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20410 Commits
Author SHA1 Message Date
Helena Rasche c545aaf4d4 [19.05] Add shapefile datatype (#7819) 
[19.05] Add shapefile datatype
 2019-05-02 10:18:40 +02:00
John Chilton 6297ca6556 Rev pulsar for latest fixes. 
Should fix the problem when that same input is sent to a tool more than once.
 2019-05-01 09:03:33 -04:00
Dannon Baker 642c97e1b7 Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-01 08:54:27 -04:00
Nate Coraor 1994c3598f Merge pull request #7855 from mvdbeek/fix_workflow_extraction 
[19.01] Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset
 2019-04-30 14:48:40 -04:00
Nicola Soranzo 170bd027cd [19.01] Use just the env name when checking `CONDA_DEFAULT_ENV` (#7853) 
[19.01] Use just the env name when checking ``CONDA_DEFAULT_ENV``
 2019-04-30 19:36:06 +01:00
Kidane M. Tekle 14628e1fe7 added elixir oidc backend, python soical auth version upgraded 2019-04-30 19:21:19 +02:00
Nicola Soranzo 96ed324131 Ensure that also $CONDA_DEFAULT_ENV is just the env name 
That's not the case e.g. for conda 4.1.1 when using `conda_exec` not inside `conda_prefix`.
 2019-04-30 17:49:49 +01:00
mvdbeek 4af1c0a6cc Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset 
To test this run a tool that generates discovered datsets twice,
with the second run taking the first output as input.
 2019-04-30 18:31:19 +02:00
mvdbeek 8fd0652d76 CONDA_DEFAULT_NAME is just the env name 
This will still write the conda activate part out multiple times,
but fix the check that would otherwise lead to repeated activation
of the conda env. Fixes the slowness reported in https://github.com/galaxyproject/galaxy/issues/7849
 2019-04-30 14:02:42 +02:00
Björn Grüning cf6f104313 add remove the logging, thanks Marius 2019-04-30 13:50:26 +02:00
Björn Grüning 5000d290ed remove logging module 2019-04-30 13:41:47 +02:00
Bjoern Gruening 102b619c43 make tests stricter 2019-04-30 09:47:06 +02:00
Aysam Guerler ea7f9c6326 Merge pull request #7749 from dannon/fix_user_reg 
Fix automatic user registration
 2019-04-30 02:07:23 -04:00
mvdbeek 7303ee6777 Open tempfile in writing mode for python3 compatibility 2019-04-30 00:26:59 +02:00
Bérénice Batut 3dc68dbe92 Add extra column metadata check for minimal biom1 file 2019-04-29 18:59:25 +01:00
John Chilton 7b4b6336ca Update version to 19.05.rc1 2019-04-29 08:45:32 -04:00
John Chilton d008e47303 Merge remote-tracking branch 'upstream/release_19.01' into dev 2019-04-29 08:43:11 -04:00
Marius van den Beek 2d0a68429d Merge pull request #7832 from pcm32/patch-3 
Fix failure in resubmitting job more than once
 2019-04-29 10:48:50 +02:00
Nicola Soranzo 084296c92a Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-04-27 00:09:31 +01:00
Bjoern Gruening 89996dcd93 remove redundant datatype def 2019-04-26 22:34:20 +02:00
Pablo Moreno 96256b21f0 Fix failure in resubmitting job more than once 2019-04-26 18:42:38 +01:00
John Chilton 003cdb83fd Merge pull request #7823 from mvdbeek/fix_token_replacement_py3 
Fix nested macro/token expansion on python 3
 2019-04-26 10:59:38 -04:00
John Chilton c0291c4267 Merge pull request #7826 from mvdbeek/fix_value_wrapper_comparison 
Fix InputValueWrapper gt/ge/lt/le comparisons
 2019-04-26 10:58:13 -04:00
Dannon Baker c20a6d139d Drop autoregistration flag; we'll use create instead. 2019-04-26 09:42:13 -04:00
mvdbeek 8886558e3d Allow specifying maxseconds in verify_tool 
And passing in tool_test_dicts, which shouold be helpful when
testing tools with many tests.
 2019-04-26 10:31:06 +02:00
guerler d3ba390bf0 Do not store password of autoregistration users 2019-04-25 21:32:41 -04:00
guerler ee0ae1c972 Use trans to access config 2019-04-25 20:58:24 -04:00
guerler 53aa894d3b Remove unused variables 2019-04-25 20:52:51 -04:00
guerler d726ff0a06 Call create instead of register in autoregistration 2019-04-25 20:48:50 -04:00
mvdbeek 60d87107ee Fix InputValueWrapper gt/ge/lt/le comparisons 2019-04-25 21:32:47 +02:00
mvdbeek 77ae679746 Fix nested macro/token expansion on python 3 
I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
 2019-04-25 19:51:25 +02:00
Dannon Baker cd704719e4 Typo... 2019-04-25 13:45:07 -04:00
Martin Cech 6c460bab23 Merge pull request #7812 from nsoranzo/fix_7809 
Encode email messages using UTF-8
 2019-04-24 22:01:14 -04:00
John Chilton 616446e09f Merge pull request #7799 from mvdbeek/fix_parameter_workflow_outputs 
Don't let parameter_input steps be workflow outputs
 2019-04-24 17:16:42 -04:00
Nicola Soranzo 88c35132d0 Encode email messages using UTF-8 
Fix https://github.com/galaxyproject/galaxy/issues/7809
 2019-04-24 20:12:02 +01:00
John Chilton 343e6e4cd3 Merge pull request #7786 from natefoo/job-fail-destination-loop 
[19.01] Fix the use of JobMappingException
 2019-04-24 14:00:27 -04:00
mvdbeek 9f18fcf10a Skip recording workflow outputs for input parameters 
These can come in as a literal parameter value, or as a dictionary like
{'id': 'encoded_id', 'src': 'hda'}, none of which is quite right.
 2019-04-24 18:25:20 +02:00
Dannon e34951f436 Merge pull request #7806 from nsoranzo/api_get_nonexistent_dataset 
Return HTTP 400 for `GET /api/datasets/nonexistent_id`
 2019-04-24 12:11:54 -04:00
Dannon Baker f86a982958 Fix filterlist for registration params 2019-04-24 10:43:18 -04:00
Dannon Baker ea973e0b51 Filter kwds, use direct params for inner-layer manager args 2019-04-24 10:42:12 -04:00
Dannon dff3be5e55 Merge pull request #7805 from mvdbeek/gops_fix 
gops_intersect_1 imports galaxy
 2019-04-24 09:57:26 -04:00
Nicola Soranzo dbf33e7279 Return HTTP 400 for GET /api/datasets/nonexistent_id 
Previously it was returning HTTP status code 200 and the exception
message as content.
 2019-04-24 14:02:28 +01:00
mvdbeek 11d4305e3b gops_intersect_1 imports galaxy 2019-04-24 13:48:11 +02:00
Marius van den Beek 4bd8644b24 Merge pull request #7800 from nsoranzo/fix_deprecations 
Fix various Python deprecations
 2019-04-24 10:52:34 +02:00
Dannon Baker 8c4943e97f Add autoregistration bypass for user manager 2019-04-23 16:38:31 -04:00
John Chilton 2589d4d394 Merge pull request #7796 from mvdbeek/param_parser_tool 
Add general purpose expression tool
 2019-04-23 16:20:39 -04:00
Martin Cech da127e1c12 Merge pull request #7773 from bgruening/geojson 
Add GeoJSON datatype
 2019-04-23 15:57:43 -04:00
guerler 7a4ec2739c Fix ui message for submitted activation emails 2019-04-23 15:52:51 -04:00
Martin Cech 9c8f0e70e9 add newline 2019-04-23 13:21:28 -04:00
Nicola Soranzo d53112aa43 Use `yaml.safe_load() instead of load()` 
See https://msg.pyyaml.org/load
 2019-04-23 16:50:55 +01:00