Miriam Baglioni
fd48ae3b85
changed because of #40 (comment)
2020-08-13 12:19:15 +02:00
Miriam Baglioni
04a3e1ab38
disabled tests
2020-08-13 12:18:13 +02:00
Miriam Baglioni
2ede397933
Apply change because of #40 (comment)
2020-08-13 12:16:39 +02:00
Miriam Baglioni
bfd1fcde6d
removed not useful method and changed because of #40 (comment) and #40 (comment)
2020-08-13 12:14:37 +02:00
Miriam Baglioni
7fd8397123
apply changes in #40 (comment)
2020-08-13 12:13:15 +02:00
Miriam Baglioni
753d448cc9
apply changes in #40 (comment)
2020-08-13 12:12:58 +02:00
Miriam Baglioni
c0e071fa26
apply changes in #40 (comment)
2020-08-13 12:12:40 +02:00
Miriam Baglioni
526db915bc
apply changes in #40 (comment)
2020-08-13 12:12:16 +02:00
Miriam Baglioni
b0fab0d138
apply changes in #40 (comment)
2020-08-13 12:11:57 +02:00
Miriam Baglioni
1b6320b251
apply changes in #40 (comment)
2020-08-13 12:11:41 +02:00
Miriam Baglioni
743d31be22
apply changes in #40 (comment)
2020-08-13 12:11:22 +02:00
Miriam Baglioni
65b48df652
apply changes in #40 (comment)
2020-08-13 12:11:06 +02:00
Miriam Baglioni
90b54d3efb
apply changes in #40 (comment)
2020-08-13 12:08:24 +02:00
Miriam Baglioni
69bbb9592a
apply changes in #40 (comment)
2020-08-13 12:07:39 +02:00
Miriam Baglioni
945323299a
apply changes in #40 (comment)
2020-08-13 12:07:24 +02:00
Miriam Baglioni
e04c993247
apply changes in #40 (comment)
2020-08-13 12:07:07 +02:00
Miriam Baglioni
ed0812d0ce
apply changes in #40 (comment)
2020-08-13 12:06:49 +02:00
Miriam Baglioni
d55cfe0ea5
apply changes in #40 (comment)
2020-08-13 12:06:20 +02:00
Miriam Baglioni
80866bec7d
apply changes in #40 (comment)
2020-08-13 12:06:05 +02:00
Miriam Baglioni
1400978c0a
apply changes in #40 (comment)
2020-08-13 12:05:44 +02:00
Miriam Baglioni
7b941a2e0a
apply changes in #40 (comment)
2020-08-13 12:05:17 +02:00
Miriam Baglioni
f7474f50fe
apply changes in #40 (comment)
2020-08-13 12:04:52 +02:00
Miriam Baglioni
367203f412
apply changes in #40 (comment)
2020-08-13 12:04:33 +02:00
Miriam Baglioni
3ab4809d31
apply changes in #40 (comment)
2020-08-13 12:04:10 +02:00
Miriam Baglioni
02a4986e7b
Applying changed from code reviews #40 (comment) and #40 (comment) and #40 (comment)
2020-08-13 11:53:01 +02:00
Miriam Baglioni
235d4e4d6e
moved Context as relevant for Communities dump
2020-08-12 18:16:45 +02:00
Miriam Baglioni
adf9f96a67
test for extraction of relation between organizations and context
2020-08-12 10:04:47 +02:00
Miriam Baglioni
7400cd019d
removed not needed variable
2020-08-12 10:03:33 +02:00
Miriam Baglioni
98d28bab5c
fixed missing _ in context nsprefix
2020-08-12 10:00:18 +02:00
Miriam Baglioni
8f48cb29f4
changed resource because of a change in the XQuery that returned the XML to be parsed. The main Zenodo community is no more a separate element, but part of the <zenodocommunities> element
2020-08-11 18:04:38 +02:00
Miriam Baglioni
c3672b162b
merge branch with master
2020-08-11 17:53:04 +02:00
Miriam Baglioni
a16bbf3202
changed test resource to mirror change in the Xquery that produced data to be parsed. The main Zenodo community it is no more provided in a different element, but it is part of the <zenodocommunities>
2020-08-11 17:48:44 +02:00
Miriam Baglioni
25f4fbceea
draft of test and resources
2020-08-11 17:37:22 +02:00
Miriam Baglioni
30a2b19b65
changed metadata for deposition od covid-19 dump in Zenodo
2020-08-11 17:36:56 +02:00
Claudio Atzori
f7cc52ab02
Merge pull request 'enrichment_wfs' ( #39 ) from enrichment_wfs into master
...
LGTM
2020-08-11 17:26:13 +02:00
Miriam Baglioni
49788b532a
changed to mirror changes in the schema
2020-08-11 16:05:03 +02:00
Miriam Baglioni
b08511287b
-
2020-08-11 16:01:36 +02:00
Miriam Baglioni
7e81a17068
changed the XQUERY to mirror the change in the code
2020-08-11 16:00:33 +02:00
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
77a390878c
merge upstream
2020-08-11 15:45:48 +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
Sandro La Bruzzo
fe8d640aee
fixed error on oozie workflow
2020-08-11 09:43:03 +02:00
304590e854
updated workflow of indexing to start from begin
2020-08-11 09:17:47 +02:00
eaf0dc68a2
fixed indexing
2020-08-11 09:17:03 +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
Claudio Atzori
cf6b68ce5a
Merge pull request 'data provision workflow: add nodes to perform DELETE BY QUERY before the indexing begins and COMMIT after the indexing is completed' ( #36 ) from provision_indexing into master
2020-08-10 11:16:29 +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
Sandro La Bruzzo
ddb1446ceb
fixed test
2020-08-07 11:34:33 +02:00
Sandro La Bruzzo
718bc7bbc8
implemented provision workflows using the new implementation with Dataset
2020-08-07 11:05:18 +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
a44e5abaa7
reformat code
2020-08-06 10:30:22 +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
88e4c3b751
added default trust to context bulktagged
2020-08-04 10:13:25 +02:00
Miriam Baglioni
f9342cb484
added constant
2020-08-03 18:32:35 +02:00
Miriam Baglioni
96c3c891f4
added trust
2020-08-03 18:32:17 +02:00
Miriam Baglioni
53656600ad
changed XQuery to select only community and ri with status not hidden
2020-08-03 18:29:30 +02:00
Miriam Baglioni
b34177d8ef
merge upstream
2020-08-03 18:13:42 +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
Claudio Atzori
3a11a387a9
data provision workflow enhancement: added nodes to perform DELETE BY QUERY before the indexing begins and COMMIT after the indexing is completed
2020-08-03 14:28:08 +02:00
Alessia Bardi
8cc067fe76
specific test for claims
2020-08-03 11:17:50 +02:00
Claudio Atzori
a89b6cc3ba
Merge pull request 'nsprefix_blacklist' ( #34 ) from nsprefix_blacklist into master
2020-07-31 11:52:23 +02:00
0c3bc9ea4b
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-31 09:07:18 +02:00
168bfb496a
adopted dedup to the new schema
2020-07-31 09:06:57 +02:00
Michele Artini
652b13abb6
Merge branch 'master' into nsprefix_blacklist
2020-07-31 07:58:37 +02:00
Enrico Ottonello
0377b40fba
output to one parquet file
2020-07-30 18:38:07 +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
Enrico Ottonello
196f36c6ed
fix publication dataset creation
2020-07-30 13:38:33 +02:00
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
9e997e63a2
merge upstream
2020-07-29 17:38:14 +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
Michele Artini
8ba94833bd
added an es prop
2020-07-29 14:16:08 +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
Enrico Ottonello
c82b15b5f4
migrate configuration to ocean, fix publication dataset creation
2020-07-28 15:23:52 +02:00
Claudio Atzori
6f11c0496e
fixed typo in module name dhp-worfklow-profiles -> dhp-workflow-profiles
2020-07-28 15:01:58 +02:00
Claudio Atzori
f680eb3e12
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
2020-07-28 14:10:56 +02:00
Claudio Atzori
985b360c31
fixed typo in module name dhp-worfklow-profiles -> dhp-workflow-profiles
2020-07-28 14:10:52 +02:00
Michele Artini
3acd632123
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-28 12:02:30 +02:00
Michele Artini
35e6e9c064
tests
2020-07-28 12:02:15 +02:00
Enrico Ottonello
a6acb37689
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi
2020-07-28 08:07:40 +02:00
Claudio Atzori
ee832f358e
Merge pull request 'stats_wf_extensions_and_corrections' ( #28 ) from spyros/dnet-hadoop:stats_wf_extensions_and_corrections into master
...
Thank you Guys! The update workflow will be made available to the beta & production orchestration systems under the HDFS path
```/lib/dnet/oa/graph/stats/oozie_app```
2020-07-27 16:02:03 +02:00
Antonis Lempesis
4ac8ebe427
correctly calculating the project duration
2020-07-24 19:50:40 +03:00
Antonis Lempesis
18d9464b52
creating shadow db only if it not exists...
2020-07-24 19:50:40 +03:00
Antonis Lempesis
e217d496ab
added the dest db...
2020-07-24 19:50:40 +03:00
Antonis Lempesis
b16bb68b9f
added the target db name...
2020-07-24 19:50:40 +03:00
Antonis Lempesis
1ee7eeedf3
added the source db name...
2020-07-24 19:50:40 +03:00
Antonis Lempesis
cecbbfa0fc
added missing tables and views: contexts, creation_date, funder
2020-07-24 19:50:40 +03:00
Antonis Lempesis
25b7a615f5
moved datasource_sources table creating in the datasource section
2020-07-24 19:50:40 +03:00
Antonis Lempesis
a8da4ab9c0
years in projects are now integers
2020-07-24 19:50:40 +03:00
Antonis Lempesis
c9cfc165d9
not using impala since the resulting tables are not visible
2020-07-24 19:50:40 +03:00
Antonis Lempesis
dd3d6a6e15
compute stats for the used and new impala tables
2020-07-24 19:50:40 +03:00
Antonis Lempesis
e6f50de6ef
Separated impala from hive steps
2020-07-24 19:50:40 +03:00
Antonis Lempesis
de49173420
fixed a typo in queries
2020-07-24 19:50:40 +03:00
391cf80fb8
Added peer-reviewed, green, gold tables and fields in result. Added shortcuts from result-country
2020-07-24 19:50:40 +03:00
68389d0125
Corrected the script used by the last step of the wf
2020-07-24 19:50:40 +03:00
ec52141f1a
changed refereed type from value to clssname
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
63cd797aba
Comment out step 15 to make it work with the new schema of Claudio
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
138c6ddffa
Insert statement to datasource table that takes into account the piwik_id of the openAIRE graph
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
3630794cef
Fix to consider the relationships that have been 'virtually deleted' for project_results - defect #5607
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
5546f29e63
Corrections on the shadow schema and the impala table stats calculation
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
adf8a025d2
Adding more relations (Sources, Licences, Additional) and shadow schema as provided and discussed with Antonis Lempesis
2020-07-24 19:50:40 +03:00
Spyros Zoupanos
657a40536b
Corrections by Spyros: Scipt cleanup, corrections and re-arrangement
2020-07-24 19:50:40 +03:00
477fa6234d
Script re-organisation and adding table invalidations needed for impala
2020-07-24 19:50:40 +03:00
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
2a15494b16
merge upstream
2020-07-20 18:05:01 +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
b904e0699a
-
2020-07-20 18:02:53 +02:00
Miriam Baglioni
3aab7680f6
changed the test results
2020-07-20 18:00:43 +02:00
Miriam Baglioni
cde0300801
moved from projects to project
2020-07-20 17:57:35 +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
Claudio Atzori
0937c9998f
Merge branch 'deduptesting'
2020-07-20 10:00:20 +02:00
Claudio Atzori
de72b1c859
cleanup
2020-07-20 09:59:11 +02:00
Michele Artini
331a3cbdd0
fixed originalId
2020-07-20 09:50:29 +02:00
Michele Artini
c59c5369b1
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-18 09:40:54 +02:00
Michele Artini
346a1d2b5a
update eventId generator
2020-07-18 09:40:36 +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
d7d84c8217
-
2020-07-17 14:03:23 +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
Michele Artini
3adedd0a68
trust truncated to 3 decimals
2020-07-17 11:58:11 +02:00
Claudio Atzori
1781609508
code formatting
2020-07-16 19:06:56 +02:00
Claudio Atzori
db8b90a156
renamed CORE -> BETA
2020-07-16 19:05:13 +02:00
Miriam Baglioni
44e1c40c42
merge upstream
2020-07-16 18:49:38 +02:00
Claudio Atzori
878f2b931c
Merge branch 'master' into merge_graph
2020-07-16 16:34:24 +02:00
Claudio Atzori
cc5d13da85
introduced parameter shouldIndex (true|false)
2020-07-16 13:46:39 +02:00
Claudio Atzori
b098cc3cbe
avoid repeating identical values for fields: source, description
2020-07-16 13:45:53 +02:00
Claudio Atzori
805de4eca1
fix: filter the blocks with size = 1
2020-07-16 10:11:32 +02:00
Claudio Atzori
4b9fb2ffb8
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
2020-07-15 11:26:04 +02:00
Claudio Atzori
b90389bac4
code formatting
2020-07-15 11:24:48 +02:00
Claudio Atzori
4e6f46e8fa
filter blocks with one record only
2020-07-15 11:22:20 +02:00
Michele Artini
262c29463e
relations with multiple datasources
2020-07-15 09:18:40 +02:00
Claudio Atzori
7d6e269b40
reverted CreateRelatedEntitiesJob_phase1 to its previous state
2020-07-13 22:54:04 +02:00
Claudio Atzori
8e97598eb4
avoid to NPE in case of null instances
2020-07-13 20:46:14 +02:00
Claudio Atzori
06def0c0cb
SparkBlockStats allows to repartition the input rdd via the numPartitions workflow parameter
2020-07-13 20:09:06 +02:00
b52c246aed
merge done
2020-07-13 19:57:02 +02:00
b8a45041fd
minor changes
2020-07-13 19:53:18 +02:00
Claudio Atzori
66f9f6d323
adjusted parameters for the dedup stats workflow
2020-07-13 19:26:46 +02:00
03ecfa5ebd
implementation of the test class for the new block stats spark action
2020-07-13 18:48:23 +02:00
10e08ccf45
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-13 18:22:45 +02:00
9258e4f095
implementation of a new workflow to compute statistics on the blocks
2020-07-13 18:22:34 +02:00
Claudio Atzori
c6f6fb0f28
code formatting
2020-07-13 16:46:13 +02:00
Claudio Atzori
8d2102d7d2
Merge branch 'deduptesting'
2020-07-13 16:32:43 +02:00
Claudio Atzori
344a90c2e6
updated assertions in propagateRelationTest
2020-07-13 16:32:04 +02:00
Claudio Atzori
1143f426aa
WIP SparkCreateMergeRels distinct relations
2020-07-13 16:13:36 +02:00
Claudio Atzori
8c67938ad0
configurable number of partitions used in the SparkCreateSimRels phase
2020-07-13 16:07:07 +02:00
Claudio Atzori
c73168b18e
Merge branch 'deduptesting' of https://code-repo.d4science.org/D-Net/dnet-hadoop into deduptesting
2020-07-13 15:54:58 +02:00
Claudio Atzori
c8284bab06
WIP SparkCreateMergeRels distinct relations
2020-07-13 15:54:51 +02:00
Sandro La Bruzzo
1d133b7fe6
update test
2020-07-13 15:52:41 +02:00
Michele Artini
3635d05061
poms
2020-07-13 15:52:23 +02:00
Claudio Atzori
7dd91edf43
parsing of optional parameter
2020-07-13 15:40:41 +02:00
Claudio Atzori
4c101a9d66
WIP SparkCreateMergeRels distinct relations
2020-07-13 15:31:38 +02:00
Claudio Atzori
8a612d861a
WIP SparkCreateMergeRels distinct relations
2020-07-13 15:30:57 +02:00
Sandro La Bruzzo
9ef2385022
implemented test for cut of connected component
2020-07-13 15:28:17 +02:00
Sandro La Bruzzo
d561b2dd21
implemented cut of connected component
2020-07-13 14:18:42 +02:00
Miriam Baglioni
8e0e090d7a
merge upstream
2020-07-13 12:46:55 +02:00
Claudio Atzori
e2093e42db
Merge branch 'master' into deduptesting
2020-07-13 10:57:49 +02:00
Michele Artini
2c4ed9a043
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-13 10:55:39 +02:00
Michele Artini
ccbe5c5658
fixed import of eu.dnetlib.dhp:dnet-openaire-broker-common
2020-07-13 10:55:27 +02:00
Claudio Atzori
7a3fd9f54c
dedup relation aggregator moved into dedicated class
2020-07-13 10:11:36 +02:00
Alessia Bardi
7e96105947
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
2020-07-12 19:29:12 +02:00
Alessia Bardi
b7a39731a6
assert, not print
2020-07-12 19:28:56 +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
770adc26e9
WIP aggregator to make relationships unique
2020-07-10 19:35:10 +02:00
Claudio Atzori
ecf119f37a
Merge branch 'master' into deduptesting
2020-07-10 19:04:16 +02:00
Claudio Atzori
31071e363f
Merge branch 'provision_indexing'
2020-07-10 19:03:57 +02:00
Claudio Atzori
06c1913062
added different limits for grouping by source and by target, incremented spark.sql.shuffle.partitions for the join operations
2020-07-10 19:03:33 +02:00
Claudio Atzori
cc77446dc4
added dbSchema parameter to the raw_db workflow
2020-07-10 19:01:50 +02:00
Claudio Atzori
4c3836f62e
materialize the related entities before joining them
2020-07-10 19:00:44 +02:00
Michele Artini
e1ae964bc4
stats
2020-07-10 16:12:08 +02:00
Claudio Atzori
752d28f8eb
make the relations produced by the dedup SparkPropagateRelation jon unique
2020-07-10 15:09:50 +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
b21866a2da
allow to set different to relations cut points by source and by target; adjusted weight assigned to relationship types
2020-07-10 13:59:48 +02:00
Claudio Atzori
ff4d6214f1
experimenting with pruning of relations
2020-07-10 10:06:41 +02:00
Miriam Baglioni
faea30cda0
-
2020-07-09 14:05:21 +02:00
Michele Artini
2d742a84ae
DedupConfig as json file
2020-07-09 12:53:46 +02:00
Miriam Baglioni
a634794242
merge upstream
2020-07-09 11:46:51 +02:00
Michele Artini
a44b9b36b9
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-09 11:02:31 +02:00
Michele Artini
1c6a171633
updated pom
2020-07-09 11:02:09 +02:00
Claudio Atzori
3c728aaa0c
trying to overcome OOM errors during duplicate scan phase
2020-07-08 22:39:51 +02:00
Claudio Atzori
18c555cd79
Merge branch 'master' into deduptesting
2020-07-08 22:32:01 +02:00
Claudio Atzori
4365cf41d7
trying to overcome OOM errors during duplicate scan phase
2020-07-08 22:31:46 +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
Alessia Bardi
853e8d7987
test for software merge
2020-07-08 17:03:53 +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
Claudio Atzori
e2ea30f89d
updated graph construction workflow definition: cleaning wf moved at the bottom to include cleaning of the information produced by the enrichment workflows
2020-07-08 12:16:24 +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
Michele Artini
dffa0b01a2
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-07 15:37:29 +02:00
Michele Artini
efadbdb2bc
fixed a bug with duplicated events
2020-07-07 15:37:13 +02:00
Claudio Atzori
8af8e7481a
code formatting
2020-07-07 14:23:34 +02:00
Claudio Atzori
b383ed42fa
pass optional parameter relationFilter to the PrepareRelationJob implementation
2020-07-07 14:21:28 +02:00
Claudio Atzori
911894a987
Merge branch 'deduptesting'
2020-07-07 14:20:43 +02:00
Miriam Baglioni
c19818a3f8
merge branch with fork master
2020-07-06 13:58:23 +02:00
Miriam Baglioni
d22240c0ba
merge upstream
2020-07-06 13:58:02 +02:00
Enrico Ottonello
ca37d3427b
separate workflow to parse orcid summaries, activities and generate dataset with no doi publications; test
2020-07-03 23:30:31 +02:00
Michele Artini
edf6c6c4dc
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-03 11:48:24 +02:00
Michele Artini
04bebb708c
some fixes
2020-07-03 11:48:12 +02:00
Enrico Ottonello
1729cc5cf3
publication conversion from json to oaf test
2020-07-02 18:46:20 +02:00
Claudio Atzori
c3d67f709a
adjusted dedup configuration for result entities: using new wordssuffixprefix clustering function, removed ngrampairs, adjusted queueMaxSize (800) and slidingWindowSize (80)
2020-07-02 17:35:22 +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
Miriam Baglioni
c133a23cf0
merge upstream
2020-07-02 14:24:57 +02:00
Claudio Atzori
1d39f7901c
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
2020-07-02 12:45:01 +02:00
Claudio Atzori
0f77cac4b5
fix: deduper must use queueMaxSize instead of groupMaxSize for the block definition
2020-07-02 12:43:51 +02:00
Sandro La Bruzzo
18b9330312
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-02 12:43:19 +02:00
Michele Artini
b413db0bff
white/blacklists
2020-07-02 12:43:03 +02:00
Claudio Atzori
d380b85246
unit test for the preparation of the relations
2020-07-02 12:42:13 +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
07f0723fa7
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
2020-07-02 12:37:49 +02:00
Miriam Baglioni
Claudio Atzori
Sandro La Bruzzo
Sandro La Bruzzo
Alessia Bardi
Michele Artini
Enrico Ottonello
Antonis Lempesis
antleb
Spyros Zoupanos
Giorgos Alexiou
miconis