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617 Commits
Author SHA1 Message Date
John Chilton 82a8eb05d6 Merge remote-tracking branch 'jmchilton/release_18.09' into dev_merge_1 2018-11-06 09:10:22 -05:00
Marius van den Beek c3dc2392ce Merge pull request #6954 from jmchilton/workflow_tests_2 
Small API Workflow Test Improvements.
 2018-11-05 14:22:59 +01:00
mvdbeek 9b42032098 Fill in default state for test_optional_workflow_output 2018-11-05 13:09:31 +01:00
M Bernt 4e098c5d52 tests: add parameter to output_filter 2018-11-01 17:23:17 +01:00
John Chilton f035d642ce Merge pull request #6844 from jmchilton/compressed_types_and_extra_files 
Infrastructure/API Support for Composite Uploads/Downloads
 2018-11-01 10:57:09 -04:00
John Chilton 06aea92eb8 cleaner test test_run_subworkflow_runtime_parameters 2018-11-01 10:37:51 -04:00
John Chilton d4b6bf28b5 Test for parameter replacement of GUI-style normalized parameters. 2018-11-01 10:37:49 -04:00
John Chilton 7bd7abb5ee Fix linting of dev. 2018-10-26 10:01:56 -04:00
Marius van den Beek dda297c408 Merge pull request #6776 from jmchilton/gxformat2_integration 
Allow API import/export of format 2 workflows.
 2018-10-26 14:10:33 +02:00
John Chilton e3bc005a86 Implement API endpoint for indexing extra files in a dataset. 2018-10-24 09:55:25 -04:00
John Chilton dd6b185ab8 Implement composite uploads on arbitrary datatypes. 
Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files.

These may be specified one at a time or in directory structures via tar files.
 2018-10-24 09:55:25 -04:00
Pierrick ROGER 35093e38fc Remove spaces in blank line. 2018-10-18 11:16:29 +02:00
Pierrick ROGER efc7864cab Merge branch 'dev' into feature/isa_data_type 2018-10-18 10:36:49 +02:00
John Chilton cdd1520434 Rework most test workflows to label maps for step definitions 2018-10-12 13:41:13 -04:00
John Chilton 14978355ee Support for de-duplicated workflow import. 2018-10-12 13:41:06 -04:00
John Chilton b0334c0c06 Add CWL-style doc keyword to format2 workflows, map to annotations. 2018-10-12 13:41:06 -04:00
John Chilton 00625839b3 Allow downloading Galaxy workflows as format 2 workflows. 2018-10-12 13:41:06 -04:00
John Chilton feddcfaa5a Allow upload format 2 workflows to Galaxy. 2018-10-12 13:41:06 -04:00
Nate Coraor ca95d7a26e Merge remote-tracking branch 'upstream/release_18.09' into dev 2018-10-12 10:32:43 -04:00
John Chilton f3da0864b4 Test case for regression #6856. 2018-10-12 09:03:12 -04:00
John Chilton fb52755601 Merge pull request #6811 from jmchilton/gxformat2_060 
Support for Enhancements to gxformat2 (part II)
 2018-10-10 08:42:37 -04:00
John Chilton a8843ece34 Allow CWL-style id map for workflow inputs 2018-10-09 08:18:29 -04:00
John Chilton 915c1a9b66 Remove unused variable in test_workflows. 2018-10-09 08:18:29 -04:00
John Chilton 8ba76c9704 Switch to CWL-style format 2 workflow output definitions. 2018-10-09 08:18:29 -04:00
John Chilton 1e2080242c Toward newer style gxformat2 definitions. 2018-10-09 08:18:29 -04:00
Nicola Soranzo 6b3f672770 Replace deprecated assertEquals() method 
Fix warnings during py34-unit tests like:

```
/home/travis/build/galaxyproject/galaxy/test/unit/workflows/test_extract_summary.py:46: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(job_dict[hda.job], [('out1', derived_hda_2)])
```

See e.g. https://travis-ci.org/galaxyproject/galaxy/jobs/438829277
 2018-10-09 12:37:15 +01:00
John Chilton d010077830 Allow workflow import of workflows with connections that don't have matching empty tool state entries. 
There is a long conversation in the added doc string.
 2018-10-06 09:39:21 -04:00
John Chilton c7fa2860d8 Toward new format2 syntaxes in test workflows. 2018-10-06 09:39:21 -04:00
John Chilton 319c29937e gxformat2 - allow CWL style 'in' declarations for step connections. 
Makes gxformat2 look a lot closer to CWL workflows with Galaxy tools and state.
 2018-10-06 09:39:21 -04:00
Marius van den Beek 10e984ce85 Merge pull request #6746 from jmchilton/workflow_state_touch_1 
Fill in needed state defaults when importing manually crafted workflows.
 2018-10-06 10:17:41 +02:00
Dannon Baker 55c90960e9 Merge remote-tracking branch 'upstream/release_18.09' into dev 2018-10-01 10:53:11 -04:00
mvdbeek ab660686c2 Add test for single and multi-input identifiers 
test_identifier_map_over_input_in_conditional fails at the
moment (same issue as in https://github.com/galaxyproject/galaxy/issues/6182)
 2018-09-28 19:01:28 +02:00
Dannon Baker ad76a0d57f Merge branch 'release_18.09' into dev 2018-09-28 12:49:42 -04:00
mvdbeek 70e325574c Use with statement for all file uploads 2018-09-27 22:20:00 +02:00
mvdbeek 53b062f804 Add bam upload test 
`test_upload_bam_file` fails on release_18.09 but passes on 18.05.
 2018-09-27 20:31:33 +02:00
Dannon Baker 7787d3ae8e Merge remote-tracking branch 'upstream/release_18.09' into dev 2018-09-26 10:46:58 -04:00
John Chilton 3e774713a9 Fill in needed state defaults when importing manually curated workflows. 2018-09-24 09:38:34 -04:00
John Chilton 50019e503a Refactor method for running format 2 workflows into populators.py for reuse. 2018-09-24 09:38:34 -04:00
John Chilton 7eac08979b Undo auto-propagation of group tags. 
@mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool.
 2018-09-20 14:15:29 -04:00
Martin Cech 3072889905 Merge branch 'release_18.05' into release_18.09 2018-09-20 11:48:45 -04:00
Dannon 02c177152b Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes 
[18.05] Backport tool version select fixes
 2018-09-20 09:41:15 -04:00
Nicola Soranzo bae08f3ca2 Merge branch 'release_18.09' into dev 2018-09-20 10:16:40 +01:00
Nicola Soranzo 5eb7e5ce6f Merge branch 'release_18.05' into release_18.09 2018-09-20 09:49:39 +01:00
mvdbeek f5dcf60561 Fix and test anonymous error reports 
Fixes https://github.com/galaxyproject/galaxy/issues/6675
 2018-09-19 21:00:50 +02:00
mvdbeek 3017568e77 Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test 2018-09-19 16:40:59 +02:00
mvdbeek 5635a05a2a Look up collection_type if collection_type_source is set 
We do this in the wf-editor and in the backend, so this works for
subworkflows. This should make quite some tools more usable in a
workflow scenario. Should fix
- https://github.com/galaxyproject/galaxy/issues/6514
- https://github.com/galaxyproject/galaxy/issues/6012
- https://github.com/galaxyproject/galaxy/issues/6569
- https://github.com/galaxyproject/galaxy/issues/1889
and perhaps more issues related to this.
 2018-09-19 09:48:25 -04:00
mvdbeek f6f526a0a5 Use tool_version instead of version parameter 
To be consistent with other routes that accept this parameter.
 2018-09-19 15:39:00 +02:00
mvdbeek 806beaca9b Test that newest version will be returned if tool id or version don't match 2018-09-19 15:39:00 +02:00
John Chilton da421294f8 Merge pull request #6732 from mvdbeek/propagate_collection_type 
Look up collection_type if collection_type_source is set
 2018-09-19 08:28:51 -04:00
Dannon Baker ed147ee052 Merge branch 'release_18.09' into dev 2018-09-18 13:51:56 -04:00