Martin Cech
f6b978be8c
prevent XSS on toolshed when browsing repo changeset
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fix invalid changeset ts test, fix flake8
Revert "fix invalid changeset ts test, fix flake8"
This reverts commit 84864fe82a9f3b9ffa1cd5ef272f979e867e2002.
tweak the invalid changeset test and add a new one
2019-01-08 12:52:28 -05:00
Martin Cech
46ad1992bd
Merge pull request #7071 from mvdbeek/fix_process_key
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[18.09] Fix process key
2018-12-04 10:26:49 -05:00
mvdbeek
3a93fd4f23
Add test for proper nesting in process_keys
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and a unit test for https://github.com/galaxyproject/galaxy/issues/7048
2018-12-04 14:02:20 +01:00
Dannon Baker
2620367a5a
Merge remote-tracking branch 'upstream/release_18.05' into release_18.09
2018-11-27 08:34:42 -05:00
Dannon Baker
9a6fddcdca
Merge remote-tracking branch 'upstream/release_18.01' into release_18.05
2018-11-27 08:28:21 -05:00
mvdbeek
1e4821c644
Provide element_identifier attribute in DatsetCollectionWrapper
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This allows accessing `$input1.element_identifier` for an `input1` of
collection_type `list:pair`.
2018-11-20 16:13:29 +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
M Bernt
717605af96
added test
2018-10-31 12:52:25 +01:00
Marius van den Beek
01f1f1b95f
Merge pull request #6858 from jmchilton/fix_metadata_revert
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[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
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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
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Thanks @nsoranzo.
2018-10-10 14:56:05 +02:00
mvdbeek
5844bdc7aa
Add integration test for remote shell CLI runners
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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.
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Fixes GX-2018-0006.
2018-10-04 11:32:52 -04:00
mvdbeek
ab660686c2
Add test for single and multi-input identifiers
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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
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[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
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`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
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Similar to 366701cfb2
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.
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@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
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[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
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[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...
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... instead of raw sleep.
2018-09-19 20:14:08 -04:00
mvdbeek
f5dcf60561
Fix and test anonymous error reports
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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
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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
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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.
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Ensure #6334 is fixed I think.
2018-09-18 11:29:58 -04:00
Dannon
d349d4763d
Merge pull request #6678 from jmchilton/subworkflow_parameters
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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
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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
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document config for sniffing compressed files, enable by default
2018-09-08 00:32:08 +01:00
John Chilton
8f979b4da1
Workflow replacement parameters polish.
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- 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
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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
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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
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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
Martin Cech