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612 Commits

Author SHA1 Message Date
Miriam Baglioni 37ad2f28e9 removed added | in prefix for datasource 2020-08-11 15:55:06 +02:00
Miriam Baglioni f31c2e9461 enabled test 2020-08-11 15:49:25 +02:00
Miriam Baglioni 2d67476417 merge branch with master 2020-08-11 15:46:04 +02:00
Miriam Baglioni 6d3804e24c - 2020-08-11 15:45:12 +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 7dfd56df9d - 2020-08-11 15:42:35 +02:00
Miriam Baglioni a169d7e7c1 added test file for the MakeTar class 2020-08-11 15:40:41 +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 c378c38546 disabled test. The testing functionalities for hte upload in Zenode are moved to common 2020-08-10 12:41:11 +02:00
Miriam Baglioni 63ad0ed209 changed to use communityMapPath instead of IsLookUp 2020-08-10 12:40:19 +02:00
Miriam Baglioni cec795f2ea changed resources to mirror changes in the model 2020-08-10 12:39:35 +02:00
Miriam Baglioni f50e3e7333 changed the class for which to generate the schema 2020-08-10 12:03:49 +02:00
Miriam Baglioni b8c26f656c test using communityMapPath instead of isLookUp 2020-08-10 12:02:55 +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
Sandro La Bruzzo 0ade33ad15 updated mergeFrom function for DLI Unknown 2020-08-10 10:18:35 +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 931fa2ff00 removed dependencies 2020-08-07 16:46:37 +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 adf0ca5aa7 test to send is from hdfs 2020-08-05 14:24:43 +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
Alessia Bardi 09a323d18d testing a dataset from Nakala 2020-08-04 12:50:52 +02:00
Alessia Bardi c35bf486cc added handle among the possible PIDs 2020-08-04 12:50:12 +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 fa38cdb10b added resource 2020-08-03 18:11:12 +02:00
Miriam Baglioni e9fcc0b2f1 commented test unit - to decide change for mirroring the changed logics 2020-08-03 18:10:53 +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 ec4b392d12 added new dependencies for writing on s3 2020-08-03 17:57:04 +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
Alessia Bardi 8cc067fe76 specific test for claims 2020-08-03 11:17:50 +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 872d7783fc - 2020-07-30 16:50:36 +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 487226f669 Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-07-30 09:25:39 +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 ee8420c6b3 added resource for datasource test 2020-07-29 18:28:43 +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 ef1d8aef17 added one test to verify the dump for the datasources 2020-07-29 18:27:46 +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 1433db825d refactorign 2020-07-29 17:43:24 +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
Miriam Baglioni 536e7f6352 added and changed resources for testing of the whole graph dump and of community related products dumps 2020-07-29 17:33:34 +02:00
Miriam Baglioni 4d7f590493 testings for the whole graph dump 2020-07-29 17:32:37 +02:00
Miriam Baglioni a2f73ec2c7 changed due to changes in the model 2020-07-29 17:32:02 +02:00
Miriam Baglioni 481585e9d3 - 2020-07-29 17:31:41 +02:00
Miriam Baglioni 40a8dafbdc - 2020-07-29 17:30:44 +02:00
Miriam Baglioni de2ebb467e changed due to changes in the model 2020-07-29 17:08:02 +02:00
Miriam Baglioni d0ff2a56fb - 2020-07-29 17:06:53 +02:00
Miriam Baglioni b96dedb56b changed due to changes in the model 2020-07-29 17:05:31 +02:00
Miriam Baglioni 6d0f08277b classes to implement the dump of the whole graph. 2020-07-29 17:03:19 +02:00
Miriam Baglioni 8d4327b292 input parameters and workflow definition for the dump of the whole graph 2020-07-29 17:00:34 +02:00
Miriam Baglioni b5f995ab12 refactoring 2020-07-29 16:59:48 +02:00
Miriam Baglioni f7a87cc447 added new constants value 2020-07-29 16:58:40 +02:00
Miriam Baglioni b71d12cf26 refactoring 2020-07-29 16:52:44 +02:00
Miriam Baglioni a8d65b68cb changed to delete the part to check if it was a test or a real execution 2020-07-29 16:47:57 +02:00
Miriam Baglioni 3ec2392904 Added new class to move the place the split is effectively run 2020-07-29 16:46:50 +02:00
Miriam Baglioni 178c2729a7 changed the path to reach the java class to be executed 2020-07-29 12:29:51 +02:00
Miriam Baglioni 437ac12139 removed unused parameter 2020-07-29 12:28:16 +02:00
Michele Artini 35e6e9c064 tests 2020-07-28 12:02:15 +02:00
Miriam Baglioni 6c2223d1fc added code to get the openaire id for contexts 2020-07-24 17:30:15 +02:00
Miriam Baglioni afd54c1684 removed not needed upload and refactoring 2020-07-24 17:28:56 +02:00
Miriam Baglioni 7b0569d989 changed to map also the result associated to the whole graph 2020-07-24 17:28:11 +02:00
Miriam Baglioni 082225ad61 - 2020-07-24 17:27:26 +02:00
Miriam Baglioni 968c59d97a added teh logic to dump also the products for the whole graph. They will miss collected from and context information that will be materialized as new relations 2020-07-24 17:25:19 +02:00
Miriam Baglioni 332258d199 split the classes related to the communities dump and to the whole graph dump 2020-07-24 17:21:48 +02:00
Claudio Atzori 56bbfdc65d introduced parameter 'numParitions', driving the hive DB table data partitioning. Currently specified only for table 'project' 2020-07-23 08:54:10 +02:00
Sandro La Bruzzo 9ab594ccf6 fixed test 2020-07-21 10:36:21 +02:00
Claudio Atzori ebf60020ac map results as OPRs in case of missing //CobjCategory/@type and the vocabulary dnet:result_typologies doesn't resolve the super type 2020-07-20 19:01:10 +02:00
Miriam Baglioni 355d7e426e added dumo for project - not finished 2020-07-20 18:54:43 +02:00
Miriam Baglioni a2f01e5259 added getter and setter 2020-07-20 18:54:17 +02:00
Miriam Baglioni 40bbe94f7c merge with master fork 2020-07-20 18:10:03 +02:00
Miriam Baglioni 23160b4d29 realignment of the workflow classes with the changes in the structure of the module 2020-07-20 18:04:30 +02:00
Miriam Baglioni 3aab7680f6 changed the test results 2020-07-20 18:00:43 +02:00
Miriam Baglioni 5076e4f320 changed test to comply with the modifications 2020-07-20 17:55:18 +02:00
Miriam Baglioni 08dbd99455 changed to dump the whole results graph by usign classes already implemented for communities. Added class to dump also organization 2020-07-20 17:54:28 +02:00
Miriam Baglioni e47ea9349c extended some types by adding provenance as the couple (provenance, trust) and moved some classes to be used by the complete graph dump also 2020-07-20 17:46:27 +02:00
Claudio Atzori 32f5e466e3 imports cleanup 2020-07-20 17:42:58 +02:00
Claudio Atzori 54ac583923 code formatting 2020-07-20 17:37:08 +02:00
Claudio Atzori 124e7ce19c in case of missing attribute //dr:CobjCategory/@type the resulttype is derived by looking up the vocabulary dnet:result_typologies with the 1st instance type available 2020-07-20 17:33:37 +02:00
Claudio Atzori 050dda223d Merge pull request 'removed duplicated fields' (#25) from unique_field_in_lists into master 
Looks good as a temporary workaround. I agree the model could seamlessly make the distinct operation by using HashSets instead of Linked (or Array) Lists.

The task to update the model in such a way is added on #9#issuecomment-1583

Thanks!
 2020-07-20 12:12:50 +02:00
Claudio Atzori e0c4cf6f7b added parameter to drive the graph merge strategy: priority (BETA|PROD) 2020-07-20 10:48:01 +02:00
Claudio Atzori 94ccdb4852 Merge branch 'master' into merge_graph 2020-07-20 10:14:55 +02:00
Michele Artini 331a3cbdd0 fixed originalId 2020-07-20 09:50:29 +02:00
Sandro La Bruzzo 9116d75b3e Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-07-17 18:01:30 +02:00
Miriam Baglioni 47c7122773 changed priority from beta to production 2020-07-17 12:56:35 +02:00
Michele Artini 442f30930c removed duplicated fields 2020-07-17 12:25:36 +02:00
Claudio Atzori 1781609508 code formatting 2020-07-16 19:06:56 +02:00
Claudio Atzori 878f2b931c Merge branch 'master' into merge_graph 2020-07-16 16:34:24 +02:00
Miriam Baglioni f9ad6f3255 Merge branch 'dump' of code-repo.d4science.org:miriam.baglioni/dnet-hadoop into dump 2020-07-10 19:42:53 +02:00
Miriam Baglioni c27f12d6e8 avoid to consider _SUCCESS file 2020-07-10 19:42:23 +02:00
Claudio Atzori 31071e363f Merge branch 'provision_indexing' 2020-07-10 19:03:57 +02:00
Claudio Atzori cc77446dc4 added dbSchema parameter to the raw_db workflow 2020-07-10 19:01:50 +02:00
Michele Artini e1ae964bc4 stats 2020-07-10 16:12:08 +02:00
Sandro La Bruzzo c01efed79b Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop 2020-07-10 14:44:57 +02:00
Sandro La Bruzzo a7d3977481 added generation of EBI Dataset 2020-07-10 14:44:50 +02:00
Claudio Atzori 67e1d222b6 bulk cleaning when found null or empty, sets bestaccessrights evaluating the result instances 2020-07-08 17:53:35 +02:00
Claudio Atzori 610d377d57 first implementation of the BETA & PROD graphs merge procedure 2020-07-08 16:54:26 +02:00
Alessia Bardi 9a898c0e4c Json schema generator 2020-07-08 12:52:00 +02:00
Alessia Bardi 636f9ce7d6 json schema generator lib 2020-07-08 12:50:57 +02:00
Alessia Bardi 8f83b726fa Dump json schema compliant to json schema Draft 7 2020-07-08 12:48:46 +02:00
Miriam Baglioni 1b0b968548 fixed issue on substring 2020-07-08 12:11:51 +02:00
Miriam Baglioni 7fe00cb4fb - 2020-07-08 10:29:37 +02:00
Miriam Baglioni 375ef07d7b changed the description for the upload 2020-07-07 18:41:27 +02:00
Miriam Baglioni 35c8265793 added the json extention to filename 2020-07-07 18:29:49 +02:00
Miriam Baglioni 81434f8e5e added method newInstance 2020-07-07 18:26:10 +02:00
Miriam Baglioni 817cddfc52 - 2020-07-07 18:25:12 +02:00
Miriam Baglioni a66aa9bd83 removed unuseful tests 2020-07-07 18:25:00 +02:00
Miriam Baglioni 9b20a21b24 removed unuseful tests 2020-07-07 18:23:37 +02:00
Miriam Baglioni 8a1b42ff21 added check to verify that dump contains at least one product 2020-07-07 18:21:35 +02:00
Miriam Baglioni d86adb82a7 - 2020-07-07 18:20:51 +02:00
Miriam Baglioni b2782025f6 enabled the whole workflow to run. Added property to give priority to depenedency in the classpath - to solve conflicts 2020-07-07 18:10:47 +02:00
Miriam Baglioni 83d2c84b77 added constraints to xquery so that to get only profiles with status manager or all 2020-07-07 18:09:48 +02:00
Miriam Baglioni 4c8d86493c - 2020-07-07 18:09:06 +02:00
Miriam Baglioni 0208bc18f3 added new resource for testing 2020-07-07 17:47:24 +02:00
Miriam Baglioni f5bb65c9ef the json schema for the dump of the results 2020-07-07 17:34:40 +02:00
Miriam Baglioni c19818a3f8 merge branch with fork master 2020-07-06 13:58:23 +02:00
Miriam Baglioni f8bf4acd76 - 2020-07-02 16:03:11 +02:00
Miriam Baglioni e6c79d44e6 - 2020-07-02 16:02:02 +02:00
Miriam Baglioni d7f6f0c216 changed code to use other lib 2020-07-02 16:01:34 +02:00
Miriam Baglioni 8fdc9e070c added dependency to OkHttp 2020-07-02 16:01:08 +02:00
Miriam Baglioni 94500a581b merge branch with fork master 2020-07-02 14:25:39 +02:00
Claudio Atzori ed1c7e5d75 fixed workflow for the import of the claims alone 2020-07-02 12:40:21 +02:00
Sandro La Bruzzo 1d420eedb4 added generation of EBI Dataset 2020-07-02 12:37:43 +02:00
Claudio Atzori e4a29a4513 fixed workflow for the import of the claims alone 2020-07-02 12:36:33 +02:00
Claudio Atzori 6f5771c1c9 sets author.rank when null 2020-06-25 14:06:21 +02:00
Claudio Atzori 2d77d3a388 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop 2020-06-25 12:54:30 +02:00
Miriam Baglioni 05a99cfb61 change the position of value and description elements in the workflow definition 2020-06-25 12:36:08 +02:00
Claudio Atzori 7df2712824 Merge branch 'provision_indexing' 2020-06-25 12:22:41 +02:00
Michele Artini abcbebcbb4 fixed generation of ids 2020-06-25 09:50:46 +02:00
Michele Artini 77d2a1b1c4 params to choose sql queries for beta or production 2020-06-25 09:28:13 +02:00
Claudio Atzori 0e723d378b added default from vocab for missing instance.refereed; remove spurious prefixes from orcid values; WIP: prepare relation job 2020-06-24 18:34:42 +02:00
Miriam Baglioni 3e5570de7a - 2020-06-23 15:44:54 +02:00
Michele Artini 38bb45d0b6 test osf:refereed 2020-06-23 10:14:39 +02:00
Miriam Baglioni e4b21be004 - 2020-06-22 17:31:50 +02:00
Miriam Baglioni afa19b0c84 changed the way to PUT the files to the rest API 2020-06-22 17:20:07 +02:00
Miriam Baglioni 250fd1c854 merge branch with fork master 2020-06-22 16:25:48 +02:00
Claudio Atzori 9cd27183b6 [maven-release-plugin] prepare for next development iteration 2020-06-22 11:27:44 +02:00
Claudio Atzori 1e3dab0631 [maven-release-plugin] prepare release dhp-1.2.3 2020-06-22 11:27:39 +02:00
Miriam Baglioni df80ae5c1b merge branch with fork master 2020-06-22 10:51:23 +02:00
Miriam Baglioni e8f914f8b3 - 2020-06-22 10:50:41 +02:00
Miriam Baglioni edeb862476 excluded dependency in module that generates conflict 2020-06-22 10:49:56 +02:00
Miriam Baglioni 185facb8e5 change the deprecated DefaultHttpClient with the CLoseableHttpClient 2020-06-22 10:49:10 +02:00
Claudio Atzori 7d416f08d8 graph cleaning workflow: set hostedby to unknown repository when defined as NULL 2020-06-22 09:50:43 +02:00