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4346 Commits

Author SHA1 Message Date
Lampros Smyrnaios d7da4f814b Minor updates to the copying operation to Impala Cluster: 
- Improve logging.
- Code optimization/polishing.
 2024-04-12 18:12:06 +03:00
Lampros Smyrnaios 14719dcd62 Miscellaneous updates to the copying operation to Impala Cluster: 
- Update the algorithm for creating views that depend on other views.
- Add check for successful execution of the "hadoop distcp" command.
- Add a check for successful copy operation of all entities.
- Upon facing an error in a DB, exit the method, instead of the whole script.
- Improve logging.
- Code polishing.
 2024-04-12 15:36:13 +03:00
Sandro La Bruzzo 41a42dde64 code formatted 2024-04-11 17:43:48 +02:00
Sandro La Bruzzo 843dc95340 resolved conflict 2024-04-11 17:38:16 +02:00
Sandro La Bruzzo 1e30454ee0 added vocabulary tu instanceTypeMApping of Mag 2024-04-11 17:32:30 +02:00
Sandro La Bruzzo 2581672c11 updated wf of MAG and crossref to use transaction 2024-04-11 17:27:49 +02:00
Lampros Smyrnaios 22745027c8 Use the "HADOOP_USER_NAME" value from the "workflow-property", in "copyDataToImpalaCluster.sh", in "stats-monitor-updates". 2024-04-11 17:46:33 +03:00
Lampros Smyrnaios abf0b69f29 Upgrade the copying operation to Impala Cluster: 
- Use only hive commands in the Ocean Cluster, as the "impala-shell" will be removed from there to free-up resources.
- Hugely improve the performance in every aspect of the copying process: a) speedup file-transferring and DB-deletion, b) eliminate permissions-assignment, "load" operations and "use $db" queries, c) retry only the "create view" statements and only as long as they depend on other non-created views, instead of trying to recreate all tables and views 5 consecutive times.
- Add error-checks for the creation of tables and views.
 2024-04-11 17:12:12 +03:00
Sandro La Bruzzo a0642bd190 added instanceTypeMapping field on MAG 2024-04-11 13:10:12 +02:00
Sandro La Bruzzo 98dc042db5 mapping generated for MAG, 
missing generation of Organization Action set
 2024-04-05 18:12:53 +02:00
Sandro La Bruzzo ef582948a7 Updated mapping 2024-04-05 11:10:44 +02:00
Sandro La Bruzzo 5142f462b5 completed mapping from paper to OAF, not tested 2024-04-04 21:06:04 +02:00
Miriam Baglioni 0794e0667b Merge branch 'doidoost_dismiss' of https://code-repo.d4science.org/D-Net/dnet-hadoop into doidoost_dismiss 2024-04-04 09:16:18 +02:00
Miriam Baglioni 4b1de076ac [DataciteHostedByMap] added entry for EBRAINS 2024-04-04 09:16:14 +02:00
Miriam Baglioni c8a88b2187 [DataciteHostedByMap] added entry for EBRAINS 2024-04-04 09:14:58 +02:00
Sandro La Bruzzo 31e152d2bb Merge remote-tracking branch 'origin/doidoost_dismiss' into doidoost_dismiss 2024-04-03 17:08:35 +02:00
Sandro La Bruzzo 6f3e925cae Implemented first part of the new MAG mapping 2024-04-03 17:07:14 +02:00
Miriam Baglioni f0f6abf892 [MapToFunderLink]added references for HFRI and Erasmus+ for the creation of links for funders 2024-04-03 14:59:09 +02:00
Claudio Atzori 26b97aa5ed Merge pull request '[BETA] fixed the result_country definition and updated the stats DB copy procedure' (#416) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #416
 2024-04-03 12:36:03 +02:00
Lampros Smyrnaios b7c8acc563 - Update the code which acquires the "IMPALA_HDFS_NODE", to test the "tmp"-dir, instead of the base-dir and introduce retries, to overcome potential file-system failures. This change was suggested by "Sebastian Tymkow" and "Grzegorz Bakalarski". 
- Fix typos.
 2024-04-03 13:15:37 +03:00
Miriam Baglioni 50fbebf186 [NOAMI] removed entry for Health and Social Care Board from the list of funders. Modified IRC putting 1596 and 1597 as synonyms, as required in ticket 9635 2024-04-03 11:45:40 +02:00
Michele Artini 71d6e02886 Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2024-04-03 09:50:41 +02:00
Michele Artini 02c9a311c8 base datainfo with trust=0.89 2024-04-03 09:50:21 +02:00
Miriam Baglioni 42846d3b91 [OpenCitation] add compression option when writing the sequence file 2024-04-03 09:25:00 +02:00
Miriam Baglioni 4f0a044245 Merge pull request 'Add action set creation for Datacite affiliations' (#413) from 9647_datacite_affiliations into beta 
Reviewed-on: #413
 2024-04-02 17:33:38 +02:00
Serafeim Chatzopoulos cbe13a5c61 Fix datacite input path in properties file 2024-04-02 18:00:35 +03:00
Miriam Baglioni 9c9a9562ae [UsageCount] fixed error 2024-04-02 16:56:37 +02:00
Miriam Baglioni b42bdd5fb3 [UsageCount] add check in case the datasource is not matched against those present in the graph 2024-04-02 16:28:27 +02:00
Miriam Baglioni 64cbd8abe9 Merge pull request '[UsageCount] Usage count per result split by datasource' (#318) from UsageStatsRecordDS into beta 
Reviewed-on: #318
 2024-04-02 10:21:39 +02:00
Antonis Lempesis df6e3bda04 added new orgs in monitor 2024-04-01 22:45:29 +03:00
Antonis Lempesis 573b081f1d added new orgs in monitor 2024-04-01 22:24:46 +03:00
Serafeim Chatzopoulos 0eb0701b26 Add action set creation for Datacite affiliations 2024-04-01 17:23:26 +03:00
Antonis Lempesis 0bf2a7a359 fixed the result_country definition 2024-04-01 15:23:22 +03:00
Claudio Atzori 24227ab598 Merge pull request '[BETA] fixed typo in indicator query' (#411) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #411
 2024-03-27 13:56:43 +01:00
Antonis Lempesis 9ff44eed96 fixed typo in indicator query 
added more institutions
 2024-03-27 14:39:01 +02:00
Claudio Atzori cff6040424 Merge pull request '[BETA] added missing EOS, Generate tables with parquet-files, instead of csv in the contexts.sh script' (#409) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #409
 2024-03-27 12:04:04 +01:00
Antonis Lempesis 1fee4124e0 added missing EOS 2024-03-27 12:58:25 +02:00
Sandro La Bruzzo 73a67c0e4a Improved Crossref mapping to include also unpaywall tested 2024-03-26 17:26:47 +01:00
Claudio Atzori 75551ad4ec code formatting 2024-03-26 14:53:16 +01:00
Miriam Baglioni 94b931f7bd [BulkTagging - tag datasource and projects]merging with branch beta 2024-03-26 14:25:19 +01:00
Miriam Baglioni 3b209261f2 [BulkTagging - tag datasource and projects]merging with branch beta 2024-03-26 14:21:27 +01:00
Lampros Smyrnaios 036ba03fcd Generate tables with parquet-files, instead of csv, in "dhp-stats-update/.../contexts.sh" script. 2024-03-26 13:29:04 +02:00
Claudio Atzori 730eaffc85 Merge pull request 'correctly selecting the active hdfs node for the impala cluster' (#405) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #405
 2024-03-26 12:07:46 +01:00
Lampros Smyrnaios bc8c97182d Automatically select the ACTIVE HDFS NODE for Impala cluster, in all "copyDataToImpalaCluster.sh" scripts. 2024-03-26 13:01:12 +02:00
Lampros Smyrnaios 92cc27e7eb Use the ACTIVE HDFS NODE for Impala cluster, in "copyDataToImpalaCluster.sh" script. 2024-03-26 12:34:11 +02:00
Claudio Atzori ef52128c55 included new stats* workflows in parent pom list of modules, code formatting 2024-03-26 10:42:10 +01:00
Claudio Atzori bfba71a95c further follow up changes from integrating the mergeutils branch 2024-03-26 09:01:18 +01:00
Claudio Atzori d72e7b7487 Merge pull request 'Changes to indicators and funders definition' (#372) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #372
 2024-03-26 08:46:20 +01:00
Sandro La Bruzzo ece56f0178 update crossref mapping to be transformed together with UnpayWall 2024-03-25 18:18:10 +01:00
Claudio Atzori 538b180fe0 Merge branch 'beta' into oaf_country_beta 2024-03-25 16:13:20 +01:00
Claudio Atzori 82fc609c4f Merge branch 'beta' into index_records 2024-03-25 16:12:49 +01:00
Claudio Atzori 74e5d05577 Merge branch 'beta' into ocnew 2024-03-25 16:10:31 +01:00
Claudio Atzori 6c3b692f60 integrated minor change from beta branch 2024-03-25 16:10:23 +01:00
Claudio Atzori 9a5b134ddf Merge branch 'beta' into FOSNew 2024-03-25 16:07:37 +01:00
Claudio Atzori 71c1f81b54 Merge branch 'beta' into exception_on_invalid_transofmation_rule 2024-03-25 16:05:11 +01:00
Claudio Atzori 91b61687fa Merge branch 'beta' into bulkTaggingPathMapExtention 2024-03-25 15:50:18 +01:00
Claudio Atzori 54936b7f42 Merge branch 'beta' into transformativeagreement 2024-03-25 15:42:22 +01:00
Michele Artini e1149eb5c4 xslt rules and tests 2024-03-25 15:01:42 +01:00
Michele Artini 3f174ad90f Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2024-03-25 12:16:02 +01:00
Michele Artini 6ffb1faf09 fixed a problem with multiple nodes 2024-03-25 12:15:51 +01:00
Giambattista Bloisi 3f22c101d9 Merge pull request 'Enrich authors with ORCID info using new matching algorithm' (#398) from new_orcid_enhancement into beta 
Reviewed-on: #398
 2024-03-22 17:29:20 +01:00
Giambattista Bloisi 0ff7faad72 Fix conditions that prevented ORCID Enrichment 2024-03-22 16:24:49 +01:00
Michele Artini 7faa115ba0 Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2024-03-22 11:08:59 +01:00
Michele Artini f9c74c98fa fixed an identifier xpath 2024-03-22 11:08:45 +01:00
Antonis Lempesis 4c40c96e30 code cleanup 2024-03-22 10:16:49 +02:00
Antonis Lempesis 459167ac2f Merge branch 'beta' of https://code-repo.d4science.org/antonis.lempesis/dnet-hadoop into beta 2024-03-21 12:44:58 +02:00
Antonis Lempesis 07f634a46d code cleanup 2024-03-21 12:44:30 +02:00
Antonis Lempesis 9521625a07 code cleanup 2024-03-21 11:45:08 +02:00
Sandro La Bruzzo 58dbe71d39 update crossref mapping to be runnable separately as a single datasource outside doiboost 2024-03-20 17:04:52 +01:00
Antonis Lempesis 67a5aa0a38 Merge branch 'beta' of https://code-repo.d4science.org/antonis.lempesis/dnet-hadoop into beta 2024-03-19 11:24:54 +02:00
dimitrispie a3a570e9a0 Commit monitor-updates-wf 2024-03-19 09:42:21 +02:00
Giambattista Bloisi 664a381d31 Unify merge logic of entities in MergeUtils.class 2024-03-18 16:04:49 +01:00
Michele Artini cb29b9773c xslt rules 2024-03-18 15:31:34 +01:00
Michele Artini 85b844d57e updated BASE filter param 2024-03-15 15:03:27 +01:00
Michele Artini 455f2e1e07 apply commits from master 2024-03-15 14:56:39 +01:00
Michele Artini 30167aa882 mapped oaf:country from results 2024-03-15 11:24:16 +01:00
Michele Artini 88fef367b9 new plugin to collect from a dump of BASE 2024-03-15 10:47:52 +01:00
Claudio Atzori 078169b922 cleanup 2024-03-15 09:56:04 +01:00
Claudio Atzori af154d4456 implemented changes from #9497: sort abstracts by string length, included author fullnames in the related results, expanded instance details within each children/result XML element 2024-03-14 16:21:23 +01:00
Claudio Atzori 7863c92466 expanded paper abstract in the result/children XML element (ticket #9497) 2024-03-13 16:25:31 +01:00
Claudio Atzori eb5887cb9a including related organization url in the XML record serialization (ticket #9498) 2024-03-13 14:46:00 +01:00
Sandro La Bruzzo 5281f010a5 applied cherry pick 2024-03-13 09:59:20 +01:00
Sandro La Bruzzo ee1fcb672b code refactor 2024-03-13 09:46:31 +01:00
Miriam Baglioni 5a32bb9578 [OC New] last fix 2024-03-13 09:36:18 +01:00
Sandro La Bruzzo c532831718 Moved Crossref Mapping on dhp-aggregations, 
refactored code, avoid to use utility for create part of the oaf defined in DOIBoostMappingUtils, used instead utility in OafMappingUtils
 2024-03-13 06:56:10 +01:00
Miriam Baglioni 48c052215c [OC New] last fix 2024-03-12 23:12:32 +01:00
Claudio Atzori db66555ebb WIP: updated provision workflow to create a JSON based representation of the payload 2024-03-12 09:56:09 +01:00
Antonis Lempesis f74c7e8689 selecting distinct peer_reviewed 2024-03-12 02:13:04 +02:00
Giambattista Bloisi 9092075760 Enrich authors with ORCID info using new matching algorithm 2024-03-11 13:23:59 +01:00
Sandro La Bruzzo cbd4e5e4bb update mag mapping 2024-03-08 16:31:40 +01:00
Claudio Atzori d4871b31e8 WIP: extended provision workflow to create the JSON based payload 2024-03-08 11:43:20 +01:00
Antonis Lempesis 3c79720342 fixed the irish result subset 2024-03-07 14:08:57 +02:00
Antonis Lempesis 5ae4b4286c Merge branch 'beta' of https://code-repo.d3science.org/antonis.lempesis/dnet-hadoop into beta 2024-03-07 12:15:19 +02:00
Miriam Baglioni 5180b6ec8a [FOSNEW] removed test class 2024-03-07 10:47:13 +01:00
Miriam Baglioni 7827a2d66b [OCNEW] added creation of the actionset for the results classified with FoS based ont he OpenAIRE identifier 2024-03-07 10:36:30 +01:00
Antonis Lempesis 316d585c8a using distinct apcs per publication to avoid huge sums 2024-03-07 02:07:59 +02:00
Miriam Baglioni fd34372c40 [OCNEW] first implementation 2024-03-06 13:42:00 +01:00
Sandro La Bruzzo d34cef3f8d Merge remote-tracking branch 'origin/beta' into doidoost_dismiss 2024-03-05 11:45:31 +01:00
Sandro La Bruzzo 3b837d38ce added oozie workflow 2024-03-05 11:44:59 +01:00
Sandro La Bruzzo f417515e43 Implemented class that generates a normalized table of MAG, which is the starting point for the creation of the mag source 2024-03-04 17:15:13 +01:00
Sandro La Bruzzo ad0e9aa80c added first part of refactoring of the code generating MAG, 
make it more readable using spark sql queries
 2024-02-29 18:16:15 +01:00
Sandro La Bruzzo 9d94648f3b code formatted 2024-02-29 18:15:20 +01:00
Giambattista Bloisi 3cd5590f3b When converting json to XML, remove characters that are not allowed in the XML 1.0 specs, as they will cause xpath failures even if escaped 2024-02-28 15:14:18 +01:00
Giambattista Bloisi 56dd05f85c Merge pull request 'Revised procedure when converting json data into xml' (#395) from restiterator_xmlcleanup into beta 
Reviewed-on: #395
 2024-02-28 10:38:54 +01:00
Claudio Atzori 6fcf872daa Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into index_records 2024-02-28 10:27:28 +01:00
Claudio Atzori 3f07390a58 WIP 2024-02-28 10:10:10 +01:00
Sandro La Bruzzo 7d806a434c formatted code 2024-02-28 09:31:58 +01:00
Sandro La Bruzzo b63994dcc4 Merge remote-tracking branch 'origin/beta' into orcid_update 2024-02-28 09:11:18 +01:00
Sandro La Bruzzo 915a76a796 following the comment on the pull requests: 
- Added #NUM_OF_THREADS complete job in the queue at the end of  the main loop to avoid deadlock
 2024-02-28 09:10:55 +01:00
Giambattista Bloisi 773e856550 Revised procedure when converting json data into xml: 
- json object keys are renamed to be conformant to xml tag elements, special characters are substituted or removed
- json string values are no longer post-processed as they are already escaped by the org.json.XML.toString method
 2024-02-24 16:54:30 +01:00
Sandro La Bruzzo a712df1e1d Merge remote-tracking branch 'origin/beta' into orcid_update 2024-02-23 10:12:25 +01:00
Sandro La Bruzzo b32a9d1994 Implemented workflow for updating table , added step to check if the new generated table is valid 2024-02-23 10:04:28 +01:00
Michele Artini 3268570b2c mapping of project PIDs 2024-02-22 14:47:21 +01:00
Miriam Baglioni 72bae7af76 [Transformative Agreement] removed the relations from the ActionSet waiting to have the gree light from Ioanna 2024-02-19 16:20:12 +01:00
Miriam Baglioni 43da7e1191 [Tagging Projects and Datasource] changed the way the pathMap parameter is passed. It was too long and was truncated 2024-02-19 16:12:59 +01:00
Serafeim Chatzopoulos f0dc12634b Add Action Set creation for affiliations inferred from the OpenAPC data 2024-02-18 18:02:09 +02:00
Claudio Atzori a63b091bae Merge branch 'beta' into import_orps_fix 2024-02-15 15:01:56 +01:00
Miriam Baglioni 8dae10b442 - 2024-02-14 14:57:08 +01:00
Miriam Baglioni 83bb97be83 [Tagging Projects and Datasource] added test to check datasource tagging. Fixed issue 2024-02-14 11:23:47 +01:00
Miriam Baglioni 6e1f383e4a [Tagging Projects and Datasource] first extention of bulktagging to add the context to projects and datasource 2024-02-13 16:37:14 +01:00
Miriam Baglioni 3f7d262a4e mergin with branch beta 2024-02-13 14:05:58 +01:00
Miriam Baglioni eca021f4d6 [Transformative Agreement] add results with information abount the agreement and the country of the organization paid for it 2024-02-13 12:21:07 +01:00
Miriam Baglioni bdb6bbb365 mergin with branch beta 2024-02-12 15:50:43 +01:00
Claudio Atzori d85d2df6ad [graph raw] fixed mapping of the original resource type from the Datacite format 2024-02-09 10:20:20 +01:00
Giambattista Bloisi b19643f6eb Dedup aliases, created when a dedup in a previous build has been merged in a new dedup, need to be marked as "deletedbyinference", since they are "merged" in the new dedup 2024-02-08 15:34:59 +01:00
Antonis Lempesis dd4c27f4f3 added 2 new institutions in monitor 2024-02-08 12:57:57 +02:00
Claudio Atzori 38c9001147 fixed import of ORPs stored on HDFS in the internal graph format (e.g. Datacite) 2024-02-07 17:02:05 +01:00
Claudio Atzori fd17c1f17c [actiosets] fixed join type 2024-02-05 16:55:36 +02:00
Claudio Atzori 009dcf6aea [actiosets] introduced support for the PromoteAction strategy 2024-02-05 16:43:40 +02:00
Claudio Atzori 42f5506306 [orcid enrichment] fixed directory cleanup before distcp 2024-02-05 09:45:36 +02:00
Alessia Bardi f2a08d8cc2 test for Italian records from IRS repositories 2024-01-30 19:20:14 +01:00
Antonis Lempesis a512ead447 changed orcid ids to all capital 2024-01-30 16:54:47 +02:00
Miriam Baglioni 07a373a0bd [bulkTagging] removing checks while performing the substring action so that it will fire an Exception if the paramneters are wrongly set 2024-01-30 13:51:11 +01:00
Miriam Baglioni ead08b0dd4 mergin with branch beta 2024-01-30 12:19:10 +01:00
Antonis Lempesis bb10a22290 merged changes from dnet-hadoop 2024-01-29 21:51:47 +02:00
Miriam Baglioni a5995ab557 [orcid-enrichment] change the value of parameters. 2024-01-29 18:19:48 +01:00
Miriam Baglioni a418dacb47 [UsageCount] code extention to include also the name of the datasource 2024-01-29 18:12:33 +01:00
Miriam Baglioni e9131f4e4a mergin with branch beta 2024-01-29 16:27:18 +01:00
Sandro La Bruzzo 9aebca77a0 Added exception throwing in Hadoop transformation when TR is not syntactically valid 2024-01-29 14:41:02 +01:00
Claudio Atzori 926903b06b Merge branch 'beta' into stats_with_spark_sql 2024-01-29 09:11:45 +01:00
Giambattista Bloisi 078df0b4d1 Use SparkSQL in place of Hive for executing step16-createIndicatorsTables.sql of stats update wf 2024-01-26 21:56:55 +01:00
Claudio Atzori ce3200263e Merge branch 'beta' into crossref_missing_author_fix 2024-01-26 15:57:04 +01:00
Sandro La Bruzzo e889808daa Fixed problem on missing author in crossref Mapping 2024-01-26 12:19:04 +01:00
Antonis Lempesis c548796463 Changed step16-createIndicatorsTables to use a spark oozie action instead of hive 2024-01-26 02:04:48 +02:00
Sandro La Bruzzo 0386f36385 Added workflow to update ORCID and replaced some parsing, because the update works and employments xml differs from the dump one. 2024-01-25 19:40:59 +01:00
Antonis Lempesis a7115cfa9e max mem of joins (hive.mapjoin.followby.gby.localtask.max.memory.usage) now 80%, up from 55%. 2024-01-25 15:13:16 +01:00
Antonis Lempesis fd43b0e84a max mem of joins (hive.mapjoin.followby.gby.localtask.max.memory.usage) now 80%, up from 55%. 2024-01-25 15:06:34 +01:00
Claudio Atzori 9b13c22e5d [graph provision] retrieve all the context information by adding all=true to the requests issued to thr API 2024-01-23 15:36:08 +01:00
Sandro La Bruzzo 43e0bba7ed logg added during download 2024-01-23 15:04:49 +01:00
Miriam Baglioni f7d06dc661 compilation after merging 2024-01-23 11:43:08 +01:00