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
35,154 Commits 64 Branches 246 Tags
d7a245608ead868c8104f2e6dbbbc9fc9ef20dcc
Commit Graph
35154 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
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
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Dannon Baker b8fa78358c Remove outdated comment; I refactored to handle this. 2018-08-28 13:21:35 -04:00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
John Chilton 7e445be502 Merge pull request #6602 from phac-nml/ie_documentation_fix 
[18.05] Fix Location of Plugin Static Content In Documentation for 18.05
 2018-08-15 09:58:44 -04:00
Matthew Spelchak 6cbb574553 Fix Location of Plugin Static Content 2018-08-14 13:15:39 -05:00
Dannon Baker 1cd36e3f81 Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? 2018-08-10 11:27:17 -04:00
Dannon Baker 2839475967 Update ucsc genome-test server URL. 2018-08-10 11:19:13 -04:00
Dannon 1ddaf4a64d Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue 
[18.05] Use object store to check for existence of extra_files_path
 2018-08-10 08:33:19 -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
John Chilton d7398672a1 Merge pull request #6574 from dannon/release_18.05 
[18.05] Client rebuild to include uploadbox value fix in release branch.
 2018-08-08 09:06:55 -04:00
Dannon Baker ec60327f98 Client rebuild to include uploadbox value fix in release branch. 2018-08-07 15:48:21 -04:00
Dannon f992980d45 Merge pull request #6573 from guerler/fix_upload_naming 
[18.05] Fix upload file selector value resetting
 2018-08-07 15:24:27 -04:00
guerler 1d0f51a05e Fix upload file selector value resetting 
Fix
 2018-08-07 14:47:23 -04:00
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
Dannon 6d9df51f36 Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery 
[18.01] Use subworkflow index when setting auto-label
 2018-08-06 20:14:56 -04:00
Marius van den Beek 6c7b9a3c7d Merge pull request #6532 from dannon/fix-dataset-copy-tags 
[18.05] Fix dataset copy tags
 2018-08-06 21:14:16 +02:00
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
mvdbeek ba47188f5e Introduce test for auto-labelling subworkflow workflow outputs 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
Björn Grüning 0a9010156e Merge pull request #6538 from jmchilton/tool_output_io 
[18.01] Fix to_dict with io_details=True for tools with collection outputs.
 2018-07-26 22:26:41 +02:00
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
John Chilton 50b3418539 Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0 
[18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
 2018-07-23 11:30:07 -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
Martin Cech ef702e1458 Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b 
[18.05] Fix infinite loop in uploads
 2018-07-17 14:52:26 -04:00
John Chilton 7b8e4f9e74 Fix empty datatypes. 2018-07-17 17:56:19 +01:00
Marius van den Beek fd33c5c6d6 Merge pull request #6497 from martenson/backport-takadonet 
[18.05] backport ftp purge fix
 2018-07-13 11:51:09 +02:00
Nicola Soranzo dfc996c8d6 Merge branch 'release_18.01' into release_18.05 2018-07-13 01:01:13 +01:00
takadonet 4b0ae30a83 Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 2018-07-12 16:35:35 -04:00