opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-30 18:13:23 +08:00
Code Issues Packages Projects Releases Wiki Activity
35,184 Commits 64 Branches 246 Tags
02c177152bd7dbef02d4ea5d40449745e913b38b
Commit Graph
35184 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
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
Martin Cech d014469f07 Merge pull request #6742 from mvdbeek/fix_error_reporting 
[18.05] Fix and test anonymous error reports
 2018-09-19 21:02:05 -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
Martin Cech 8400417445 Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 
[18.05] Decode tool id and version in the client, not in the API
 2018-09-19 10:58:42 -04:00
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 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 3ea9d086bf Sort rval so that newest tool appears last in rval 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 c8552970dd Sort by tool version when picking a tool with an unavailable version 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
Nicola Soranzo 35754dc49a Fix symlinking during plugin staging 
Remove also broken symlinks before creating the new ones.
 2018-09-19 11:16:54 +01:00
Nicola Soranzo 7f38e61cae Remove again lib/galaxy/dependencies/requirements.txt 
It was reintroduced (empty) by mistake in
https://github.com/galaxyproject/galaxy/pull/4474 .
 2018-09-19 10:18:02 +01:00
Nicola Soranzo 18d99deb95 Decode tool id and version in the client, not in the API 
using `decodeUriComponent` from `decode-uri-component` JS package.

Revert https://github.com/galaxyproject/galaxy/pull/6707

Remove unused `_get_tool()` method in
`lib/galaxy/webapps/galaxy/api/workflows.py` .

Rebuild client with:
```
make client-production-maps
```
 2018-09-19 10:17:26 +01:00
Martin Cech 6993dbb6fc Merge pull request #6705 from natefoo/slurm-cgroup-enospc 
[18.05] Catch additional permutations of Slurm cgroup creation warnings
 2018-09-14 15:38:18 -04:00
Nate Coraor 3d508a01d3 Improvements from @nsoranzo 2018-09-14 14:39:01 -04:00
Dannon f513594c31 Merge pull request #6707 from martenson/unqoute_tool_version 
[18.05] unquote the tool_version in the tools API
 2018-09-14 09:16:44 -04:00
Martin Cech 1b6d422afd unquote similarly to previous commit but in the workflow controller 2018-09-13 13:00:18 -04:00
Martin Cech f7c1d31dbc unquote the tool_version in the tools API 
if the tool version includes '+', which is a recommended way
of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-versions
this would fail the comparison down the line in the toolbox.get_tool() method

this commit also downgrades the unquote_plus to unquote for tool_id
for similar reasons since it also contains the version
 2018-09-12 14:49:10 -04:00
Nate Coraor 7e2a77e8af Catch additional permutations of Slurm cgroup creation warnings 2018-09-12 13:59:26 -04:00
Dannon 1dacc35332 Merge pull request #6703 from davebx/updates_api 
[18.05] Add missing route for API endpoint.
 2018-09-12 13:31:21 -04:00
Dave B bddabe3029 Add missing route for API endpoint. 2018-09-12 12:28:10 -04:00
Marius van den Beek 2a79ae0ce1 Merge pull request #6691 from jmchilton/backport_6326 
[18.05] Backport #6326
 2018-09-12 10:25:03 +02:00
John Chilton a937bc5539 Client build. 2018-09-11 11:22:02 -04:00
Sebastian Kapust 4fc9fe2150 Fix target update for rule collection builder after input selection 2018-09-11 09:39:25 -04:00
Nate Coraor 9217680ab6 Merge pull request #6647 from dannon/page_fixes 
[18.05] Pages - fixes for encoded ids in the database
 2018-09-10 16:21:46 -04:00
Dannon Baker 1ee673306c Skip the commit attempt, just flush on success 2018-09-07 13:20:34 -04:00
Dannon Baker eba93525af Minor refactoring/dedupe 2018-09-07 11:32:46 -04:00
Dannon Baker fa64299fd1 Drop redundant decode; this is handled in either path of the logic above. 2018-09-07 11:28:02 -04:00
Dannon Baker 3571df4e4d Use PAGE_MAXRAW in both places (refactor this after it all works perfectly) 2018-09-07 11:20:02 -04:00
Dannon Baker d7a245608e Fix lint 2018-09-06 07:36:55 -04:00
Dannon Baker cf9d7c53f0 Restructure to allow individual successful conversions to commit, only rolling back individual fails instead of the entire transaction. This is going to be necessary for complicated deployments like main, where we have ~95% working fine but the otehr 5% were busted to start with (and won't parse), etc. Also swap dryrun to difflib display. 2018-09-05 14:11:11 -04:00
Nicola Soranzo d645d80443 Update bx-python to 0.8.2 
to include https://github.com/bxlab/bx-python/pull/35 .

Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 .
 2018-09-05 09:17:28 -04:00
Dannon Baker 4ec42d2836 Enforce PAGE_MAXRAW, otherwise we have no way to differentiate between potentially all-integer 16 character identifiers. I can't think of a better way to do this, unfortunately. 2018-09-04 14:28:17 -04:00
Dannon Baker a3799350ff Fix hda security check. 2018-09-04 13:11:18 -04:00
Dannon Baker f2072310af Swap placeholder template string back to a single line. 2018-09-04 10:47:45 -04:00
Dannon Baker eab6dd8581 Add dry run mode for script to test 2018-08-29 16:27:01 -04:00
Dannon Baker 5ffff7f1b4 Client build. Looks like we accidentally committed the map references? Leaving that in place, but we had agreed to drop them. 2018-08-29 16:05:33 -04:00
Dannon Baker f8273572f7 Fix (unrelated to the changes in this PR -- bonus bug) name injection for embedded objects. 2018-08-29 16:00:44 -04:00
Dannon Baker 4fa1cc38ea Rename page 'fixer' script 2018-08-29 13:08:26 -04:00
Dannon Baker 2fa6dedf4e Only display encoded ids in editor as well. 2018-08-29 13:07:05 -04:00
Dannon Baker eb8d80b6d2 Handle item name fetching, enforce accessible 2018-08-29 12:18:27 -04:00
Dannon Baker f01726dc6f Almost there, one more (preexisting) bug to fix. This adds validation on save and correct processing to the page writer. 2018-08-29 11:01:33 -04:00
Dannon Baker f9d791c228 Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully. 2018-08-28 16:02:07 -04:00
Dannon Baker b8fa78358c Remove outdated comment; I refactored to handle this. 2018-08-28 13:21:35 -04:00
Dannon Baker a23e5d77a5 Allow pages to read both encoded and unencoded ids out of the database. Always save unencoded version, with the additional benefit of using a simpler, smaller placeholder. 2018-08-28 13:19:11 -04:00
Dannon Baker c0c587abdf Add page_to_raw to decode ids in the database. 2018-08-28 13:19:11 -04:00
Marius van den Beek 03c485ee45 Merge pull request #6639 from bwlang/patch-2 
[18.05] row ids that are all numeric become ints...
 2018-08-27 14:19:56 +02:00
mvdbeek 55d350d015 Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 2018-08-26 20:36:51 +02:00
Brad Langhorst 296105ee39 row ids that are all numeric become ints... 
Since the "F" prefix is checked with substring, row_id must always be a string
 2018-08-26 20:31:38 +02:00
John Chilton 709e49f104 Merge pull request #6591 from dannon/ucsc-test-server-domain 
[18.05] Update UCSC genome-test server URLs
 2018-08-15 10:05:07 -04:00