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425 Commits

Author SHA1 Message Date
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
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 baed5e3337 test classes moved in specific components 2021-08-13 12:14:47 +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
Miriam Baglioni 01db1f8bc4 GetCSV refactoring - removed not needed import 2021-08-13 10:14:17 +02:00
Claudio Atzori 9587d4aee8 Merge branch 'beta' into hostedbymap 2021-08-12 17:04:30 +02:00
Claudio Atzori 86d940044c added test to verify bad records from FWF-E-Book-Library 2021-08-12 11:32:56 +02:00
Claudio Atzori 8cdce59e0e [graph raw] let the mapping exceptions propagate 2021-08-12 11:32:26 +02:00
Miriam Baglioni 785db1d5b2 refactoring 2021-08-11 17:44:07 +02:00
Miriam Baglioni 8229632839 adding assertions to the mapping of the unibi part of gold list 2021-08-11 16:36:01 +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 61d811ba53 suggestions from intellij 2021-08-11 12:18:20 +02:00
Claudio Atzori 2ee21da43b suggestions from SonarLint 2021-08-11 12:13:22 +02:00
Miriam Baglioni b954fe9ba8 mergin with branch beta 2021-08-11 10:12:46 +02:00
Miriam Baglioni b688567db5 hostedbymap - modified part of test to check the bestaccessright changed 2021-08-11 10:12:10 +02:00
Miriam Baglioni a90bac3bc9 Graph Dump - added method to test class to verify addition of validation date in projects for community result 2021-08-09 16:36:54 +02:00
Miriam Baglioni bc9e3a06ba Graph Dump - extended the test class 2021-08-09 15:46:06 +02:00
Miriam Baglioni eff499af9f added new tests and changed the test example 2021-08-09 11:12:30 +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 ee13da9258 merge branch with master 2021-08-05 11:34:20 +02:00
Claudio Atzori 83c04e5d28 mapping test for dataset records adapted to reflect the delegated pid authority (zenodo) 2021-08-04 10:37:57 +02:00
Miriam Baglioni eb8c3f8594 Hosted By Map - test modified because of the application of the new aggregator on datasources 2021-08-04 10:19:17 +02:00
Miriam Baglioni ee7ccb98dc Hosted By Map - test class to verify the application of the hbm to results and datasource 2021-08-02 19:36:18 +02:00
Miriam Baglioni 90e91486e2 Hosted By Map - test class to verify each step in the preparation process 2021-08-02 19:35:52 +02:00
Miriam Baglioni 1695d45bd4 Hosted By Map - Test class to verify the preparation of the intermediate information 2021-07-30 17:57:01 +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 081fe92a21 Merge branch 'fct_project_id_replacement' of https://code-repo.d4science.org/D-Net/dnet-hadoop into fct_project_id_replacement 2021-07-30 10:13:56 +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 a9961a1835 [cleaning] title cleaning based on the me.xuender:unidecode library 2021-07-28 16:36:33 +02:00
Claudio Atzori e1797c0a42 Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta 2021-07-28 16:21:36 +02:00
Claudio Atzori 6dddad86ee [cleaning] title cleaning based on the me.xuender:unidecode library 2021-07-28 16:21:29 +02:00
Alessia Bardi c806387d4b tests for enermaps 2021-07-28 11:54:36 +02:00
Claudio Atzori 2fff24df55 code formatting 2021-07-28 11:34:19 +02:00
Michele Artini 9f1c7b8e17 tests 2021-07-28 11:32:34 +02:00
Miriam Baglioni 708d0ade34 Merge branch 'beta' into hostedbymap 2021-07-28 10:37:22 +02:00
Miriam Baglioni 0424f47494 HostedByMap fixing issues 2021-07-28 10:24:13 +02:00
Claudio Atzori 5aa7d16d1b updated assertions in eu.dnetlib.dhp.oa.graph.raw.MappersTest 2021-07-27 15:11:58 +02:00
Claudio Atzori 998b66855a updated assertions in eu.dnetlib.dhp.oa.graph.raw.MappersTest 2021-07-27 15:11:37 +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
Alessia Bardi 9069958479 tests for enermaps 2021-07-20 19:31:43 +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 618d2de2da minor changes and refactoring 2021-07-13 17:10:02 +02:00
Miriam Baglioni 59615da65e Add test to verify the creation of relation between context and projects 2021-07-13 17:09:15 +02:00
Miriam Baglioni 5295d10691 added check not to dump deletedByInference entities 2021-07-13 16:11:46 +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 6410ab71d8 added APC in the dump and test method 2021-07-13 15:13:58 +02:00
Miriam Baglioni 87a6e2b967 extended test class 2021-07-13 14:38:28 +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 c952c8d236 generate first side of scholix mapping 2021-07-06 09:53:14 +02:00
Sandro La Bruzzo c6fa8598e1 massive code refactor: 
removed modules dhp-*-scholexplorer
 2021-07-01 22:13:45 +02:00
Sandro La Bruzzo 623a0c4edb code Refactor, renaming packages 2021-06-30 11:09:30 +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 2e8fd2c531 cleanup 2021-06-23 14:38:24 +02:00
Sandro La Bruzzo 080a280bea added pdb to Oaf Transformation 2021-06-21 16:23:59 +02:00
Sandro La Bruzzo 4fe7b75644 renamed packages 2021-06-18 16:41:24 +02:00
Sandro La Bruzzo cc0f2b11fb Implemented mapping from pubmed baseline to OAF 2021-06-16 14:56:24 +02:00
Claudio Atzori 2039bb9f5f orcid / orcid_pending cleaning backported from master branch 2021-06-14 09:40:50 +02:00
Claudio Atzori dd19c4ac5a Merge pull request 'import_new_mdstores' (#112) from import_new_mdstores into stable_ids 
Reviewed-on: #112
 2021-06-14 09:23:55 +02:00
Claudio Atzori a900bfb874 delegating the date parsing to https://github.com/sisyphsu/dateparser 2021-06-11 16:53:01 +02:00
Sandro La Bruzzo e57294ac99 implemented changes on PUBMed dataflow 2021-06-03 10:52:09 +02:00
Michele Artini f0fbfdcfae Merge branch 'stable_ids' into import_new_mdstores 2021-06-01 12:03:00 +02:00
Michele Artini 03a510859a removed coalesce(1) 2021-05-31 14:10:51 +02:00
Michele Artini e9f2b6037c patch of mdstore records 2021-05-31 11:36:26 +02:00
Claudio Atzori 6e3a4e9237 updated test expectations 2021-05-28 09:37:50 +02:00
Claudio Atzori 9d725efdc1 reverted implementation of the mdstore client 2021-05-20 18:26:09 +02:00
Claudio Atzori ae5c28e54f code formatting 2021-05-20 16:13:06 +02:00
Claudio Atzori 232dce83db fixes #6701: xpath for titles to support both datacite and Guidelines v4 mapping 2021-05-20 14:41:15 +02:00
Claudio Atzori 23b8883ab1 applied intellij code cleanup 2021-05-14 10:58:12 +02:00
Claudio Atzori d1cbee8413 imported methods from CleaningFunctions, defined in GraphCleaningFunctions 2021-05-10 16:43:39 +02:00
Claudio Atzori d4a30fabe3 clean up tests 2021-05-05 17:28:15 +02:00
Claudio Atzori dccaf173cf fixed mapping applied to ODF records. Added unit test to verify the mapping for OpenTrials 2021-05-05 16:36:15 +02:00
Claudio Atzori 2e1eb96f9a code formatting 2021-05-05 11:23:57 +02:00
Claudio Atzori fb930b84d3 Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids 2021-05-04 18:06:30 +02:00
Claudio Atzori 923d19ea8e mdstore read lock/unlock when bulk copying records from mongodb to hdfs 2021-05-04 18:06:21 +02:00
Sandro La Bruzzo 714b71bd21 updated pubmed 2021-05-04 14:54:12 +02:00
Sandro La Bruzzo 2129e9caa7 updated pangaea transformation to parse directly the xml 2021-04-28 10:21:03 +02:00
Claudio Atzori 5afa7d3e0c core utilities in dhp-common moved in external module dhp-schemas 2021-04-27 15:44:01 +02:00
Sandro La Bruzzo 7f8848ecdd added first implementation of Pangaea Mapping 2021-04-27 11:30:37 +02:00
Claudio Atzori d0d477cca3 code formatting 2021-04-20 12:50:34 +02:00
miconis 0393cdce42 addition of alternative names in export queries 2021-04-20 12:45:21 +02:00
Claudio Atzori d1ca025b0b [cleaning] remiving authors without fullname or providing 'deactivated' keyword. Removing test test titles 2021-04-13 14:32:41 +02:00
Claudio Atzori 827e7e37db [Cleaning] drop instance.alternateIdentifier elements when they are available among instance.pid 2021-03-25 11:07:59 +01:00
Claudio Atzori 751125fdf9 [Actionmanager] zero function considers empty entity.id as well as rel.source/rel.target 2021-03-23 17:34:32 +01:00
Claudio Atzori b4febed138 updated mapping tests as consequence of the special treatment reserved to Handle PIDs 2021-03-23 09:37:48 +01:00
Claudio Atzori 431cbe9955 handle missing instance.pid during bulk cleaning 2021-03-23 09:28:58 +01:00
Sandro La Bruzzo c73072079d fix conflicts 2021-03-22 16:36:31 +01:00
Claudio Atzori 8257f9a2bc result.pid: adjusted the mapping applied to the contents from the aggregator 2021-03-17 12:45:38 +01:00
Claudio Atzori 640b885706 added instance.alternativeIdentifiers to the graph model, adjusted the mapping applied to the contents from the aggregator 2021-03-16 14:19:32 +01:00
Claudio Atzori 01630f638d IdentifierFactory implementation based on the list of datasources authoritative for a given pid type 2021-03-09 17:11:50 +01:00
Claudio Atzori 59532b0919 [#6281 Provenance of product PIDs] Added PIDs to the Instance type; extended mapping for OAF/ODF records 2021-03-09 11:14:45 +01:00
Claudio Atzori f468c7f0d7 merged from master 2021-03-09 09:12:41 +01:00
Claudio Atzori 8d2bb24512 merged from master 2021-03-08 15:44:34 +01:00
Alessia Bardi c4d1feca74 mapper test with validated link to project 2021-02-10 11:22:54 +01:00
Alessia Bardi c67329d3ad updated test for EU Open Data portal datasets 2021-02-03 17:06:48 +01:00
Alessia Bardi fd705404a1 tests for EU Open Data portal dataset mapping 2021-02-03 10:28:17 +01:00
Sandro La Bruzzo 686e7b507c Merge branch 'hadoop_aggregator' of code-repo.d4science.org:D-Net/dnet-hadoop into aggregation_on_hadoop 2021-01-28 10:02:13 +01:00
Sandro La Bruzzo 98b9498b57 Removed old messaging system not quite used from collection and Transformation workflow 
code refactor
 2021-01-28 09:51:17 +01:00
Sandro La Bruzzo 150a617bd1 Merge pull request 'aggregation_on_hadoop' (#90) from sandro.labruzzo/dnet-hadoop:aggregation_on_hadoop into hadoop_aggregator 
Wonderfull code... You're the Best Sandro
 2021-01-26 16:00:47 +01:00
Alessia Bardi 505477f36f format code 2021-01-25 18:02:49 +01:00
Alessia Bardi ded6ed8d7d no ',' author, if there are no author in ODF records 2021-01-25 17:57:51 +01:00
Sandro La Bruzzo a54848a59c Moved Vocabulary stuff to common module 2021-01-25 15:43:04 +01:00
Claudio Atzori 47270d9af5 lenient mock can be lenient 2020-12-18 15:38:59 +01:00
Claudio Atzori 12e2f930c8 resolved conflicts 2020-12-10 10:57:39 +01:00
Alessia Bardi 112da6d76a in theory, just auto-formatting after mvn compile 2020-12-09 20:00:27 +01:00
Alessia Bardi bece04b330 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-12-09 19:54:43 +01:00
Alessia Bardi 426b76ee8e more asserts for TextGrid record 2020-12-09 19:46:11 +01:00
Claudio Atzori 4705144918 Merge pull request 'rel_project_validation' (#69) from rel_project_validation into master 
LGTM
 2020-12-09 19:01:20 +01:00
Michele Artini 370a5e650b validation attributes in resultProject relations 2020-12-09 11:18:26 +01:00
Miriam Baglioni 5fb65ffc4a merge branch with master 2020-12-03 11:24:35 +01:00
Alessia Bardi a417624670 tests for raw graph mapping 2020-12-02 10:15:26 +01:00
Claudio Atzori 2c407e775e GenerateEntitiesApplication can be configured to hash the id value or not 2020-11-30 12:00:38 +01:00
Miriam Baglioni 124591a7f3 refactoring 2020-11-25 18:23:28 +01:00
Miriam Baglioni 1a89f8211c #61 (comment) 2020-11-25 18:12:40 +01:00
Miriam Baglioni d4ddde2ef2 changed because of #61 (comment) 2020-11-25 18:01:01 +01:00
Miriam Baglioni 90d4369fd2 added test to verify the compression in writing community info on hdfs 2020-11-25 14:34:58 +01:00
Miriam Baglioni bde6d337dd test classes for dump of results related to funders 2020-11-25 13:42:01 +01:00
Miriam Baglioni b37b9352d7 added constant value for semantic relationship between projects and results 2020-11-25 13:41:08 +01:00
Claudio Atzori e1a1bb3ee4 moved class CleaningFunctions in the correct package. Remove newlines from titles, descriptions, subjects 2020-11-24 18:34:03 +01:00
Miriam Baglioni 54a309bb6b refactoring 2020-11-24 14:45:30 +01:00
Miriam Baglioni 35ecea8842 changed to consider the modification for the specification of the type of dump 2020-11-24 14:45:15 +01:00
Claudio Atzori 3f34757c63 merged from master 2020-11-19 14:34:54 +01:00
Claudio Atzori ede7fae6c8 Merge pull request 'XML record indexing test' (#58) from provision_indexing into master 2020-11-18 17:04:34 +01:00
Claudio Atzori 8177ce7939 test for XmlIndexingJob based on a local miniSolrCluster 2020-11-18 10:58:05 +01:00
Michele Artini 33da2e3d6c xpaths for dateOfCollection and dateOfTransformation 2020-11-18 09:26:20 +01:00
Alessia Bardi 7e0a76a8ac test fr TextGrid 2020-11-17 18:39:25 +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 13e36a4da0 WIP: added oozie workflow for grouping graph entities by id 2020-11-13 10:05:02 +01:00
Claudio Atzori 9b0fb9e958 merged from master 2020-11-12 09:27:12 +01:00
Sandro La Bruzzo 027ef2326c Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-11-06 17:12:42 +01:00
Sandro La Bruzzo cd27df91a1 fixed bug on missing relation in ANDS 2020-11-06 17:12:31 +01:00
Claudio Atzori d10447e747 re-packaged graph dump workflow sources 2020-11-05 17:38:18 +01:00
Miriam Baglioni 56150d7e5e removed all code related to the dump of pids graph 2020-11-04 17:13:12 +01:00
Miriam Baglioni c010a8442f fixed issue on test code 2020-11-03 17:26:51 +01:00
Miriam Baglioni 8ec7a61188 merge branch with master 2020-11-03 16:59:08 +01:00
Claudio Atzori 86d6fbe95b refactoring: CleaningFunctions and OafMapperUtils moved in dhp-commong 2020-11-03 12:19:46 +01:00
Claudio Atzori 3fcd669e99 result merge operation leverage on custom ResultTypeComparator in the aggregator graph construction 2020-11-03 10:53:23 +01:00