opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-31 02:28:09 +08:00
Code Issues Packages Projects Releases Wiki Activity
35,163 Commits 64 Branches 246 Tags
2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2
Commit Graph
17817 Commits
Author SHA1 Message Date
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 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
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 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Dannon Baker b8fa78358c Remove outdated comment; I refactored to handle this. 2018-08-28 13:21:35 -04:00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
mvdbeek 2f87087ba2 Use object store to check for existence of extra_files_path 
This should fix https://github.com/galaxyproject/galaxy/issues/6585
 2018-08-09 21:42:45 +02:00
Dannon ea085b07a0 Merge pull request #6571 from guerler/fix_link 
[18.05] Fix workflow run link for extracted workflows
 2018-08-06 20:19:41 -04:00
Dannon Baker d7959568f8 Merge branch 'release_18.01' into release_18.05 2018-08-06 20:19:18 -04:00
guerler ffdf674c75 Fix worklfow run link for extracted workflows 2018-08-06 12:39:30 -04:00
mvdbeek 21fd74e640 Use subworkflow index when setting auto-label 
Previously this would reference the parent workflow index, while the
get_data module would use the subworkflow index. This means defining
workflows worked fine, but executing would fail when trying to find the
output to replace. Using the subworkflow index here seems like the
correct thing to do.

Fixes https://github.com/galaxyproject/galaxy/issues/6560
 2018-08-06 15:55:27 +02:00
Dannon Baker 9630699c21 Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) 2018-07-31 16:04:18 -04:00
Dannon 66e74d0e47 Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend 
[18.05] Fix "filter empty" rule in Python rule handling framework.
 2018-07-30 15:35:58 -04:00
Dannon a88bf0a2be Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values 
[18.05] Allow invalid optional param values for tools profile versions < 18.09
 2018-07-26 11:14:51 -04:00
John Chilton 5f19b8752d Fix empty handling rule. 2018-07-26 09:52:07 -04:00
John Chilton 9794d835e5 Fix to_dict with io_details=True for tools with collection outputs. 
Fixes #6537 and includes a test case.
 2018-07-25 12:32:38 -04:00
Nicola Soranzo a8b9899681 Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 
Since v2.27.0 (see
https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f07c9a75 ),
`bedtools genomecov` emits this warning:
```
*****
*****WARNING: Genome (-g) files are ignored when BAM input is provided.
*****
```
if both `-ibam` and `-g` option are specified, which causes the converters to
always fail.

Also:
- Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from
  creating other issues.
- Fix input format in `CONVERTER_sam_to_bigwig_0`.
 2018-07-23 14:23:43 +01:00
John Chilton 7b8e4f9e74 Fix empty datatypes. 2018-07-17 17:56:19 +01:00
Nicola Soranzo dfc996c8d6 Merge branch 'release_18.01' into release_18.05 2018-07-13 01:01:13 +01:00
John Chilton 20565a2b85 Merge pull request #6375 from dannon/sentry_transport_fix 
[18.05] Specify standard HTTPTransport for Sentry
 2018-07-11 13:34:54 -04:00
John Chilton 93fc3a6350 Merge pull request #6369 from guerler/pages 
[18.05] Make sure that the workflow step has a proper state available
 2018-07-11 13:33:43 -04:00
Devon Ryan bc95f25636 Fix the --log-file option in the job handlers 
(cherry picked from commit 97c344a17a)
 2018-07-09 12:46:22 -04:00
thobalose 0c97d4ff5c GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 2018-07-04 11:33:32 -04:00
John Chilton 6654a83752 Hack around #6299. 2018-07-01 10:01:57 -07:00
Nicola Soranzo e0c269291a Merge branch 'release_18.01' into release_18.05 2018-06-23 00:04:32 +01:00
Dannon Baker fa2b6baef7 Revert "Remove bam to bai converter" 
This reverts commit 7e2727bc0a.
 2018-06-22 13:22:51 -04:00
guerler 9967639bac Comma-separate tool names in missing tools error message 2018-06-22 00:30:17 -04:00
guerler f94a073e86 Make sure that the workflow step has a proper state available 2018-06-21 16:44:26 -04:00
Dannon Baker 603b2365b6 Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations 2018-06-21 10:25:42 -04:00
Martin Cech 6d5be41b32 Merge pull request #6366 from jmchilton/job_log_bug 
[18.05] Fix small bug in logging output name in job finish.
 2018-06-20 21:16:18 -05:00
Nicola Soranzo d0a0fa8319 Merge branch 'release_18.01' into release_18.05 2018-06-20 22:43:33 +01:00
John Chilton c6403acd0f Fix logging bug. 2018-06-20 15:37:29 -04:00
mvdbeek 333d660556 Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over 2018-06-20 09:54:42 -04:00
mvdbeek 5e32d78aa7 Consider mapping-over when picking collection_type for dynamically discovered collections 2018-06-20 09:54:41 -04:00
mvdbeek f5aec1cdf1 Fix inferring output structure when mapping over 
Previously this would have always generated `list:list` structures,
even when the input is a list:pair. I'm not 100% convinced
this is correct, but this seems to work.
 2018-06-20 09:54:38 -04:00
mvdbeek b53d2ae381 Fix can_map_over for mapping over paired inputs 
We'd only try mapping over the first collection type description
otherwise. I suppose we didn't notice because the first type is `list`
and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640.
 2018-06-20 09:54:37 -04:00
mvdbeek 9e3de244d7 Fix mapping list over multidata input 2018-06-20 09:54:02 -04:00
mvdbeek 6b8b862e4d Fix up subcollection_type 2018-06-20 09:53:42 -04:00
John Chilton c601a9d491 Fix collection mapping to allow mapping over multi-data inputs. 
It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work.
 2018-06-20 09:53:41 -04:00
John Chilton 470299a2ce Merge pull request #6234 from mvdbeek/fix_relabel_non_strict 
[18.01] Fix non-strict tabular relabel operation
 2018-06-18 15:08:36 -04:00
Nicola Soranzo cddee94e4b Small fixes 2018-06-15 20:08:18 +01:00