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342 Commits

Author SHA1 Message Date
Sandro La Bruzzo c6fa8598e1 massive code refactor: 
removed modules dhp-*-scholexplorer
 2021-07-01 22:13:45 +02:00
Miriam Baglioni bc34347643 added assertions to verify doi normalization 2021-06-30 14:37:08 +02:00
Miriam Baglioni 86f47afcc7 slight modification of the resource to accomodate also doi normalization tests 2021-06-30 14:36:49 +02:00
Miriam Baglioni 03767ea8e6 slight modification of the resource to accomodate also doi normalization tests 2021-06-30 13:21:24 +02:00
Miriam Baglioni f8eec0ca9a added resource to test the normalization of doi during the import of MAG 2021-06-30 13:19:54 +02:00
Miriam Baglioni 149f85ddf5 added tests for the normalization of the dois 2021-06-30 13:00:52 +02:00
Miriam Baglioni e487b5544c added tests for the normalization of the dois 2021-06-30 12:57:11 +02:00
Miriam Baglioni 1503ccbbb5 added tests for the normalization of the dois 2021-06-30 12:55:37 +02:00
Miriam Baglioni 1299bfb357 Added class to test the normalization of doi 2021-06-30 12:53:27 +02:00
Miriam Baglioni cf758f4f91 added normalization step for the doi 2021-06-30 10:03:15 +02:00
Miriam Baglioni 801763a0fa there is no more the need to lower case the doi since it is done in the first step. Also changed the creation of the id by using the factory 2021-06-29 19:07:23 +02:00
Miriam Baglioni a74de1cda2 added normalization step to the doi 2021-06-29 18:51:11 +02:00
Miriam Baglioni 06074ea7d3 added normalization step to the doi 2021-06-29 18:46:08 +02:00
Miriam Baglioni 8b8ffe82dc added step of normalization for the doi 2021-06-29 18:41:39 +02:00
Miriam Baglioni 50cc21d92e Added method to normalize doi values (lower case, remove all preceeding 10., filtering out doi not starting with 10.) 2021-06-29 18:35:28 +02:00
Sandro La Bruzzo 80e15cc455 implemented mapping from uniprot, pdb and ebi links 2021-06-24 17:20:00 +02:00
Sandro La Bruzzo a167543637 Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_id_scholexplorer 2021-06-21 09:14:11 +02:00
Miriam Baglioni 13c96622c9 - 2021-06-18 09:45:16 +02:00
Miriam Baglioni b486ae498f added test and test resource to verify the generation of the date of acceptance from the input extracted from the dump 2021-06-18 09:43:32 +02:00
Miriam Baglioni 464c2ddde3 changed to split in two steps the generation of the crossref dataset 2021-06-18 09:42:31 +02:00
Miriam Baglioni 6aca0d8ebb added kryo encoding for input files 2021-06-18 09:42:07 +02:00
Miriam Baglioni 3585e53da3 changed to split in two steps the generation of the crossref dataset 2021-06-18 09:41:23 +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
Miriam Baglioni 95885bcf12 forces executor Executor memory and driver executor memory to be 7G (trying to avoid OOM) 2021-06-16 10:17:52 +02:00
Miriam Baglioni 2550a73981 - 2021-06-16 10:04:41 +02:00
Miriam Baglioni 1c47c0d786 modified the number of executors trying to avoid OOM exception 2021-06-15 21:05:39 +02:00
Miriam Baglioni 7deac55138 added one option for resume from in the wf 2021-06-15 18:38:20 +02:00
Miriam Baglioni 66e7ef892f changed the parameter name 2021-06-15 11:08:54 +02:00
Miriam Baglioni 4f47ad0891 no need to rename the folders, just write in overwrite mode, so I changed the name of the output folder 2021-06-15 09:28:31 +02:00
Miriam Baglioni 9f9dd00b94 refactoring 2021-06-15 09:24:46 +02:00
Miriam Baglioni 63d74ee379 refactoring 2021-06-15 09:24:11 +02:00
Miriam Baglioni 6ebc236657 added needed property: outputPath 2021-06-15 09:23:24 +02:00
Miriam Baglioni f7379255b6 changed the workflow to extract info from the dump 2021-06-15 09:22:54 +02:00
Miriam Baglioni d6e21bb6ea creates the crossref dataset used for doiboost together with unpacking part from tar 2021-06-14 17:27:19 +02:00
Miriam Baglioni ce0cfd79e0 creates the crossref dataset used for doiboost 2021-06-14 13:40:19 +02:00
Miriam Baglioni 93efe4de82 split the construction of crossref dataset in two parts. This one just unpacks the tar entries 2021-06-14 13:39:40 +02:00
Miriam Baglioni 8873e6b6d1 workflow and parameter 2021-06-14 10:15:57 +02:00
Miriam Baglioni 0f1acdf6b6 workflow and parameter 2021-06-14 10:08:55 +02:00
Sandro La Bruzzo efbea1e01a minor fix 2021-06-14 09:45:14 +02:00
Miriam Baglioni 75780fc636 extraction of the tar for the dump of crossref, and creation of the dataset 2021-06-14 09:45:07 +02:00
Miriam Baglioni 8d2e086e48 changes to avoid reassignment to val 2021-06-07 17:50:37 +02:00
Miriam Baglioni f33521d338 Aggiornare 'dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala' 
to be able to replace the aboject assigned to author val has been replaced by var
 2021-06-07 17:27:07 +02:00
Miriam Baglioni bc12e9819e Aggiornare 'dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala' 
The change is to fix the issue that arises when the same work appears more than once on the same ORCID profile. The change avoid to replicate the association doi -> author when the orcid id is already associated to the doi.
 2021-06-07 16:37:01 +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 c4a23c2f4d fix: preserving the old identifier among the originalIds in the doiboost construction process, trying to avoid UnsupportedOperationException while adding elements to the originalIds 2021-05-19 16:01:52 +02:00
Claudio Atzori ba03f549d7 fix: preserving the old identifier among the originalIds in the doiboost construction process 2021-05-19 15:43:26 +02:00
Claudio Atzori 2cbf15f4fb using ModelConstants 2021-05-17 09:54:45 +02:00
Claudio Atzori f19feceaf0 set the old identifier before switching to the new one 2021-05-14 12:53:40 +02:00
Claudio Atzori 1bd70fa2c6 preserving the old identifier among the originalIds in the doiboost construction process 2021-05-14 11:30:41 +02:00
Claudio Atzori ca3f3a7687 using ModelConstants 2021-05-14 11:29:49 +02:00
Claudio Atzori 23b8883ab1 applied intellij code cleanup 2021-05-14 10:58:12 +02:00
Enrico Ottonello c537986b7c deleted folders with merged data immediately before merge phases 2021-04-28 11:25:25 +02:00
Claudio Atzori 5afa7d3e0c core utilities in dhp-common moved in external module dhp-schemas 2021-04-27 15:44:01 +02:00
Claudio Atzori e5abbec2ba [orcid] download of the lambda file defined in a script 2021-04-22 11:22:10 +02:00
Claudio Atzori 55964cbd81 [orcid] large oozie workflow cleanup; updated workflow for the orcidnodoi actionset creation 2021-04-22 10:18:09 +02:00
Claudio Atzori 52244f813a merging from enrico.ottonello/dnet-hadoop:orcid-no-doi 2021-04-21 12:24:09 +02:00
Sandro La Bruzzo a16e5299f9 applied unique function on the final dataset 2021-04-16 17:36:48 +02:00
Enrico Ottonello 27068aacd1 wf to move orcid-no-doi dataset on the folder ready the import 2021-04-16 17:17:47 +02:00
Sandro La Bruzzo 67085da305 fixed NPE 2021-04-16 11:05:58 +02:00
Sandro La Bruzzo 7d6a80e2f2 added new type on MAG mapping 2021-04-16 09:14:15 +02:00
Sandro La Bruzzo 3f77bfceb0 fixed test failure on jenkins 2021-04-14 10:03:01 +02:00
Sandro La Bruzzo 479abd10cb Add into ORCID workflow a method that extracts orcid directly to the dump generated by Enrico 2021-04-13 17:47:43 +02:00
Claudio Atzori e686b8de8d [ORCID-no-doi] integrating PR#98 D-Net/dnet-hadoop#98 2021-04-01 17:11:03 +02:00
Claudio Atzori ee34cc51c3 [ORCID-no-doi] integrating PR#98 D-Net/dnet-hadoop#98 2021-04-01 17:07:49 +02:00
Claudio Atzori 7941d7be29 WIP: using common definitions from ModelConstants 2021-03-31 18:33:57 +02:00
Enrico Ottonello 59ec5137e1 improvement related to https://issue.openaire.research-infrastructures.eu/issues/6501 2021-03-31 16:25:41 +02:00
Sandro La Bruzzo 616d2ecce2 splitted workflow collecting datacite into two workflows. 
Released on beta
 2021-03-31 15:45:58 +02:00
Sandro La Bruzzo 1dfda3624e improved workflow importing datacite 2021-03-26 13:56:29 +01:00
Enrico Ottonello ebd67b8c8f removed duplicates orcid data on authors set 2021-03-25 11:20:52 +01:00
Sandro La Bruzzo 625e4c29c4 added model constants 2021-03-23 09:39:56 +01:00
Sandro La Bruzzo c392936b97 fixed error on best access right 2021-03-23 09:23:22 +01:00
Sandro La Bruzzo c73072079d fix conflicts 2021-03-22 16:36:31 +01:00
Sandro La Bruzzo 098914dcff fix wrong relation with source null 2021-03-22 11:35:02 +01:00
Sandro La Bruzzo 25d5663d97 added filter 2021-03-18 10:24:42 +01:00
Sandro La Bruzzo 5f98ea74a9 Added fix for pid generation in stableIds 2021-03-17 15:53:24 +01:00
Sandro La Bruzzo cc5bbafa5d some fix to make workflows runs 2021-03-17 12:12:56 +01:00
Sandro La Bruzzo 4bb3bcafa5 add author sequence number 2021-03-11 11:32:32 +01:00
Sandro La Bruzzo a8e5d0ea0d updated test and fixed assign of access right 2021-03-11 10:41:24 +01:00
Sandro La Bruzzo f5e7c57654 Fixed ticket 6282 2021-03-11 10:32:45 +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
Sandro La Bruzzo a2169ccf07 // implemented Ticket #6281 added pid to Instance in doiBoost 2021-03-09 10:46:36 +01:00
Claudio Atzori 8d2bb24512 merged from master 2021-03-08 15:44:34 +01:00
Enrico Ottonello 70cb100647 added updating last orcid dataset folders after completion 2021-03-01 10:17:04 +01:00
Enrico Ottonello bd3b16402b added result typologies 2021-03-01 10:16:02 +01:00
Enrico Ottonello 53d7023460 dateOfCollection taken from orcid last_update.txt on hdfs; cleaned wf parameters 2021-02-25 18:43:29 +01:00
Enrico Ottonello d43ea88caf aligned orcid result typologies with openaire vocabulary 2021-02-25 15:02:10 +01:00
Enrico Ottonello 975823b968 data from last updated orcid 2021-02-23 15:35:04 +01:00
Enrico Ottonello ee4ba7298b fix last update read/write from file on hdfs 2021-02-09 23:24:57 +01:00
Enrico Ottonello c238561001 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi 2021-02-04 10:44:21 +01:00
Enrico Ottonello 465ce39f75 job execution now based on file last_update.txt on hdfs 2021-02-04 10:44:04 +01:00
Sandro La Bruzzo 99cf3a8ea4 Merged Datacite transfrom into this branch 2021-01-28 16:34:46 +01:00
Claudio Atzori ab2fe9266a [DOIBoost] minor fixes in workflow definition 2021-01-05 10:26:39 +01:00
Claudio Atzori 7c722f3fdc [DOIBoost] fixed typo 2021-01-05 10:25:54 +01:00
Claudio Atzori 8879704ba0 [DOIBoost] configurable ES server url and index name in crossref importer 2021-01-05 10:00:13 +01:00
Sandro La Bruzzo 7834a35768 avoid to save intermediate dataset before generation of Sequence file 2021-01-04 17:54:57 +01:00
Sandro La Bruzzo e79445a8b4 minor fix for claudio polemica 2021-01-04 17:39:25 +01:00
Sandro La Bruzzo 8765020b85 minor fix 2021-01-04 17:37:08 +01:00
Sandro La Bruzzo b0dc92786f defined a single oozie workflow for the generation of doiboost 2021-01-04 17:01:35 +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
Sandro La Bruzzo 1f6c8a9e83 added orcid_pending type to records coming from Crossref 2020-12-15 11:47:15 +01:00
Enrico Ottonello b2de598c1a all actions from download lambda file to merge updated data into one wf 2020-12-15 10:42:55 +01:00
Enrico Ottonello efe4c2a9c5 authors and works are now updated in two separate spark actions of the wf 2020-12-12 02:06:21 +01:00
Enrico Ottonello 858efbfad1 fix dataset creation for downloaded works 2020-12-11 16:49:54 +01:00
Claudio Atzori d9532446eb imported more diffs from master branch; code formatting 2020-12-10 16:14:16 +01:00
Claudio Atzori 12e2f930c8 resolved conflicts 2020-12-10 10:57:39 +01:00
Enrico Ottonello 2233750a37 original orcid xml data are stored in a field of the class that models orcid data 2020-12-09 09:45:19 +01:00
Sandro La Bruzzo 302baab67b fixed doiboost mapping and workflows 2020-12-07 19:59:33 +01:00
Enrico Ottonello 5c65e602d3 wf doi_authors generates one json data foreach row 2020-12-07 15:28:10 +01:00
Enrico Ottonello fa1855a4b8 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi 2020-12-07 11:02:59 +01:00
Enrico Ottonello b1b589ada1 wf to generate orcid dataset 2020-12-07 11:02:32 +01:00
Sandro La Bruzzo b31dd126fb fixed crossref workflow added common ORCID Class 2020-12-07 10:42:38 +01:00
Enrico Ottonello 8812ab65e1 completed download function to wf; added accumulators 2020-12-04 21:13:49 +01:00
Enrico Ottonello 53b22c1937 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi 2020-12-02 23:21:27 +01:00
Enrico Ottonello 1b1e9ea67c wf to generate doi_author_list for doiboost; wf to download updated works 2020-12-02 23:20:16 +01:00
Sandro La Bruzzo 7da679542f fixed wrong projectId 2020-12-02 14:28:09 +01:00
Sandro La Bruzzo 6ba8037cc7 fixed failure to test due to changing of input 2020-12-02 11:34:46 +01:00
Claudio Atzori cfb55effd9 code formatting 2020-12-02 11:23:49 +01:00
Enrico Ottonello f2df3ead74 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi 2020-11-30 14:22:46 +01:00
Enrico Ottonello 40c4559e92 added datainfo on authors pid with "sysimport:crosswalk:entityregistry", 2020-11-30 14:19:22 +01:00
Claudio Atzori a104d2b6ad cleanup 2020-11-26 11:12:00 +01:00
Claudio Atzori db0181b8af Merge pull request 'added bidirectionality to relations from project and result coming from crossref' (#60) from miriam.baglioni/dnet-hadoop:sxBidirectionality into master 2020-11-25 17:17:40 +01:00
Sandro La Bruzzo ec3e238de6 Fixed problem on duplicated identifier 2020-11-25 17:15:54 +01:00
Sandro La Bruzzo 264723ffd8 updated stuff for zenodo upload 2020-11-25 11:56:07 +01:00
Enrico Ottonello 99a086f0c6 max concurrent executors set to 10, according to ORCID Director of Technology mail request 2020-11-24 17:49:32 +01:00
Miriam Baglioni 00874a8ce6 added bidirectionality to relations from project and result 2020-11-24 15:17:23 +01:00
Enrico Ottonello 5c17e768b2 set wf configuration with spark.dynamicAllocation.maxExecutors 20 over 20 input partitions 2020-11-23 16:01:23 +01:00
Enrico Ottonello 97c8111847 action to convert lambda file in seq file; spark action to download updated authors 2020-11-23 09:49:22 +01:00
Enrico Ottonello c0c2e05eae added wf to extracting authors and works xml data from orcid dump to hdfs; added wf to download the lamda file (containing last orcid update informations) from orcid to hdfs 2020-11-17 18:23:12 +01:00
Enrico Ottonello 005f849674 added compression to output dataset 2020-11-13 12:45:31 +01:00
Enrico Ottonello 9a2fa9dc2f added test for other names parsing from summaries dump 2020-11-13 10:25:34 +01:00
Enrico Ottonello 13f28fa225 moved AuthorData to dhp-schemas; added other names to author data 2020-11-12 17:43:32 +01:00
Claudio Atzori 9b0fb9e958 merged from master 2020-11-12 09:27:12 +01:00
Enrico Ottonello 1f861f2b0d now wf output is a sequence file with the format seq("eu.dnetlib.dhp.schema.oaf.Publication",eu.dnetlib.dhp.schema.action.AtomicActions) 2020-11-11 17:38:50 +01:00
Enrico Ottonello fea2451658 Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi 2020-11-10 11:49:43 +01:00
Enrico Ottonello 1513174d7e added further test case 2020-11-10 11:44:55 +01:00
Sandro La Bruzzo 8e1d43aab2 Implemented ID generation using IdentifierRecordFactory on DOIBoost 2020-11-09 11:53:55 +01:00
Sandro La Bruzzo cd27df91a1 fixed bug on missing relation in ANDS 2020-11-06 17:12:31 +01:00
Enrico Ottonello 6bc7dbeca7 first version of dataset successful generated from orcid dump 2020 2020-11-06 13:47:50 +01:00
Sandro La Bruzzo 39337d8a8a fixed test 2020-11-02 09:26:25 +01:00
Enrico Ottonello 9818e74a70 added dependency version in main pom.xml for orcid no doi 2020-10-22 16:38:00 +02:00
Enrico Ottonello 210a50e4f4 replaced null value 2020-10-22 16:24:42 +02:00
Enrico Ottonello a38ab57062 let run test methods 2020-10-22 15:43:50 +02:00
Enrico Ottonello 1139d6568d replaced null value with a more safe empty string as return value 2020-10-22 15:32:26 +02:00
Enrico Ottonello c58db1c8ea added filter on null value after map function 2020-10-22 15:11:02 +02:00
Enrico Ottonello 846ba30873 if typologies mapping fails, an exception will be propagated 2020-10-22 14:36:18 +02:00
Enrico Ottonello c3114ba0ae replaced null as return value with a more safe empty string 2020-10-22 14:21:31 +02:00
Enrico Ottonello c295c71ca0 added comment 2020-10-22 14:07:26 +02:00
Enrico Ottonello ab083f9946 propagate exception on parsing work (PR request) 2020-10-22 14:02:32 +02:00
sandro 3a81a940b7 solved bug on merge publication 2020-10-21 22:41:55 +02:00
Sandro La Bruzzo 34bf64c94f fixed export Scholexplorer to OpenAire 2020-10-13 08:47:58 +02:00