Nicola Soranzo
8fbecfefff
Disallow also fastapi 0.70.1
2022-01-06 19:21:15 +00:00
Nicola Soranzo
a28880ea37
Specify galaxybot as commit author
2022-01-06 05:15:11 +00:00
ic4f
5cb4314ebb
Update Python dependencies
2022-01-01 03:14:02 +00:00
Björn Grüning
f978de75ac
Merge pull request #13078 from martenson/parquet_converter
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add implicit parquet>csv converter
2021-12-28 17:35:14 +01:00
Marius van den Beek
a3ac2ab611
Merge pull request #12940 from nuwang/vault_impl
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Vault abstraction for Galaxy
2021-12-27 18:59:13 +01:00
Marius van den Beek
aeddd9c34c
Merge pull request #13102 from bioflowy/disable_cleanup_thread_in_set_metadata
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Disable cleanup thread for cloud object store in set metadata
2021-12-24 11:09:09 +01:00
Uehara.Keizo
009760b6d0
open cache file with binary mode
2021-12-23 01:33:14 +00:00
Uehara.Keizo
992f18e127
Disable cleanup thread of cloud objectstore in set_metadata.py
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Apply the following fixes for s3.py to cloud.py
Be more explcit about starting cache monitor thread 494c15cb9d6a56f3a5de7a63fd1db2
2021-12-23 01:32:16 +00:00
Nuwan Goonasekera
01ca66fa98
Merge branch 'dev' into vault_impl
2021-12-22 23:55:37 +05:30
Sergey Golitsynskiy
bf58b5cc30
Merge pull request #13099 from ic4f/dev_migratetools
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Drop tool migration scripts and related code
2021-12-21 14:35:35 -05:00
Sergey Golitsynskiy
263f2db982
Drop tool_migration_manager and all references to it (see note)
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The from_tool_migration_manager parameter as False as its default value.
The only case where it's called with the value True is when it's called
from the from_tool_migration_manager module - which is now deleted.
Therefore, now the value is always False and, therefore, it is safe to
drop this parameter and adjust the code that checks its value accordingly.
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
af270403c0
Fix packages test: do not import deleted packages
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
ecebe46831
Drop get_executable(): no longer used
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
ddc95d8456
Delete migrate directory
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
8682e49016
Remove unused parameter
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
bc6f766d5a
Update migrated_tools_config schema description, run config-rebuild
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
91af9c51ed
Run make config-rebuild
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
5f87739c60
Remove references to check_migrate_tools
2021-12-21 10:54:28 -05:00
Martin Cech
fad9eeab89
import the pyarrow modules explicitly
2021-12-21 10:34:27 +01:00
Marius van den Beek
f041b13d36
Merge pull request #13048 from bernt-matthias/topic/fix-optional-column-select
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Fix dynamic optional + multiple select parameters: allow to select no option
2021-12-21 10:13:57 +01:00
Marius van den Beek
9244f6ed1f
Merge pull request #13073 from qiagu/ludwig
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Add ludwig model datatype
2021-12-21 10:10:14 +01:00
Marius van den Beek
9debf1fc6e
Merge pull request #13082 from bernt-matthias/topic/doc-param-metadata
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Add documentation for test/param/metadata in xsd
2021-12-21 10:08:56 +01:00
Marius van den Beek
9c92c1bde9
Merge pull request #12500 from nuwang/papercut_file_sources
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File sources for gdrive, gcs, onedata, basespace
2021-12-21 10:08:24 +01:00
Marius van den Beek
98248892ea
Merge pull request #13097 from davelopez/beta_history_additional_collection_fixes
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Beta History: additional small fixes at collection level
2021-12-21 09:53:15 +01:00
Qiang Gu and Sergey Golitsynskiy
fb76243737
Update lib/galaxy/datatypes/binary.py
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Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com >
2021-12-20 11:55:50 -08:00
Nuwan Goonasekera
0924628d10
Refactor file source tests
2021-12-21 00:56:17 +05:30
Nuwan Goonasekera
5d72ddba11
Make gcsfs test optional
2021-12-21 00:43:39 +05:30
davelopez
e9ebc20a67
Fix DatasetCollection.isHomogeneous condition
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HDCAs provide `elements_datatypes` property but `DatasetCollection` instances don't.
2021-12-20 18:23:21 +01:00
Martin Cech
1b8e5af742
import whole library instead of modules
2021-12-20 18:17:26 +01:00
davelopez
4ee67bf14a
Fix DatasetCollection.totalElements condition
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- The `element_count` property sometimes exists but is null, so the paired condition may never be evaluated.
2021-12-20 18:02:24 +01:00
davelopez
7e3f757dca
Move Download collection button to CollectionOperations
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- Create the CollectionOperations component as a toolbar for operations on collections
- Move the Download Collection button from the top `localNav` to the `listcontrols` slot. The button was quite hidden up there and also, if the name of the collection was long, it was completely inaccesible.
2021-12-20 17:22:19 +01:00
Sergey Golitsynskiy
36e4c33210
Merge pull request #13067 from quacksawbones/dev
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Change default `file_path` variable for galaxy reports
2021-12-20 10:39:40 -05:00
Martin Cech
17766735c0
remove lint
2021-12-20 16:10:19 +01:00
Martin Cech
127a817043
update test file names
2021-12-20 16:04:16 +01:00
Nuwan Goonasekera
e8cb3d789c
Merge pull request #12345 from almahmoud/data_pvc
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Separated data PVC
2021-12-20 19:32:22 +05:30
Nuwan Goonasekera and Enis Afgan
d4fe61a424
Update vault docs
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Co-authored-by: Enis Afgan <afgane@gmail.com >
2021-12-20 18:40:20 +05:30
Nuwan Goonasekera
be9f210901
Change vault api test case to integration test case and add missing conditional requirements
2021-12-20 18:23:00 +05:30
Nuwan Goonasekera and Marius van den Beek
592603eb41
Add file upload test to vault
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-20 18:00:53 +05:30
Marius van den Beek
81cf9c57d7
Merge pull request #13074 from bioflowy/dev
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Fix Cloud object store
2021-12-20 13:05:15 +01:00
Marius van den Beek
ce062553ca
Merge pull request #13088 from nsoranzo/reports_startup_gh_wf
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Add tox environment and GitHub workflow for reports startup test
2021-12-20 13:03:02 +01:00
Nuwan Goonasekera
d1f804921c
Add support for anonymous gcs file source access
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
15b7b88d8b
Streamline access tokens needed to run gcsfs and gdrive storage tests
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
cb22970426
Added support for illumina basespace filesource
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
d1185fcd18
Added one data
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
b8bdb6878e
Added file source for google cloud storage
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
71862f540c
Use separate env vars for each required param in google drive credentials
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
482fb2827c
Added google drive to conditional requirements
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
ae8a832b7b
Added unit tests for google drive file source
2021-12-20 11:08:42 +05:30
Nuwan Goonasekera
9bb6ec20f7
Added google drive file source
2021-12-20 11:08:41 +05:30
Nuwan Goonasekera
2ed66ea25a
Refactor extra pvc volume handling in k8s
2021-12-19 20:32:24 +05:30
Nicola Soranzo