https://github.com/galaxyproject/galaxy

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907130d Fix repository uploads with remove_repo_files_not_in_tar This fixes erroneously deleting the just uploaded files, which otherwise happens in ``` if full_name not in filenames_in_archive: files_to_remove.append(full_name) ``` 21 February 2022, 09:28:41 UTC
76a8e12 Merge pull request #13325 from mvdbeek/remap_fix_sentry [21.09] Fix resuming job when job has optional data parameters 10 February 2022, 10:19:20 UTC
76d2f63 Merge pull request #13326 from dannon/backport-blame-ignore-revs 08 February 2022, 16:04:13 UTC
9cb0c45 Add .git-blame-ignore-revs to 21.09. Without this, if you have set the file up in git config blame will blow up with something like `could not open object name list: .git-blame-ignore-revs`. I only included the relevant hashes here, will need to handle a merge as it goes forward. 08 February 2022, 14:57:50 UTC
bec9d4b Fix resuming job when job has optional data parameters This fixes ``` ERROR galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun self.__remap_parameters(job_to_remap, jtid, jtod, out_data) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters} File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp> input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters} File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads raise TypeError(f'the JSON object must be str, bytes or bytearray, ' TypeError: the JSON object must be str, bytes or bytearray, not NoneType ``` Optional data inputs or optional selects are stored as `None` (super inconsistent, since most other parameters are stored as JOSN. We should create "basic_2.py" using pydantic at one point not too far into the future ...). This means we can't call `json.loads` on these. Fortunately this is the only place we do it, and we don't need to consider optional parameters here anyway. 08 February 2022, 14:45:01 UTC
00b0846 Merge branch 'release_21.05' into release_21.09 08 February 2022, 13:29:08 UTC
d27ded4 Merge pull request #13315 from mvdbeek/restore_metadata_size_limit 08 February 2022, 11:14:26 UTC
e5455a4 Merge pull request #13316 from mvdbeek/fix_failure_to_fail_job [21.09] Make __link_file_check more robust 07 February 2022, 14:29:56 UTC
83c0683 Restore Metadata size limit Broke in https://github.com/galaxyproject/galaxy/pull/11902 07 February 2022, 14:02:02 UTC
37846b2 Make __link_file_check more robust There's no need to load the job and job parameters if the tool isn't upload1. This should fix https://github.com/galaxyproject/galaxy/issues/13311 07 February 2022, 10:33:18 UTC
44644a0 Merge pull request #13304 from mvdbeek/fix_stopping_its_slurm [21.09] Fix stopping ITs on slurm 04 February 2022, 12:46:28 UTC
bb299b9 Merge pull request #13301 from Smithsonian/Fixfor13297 [21.09] Fix univa job runner setup without nativeSpecification 04 February 2022, 12:13:46 UTC
a60a898 Fix stopping ITs on slurm If slurm decided the job is in error. There are configurations of slurm that error out when cancelling the job monitor script, and others that don't do this. 04 February 2022, 09:44:19 UTC
10a6db4 Fix for traceback: ``` Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 707, in monitor self.check_watched_items() File "lib/galaxy/jobs/runners/drmaa.py", line 338, in check_watched_items if self._complete_terminal_job(ajs, drmaa_state=state) is not None: File "lib/galaxy/jobs/runners/univa.py", line 85, in _complete_terminal_job time_granted, mem_granted = _parse_native_specs(ajs.job_id, native_spec) File "lib/galaxy/jobs/runners/univa.py", line 572, in _parse_native_specs m = re.search(r"rt=([0-9:]+)[\s,]*", native_spec) File "/pool/spare/galaxy/galaxy/.venv/lib64/python3.6/re.py", line 182, in search return _compile(pattern, flags).search(string) TypeError: expected string or bytes-like object ``` See https://github.com/galaxyproject/galaxy/issues/13297 reported by @ajs6f fix from @mvdbeek 03 February 2022, 16:46:42 UTC
213f6ee Merge pull request #13290 from mvdbeek/fix_dataset_details_and_drag_and_drop [21.09] Fix dataset details and drag and drop 02 February 2022, 00:03:10 UTC
04c340a Drop leftover debug log Co-authored-by: Dannon <dannon.baker@gmail.com> 01 February 2022, 22:58:39 UTC
69c635b Fix link to dataset details for datasets in running collection 01 February 2022, 19:57:54 UTC
51bca9d Fix drag and drop of unexpanded collection elements 01 February 2022, 19:54:41 UTC
81f27cb Merge pull request #13254 from davelopez/fix_edit_imported_subworkflow [21.09] Fix imported sub-workflows cannot be edited 27 January 2022, 17:20:52 UTC
6cb59a5 Fix imported subworkflows cannot be edited There may be no StoredWorkflow associated with the imported subworkflow yet, so trying to edit the subworkflow without it will fail. xref https://github.com/galaxyproject/galaxy/pull/10160 27 January 2022, 14:25:06 UTC
004d69f Merge pull request #13249 from mvdbeek/hgutil_fix 26 January 2022, 19:36:56 UTC
2d70fa5 Fix one usage of hg_util.remove_file I missed this one in https://github.com/galaxyproject/galaxy/pull/13230 26 January 2022, 15:54:45 UTC
5845b3d Merge pull request #13230 from mvdbeek/fix_mercurial_new_file [21.09] Fix adding new files via tarball upload 25 January 2022, 13:32:38 UTC
0f59f70 Merge pull request #13231 from simonbray/wf-au-fix [21.09] Ensure tool_id/content_id is updated when refactoring workflows 24 January 2022, 14:38:59 UTC
381d218 ensure tool_id/content_id is updated when refactoring workflows 24 January 2022, 12:39:27 UTC
5c39169 Partial unit tests for hgutil.py 24 January 2022, 11:28:06 UTC
956ad81 Fix adding new files via tarball upload The API of `repo.dirstate.write` has changed and takes a `tr` parameter now. I've removed the whole fallback since it fails and uses internals of mercurial that we should probably not be using anyway. Instead we're going to delete untracked files in hg_util.remove_file() 24 January 2022, 10:58:30 UTC
f2c6666 Merge pull request #13174 from mvdbeek/fix_display_in_upload_false_connections [21.09] Fix workflow connections for outputs that are not displayed in uploads 24 January 2022, 08:17:12 UTC
15e1158 Merge pull request #13227 from mvdbeek/drop_unnecessary_tests [21.09] Skip non-Selenium tests if only lib/galaxy_test/selenium is touched 23 January 2022, 12:43:55 UTC
31f0cb4 Don't sort array in place, fixes infinite update loop 23 January 2022, 12:43:06 UTC
f7fde81 Print exception 23 January 2022, 12:43:06 UTC
f66b673 Drop indented, fenced galaxy blocks from test https://github.com/galaxyproject/galaxy/issues/13181 23 January 2022, 09:48:22 UTC
036dddc Wait for data and datatype before rendering HistoryDatasetsDisplay 23 January 2022, 09:48:22 UTC
65b3157 Search datatype before selecting it We now return more datatypes in the list, so bam fell out of the intial items that select2 displays without scrolling. 23 January 2022, 09:48:22 UTC
bb2c6ba Fix workflow connections for outputs that are not displayed in uploads and apply the same fix for tool recommendations. Fixes https://github.com/galaxyproject/galaxy/issues/13173 23 January 2022, 09:48:21 UTC
6c7f4b0 Skip api tests if lib/galaxy_test/selenium is touched (and other unrelated test). 23 January 2022, 09:42:34 UTC
59393dc Merge pull request #13216 from mvdbeek/fix_unique_constraint_exceptions [21.09] Handle unique tag name constraints 22 January 2022, 15:26:47 UTC
296b31e Merge pull request #13193 from davelopez/fix_wf_invocation_name_overflow [21.09] Fix workflow invocation name overflow 21 January 2022, 20:42:18 UTC
29f8b18 Handle unique tag name constraints The idea is to create the tag one by one in a separate session, and catch any violations. 21 January 2022, 13:50:16 UTC
ad9b422 Fix column text overflow after wrapping in div And slightly enhance switch to history tooltip 21 January 2022, 13:45:56 UTC
bac2cc2 Move `toggle-invocation-details` class to expand column 21 January 2022, 13:26:24 UTC
407c04d Fix tooltip position The tooltip was ignoring the text-overflow when the full name was truncated and was positioned in the center of where the full text would be. Putting the tooltip into a wrapping div seems to solve the issue. 21 January 2022, 12:44:28 UTC
36a0f56 Truncate history name too 21 January 2022, 12:42:08 UTC
851bc56 Merge pull request #13210 from mvdbeek/backport_non_data_map_over_fix [21.09] Backport allow mapping of collection outputs to parameter inputs 21 January 2022, 12:09:19 UTC
10fc135 Merge pull request #13214 from davelopez/fix_hide_collection_batch [21.09] Fix hide collections in batch 21 January 2022, 12:08:53 UTC
de633e9 Fix column index in unit tests After adding a new "first" column for expanding 21 January 2022, 11:43:14 UTC
5e603a9 Add explicit row expand button - Makes more obvious that the row can be expanded. - Allows to display the full name in the tooltip when truncated. 21 January 2022, 11:28:34 UTC
71e3fd4 Add min-width to table This will prevent the workflow name column to completely dissapear in small resolutions 21 January 2022, 11:26:40 UTC
0bc41e0 Fix dataset collections not hiding when updating in batch NOTE: this commit can be dropped when merging forward as this is already refactored and fixed in the dev branch 20 January 2022, 18:39:03 UTC
4f104cf Add API test for dataset collections batch update When merging forward replace `_raw_update_batch` to `_update_batch` 20 January 2022, 18:25:45 UTC
2a005df Separate qunit test cases for data and parameter input terminals 20 January 2022, 15:20:32 UTC
f7fb4ed Remove currently unused options from qunit terminal creation helpers 20 January 2022, 15:20:32 UTC
b5f35c7 Add test to validate correct mapping of parameter input terminals 20 January 2022, 15:20:32 UTC
dce483e Call setMapOver routine in input parameter terminals to detect mapped collections 20 January 2022, 15:20:31 UTC
7f0ce0e Add selenium test to check map over state for parameter steps 20 January 2022, 15:20:31 UTC
6805a34 Merge pull request #13196 from mvdbeek/fix_tool_id_update [21.09] Fix tool id update when updating tool shed tools in editor 19 January 2022, 21:26:14 UTC
25ba40e Merge pull request #13203 from simonbray/patch-2 19 January 2022, 19:20:53 UTC
178d972 Merge pull request #13202 from mvdbeek/fix_metadata_source_access 19 January 2022, 18:40:47 UTC
b920bfb Set table columns widths as suggested in comments 19 January 2022, 17:36:50 UTC
9ba9783 Use break-word on overflow-wrap 19 January 2022, 17:35:26 UTC
2ed8cf6 Consistently parse content id for workflow modules when updating states 19 January 2022, 17:18:27 UTC
ee62798 fix error getting toolshed repo metadata when no repo found 19 January 2022, 16:54:31 UTC
98b7b12 Fix metadata source access in tool shed Fixes: ``` Unexpected HTTP status code: 500: {"err_msg": "Metadata may have been defined for some items in revision '8f1b150a2487'. Correct the following problems if necessary and reset metadata.<br/><b>abyss-pe.xml<\/b> - 'NoneType' object has no attribute 'get_biotools_metadata'<br/>"} ``` in https://github.com/galaxyproject/tools-iuc/runs/4792653893?check_suite_focus=true 19 January 2022, 16:32:47 UTC
d3d6c60 Fix embedding subworkflow 19 January 2022, 14:49:05 UTC
d5b31ee Fix tool id not getting updated on tool update 19 January 2022, 13:46:31 UTC
97c5f8d Properly replace tool version in tool identifer string 19 January 2022, 11:34:19 UTC
60cd5fc Fix workflow invocation name overflow This will force wrapping the name of the workflow when it overflows 19 January 2022, 10:44:58 UTC
6c354e2 Merge pull request #13182 from kxk302/release_21.09 [21.09] Backport of iRODS Object Store path name fix in #13080 18 January 2022, 17:57:46 UTC
043371e Merge pull request #13179 from rhpvorderman/patch-5 [21.09] Catch exceptions when job.user is None 18 January 2022, 17:57:17 UTC
2b70e34 Revised code based on code review 18 January 2022, 15:14:35 UTC
28423d2 Clear the cache before fetching a file from irods object store, to verify file is fetched from the object store, not from the cache 18 January 2022, 14:51:56 UTC
faddbee Use job.get_user_email systematically 18 January 2022, 13:21:09 UTC
9e546f7 Catch exceptions when job.user is None prevents the following error: galaxy.web.framework.decorators ERROR 2022-01-17 14:52:09,619 [p:18,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 282, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/jobs.py", line 113, in index j['user_email'] = job.user.email AttributeError: 'NoneType' object has no attribute 'email' 18 January 2022, 13:21:08 UTC
48e7257 Merge pull request #13176 from mvdbeek/fix_yaml_downloaded_in_preview [21.09] Show yaml files in preview 17 January 2022, 11:27:08 UTC
ea24c7c Show yaml files in preview The `application/yaml` mediatype might be the logical mediatype for yaml (there's no standard yet), but we want to see a textual preview (in the absence of a viewer). Fixes https://github.com/galaxyproject/galaxy/issues/13168 17 January 2022, 09:15:57 UTC
53ec65f Merge pull request #13157 from mvdbeek/fix_hiding_on_rerun [21.09] Fix re-run with rerun_remap_job_id hiding collection 14 January 2022, 16:02:25 UTC
fc8fb85 Set collection update_time when replacing failed elements That allows the new history to update the collection. 14 January 2022, 11:59:36 UTC
2a76f41 Merge pull request #13154 from mvdbeek/limit_repository_cache_lifetime [21.09] Limit lifetime of repository cache 13 January 2022, 15:10:40 UTC
bf71267 Drop refresh argument of get_installed_repository 13 January 2022, 12:35:36 UTC
afd9421 Don't need to use a joinedload anymore The cache is only used on startup, not during dependency resolution. Also rename _rebuild, since we only use it once now. 13 January 2022, 11:26:56 UTC
a327e34 Limit lifetime of repository cache 13 January 2022, 11:26:55 UTC
855e9f9 Fix re-run with rerun_remap_job_id hiding collection Fixes https://github.com/galaxyproject/galaxy/issues/13052 12 January 2022, 19:10:08 UTC
a2c4f12 Merge pull request #13156 from mvdbeek/fix_logo_url [21.09] Fix staticUrlToPrefixed url rewriting 12 January 2022, 16:40:09 UTC
817a2d4 Fix staticUrlToPrefixed url rewriting 12 January 2022, 14:12:14 UTC
1e889ad Merge pull request #13138 from mvdbeek/prefix_fixes_backports [21.09] Backport of prefix fixes 10 January 2022, 23:06:17 UTC
89c814d Fix logo link when using prefix 09 January 2022, 18:06:19 UTC
2af7abd Fix Save and View url 09 January 2022, 18:01:34 UTC
0c27185 Fix (per-domain) favicon url 09 January 2022, 18:01:18 UTC
8e1e225 Fix old-style page editor load when using prefix 09 January 2022, 18:00:51 UTC
ab6e245 Fix tour builder for instances with prefix 09 January 2022, 18:00:43 UTC
ba33eca Fix tagService for url prefix 09 January 2022, 18:00:20 UTC
74a7ef0 Strip trailing slash from cookie path 09 January 2022, 18:00:00 UTC
1328b45 Merge pull request #13134 from mvdbeek/fix_import_of_history_archives_with_tag [21.09] Fix history import for datasets with tags 08 January 2022, 10:23:25 UTC
2086ce9 Check response status code Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 08 January 2022, 07:51:46 UTC
a2ede03 Fix history import for datasets with tags and tag dataset used for history import/export tests 07 January 2022, 16:16:45 UTC
7fecc4b Merge pull request #13126 from thepineapplepirate/master added description of inpcrd and prmtop 07 January 2022, 09:04:48 UTC
34cdf6d added description of inpcrd and prmtop 06 January 2022, 15:57:00 UTC
3f8bb2d Merge pull request #13092 from mvdbeek/fix_dataset_details_prefix [21.09] Fix dataset details button when using prefix 28 December 2021, 16:33:08 UTC
4beeac3 Merge pull request #13096 from mvdbeek/trim_stdout_stderr [21.09] Limit possible size of info field, read only 100 MB of stdio 21 December 2021, 08:48:29 UTC
11c5a19 Limit possible size of info field, read only 100 MB of stdio 20 December 2021, 16:53:42 UTC
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