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Author SHA1 Message Date
mvdbeek 3af877573a Cleanup add_index/drop_index 2020-10-02 11:41:37 +02:00
mvdbeek d97606186c Add missing indexes 2020-10-01 20:21:08 +02:00
mvdbeek 04186715e9 Drop unused models 2020-10-01 20:21:08 +02:00
mvdbeek 812015421d Drop msg from _archive_composite_dataset signature 2020-09-30 15:32:03 +02:00
Marius van den Beek acfa2663cf Merge pull request #15 from nsoranzo/simplify__archive_composite_dataset 
Simplify `Data._archive_composite_dataset()`
 2020-09-30 15:25:38 +02:00
Nicola Soranzo 5ce78cb5cd Simplify Data._archive_composite_dataset() 2020-09-30 12:21:20 +01:00
mvdbeek a980a65b8d Fix composite data download from collection 
We wrongly pass hdca (and element_identifier) into
_archive_composite_dataset, which breaks downloading composite datasets
from a collection. Fixes
https://sentry.galaxyproject.org/sentry/main/issues/290622/:
```
Exception: Unknown parameter type (<class 'galaxy.model.HistoryDatasetCollectionAssociation'>)
  File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__
    iterable = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 33, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 141, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 220, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 186, in display
    return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd)
  File "galaxy/datatypes/data.py", line 444, in display_data
    return self._archive_composite_dataset(trans, data, **kwd)
  File "galaxy/datatypes/data.py", line 266, in _archive_composite_dataset
    params = util.Params(kwd)
  File "galaxy/util/__init__.py", line 822, in __init__
    self.__dict__[key] = sanitize_param(value)
  File "galaxy/util/__init__.py", line 596, in sanitize_param
    raise Exception('Unknown parameter type (%s)' % (type(value)))
```
 2020-09-30 12:05:34 +02:00
Nicola Soranzo 9d3d5cb757 Merge pull request #10302 from dannon/backport-dependabot 
[20.09] Backport tensorflow bump by dependabot.
 2020-09-26 00:52:19 +01:00
John Chilton 4c778a4a52 Merge pull request #10301 from dannon/fix-quotameter-backport 
[20.09] Revise quota meter style - backport.
 2020-09-25 19:22:15 -04:00
dependabot[bot] 167ee545d6 Tape resource used based on a cuttoff date 2020-09-25 16:14:12 -04:00
guerler 9fbd70ed7d Revise quota meter style 2020-09-25 14:44:15 -04:00
Marius van den Beek 79791acd62 Merge pull request #10295 from mvdbeek/datatype_test_fix_backport 
[20.09] Backport #10272 datatype test fix
 2020-09-25 15:28:52 +02:00
Nicola Soranzo 5a3028c61b Merge branch 'release_20.05' into release_20.09 2020-09-25 12:40:23 +01:00
Marius van den Beek 3ba6e80316 Merge pull request #10293 from ic4f/2009_anndata_fix 
[20.09] Fix tuple assignment (fixes anndata, scanpy tool tests)
 2020-09-25 10:51:54 +02:00
Simon BrayandNicola Soranzo d7ab012060 clarify comment on api test 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-09-25 10:48:09 +02:00
Simon Bray 53357e4199 fix test 2020-09-25 10:48:09 +02:00
Simon Bray 87936d1f1d change to RequestParameterInvalidException 2020-09-25 10:48:09 +02:00
Simon Bray 261f7391fc use cat_data_and_sleep tool for datatype change api test 2020-09-25 10:48:09 +02:00
Marius van den Beek ae2f67066a Merge pull request #10242 from torfinnnome/release_20.05 
[20.05] Make cached container resolver pick newest build
 2020-09-25 10:40:24 +02:00
Sergey Golitsynskiy fa3829df97 Fix tuple assignment 
tuple() expects iterable; just use values in parens instead.
 2020-09-24 23:10:16 -04:00
Dannon 74df929899 Merge pull request #10286 from mvdbeek/fix_histories_shared_with_me_message 
[20.09] Fix histories shared with me message
 2020-09-24 16:29:01 -04:00
mvdbeek 9c1426d6bb Fix histories shared with me message 
Fixes https://github.com/galaxyproject/galaxy/issues/10285
 2020-09-24 18:04:47 +02:00
Dannon 5341fcb9e2 Merge pull request #10282 from mvdbeek/bump_up_log_level 
[20.09] Bump up failing job log message to info
 2020-09-24 10:46:43 -04:00
Marius van den Beek f86469310c Merge pull request #10281 from mvdbeek/persist_tool_cache_data_dir 
[20.09] Persist tool_cache_data_dir tag if specified
 2020-09-24 16:39:30 +02:00
mvdbeek b66afca107 Bump up failing job log message to info 2020-09-24 16:23:42 +02:00
mvdbeek 6a50c67463 Persist tool_cache_data_dir tag if specified 
We noticed that the tag was getting lost when installing new tools,
this fixes that.
 2020-09-24 15:39:42 +02:00
Dannon Baker b99f14eda3 Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 2020-09-23 21:29:26 -04:00
Dannon Baker f27a6fa081 Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 2020-09-23 21:07:42 -04:00
Dannon 806f2f235d Merge pull request #10274 from almahmoud/filtering_20.01 
Backporting #10266 to 20.01
 2020-09-23 20:42:15 -04:00
Alexandru Mahmoud 7944706467 filtering.py check_expression adding 'Constant' 2020-09-23 16:57:26 -04:00
Marius van den Beek f1bfa2ae5c Merge pull request #10269 from ic4f/release_20.09 
[20.09] Remove references to missing types from sample config file
 2020-09-23 10:03:55 +02:00
Sergey Golitsynskiy d167848b3e Remove references to missing types from sample config file 2020-09-22 21:46:01 -04:00
Dannon bfd4172968 Merge pull request #10263 from mvdbeek/fix_optional_input_submission 
[20.09] Fix submission via UI of workflows with optional inputs
 2020-09-22 15:01:14 -04:00
Marius van den Beek f31291554f Merge pull request #10261 from mvdbeek/version-20.09 
Update version to 20.09.rc1
 2020-09-22 16:18:24 +02:00
mvdbeek e46273060c Update version to 20.09.rc1 2020-09-22 16:17:09 +02:00
mvdbeek ebcf9e67bd Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-09-22 16:16:19 +02:00
mvdbeek 95bb58d739 Fix submission via UI of workflows with optional inputs 
A typical payload from the UI looks like this:
```
{'0': None, '1': {'hid': 56, 'id': '0fe36ab5a28e309f', 'keep': False, 'name': 'Select first on data 55', 'src': 'hda', 'tags': [...]}}
```
where '0' is an optional data input step.
Just skipping `None` inputs should be fine here.
 2020-09-22 16:08:05 +02:00
Dannon 95045eb75f Merge pull request #10259 from mvdbeek/dev 
Merge 20.05 into dev
 2020-09-22 10:07:52 -04:00
mvdbeek 8ef1a8f51e Make force_datatype a computated property 
This is effectively the same as
https://github.com/galaxyproject/galaxy/pull/10237 which doesn't apply
to dev anymore.
 2020-09-22 15:19:34 +02:00
Torfinn Nome 2b76855e3e Replace tag with version 
I assume you meant version and not tag here.
 2020-09-22 13:58:42 +02:00
mvdbeek b6c43e40ba Merge branch 'release_20.05' into dev 2020-09-22 13:26:05 +02:00
Torfinn Nome 2014062833 Merge pull request #1 from mvdbeek/cached_resolver_image_sorting 
Make sure cached images are properly sorted by build build_number and…
 2020-09-22 13:05:37 +02:00
Marius van den Beek bae72b948a Merge pull request #9915 from xgaia/release_20.05_askomics_it_4.0.0 
Update AskOmics IT to askomics 4.0.0
 2020-09-22 12:24:18 +02:00
Marius van den Beek 3c53c5085e Merge pull request #10199 from juleengraham/existing-acct-error 
Display proper clientside error
 2020-09-22 12:16:39 +02:00
Marius van den Beek c905535745 Merge pull request #9374 from simonbray/add-ext 
Add dataset deserializer for 'datatype'
 2020-09-22 12:12:41 +02:00
mvdbeek 234cc4f9cf Make sure cached images are properly sorted by build build_number and build_version 2020-09-22 11:28:14 +02:00
Simon Bray 1d7c20bf0e update exception message 2020-09-22 11:15:51 +02:00
Marius van den Beek 69e0ff772a Merge pull request #9744 from juleengraham/tool-search 
Allow tool search on tool id and wildcard before search string
 2020-09-22 11:09:39 +02:00
Simon Bray 0b5499916b fix assertion 2020-09-22 10:31:12 +02:00
Simon Bray a55a606e20 changes to datatype change test 2020-09-22 10:11:32 +02:00