D-Net
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929 Commits

Author SHA1 Message Date
Michele Artini 83132ee99a fixed a problem with empty mdstore list 2021-06-14 11:57:00 +02:00
Sandro La Bruzzo aeb8132627 Merged branch stable_ids 2021-06-14 10:07:29 +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
Sandro La Bruzzo 5b724d9972 added relations to datacite mapping 2021-06-04 10:14:22 +02:00
Sandro La Bruzzo e57294ac99 implemented changes on PUBMed dataflow 2021-06-03 10:52:09 +02:00
Michele Artini ede2749822 orcid pid type 2021-06-01 12:42:43 +02:00
Michele Artini f0fbfdcfae Merge branch 'stable_ids' into import_new_mdstores 2021-06-01 12:03:00 +02:00
Michele Artini e950750262 add nodes to import hdfs mdstores 2021-06-01 10:48:50 +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
Michele Artini ad56a44fda save as gzipped sequence file 2021-05-28 14:45:39 +02:00
Michele Artini 4fa5671d16 first implementation of Hdfs Mdstores Importer 2021-05-27 16:22:07 +02:00
Claudio Atzori 5e4b91d9ef more pervasive use of constants from ModelConstants, especially for ORCID 2021-05-26 18:20:23 +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 d4c3476152 mapping datasource.journal only when an issn is available, null otherwhise 2021-05-11 11:08:54 +02:00
Claudio Atzori d1cbee8413 imported methods from CleaningFunctions, defined in GraphCleaningFunctions 2021-05-10 16:43:39 +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 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
Alessia Bardi 9a20057615 fixed query for organisations' pids 2021-04-29 15:23:39 +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 74484d2823 bug fixing 2021-04-27 12:13:44 +02:00
Sandro La Bruzzo 7f8848ecdd added first implementation of Pangaea Mapping 2021-04-27 11:30:37 +02:00
Claudio Atzori c25238480c making ODF record parsing namespace unaware (#6629) 2021-04-23 17:34:57 +02:00
miconis 0393cdce42 addition of alternative names in export queries 2021-04-20 12:45:21 +02:00
miconis cadd0a5de8 modification of the queries for openorgs: they now consider also pending orgs 2021-04-20 12:06:56 +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
miconis 11b22b2d23 bug fix in the query, it now exports only relations with non-hidden organizations 2021-04-08 11:51:47 +02:00
miconis 0857100fb8 implementation of the tests for the openorgs integration in the openaire provision 2021-04-07 18:42:16 +02:00
miconis bf685d849f addition of pids in the query for the export of openorgs for the provision, addition of ec_fields in the openorgs model 2021-04-07 14:27:43 +02:00
miconis eaaefb8b4c implementation of the procedure to reuse content of different dbs when creating the raw graph 2021-04-06 14:35:51 +02:00
miconis c39c82dfe9 modification of the jobs for the integration of openorgs in the provision, dedup records are no more created by merging but simply taking results of openorgs portal 2021-04-06 14:31:00 +02:00
Claudio Atzori 7941d7be29 WIP: using common definitions from ModelConstants 2021-03-31 18:33:57 +02:00
Claudio Atzori 72ce741ea6 WIP: using common definitions from ModelConstants 2021-03-31 17:07:13 +02:00
Claudio Atzori 9237d55d7f [OpenOrgsWf] cleanup 2021-03-29 17:40:34 +02:00
Claudio Atzori 7f4e9479ec [OpenOrgsWf] graph construction wf: allow to skip the import openorgs node (importOpenorgs true|false) 2021-03-29 16:59:16 +02:00
miconis 2709d08fc2 Merge branch 'stable_ids' into openorgswf 2021-03-29 16:39:07 +02:00
miconis f446580e9f code refactoring (useless classes and wf removed), implementation of the test for the openorgs dedup 2021-03-29 16:10:46 +02:00
miconis 2355cc4e9b minor changes and bug fix 2021-03-29 10:07:12 +02:00
miconis 28c1cdd132 merged stable_ids into openorgswf 2021-03-25 10:44:49 +01:00
miconis 348b0ef921 bug fix, implementation of the workflow for the creation of raw_organizations (openorgs dedup), addition of the pid lists to the openorgs postgres db 2021-03-24 15:51:27 +01:00
Sandro La Bruzzo c73072079d fix conflicts 2021-03-22 16:36:31 +01:00
Claudio Atzori 5a043e95ea code formatting 2021-03-19 11:37:27 +01:00
Claudio Atzori a4e82a65aa integrated filter applied when merging BETA & PROD graphs to rule our records from Datacite 2021-03-19 11:34:44 +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 d525785497 [#6282 open access status in the Graph] Result.Instance.accessRight defined with dedicated data type that includes the open access color. 2021-03-09 11:12:55 +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
miconis 1a85020572 bug fix in graph-mapper, changes in the implementation of the openorgs wf to create relations and populate openorgs db 2021-02-26 10:19:28 +01:00
Claudio Atzori b830e33392 mdstore collector plugin 2021-02-25 12:30:30 +01:00
Claudio Atzori fc3fa5e343 implemented mdstore collector plugin 2021-02-24 15:07:24 +01:00
miconis 4b2124a18e implementation of the openorgs wfs, implementation of the raw_all wf to migrate openorgs db entities 2021-02-10 11:51:50 +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
Claudio Atzori 885e0dd926 [Cleaning] filter authors not providing word characters in the fullname 2021-01-26 09:48:53 +01:00
Claudio Atzori 2890511613 [Cleaning] normalise missing Result.country 2021-01-26 09:41:44 +01:00
Claudio Atzori 4eb9ed35b1 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2021-01-25 18:12:24 +01:00
Claudio Atzori cd379eb5e3 [Cleaning] trying to avoid NPEs, this time by ruling out authors without a defined fullname 2021-01-25 18:11:49 +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
Claudio Atzori 3465c8ccee [Cleaning] trying to avoid NPEs 2021-01-25 16:54:53 +01:00
Sandro La Bruzzo a54848a59c Moved Vocabulary stuff to common module 2021-01-25 15:43:04 +01:00
Claudio Atzori 07a0ccfc96 [Cleaning] trying to avoid NPEs 2021-01-25 13:36:01 +01:00
Claudio Atzori 34d653de41 [Cleaning] updated cleaning rule for DOIs 2021-01-22 14:16:33 +01:00
Claudio Atzori 26e9d55c13 code formatting 2021-01-05 09:59:26 +01:00
Claudio Atzori 7185158942 ignore missing properties 2020-12-29 11:06:28 +01:00
Claudio Atzori 28460c2cd1 using com.fasterxml.jackson.databind.ObjectMapper instead of org.codehaus.jackson.map.ObjectMapper 2020-12-23 16:59:52 +01:00
Claudio Atzori 723b01f9e9 trivial: the less magic numbers and values around, the better 2020-12-23 12:22:48 +01:00
Claudio Atzori 6cb0dc3f43 extended OCRID cleaning procedure 2020-12-21 11:40:17 +01:00
Michele Artini 991e675dc6 validation in claim rels 2020-12-14 15:41:25 +01:00
Claudio Atzori 12e2f930c8 resolved conflicts 2020-12-10 10:57:39 +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
Claudio Atzori ada21ad920 Merge pull request 'dump of the results related to at least one project' (#61) from miriam.baglioni/dnet-hadoop:dump into master 
LGTM
 2020-12-09 17:22:56 +01:00
Michele Artini 1bc9adc10d default trust for validated rels 2020-12-09 16:18:37 +01:00
Michele Artini 5f21a356fd reindent 2020-12-09 11:24:30 +01:00
Michele Artini 370a5e650b validation attributes in resultProject relations 2020-12-09 11:18:26 +01:00
Claudio Atzori a104a632df cleanup 2020-12-04 16:32:47 +01:00
Miriam Baglioni 5fb65ffc4a merge branch with master 2020-12-03 11:24:35 +01:00
Miriam Baglioni ea88dc3401 fixed issue in property name 2020-12-03 11:24:23 +01:00
Claudio Atzori cfb55effd9 code formatting 2020-12-02 11:23:49 +01:00
Claudio Atzori 57f448b7a4 graph cleaning workflow separate orcid_pending from orcid, depending on the author pid provenance 2020-12-02 10:44:05 +01:00
Claudio Atzori 893ac4a77b GenerateEntitiesApplication can be configured to hash the id value or not 2020-12-02 09:30:06 +01:00
Claudio Atzori 2c407e775e GenerateEntitiesApplication can be configured to hash the id value or not 2020-11-30 12:00:38 +01:00
Claudio Atzori e731a7658d cleaning texts to remove tab characters too 2020-11-27 09:00:04 +01:00
Claudio Atzori c1b9a4045a grouping of records will be performed by the dedup workflow 2020-11-26 10:59:10 +01:00
Miriam Baglioni 124591a7f3 refactoring 2020-11-25 18:23:28 +01:00
Miriam Baglioni 5fbe54ef54 #61 (comment) 2020-11-25 18:10:28 +01:00
Miriam Baglioni ed01e5a5e1 #61 (comment) 2020-11-25 18:09:34 +01:00
Miriam Baglioni f5e5e92a10 changed because of #61 (comment) 2020-11-25 17:58:53 +01:00
Miriam Baglioni 1df94b85b4 changed because of #61 (comment) 2020-11-25 17:57:43 +01:00
Claudio Atzori dfd6205b95 Consistency graph workflow merges all the entities by ID 2020-11-25 14:55:32 +01:00
Miriam Baglioni 6750e33d69 merge branch with master 2020-11-25 14:09:01 +01:00
Miriam Baglioni b2c455f883 added java doc 2020-11-25 14:08:09 +01:00
Miriam Baglioni e758d5d9b4 refactoring 2020-11-25 13:46:39 +01:00
Miriam Baglioni 87a9f616ae refactoring and addition of the funder nsp first part as nome for the dump insteasd of the whole nsp 2020-11-25 13:45:41 +01:00
Miriam Baglioni e7e418e444 added decision node to verify if to upload in Zenodo 2020-11-25 13:44:10 +01:00
Miriam Baglioni 21ce175d17 added FilterFunction specification if filter operation 2020-11-25 13:42:31 +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 36173c13a5 reverted filters in the clening process 2020-11-25 10:24:42 +01:00
Claudio Atzori eeebd5a920 Cleanig workflow: remove newlines from titles, descriptions, subjects 2020-11-24 18:40:25 +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 72bb0fe360 changed directory name 2020-11-24 16:47:07 +01:00
Miriam Baglioni 39f4a20873 chenged the path and the name for saving the communities_infrastructures dump file 2020-11-24 14:47:32 +01:00
Miriam Baglioni 7e14452a87 final versione of the wf to get the dump of results associated to at least one funder per funder 2020-11-24 14:46:34 +01:00
Miriam Baglioni c167a18057 added new parameter for the dumpType 2020-11-24 14:45:50 +01:00
Miriam Baglioni b9b6bdb2e6 fixing issue on previous implementation 2020-11-24 14:44:53 +01:00
Miriam Baglioni 7e940f1991 changed to consider the modification for the specification of the type of dump 2020-11-24 14:43:34 +01:00
Miriam Baglioni 62928ef7a5 changed to save the communities_infrastructures information as the other entity dumps: in a json.gz file 2020-11-24 14:42:41 +01:00
Claudio Atzori 33bae02451 reverted behaviour of the cleaning workflow: grouping entities by ID will be managed differently 2020-11-24 14:42:33 +01:00
Miriam Baglioni 3319440c53 changed the direction of the relation between projects and result considered to select the results linked to projects 2020-11-24 14:41:09 +01:00
Miriam Baglioni 00c377dac2 added specification of MapFunction types in map 2020-11-24 14:40:22 +01:00
Miriam Baglioni 44db258dc4 added enumerated for the dump type 2020-11-24 14:38:06 +01:00
Miriam Baglioni 1832708c42 modified boolean variable with string one whcih specify the type of dump we are performing: complete, community or funder 2020-11-24 14:37:36 +01:00
Miriam Baglioni 259c67ce36 fixed issue in path name 2020-11-20 12:32:23 +01:00
Miriam Baglioni 0a9db67eec - 2020-11-20 12:21:33 +01:00
Miriam Baglioni cf3f47563f new parameter files 2020-11-19 19:16:05 +01:00
Miriam Baglioni 24c56fa7a3 new logic and workflow for dump of results with link to projects. In this implementation the result match the model of the communityresult. 2020-11-19 19:15:39 +01:00
Claudio Atzori fcbb05eb21 cleanup 2020-11-19 15:14:33 +01:00
Claudio Atzori 3f34757c63 merged from master 2020-11-19 14:34:54 +01:00
Miriam Baglioni fafb688887 - 2020-11-18 18:56:48 +01:00
Miriam Baglioni 906db690d2 - 2020-11-18 17:43:08 +01:00
Miriam Baglioni 5402062ff5 changed parameter file with the ono associated to the job 2020-11-18 16:58:20 +01:00
Miriam Baglioni a172a37ad1 fixed typo 2020-11-18 16:55:07 +01:00
Miriam Baglioni 46ba3793f6 code, workflow and parameters for the dump of the results associated to funders 2020-11-18 16:47:31 +01:00
Miriam Baglioni 57cac36898 changed the workflow name 2020-11-18 13:38:03 +01:00
Alessia Bardi 10e673660f Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-11-18 10:01:23 +01:00
Alessia Bardi be7b310cef rel semantcis ignore case 2020-11-18 10:01:20 +01:00
Michele Artini 33da2e3d6c xpaths for dateOfCollection and dateOfTransformation 2020-11-18 09:26:20 +01:00
Alessia Bardi 8f87020a50 #56: map relevantDates from aggregated ODF records 2020-11-17 18:42:09 +01:00
Claudio Atzori cfc01f136e PID filtering based on a blacklist 2020-11-17 12:27:06 +01:00
Claudio Atzori 6ab1ce53c9 fixed condition in result pid cleaning; cleanup 2020-11-16 10:09:17 +01:00
Claudio Atzori 4de8c8b237 fixed workflow variable name 2020-11-16 10:03:11 +01:00
Claudio Atzori 5d4e34e26a fixed typo in variable name 2020-11-14 10:32:26 +01:00
Claudio Atzori 768bc5304c Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-11-13 15:40:34 +01:00
Claudio Atzori 93f7b7974f Merge pull request 'trust truncated to 3 decimals' (#24) from trunc_trust into master 
LGTM
 2020-11-13 15:40:02 +01:00
Claudio Atzori 528231a287 grouping graph entities by id turned out to be an easy extension for the already existing cleaning workflow 2020-11-13 15:37:48 +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
Michele Artini 40160d171f organizations pids 2020-11-09 12:58:36 +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
Claudio Atzori 2d76497488 cleanup 2020-11-05 17:10:24 +01:00
Miriam Baglioni f8e9bda24c merge branch with master 2020-11-05 16:31:18 +01:00
Miriam Baglioni be5ed8f554 added check to avoid sending empty metadata. 2020-11-05 16:10:17 +01:00
Claudio Atzori 2148a51fae minor changes 2020-11-05 11:24:12 +01:00
Claudio Atzori 4625b7486e code formatting 2020-11-04 18:12:43 +01:00
Miriam Baglioni e9ac471ae9 removed dependency from classes for the pid graph dump 2020-11-04 18:04:42 +01:00
Miriam Baglioni b90a945c49 removed property files for pid graph dump 2020-11-04 17:28:33 +01:00
Miriam Baglioni bac307155a removed properties specific for pid graph dump 2020-11-04 17:28:04 +01:00
Miriam Baglioni 9c9d50f486 removed code specific for pid graph dump 2020-11-04 17:26:22 +01:00
Miriam Baglioni 5669890934 removed commented lines 2020-11-04 17:15:21 +01:00
Miriam Baglioni 6a89f59be9 removed commented lines 2020-11-04 17:13:59 +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 16c54a96f8 removed pid dump 2020-11-04 17:11:32 +01:00
Alessia Bardi 51808b5afd Updated descriptions 2020-11-04 12:29:48 +01:00
Alessia Bardi e6becf8659 Updated descriptions 2020-11-04 12:17:57 +01:00
Alessia Bardi 0abe0eee33 Updated descriptions 2020-11-04 12:15:30 +01:00
Alessia Bardi f6ab238f5d Updated descriptions 2020-11-04 11:50:47 +01:00
Miriam Baglioni 8ec7a61188 merge branch with master 2020-11-03 16:59:08 +01:00
Miriam Baglioni c209284ca7 new schemas for the entities in the dump with added descriptions 2020-11-03 16:58:08 +01:00
Miriam Baglioni 08806deddf added the splitSize non mandatory parameter. Default size 10G 2020-11-03 16:57:34 +01:00
Miriam Baglioni 7d2eda43ca added new non mandatory property publish to determine if to publish the upload or leave it pending. Default value flase 2020-11-03 16:57:01 +01:00
Miriam Baglioni cbbb1bdc54 moved business logic to new class in common for handling the zip of hte archives 2020-11-03 16:55:50 +01:00
Miriam Baglioni d4382b54df moved the tar archive with maz size on common module 2020-11-03 16:54:50 +01:00
Claudio Atzori 86d6fbe95b refactoring: CleaningFunctions and OafMapperUtils moved in dhp-commong 2020-11-03 12:19:46 +01:00
Claudio Atzori 8471888ad3 Merge branch 'graph_cleaning' into stable_ids 2020-11-03 11:52:47 +01:00
Claudio Atzori 5310e56dba remove empy PIDs 2020-11-03 11:52:10 +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
Claudio Atzori 09e44dabff Merge branch 'master' into stable_ids 2020-11-02 12:16:01 +01:00
Miriam Baglioni dabb33e018 changed the discriminant for which split the file 2020-10-30 17:52:22 +01:00
Miriam Baglioni 0fba08eae4 max allowed size per file 10 Gb 2020-10-30 16:05:55 +01:00
Miriam Baglioni b828587252 prevent the code to cicle indefinetly 2020-10-30 15:01:25 +01:00
Miriam Baglioni f747e303ac classes for dumping of the graph as ttl file 2020-10-30 14:13:45 +01:00
Miriam Baglioni 16baf5b69e formatting 2020-10-30 14:13:14 +01:00
Miriam Baglioni a9eef9c852 added check for possible Optional value in relation dataInfo 2020-10-30 14:12:28 +01:00
Miriam Baglioni 5f4de9a962 formatting 2020-10-30 14:11:40 +01:00
Miriam Baglioni 14bf2e7238 added option to split dumps bigger that 40Gb on different files 2020-10-30 14:09:04 +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
Miriam Baglioni 78fdb11c3f merge branch with master 2020-10-29 12:55:22 +01:00
Sandro La Bruzzo 1d9fdb7367 fixed spark memory issue in SparkSplitOafTODLIEntities 2020-10-28 12:30:32 +01:00
Miriam Baglioni d2374e3b9e added code to handle cases where the funding tree is not existing 2020-10-27 16:15:21 +01:00
Miriam Baglioni 5d3012eeb4 changed code to dump only the programme list and not the classification list 2020-10-27 16:14:18 +01:00
Miriam Baglioni 3241ec1777 added connection timeout and socket timeout 600 sec 2020-10-27 16:12:11 +01:00
Claudio Atzori 266bf1a221 common IdentifierFactory in use on the mapping from the aggregator data; merge the entities sharing the same id; code formatting 2020-10-16 17:02:10 +02:00
Claudio Atzori 34f1d0904b common IdentifierFactory in use on the mapping from the aggregator data 2020-10-16 16:00:19 +02:00
Sandro La Bruzzo fed711da80 Merge remote-tracking branch 'origin/master' into merge_record_to_common 2020-10-13 15:32:45 +02:00
Alessia Bardi 8775a64bc1 Merge pull request 'Merging different compatibility levels (pinocchio operator)' (#47) from merge_graph into master 2020-10-09 14:44:52 +02:00
Claudio Atzori e751c1402f Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-10-09 13:53:21 +02:00
Claudio Atzori b961dc7d1e added originalid to the fields in the result graph view 2020-10-09 13:53:15 +02:00
Sandro La Bruzzo eec418cd26 moved AuthoreMerger into dhp-common 2020-10-08 10:33:55 +02:00
Sandro La Bruzzo cd9c377d18 adpted scholexplorer Dump generation to the new Dataset definition 2020-10-08 10:10:13 +02:00
Claudio Atzori a3f37a9414 javadoc 2020-10-07 16:44:22 +02:00
Claudio Atzori 8d85a2fced [BETA wf only] datasources involved in the merge operation doesn't obey to the infra precedence policy, but relies on a custom behaviour that, given two datasources from beta and prod returns the one from prod with the highest compatibility among the two 2020-10-07 16:28:52 +02:00
Miriam Baglioni ae08b3c0dd merge branch with master 2020-10-05 11:35:55 +02:00
Miriam Baglioni 11b7eaae09 changed the name of the folder where to store the context entity from context to communities_infrastructures 2020-10-05 11:24:54 +02:00
Miriam Baglioni 32bffb0134 changed the name from communities_infrastructures to communities_infrastuctures.json 2020-10-05 11:24:17 +02:00
Miriam Baglioni 25cbcf6114 changed to solve issues about names. context renamed communities_infrastructure.json and removed the double json.gz extention to the name of the part in the tar 2020-10-02 12:17:46 +02:00
Claudio Atzori 49ae3450a9 code formatting 2020-10-02 09:43:24 +02:00
Claudio Atzori c2a6e2a9bf fixed mapping for datasource journal info (ISSNs) 2020-10-02 09:37:08 +02:00
Miriam Baglioni 01117a46e1 whole workflow activated 2020-10-01 17:19:21 +02:00
Miriam Baglioni cfb5766c6b removed double json.gz from names of files in the tar 2020-10-01 17:18:34 +02:00
Miriam Baglioni fcaedac980 merge branch with master 2020-10-01 16:46:59 +02:00
Miriam Baglioni c6e6ed1bd8 merge branch with master 2020-10-01 16:24:41 +02:00
Claudio Atzori 2e9e13444d author pids made unique by value 2020-10-01 12:50:40 +02:00
Claudio Atzori e265c3e125 cleaning functions factored out in a dedicated class 2020-10-01 10:50:15 +02:00
Claudio Atzori 4287164aba include relevantdate field in the result view 2020-10-01 10:28:55 +02:00
Miriam Baglioni 7b6a7333e6 merge branch with master 2020-09-25 16:42:07 +02:00
Miriam Baglioni 983a12ed15 temporary modification to allow the upload of files in the sandbox without the neew to recreate the mapping from scratch 2020-09-25 16:41:51 +02:00
Miriam Baglioni 8b36d19182 added property depositionId and chenage property newVersion that became string from boolean to handle the three possible distinct values 2020-09-25 16:41:15 +02:00
Miriam Baglioni ed5239f9ec added new code to handle the new possibility to upload files to an already open deposition 2020-09-25 16:34:32 +02:00
Miriam Baglioni 3a8c524fce refactor 2020-09-25 16:34:02 +02:00
Miriam Baglioni 54800fb9b0 enabled only the step to upload in zenodo 2020-09-25 14:40:22 +02:00
Miriam Baglioni de6c4d46d8 fixed conflicts 2020-09-24 15:35:01 +02:00
Claudio Atzori 044d3a0214 fixed query used to load datasources in the Graph 2020-09-24 13:48:58 +02:00
Claudio Atzori 42f55395c8 fixed order of the ISSNs returned by the SQL query 2020-09-24 12:09:58 +02:00
Claudio Atzori 9a7e72d528 using concat_ws to join textual columns from PSQL. When using || to perform the concatenation, Null columns makes the operation result to be Null 2020-09-24 10:42:47 +02:00
Claudio Atzori 9e3e93c6b6 setting the correct issn type in the datasource.journal element 2020-09-24 10:39:16 +02:00
Miriam Baglioni 39eb8ab25b changed the dump to move from h2020programme to h2020classification 2020-09-23 17:33:00 +02:00
Miriam Baglioni e2ceefe9be - 2020-09-14 14:33:28 +02:00
Miriam Baglioni 1f893e63dc - 2020-09-14 14:33:10 +02:00
Claudio Atzori 8a523474b7 code formatting 2020-09-07 11:40:16 +02:00
Miriam Baglioni 8694bb9b31 refactoring due to compilation 2020-08-24 17:07:34 +02:00
Miriam Baglioni 8a069a4fea - 2020-08-24 17:01:30 +02:00
Miriam Baglioni 34fa96f3b1 - 2020-08-24 17:00:20 +02:00
Miriam Baglioni 5fb2949cb8 added utils methods 2020-08-24 17:00:09 +02:00
Miriam Baglioni 2a540b6c01 added constants for the pid graph dump 2020-08-24 16:55:35 +02:00
Miriam Baglioni 40c8d2de7b test resources for the dump of the pids graph 2020-08-24 16:50:39 +02:00
Miriam Baglioni bef79d3bdf first attempt to the dump of pids graph 2020-08-24 16:49:38 +02:00
Miriam Baglioni 85203c16e3 merge branch with master 2020-08-19 11:49:03 +02:00
Miriam Baglioni 1c593a9cfe - 2020-08-19 11:29:51 +02:00
Miriam Baglioni e42b2f5ae2 - 2020-08-19 11:29:09 +02:00
Miriam Baglioni f81ee22418 changed to mirror the changes in the model (Instance, CommunityInstance, GraphResult) 2020-08-19 11:28:26 +02:00
Miriam Baglioni 387be43fd4 changed to discriminate if dumping all the results type together or each one in its own archive 2020-08-19 11:25:27 +02:00
Miriam Baglioni c5858afb88 added parameter to guide the dump for the result (resultAggregation). true if all the result types should be dump together, false otherwise. 2020-08-19 11:24:14 +02:00
Miriam Baglioni 5570678c65 changed parameter name from hfdsNameNode to nameNode 2020-08-19 10:59:26 +02:00
Miriam Baglioni dc5096a327 refactoring due to compilation 2020-08-19 10:57:36 +02:00
Miriam Baglioni 09f5b92763 added specific reference to class 2020-08-14 20:00:09 +02:00
Miriam Baglioni 37e7c43652 changed parameter name from hdfsNaemNode to nameNode 2020-08-14 18:18:25 +02:00
Miriam Baglioni a5043de5da added method to get the mapped instance 2020-08-13 18:45:50 +02:00
Miriam Baglioni fcd10f452c changed because of #40 (comment) 2020-08-13 12:55:32 +02:00
Miriam Baglioni bfd1fcde6d removed not useful method and changed because of #40 (comment) and #40 (comment) 2020-08-13 12:14:37 +02:00
Miriam Baglioni 7fd8397123 apply changes in #40 (comment) 2020-08-13 12:13:15 +02:00
Miriam Baglioni 753d448cc9 apply changes in #40 (comment) 2020-08-13 12:12:58 +02:00
Miriam Baglioni c0e071fa26 apply changes in #40 (comment) 2020-08-13 12:12:40 +02:00
Miriam Baglioni 526db915bc apply changes in #40 (comment) 2020-08-13 12:12:16 +02:00
Miriam Baglioni b0fab0d138 apply changes in #40 (comment) 2020-08-13 12:11:57 +02:00
Miriam Baglioni 1b6320b251 apply changes in #40 (comment) 2020-08-13 12:11:41 +02:00
Miriam Baglioni 743d31be22 apply changes in #40 (comment) 2020-08-13 12:11:22 +02:00
Miriam Baglioni 65b48df652 apply changes in #40 (comment) 2020-08-13 12:11:06 +02:00
Miriam Baglioni 90b54d3efb apply changes in #40 (comment) 2020-08-13 12:08:24 +02:00
Miriam Baglioni 69bbb9592a apply changes in #40 (comment) 2020-08-13 12:07:39 +02:00
Miriam Baglioni 945323299a apply changes in #40 (comment) 2020-08-13 12:07:24 +02:00
Miriam Baglioni e04c993247 apply changes in #40 (comment) 2020-08-13 12:07:07 +02:00
Miriam Baglioni ed0812d0ce apply changes in #40 (comment) 2020-08-13 12:06:49 +02:00
Miriam Baglioni d55cfe0ea5 apply changes in #40 (comment) 2020-08-13 12:06:20 +02:00
Miriam Baglioni 80866bec7d apply changes in #40 (comment) 2020-08-13 12:06:05 +02:00
Miriam Baglioni 1400978c0a apply changes in #40 (comment) 2020-08-13 12:05:44 +02:00
Miriam Baglioni 7b941a2e0a apply changes in #40 (comment) 2020-08-13 12:05:17 +02:00
Miriam Baglioni f7474f50fe apply changes in #40 (comment) 2020-08-13 12:04:52 +02:00
Miriam Baglioni 367203f412 apply changes in #40 (comment) 2020-08-13 12:04:33 +02:00
Miriam Baglioni 3ab4809d31 apply changes in #40 (comment) 2020-08-13 12:04:10 +02:00
Miriam Baglioni 235d4e4d6e moved Context as relevant for Communities dump 2020-08-12 18:16:45 +02:00
Miriam Baglioni 7400cd019d removed not needed variable 2020-08-12 10:03:33 +02:00
Miriam Baglioni 98d28bab5c fixed missing _ in context nsprefix 2020-08-12 10:00:18 +02:00
Miriam Baglioni 2d67476417 merge branch with master 2020-08-11 15:46:04 +02:00
Miriam Baglioni 0603ec4757 changed test to upload the dump for covid-19 community 2020-08-11 15:43:25 +02:00
Miriam Baglioni acb0926b2e json schemas for the dumped entities and relation 2020-08-11 15:39:48 +02:00
Miriam Baglioni ff52c51f92 added the communityMapPath parameter and removed the isLookUpUrl parameter 2020-08-11 15:39:22 +02:00
Miriam Baglioni 6f43acda5e added the maketar and send to zenodo step. Adjusted wf parameters 2020-08-11 15:38:20 +02:00
Miriam Baglioni ddc19de2e9 removed the isLookUpUrl among the parameters 2020-08-11 15:37:47 +02:00
Miriam Baglioni 592a8ea573 added parameter file for maketar class 2020-08-11 15:37:14 +02:00
Miriam Baglioni 77a0951b32 added the make archive step in the workflow 2020-08-11 15:32:32 +02:00
Miriam Baglioni cf4d918787 added description, changed parameter name and added method 2020-08-11 15:27:31 +02:00
Miriam Baglioni dc5fc5366d Creation of an archive for each related dump part 2020-08-11 15:26:06 +02:00
Miriam Baglioni 0ce49049d6 added description 2020-08-11 15:25:11 +02:00
Miriam Baglioni 9bae991167 added description of the class 2020-08-11 11:20:43 +02:00
Miriam Baglioni 341dc59ead removed the repartition(1). Added code for the creation of an archive containing all the parts dumped for each community 2020-08-11 11:18:58 +02:00
Miriam Baglioni 1991a49f70 removed reference to isLookUp to get the communityMap 2020-08-10 18:02:56 +02:00
Miriam Baglioni fe88904df0 changed the wf definition 2020-08-10 12:01:14 +02:00
Miriam Baglioni 87856467e2 removed isLookUpUrl and added code to read from HDSF the communitymap 2020-08-10 11:38:41 +02:00
Miriam Baglioni 1cf7043e26 removed isLookUoUrl from the parameters 2020-08-10 11:38:03 +02:00
Miriam Baglioni 46986aae2d added the new parameter for newdeposion/newversion and concept_record_id 2020-08-07 18:00:06 +02:00
Miriam Baglioni 3aedfdf0d6 added option to do a new deposition or new version of an old deposition 2020-08-07 17:49:14 +02:00
Miriam Baglioni 1b3ad1bce6 filter out authors pid (only orcid). Added check to get unique provenance for context id. filtr out countries with code UNKNOWN 2020-08-07 17:48:18 +02:00
Miriam Baglioni 5ceb8c5f0a moved constants from graph.Constants 2020-08-07 17:46:47 +02:00
Miriam Baglioni 6c65c93c0e refactoring 2020-08-07 17:45:35 +02:00
Miriam Baglioni 68adf86fe4 refactoring 2020-08-07 17:43:20 +02:00
Miriam Baglioni 26d2ad6ebb refactoring 2020-08-07 17:41:56 +02:00
Miriam Baglioni 9675af7965 refactoring 2020-08-07 17:41:07 +02:00
Miriam Baglioni 346a91f4d9 Added constants 2020-08-07 17:35:39 +02:00
Miriam Baglioni d52b0e1797 no use of IsLookUp. The query is done once and its result stored on HDFS. The path to the result is given instead of the isLookUpUrl 2020-08-07 17:34:40 +02:00
Miriam Baglioni ae1b7fbfdb changed method signature from set of mapkey entries to String representing path on file system where to find the map 2020-08-07 17:32:27 +02:00
Miriam Baglioni 545ea9f77e moved in common. Zenodo response model and APIClient to deposit in Zenodo 2020-08-07 16:44:51 +02:00
Miriam Baglioni da9b012c15 fixed dewcription 2020-08-06 11:55:44 +02:00
Miriam Baglioni 6dbadcf181 the new schema for the dumped result 2020-08-06 11:05:56 +02:00
Sandro La Bruzzo 4fb1821fab Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-08-06 10:28:31 +02:00
Sandro La Bruzzo 9d9e9edbd2 improved extractEntity Relation workflows using dataset 2020-08-06 10:28:24 +02:00
Miriam Baglioni 14eda4f46e added method to try to put inputstream to zenodo 2020-08-05 14:18:25 +02:00
Miriam Baglioni e737a47270 added classes to try to send input stream to zenodo for the upload 2020-08-05 14:17:40 +02:00
Miriam Baglioni 873e9cd50c changed hadoop setting to connect to s3 2020-08-04 15:37:25 +02:00
Alessia Bardi a29565ff57 code formatting 2020-08-04 12:55:27 +02:00
Alessia Bardi 01db29e208 fixes redmine issue #5846: datacite and its different namespace declarations 2020-08-04 12:53:48 +02:00
Alessia Bardi b4e4e5f858 do not duplicate result PIDs 2020-08-04 12:52:14 +02:00
Miriam Baglioni 5b651abf82 merge branch with master 2020-08-04 10:14:07 +02:00
Miriam Baglioni 901ae37f7b added step to workflow 2020-08-03 18:12:54 +02:00
Miriam Baglioni e43aeb139a added new property file and changed some parameter to old files 2020-08-03 18:07:28 +02:00
Miriam Baglioni aa9f3d9698 changed logic for save in s3 directly 2020-08-03 18:06:18 +02:00
Miriam Baglioni d465f0eec9 added fulltext to result 2020-08-03 18:03:27 +02:00
Miriam Baglioni c892c7dfa7 changed to query for community map just once and save the result for remaining executions 2020-08-03 17:56:31 +02:00
Michele Artini 652b13abb6 Merge branch 'master' into nsprefix_blacklist 2020-07-31 07:58:37 +02:00
Claudio Atzori cd631bb5bc defaults fixed in the cleaning workflow forces result.publisher to NULL when result.publisher.value in empty 2020-07-30 17:03:53 +02:00
Miriam Baglioni 57c87b7653 re-implemented to fix issue on not serializable Set<String> variable 2020-07-30 16:43:43 +02:00
Miriam Baglioni ef8e5957b5 added specific directory where to save results 2020-07-30 16:42:46 +02:00
Miriam Baglioni 75f3361c85 - 2020-07-30 16:41:31 +02:00
Miriam Baglioni 3f695b25fa refactoring 2020-07-30 16:40:15 +02:00
Miriam Baglioni e623f12bef refactoring 2020-07-30 16:32:59 +02:00
Miriam Baglioni ff7d05abb4 added support class to store the couple organizationId representativeId gaot from sql query on hive 2020-07-30 16:32:04 +02:00
Miriam Baglioni cf6d80b2ab added command to close the writer 2020-07-30 16:31:22 +02:00
Miriam Baglioni f985bca37b added USER_CLAIM constant value 2020-07-30 16:25:26 +02:00
Claudio Atzori 4bbfcf1ac6 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-07-30 16:25:06 +02:00
Claudio Atzori 4ff8007518 added function to set the missing vocabulary names, used in the cleaning workflow as a pre-cleaning step 2020-07-30 16:24:39 +02:00
Miriam Baglioni 6f1c40a933 - 2020-07-30 16:24:28 +02:00
Miriam Baglioni 2b66a93f9e added property file that was missing 2020-07-30 16:24:17 +02:00
Michele Artini bdece15ca0 blacklist of nsprefix 2020-07-30 16:13:38 +02:00
Sandro La Bruzzo c97c8f0c44 implemented new oozie job to extract entities in a separate dataset 2020-07-30 12:13:58 +02:00
Sandro La Bruzzo 3010a362bc updated changing in the workflow of provision in the phase of aggregation. Removed serialization in JSON RDD and used spark Dataset 2020-07-30 09:25:56 +02:00
Sandro La Bruzzo 16ae3c9ccf updated changing in the workflow of provision in the phase of aggregation. Removed serialization in JSON RDD and used spark Dataset 2020-07-30 09:25:32 +02:00
Miriam Baglioni 76bcab98ce added code to filter out null originalId from the dump 2020-07-29 18:28:21 +02:00
Miriam Baglioni 86bab79512 - 2020-07-29 18:20:22 +02:00
Miriam Baglioni 31791dcf3d fixed wrong property file path name 2020-07-29 18:20:08 +02:00
Miriam Baglioni 9e722aa1ef - 2020-07-29 18:00:08 +02:00
Miriam Baglioni d22f106f27 added constant to identify datasource associated to funders 2020-07-29 17:56:55 +02:00
Miriam Baglioni 40e194fe2f added check to not dump datasources related to funders 2020-07-29 17:56:18 +02:00
Miriam Baglioni b48934f6df changed the workflow name 2020-07-29 17:43:43 +02:00
Miriam Baglioni 074e9ab75e refactoring 2020-07-29 17:42:50 +02:00
Miriam Baglioni 8ad8dac7d4 merge branch with fork master 2020-07-29 17:38:28 +02:00
Miriam Baglioni 9fa82dc93b fixed issue 2020-07-29 17:36:16 +02:00
Miriam Baglioni 8907648d6a - 2020-07-29 17:35:47 +02:00