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
Claudio Atzori
41b551562e
applying PR#115 (DatePicker) on stable_ids
2021-06-17 09:33:50 +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
Claudio Atzori
74833d04f1
Merge branch 'pids_beta' of https://code-repo.d4science.org/antonis.lempesis/dnet-hadoop into stable_ids
2021-06-16 15:54:18 +02:00
Claudio Atzori
7243a40c88
code formatting
2021-06-16 15:03:03 +02:00
Sandro La Bruzzo
dfcf78cf24
removed wrong code
2021-06-16 14:57:42 +02:00
Sandro La Bruzzo
cc0f2b11fb
Implemented mapping from pubmed baseline to OAF
2021-06-16 14:56:24 +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
Antonis Lempesis
f7c0b80e35
storing result_instance as parquet
2021-06-15 14:45:48 +03:00
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
4da141bd7c
Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids
2021-06-14 13:41:02 +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
Michele Artini
ada063ce70
fixed a problem with empty mdstore list (2)
2021-06-14 12:04:47 +02:00
Michele Artini
83132ee99a
fixed a problem with empty mdstore list
2021-06-14 11:57:00 +02:00
Miriam Baglioni
cf360d7c97
Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids
2021-06-14 10:19:49 +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
aeb8132627
Merged branch stable_ids
2021-06-14 10:07:29 +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
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: D-Net/dnet-hadoop#112
2021-06-14 09:23:55 +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
Antonis Lempesis
d413b24611
added instances, orgs for monitor, totalcost for projects, apcs
2021-06-10 02:35:46 +03:00
Claudio Atzori
741077dbca
Merge pull request 'Fix in Affiliation Propagation' ( #113 ) from miriam.baglioni/dnet-hadoop:master into stable_ids
...
Reviewed-on: D-Net/dnet-hadoop#113
2021-06-09 18:42:42 +02:00
Miriam Baglioni
32b0c27217
Aggiornare 'dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java'
...
fix in SQL query: while writing the blacklist constraint it used d.id to indicate the datasource id, but no alias for the datasource was defined. So I removed the alias
2021-06-09 18:36:11 +02:00
Sandro La Bruzzo
0d1f37302f
Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_id_scholexplorer
2021-06-09 09:35:16 +02:00
Miriam Baglioni
dc07f1079b
added check in case the author set to be enriched is null
2021-06-08 12:06:10 +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
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
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
Sandro La Bruzzo
02ef46535f
Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_ids
2021-05-31 09:50:15 +02:00
Sandro La Bruzzo
aeadc5a366
updated wf Datacite Import to retrieve the block size as parameter
2021-05-31 09:49:53 +02:00
Claudio Atzori
96238152cb
added serialization for alternateIdentifiers and pids within each record instance
2021-05-28 16:57:30 +02:00
Michele Artini
ad56a44fda
save as gzipped sequence file
2021-05-28 14:45:39 +02:00
Claudio Atzori
83722ebc47
pull #111 replied on stable_ids
2021-05-28 14:11:46 +02:00
Claudio Atzori
6e3a4e9237
updated test expectations
2021-05-28 09:37:50 +02:00
Michele Artini
4fa5671d16
first implementation of Hdfs Mdstores Importer
2021-05-27 16:22:07 +02:00
Claudio Atzori
d512062b58
integrating pull #109 , H2020Classification
2021-05-27 12:22:47 +02:00
Claudio Atzori
5e4b91d9ef
more pervasive use of constants from ModelConstants, especially for ORCID
2021-05-26 18:20:23 +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
abd88f663d
changed test resource to mirror change in the input file
2021-05-21 15:20:47 +02:00
Miriam Baglioni
c844877de2
changed workflow flow to possibly parallelize also the programme and project preparation steps
2021-05-21 14:41:57 +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
Enrico Ottonello
abdd0ade1f
added temporary output folder as workflow parameter
2021-05-21 12:08:16 +02:00
Miriam Baglioni
53b9d87fec
new prepareProgramme according to the new file
2021-05-21 11:49:31 +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
54f6e2f693
changed to get the needed information to build the action set as parallel jobs
2021-05-21 11:47:00 +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
Enrico Ottonello
d0945c3c78
added temporary output folder, because of folder access rights are different on beta and prod
2021-05-20 19:14:31 +02:00
Enrico Ottonello
1265dadc90
workflow aligned with stable_ids
2021-05-20 19:01:28 +02:00
Enrico Ottonello
0821d8e97d
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi
2021-05-20 18:33:18 +02:00
Enrico Ottonello
ae7bd24d79
removed old workflows
2021-05-20 18:32:22 +02:00
Claudio Atzori
9d725efdc1
reverted implementation of the mdstore client
2021-05-20 18:26:09 +02:00
Miriam Baglioni
9610224671
added param to workflow property
2021-05-20 18:21:12 +02:00
Claudio Atzori
863b56b6ce
using constants from ModelConstants
2021-05-20 16:23:58 +02:00
Claudio Atzori
ae5c28e54f
code formatting
2021-05-20 16:13:06 +02:00
Miriam Baglioni
aa45b4df9b
-
2021-05-20 15:57:40 +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
Claudio Atzori
ea9b00ce56
adjusted test
2021-05-20 15:31:42 +02:00
Claudio Atzori
b572f56763
Merge branch 'master' into master
2021-05-20 15:22:35 +02:00
Claudio Atzori
2578b7fbb3
code formatting
2021-05-20 14:59:02 +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
232dce83db
fixes #6701 : xpath for titles to support both datacite and Guidelines v4 mapping
2021-05-20 14:41:15 +02:00
Claudio Atzori
aef2977ad0
fixes #6701 : xpath for titles to support both datacite and Guidelines v4 mapping
2021-05-20 14:40:22 +02:00
Miriam Baglioni
02b80cf24f
resolved conflicts
2021-05-20 10:59:39 +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
239d0f0a9a
ROR actionset import workflow backported from branch stable_ids
2021-05-18 16:12:11 +02:00
Antonis Lempesis
168edcbde3
added the final steps for the observatory promote wf and some cleanup
2021-05-18 15:23:20 +03:00
Michele Artini
e56ccec536
Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_ids
2021-05-18 14:00:28 +02:00
Michele Artini
c1e20de7cf
fixed the deserialization of a json property
2021-05-18 14:00:14 +02:00
Claudio Atzori
a9f512103b
using constants from ModelConstants
2021-05-18 11:19:07 +02:00
Claudio Atzori
eeb8bcf075
using constants from ModelConstants
2021-05-18 11:10:07 +02:00
Claudio Atzori
2cbf15f4fb
using ModelConstants
2021-05-17 09:54:45 +02:00
Enrico Ottonello
e13926cdd0
merged with master
2021-05-14 18:10:31 +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
Claudio Atzori
609eb711b3
IndexRecordTransformerTest for producing a record that can be manually submitted to solr
2021-05-13 16:13:28 +02:00
Claudio Atzori
1517bf7c92
IndexRecordTransformerTest for producing a record that can be manually submitted to solr
2021-05-13 16:11:22 +02:00
Sandro La Bruzzo
d9a0bbda7b
implemented new phase in doiboost to make the dataset Distinct by ID
2021-05-13 12:25:14 +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
d4c3476152
mapping datasource.journal only when an issn is available, null otherwhise
2021-05-11 11:08:54 +02:00
Claudio Atzori
da9d6f3887
mapping datasource.journal only when an issn is available, null otherwhise
2021-05-11 10:45:30 +02:00
Sandro La Bruzzo
54217d73ff
removed old parameters from oozie workflow
2021-05-11 09:59:02 +02:00
Claudio Atzori
d1cbee8413
imported methods from CleaningFunctions, defined in GraphCleaningFunctions
2021-05-10 16:43:39 +02:00
Claudio Atzori
3797543600
MDStoreManager model classes moved in dhp-schemas
2021-05-10 14:32:05 +02:00
Claudio Atzori
25254885b9
[ActionManagement] reduced number of xqueries used to access ActionSet info
2021-05-07 17:32:03 +02:00
Claudio Atzori
8a0de2fc18
[ActionManagement] reduced number of xqueries used to access ActionSet info
2021-05-07 17:31:32 +02:00
Sandro La Bruzzo
7dc824fc23
imported changes in stable_id into master
2021-05-07 12:53:50 +02:00
Michele Artini
d82071ba6c
originalId with prefix
2021-05-06 15:34:48 +02:00
Claudio Atzori
d4a30fabe3
clean up tests
2021-05-05 17:28:15 +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
8c96a82a03
fixed mapping applied to ODF records. Added unit test to verify the mapping for OpenTrials
2021-05-05 15:30:06 +02:00
Claudio Atzori
2e1eb96f9a
code formatting
2021-05-05 11:23:57 +02:00
Sandro La Bruzzo
1adfc41d23
merged manually changes on stable_id for doiboost into master
2021-05-05 10:23:32 +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
Claudio Atzori
ba86835951
using common constants from ModelConstants
2021-05-04 11:51:52 +02:00
Michele Artini
f4bd2b5619
recert file SparkDedupTest.java
2021-05-04 10:26:14 +02:00
Michele Artini
b4877da363
Merge branch 'stable_ids' into prepare_ror_actionset
2021-05-03 08:13:55 +02:00
Alessia Bardi
9a20057615
fixed query for organisations' pids
2021-04-29 15:23:39 +02:00
Michele Artini
6692128234
Merge branch 'stable_ids' into prepare_ror_actionset
2021-04-29 13:24:08 +02:00
Alessia Bardi
a801999e75
fixed query for organisations' pids
2021-04-29 12:18:42 +02:00
Michele Artini
a278d67175
parse input file
2021-04-29 11:34:47 +02:00
Claudio Atzori
f6ccd54d87
Merge branch 'stable_ids' of https://code-repo.d4science.org/D-Net/dnet-hadoop into stable_ids
2021-04-29 10:10:01 +02:00
Claudio Atzori
91e7220f20
cleaned up workflow for actionset migration, adjusted dnet|cnr* dependency versions
2021-04-29 10:09:52 +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
Enrico Ottonello
c537986b7c
deleted folders with merged data immediately before merge phases
2021-04-28 11:25:25 +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
Alessia Bardi
e6075bb917
updated json schema for results - added instances and accessright definition
2021-04-27 15:15:08 +02:00
Sandro La Bruzzo
63c0303137
removed unused import, add log
2021-04-27 12:17:23 +02:00
Sandro La Bruzzo
74484d2823
bug fixing
2021-04-27 12:13:44 +02:00
Sandro La Bruzzo
c74b03d59c
Merge branch 'stable_ids' of code-repo.d4science.org:D-Net/dnet-hadoop into stable_ids
2021-04-27 11:31:07 +02:00
Sandro La Bruzzo
7f8848ecdd
added first implementation of Pangaea Mapping
2021-04-27 11:30:37 +02:00
Claudio Atzori
27ab8a704d
adjusted poms to align with the external dhp-schema module
2021-04-27 10:12:27 +02:00
Claudio Atzori
a7cf449b36
cleanup
2021-04-27 10:11:26 +02:00
Claudio Atzori
fa42026590
fixed PersonCleaner extension functions
2021-04-27 10:10:06 +02:00