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Sync with NCBO upstream #10

Merged
merged 98 commits into from
Nov 29, 2023
Merged

Sync with NCBO upstream #10

merged 98 commits into from
Nov 29, 2023

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syphax-bouazzouni
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@syphax-bouazzouni syphax-bouazzouni commented Nov 29, 2023 •
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syphax-bouazzouni and others added 30 commits March 1, 2022 18:01
@syphax-bouazzouni
fix to use the unzipped file in the diff process
408314c
@syphax-bouazzouni
fix and update the way the diff output folder is computed
b10b9bf
@syphax-bouazzouni
adding gzip support
3ea86a9
@syphax-bouazzouni
Merge branch 'upstream' into pl/fix-diff-zip-and-output-folder-bugs
03b1c01
@syphax-bouazzouni
fix function argument default
3024620
@syphax-bouazzouni
add the owlapi_parser builder
a8711f5
@syphax-bouazzouni
use the owlapi_parser builder in the submission generate_rdf
6a1dcba
@syphax-bouazzouni
add the parsable? method to the submissions
1cec803
@syphax-bouazzouni
use zipped? in the master_file_path method
5360eb5
@syphax-bouazzouni
make the owlapi_parser builder private
3255281
@syphax-bouazzouni
use the uploadFilePath as path for missing_labels and obsolete_classes
de1a207
@syphax-bouazzouni
bring the uploadFilePath before doing the diff
4b46464
@syphax-bouazzouni
add url prefix replacement utilities functions to base model
e758198
@syphax-bouazzouni
update with the new replace_url_prefix_to_id in the base find
22aefee
@syphax-bouazzouni
update with the new replace_url_prefix_to_id every where its used
65740af
@syphax-bouazzouni
refactor rest mappings tests by extracting some commun methods
454e87d
@syphax-bouazzouni
add get_rest_mapping unit test
f365f83
@syphax-bouazzouni
save the created rest mapping id with the initializer
94eeb65
@syphax-bouazzouni
use replace_url_prefix_to_id in the get_rest_mapping method
dc35d50
@mdorf
improved exception handling for datatype mismatch errors
0b56a04
@mdorf
fixed a case described in ncbo/bioportal-project#251
9358ab4
@mdorf
another fix to ncbo/bioportal-project#251
5922343
@mdorf
a partial fix to ncbo/bioportal-project#251
a00dac9
@mdorf
Gemfile.lock update
6080753
@alexskr
Bump up version of actions/checkout
323696d 
to address node.js 12 deprecation warning
@alexskr
Remove duplicate file
a9a28f4
@jvendetti
New version of the owlapi-wrapper JAR (v 1.4.1)
8628abe
@alexskr
Merge branch 'develop'
4f9139d
@alexskr
Use dedicated solr containers for term search and property search.
fb024ac 
Split up single solr container hosting both term search and property
search into to two separate solr containers running single core each.
This simplifies core creation command in docker-compose file.
@syphax-bouazzouni
Merge branch 'master' into pl/enhance-zipped-submissions-support
29153b6
mdorf and others added 28 commits September 5, 2023 15:14
@mdorf
fixed unit tests after merging ncbo/goo#138 and ncbo/goo#139
9f5c7e3
@mdorf
Gemfile.lock update
69b6e60
@mdorf
had to remove a redundant block of code during merge
629aa39
@mdorf
Gemfile.lock update
663baa3
@mdorf
Merge branch 'ontoportal-lirmm-pl/enhance-zipped-submissions-support'
aae2e20
@mdorf
Merge pull request #144 from master
f797d9d
@mdorf
fix for pull request #144
e33a0e4
@mdorf
Merge staging for release
6f88452
@mdorf
fixed Gemfile after merging from master
89474fa
@alexskr
fix mimitype string for gzip files
7d26cfb 
application/x-gzip is a deprecated mimetype
add unit test for determining gzip mimetype
@alexskr
fix filename
5ddd9ae
@alexskr
parse sumbission for .gz file to test gzip support
72c950a
@alexskr
Revert "parse sumbission for .gz file to test gzip support"
8d1209e 
This reverts commit 72c950a.
@alexskr
add unit test for parsing gzipped submission
4f9fcd3
@syphax-bouazzouni
use "zlib" to read and unzip Gz files and raise an error if unsupport…
ce4d2c4 
…ed file submitted
@syphax-bouazzouni
make sure the gzip process test assert that parsed content is not empty
299a01c
@alexskr
Merge pull request #174 from ontoportal-lirmm/pl/enhance-zipped-submi…
711ebf2 
…ssions-support

Fix: Enhance zipped submissions support - follow up
@alexskr
Merge branch 'develop'
f430fd3
@alexskr
Gemfile.lock update
a7ad210
@syphax-bouazzouni
Merge remote-tracking branch 'upstream/master' into upstream
8615bca
@syphax-bouazzouni
make the slice acronym validator not accepting underscores
c9e05b2
@mdorf
Merge pull request #176 from ontoportal-lirmm/pr/feature/extend-slice…
d5bbed1 
…-acronym-validator

Merging in order to fulfill a dependency required by ncbo/ontologies_api#87
@mdorf
merged PR #176 and updated Gemfile.lock
ff10e5f
@mdorf
Gemfile.lock update
32e93d5
@mdorf
added more informative exception output to cases of bad data
5600020
@jvendetti
New version of the owlapi-wrapper JAR (v 1.4.2)
9487c7f
@alexskr
Merge branch 'develop'
c391037
@alexskr
Gemfile update
7783784
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@syphax-bouazzouni syphax-bouazzouni merged commit f36641f into ontoportal:master Nov 29, 2023
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5 participants
@syphax-bouazzouni @codecov-commenter @mdorf @alexskr @jvendetti