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3061 Commits

Author SHA1 Message Date
Sandro La Bruzzo 35e20b0647 updated resolution wf: 
- generate a new version of the graph
 - changed merge from union to join
 2021-11-22 11:48:55 +01:00
Miriam Baglioni fdb75b180e [Cleaning] added couple of tests for DOIBOOST publications 2021-11-21 16:35:22 +01:00
Miriam Baglioni 0506fa2654 [Graph Dump] changed to mirror the changes in the model 2021-11-19 15:56:25 +01:00
Sandro La Bruzzo 3426451d3f Merge remote-tracking branch 'origin/beta' into beta 2021-11-19 14:49:04 +01:00
Sandro La Bruzzo 4542a2338b updated site configuration to deploy on website 2021-11-19 13:44:08 +01:00
Claudio Atzori e5a2c596b2 Merge branch 'beta' into preserve_openorg_parent_child_relations 2021-11-19 11:35:46 +01:00
Claudio Atzori f4538f3c4c cleanup 2021-11-19 11:33:10 +01:00
Claudio Atzori 2b46b87f56 fixed filtering criteria applied in SparkCopyRelationsNoOpenorgs to keep the parent/child relations from OpenOrgs 2021-11-19 11:30:29 +01:00
Miriam Baglioni 9fae872181 [Graph Dump] changed to mirror the changes in the model 2021-11-19 11:25:50 +01:00
Sandro La Bruzzo fc03c99805 fixed javadocs url after deploying site 2021-11-19 10:46:33 +01:00
Sandro La Bruzzo 0c0d561bc4 added public class into tests to create correct javadoc 2021-11-19 09:54:22 +01:00
Claudio Atzori 62fa61f3cf merge from beta 2021-11-19 09:23:42 +01:00
Claudio Atzori bd9a43cefd Revert to 4094f2bb9a 2021-11-19 09:20:43 +01:00
Claudio Atzori 3974fa7dc1 Merge branch 'beta' into affiliationPropagation 2021-11-18 18:06:26 +01:00
Claudio Atzori a24b9f8268 [dedup] trivial refactoring 2021-11-18 17:12:02 +01:00
Claudio Atzori c0750fb17c avoid non necessary count operations over large spark datasets 2021-11-18 17:11:31 +01:00
Claudio Atzori bb5dca7979 cleanup 2021-11-18 17:10:46 +01:00
Miriam Baglioni 793b5a8e5f Aggiornare 'dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java' 
Removing the dump of Measure at the level of the result. We decided not to map it
 2021-11-18 14:49:38 +01:00
Miriam Baglioni 5dc5792722 [Graph Dump] Change test resource to mirror the movement of the measure element 2021-11-18 14:39:12 +01:00
Miriam Baglioni 0136a8c266 [Graph Dump] Change test to mirror that measure is at the level of the isntance 2021-11-18 14:38:33 +01:00
Miriam Baglioni 1b79c0ee79 mergin with branch beta 2021-11-18 11:01:00 +01:00
Antonis Lempesis cb3adb90f4 Merge branch 'beta' into beta 2021-11-17 14:33:45 +01:00
Antonis Lempesis c283406829 added Universidad Polytecnica de Madrid 2021-11-17 15:33:00 +02:00
Claudio Atzori e0395719d7 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2021-11-17 14:17:27 +01:00
Claudio Atzori 82a4e4efae [cleaning wf] fixed methodology to rule out invalid result titles, based on https://support.openaire.eu/issues/7206 2021-11-17 14:17:22 +01:00
Miriam Baglioni 6d4a1c57ee [Resolve Entities] Change test dataset to mirror the modification in the creation of the map between the pids and the unresolved 2021-11-17 12:41:52 +01:00
Sandro La Bruzzo 9c82d670b8 make class public in order to create javadoc 2021-11-17 12:31:02 +01:00
Sandro La Bruzzo 1f5ee116ed code refactor, created and moved scala code on the correct maven folder under src/main/scala and src/test/scala 
fixed test
 2021-11-17 12:23:52 +01:00
Sandro La Bruzzo 2fd9ceac13 code refactor, created and moved scala code on the correct maven folder under src/main/scala and src/test/scala 2021-11-17 11:35:22 +01:00
Sandro La Bruzzo 2506d7a679 Merge branch 'mvn_site_documentation' of code-repo.d4science.org:D-Net/dnet-hadoop into mvn_site_documentation 2021-11-17 11:07:24 +01:00
Sandro La Bruzzo cded363b55 code refactor, created and moved scala code on the correct maven folder under src/main/scala and src/test/scala 2021-11-17 11:06:35 +01:00
Miriam Baglioni 4094f2bb9a added integration md file 2021-11-17 10:04:52 +01:00
Miriam Baglioni ec8b0219ff [Documentation] Added first page for Integration via unresolved entities generation 2021-11-16 17:41:34 +01:00
Miriam Baglioni 2bbece2ca5 mergin with branch beta 2021-11-16 16:35:40 +01:00
Sandro La Bruzzo 2d67020c59 added dhp-enrichment maven site template 2021-11-16 16:01:08 +01:00
Miriam Baglioni 28ea532ece [Affilaition Propagation] moved the selection of graph relation as a preparation step 2021-11-16 15:24:19 +01:00
Sandro La Bruzzo 18c1d70ef4 Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into mvn_site_documentation 2021-11-16 15:16:49 +01:00
Sandro La Bruzzo a1cafaf2e3 added mvn site for dnet-hadoop project 2021-11-16 15:16:28 +01:00
Miriam Baglioni 7c96e3fd46 removed not useful dir 2021-11-16 13:57:26 +01:00
Miriam Baglioni c7c0c3187b [AFFILIATION PROPAGATION] Applied some SonarLint suggestions 2021-11-16 13:56:32 +01:00
Miriam Baglioni c6a9f0a1a8 mergin with branch beta 2021-11-16 12:04:40 +01:00
Miriam Baglioni 99d86134f5 [Graph Dump] changed the dump since the measures have been moded at the level of the instance 2021-11-16 12:04:21 +01:00
Claudio Atzori 0a727d325d [dedup] increased number of partitions in the consistency phase 2021-11-16 08:43:41 +01:00
Claudio Atzori bafa2990f3 code formatting 2021-11-15 17:07:16 +01:00
Claudio Atzori 668ac25224 [graph resolution] using existing argument parser file name 2021-11-15 17:02:45 +01:00
Claudio Atzori 7d0a03f607 [graph resolution] minor 2021-11-15 14:45:54 +01:00
Claudio Atzori 941a50a2fc Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2021-11-15 14:42:49 +01:00
Claudio Atzori 7c804acda8 [graph resolution] minor 2021-11-15 14:42:43 +01:00
Sandro La Bruzzo efa09057db Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2021-11-15 14:32:09 +01:00
Sandro La Bruzzo 48923e46a1 added documentation to Pubmed Class and also added mvn site for dhp-aggregations 2021-11-15 14:32:01 +01:00
Claudio Atzori d2c787d416 [graph resolution] fixed sequence of the workflow steps 2021-11-15 14:31:15 +01:00
Claudio Atzori 975b10b711 [actionmanager] increased spark.sql.shuffle.partitions to 5000 2021-11-15 12:31:45 +01:00
Miriam Baglioni 4ec88c718c merge with beta - resolved conflict in pom 2021-11-15 10:52:16 +01:00
Miriam Baglioni 6f1a434e90 [Bypass Action Set] Fixed test to consider the new identifier utils 2021-11-15 09:59:23 +01:00
Miriam Baglioni 157d33ebf9 [Bypass Action Set] Refactoring 2021-11-15 09:58:48 +01:00
Miriam Baglioni 6595135a1a [Dump Schemas] changed the schema of the dumped result according to the modifications in the bestAccessRight type 2021-11-12 11:45:38 +01:00
Miriam Baglioni 43cae4ad88 Merge branch 'dump' of https://code-repo.d4science.org/D-Net/dnet-hadoop into dump 2021-11-12 11:36:54 +01:00
Miriam Baglioni b3f9370125 merge with beta - resolved conflict in pom 2021-11-12 11:25:26 +01:00
Miriam Baglioni 92d0e18b55 [Bypass Action Set] used constant DOI instead of "doi" 2021-11-12 10:56:58 +01:00
Miriam Baglioni 881113743f [Bypass Action Set] refactoring 2021-11-12 10:55:50 +01:00
Miriam Baglioni 47ccb53c4f [Bypass Action Set] modification for comment #157 (comment) 2021-11-12 10:54:09 +01:00
Miriam Baglioni ffb0ce1d59 merge with beta - resolved conflict in pom 2021-11-12 10:19:59 +01:00
Miriam Baglioni 716021546e [Bypass Action Set] minor fix 2021-11-12 10:18:01 +01:00
Sandro La Bruzzo 3469cc2b1d Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta 2021-11-12 09:56:52 +01:00
Sandro La Bruzzo a7763d2492 removed alternate identifier in resolutionMap 2021-11-12 09:56:45 +01:00
Miriam Baglioni b8bdabfae9 [Graph DUmp] removed OpenAccessRoute from test in best access right 2021-11-11 16:16:48 +01:00
Miriam Baglioni e5498052e8 [Graph DUmp] removed OpenAccessRoute from test in best access right 2021-11-11 16:14:10 +01:00
Miriam Baglioni 935062edec [Bypass Action Set] creation of unresolved entities 2021-11-11 16:11:25 +01:00
Antonis Lempesis 26f086dd64 removed the too restrctive clause. will discuss again 2021-11-11 12:57:19 +02:00
Claudio Atzori 148289150f Merge branch 'beta' into doiboost_url 2021-11-11 10:40:19 +01:00
Sandro La Bruzzo 2ca0a436ad added SparkResolveEntities node to the oozie wf 2021-11-11 10:25:42 +01:00
Sandro La Bruzzo 9cb195314f implemented and tested resolution of entities 2021-11-11 10:17:40 +01:00
Miriam Baglioni 6d3c4c4abe mergin with branch beta 2021-11-11 08:59:53 +01:00
Miriam Baglioni 8cc50ecee0 [Graph Dump] changed AccessRight with BestAccessRight in the dump and modified the dependency to the schema to the SNAPSHOT 2021-11-11 08:59:20 +01:00
Miriam Baglioni 88b73f4f49 mergin with branch beta 2021-11-10 17:00:52 +01:00
Miriam Baglioni c371b23077 - 2021-11-10 17:00:37 +01:00
Miriam Baglioni 9e214ce0eb [BypassAS] addition of OC relations 2021-11-09 12:07:19 +01:00
Sandro La Bruzzo 6477a40670 implement filter of openCitation 2021-11-09 11:27:12 +01:00
Miriam Baglioni 6f7ca539c6 [BypassAS] update of results for bipFinder and FOS 2021-11-09 11:25:41 +01:00
Miriam Baglioni a7d50c499b [BypassAS] prepare FOS subject, test and model for FOS and BipFinder scores 2021-11-08 16:44:19 +01:00
Antonis Lempesis 91354c6068 - fetching all context related results 
- storing tables as parquet
 2021-11-08 15:15:46 +02:00
Miriam Baglioni 94918a673c [Graph DUMP] Fix issue for empty origilaId list 2021-11-08 10:25:28 +01:00
Miriam Baglioni 4c70201412 mergin with branch beta 2021-11-05 12:29:56 +01:00
Miriam Baglioni 8442efd8d1 [Graph DUMP] Filtering out from the originalIds the id of the result in OpenAIRE 2021-11-05 12:29:22 +01:00
Claudio Atzori 5681e89544 Update 'dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/schemas/result_schema.json' 2021-11-05 12:18:24 +01:00
Miriam Baglioni a22c29fba1 [Graph DUMP] Filtering out from the originalIds the id of the result in OpenAIRE 2021-11-05 12:08:33 +01:00
Miriam Baglioni c10ff6928c [Graph DUMP] add schema of the dump related to the model as in dhp-schemas.2.8.31. Note the measere element at the level of the result has been removed because of issues on where to display it: at the level of the result or at the level of the entity 2021-11-05 11:36:21 +01:00
Miriam Baglioni 0857849a86 [Graph DUMP] Remove dump of measure until it will be clear where to put it (at the level of result or at the level of the instance) 2021-11-05 11:02:37 +01:00
Miriam Baglioni df7ee77c7a [DOIBoost Mapping] removed not needed comments 2021-11-04 16:24:07 +01:00
Miriam Baglioni de63d29b6f [DOIBoost Mapping] Fix to avoid to produce results with null as identifier (probably due to the filtering function in the factory for the creation of the id) 2021-11-04 16:16:40 +01:00
Miriam Baglioni d50057b2d9 [DOIBoost Mapping] changed the way to create the url for the instance: we use the crooref guidelines https://doi.org/doi 2021-11-03 16:59:37 +01:00
Miriam Baglioni edf55395e9 added test resourse 2021-11-03 16:49:30 +01:00
Miriam Baglioni d97ea82a29 [DOIBoost Mapping] Added test to verify the instance created for Crossref will have just the url related to the doi 2021-11-03 16:45:15 +01:00
Miriam Baglioni 96769b4481 [DOIBoost - Mapping] Changed the logic which brought in in the instance urls that should not be there: The urld of the doi in the json is reachable from the root (json/"URL") other urls where added from the links element. Now the mapping from the link element has been removed 2021-11-03 16:43:36 +01:00
Miriam Baglioni 683fe093cf [DOIBoost - Mapping] Remove the addition of the instance to the MAG publication record 2021-11-03 15:51:26 +01:00
Miriam Baglioni b2bb8d9d79 [DOIBoost - Mapping] selecting the url from Crossref containing the doi 2021-11-03 15:44:57 +01:00
Miriam Baglioni 779318961c [DOIBoost - Mapping] removed the url from crossref containing the api.elsevier.com... string in the url 2021-11-03 14:38:52 +01:00
Miriam Baglioni 2480e590d1 [DOIBoost - Mapping] changed the type on which to map dissertation from Crossref: from 006 Doctoral thesis to 0044 Thesis since dissertation could be either Doctoral or master thesis 2021-11-03 14:25:23 +01:00
Miriam Baglioni b9d124bb7c [Enrichment: Propagation through parent-child relationships] Added counters, and changed constraint to verify if filtering out the relation (from classname = harvested to classid != propagation) 2021-11-03 13:55:37 +01:00
Sandro La Bruzzo 7bd224f051 implement first version of scholexplorer integration for the generation of final graph 2021-11-02 15:58:15 +01:00
Claudio Atzori 7fa49f6956 Merge pull request 'removed hardcoded reference' (#154) from antonis.lempesis/dnet-hadoop:beta into beta 
Reviewed-on: #154
 2021-11-02 09:11:30 +01:00
Antonis Lempesis f78afb5ef9 removed hardcoded reference 2021-11-01 15:42:29 +02:00
Miriam Baglioni 2aca6bfa0a mergin with branch beta 2021-10-29 11:20:45 +02:00
Miriam Baglioni 09f36cffb8 [Enrichment: Propagation through parent-child relationships] First implementation, testing, and wf for propagation of result to organization through semantic relation 2021-10-29 11:20:03 +02:00
Claudio Atzori 1225ba0b92 [resolution] increasing number of partitions to avoid OOM 2021-10-28 16:18:17 +02:00
Sandro La Bruzzo d9cbca83f7 moved filter on next phase 2021-10-28 16:13:24 +02:00
Sandro La Bruzzo 1be9aa0a5f Removed filter of datacite items from the raw graph merging phase, Datacite is not an actionset anymore in beta 2021-10-26 17:52:20 +02:00
Sandro La Bruzzo 4acfa8fa2e Scholexplorer Datasource Aggregation: 
- Added collectedfrom in the inverse relation generated
Relation resolution:
- increased number of partitions in workflow.xml
- using classid instead of classname to build the pid-dnetId mapping
 2021-10-26 17:51:20 +02:00
Miriam Baglioni d0ef7d91c5 adding test resource 2021-10-26 17:34:11 +02:00
Sandro La Bruzzo 034304b33a conflict resolved on merge 2021-10-26 09:40:47 +02:00
Claudio Atzori d147295c2f avoiding java.io.NotSerializableException: java.util.HashMap 2021-10-21 14:15:57 +02:00
Claudio Atzori 3702fe478d cleanup 2021-10-21 12:05:02 +02:00
Sandro La Bruzzo ac36aa7d1c fixed wrong Encoding during a map phase 2021-10-21 11:35:02 +02:00
Sandro La Bruzzo aeeebd573b code refactor renamed datacite package 2021-10-20 17:37:42 +02:00
Sandro La Bruzzo ab3a99d3e9 removed old datacite oozie workflow 2021-10-20 17:19:47 +02:00
Sandro La Bruzzo ae4e99a471 Adapted workflow of resolution of PID to work into OpenAIRE data workflow 
- Added relations in both verse on all Scholexplorer datasources
 2021-10-20 17:12:16 +02:00
Claudio Atzori 4f8970f8ed [stats] reducing the step22 wait time 2021-10-20 14:14:53 +02:00
Claudio Atzori 00b78b9c58 cleanup: mapping contents in the graph already defined in the OAF graph model doesn't require to be aware of the vocabularies 2021-10-20 14:04:45 +02:00
Claudio Atzori c01dd0c925 registered oaf model classes for the KryoSerializer 2021-10-20 13:55:07 +02:00
Miriam Baglioni 652114c641 [affiliationPropagation] first try. preparetion 2021-10-20 11:44:23 +02:00
Claudio Atzori 59f76b50d4 Merge branch 'beta' into hierarchical_orgs_relations 2021-10-20 09:42:35 +02:00
Antonis Lempesis 241dcf6df1 Merge branch 'beta' into beta 2021-10-19 23:54:21 +02:00
Claudio Atzori 515e068a78 Merge branch 'beta' into hierarchical_orgs_relations 2021-10-19 16:46:06 +02:00
Claudio Atzori 512e7b0170 code formatting 2021-10-19 16:19:29 +02:00
Claudio Atzori e9157c67aa Merge branch 'beta' into dump 2021-10-19 16:15:03 +02:00
Claudio Atzori 98f37c8d81 WIP: worflow nodes for including Scholexplorer records in the RAW graph 2021-10-19 16:14:40 +02:00
Claudio Atzori c8850456e9 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2021-10-19 16:09:54 +02:00
Sandro La Bruzzo c9870c5122 code formatted 2021-10-19 15:24:59 +02:00
Sandro La Bruzzo f8329bc110 since dhp-schemas changed, introducing new Relation inverse model, this class has been updated 2021-10-19 15:24:22 +02:00
Claudio Atzori 7a73010acd WIP: worflow nodes for including Scholexplorer records in the RAW graph 2021-10-19 11:59:16 +02:00
Miriam Baglioni c7f6cd2591 added again the setting for saXReader 2021-10-19 10:15:26 +02:00
miconis 5f780a6ba1 bug fix in migrate entities: parameter name was wrong 2021-10-18 23:30:40 +02:00
Miriam Baglioni 1315952702 merge with branch beta 2021-10-18 14:17:09 +02:00
Miriam Baglioni 1cc09adfaa Opencitations: chenaged the test class to mirror the creation or not of duplicate dois for .refs oc original plus added optional parameter to duplicate the relation 2021-10-18 14:11:27 +02:00
Miriam Baglioni 76d41602be Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2021-10-18 10:53:22 +02:00
Miriam Baglioni 46f82c7c8f removed not needed folder deletion 2021-10-18 10:53:16 +02:00
Sandro La Bruzzo 7b15b88d4c renamed wrong package, implemented last aggregation workflow for scholexplorer 2021-10-15 15:00:15 +02:00
Antonis Lempesis 41ecb1eb61 invalidating medatadata before context thingies 2021-10-15 13:42:55 +03:00
Antonis Lempesis 4b7c8dff2d fetching affiliated results for 4 orgs in monitor. fixed affiliated orgs in stats db 2021-10-14 18:53:35 +03:00
Sandro La Bruzzo 51a03c0a50 refactor code for EBI from dhp-graph-mapper into dhp-aggregation 2021-10-14 14:23:13 +02:00
Claudio Atzori 14fbf92ad6 Merge branch 'beta' into beta_solr_config 2021-10-14 11:08:44 +02:00
Claudio Atzori b292e4a700 [stats wf] added extra logging in the context data retrieval phase 2021-10-13 17:31:53 +02:00
miconis 995c1eddaf minor change 2021-10-13 17:07:10 +02:00
Miriam Baglioni 5d9cc2452d changed the working path parameter value as dependant from the dnet-workflow working dir parameter 2021-10-13 15:33:50 +02:00
miconis 326bf63775 integration of parent child orgs relations 2021-10-13 12:24:48 +02:00
Miriam Baglioni 16b28494a9 added new parameter in the doiboost process workflow to specify a folder for the process of MAG dataset 2021-10-13 11:34:24 +02:00
Miriam Baglioni 63933808d4 added fix for mixing result types, added configuration default to funder subworkflow 2021-10-13 11:28:28 +02:00
Sandro La Bruzzo 7387416e90 added params skip update to direct transform in OAF, this should be set to true in production 2021-10-12 12:36:30 +02:00
Sandro La Bruzzo 511da98d0c - fixed bug on download pmc Article 
- removed unused line of code in SparkCreateActionset
 2021-10-12 11:47:49 +02:00
Miriam Baglioni fec40bdd95 merging with branch beta - resolved conflicts 2021-10-12 09:16:36 +02:00