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
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
John Chilton
376516610e
Bugfix - missing tests for data source sniffing.
...
Ensure #6334 is fixed I think.
2018-09-18 11:29:58 -04:00
mvdbeek
a44baa5642
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.
2018-09-18 17:11:40 +02:00
mvdbeek
17d148eb8f
Use tool_version instead of version parameter
...
To be consistent with other routes that accept this parameter.
2018-09-13 20:30:52 +02:00
mvdbeek
943e67e4e5
Test that newest version will be returned if tool id or version don't match
2018-09-13 13:25:09 +02:00
Dannon
d349d4763d
Merge pull request #6678 from jmchilton/subworkflow_parameters
...
Workflow replacement parameters polish.
2018-09-10 15:28:05 -04:00
Nicola Soranzo
64bb339a31
Merge pull request #6641 from martenson/rename-and-document-config-value
...
document config for sniffing compressed files, enable by default
2018-09-08 00:32:08 +01:00
John Chilton
8f979b4da1
Workflow replacement parameters polish.
...
- Selenium test case demonstrating their use in simple workflows.
- API test demonstrating they work with nested workflows from the run perspective.
- Update run variant of workflow to_dict to parse out replacement parameters to display on the backend and tweak the client to just accept these.
- Parse out replacement parameters for subworkflows recursively, include in new run output attribute - nested workflow replacement parameters work now.
- Selenium test case demosntrating subworkflow replacement parameters are rendered and used when submitted.
2018-09-07 11:22:20 -04:00
Marius van den Beek
da18624067
Merge pull request #6664 from jmchilton/runtime_parameters
...
Implement runtime parameters for subworkflows.
2018-09-07 10:26:17 +02:00
John Chilton
fc75d4f9fb
Test case - verify step parameters replace after workflow invoke pauses.
2018-09-06 14:43:22 -04:00
John Chilton
7806a84d1c
Implement runtime parameters in nested workflows.
2018-09-06 14:43:22 -04:00
John Chilton
6a266a19a9
More tests for runtime workflow parameters.
2018-09-06 09:02:55 -04:00
mvdbeek
64652c28cf
Drop wait from cached job tests
2018-09-05 12:16:08 +02:00
Martin Cech
9b5724d62d
add back the unstable flags for bed.gz datasets
...
I expect the datatypes_conf.xml bed compress default will change in near future
2018-08-30 13:09:32 -04:00
Martin Cech
4a21ac30ea
Merge branch 'rename-and-document-config-value' of github.com:martenson/galaxy into rename-and-document-config-value
2018-08-30 10:41:44 -04:00
Martin Cech
e1b3236802
fix tests for the bed.gz dtaatype
...
compressed beds are not part of the datatypes_conf.xml.sample
2018-08-30 10:40:24 -04:00
John Chilton