D-Net
/
dnet-hadoop
14
5
Fork 11
Code Issues 14 Pull Requests 12 Projects 2 Releases 2 Wiki Activity
4,677 Commits 99 Branches 20 Tags 658 MiB
Commit Graph

362 Commits

Author SHA1 Message Date
Sandro La Bruzzo ae4e99a471 Adapted workflow of resolution of PID to work into OpenAIRE data workflow 
- Added relations in both verse on all Scholexplorer datasources
 2021-10-20 17:12:16 +02:00
Miriam Baglioni 1cc09adfaa Opencitations: chenaged the test class to mirror the creation or not of duplicate dois for .refs oc original plus added optional parameter to duplicate the relation 2021-10-18 14:11:27 +02:00
Sandro La Bruzzo 7b15b88d4c renamed wrong package, implemented last aggregation workflow for scholexplorer 2021-10-15 15:00:15 +02:00
Sandro La Bruzzo 51a03c0a50 refactor code for EBI from dhp-graph-mapper into dhp-aggregation 2021-10-14 14:23:13 +02:00
Sandro La Bruzzo 7387416e90 added params skip update to direct transform in OAF, this should be set to true in production 2021-10-12 12:36:30 +02:00
Sandro La Bruzzo 511da98d0c - fixed bug on download pmc Article 
- removed unused line of code in SparkCreateActionset
 2021-10-12 11:47:49 +02:00
Sandro La Bruzzo 5606014b17 code refactor see ticket #7065 2021-10-12 08:11:53 +02:00
Sandro La Bruzzo 66702b1973 Added node to update datacite 2021-09-28 08:59:06 +02:00
Miriam Baglioni 5ec69889db OpenCitations: creation of AS from OC 2021-09-27 16:02:06 +02:00
Miriam Baglioni f2118d771a first steps in the implementation of the integration of opencitations 2021-09-22 15:18:05 +02:00
Claudio Atzori 663b1556d7 manually integrating PR#140 #140 2021-09-15 16:40:25 +02:00
Sandro La Bruzzo aed29156c7 changed behavior in transformation job, that doesn't fail at first error 2021-09-07 19:05:46 +02:00
Sandro La Bruzzo 3c6fc2096c fix bug on oai iterator that skip record cleaned 2021-09-07 10:46:26 +02:00
Sandro La Bruzzo e8b3cb9147 Implemented method to download delta updates in EBI Links 2021-08-30 09:32:45 +02:00
Claudio Atzori 3359f73fcf cleanup & best practices 2021-08-13 12:00:42 +02:00
Miriam Baglioni 32fd75691f refactoring 2021-08-13 10:15:42 +02:00
Miriam Baglioni 5cd5714530 GetCSV refactoring - added ignore annotation for fields not in input csv 2021-08-13 10:06:49 +02:00
Miriam Baglioni 8769dd8eef GetCSV refactoring - refactoring due to movement of classes 2021-08-12 18:20:56 +02:00
Miriam Baglioni 6b9e1bf2e3 GetCSV refactoring - removing not needed dependency 2021-08-12 18:17:50 +02:00
Miriam Baglioni 335a824e34 GetCSV refactoring - fixed issue 2021-08-12 18:10:10 +02:00
Miriam Baglioni f0845e9865 GetCSV refactoring - refactoring due to movement of classes 2021-08-12 18:04:58 +02:00
Miriam Baglioni 7a789423aa GetCSV refactoring - refactoring due to movement of classes 2021-08-12 18:04:27 +02:00
Miriam Baglioni e9fc3ef3bc GetCSV refactoring - changed to use the new class to get and write the csv file 2021-08-12 18:03:41 +02:00
Miriam Baglioni 4317211a2b GetCSV refactoring - refactoring due to movement 2021-08-12 18:03:14 +02:00
Miriam Baglioni b62cd656a7 GetCSV refactoring - changed the model to store only the information needed 2021-08-12 18:01:10 +02:00
Miriam Baglioni d36e925277 GetCSV refactoring - moved under model package 2021-08-12 18:00:21 +02:00
Miriam Baglioni 6e84b3951f GetCSV refactoring - moving classes to dhp-common that have dependency with GetCSV class (that was located in graph-mapper) 2021-08-12 17:57:41 +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 2ee21da43b suggestions from SonarLint 2021-08-11 12:13:22 +02:00
Miriam Baglioni 1d6ac3715b merge branch with beta 2021-07-30 11:58:29 +02:00
Sandro La Bruzzo 3721df7aa6 refactoring create actionset of scholexplorer, moved on package dhp-aggregation 2021-07-29 10:45:35 +02:00
Sandro La Bruzzo 3d8f0f629b implemented workflow of creation action set for scholexplorer 2021-07-28 16:15:34 +02:00
Miriam Baglioni cc0d3d8a7b mergin with branch beta 2021-07-28 11:24:46 +02:00
Miriam Baglioni 708d0ade34 Merge branch 'beta' into hostedbymap 2021-07-28 10:37:22 +02:00
Sandro La Bruzzo 16c91203bd implemented workflow of creation action set for scholexplorer 2021-07-28 10:30:49 +02:00
Sandro La Bruzzo 825d9f0289 fixed datacite workflow starting from Importing delta 2021-07-27 16:09:46 +02:00
Miriam Baglioni 74f801b689 mergin with branch beta 2021-07-27 13:18:31 +02:00
Claudio Atzori a0393607a7 mapping funding relations from Datacite should be done according to the actual result identifier 2021-07-23 18:15:08 +02:00
Miriam Baglioni 63553a76b3 added code to download gold issn list from unibi 2021-07-22 12:01:48 +02:00
Sandro La Bruzzo bbe8193930 merged stable ids 2021-07-12 17:00:43 +02:00
Sandro La Bruzzo cd17e19044 implemented branch workflow to import datacite and crossref in scholexplorer 2021-07-08 21:20:19 +02:00
Claudio Atzori 777536ce91 [aggregation] string values used as regular expressions in the OAI collection classes are defined in a single point as constants, to be reused across the code (PR#122) 2021-07-07 11:23:48 +02:00
Claudio Atzori bc014023c8 Merge pull request 'to solve the scala SI-3623' (#122) from andreas.czerniak/BrStableId_dnet-hadoop:stable_ids into stable_ids 
Reviewed-on: #122
 2021-07-07 11:13:51 +02:00
Andreas Czerniak ebf3f47a02 from&until more OAI2.0 compl., adding tfs 2021-07-07 09:29:49 +02:00
Claudio Atzori 70ded407bb HttpClient used in metadata collection retries also on 404 2021-07-05 18:04:30 +02:00
Sandro La Bruzzo db933ebd21 Merge remote-tracking branch 'origin/stable_ids' into stable_id_scholexplorer 2021-06-29 14:16:12 +02:00
Sandro La Bruzzo 7e08655e5f added relation dates in all scholexplorer Datasources 2021-06-29 12:02:03 +02:00
Claudio Atzori af42377d0e HttpClient used in metadata collection retries on 502, 503, 504 2021-06-28 09:34:30 +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 5edcc6832a applying sonarLint suggestions 2021-06-23 09:53:29 +02:00
Sandro La Bruzzo 1dc0c59e20 merged fix thai dates from stable_ids 2021-06-21 10:39:46 +02:00
Sandro La Bruzzo 3990165d05 changed typologies of unresolved relation 2021-06-18 11:43:59 +02:00
Sandro La Bruzzo aeb8132627 Merged branch stable_ids 2021-06-14 10:07:29 +02:00
Claudio Atzori e9e86a237d Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids 2021-06-11 17:00:02 +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 dd997c49e0 fix wrong relation id 
fix date thai ticket #6791
 2021-06-10 14:47:18 +02:00
Sandro La Bruzzo 0cdb7ccdaa added inverse relations to datacite mapping 2021-06-04 15:10:20 +02:00
Sandro La Bruzzo 5b724d9972 added relations to datacite mapping 2021-06-04 10:14:22 +02:00
Claudio Atzori d512062b58 integrating pull #109, H2020Classification 2021-05-27 12:22:47 +02:00
Sandro La Bruzzo bced804151 updated wf Datacite Import to retrieve the block size as parameter 2021-05-26 17:06:50 +02:00
Miriam Baglioni 073d76864d refactoring 2021-05-21 14:41:03 +02:00
Miriam Baglioni 4c8b4a774c removed not needed code 2021-05-21 14:40:07 +02:00
Miriam Baglioni 1ee8f13580 refactoring and added "left" as join type to be 100% sure to get the whole set of projects 2021-05-21 11:49:05 +02:00
Miriam Baglioni e07c3ba089 due to change in the input file the filtering step is no more needed 2021-05-21 11:47:43 +02:00
Miriam Baglioni 7180505519 removed non needed variable 2021-05-21 11:46:13 +02:00
Miriam Baglioni 2eb1a8b344 changed because the input file changed 2021-05-21 11:40:20 +02:00
Claudio Atzori 9d725efdc1 reverted implementation of the mdstore client 2021-05-20 18:26:09 +02:00
Miriam Baglioni 052c837843 - 2021-05-20 15:54:44 +02:00
Claudio Atzori b695932ae4 integrated pull#108 2021-05-20 15:34:04 +02:00
Miriam Baglioni dc0ad8d2e0 fixed issue related to change in the file name downloaded. Added sheet name as parameter and also a check if the name should change 2021-05-20 14:53:53 +02:00
Claudio Atzori 239d0f0a9a ROR actionset import workflow backported from branch stable_ids 2021-05-18 16:12:11 +02:00
Michele Artini c1e20de7cf fixed the deserialization of a json property 2021-05-18 14:00:14 +02:00
Claudio Atzori 23b8883ab1 applied intellij code cleanup 2021-05-14 10:58:12 +02:00
Sandro La Bruzzo 6424cd9062 Added passing of the following parameters: 
-varDataSourceId
-varOfficialName

in Each transformation Rule
 2021-05-11 15:17:38 +02:00
Sandro La Bruzzo 073dcea2aa Added passing of the following parameters: 
-varDataSourceId
-varOfficialName

in Each transformation Rule
 2021-05-11 15:05:58 +02:00
Claudio Atzori 3797543600 MDStoreManager model classes moved in dhp-schemas 2021-05-10 14:32:05 +02:00
Michele Artini d82071ba6c originalId with prefix 2021-05-06 15:34:48 +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
Claudio Atzori ba86835951 using common constants from ModelConstants 2021-05-04 11:51:52 +02:00
Michele Artini a278d67175 parse input file 2021-04-29 11:34:47 +02:00
Michele Artini f77ba34126 pid types 2021-04-29 09:50:05 +02:00
Michele Artini 7c5cd86927 annotations and tests 2021-04-29 09:29:19 +02:00
Michele Artini b5cf505cc6 partial implementation of the ROR->actionset workflow 2021-04-28 16:00:24 +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 63c0303137 removed unused import, add log 2021-04-27 12:17:23 +02:00
Claudio Atzori fa42026590 fixed PersonCleaner extension functions 2021-04-27 10:10:06 +02:00
Claudio Atzori d0d477cca3 code formatting 2021-04-20 12:50:34 +02:00
Sandro La Bruzzo dbe0d0378e resolved ticket #6377 2021-04-20 09:44:44 +02:00
Sandro La Bruzzo 524e5f3092 Improved parallelization on transformation wf on hadoop 2021-04-19 15:17:25 +02:00
Sandro La Bruzzo cdfe01bbae improved parallelization on transformation job 2021-04-19 15:14:52 +02:00
Andreas Czerniak 3b694074ff add xslt, personname cleaner 2021-04-13 07:04:27 +02:00
Claudio Atzori 7941d7be29 WIP: using common definitions from ModelConstants 2021-03-31 18:33:57 +02:00
Claudio Atzori 879e8cc7ef WIP: using common definitions from ModelConstants 2021-03-31 17:12:01 +02:00
Claudio Atzori 72ce741ea6 WIP: using common definitions from ModelConstants 2021-03-31 17:07:13 +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
Sandro La Bruzzo c73072079d fix conflicts 2021-03-22 16:36:31 +01:00
Claudio Atzori 61a2551e74 migrated last changes from svn (dnet45) 2021-03-15 17:17:55 +01:00
Claudio Atzori acbe3119a4 RestCollectorPlugin imported from dne45 2021-03-08 09:44:09 +01:00
Claudio Atzori 36f750cd1d removed unused classes 2021-03-03 10:22:29 +01:00
Claudio Atzori b73dce3e3a more logging on the MDStore mongodb client. Forcing UTF_8 encoding on the content 2021-03-03 10:17:16 +01:00
Claudio Atzori e76c4f62c1 MetadataRecord moved in dhp-schemas 2021-02-26 10:58:48 +01:00
Claudio Atzori 7df2461ccc indent XML records collected from oai-pmh endpoints 2021-02-25 16:19:12 +01:00
Claudio Atzori b830e33392 mdstore collector plugin 2021-02-25 12:30:30 +01:00
Claudio Atzori 271e88537b code formatting 2021-02-25 12:28:56 +01:00
Claudio Atzori 9c899f4433 cleanup on transformation functions and the relative tests 2021-02-24 15:07:59 +01:00
Claudio Atzori fc3fa5e343 implemented mdstore collector plugin 2021-02-24 15:07:24 +01:00
Claudio Atzori e7eba9f7e7 WIP: transformation workflow error reporting; cleanup 2021-02-17 16:54:08 +01:00
Claudio Atzori 58467aaf1e WIP: transformation workflow error reporting 2021-02-17 16:14:41 +01:00
Claudio Atzori cc88701f29 retry for any Socket exception 2021-02-17 16:13:54 +01:00
Claudio Atzori 545f8f3e48 using jackson objectmapper instead of GSon to serialise the aggregation report 2021-02-17 12:15:00 +01:00
Claudio Atzori b592d78bb4 WIP: collectorWorker error reporting, generalised reported implementation 2021-02-17 10:28:01 +01:00
Claudio Atzori cf27905a71 WIP: collectorWorker error reporting, added report messages 2021-02-16 16:53:14 +01:00
Claudio Atzori 1abe6d1ad7 WIP: collectorWorker error reporting, added report messages 2021-02-15 15:08:59 +01:00
Claudio Atzori 523a6bfa97 Merge pull request 'first commit to the correct branch' (#94) from andreas.czerniak/BrAggr_dnet-hadoop:hadoop_aggregator into hadoop_aggregator 
Looks good to me, thanks Andreas!
 2021-02-15 12:15:31 +01:00
Sandro La Bruzzo 7edcc87ed4 changed xslt behaviour on failure 2021-02-12 17:27:08 +01:00
Sandro La Bruzzo b3f5c2351d Merge branch 'hadoop_aggregator' of code-repo.d4science.org:D-Net/dnet-hadoop into hadoop_aggregator 
 Conflicts:
	dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
 2021-02-12 16:37:14 +01:00
Sandro La Bruzzo f216277219 Implemented cleaning date 2021-02-12 16:34:52 +01:00
Andreas Czerniak 5a9017cf18 clone, min. changes, test, run 2021-02-12 14:32:36 +01:00
Claudio Atzori aa55dedb8a Merge branch 'hadoop_aggregator' of https://code-repo.d4science.org/D-Net/dnet-hadoop into hadoop_aggregator 2021-02-12 12:31:05 +01:00
Claudio Atzori 29c6f7e255 classes related to the collection workflow moved into common package; implemented MongoDB collection plugins 2021-02-12 12:31:02 +01:00
Sandro La Bruzzo 17e6f1934e fixed NPE on cleaner 2021-02-12 11:48:11 +01:00
Sandro La Bruzzo ebcc3ec14f updated wrong datacite identifier in trasformation 2021-02-11 16:25:51 +01:00
Claudio Atzori bae029f828 collection_java_xmx allows to declare the heap size allocated for the java actions involved in the metadata collectionw workflow 2021-02-08 18:07:23 +01:00
Claudio Atzori bebc54d5bf seq file storing native records is now compressed 2021-02-08 18:06:25 +01:00
Claudio Atzori 50add4c61b added requestDelay to HttpConnector2 configuration; Aggregation workflow constants moved in dhp-common 2021-02-08 12:19:38 +01:00
Claudio Atzori 40df0f987d better logging, WIP: collectorWorker error reporting; common functions moved in DHPUtils 2021-02-06 20:12:00 +01:00
Claudio Atzori a8a758925e better logging, WIP: collectorWorker error reporting 2021-02-05 19:18:05 +01:00
Claudio Atzori 730973679a Merge branch 'hadoop_aggregator' of https://code-repo.d4science.org/D-Net/dnet-hadoop into hadoop_aggregator 2021-02-04 17:25:00 +01:00
Claudio Atzori deb85706db imported HttpConnector from https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-modular-collector-service/trunk/src/main/java/eu/dnetlib/data/collector/plugins/HttpConnector.java as HttpConnector2 2021-02-04 17:24:52 +01:00
Sandro La Bruzzo 4dae5e605d implemented messaging btween collection worker and Dnet 2021-02-04 15:51:15 +01:00
Claudio Atzori 40764cf626 better logging, WIP: collectorWorker error reporting 2021-02-04 14:06:02 +01:00
Claudio Atzori e04045089f better logging, WIP: collectorWorker error reporting 2021-02-03 17:58:22 +01:00
Claudio Atzori 0e8a4f9f1a better logging, WIP: collectorWorker error reporting 2021-02-03 12:33:41 +01:00
Claudio Atzori ac46c247d2 code formatting 2021-02-02 14:24:00 +01:00
Claudio Atzori bde14b149a fixed transformation target paths 2021-02-02 12:49:29 +01:00
Claudio Atzori ca4391aa1c minor changes 2021-02-02 12:44:04 +01:00
Claudio Atzori bb89b99b24 code formatting 2021-02-02 12:34:14 +01:00
Claudio Atzori 75807ea5ae factored out constants 2021-02-02 12:28:21 +01:00
Sandro La Bruzzo 0634674add implemented transformation test 2021-02-02 12:12:14 +01:00
Claudio Atzori 8eaa1fd4b4 WIP: metadata collection in INCREMENTAL mode and relative test 2021-02-01 19:29:10 +01:00
Sandro La Bruzzo bead34d11a code refactor 2021-02-01 14:58:06 +01:00
Sandro La Bruzzo 6ff234d81b Implemented a first prototype of incremental harvesting and trasformation using readlock 2021-02-01 13:56:05 +01:00
Sandro La Bruzzo b6b835ef49 update transformation Factory to get Transformation Rule by Id and not by Title 2021-02-01 08:49:42 +01:00
Sandro La Bruzzo 8ee82576c6 Collection on Refresh WORKS!!! 2021-01-29 17:02:46 +01:00
Sandro La Bruzzo 0276180039 WIP mdstore 
transaction implemented on hadoop side
 2021-01-29 16:42:41 +01:00
Sandro La Bruzzo 0f8e2ecce6 Merged Datacite transfrom into this branch 2021-01-29 10:45:07 +01:00
Sandro La Bruzzo 99cf3a8ea4 Merged Datacite transfrom into this branch 2021-01-28 16:34:46 +01:00