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181 Commits

Author SHA1 Message Date
Claudio Atzori d9e07a242b extended XmlIndexingJob to accept an optional parameter: outputPath. When present, forces the job to write its output on the specified HDFS location 2020-11-18 14:34:55 +01:00
Claudio Atzori 29dcff0f34 spark complains about missing classes, so here they are again 2020-11-18 14:32:32 +01:00
Claudio Atzori 8177ce7939 test for XmlIndexingJob based on a local miniSolrCluster 2020-11-18 10:58:05 +01:00
Claudio Atzori 2bed29eb09 WIP: added oozie workflow for grouping graph entities by id 2020-11-13 10:05:12 +01:00
Claudio Atzori 9b0fb9e958 merged from master 2020-11-12 09:27:12 +01:00
Claudio Atzori 822971f54f no need to filter relations in CreateRelatedEntitiesJob_phase1; replaced 'left outer' join with 'left' join in CreateRelatedEntitiesJob_phase2; cleanup; 2020-11-12 09:22:59 +01:00
Claudio Atzori 18d9aad70c improved documentation in dhp-graph-provision 2020-11-10 11:48:55 +01:00
Claudio Atzori 58f28296ea ProvisionConstants moved as ModelHardLimits in dhp-common and applied to truncate long abstracts (len > 150000). Further filtering for empty PID values 2020-10-30 10:56:42 +01:00
Claudio Atzori 1871d1c6f6 solve error java.lang.NoSuchFieldError: INSTANCE when instantiating Solr client 2020-08-14 11:18:30 +02:00
Claudio Atzori 3a11a387a9 data provision workflow enhancement: added nodes to perform DELETE BY QUERY before the indexing begins and COMMIT after the indexing is completed 2020-08-03 14:28:08 +02:00
Claudio Atzori cc5d13da85 introduced parameter shouldIndex (true|false) 2020-07-16 13:46:39 +02:00
Claudio Atzori b098cc3cbe avoid repeating identical values for fields: source, description 2020-07-16 13:45:53 +02:00
Claudio Atzori 7d6e269b40 reverted CreateRelatedEntitiesJob_phase1 to its previous state 2020-07-13 22:54:04 +02:00
Claudio Atzori 8e97598eb4 avoid to NPE in case of null instances 2020-07-13 20:46:14 +02:00
Claudio Atzori 06c1913062 added different limits for grouping by source and by target, incremented spark.sql.shuffle.partitions for the join operations 2020-07-10 19:03:33 +02:00
Claudio Atzori 4c3836f62e materialize the related entities before joining them 2020-07-10 19:00:44 +02:00
Claudio Atzori b21866a2da allow to set different to relations cut points by source and by target; adjusted weight assigned to relationship types 2020-07-10 13:59:48 +02:00
Claudio Atzori ff4d6214f1 experimenting with pruning of relations 2020-07-10 10:06:41 +02:00
Claudio Atzori b383ed42fa pass optional parameter relationFilter to the PrepareRelationJob implementation 2020-07-07 14:21:28 +02:00
Claudio Atzori d380b85246 unit test for the preparation of the relations 2020-07-02 12:42:13 +02:00
Claudio Atzori 7817338e05 added test to verify the relation pre-processing 2020-06-26 17:58:33 +02:00
Claudio Atzori 8d59fdf34e WIP: dataset based PrepareRelationsJob 2020-06-26 14:32:58 +02:00
Claudio Atzori 216975c4ec restored complete provision workflow 2020-06-25 12:55:52 +02:00
Claudio Atzori 93f627ea51 code formatting 2020-06-25 12:54:21 +02:00
Claudio Atzori e62333192c WIP: prepare relation job 2020-06-25 12:22:18 +02:00
Claudio Atzori 6933ec11fb WIP: prepare relation job 2020-06-25 11:04:12 +02:00
Sandro La Bruzzo a6c0faac70 added test to verify secondary sorting 2020-06-25 10:48:15 +02:00
Claudio Atzori 69b0391708 WIP: prepare relation job 2020-06-25 10:19:56 +02:00
Claudio Atzori 46e76affeb WIP: prepare relation job 2020-06-24 19:01:15 +02:00
Claudio Atzori 0e723d378b added default from vocab for missing instance.refereed; remove spurious prefixes from orcid values; WIP: prepare relation job 2020-06-24 18:34:42 +02:00
Claudio Atzori 9cd27183b6 [maven-release-plugin] prepare for next development iteration 2020-06-22 11:27:44 +02:00
Claudio Atzori 1e3dab0631 [maven-release-plugin] prepare release dhp-1.2.3 2020-06-22 11:27:39 +02:00
Claudio Atzori c4d9f1837f [maven-release-plugin] prepare for next development iteration 2020-06-12 12:21:08 +02:00
Claudio Atzori f0746a7605 [maven-release-plugin] prepare release dhp-1.2.2 2020-06-12 12:21:03 +02:00
Claudio Atzori 463489f59f code formatting 2020-06-12 12:03:25 +02:00
Claudio Atzori 4bcad1c9c3 Merge branch 'graph_cleaning' 2020-06-12 11:40:25 +02:00
Alessia Bardi e79943965b Fixes #5604: field oamandatepublications in XML 2020-06-11 12:49:31 +02:00
Claudio Atzori 67c7b31ba6 Merge branch 'master' into graph_cleaning 2020-06-10 15:00:35 +02:00
Claudio Atzori ce12f236bb disabled test, need to need to update the joined_entity.json file 2020-06-09 20:07:36 +02:00
Claudio Atzori a2fdf85ba1 WIP: graph cleaner implementation 2020-06-09 19:52:53 +02:00
Claudio Atzori 05f269a1c0 kryo based parallel implementation of CreateRelatedEntitiesJob_phase2, now works by OafType; introduced custom aggregator in AdjacencyListBuilderJob 2020-06-01 00:32:42 +02:00
Claudio Atzori 6f5f498c78 restored common properties driving executor-cores and executor-memory in join_organization_relations wf node 2020-05-29 11:22:00 +02:00
Claudio Atzori b2f9564f13 WIP: fixed PrepareRelationsJob; parallel implementation of CreateRelatedEntitiesJob_phase2, now works by OafType; introduced custom aggregator in AdjacencyListBuilderJob 2020-05-29 10:58:15 +02:00
Claudio Atzori a57965a3ea limiting the dimensions of outliers 2020-05-28 17:36:37 +02:00
Claudio Atzori 821be1f8b6 experimental implementation of custom aggregation using kryo encoders 2020-05-28 13:53:13 +02:00
Claudio Atzori 83504ecace limiting the maximum number of authors allowed in XML records to MAX_AUTHORS = 200; authors with ORCID can exceed that limit 2020-05-28 13:52:30 +02:00
Claudio Atzori ef11593068 JoinedEntity.links defined as empty list by default 2020-05-28 13:50:44 +02:00
Claudio Atzori 5dea155a87 increased number of partitions produced by the join_all_entities phase as well as spark.sql.shuffle.partitions in adjancency_lists phase 2020-05-28 13:49:59 +02:00
Claudio Atzori fdd54bad1c code formatting 2020-05-27 19:31:54 +02:00
Claudio Atzori cfd753217c repartition the join_entities in 24k files 2020-05-27 12:44:01 +02:00
Claudio Atzori 2f1a623d09 sync from master branch 2020-05-27 12:39:58 +02:00
Claudio Atzori 9e4ec1543b updated test 2020-05-27 12:38:42 +02:00
Claudio Atzori 8047d16dd9 added RDD based adjacency list creation procedure 2020-05-27 12:38:12 +02:00
Claudio Atzori f057dcdf65 limit the max number of externalreferences to MAX_EXTERNAL_ENTITIES 2020-05-27 12:37:33 +02:00
Claudio Atzori 4e36d689dd fixed XML serialization for children sub-elements (duplicates & externalreferences) 2020-05-26 18:30:40 +02:00
Claudio Atzori b8e541a454 fixing repeated organization.websiteurl in organization entities (#5645) as well as project.ecinternationalorganizationeurinterests 2020-05-26 10:30:09 +02:00
Claudio Atzori 7582532e73 [maven-release-plugin] prepare for next development iteration 2020-05-25 19:48:18 +02:00
Claudio Atzori 01c2e93395 [maven-release-plugin] prepare release dhp-1.2.1 2020-05-25 19:48:14 +02:00
Claudio Atzori 925d933204 making XmlRecordFactory immune to graph encoding changes (mostly to avoid NPEs) 2020-05-22 08:50:44 +02:00
Claudio Atzori b33dd58be4 replaced parameter 'reuseRecords' with 'resumeFrom', allowing to restart the provision workflow execution from any step, useful for manual submissions or debugging 2020-05-22 08:50:06 +02:00
Claudio Atzori dbfb9c19fe minor changes 2020-05-21 10:00:14 +02:00
Claudio Atzori d7d2a0637f added extra parameters to the provision indexing workflow 2020-05-20 14:55:38 +02:00
Claudio Atzori 0bdfbb0a57 reintroduced RDD based relation cut off procedure 2020-05-19 15:02:21 +02:00
Claudio Atzori 60c40618d3 [maven-release-plugin] prepare for next development iteration 2020-05-11 10:17:14 +02:00
Claudio Atzori c267d958d5 [maven-release-plugin] prepare release dhp-1.2.0 2020-05-11 10:17:10 +02:00
Claudio Atzori 42f1a2bf94 bumped project version to 1.2.0-SNAPSHOT 2020-05-11 10:05:57 +02:00
Claudio Atzori 0ccc864ad9 [maven-release-plugin] prepare for next development iteration 2020-05-08 17:01:31 +02:00
Claudio Atzori 6e47c724c6 [maven-release-plugin] prepare release dhp-1.1.7 2020-05-08 17:01:27 +02:00
Claudio Atzori 8c67073a07 force speculative execution to false 2020-05-08 09:42:21 +02:00
Claudio Atzori bac37b3973 fixed children expansion in XML records 2020-05-04 11:51:17 +02:00
Claudio Atzori 077ccd8743 stats wf properties cleanup 2020-05-04 11:41:46 +02:00
Claudio Atzori 439c6255a2 cleanup 2020-04-29 19:09:07 +02:00
Claudio Atzori 6f5b899038 reformatted code according to the updated style descriptor 2020-04-28 11:23:29 +02:00
Claudio Atzori a0bdbacdae switched automatic code formatting plugin to net.revelc.code.formatter:formatter-maven-plugin 2020-04-27 14:52:31 +02:00
Claudio Atzori 7a3f8085f7 switched automatic code formatting plugin to net.revelc.code.formatter:formatter-maven-plugin 2020-04-27 14:45:40 +02:00
Claudio Atzori 1e7583c5a6 filtered invisible records in data provision workflow 2020-04-23 07:51:34 +02:00
Claudio Atzori 0b55795d4d small adjustments in the provisioning workflow 2020-04-21 16:15:04 +02:00
Claudio Atzori d772d967aa restored changes from master branch 2020-04-20 18:53:06 +02:00
miconis 4da13e4570 Revert "Merge branch 'master' into deduptesting" 
This reverts commit 772f75d167, reversing
changes made to 5f45f2c77f.
 2020-04-20 16:04:49 +02:00
Claudio Atzori d714bfb4d4 collectedfrom field moved in common parent class Oaf.java 2020-04-20 12:25:19 +02:00
Claudio Atzori ad7a131b18 introduced common project code formatting plugin, works on the commit hook, based on https://github.com/Cosium/git-code-format-maven-plugin, applied to each java class in the project 2020-04-18 12:42:58 +02:00
Claudio Atzori d74e128aa6 Utility classes moved in dhp-common and dhp-schemas 2020-04-07 11:56:22 +02:00
Claudio Atzori 1a1a026a18 we do expect to find field bestaccessright already defined. No need to add it again 2020-04-07 08:55:33 +02:00
Claudio Atzori fbdd18a96b using dataset based relation preparation procedure 2020-04-07 08:54:39 +02:00
Claudio Atzori 77f59b1b10 dataset based provision WIP 2020-04-06 19:37:27 +02:00
Claudio Atzori e355961997 dataset based provision WIP 2020-04-06 17:34:25 +02:00
Claudio Atzori ca345aaad3 dataset based provision WIP 2020-04-06 15:33:31 +02:00
Claudio Atzori c8f4b95464 dataset based provision WIP 2020-04-06 08:59:58 +02:00
Claudio Atzori eb2f5f3198 dataset based provision WIP 2020-04-04 17:41:31 +02:00
Claudio Atzori 3d1b637cab dataset based provision WIP 2020-04-04 14:03:43 +02:00
Claudio Atzori 24b2c9012e dataset based provision WIP 2020-04-02 18:44:09 +02:00
Claudio Atzori daa26acc9d dataset based provision WIP, fixed spark2EventLogDir 2020-04-02 16:15:50 +02:00
Claudio Atzori 9c7092416a dataset based provision WIP 2020-04-01 19:07:30 +02:00
Claudio Atzori 1402eb1fe7 cleanup 2020-04-01 15:38:50 +02:00
Claudio Atzori adcdd2d05e WIP: reimplementing the adjacency list construction process using spark Datasets 2020-04-01 14:56:57 +02:00
Claudio Atzori 377e1ba840 [maven-release-plugin] prepare for next development iteration 2020-03-30 20:06:00 +02:00
Claudio Atzori 76d9315129 [maven-release-plugin] prepare release dhp-1.1.6 2020-03-30 20:05:56 +02:00
Claudio Atzori ef429010ee removed log file and job-override.properties 2020-03-30 20:00:58 +02:00
Claudio Atzori 0fbec69b82 use oozie prepare statement to cleanup working directories 2020-03-30 19:48:41 +02:00
Claudio Atzori f3f9affd49 allow dynamic executors to build XML records 2020-03-30 13:12:11 +02:00