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Author SHA1 Message Date
Dannon Baker b8fa78358c Remove outdated comment; I refactored to handle this. 2018-08-28 13:21:35 -04:00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
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
John Chilton 23666c94a2 Merge pull request #6477 from natefoo/backport-pr-6351 
[18.01] Fix the --log-file option in the job handlers
 2018-07-11 09:29:22 -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
Nicola Soranzo 3fe88a9bfe Merge pull request #6465 from dannon/backport-gie-static-again 
[18.05] Backport of IE static url fix (to actual 18.05)
 2018-07-05 08:56:58 +01:00
thobalose 0c97d4ff5c GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 2018-07-04 11:33:32 -04:00
Martin Cech 39d7cf2eb7 Merge pull request #6433 from jmchilton/hack_6299 
[18.05] decode potential encoded id
 2018-07-01 16:14:13 -07:00
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
Martin Cech 36706e9eb3 Merge pull request #6385 from dannon/revert-baiconverter-removal 
[18.01] Revert "Remove bam to bai converter"
 2018-06-22 13:08:13 -05:00
mvdbeek 5f24794efd Add basic .bai datatype 2018-06-22 19:50:43 +02:00
Dannon Baker fa2b6baef7 Revert "Remove bam to bai converter" 
This reverts commit 7e2727bc0a.
 2018-06-22 13:22:51 -04:00
Dannon 22d383c398 Merge pull request #6378 from guerler/commaseperror 
[18.05] Comma-separate tool names in missing tools error message
 2018-06-22 08:24:22 -04:00