Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 14cfb26ca1b888156ae517dc33ebeefc099bac6f
https://github.com/galaxyproject/galaxy/commit/14cfb26ca1b888156ae517dc33eb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Give NO_REPLACEMENT constant object a str value.
Shows up in logging a lot and such - make it more clear.
Commit: 95962d9e5aa2b3b8e60755767b0dbc06ef341782
https://github.com/galaxyproject/galaxy/commit/95962d9e5aa2b3b8e60755767b0d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M test/base/populators.py
Log Message:
-----------
More correct file_data handling in populators.py.
Any of file_N|file_data fields can have attached data.
Commit: 31640840e310f76dc38e24f4147c0d4d1959f178
https://github.com/galaxyproject/galaxy/commit/31640840e310f76dc38e24f4147c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
Log Message:
-----------
Fix consumption of macro paths from tool spec.
Commit: 5551611aff92f55c7b1e00f573c44473b6b2823a
https://github.com/galaxyproject/galaxy/commit/5551611aff92f55c7b1e00f573c4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M lib/galaxy/model/mapping.py
Log Message:
-----------
Drop old comment, we use this variable now and have for some time.
Commit: b50ae948368abae7f91af8e2d4f3cbc69418ab92
https://github.com/galaxyproject/galaxy/commit/b50ae948368abae7f91af8e2d4f3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-15 (Tue, 15 May 2018)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Move workflow api test helpers into base class for more reuse.
Commit: 5a27b0cf4d4105f61c7660b63de97d812346df13
https://github.com/galaxyproject/galaxy/commit/5a27b0cf4d4105f61c7660b63de9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/populators.py
Log Message:
-----------
Merge pull request #6148 from jmchilton/cwl-small-stuff-2
Small fixes and small refactorings toward reuse in CWL branch (retry)
Compare: https://github.com/galaxyproject/galaxy/compare/d514ebce3bfe...5a27b0cf4d41
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6e78a440b308a0a0df541b6d98891d17b99a2a46
https://github.com/galaxyproject/galaxy/commit/6e78a440b308a0a0df541b6d9889…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-18 (Fri, 18 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add impersonate to main user grid when it's enabled
Commit: 96b4532e9999b816df3dcc5de6e7c2d7607b5ec6
https://github.com/galaxyproject/galaxy/commit/96b4532e9999b816df3dcc5de6e7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-18 (Fri, 18 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
M templates/admin/impersonate.mako
Log Message:
-----------
Drop emails query we weren't actually even using...
Commit: 3bd8b3b18b6032e8844795fae488e501074cd573
https://github.com/galaxyproject/galaxy/commit/3bd8b3b18b6032e8844795fae488…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-18 (Fri, 18 May 2018)
Changed paths:
M client/galaxy/scripts/apps/panels/admin-panel.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/admin/impersonate.mako
M templates/webapps/galaxy/admin/center.mako
Log Message:
-----------
Impersonation refactoring, condense functionality into user grid, optimize some stuff.
Commit: ce2893d50d1e2914fa2193aea26d563258a11bc9
https://github.com/galaxyproject/galaxy/commit/ce2893d50d1e2914fa2193aea26d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Add APIKey generation operation to user grid.
Commit: 5e9cd276ebbef84a0091ef3b531d4b5553874bff
https://github.com/galaxyproject/galaxy/commit/5e9cd276ebbef84a0091ef3b531d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Match existing formatting.
Commit: c3d01f0505a42903f4fd2bc42d8e5bdce13315d3
https://github.com/galaxyproject/galaxy/commit/c3d01f0505a42903f4fd2bc42d8e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Actually include new_key in msgstring
Commit: fb199c5f8c8083e78cc50d62b1c77c9fec21f249
https://github.com/galaxyproject/galaxy/commit/fb199c5f8c8083e78cc50d62b1c7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Slight safeguarding of user selection, respond with a more contextualized message
Commit: 61e2e82a09047b5b1d4194259012178bc8dfd7f8
https://github.com/galaxyproject/galaxy/commit/61e2e82a09047b5b1d4194259012…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
R client/galaxy/scripts/components/admin/UserAPIKeys.vue
Log Message:
-----------
Drop individual UserAPIKeys.vue; this functionality is included in the standard user grid now.
Commit: 9dcb1019c5afe76c864cb4e361509b4f47f215c2
https://github.com/galaxyproject/galaxy/commit/9dcb1019c5afe76c864cb4e36150…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-05-21 (Mon, 21 May 2018)
Changed paths:
M templates/webapps/galaxy/admin/center.mako
Log Message:
-----------
Drop separate APIKeys blurb
Commit: d514ebce3bfe936091f57d22bbafbca48d419fa8
https://github.com/galaxyproject/galaxy/commit/d514ebce3bfe936091f57d22bbaf…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
R client/galaxy/scripts/components/admin/UserAPIKeys.vue
M lib/galaxy/webapps/galaxy/controllers/admin.py
R templates/admin/impersonate.mako
M templates/webapps/galaxy/admin/center.mako
Log Message:
-----------
Merge pull request #6176 from dannon/user_grid_impersonate
Add impersonate to main user grid when it's enabled
Compare: https://github.com/galaxyproject/galaxy/compare/542dbe63e896...d514ebce3bfe
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f59b13c1cdb8e688d6738463ce54027e53d61cb7
https://github.com/galaxyproject/galaxy/commit/f59b13c1cdb8e688d6738463ce54…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
Log Message:
-----------
Replace non-existent `tab` format with `tabular` in 2 tools
Also:
- Remove deprecated `interpreter` attribute of `<command>`
- Single-quote text and data parameters inside the command
- Fix wrong `name` attribute of `output` in 3 tests
- Linting and cleanups
Commit: b454bef75de0730b80820326eb53c2501b8baa05
https://github.com/galaxyproject/galaxy/commit/b454bef75de0730b80820326eb53…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-04 (Mon, 04 Jun 2018)
Changed paths:
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
Log Message:
-----------
Fix indentation
Commit: 542dbe63e89689daec88ab0d075ad7f1f77bf0b0
https://github.com/galaxyproject/galaxy/commit/542dbe63e89689daec88ab0d075a…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
Log Message:
-----------
Merge pull request #6269 from nsoranzo/phenotype_association_tools
Fixes for phenotype association tools
Compare: https://github.com/galaxyproject/galaxy/compare/9b9ab6a1cf44...542dbe63e896
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 713bca04f63f464ccbb47ced90d971624ed075b6
https://github.com/galaxyproject/galaxy/commit/713bca04f63f464ccbb47ced90d9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Allow #if $datasets #end if patern for file lists
Otherwise the following exception occurs:
```
Traceback (most recent call last):
File "/home/wolffj/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job
job_wrapper.prepare()
File "/home/wolffj/src/galaxy/lib/galaxy/jobs/__init__.py", line 858, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/home/wolffj/src/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build
raise e
AttributeError: 'DatasetListWrapper' object has no attribute 'value'
```
This is because DatasetListWrapper inherits `__bool__` from ToolParameterValueWrapper
which defines bool as
```
def __bool__(self):
return bool(self.value)
__nonzero__ = __bool__
```
while DatasetListWrapper has no `value` attribute.
Fixes https://github.com/galaxyproject/galaxy/issues/6314 reported by
@joachimwolff (many thanks for the detailed report!).
Commit: 0a29e533d3362e3a0dd7bfc202e8fff799a9e6ee
https://github.com/galaxyproject/galaxy/commit/0a29e533d3362e3a0dd7bfc202e8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M test/functional/tools/multi_data_optional.xml
Log Message:
-----------
Use #if $datasets #end if pattern in test tool
Commit: 6f213b36975b5b8f66b0b02f8920744a5e2d0064
https://github.com/galaxyproject/galaxy/commit/6f213b36975b5b8f66b0b02f8920…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Fix __bool__ for empty optional multidata parameters
Commit: 550eb882100a3a9210689dbe789b67a1eb2ba5c2
https://github.com/galaxyproject/galaxy/commit/550eb882100a3a9210689dbe789b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M test/functional/tools/multi_data_optional.xml
Log Message:
-----------
Add a test for not providing an optional input
Commit: 9b9ab6a1cf4485920c88b252d27642f6f20c3525
https://github.com/galaxyproject/galaxy/commit/9b9ab6a1cf4485920c88b252d276…
Author: Helena Rasche <hxr(a)hx42.org>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/wrappers.py
M test/functional/tools/multi_data_optional.xml
Log Message:
-----------
Merge pull request #6317 from mvdbeek/fix_6314
Allow #if $datasets #end if pattern for file lists
Compare: https://github.com/galaxyproject/galaxy/compare/c08f7c9a4cfd...9b9ab6a1cf44
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6c2f1957a9c49943182b8b971097f9a8ef511bab
https://github.com/galaxyproject/galaxy/commit/6c2f1957a9c49943182b8b971097…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-04 (Fri, 04 May 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/base/data/rules_dsl_spec.yml
Log Message:
-----------
Rules - test case and bug fixes for adding cols for regex groups.
Commit: 898e73eca1eccfb9fb707cdb5af75ee72c3d7565
https://github.com/galaxyproject/galaxy/commit/898e73eca1eccfb9fb707cdb5af7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-04 (Fri, 04 May 2018)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Rules - bug fix for apply_rules tool on nested collections.
Commit: ec723829bf788b3100bfb56f72c22dd4981e3fdf
https://github.com/galaxyproject/galaxy/commit/ec723829bf788b3100bfb56f72c2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-04 (Fri, 04 May 2018)
Changed paths:
M lib/galaxy/tools/apply_rules.xml
Log Message:
-----------
Rules - fix poor name for Apply Rules output collection.
Commit: 050c9e99c6c981518f160d99aeaa2f395a84e4b5
https://github.com/galaxyproject/galaxy/commit/050c9e99c6c981518f160d99aeaa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-05-05 (Sat, 05 May 2018)
Changed paths:
A test-data/rules/treated1fb.txt
A test-data/rules/treated2fb.txt
A test-data/rules/treated3fb.txt
A test-data/rules/untreated1fb.txt
A test-data/rules/untreated2fb.txt
A test-data/rules/untreated3fb.txt
A test-data/rules/untreated4fb.txt
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Rules - test case for apply rules tutorial.
Demonstrates using the Apply Rules collection operation tool against existing collections to:
- Use grouping to build nested lists from flat ones.
- Invert nested collections.
- Filter collections.
- Filter while also grouping to build nested collections.
Based on count data used in the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq…), originally from the Bioconductor Pasilla package (http://bioconductor.org/packages/release/data/experiment/html/pasilla.html). Citation: Huber W, Reyes A (2018). pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.. R package version 1.8.0.
Commit: 1b50504678dc5c84fa292236ac58697591611aa4
https://github.com/galaxyproject/galaxy/commit/1b50504678dc5c84fa292236ac58…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-06-12 (Tue, 12 Jun 2018)
Changed paths:
M lib/galaxy/tools/apply_rules.xml
A test-data/rules/treated1fb.txt
A test-data/rules/treated2fb.txt
A test-data/rules/treated3fb.txt
A test-data/rules/untreated1fb.txt
A test-data/rules/untreated2fb.txt
A test-data/rules/untreated3fb.txt
A test-data/rules/untreated4fb.txt
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #6066 from jmchilton/apply_rules_tutorials
Rules - test case for apply rules tutorial.
Compare: https://github.com/galaxyproject/galaxy/compare/178486b840b6...1b50504678dc
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 940ed5f5dd1f34456d81513db8bbf0a66476e683
https://github.com/galaxyproject/galaxy/commit/940ed5f5dd1f34456d81513db8bb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M test/functional/tools/for_workflows/cat_collection.xml
Log Message:
-----------
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.
Commit: cb97f89d129cf7f0b7cf7146c0c15309b3dcb0c7
https://github.com/galaxyproject/galaxy/commit/cb97f89d129cf7f0b7cf7146c0c1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-08 (Fri, 08 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/history_query.py
Log Message:
-----------
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.
Commit: 9b19d5c267900409b5aace9f2c554b2da13ce8e7
https://github.com/galaxyproject/galaxy/commit/9b19d5c267900409b5aace9f2c55…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
Log Message:
-----------
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.
Commit: fd16302d65193f13eb04456b610044343ca54adb
https://github.com/galaxyproject/galaxy/commit/fd16302d65193f13eb04456b6100…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M test/api/test_workflows.py
A test/functional/tools/collection_type_source_map_over.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
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.
Commit: 258ccb89bd5190e703f9d1705ec888b65ce77724
https://github.com/galaxyproject/galaxy/commit/258ccb89bd5190e703f9d1705ec8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Consider mapping-over when picking collection_type for dynamically discovered collections
Commit: fc06a7a168d5d36fabb3f6f420a4ef0b12363f2c
https://github.com/galaxyproject/galaxy/commit/fc06a7a168d5d36fabb3f6f420a4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over
Commit: 178486b840b64c2bfb1b4cffefd44c945a8ccb3e
https://github.com/galaxyproject/galaxy/commit/178486b840b64c2bfb1b4cffefd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-11 (Mon, 11 Jun 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/history_query.py
M test/api/test_workflows.py
A test/functional/tools/collection_type_source_map_over.xml
M test/functional/tools/for_workflows/cat_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6278 from mvdbeek/fix_paired_mapping_over
Various fixes for mapping over collections
Compare: https://github.com/galaxyproject/galaxy/compare/cd2feb7dcb81...178486b840b6
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.