandro La Bruzzo 859babf722 added some useful comment 2024-01-10 19:51:13 +01:00
Sandro La Bruzzo 39ebb60b38 Merge remote-tracking branch 'origin/beta' into orcid_update 2024-01-10 19:50:00 +01:00
Sandro La Bruzzo 9d5a7c3b22 code refactor 2024-01-10 19:42:34 +01:00
Sandro La Bruzzo 8f61063201 Added workflow 2024-01-10 19:42:22 +01:00
Sandro La Bruzzo 1a42a5c10d Implemented Download update of ORCID 2024-01-10 18:03:20 +01:00
Miriam Baglioni e711a05229 fixed conflicts 2024-01-10 11:03:42 +01:00
Miriam Baglioni 71d6f30711 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2024-01-10 10:59:58 +01:00
Miriam Baglioni cb14470ba6 added properties file in the forlder for the workflow of result to organization from inst repo propagation. Changes the path in the classes implementing the propagation 2023-12-22 14:50:05 +01:00
Miriam Baglioni 9f966b59d4 added properties file in the forlder for the workflow of result to community from semrel propagation. Changes the path in the classes implementing the propagation 2023-12-22 14:11:47 +01:00
Miriam Baglioni 2f3b5a133d added properties file in the forlder for the workflow of result to community from organization propagation. Changes the path in the classes implementing the propagation 2023-12-22 13:56:40 +01:00
Miriam Baglioni 2f7b9ad815 added properties file in the forlder for the workflow of project to result propagation. Changes the path in the classes implementing the propagation 2023-12-22 11:46:15 +01:00
Miriam Baglioni f2352e8a78 changed in the classes the path for the property files for the propagation of community from project 2023-12-22 11:43:34 +01:00
Miriam Baglioni 009730b3d1 added properties file in the forlder for the workflow of orcid propagation. Changes the path in the classes implementing the propagationchanged the path to the parameter file in the class for entitytoorganization propagation 2023-12-22 11:42:09 +01:00
Miriam Baglioni 89f269c7f4 changed the path to the parameter file in the class for entitytoorganization propagation 2023-12-22 11:37:50 +01:00
Miriam Baglioni b06aea0adf adding the bulkTag parameter file in the folder for the oozie workflow for bulkTagging. Changes the path in the class 2023-12-22 11:35:37 +01:00
Miriam Baglioni 3afd4aa57b adjustments for country propagation 2023-12-22 11:27:30 +01:00
Claudio Atzori 62104790ae added metaresourcetype to the result hive DB view 2023-12-21 12:27:10 +01:00
Miriam Baglioni 5011c4d11a refactoring after compiletion 2023-12-20 15:57:26 +01:00
Miriam Baglioni 4740c808f7 - 2023-12-20 14:26:54 +01:00
Miriam Baglioni d410ea8a41 added needed parameter 2023-12-19 12:15:01 +01:00
Sandro La Bruzzo 15fd93a2b6 uploaded input parameters on CreateBaseline WF 2023-12-18 12:21:55 +01:00
Sandro La Bruzzo 9d342a47da updated the transformation Baseline workflow to include mdstore rollback/commit action 2023-12-18 11:48:57 +01:00
Miriam Baglioni 3eca5d2e1c - 2023-12-18 09:55:27 +01:00
Miriam Baglioni 01ce0b9c76 [doiboost - preprocess] remove transition to orcid preparation from sequence of steps at the beginning of the workflow 2023-12-15 12:24:55 +01:00
Miriam Baglioni 0d8e496a63 - 2023-12-15 12:16:43 +01:00
Claudio Atzori ff924215b8 [graph provision] added tests for new peerreviewed field 2023-12-12 11:21:30 +01:00
Claudio Atzori 7e8eff40c1 [graph provision] added tests for the new model fields 2023-12-12 08:54:15 +01:00
Miriam Baglioni 8752d275fa removed not needed parameter 2023-12-09 15:24:45 +01:00
Miriam Baglioni d4eedada71 adjusting workflow definition 2023-12-09 15:20:11 +01:00
Claudio Atzori cb71a7936b [graph cleaning] avoid stack overflow error when navigating Oaf objects declaring an Enum 2023-12-07 23:09:54 +01:00
Claudio Atzori 70eb1796b2 logging typo 2023-12-07 14:08:04 +01:00
Claudio Atzori c381bacee0 [enrichment] passing the community API base URL 2023-12-07 14:07:11 +01:00
Miriam Baglioni 336fb31d87 [community_result_propagation] adjusting starting poit of workflow 2023-12-07 10:27:25 +01:00
Miriam Baglioni c0cde53bf6 [bulktagging] setting first step of bulktaggin as the copy of the entities and relations not involved in the tagging' 2023-12-07 10:08:35 +01:00
Miriam Baglioni 616622d2bb first version of the workflow single step 2023-12-07 09:59:52 +01:00
Claudio Atzori 259c69e446 [orcid enrichment] fixed workflow definition 2023-12-06 19:41:53 +01:00
Claudio Atzori 431c6bb08a [dedup] added isLookupUrl to the graph consistency workflow definition, required now by the entity grouping phase 2023-12-06 11:06:46 +01:00
Claudio Atzori 321922772b added serialization for the new fields imported for the Irish tender 2023-12-05 16:37:04 +01:00
Claudio Atzori c5b7253130 [community_organization propagation] fixed workflow parameters 2023-12-05 09:13:33 +01:00
Claudio Atzori 3c3bdb8318 [bulktagging] fixed workflow parameters 2023-12-05 09:08:48 +01:00
Claudio Atzori 2a233a89aa [graph grouping] added isLookupUrl to the workflow definition, passed to the grouping spark aciton 2023-12-03 13:32:52 +01:00
Claudio Atzori 178a14c491 code formatting 2023-12-03 13:31:58 +01:00
Sandro La Bruzzo 3caf6ff27e Extracted the correct original type to pass to instanceTypeMapping in Crossref Mapping 2023-12-01 16:33:56 +01:00
Claudio Atzori 511a98dd80 fixed doiboost process workflow, removed references to the ProcessORCID step 2023-12-01 16:21:53 +01:00
Claudio Atzori 09d061e90b Merge branch 'beta' into orcid_import 2023-12-01 15:05:35 +01:00
Claudio Atzori 93a700742a Merge pull request 'Changes for tables and creation of the new indicator indi_is_result_accessible' (#363) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#363
 2023-12-01 15:05:23 +01:00
Claudio Atzori 0c3c9ea43d Merge pull request 'StatsDB workflow to export actionsets about OA routes, diamond, and publicly-funded' (#355) from dimitris.pierrakos/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#355
 2023-12-01 15:03:56 +01:00
Claudio Atzori 33cb483c75 using objectSubType as originalType in Crossref2Oaf, code formatting 2023-12-01 15:03:05 +01:00
dimitrispie c9d995dde0 New institutions added 2023-12-01 15:44:35 +02:00
dimitrispie a397112cb8 Add new indicator 
Add indi_pub_publicly_funded
 2023-12-01 15:00:18 +02:00
dimitrispie 76594ded23 Changes to indicators 
Fixes on open access colours indicators
- indi_pub_green_oa
- indi_pub_gold_oa
- indi_pub_hybrid
- indi_pub_bronze_oa
- indi_pub_diamond
 2023-12-01 13:38:19 +02:00
Claudio Atzori 622fafbd2e Merge branch 'beta' into orcid_import 2023-12-01 12:28:14 +01:00
Sandro La Bruzzo bf0fd27c36 Removed unused function 
Applied PR Comment of Giambattista in the PR
 2023-12-01 12:16:42 +01:00
dimitrispie 48430a32a6 Update StatsAtomicActionsJob.java 
Added indi_funded_result_with_fundref indicator
 2023-12-01 11:35:01 +02:00
Sandro La Bruzzo cdfb7588dd code formatting 2023-11-30 15:31:42 +01:00
Sandro La Bruzzo 5e22b67b8a Merge remote-tracking branch 'origin/beta' into orcid_import 2023-11-30 15:27:46 +01:00
Sandro La Bruzzo f718caaac9 Added copy of the untouched entities of the graph 2023-11-30 14:51:00 +01:00
Sandro La Bruzzo 7b5e04f37e removed Orcid intersection on DOIBoost 2023-11-30 14:36:50 +01:00
Claudio Atzori 6f10791e77 Merge branch 'beta' into propagationapi 2023-11-30 14:20:18 +01:00
Claudio Atzori 4e1aac2e2f resolved conflict in pom.xml before applying the changes from [COAR based resource types & Irish tender] #350 2023-11-29 14:37:52 +01:00
Sandro La Bruzzo 86b5775e08 added vocabulary in instanceTypeMapping for 
- DOIBoost
- Datacite
- PubMed
- Scholexplorer Datasource
 2023-11-29 13:15:43 +01:00
Sandro La Bruzzo c96ff54b45 Merge remote-tracking branch 'origin/resource_types' into resource_types 2023-11-29 12:45:41 +01:00
Sandro La Bruzzo af1c2634b3 added instanceTypeMapping original field in the mapping of 
- DOIBoost
- Datacite
- PubMed
- Scholexplorer Datasource
 2023-11-29 12:45:30 +01:00
Sandro La Bruzzo 279100fa52 added test 2023-11-29 11:17:58 +01:00
Sandro La Bruzzo 59111713fa added comment 2023-11-28 09:00:48 +01:00
Sandro La Bruzzo 6f4d0c05ea Implemented Author MErger for ORCID that takes in account the case when name and surname are swapped 2023-11-28 08:43:56 +01:00
Miriam Baglioni 8eb70e6657 refactoring 2023-11-27 15:13:15 +01:00
Miriam Baglioni e3cce9a5a0 mergin with branch beta 2023-11-27 15:10:55 +01:00
Miriam Baglioni 48e0427a23 changed the parameter from production to baseURL. Fixed issue in tagging configuration 2023-11-27 15:10:27 +01:00
Sandro La Bruzzo 34a4b3cbdf Implemented ORCID Enrichment 2023-11-24 12:39:58 +01:00
dimitrispie 359e81b7a6 Update StatsAtomicActionsJob.java 
Bug fix for duplicate bronze checks
 2023-11-23 10:48:55 +02:00
Claudio Atzori 2c77638bf5 Merge branch 'beta' into cleaning_8898 2023-11-22 14:00:10 +01:00
Claudio Atzori 745039ad5b Merge branch 'beta' into 9117_pubmed_affiliations 2023-11-22 13:52:53 +01:00
Claudio Atzori 11a1207f9c [graph cleaning] applying coar based vocabularies in bulk 2023-11-22 12:22:14 +01:00
dimitrispie a94a54a2d0 Changes for tables and creation of the new indicator indi_is_result_accessible 
- Drop table statements for all tables to avoid duplicates in case of wf rerun
- Add pdfsaggregated step to create the indi_is_result_accessible table. This step is executed on the new impala cluster only, since the pdfaggregation_i is updated on this cluster.
 2023-11-15 14:32:18 +02:00
Miriam Baglioni eaf0a702de - 2023-11-14 14:53:34 +01:00
Sandro La Bruzzo 6ce36b3e41 Implemented ORCID Workflow on DHP-Aggregation for retrieving ORCID DUMP and generating tables 2023-11-14 12:04:29 +01:00
dimitrispie d524e30866 Changes to actionsets 
Resolve comments from
D-Net/dnet-hadoop#355
 2023-11-14 09:46:52 +02:00
Miriam Baglioni 5bc97615d5 - 2023-11-03 15:35:10 +01:00
Miriam Baglioni 7b1e34f159 refactoring 2023-11-03 15:30:01 +01:00
Miriam Baglioni 638ad9e74f changing test for new implementation 2023-11-03 15:06:50 +01:00
Miriam Baglioni edcb17ca98 refactoring and test 2023-11-03 13:01:14 +01:00
Miriam Baglioni 937ff6a7c7 - 2023-10-31 15:56:08 +01:00
Miriam Baglioni a737dd47b6 removed not needed test class 2023-10-31 15:54:49 +01:00
Miriam Baglioni c80b768af0 test for project propagation 2023-10-31 15:49:42 +01:00
Miriam Baglioni e9a20fc8f6 mergin with branch beta 2023-10-31 14:36:03 +01:00
Claudio Atzori 262d7c581b [graph cleaning] implemented further suggestions from https://support.openaire.eu/issues/8898 2023-10-31 14:34:10 +01:00
Serafeim Chatzopoulos 2090003ea9 Adjust tests to new WF input params 2023-10-26 13:47:06 -07:00
Serafeim Chatzopoulos a82aaf57b2 Renaming input param for crossref input path 2023-10-25 12:05:02 -07:00