Dannon Baker
f9ba72f0ae
Merge remote-tracking branch 'upstream/release_18.05' into dev
2018-06-20 10:15:29 -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
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[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
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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
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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
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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
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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.
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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
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[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
Dannon
bde05ac88b
Merge pull request #6354 from martenson/superdefensive-grt
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[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
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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
1c7387c53a
Merge pull request #6072 from mvdbeek/add_resume_job_api
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Add resume job api
2018-06-18 15:11:14 -04:00
Björn Grüning
e9efb47b59
Merge pull request #6302 from davebx/cuffdiff_datatype
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Add specific datatype for CuffDiff SQLite database.
2018-06-18 20:58:22 +02:00
Nicola Soranzo
6e02c9aff7
Merge branch 'release_18.05' into dev
2018-06-17 13:11:47 +01:00
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
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[18.01] Backport backbone url fixes (flattened)
2018-06-17 12:32:48 +02:00
Marius van den Beek
02974b79c7
Merge pull request #5640 from Mataivic/patch-1
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Add a FilterEmptyDatasetsTool and allow filtering tools to apply to arbitrary collection structures
2018-06-17 12:25:03 +02:00
John Chilton
a2ff5efbce
Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd
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[18.05] Added missing level fatal_oom to xsd
2018-06-16 08:47:32 -04:00
John Chilton
db11a2549d
Merge pull request #6349 from dpryan79/preventExceptionOnFileAccess
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Prevent throwing an exception if a dataset doesn't exist (and never w…
2018-06-16 08:33:09 -04:00
Martin Cech
12a05c7820
Merge pull request #6344 from dannon/python_static_staging
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[18.05] Visualization static staging
2018-06-15 17:08:44 -05:00
dpryan79
82c965f1c6
Prevent throwing an exception if a dataset doesn't exist (and never will) due to a job error. This is an alternative (and better) solution to #6337 when jobs set metadata externally.
2018-06-15 21:38:16 +02:00
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
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[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
Dannon Baker
fc47618f67
Initial python-based plugin staging. to be used from common startup.
2018-06-15 11:41:06 -04:00
M Bernt
8d75a67386
also added missing documentation
2018-06-15 16:42:16 +02:00
M Bernt
c2307f3f1a
added missing level fatal_oom to xsd
2018-06-15 15:54:45 +02:00
Dannon Baker
2e7dd84583
Rebuild client w/ maps.
2018-06-14 10:03:05 -04:00
Dannon Baker
3a17db8f20
Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things
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Convert history-contents urlroot to instance var
remove outdated comment
2018-06-14 09:48:05 -04:00
mvdbeek
72dd53f55e
Update comments to the fact that we're processing list or list:paired collections
2018-06-13 20:50:05 +02:00
Dannon
b41af6abe9
Merge pull request #6303 from guerler/history_polling
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Stop listening to history changes after job submission
2018-06-13 13:43:18 -04:00
mvdbeek
5992629619
Map over list or list:paired collection in filter collection tools
2018-06-13 16:38:37 +02:00
mvdbeek
0507818bbe
Add tests for filtering list:pair and list:list:pair collections
2018-06-13 16:38:37 +02:00
mvdbeek
46d8b318ba
Correct help text of filter_failed_collection and filter_empty_collection tools
2018-06-13 16:38:37 +02:00
mvdbeek
babe2e5cc5
Change get_new_elements to _get_new_elements
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And use same order for arguments in signature and caller.
2018-06-13 16:32:01 +02:00
Dannon Baker