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4638 Commits

Author SHA1 Message Date
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 0515d81c7c Merge pull request 'Rewrite SparkPropagateRelation exploiting Dataframe API' (#330) from propagate_relation_rewrite into beta 
Reviewed-on: D-Net/dnet-hadoop#330
 2023-08-29 10:47:14 +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
Miriam Baglioni 35b8deb2c6 Merge pull request 'DispatchEntitiesSparkJob: manage all entity types together, support filtering by dataInfo.invisible flag' (#329) from dispatch_filter_invisible_entities into beta 
Reviewed-on: D-Net/dnet-hadoop#329
 2023-08-10 12:56:18 +02:00
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 b9dddbfe54 rule out records with NULL dataInfo, except for Relations 2023-07-31 17:53:54 +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 1275a07d45 Merge pull request '[graph indexing] expand the instance level fulltext in the XML records' (#326) from instance_fulltext_xml into beta 
Reviewed-on: D-Net/dnet-hadoop#326
 2023-07-27 15:02:07 +02:00
Claudio Atzori a72b9e96ac expand the instance level fulltext in the XML records 2023-07-27 14:57:38 +02:00
Claudio Atzori d8435a6512 inverted condition 2023-07-25 17:39:57 +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
Claudio Atzori 8c63e4a864 Merge pull request 'Refactor Dedup using Spark Dataframe API, initial support for scala 2.12 and Spark 3.4' (#324) from dedup-with-dataframe-2 into beta 
Reviewed-on: D-Net/dnet-hadoop#324
 2023-07-25 10:17:17 +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
Claudio Atzori 002b24e06f Merge pull request '[graph cleaning] fixed regex behaviour for cleaning ROR and GRID identifiers, added tests' (#315) from pid_cleaning into beta 
Reviewed-on: D-Net/dnet-hadoop#315
 2023-07-24 10:49:44 +02:00
Claudio Atzori c754397a19 Merge branch 'beta' into pid_cleaning 2023-07-24 10:49:31 +02:00
Claudio Atzori f0678cda09 Merge pull request 'fix_beta_tests' (#323) from fix_beta_tests into beta 
Reviewed-on: D-Net/dnet-hadoop#323
 2023-07-24 10:47:35 +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
Giambattista Bloisi 38dfebfbe6 Disable MdStoreClientTest test as it requires a local mongodb running and it does not perform any assertions 2023-07-19 14:18:56 +02:00