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769 Commits

Author SHA1 Message Date
Sandro La Bruzzo 7bd224f051 implement first version of scholexplorer integration for the generation of final graph 2021-11-02 15:58:15 +01:00
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
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 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 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
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 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
miconis 995c1eddaf minor change 2021-10-13 17:07:10 +02:00
miconis 326bf63775 integration of parent child orgs relations 2021-10-13 12:24:48 +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
Miriam Baglioni fec40bdd95 merging with branch beta - resolved conflicts 2021-10-12 09:16:36 +02:00
Sandro La Bruzzo 5606014b17 code refactor see ticket #7065 2021-10-12 08:11:53 +02:00
Sandro La Bruzzo 2557bb41f5 Implemented new method for update baseline inside scala node 2021-10-06 16:41:08 +02:00
Sandro La Bruzzo b84e0cabeb Implemented new method for update baseline 2021-10-05 16:34:47 +02:00
Sandro La Bruzzo 991b06bd0b removed generation of EBI links from old dump, now EBI link dump is created by another wf 2021-10-05 10:21:33 +02:00
Miriam Baglioni e653756e3d applied some suggestiond from Sonar Lint 2021-10-04 18:40:07 +02:00
Miriam Baglioni c4ccd7b32c - 2021-10-01 12:59:47 +02:00
Miriam Baglioni c8321ad31a merge with branch beta 2021-10-01 12:59:08 +02:00
Claudio Atzori ebf53a1616 added cleaning for relation fields: subRelType & relClass according to dedicated vocabs 2021-09-15 16:10:37 +02:00
Sandro La Bruzzo e8b3cb9147 Implemented method to download delta updates in EBI Links 2021-08-30 09:32:45 +02:00
Alessia Bardi ccf4103a25 keep the original url if the decoder fails for any reason 2021-08-25 10:07:58 +02:00
Sandro La Bruzzo 45898c71ac fixed wrong doi in pubmed 2021-08-24 15:20:04 +02:00
Alessia Bardi 931f430129 Merge branch 'beta' into datasource_model_eosc_beta 2021-08-23 11:57:21 +02:00
Alessia Bardi 4c1474e693 Dealing with #6859#note-2: we have to decode URLs to avoid & and other chars encoded becasue of the original XML representation of data 2021-08-20 17:03:30 +02:00
Miriam Baglioni e5cf11d088 change open access route to result matching hbm to gold 2021-08-19 10:29:04 +02:00
Claudio Atzori f74adc4752 added DownloadCSV2 as alternative implementation of the same download procedure 2021-08-13 15:52:15 +02:00
Claudio Atzori 5f0903d50d fixed CSV downloader & tests 2021-08-13 14:17:54 +02:00
Claudio Atzori 7ee2757fcd fixed DownloadCSV parameters spec; workflow patching the hostedby replaces the graph content (publication, datasource) rather than creating a copy 2021-08-13 12:41:01 +02:00
Claudio Atzori c3ad4ab701 minor fixes 2021-08-13 12:23:15 +02:00
Claudio Atzori 3359f73fcf cleanup & best practices 2021-08-13 12:00:42 +02:00
Miriam Baglioni f4ec81c92c mergin with branch beta 2021-08-13 10:31:35 +02:00
Miriam Baglioni 32fd75691f refactoring 2021-08-13 10:15:42 +02:00
Claudio Atzori 9587d4aee8 Merge branch 'beta' into hostedbymap 2021-08-12 17:04:30 +02:00
Claudio Atzori 8cdce59e0e [graph raw] let the mapping exceptions propagate 2021-08-12 11:32:26 +02:00
Miriam Baglioni b1c6140ebf removed all comments in Italian 2021-08-11 16:23:33 +02:00
Miriam Baglioni 8da3a25cf6 merging with branch beta 2021-08-11 15:55:34 +02:00
Claudio Atzori 9f4db73f30 updated/fixed unit tests 2021-08-11 15:02:51 +02:00
Claudio Atzori 2ee21da43b suggestions from SonarLint 2021-08-11 12:13:22 +02:00
Miriam Baglioni 9731a6144a hostedbymap - in case the journal is open access the access may be changed also for the best access right in the result 2021-08-10 17:49:45 +02:00
Miriam Baglioni c3931557e3 extended the logic of the dump to consider the validation date in the relation (also in the dumped result for communities and funders at the level of the project), the extention on the instance for the APC, the pid, the alternate identifiers, and the extention of the AccessRight to store the OpenAccessRoute. Added new resourec for testing and extended the old class to verify the new dump. Fixed also issue on relation dump: only relation whose source and target are entities in the graph are dumped. The same hold for references to projects 2021-08-06 18:56:18 +02:00
Miriam Baglioni 6bd1eca7e0 merge branch with beta 2021-08-05 15:23:32 +02:00
Miriam Baglioni 73dc082927 added new dumped field (openaccessroute, pid and alternate identifier at the level of the instance) and the bipFinder measure at the level of the result 2021-08-05 15:20:50 +02:00
Miriam Baglioni ee13da9258 merge branch with master 2021-08-05 11:34:20 +02:00
Miriam Baglioni eccf3851b0 Hosted By Map - refactoring 2021-08-04 10:16:30 +02:00
Miriam Baglioni 1e952cccf6 Hosted By Map - refactoring and deletion of not needed methods 2021-08-04 10:15:43 +02:00
Miriam Baglioni 8ba8c77f92 Hosted By Map - refactoring 2021-08-04 10:14:57 +02:00
Miriam Baglioni 8f7623e77a Hosted By Map - refactoring and application of the new aggregator 2021-08-04 10:14:20 +02:00
Miriam Baglioni a7bf314fd2 Hosted By Map - added new aggregator to get just one result per datasource id 2021-08-04 10:13:30 +02:00
Miriam Baglioni 100e54e6c8 mergin with branch beta 2021-08-03 10:47:11 +02:00
Miriam Baglioni 461b8a29a0 removed not needed class 2021-08-03 10:46:51 +02:00
Miriam Baglioni 327cddde33 Hosted By Map - refactoring 2021-08-03 10:44:13 +02:00
Miriam Baglioni 1e859706a3 Hosted By Map - Classes to apply the HBM to results and datasources 2021-08-02 19:35:23 +02:00
Miriam Baglioni 72df8f9232 Hosted By Map - removed the aggregator for the datasource (it is no more needed) and added a new aggregator for the results. Changed also the hostedBYMap aggregator 2021-08-02 19:34:44 +02:00
Miriam Baglioni ff1ce75e33 Hosted By Map - modification in the code to prepare the info needed to apply the HostedByMap. There is no need to join datasources with the hbm: all the information needed is in the hosted by map already 2021-08-02 19:32:59 +02:00
Claudio Atzori e826aae848 using constants from ModelConstants 2021-08-02 14:28:59 +02:00
Miriam Baglioni 7c6ea2f4c7 Hosted By Map - first attempt for the creation of intermedia information to be used to applu the hosted by map on the graph entities 2021-07-30 17:56:27 +02:00
Miriam Baglioni d8b9b0553b Hosted By Map - model classes to store the intermediate information to be used to apply the hosted by map 2021-07-30 17:55:39 +02:00
Miriam Baglioni 613bd3bde0 Hosted By Map - refactor of the first attemp to prepare a new hosted by map dependent on the datasource in the graph and on two external sources: the gold list from unibi ad the doaj list of open access journal. Both the lists are downloaded from provided url parameter 2021-07-30 17:54:45 +02:00
Miriam Baglioni d1807781c0 mergin with branch beta 2021-07-30 14:34:07 +02:00
Miriam Baglioni 1d6ac3715b merge branch with beta 2021-07-30 11:58:29 +02:00
Claudio Atzori 19620eed46 applying PR#131, Patch the identifiers (source/target) in the relations, refinements 2021-07-30 11:09:32 +02:00
Claudio Atzori a6a38cca9e fixed implementation of PatchRelationsApplication, refined the relative unit test 2021-07-30 11:06:11 +02:00
Claudio Atzori 576693d782 added unit test for PatchRelationsApplication 2021-07-30 10:13:33 +02:00
Miriam Baglioni baad01cadc hostedbymap 2021-07-29 13:04:39 +02:00
Claudio Atzori e87e1805c4 [raw_all] added extra workflow step for patching the identifiers in the relations, given an id mapping dataset 2021-07-29 12:13:06 +02:00
Claudio Atzori 1923c1ce21 replaced full join + filtering with a left join 2021-07-29 11:36:20 +02:00
Michele Artini e6f1773d63 mapping of new eosc fields 2021-07-28 11:17:11 +02:00
Miriam Baglioni 0424f47494 HostedByMap fixing issues 2021-07-28 10:24:13 +02:00
Claudio Atzori d267dce520 [raw_all] added extra workflow step for patching the identifiers in the relations, given an id mapping dataset 2021-07-27 17:18:29 +02:00
Miriam Baglioni 74f801b689 mergin with branch beta 2021-07-27 13:18:31 +02:00
Miriam Baglioni 35e395eae8 merge with master 2021-07-27 12:34:59 +02:00
Miriam Baglioni eb07f7f40f Hosted By Map 2021-07-27 12:27:26 +02:00
Sandro La Bruzzo 848aabbb6c minor fix 2021-07-25 12:06:41 +02:00
Sandro La Bruzzo 8fac10c91e fixed defintion wf of creation final infospace of scholexplorer 2021-07-25 11:15:37 +02:00
Sandro La Bruzzo 3920c69bc8 change implementation of resolve Relation to generate jsonRdd in output 2021-07-25 09:51:36 +02:00
Sandro La Bruzzo d9e3b89937 implemented last part of workflows to generate scholixGraph 2021-07-23 16:38:32 +02:00
Sandro La Bruzzo cfde63a7c3 fixed resolve relation join 2021-07-23 14:17:29 +02:00
Sandro La Bruzzo 4a439c3863 NPE fixed 2021-07-23 14:17:29 +02:00
Sandro La Bruzzo 43e9380cd3 update resolve relation to use the same format of openaire graph 2021-07-23 11:25:18 +02:00
Sandro La Bruzzo 62ae36a3d2 fixed NPE 2021-07-22 15:41:38 +02:00
Sandro La Bruzzo 31d2d6d41e Scholexplorer: introduction of dedup openaire 2021-07-21 18:09:32 +02:00
Claudio Atzori 65934888a1 adding record identifier among the originalIds regardless of what IdentifierFactory produces 2021-07-19 17:52:52 +02:00
Claudio Atzori 5947cddafc adding record identifier among the originalIds regardless of what IdentifierFactory produces 2021-07-19 17:52:24 +02:00
Claudio Atzori 0977baf41d contents mapped from the stores with 'claim' interpretation will not change their identifier along their way towards the graph 2021-07-19 17:43:52 +02:00
Claudio Atzori 5e5f65a3c3 contents mapped from the stores with 'claim' interpretation will not change their identifier along their way towards the graph 2021-07-19 15:56:55 +02:00
Sandro La Bruzzo 7e2caafe84 Scholexplorer: fixed mapping typologies 2021-07-15 09:53:12 +02:00
Miriam Baglioni 774cdb190e changes to mirror the last dump of the graph with the ols data model. 2021-07-13 18:57:24 +02:00
Miriam Baglioni 886617afd0 One result linked to more than on project is saved just once 2021-07-13 18:15:35 +02:00
Miriam Baglioni 320cf02d96 Changed the way to find results linked to projects. We verify to actually have the project on the graph before selecting the result 2021-07-13 18:13:32 +02:00
Miriam Baglioni 970b387b8d modification to allow dump of a single community 2021-07-13 18:08:10 +02:00
Miriam Baglioni eae10c5894 modification to allow the dump for a single community 2021-07-13 18:07:25 +02:00
Miriam Baglioni d70f8c96fd funding contains and not starts with h2020 2021-07-13 17:34:53 +02:00
Miriam Baglioni 5e38c7f42d dumping only communities with status all 2021-07-13 17:32:38 +02:00
Miriam Baglioni 618d2de2da minor changes and refactoring 2021-07-13 17:10:02 +02:00
Miriam Baglioni 084b4ef999 added the creation of the openaireId from funder and grant number if the element is not present in the context profile 2021-07-13 17:07:46 +02:00
Miriam Baglioni 8f322a73cb change because of the renaming of originalId in acronym 2021-07-13 16:22:58 +02:00
Miriam Baglioni 72397ea1ba Added fix for community of arbitrary name length 2021-07-13 16:18:35 +02:00
Miriam Baglioni 5295d10691 added check not to dump deletedByInference entities 2021-07-13 16:11:46 +02:00
Miriam Baglioni e9a17ec899 added check to verify not to add void APC 2021-07-13 15:53:35 +02:00
Miriam Baglioni 39b1a6edf6 added test class for the selection of valid relations and description 2021-07-13 15:23:09 +02:00
Miriam Baglioni 9a58f1b93d added logic to select only the valid relations: those not deletedbyinference and having both part of the relation as entities in the graph 2021-07-13 15:20:39 +02:00
Miriam Baglioni 13c66e16be changed logic to split for communities 2021-07-13 15:15:27 +02:00
Miriam Baglioni 6410ab71d8 added APC in the dump and test method 2021-07-13 15:13:58 +02:00
Miriam Baglioni 69fd40fd30 modified code to split the Croatian funder 2021-07-13 14:35:26 +02:00
Miriam Baglioni 86e50f7311 modified code to split the Croatian funder 2021-07-13 14:31:45 +02:00
Miriam Baglioni da88c850c6 changed the logic to verify if a community is contained in the list of context of a result 2021-07-13 14:22:44 +02:00
Miriam Baglioni 2f66fedfec changed the logic to verify if a community is contained in the list of context of a result 2021-07-13 14:22:23 +02:00
Sandro La Bruzzo bbe8193930 merged stable ids 2021-07-12 17:00:43 +02:00
Sandro La Bruzzo 09fccf8000 added workflow to serialize scholix and summary in json 2021-07-09 11:01:42 +02:00
Sandro La Bruzzo 0ea576745f updated CreateInputGraph because ggenerics don't work on Spark Dataset 2021-07-09 10:29:24 +02:00
Sandro La Bruzzo 8a034e46e1 updated baseline workflow 2021-07-08 11:11:41 +02:00
Claudio Atzori b7b8e0986e [raw_all] The claim merge procedure includes the claimed contexts in the merged result 2021-07-08 10:42:31 +02:00
Sandro La Bruzzo 0799ac9fb6 fixed wrong path 2021-07-08 10:36:37 +02:00
Sandro La Bruzzo 4d53402712 extended ebiLinks to create a dataset before generation of OAF 2021-07-08 10:26:21 +02:00
Sandro La Bruzzo a4a54a3786 code refactor 2021-07-08 09:08:25 +02:00
Sandro La Bruzzo a01dbe0ab0 completed workflow of generation of scholix and summaries 2021-07-07 23:10:34 +02:00
Claudio Atzori fdcff42e46 [raw_all] Aggregator graph creation merges claims (updates) with the corresponding entity 2021-07-07 19:01:59 +02:00
Claudio Atzori 32bdfdccbc [raw_all] Aggregator graph creation merges claims (updates) with the corresponding entity 2021-07-07 11:08:27 +02:00
Claudio Atzori f580cb77e1 added mapping for claim relation 'resultResult_publicationDataset_isRelatedTo' (present on BETA) 2021-07-06 21:11:11 +02:00
Sandro La Bruzzo 8535506c22 added scholix generation 2021-07-06 17:18:06 +02:00
Sandro La Bruzzo 4c54bd8742 add test to verify merge scholix on source 2021-07-06 11:32:14 +02:00
Sandro La Bruzzo 7d8db2eb8a betterRenamingMethod 2021-07-06 09:56:32 +02:00
Sandro La Bruzzo c952c8d236 generate first side of scholix mapping 2021-07-06 09:53:14 +02:00
Sandro La Bruzzo e4b84ef5d6 fixed mapping OAF to Scholix summary 2021-07-02 16:48:48 +02:00
Sandro La Bruzzo c6fa8598e1 massive code refactor: 
removed modules dhp-*-scholexplorer
 2021-07-01 22:13:45 +02:00
Sandro La Bruzzo 1a6b398968 implemented Creation of Raw Graph and Resolution 2021-06-30 17:27:55 +02:00
Sandro La Bruzzo 623a0c4edb code Refactor, renaming packages 2021-06-30 11:09:30 +02:00
Sandro La Bruzzo 7e08655e5f added relation dates in all scholexplorer Datasources 2021-06-29 12:02:03 +02:00
Sandro La Bruzzo 075055eaca added relation dates in bio mapping 2021-06-29 10:33:09 +02:00
Sandro La Bruzzo f36f92287d implemented mapping from Crossref Event Data to Oaf 2021-06-29 10:21:23 +02:00
Sandro La Bruzzo 511ec14c63 implemented mapping from EBI and Scholix Resolved to OAF 2021-06-28 22:04:22 +02:00
Sandro La Bruzzo ad50415167 Merge remote-tracking branch 'origin/stable_ids' into stable_id_scholexplorer 2021-06-24 17:20:50 +02:00
Sandro La Bruzzo 80e15cc455 implemented mapping from uniprot, pdb and ebi links 2021-06-24 17:20:00 +02:00
Claudio Atzori 50fc5a64a0 [raw_all] Aggregator graph creation merges claims (updates) with the corresponding entity 2021-06-23 11:49:42 +02:00
Sandro La Bruzzo 080a280bea added pdb to Oaf Transformation 2021-06-21 16:23:59 +02:00
Sandro La Bruzzo 507e42102a added pdb to oaf class 2021-06-21 09:36:40 +02:00
Sandro La Bruzzo 4fe7b75644 renamed packages 2021-06-18 16:41:24 +02:00
Sandro La Bruzzo 3100166d29 Merge remote-tracking branch 'origin/stable_ids' into stable_id_scholexplorer 2021-06-16 16:22:16 +02:00
Claudio Atzori 7243a40c88 code formatting 2021-06-16 15:03:03 +02:00