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4346 Commits

Author SHA1 Message Date
Miriam Baglioni 6e58d79623 mergin with branch beta 2024-01-23 11:36:47 +01:00
Miriam Baglioni e0ec800d7e [BulkTagging] extend the definition of the pathMap to include also actions that should be performed of the value extracted from the result befor applying the constraint 2024-01-23 11:34:53 +01:00
Claudio Atzori f87f3a6483 [graph provision] updated param specification for the XML converter job 2024-01-23 08:54:37 +01:00
Claudio Atzori 6fd25cf549 code formatting 2024-01-23 08:47:12 +01:00
Claudio Atzori f76852f385 Merge branch 'beta' into update_pivots_table 2024-01-22 16:37:22 +01:00
Claudio Atzori 1c6db320f4 [graph provision] obtain context info from the context API instead from the ISLookUp service 2024-01-22 15:53:17 +01:00
Claudio Atzori 2655eea5bc [orcid enrichment] drop paths before copying the non-modifyed contents 2024-01-19 16:28:05 +01:00
Claudio Atzori c6b3401596 increased shuffle partitions for publications in the country propagation workflow 2024-01-19 10:15:39 +01:00
Miriam Baglioni bcc0a13981 [enrichment single step] adding <end> element in wf definition 2024-01-18 17:39:14 +01:00
Miriam Baglioni 6af536541d [enrichment single step] moving parameter file in correct location 2024-01-18 15:35:40 +01:00
Miriam Baglioni a12a3eb143 - 2024-01-18 15:18:10 +01:00
Miriam Baglioni 82e9e262ee [enrichment single step] remove parameter from execution 2024-01-17 17:38:03 +01:00
Miriam Baglioni 67ce2d54be [enrichment single step] refactoring to fix issues in disappeared result type 2024-01-17 16:50:00 +01:00
Miriam Baglioni 59eaccbd87 [enrichment single step] refactoring to fix issue in disappeared result type 2024-01-15 17:49:54 +01:00
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
Antonis Lempesis e024718f73 creating result_instances even when no pids exist for the instance 2024-01-10 22:25:50 +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
dimitrispie b920307bdd Changes to indicators 2024-01-09 00:47:09 +02:00
dimitrispie 8b2cbb611e Changes to beta db names 2024-01-09 00:40:56 +02:00
Antonis Lempesis 2e4cab026c fixed the result_country definition 2024-01-08 16:01:26 +02:00
dimitrispie 6b823100ae Update buildIrishMonitorDB.sql 
New indicators added
 2024-01-07 22:54:39 +02:00
dimitrispie 75bfde043c Historical Snapshots Workflow 
Create historical snapshots db with parameters:

hist_db_name=openaire_beta_historical_snapshots_xxx
hist_db_name_prev=openaire_beta_historical_snapshots_xxx (previous run of wf)
stats_db_name=openaire_beta_stats_xxx
stats_irish_db_name=openaire_beta_stats_monitor_ie_xxx
monitor_db_name=openaire_beta_stats_monitor_xxx
monitor_db_prod_name=openaire_beta_stats_monitor
monitor_irish_db_name=openaire_beta_stats_monitor_ie_xxx
monitor_irish_db_prod_name=openaire_beta_stats_monitor_ie
hist_db_prod_name=openaire_beta_historical_snapshots
hist_db_shadow_name=openaire_beta_historical_snapshots_shadow
hist_date=122023
hive_timeout=150000
hadoop_user_name=xxx
resumeFrom=CreateDB
 2024-01-04 15:11:04 +02:00
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
dimitrispie ffdd03d2f4 Monitor Irish Stats WF 
Parameters (with examples):
stats_db_name=openaire_beta_stats_20231208
monitor_irish_db_name=openaire_beta_stats_monitor_ie_20231208b
monitor_irish_db_prod_name=openaire_beta_stats_monitor_ie
graph_db_name=openaire_beta_20231208
monitor_irish_db_shadow_name=openaire_beta_stats_monitor_ie_shadow
hive_timeout=150000
hadoop_user_name=dnet.beta
resumeFrom=Step1-buildIrishMonitorDB
 2023-12-22 11:05:24 +02:00
dimitrispie 40b98d8182 Changes to indicators and funders definition 
- Changes result_refereed definition
- Added result_country indicator
- Added indi_pub_green_with_license indicator
- Added country from jurisdiction to funders
 2023-12-22 10:29:20 +02:00
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
Miriam Baglioni 624f5f3f21 [Transformative Agreement] added check to verify the APC were paid byu the IReL funder 2023-12-18 15:28:19 +01:00
Miriam Baglioni 354e02e6a9 [Transformative Agreement] removed not needed class. Read directly the json and no need to pass from the csv 2023-12-18 15:20:27 +01:00
Miriam Baglioni b00771c7cc [Transformative Agreement] added code to extract relations from the transformative agreement file for the IE products got from OpenAPC 2023-12-18 15:12:44 +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
Giambattista Bloisi 613ec5ffce Add profiles for different spark versions: spark-24, spark-34, spark-35 2023-12-05 19:11:06 +01:00
Sandro La Bruzzo 52495f2cd2 used javax.xml.stream.XMLEventReader instead of deprecated scala.xml.pull.XMLEventReader 2023-12-05 19:11:06 +01:00
Sandro La Bruzzo 8c3e9a09d3 added repository openaire-third-parties 2023-12-05 19:11:06 +01:00
Giambattista Bloisi 2fa78f6071 Changes requires to build and run tests with Java 17 2023-12-05 19:11:06 +01:00
Giambattista Bloisi 326c9dc08c Changes in maven poms to build and test the project using Spark 3.4.x and scala 2.12 2023-12-05 19:11:06 +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
Claudio Atzori b3a61ea955 Merge branch 'beta' into url_validation 2023-10-25 14:22:56 +02:00
dimitrispie 89c4dfbaf4 StatsDB workflow to export actionsets about OA routes, diamond, and publicly-funded 
A new oozie workflow capable to read from the stats db to produce a new actionSet for updating results with:
- green_oa ={true, false}
- openAccesColor = {gold, hybrid, bronze}
- in_diamond_journal={true, false}
- publicly_funded={true, false}

Inputs:

- outputPath
- statsDB
 2023-10-24 09:48:23 +03:00
Claudio Atzori 7fc621cdec added defaults to the graph resolution workflow config-default.xml 2023-10-20 22:28:12 +02:00
Serafeim Chatzopoulos aad5982bf1 Change the description of the workflow 2023-10-20 12:48:21 +03:00
Miriam Baglioni a4214ced1e fixing issue on propagation organization. added --config to workflow definition. added oozie_app to communtiy project 2023-10-20 10:14:20 +02:00
Serafeim Chatzopoulos 6b19dcee80 Add actionset creation for pubmed affiliations 2023-10-19 19:58:25 +03:00
Claudio Atzori 2b9d0416ec [graph raw] URL Validator to accept double slashes 2023-10-19 16:26:37 +02:00
Claudio Atzori b0fed1725e avoid NPEs 2023-10-19 12:13:45 +02:00
Miriam Baglioni f1b898c6b4 mergin with branch beta 2023-10-19 09:04:35 +02:00
Claudio Atzori 6dfcd0c9a2 [raw graph] mapping original resource types 2023-10-16 12:57:18 +02:00
Claudio Atzori 39d24d5469 Merge branch 'beta' into resource_types 2023-10-16 11:56:38 +02:00
Sandro La Bruzzo a5a89a702f new spark parrameter updated 2023-10-16 11:46:12 +02:00
Miriam Baglioni 159388f9c2 testing and fix some issues 2023-10-16 11:26:07 +02:00
Claudio Atzori 03670bb9ce [dedup] use common saveParquet and save methods to ensure outputs are compressed 2023-10-16 10:55:47 +02:00
Claudio Atzori 54fbf09ac6 [raw graph] WIP: mapping original resource types 2023-10-16 08:57:47 +02:00
Claudio Atzori 6cf64d5d8b [SWH] renamed 'Software Heritage Identifier' to 'Software Hash Identifier' 2023-10-13 10:09:26 +02:00
Claudio Atzori 76447958bb cleanup & docs 2023-10-12 12:23:20 +02:00
Claudio Atzori dda602fff7 [AMF] docs 2023-10-12 10:05:46 +02:00
Miriam Baglioni 8e9493fad9 mergin with branch beta 2023-10-11 18:18:09 +02:00
Miriam Baglioni 89184d5b4f used the API instead of the IS for bulktagging and propagation for community through organization. Added a new propagation step for communities through projects. Still using the API and not the IS 2023-10-11 18:17:35 +02:00
Claudio Atzori 554551682d [raw graph] adopting the new COAR based vocabularies for the resource typing 2023-10-11 16:09:19 +02:00
Claudio Atzori a460ebe215 [UnresolvedEntities] updated action name 2023-10-10 15:50:11 +02:00
Claudio Atzori 66064e99fe Merge branch 'beta' into fos 2023-10-10 15:07:21 +02:00
Miriam Baglioni a431b04814 leftover for the properties and removal of bipfinder 2023-10-10 12:53:57 +02:00
Claudio Atzori ed9282ef2a removed module dhp-stats-monitor-update 2023-10-10 09:52:03 +02:00
Miriam Baglioni 110ce4b40f extend the fos model to include the level4 and the scores for level3 and level4. removed bip indicators from the instance 2023-10-10 09:46:40 +02:00
Claudio Atzori 204404b0e3 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2023-10-10 09:36:13 +02:00
Claudio Atzori 9a98f408b3 code formatting 2023-10-10 09:36:11 +02:00
Claudio Atzori 4e6fccf4f6 Merge pull request 'Beta stats wf updated' (#332) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#332
 2023-10-10 09:35:32 +02:00
Miriam Baglioni a3d01ccb24 refactoring 2023-10-09 14:52:17 +02:00
Miriam Baglioni 8448b9ebfb mergin with branch beta 2023-10-09 14:27:23 +02:00
Miriam Baglioni 3d6be20989 changes to use the API instead of the IS the get the information for the communities to be used during bulktagging and context propagation 2023-10-09 14:26:33 +02:00
dimitrispie 17586f0ff8 Update step20-createMonitorDB.sql 
Add result_orcid table to monitor dbs
 2023-10-09 14:21:31 +03:00
dimitrispie 489a082f04 Update step16-createIndicatorsTables.sql 
Change scripts for gold, hybrid, bronze indicators
 2023-10-09 14:00:50 +03:00
Claudio Atzori ef833840c3 [Doiboost] removed linkage to SFI unidentified project 2023-10-06 15:48:18 +02:00
Claudio Atzori 84a58802ab [OC] using the common pid cleaning function 2023-10-06 14:48:05 +02:00
Claudio Atzori 46034630cf [OC] compress the output actionset 2023-10-06 14:42:02 +02:00
Claudio Atzori 3bc44fbf1d Merge branch 'beta' into irish_funder 2023-10-06 14:26:41 +02:00
Claudio Atzori 3c23d5f9bc Merge branch 'beta' into SWH_integration 2023-10-06 14:15:38 +02:00
Claudio Atzori 858931ccb6 [SWH] compress the output actionset 2023-10-06 14:03:33 +02:00
Claudio Atzori f759b18bca [SWH] aligned parameter name 2023-10-06 13:43:20 +02:00
Claudio Atzori eed9fe0902 code formatting 2023-10-06 12:31:17 +02:00
Claudio Atzori 73c49b8d26 Merge branch 'beta' into SWH_integration 2023-10-06 12:21:51 +02:00
Sandro La Bruzzo 42a2dad975 implemented relation to irish funder from a Json list 2023-10-06 11:52:33 +02:00
Serafeim Chatzopoulos 1bb83b9188 Add prefix in SWH ID 2023-10-04 20:31:45 +03:00
Claudio Atzori ee8a39e7d2 cleanup and refinements 2023-10-04 12:32:05 +02:00
Serafeim Chatzopoulos e9f24df21c Move SWH API Key from constants to workflow param 2023-10-03 20:57:57 +03:00
Serafeim Chatzopoulos cae75fc75d Add SWH in the collectedFrom field 2023-10-03 16:55:10 +03:00
Serafeim Chatzopoulos b49a3ac9b2 Add actionsetsPath as a global WF param 2023-10-03 15:43:38 +03:00
Serafeim Chatzopoulos 24c43e0c60 Restructure workflow parameters 2023-10-03 15:11:58 +03:00
Serafeim Chatzopoulos 9f73d93e62 Add param for limiting repo Urls 2023-10-03 14:39:08 +03:00
Claudio Atzori 5919e488dd Merge branch 'beta' into importpoci 2023-10-03 10:43:53 +02:00
Serafeim Chatzopoulos 839a8524e7 Add action for creating actionsets 2023-10-02 23:50:38 +03:00
Miriam Baglioni d7fccdc64b fixed paths in wf to match the req of the pathname 2023-10-02 14:10:57 +02:00
Miriam Baglioni 9898470b0e Addressing comments in D-Net/dnet-hadoop#340\#issuecomment-10592 2023-10-02 12:54:16 +02:00
Claudio Atzori 7b403a920f Merge branch 'beta' into consistency_keep_mergerels 2023-10-02 11:26:00 +02:00
Claudio Atzori dc86018a5f Merge branch 'merge_entities_job' into beta 2023-10-02 11:24:48 +02:00
Claudio Atzori 7f244d9a7a code formatting 2023-10-02 11:04:36 +02:00
Giambattista Bloisi e239b81740 Fix defect #8997: GenerateEventsJob is generating huge amounts of logs because broker entity similarity calculation consistently failed 2023-10-02 11:04:18 +02:00
Miriam Baglioni e84f5b5e64 extended existing codo to accomodate import of POCI from open citation 2023-10-02 09:25:16 +02:00
Serafeim Chatzopoulos ab0d70691c Add step for archiving repoUrls to SWH 2023-09-28 20:56:18 +03:00
Serafeim Chatzopoulos ed9c81a0b7 Add steps to collect last visit data && archive not found repository URLs 2023-09-27 19:00:54 +03:00
Alessia Bardi 0935d7757c Use v5 of the UNIBI Gold ISSN list in test 2023-09-20 15:41:35 +02:00
Alessia Bardi cc7204a089 tests for d4science catalog 2023-09-20 15:38:32 +02:00
dimitrispie 9ef971a146 Update step16-createIndicatorsTables.sql 
Fix int year for:
indi_org_openess_year
indi_org_fairness_year
indi_org_findable_year
 2023-09-19 14:25:42 +03:00
Serafeim Chatzopoulos 9d44418d38 Add collecting software code repository URLs 2023-09-14 18:43:25 +03:00
Serafeim Chatzopoulos 395a4af020 Run CC and RAM sequentieally in dhp-impact-indicators WF 2023-09-13 08:59:40 +02:00
Claudio Atzori 4786aa0e09 added Archive ouverte UNIGE (ETHZ.UNIGENF, opendoar____::1400) to the Datacite hostedBy_map 2023-09-07 11:21:07 +02:00
dimitrispie 5f90cc11e9 Update step16-createIndicatorsTables.sql 
Fix indi_pub_bronze_oa
 2023-09-06 14:14:38 +03:00
Claudio Atzori adec6692ca Merge branch 'beta' into invisible_relations 2023-09-04 16:13:06 +02:00
Claudio Atzori 15666e86a8 added collectedfrom to the affiliation relations imported from Crossref 2023-09-04 15:56:06 +02:00
Claudio Atzori 5b06c9d06f [graph raw] datainfo.invisible set as true only for entities 2023-09-04 15:15:24 +02:00
Serafeim Chatzopoulos 7de0164c26 Fix import of affiliations relations from Crossref 2023-09-04 16:04:41 +03:00
Giambattista Bloisi 2caaaec42d Include SparkCleanRelation logic in SparkPropagateRelation 
SparkPropagateRelation includes merge relations
Revised tests for SparkPropagateRelation
 2023-09-04 11:33:20 +02:00
dimitrispie 964c2f553e Changes in indicators step, monitor step 
- graduatedoctorates for observatory
- result_apc_affiliations table
- new indicators
	indi_is_funder_plan_s
	indi_funder_fairness
	indi_ris_fairness
	indi_funder_openess
	indi_ris_openess
	indi_funder_findable
	indi_ris_findable
	indi_is_project_result_after
- cast year to int in composite indicators
- new institutions
     -- Universidade Católica Portuguesa
     -- Iscte - Instituto Universitário de Lisboa
     -- Munster Technological University
     -- Cardiff University
     -- Leibniz Institute of Ecological Urban and Regional Development
 2023-09-01 10:57:02 +03:00
Giambattista Bloisi 6cc7d8ca7b GroupEntities and DispatchEntites are now merged in GroupEntitiesSparkJob 2023-08-30 10:43:31 +02:00
Giambattista Bloisi 6b1c05d118 Add sparkExecutorMemoryOverhead workflow config to set off-heap memory for Spark actions. If not explicitly set it is defaulted to 1Gb 2023-08-29 16:04:19 +02:00
Claudio Atzori bf35280ea6 code formatting 2023-08-29 11:11:00 +02:00
Claudio Atzori 58665a246c Merge branch 'beta' into propagate_relation_rewrite 2023-08-29 10:47:02 +02:00
Claudio Atzori f437be80ad [impact indicators] adjusted paths in the bip ranker wf parameters 2023-08-29 09:03:03 +02:00
Giambattista Bloisi d012aec0b3 Revert PropagateRelation's argument name from outputPath to graphOutputPath in consistency workflow (#8964) 2023-08-28 22:44:54 +02:00
Giambattista Bloisi a860e19423 Fix ensure all relations are written out, not only those managed by dedup 2023-08-28 15:36:02 +02:00
Giambattista Bloisi 0d7b2bf83d Rewrite SparkPropagateRelation exploiting Dataframe API 2023-08-28 10:34:54 +02:00
Miriam Baglioni 9c8b41475a Merge pull request '8172_impact_indicators_workflow' (#284) from 8172_impact_indicators_workflow into beta 
Reviewed-on: D-Net/dnet-hadoop#284
 2023-08-14 15:50:48 +02:00
Serafeim Chatzopoulos 97c1ba8918 Merge actionsets of results and projects 2023-08-11 15:56:53 +03:00
Giambattista Bloisi 95cd2b9b1e Make filterInvisible a mandatory parameter of DispathEntitiesSparkJob 
Make filterInvisible a mandatory parameter of both dedup/consistency and graph/group oozie workflows
 2023-08-10 11:53:48 +02:00
Giambattista Bloisi fab9920271 DispatchEntitiesSparkJob: manage all entity types together, support filtering by dataInfo.invisible flag 2023-08-09 15:41:43 +02:00
Miriam Baglioni c25ac21e5e Merge pull request 'graph cleaning, suggestions from ticket 8898' (#325) from cleaning_8898 into beta 
Reviewed-on: D-Net/dnet-hadoop#325
 2023-08-08 11:14:19 +02:00
Miriam Baglioni c334fe2438 Merge pull request 'Add a "CleanRelation" action after the PropagateRelation to filter out all relations that have been deleted by inference or that are pointing to dangling entities' (#328) from cleanup_relations_after_dedup into beta 
Reviewed-on: D-Net/dnet-hadoop#328
 2023-08-08 09:49:12 +02:00
Miriam Baglioni 0e2f855807 Merge pull request 'Updates Promotion DBs' (#321) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#321
 2023-08-07 12:09:16 +02:00
Miriam Baglioni 18fbe52b20 Merge pull request 'Import affiliation relations from Crossref' (#320) from 8876 into beta 
Reviewed-on: D-Net/dnet-hadoop#320
 2023-08-07 10:45:30 +02:00
Giambattista Bloisi 97b6d1dc45 Filter ids by dataInfo.deletedbyinference and DataInfo.invisible flags 
Filter relations also by dataInfo.invisible flag
 2023-08-07 10:24:11 +02:00
Giambattista Bloisi af49424b59 Add a "CleanRelation" action after the PropagateRelation to filter out all relations that have been deleyted by inference or that are pointing to dangling entities 2023-08-04 14:27:39 +02:00
Claudio Atzori 11ffb9bd68 rule out records with NULL dataInfo 2023-07-31 12:35:33 +02:00
Serafeim Chatzopoulos 7cefe2665b Remove unnecessary classes 2023-07-28 19:14:39 +03:00
Serafeim Chatzopoulos 26a92ce762 Merge branch '8876' of https://code-repo.d4science.org/D-Net/dnet-hadoop into 8876 2023-07-28 19:03:57 +03:00
Serafeim Chatzopoulos ebfba38ab6 Add changes from code review 2023-07-28 19:03:47 +03:00
Serafeim Chatzopoulos eb8684a8cf Merge branch 'beta' into 8876 2023-07-28 13:39:33 +02:00
Claudio Atzori a72b9e96ac expand the instance level fulltext in the XML records 2023-07-27 14:57:38 +02:00
Claudio Atzori 270df939c4 partial implementation of the suggestions from https://support.openaire.eu/issues/8898 2023-07-25 17:29:50 +02:00
Giambattista Bloisi e64c2854a3 Refactor Dedup process to use Spark Dataframe API and intermediate representation with Row interface 
JsonPath cache contention fixed by using a ConcurrentHashMap
Blacklist filtering performance improvement
Minor performance improvements when evaluating similarity
Sorting in clustered elements is deterministic (by ordering and identity field, instead of ordering field only)
 2023-07-24 15:36:24 +02:00
Giambattista Bloisi bb5b845e3c Use scala.binary.version property to resolve scala maven dependencies 
Ensure consistent usage of maven properties
Profile for compiling with scala 2.12 and Spark 3.4
 2023-07-24 11:13:48 +02:00
Serafeim Chatzopoulos 3a0f09774a Add script to find score limits 2023-07-21 17:55:41 +03:00
Ilias Kanellos 06b9b71c4e Merge branch '8172_impact_indicators_workflow' of https://code-repo.d4science.org/D-Net/dnet-hadoop into 8172_impact_indicators_workflow 2023-07-21 17:42:49 +03:00
Ilias Kanellos 2374f445a9 Produce additional bip update specific files 2023-07-21 17:42:46 +03:00
Serafeim Chatzopoulos cb0f3c50f6 Format workflow.xml 2023-07-21 16:07:10 +03:00
Serafeim Chatzopoulos c64e5e588f Merge branch '8172_impact_indicators_workflow' of https://code-repo.d4science.org/D-Net/dnet-hadoop into 8172_impact_indicators_workflow 2023-07-21 15:27:02 +03:00
Serafeim Chatzopoulos 2cc5b1a39b Fixes in workflow.xml 2023-07-21 15:26:50 +03:00
Ilias Kanellos 0f96af5d56 Merge branch '8172_impact_indicators_workflow' of https://code-repo.d4science.org/D-Net/dnet-hadoop into 8172_impact_indicators_workflow 2023-07-21 13:42:35 +03:00
Ilias Kanellos 03da965162 Format bip-score based file without doi references 2023-07-21 13:42:30 +03:00
Giambattista Bloisi f03153823a Update testCitationRelations number of expected citations according to changes made in 0559d8b4 (monodirectional citations) 2023-07-21 10:48:28 +02:00
Giambattista Bloisi 54c1eacef1 SparkJobTest was failing because testing workingdir was not cleaned up after eact test 2023-07-21 10:42:24 +02:00
Giambattista Bloisi 5e15f20e6e Fix entityMerger that was excluding the authors of the first entity in the list to merge 2023-07-21 00:46:54 +02:00
Giambattista Bloisi 0210a14e43 Ignore timestamp differences in PromoteActionPayloadForGraphTableJobTest 2023-07-20 23:45:57 +02:00
Giambattista Bloisi dba34505de Fix SparkStatsTest bug where parquet tables were incorrectly read as text files leading to unpredictable count() values 2023-07-19 14:24:52 +02:00
Giambattista Bloisi e47ed1fdb2 Use DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES in json mapper to avoid that tests fail if they encounter unmapped properties 2023-07-19 14:21:40 +02:00
Serafeim Chatzopoulos db4ca43ee8 Resolve conflict 2023-07-18 18:38:26 +03:00
Serafeim Chatzopoulos be320ba3c1 Indentation fixes 2023-07-17 16:04:21 +03:00
dimitrispie be4856ef35 Update step15.sql 2023-07-17 15:33:58 +03:00
Serafeim Chatzopoulos bc1a4611aa Minor changes 2023-07-17 11:17:53 +03:00
dimitrispie 163b2ee2a8 Changes 
1. Monitor updates
2. Bug fixes during copy to impala cluster
 2023-07-13 15:25:00 +03:00
dimitrispie 76901a25f9 Updates Promotion DBs 
- Add a step for promoting the splitted monitor DBs
 2023-07-12 22:49:08 +03:00
Serafeim Chatzopoulos 4eba14a80e Add oozie workflow 2023-07-06 21:07:50 +03:00
Serafeim Chatzopoulos c2998a14e8 Add basic tests for affiliation relations 2023-07-06 20:28:16 +03:00
Serafeim Chatzopoulos bc7b00bcd1 Add bi-directional affiliation relations 2023-07-06 18:29:15 +03:00
Serafeim Chatzopoulos 12528ed2ef Refactor PrepareAffiliationRelations.java to use OafMapperUtils common functions 2023-07-06 18:08:33 +03:00
Serafeim Chatzopoulos bbc245696e Prepare actionsets for BIP affiliations 2023-07-06 15:56:12 +03:00
Ilias Kanellos 0c433eccdd Fix scores & Workflow 2023-07-06 15:06:28 +03:00
Ilias Kanellos d5c39a1059 Fix map scores to doi 2023-07-06 15:04:48 +03:00
Ilias Kanellos 772d5f0aab Make PR and AttRank serial 2023-07-06 13:47:51 +03:00
Giambattista Bloisi 801da2fd4a New sources formatted by maven plugin 2023-07-06 10:28:53 +02:00
Giambattista Bloisi bd3fcf869a rename dnet-pace-core into dhp-pace-core module and use it as dependency in other modules 2023-07-06 10:02:23 +02:00
Serafeim Chatzopoulos 347a889b20 Read affiliation relations 2023-07-06 00:51:01 +03:00
Miriam Baglioni 4c9bc4c3a5 refactoring 2023-06-30 19:05:15 +02:00
Miriam Baglioni 7738372125 [UsageCount] fixed typo in attribute name for datasource table 2023-06-30 18:56:41 +02:00
Miriam Baglioni 55ea485783 [UsageCount] split the count for result at the level of the datasource. for each indicator one unit is specified for each datasource contrinuting to that indicator value. The datasource key is the value of the key element in the unit for the measure, while the count for that datasource is in the value 2023-06-30 18:39:30 +02:00
Sandro La Bruzzo 9963fd6d29 updated log to add subentity 2023-06-28 13:36:05 +02:00
Sandro La Bruzzo ed7e2ab6d1 reverted mistake on commit workflow.xml 2023-06-28 11:40:19 +02:00
Sandro La Bruzzo 9910ce06ae added to CreateSimRel the feature to write time log 2023-06-28 11:38:16 +02:00
Miriam Baglioni 2717edafb7 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2023-06-28 11:25:14 +02:00
Miriam Baglioni 2f04c9d149 [BulkTagging] fixing left over for test 2023-06-28 11:24:42 +02:00
Sandro La Bruzzo bd17c3edc8 added to CreateSimRel the feature to write time log 2023-06-28 11:20:58 +02:00
Serafeim Chatzopoulos 60f25b780d Minor fixes in workflow.xml and job.properties 2023-06-23 12:51:50 +03:00
Michele Artini 88a1cbc37d fixed a datasource id 2023-06-22 07:56:33 +02:00
Claudio Atzori b0ebf56367 Merge pull request 'Update step15_5.sql' (#314) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#314
 2023-06-21 10:33:22 +02:00
dimitrispie 2b6370eaee Update step15_5.sql 
Bug fix
 2023-06-21 11:31:10 +03:00
Claudio Atzori 35e42a86ed Merge pull request 'Update step15_5.sql' (#313) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#313
 2023-06-21 10:26:16 +02:00
dimitrispie 74cb060bfe Update step15_5.sql 
Add "if not exists" clause
 2023-06-21 11:24:06 +03:00
Claudio Atzori 85e016df17 Merge pull request 'Update step16-createIndicatorsTables.sql' (#312) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#312
 2023-06-21 09:52:33 +02:00
dimitrispie a475cfcb7b Update step16-createIndicatorsTables.sql 
Rename a field in indi_pub_interdisciplinarity
 2023-06-21 10:42:02 +03:00
Claudio Atzori 979cf9cd87 Merge pull request 'Update step15.sql' (#311) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#311
 2023-06-21 09:20:01 +02:00
dimitrispie 4648cd88d4 Update step15.sql 
Cast score to double
 2023-06-21 10:02:19 +03:00
dimitrispie 94d2573c77 Update step15.sql 
Bug Fix
 2023-06-21 09:22:39 +03:00
Claudio Atzori 0561362de2 Merge pull request 'Update step20-createMonitorDB_institutions.sql' (#309) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#309
 2023-06-20 15:07:09 +02:00
Claudio Atzori 50d7dc0078 [graph enrichment] fixed projectOrganizationPath not being passed to the apply_resulttoorganization_propagation node 2023-06-19 15:42:44 +02:00
Claudio Atzori fbd9bf704e indent 2023-06-19 15:41:22 +02:00
dimitrispie be2caedb04 Update step20-createMonitorDB_institutions.sql 
Add openorgs____::1624ff7c01bb641b91f4518539a0c28a Vrije Universiteit Amsterdam
 2023-06-19 12:12:17 +03:00
dimitrispie 36e0a8fec4 Changes to Promotion Stats WF 
1. Add new cluster host at impala-shell commands
2. Add a step for splitting monitor dbs
3. Update workflow.xml to included the new splitting monitor dbs step
 2023-06-19 09:44:34 +03:00
dimitrispie 4c770a5e29 Update finalizeImpalaCluster.sh 
Drop views in shadow dbs before dropping the db
 2023-06-15 13:25:37 +03:00
dimitrispie e06d962a6a Update step15.sql 2023-06-15 12:20:35 +03:00
dimitrispie afcad08396 Update step20-createMonitorDB_institutions.sql 
Added openorgs____::c0b262bd6eab819e4c994914f9c010e2   -- National Institute of Geophysics and Volcanology
 2023-06-15 10:28:49 +03:00
Claudio Atzori b9748763e2 Merge pull request '[stats wf] Bug fixes' (#308) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: D-Net/dnet-hadoop#308
 2023-06-14 21:57:03 +02:00
dimitrispie 42b8ce2ba4 Update copyDataToImpalaCluster.sh 2023-06-14 19:23:42 +03:00
dimitrispie 2032b0df40 Bug fixes 
1. Remove tables/views from old databases in the new cluster, before dropping the dbs
2. Fix id in result_accessroute, indi_impact_measures, indi_pub_bronze_oa
 2023-06-14 19:09:09 +03:00
Claudio Atzori b76a47b103 [aggregator graph] added column alias when mapping organization PIDs from the OpenOrgs database 2023-06-13 11:38:10 +02:00
Claudio Atzori ad04f14b81 Merge branch 'beta' into distinct_pids_from_openorgs_beta 2023-06-12 09:58:21 +02:00
Claudio Atzori 55f002f1e9 Merge branch 'beta' into propagationProjectThroughParentChils 2023-06-12 09:56:53 +02:00
Claudio Atzori 4b00a76271 Merge branch 'beta' into fulltext_url_validation 2023-06-12 09:55:25 +02:00
Claudio Atzori de225c71cd Merge branch 'beta' into removeTaggingCondition 2023-06-12 09:50:40 +02:00
Claudio Atzori e1409ffe80 update sql query to return distinct pids 2023-06-12 09:47:45 +02:00