opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-31 18:42:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
36,715 Commits 64 Branches 246 Tags
show
Commit Graph
3643 Commits
Author SHA1 Message Date
Marius van den Beek 01f1f1b95f Merge pull request #6858 from jmchilton/fix_metadata_revert 
[18.09] Revert selective metadata flushing - breaks multiple uploads/outputs.
 2018-10-12 15:44:01 +02:00
John Chilton f3da0864b4 Test case for regression #6856. 2018-10-12 09:03:12 -04:00
Nicola Soranzo d22f652f91 Merge branch 'release_18.05' into release_18.09 2018-10-12 09:44:18 +01:00
Nicola Soranzo ac3e1ca1d0 Use Crypto to generate SSH keys 
Also remove key files in `stop_ssh_docker()`.
 2018-10-10 16:22:05 +01:00
mvdbeek b08c6219c3 Simplify ssh key handling in integration test 2018-10-10 14:56:05 +02:00
mvdbeek 5e12e509bf Fix selection of job plugin and image 
Thanks @nsoranzo.
 2018-10-10 14:56:05 +02:00
mvdbeek 5844bdc7aa Add integration test for remote shell CLI runners 
This tests both the SecureShell and Paramiko shell plugins and the
Slurm and Torque CLI runner.
 2018-10-10 10:10:51 +02:00
John Chilton 1c4a4ed8cb Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 2018-10-04 11:43:05 -04:00
John Chilton 4a345b99c3 Fix security problems when extracting untrusted tar files. 
Fixes GX-2018-0006.
 2018-10-04 11:32:52 -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 5a98515df8 Merge pull request #6789 from mvdbeek/fix_bam_upload 
[18.09] Fix bam upload resulting in 'auto' datatype
 2018-09-28 07:46:22 -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
mvdbeek becb922dc1 Strip all control characters from rules 
Similar to 366701cfb2, which is valid on its own, but here we just apply it to all rules.
 2018-09-27 16:36:31 +02:00
Dannon Baker cf62a1dafd Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-09-26 09:17:26 -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 d312c48ea7 Merge pull request #6748 from jmchilton/1809_robust_sleep 
[18.09] Make newer unit tests more robust with a looped wait...
 2018-09-20 10:16:13 +01:00
Nicola Soranzo 5eb7e5ce6f Merge branch 'release_18.05' into release_18.09 2018-09-20 09:49:39 +01:00
John Chilton 56f5bf743a Make newer unit tests more robust with a looped wait... 
... instead of raw sleep.
 2018-09-19 20:14:08 -04:00
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 94082a878d Unit test that fails if we don't return the latest version upon version mismatch 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 376516610e Bugfix - missing tests for data source sniffing. 
Ensure #6334 is fixed I think.
 2018-09-18 11:29:58 -04:00
Dannon d349d4763d Merge pull request #6678 from jmchilton/subworkflow_parameters 
Workflow replacement parameters polish.
 2018-09-10 15:28:05 -04:00
Dannon d42fb41cb0 Merge pull request #6681 from mvdbeek/continue_reloading_if_tool_is_broken 
Keep newly broken tool in toolbox
 2018-09-10 14:56:25 -04:00
mvdbeek dc49c3ea0e Provide visual feedback if tool is broken 2018-09-08 17:59:45 +02:00
mvdbeek 947389887b Add unit test that exercises reloading for broken tools 2018-09-08 11:29:24 +02:00
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 5c54793ddf Merge pull request #6669 from mvdbeek/fix_cache_tests 
Increase robustness and accuracy of job search / cache use
 2018-09-06 14:59:13 -04:00
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
Dannon 6787dbc9ee Merge pull request #6642 from natefoo/galaxy-main-import 
Allow running scripts/galaxy-main without Galaxy on sys.path
 2018-09-06 08:13:06 -04:00
Nicola Soranzo e14b871eb9 Add test for scripts/galaxy-main 2018-09-06 11:00:08 +01:00
John Chilton 7f1f8a7a4e Merge pull request #6627 from mvdbeek/test_more_tools 
Test tools shipped with Galaxy
 2018-09-05 14:43:13 -04:00
John Chilton 9b488ff291 One last Selenium fix for collection interface change. 2018-09-05 14:00:57 -04:00
mvdbeek 8b757f22d1 Exclude bed_to_bigbed and wig_to_bigwig from tests 
They work, but required hg17.len to be present.
 2018-09-05 15:25:33 +02:00
mvdbeek da4906dc56 Add GeneBed_Maf_Fasta2 to no test list 2018-09-05 14:22:01 +02:00
John Chilton 8148bd91de Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup 
Move tests to pytest setup
 2018-09-05 06:50:34 -04:00
mvdbeek 64652c28cf Drop wait from cached job tests 2018-09-05 12:16:08 +02:00
Nicola Soranzo ad02c53154 Fix many links 2018-09-03 14:34:13 +01:00
John Chilton 410ec1927c Merge pull request #6656 from jmchilton/collect_builder_fixes 
Assorted fixes for #6572
 2018-08-31 10:43:10 -04:00
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