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Author SHA1 Message Date
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
guerler 9967639bac Comma-separate tool names in missing tools error message 2018-06-22 00:30:17 -04:00
Nate Coraor d28ab2a4f3 Merge pull request #6377 from martenson/catch-sanitization-faults 
[18.05] Catch sanitization faults
 2018-06-21 18:47:54 -04:00
Martin Cech 572f38d1fb move the sanitization to the try/except block 
as it may fail (and it did, on Main)
 2018-06-21 15:44:05 -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
Dannon Baker bcf105cbb3 Client build. 2018-06-20 10:11:31 -04:00
Dannon Baker b8536c2005 Merge remote-tracking branch 'jmchilton/collection_fixes' into release_18.05 2018-06-20 10:10:17 -04:00
Dannon 128a1731e4 Merge pull request #6360 from guerler/legacy_modal_scrolling 
[18.05] Fix size handling in legacy modal view
 2018-06-20 10:04:58 -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 647ba8531a Add test tool and workflow for mapping over with mapping output 
This doesn't quite work because of the dynamic output collection,
which fails with:

```
galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms)
galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection.
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs
    collection_builder.populate()
  File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate
    elements = self.build_elements()
  File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements
    new_elements[identifier] = element.build()
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build'
```

This seems to happen because the inner collection is wrongly detected as
nested. In general I doubt that mapping over colleciton output works
with dynamically discovered output collections.
 2018-06-20 09:54:40 -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 7cfbb032f6 Break test by adding "list" to collection_type 
This will break tests trying to map over list:pair collections,
for instance test_extract_workflows_with_dataset_collections.
 2018-06-20 09:54:36 -04:00
mvdbeek 9e3de244d7 Fix mapping list over multidata input 2018-06-20 09:54:02 -04:00
mvdbeek 6b7ee55bac Test list collection mapping over multidata input 2018-06-20 09:54:01 -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
Dannon 817d043f12 Merge pull request #6361 from guerler/fix_msa 
[18.05] Add fasta datatype to msa viewer
 2018-06-19 20:49:39 -04:00
guerler b0212ff45c Add phylip for msa viewer 2018-06-19 17:23:52 -04:00
guerler f6888a32d6 Add fasta datatype to msa viewer 2018-06-19 14:14:44 -04:00
guerler 9f4926bd9a Limit modal body size to 67 percent of window height 2018-06-19 14:00:08 -04:00
guerler 69c8ce7e92 Fix size handling in legacy modal view 2018-06-19 13:11:46 -04:00
John Chilton 48fafa8096 Merge pull request #6358 from dannon/1805sharingfix 
[18.01] Fix 'share with another user'
 2018-06-19 13:03:58 -04:00
Dannon Baker eed703eef8 Fix share with another user in 18.05 2018-06-19 10:26:53 -04:00
Dannon bde05ac88b Merge pull request #6354 from martenson/superdefensive-grt 
[18.05] grt - wrap every write in try-except
 2018-06-18 18:56:22 -04:00
Martin Cech f21c8caf83 unname the exception 2018-06-18 16:47:19 -04:00
Martin Cech 2b8b4e198d grt - wrap every write in try-except 
and just fail the row if the data is crap
(like {NULL, SOH, STX, ETX} and friends)
 2018-06-18 16:16:05 -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 e8beea0d60 Merge branch 'release_18.01' into release_18.05 2018-06-17 12:05:50 +01:00
Björn Grüning 3707fb4eb1 Merge pull request #6336 from dannon/backport_url_fix_flattened 
[18.01] Backport backbone url fixes (flattened)
 2018-06-17 12:32:48 +02:00
John Chilton a2ff5efbce Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd 
[18.05] Added missing level fatal_oom to xsd
 2018-06-16 08:47:32 -04:00
Martin Cech 12a05c7820 Merge pull request #6344 from dannon/python_static_staging 
[18.05] Visualization static staging
 2018-06-15 17:08:44 -05:00
Nicola Soranzo cddee94e4b Small fixes 2018-06-15 20:08:18 +01:00
Nicola Soranzo 37ad1a8bdc Merge pull request #6345 from mvdbeek/update_pbs_python_doc 
[18.01] Update description for installing pbs-python
 2018-06-15 19:59:54 +01:00
Dannon Baker 4cdd210bb2 Use os.pardir instead of ../. Thanks @nsoranzo 2018-06-15 14:49:46 -04:00
Dannon Baker 8364ebebcd Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink 2018-06-15 14:11:19 -04:00
Dannon Baker 370ea25d2c Minor refactoring, comments. 2018-06-15 12:48:02 -04:00
mvdbeek 9ac0161891 Update description for installing pbs-python 2018-06-15 18:11:50 +02:00
Dannon Baker e110489cc5 Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently) 2018-06-15 11:46:08 -04:00