Nate Coraor
41b13f6d85
Merge branch 'release_17.09' into dev
2017-09-21 15:27:30 -04:00
Nate Coraor
4dbadc26e4
Merge branch 'release_17.05' into release_17.09
2017-09-21 15:27:05 -04:00
Nate Coraor
cfabe37d69
Merge branch 'release_17.01' into release_17.05
2017-09-21 15:26:24 -04:00
Nate Coraor
706a5b2cd2
Merge branch 'release_16.10' into release_17.01
2017-09-21 15:25:36 -04:00
Nate Coraor
e178879c0f
Merge branch 'release_16.07' into release_16.10
2017-09-21 15:25:16 -04:00
John Chilton
87d5d44023
Merge pull request #4635 from mvdbeek/reload_on_macro_changes
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Reload tools if a macro changes
2017-09-21 10:19:42 -04:00
John Chilton
e057d7d887
Merge pull request #4620 from guerler/reduce_viz_framework
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Remove unused abstraction layers from Visualizations Registry
2017-09-21 10:13:52 -04:00
John Chilton
d3d134030a
Rework #4635 to preserve backward compatibility on modules shared via galaxy-lib.
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Also cleanup comments and such in xml_macros to reflect this doesn't apply just to tools.
2017-09-21 10:09:19 -04:00
John Chilton
669f944292
Merge pull request #4664 from dannon/template_cleanup
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More unused template cleanup
2017-09-21 09:06:14 -04:00
Dannon Baker
12d9026b99
Merge branch 'admin_grid_formbuilder' into dev
2017-09-21 07:39:48 -04:00
Nate Coraor
69a87003f7
Fix modules resolver (addition of the resolver_msg property on the base
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class references name and version attributes that were not defined in
the ModuleDependecy).
2017-09-20 20:26:21 -04:00
Dannon Baker
e6fc47c495
Minor typo found while grepping around.
2017-09-20 19:30:06 -04:00
Martin Cech
b7694ef656
Update version to 18.01.dev
2017-09-19 14:32:46 -04:00
Martin Cech
eee4a17a4c
Update version to 17.09.rc1
2017-09-19 14:32:41 -04:00
John Chilton
7d394f202d
Merge pull request #4640 from martenson/datalibs-optimize-access-checks
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optimize the process of identifying public libraries
2017-09-19 14:18:18 -04:00
Martin Cech
c5d29be0a2
avoid mutable default, improve docs
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switch to set comprehension
2017-09-19 11:44:43 -04:00
mvdbeek
d980dfa162
Write registry.xml for all tools that require galaxy's python env
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This should cover the upload and data_source tools.
2017-09-19 16:02:40 +02:00
John Chilton
a17ae7b90c
Merge pull request #4617 from mvdbeek/data_manager_watch_new_tables
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Allow adding new data tables without restart
2017-09-19 09:09:38 -04:00
mvdbeek
ac10e0d224
Reload tools if a macro changes
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We do this by recording any macros that are required to load a tool. When
loading a tool we register the macro to be watched, and if the macro changes we
reload all corresponding tools.
2017-09-19 12:16:05 +02:00
mvdbeek
a3ff129743
Explicitly write registry.xml when creating a job for the upload tool
2017-09-19 11:20:25 +02:00
Martin Cech
8a4c637388
optimize the process of identifying public libraries
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this aims to speed up the library loading considerably
2017-09-18 14:50:36 -04:00
guerler
c9db5f8dfe
Merge branch 'dev' into admin_grid_formbuilder
2017-09-18 10:24:23 -04:00
Marius van den Beek
d9a8055368
Merge pull request #4636 from bgruening/find_file
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remove .git and .hg from recursive file search
2017-09-18 14:21:40 +02:00
Nicola Soranzo
ef602e1d1a
Merge branch 'release_17.05' into dev
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Conflicts:
lib/galaxy/datatypes/registry.py
lib/galaxy/jobs/__init__.py
lib/galaxy/jobs/command_factory.py
lib/galaxy/tools/actions/metadata.py
lib/galaxy/tools/evaluation.py
2017-09-18 11:09:00 +01:00
Eric Rasche
cfb0d06575
Exclude venv
2017-09-18 11:51:30 +02:00
Björn Grüning
5f635bda10
remove .git and .hg from recursive file search
2017-09-17 00:54:33 +02:00
John Chilton
4c9cc67a8f
Merge pull request #4630 from VJalili/patch-4
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Refactored a dataset variable to hda
2017-09-16 07:12:14 -04:00
John Chilton
6dbd47e661
Merge pull request #4632 from mvdbeek/fix_unintended_change
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[BUG] Restore tool provided metadata path in setup_external_metdata
2017-09-16 07:10:33 -04:00
mvdbeek
e03ee53f3c
Remove references to integrated_datatypes_config
2017-09-16 11:38:42 +02:00
mvdbeek
432d7f4405
Restore correct metadata path in setup_external_metdata
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This is a change I shouldn't have touched in
https://github.com/galaxyproject/galaxy/pull/4600
2017-09-16 09:02:33 +02:00
Vahid
2897992ab5
Refactored a dataset variable to hda
2017-09-15 14:47:32 -07:00
Vahid
604fdde424
typo
2017-09-15 14:38:09 -07:00
Vahid
3cca06a153
updated a comment.
2017-09-15 14:24:27 -07:00
Vahid
e3e26ae202
Updated a comment
2017-09-15 13:40:54 -07:00
Vahid
860f0ab6ba
Some function description updates
2017-09-15 13:20:25 -07:00
mvdbeek
2c77d386de
Write out registry once per job
2017-09-15 21:57:09 +02:00
Vahid
69af37f653
Typo fix
2017-09-15 12:24:09 -07:00
Dannon Baker
d5aba7da15
Three more looses.
2017-09-15 10:28:58 -04:00
guerler
b6949ac563
Remove unused imports
2017-09-15 09:43:11 -04:00
mvdbeek
2d844a86e7
Add watchdog to dev-requirements so it is available for integration tests
2017-09-15 14:42:48 +02:00
mvdbeek
4b40300827
Remove unused root_dir argument
2017-09-15 14:41:56 +02:00
Eric Rasche
c5ff555ec4
Merge pull request #4611 from martenson/respect-email-exposure
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respect expose_user_email configuration in datalibraries permissions list
2017-09-15 14:17:39 +02:00
mvdbeek
a4c4d826dc
Make watchdog a conditional dependency
2017-09-15 13:19:06 +02:00
mvdbeek
2e6654b18b
Linting fixes
2017-09-15 13:19:06 +02:00
mvdbeek
d06fb09f4b
Make DynamicOptions use updated tool_data_tables
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Otherwise a restart would be necessary after adding items to a data
table.
2017-09-15 13:19:06 +02:00
guerler
2d4689a8f7
Remove unused fill template caller, this handled by the plugin itself not by the registry
2017-09-14 19:48:08 -04:00
guerler
3daae84408
Remove unused template helper from previously inherited base class
2017-09-14 19:46:08 -04:00
guerler
d6dad603e8
Remove unnecessary static path caller
2017-09-14 19:42:11 -04:00
guerler
f558970ef1
Remove unused custom base url option, handle plugin route same as for interactive environments
2017-09-14 19:27:29 -04:00
guerler
9a4175e073
Move constants
2017-09-14 19:24:01 -04:00
Nate Coraor