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585 Commits

Author SHA1 Message Date
Miriam Baglioni 454b8a6a29 Merge remote-tracking branch 'upstream/master' 2020-04-18 14:09:44 +02:00
Miriam Baglioni 890ec28f0f input parameters for preparation step1 2020-04-18 14:09:37 +02:00
Miriam Baglioni fbf5c27c27 Added preparation classes before actual propagation 2020-04-18 14:09:03 +02:00
Claudio Atzori 5f45f2c77f Merge branch 'master' into deduptesting 2020-04-18 12:46:40 +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 a2938dd059 cleanup 2020-04-18 12:24:22 +02:00
Claudio Atzori 9374ff03ea Merge branch 'master' into deduptesting 2020-04-18 12:06:58 +02:00
Claudio Atzori 71813795f6 various refactorings on the dnet-dedup-openaire workflow 2020-04-18 12:06:23 +02:00
miconis 6450bb0daa test for softwares dedup added. definition of orp, dataset and sw dedup configurations 2020-04-17 17:31:59 +02:00
Miriam Baglioni 72c63a326e removed unuseful class 2020-04-17 17:14:51 +02:00
Miriam Baglioni 00c2ca3ee5 - 2020-04-17 17:14:25 +02:00
Miriam Baglioni 5cd092114f use mergeFrom method to add the new community contexts 2020-04-17 17:13:18 +02:00
Miriam Baglioni 264c82f21e minor 2020-04-17 16:54:46 +02:00
Miriam Baglioni 8c079c7a49 unit test for orcid to result propagation from semrel 2020-04-17 16:53:03 +02:00
Miriam Baglioni eacd140a98 added missing parameter(s) 2020-04-17 16:52:30 +02:00
Miriam Baglioni 390e250faf use the addPid method of the Author class to add a new pid 2020-04-17 16:52:02 +02:00
Miriam Baglioni b46b080ddc use mergeFrom method call to add the country(ies) instead of modify the result directly. 2020-04-17 16:50:54 +02:00
Miriam Baglioni c4987dd12a minor 2020-04-17 16:49:08 +02:00
Claudio Atzori 038ac7afd7 relation consistency workflow separated from dedup scan and creation of CCs 2020-04-17 13:12:44 +02:00
Claudio Atzori c92bfeeaee Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-04-17 13:07:52 +02:00
Miriam Baglioni adc11c97a7 Merge remote-tracking branch 'upstream/master' 2020-04-17 12:34:31 +02:00
Sandro La Bruzzo 01ea7721f3 Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-04-17 12:12:25 +02:00
Sandro La Bruzzo 5e2fa996aa fixed problem with conversion of long into string 2020-04-17 12:11:51 +02:00
miconis 418cf94642 implementation of the deletedbyinference test in propagating relations 2020-04-17 10:40:21 +02:00
Miriam Baglioni 5d772e5263 new implementation of propagation of community to result from organization that exploits the prepared info 2020-04-16 18:45:22 +02:00
Miriam Baglioni fff1e5ec39 classes to (de)serialize the data provided in the preparation step 2020-04-16 18:44:43 +02:00
Miriam Baglioni 3fd9d6b02f preparation phase for the propagation of community to result from organization 2020-04-16 18:43:55 +02:00
Miriam Baglioni a9120164aa added hive parameter and a step of reset of the working dir in the workflow 2020-04-16 18:42:04 +02:00
Miriam Baglioni 6afbd542ca changed the save mode to avoid NegativeArraySize... error. Needed to modify also the preparationstep2 2020-04-16 18:40:14 +02:00
Miriam Baglioni d60fd36046 changed the save method 2020-04-16 16:14:15 +02:00
Miriam Baglioni 951b13ac46 input parameters and workflow for new implementation of propagation of orcid to result from semrel and preparation phases 2020-04-16 16:13:10 +02:00
Miriam Baglioni 4d89f3dfed removed unuseful classes 2020-04-16 16:11:44 +02:00
Miriam Baglioni 5e72a51f11 - 2020-04-16 16:11:20 +02:00
Miriam Baglioni c33a593381 renamed 2020-04-16 16:09:47 +02:00
Miriam Baglioni 0e5399bf74 seconf phase of data preparation. Groups all the possible updates by id 2020-04-16 16:08:51 +02:00
Miriam Baglioni 548ba915ac first phase of data preparation. For each result type (parallel) it produces the possible updates 2020-04-16 15:58:42 +02:00
Miriam Baglioni 243013cea3 to (de)serialize the association from the resultId and the list of autoritative authors with orcid to possibly propagate 2020-04-16 15:57:29 +02:00
Miriam Baglioni ac3ad25b36 to (de)serialize needed information of the author to determine if the orcid can be passed (name, surname, fullname (?), orcid) 2020-04-16 15:56:33 +02:00
Miriam Baglioni d6cd700a32 new implementation that exploits prepared information (the list of possible updates: resultId - possible list of orcid to be added 2020-04-16 15:55:25 +02:00
Miriam Baglioni f077f22f73 minor 2020-04-16 15:54:16 +02:00
Miriam Baglioni fd5d792e35 refactoring 2020-04-16 15:53:34 +02:00
Claudio Atzori cb0952428e Merge branch 'master' into deduptesting 2020-04-16 14:42:25 +02:00
Claudio Atzori cc21bbfb1a Merge branch 'deduptesting' of https://code-repo.d4science.org/D-Net/dnet-hadoop into deduptesting 2020-04-16 14:41:37 +02:00
Claudio Atzori ec5dfc068d added spark.sql.shuffle.partitions=3840 to dedup scan wf 2020-04-16 14:41:28 +02:00
Claudio Atzori 09f356b047 Merge pull request 'Closes #7: subdirs inside graph table dirs' (#8) from przemyslaw.jacewicz/dnet-hadoop:przemyslawjacewicz_7_distcp_configuration_fix into master 
Run the code from this PR in isolation and it worked fine. Thanks!
 2020-04-16 14:38:46 +02:00
Claudio Atzori 3437383112 Merge branch 'master' into deduptesting 2020-04-16 12:46:14 +02:00
miconis 0eccbc318b Deduper class (utilities for dedup) cleaned. Useless methods removed 2020-04-16 12:36:37 +02:00
Claudio Atzori 76d23895e6 Merge branch 'deduptesting' of https://code-repo.d4science.org/D-Net/dnet-hadoop into deduptesting 2020-04-16 12:18:32 +02:00
miconis 6a089ec287 minor changes 2020-04-16 12:15:38 +02:00
Claudio Atzori 376efd67de removed prepare statement in spark action 2020-04-16 12:14:16 +02:00
miconis 9b36458b6a Merge branch 'deduptesting' of code-repo.d4science.org:D-Net/dnet-hadoop into deduptesting 2020-04-16 12:13:58 +02:00
miconis cd4d9a148f creating temporary directories in dedup test 2020-04-16 12:13:26 +02:00
Claudio Atzori b39ff36c16 improving the wf definitions 2020-04-16 12:11:37 +02:00
Claudio Atzori 011b342bc9 trying to avoid OOM in SparkPropagateRelation 2020-04-16 11:13:51 +02:00
Miriam Baglioni 08227cfcbd resources needed for running the test on propagation of result to organization from institutional repositories 2020-04-16 11:06:10 +02:00
Miriam Baglioni a97e915c24 test unit for propagation of result to organization from institutional repository 2020-04-16 11:05:21 +02:00
Miriam Baglioni b078710924 modification to the test due to the removal of unused parameters 2020-04-16 11:04:39 +02:00
Miriam Baglioni a5e5c81a2c input parameters and workflow definition for propagation of result to organization from institutional repositories 2020-04-16 11:03:41 +02:00
Miriam Baglioni 5e1bd67680 removed unuseful parameter 2020-04-16 11:02:01 +02:00
Miriam Baglioni eaf19ce01b removed unuseful class 2020-04-16 10:59:33 +02:00
Miriam Baglioni 7bd49abbef commit to delete 2020-04-16 10:59:09 +02:00
Miriam Baglioni 53f418098b added the isTest checkpoint 2020-04-16 10:53:48 +02:00
Miriam Baglioni c28333d43f minor 2020-04-16 10:52:50 +02:00
Miriam Baglioni a8100baed6 changed the way to save the results to aviod NegativeArray... error 2020-04-16 10:50:09 +02:00
Miriam Baglioni 79b978ec57 refactoring 2020-04-16 10:48:41 +02:00
Claudio Atzori 069ef5eaed trying to avoid OOM in SparkPropagateRelation 2020-04-15 21:23:21 +02:00
Claudio Atzori 8eedfefc98 try to introduce intermediate serialization on hdfs to avoid OOM 2020-04-15 18:35:35 +02:00
Przemysław Jacewicz da019495d7 [dhp-actionmanager] target dir removal added for distcp actions 2020-04-15 17:56:57 +02:00
miconis 5689d49689 minor changes 2020-04-15 16:34:06 +02:00
Claudio Atzori c439d0c6bb PromoteActionPayloadForGraphTableJob reads directly the content pointed by the input path, adjusted promote action tests (ISLookup mock) 2020-04-15 16:18:33 +02:00
Claudio Atzori ff30f99c65 using newline delimited json files for the raw graph materialization. Introduced contentPath parameter 2020-04-15 16:16:20 +02:00
Sandro La Bruzzo 3d3ac76dda Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-04-15 15:24:01 +02:00
Sandro La Bruzzo 74a7fac774 fixed problem with timestamp 2020-04-15 15:23:54 +02:00
Miriam Baglioni 3577219127 removed unuseful classes 2020-04-15 12:45:49 +02:00
Miriam Baglioni 964b22d418 modified the writing of the new relations. before: read old rels, add the new ones to them, write all the relations in new location. Now: first step of the wf copies the old relation i new location. If new relations are found, they are saved in the new location in append mode. 2020-04-15 12:32:01 +02:00
Miriam Baglioni 43f0590d4b change in the testing because the business logic is changed. 2020-04-15 12:29:50 +02:00
Miriam Baglioni 473d17767c new business logic for the actual propagation. It exploits previously computed information 2020-04-15 12:25:44 +02:00
Miriam Baglioni 6a377a7582 class to compute some information needed for the actual propagation 2020-04-15 12:25:11 +02:00
Miriam Baglioni 5a3487280d classes to serialize/deserialize the prepared data 2020-04-15 12:24:36 +02:00
Miriam Baglioni 62b09be43c added correct descritption for parameter isSparkSessionManaged 2020-04-15 12:23:06 +02:00
Miriam Baglioni 1859ce8902 minor refactoring 2020-04-15 12:21:31 +02:00
Miriam Baglioni 27f1d3ee8f minor refactoring 2020-04-15 12:21:05 +02:00
Alessia Bardi 550a9f82ed Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-04-14 17:53:01 +02:00
Alessia Bardi a68fae9bcb now supporting openaire 4.0 compliance 2020-04-14 17:52:48 +02:00
Sandro La Bruzzo c36239e693 fixed incremental indexing 2020-04-14 17:47:36 +02:00
Miriam Baglioni 3f4b579e7f new workflow. It is composed of four steps. The first removes the directory where to store the results. The second copies the relation to the new locatio, the third id the preparation phase and then the actual propagation 2020-04-14 16:49:24 +02:00
Miriam Baglioni ca2b40952e minor changes 2020-04-14 16:48:02 +02:00
Miriam Baglioni 61d39e659e parameters for the project2result propagation phase 2020-04-14 16:47:39 +02:00
Miriam Baglioni 92f19fa0a0 parameters for the project2result preparation phase 2020-04-14 16:46:57 +02:00
Miriam Baglioni cadab9b81d new implementation for result to project propagation. Use the prepared info in propagation 2020-04-14 16:46:07 +02:00
Miriam Baglioni ceb1f299bf minor changes 2020-04-14 16:45:12 +02:00
Claudio Atzori 82e8341f50 reorganizing parameter names in the provision workflow 2020-04-14 15:54:41 +02:00
Miriam Baglioni e0038bde5b Support class to serialize/deserialize the association project, set of linked results 2020-04-14 15:32:12 +02:00
Miriam Baglioni c0bebb7c35 code to compute the prepared information used in the actual propagation step. This step will produce who files: one with potential updates (association between projects and a list of results), the other already linked entities (association between projects and the list of results already linked to them) 2020-04-14 15:31:26 +02:00
Miriam Baglioni f47ee5b78e directory where to store the prepared infor before actual propagation will take place 2020-04-14 15:29:21 +02:00
Miriam Baglioni 36cc9516d8 the starting relation set for testing 2020-04-14 15:28:34 +02:00
Miriam Baglioni 4b01dc60e6 test unit for result to project propagation 2020-04-14 15:28:00 +02:00
Miriam Baglioni 8f12292daa changed the way to save the results on filesystem 2020-04-11 16:47:34 +02:00
Miriam Baglioni 87f802821e new workflow for country propagation: it is composed of the preparation step and in the propagation. The propagation part runs in parallel on the result types 2020-04-11 16:40:22 +02:00
Miriam Baglioni a562080b0b parameters to be used in the prepared Job and in the actual country propagation job 2020-04-11 16:39:17 +02:00
Miriam Baglioni 1251ad4455 removed unuseful class 2020-04-11 16:38:13 +02:00
Miriam Baglioni aef9b3aa90 new parametric implementation of country propagation. Exploits information compute before and broadcasts it to each executor 2020-04-11 16:36:59 +02:00
Miriam Baglioni a2d833d5dd step of data preparation before actual country propagation will take palce 2020-04-11 16:36:03 +02:00
Miriam Baglioni 6897c920a2 classes in support of new implementation of country propagation 2020-04-11 16:35:26 +02:00
Miriam Baglioni 85766a02d8 added dependency to use hive on local machine 2020-04-11 16:34:22 +02:00
Miriam Baglioni 79b8ea4fed prepared information to be used in actual country propagation. Subset of info 2020-04-11 16:29:41 +02:00
Miriam Baglioni 1822476613 Test for country propagation 2020-04-11 16:28:09 +02:00
Miriam Baglioni 7783b09c5b new implementation for result to project propagation. Prepare some info to be used in propagation 2020-04-11 16:26:23 +02:00
Claudio Atzori 6b5f9ca9cb raw graph creation workflow moved under dhp-graph-mapper, claims integration is included 2020-04-10 17:53:07 +02:00
Miriam Baglioni 90469789b9 two new classes fro new implementation of project to result propagation 2020-04-09 13:29:01 +02:00
Miriam Baglioni 627ad58a8b new wf definition 2020-04-09 11:33:19 +02:00
Miriam Baglioni 9c63c4840d new workflow and parameters for country propagation 2020-04-08 19:13:42 +02:00
Miriam Baglioni a2d309545b new parametrized implementation for country propagation 2020-04-08 19:12:59 +02:00
Miriam Baglioni 6dfdba9ef7 new parametrized implementation for country propagation 2020-04-08 18:14:37 +02:00
Miriam Baglioni 03f7cb6402 new parametrized implementation for country propagation 2020-04-08 18:08:41 +02:00
Miriam Baglioni df2fc4a6d7 Merge remote-tracking branch 'upstream/master' 2020-04-08 18:07:26 +02:00
Miriam Baglioni fcfef4632f input parameters for country propagation preparation job 2020-04-08 18:07:18 +02:00
miconis 0be2e72be5 further implementation of tests for the deduplication of each entity. publication dump added, empty entity files created 2020-04-08 18:02:30 +02:00
Miriam Baglioni 61045e84d9 merged conflict in pom 2020-04-08 14:23:30 +02:00
Claudio Atzori 47f3d9b757 unit test for GraphHiveImporterJob 2020-04-08 13:24:43 +02:00
Sandro La Bruzzo ba9f07a6fe fixed wrong test 2020-04-08 13:18:20 +02:00
Miriam Baglioni 540da4ab61 new busuness logic with prepared info before actual job run 2020-04-08 13:04:04 +02:00
Miriam Baglioni 8438702b3d addition in propagation constants 2020-04-08 10:54:01 +02:00
Miriam Baglioni 2afe971816 new implementation for country propagatio 2020-04-08 10:49:09 +02:00
Miriam Baglioni beebbcf66b new config for countrypropagation 2020-04-08 10:31:29 +02:00
Claudio Atzori d74e128aa6 Utility classes moved in dhp-common and dhp-schemas 2020-04-07 11:56:22 +02:00
Claudio Atzori c57cf679ca Merge branch 'provision_dataset' 2020-04-07 08:56:58 +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 6177cf36fb Merge pull request 'Closes #4: New action manager implementation' (#5) from przemyslaw.jacewicz/dnet-hadoop:przemyslawjacewicz_actionmanager_impl_prototype into master 
Nothing more to add here. Thanks for your contribution!
 2020-04-06 17:35:07 +02:00
Claudio Atzori e355961997 dataset based provision WIP 2020-04-06 17:34:25 +02:00
miconis 56fbe689f0 implementation of the tests for each spark action 2020-04-06 16:30:31 +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
miconis 53fd624c34 implemented test for sparkcreatesimrels 2020-04-03 18:32:25 +02:00
Claudio Atzori 24b2c9012e dataset based provision WIP 2020-04-02 18:44:09 +02:00
miconis a61763d149 structure for sparksimrel changed to be compliant with mockito testing 2020-04-02 18:37:53 +02:00
Claudio Atzori daa26acc9d dataset based provision WIP, fixed spark2EventLogDir 2020-04-02 16:15:50 +02:00
Przemysław Jacewicz 7b2a7e2417 [dhp-actionmanager] missing descriptions added and minor naming and formatting fixes 2020-04-02 11:48:40 +02:00
Claudio Atzori 9c7092416a dataset based provision WIP 2020-04-01 19:07:30 +02:00
miconis bfa5bc74df minor changes 2020-04-01 19:05:48 +02:00
Przemysław Jacewicz 80cf43b9c8 [dhp-actionmanager] promoting workflow added 2020-04-01 18:51:25 +02:00
Przemysław Jacewicz 5b459bcc47 [dhp-actionmanager] promoting spark job added 2020-04-01 18:49:08 +02:00
miconis 9802bcb9fe dedup testing 2020-04-01 18:48:31 +02:00
Przemysław Jacewicz e21bb89dbd [dhp-actionmanager] partitioning spark job added 2020-04-01 18:41:29 +02:00
Przemysław Jacewicz f9f7350bb9 [dhp-actionmanager] common package added with utility classes supporting hadoop and spark envs 2020-04-01 18:39:26 +02:00
Przemysław Jacewicz ad70c23b2e [dhp-actionmanager] pom updated 2020-04-01 18:36:00 +02:00