1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/db520d154716/
Changeset: db520d154716
Branch: stable
User: natefoo
Date: 2014-09-04 16:00:23
Summary: Update tag latest_2014.08.11 for changeset e8453771b1db
Affected #: 1 file
diff -r e8453771b1dbfe462974b63216e00752fb8c4097 -r db520d1547165e56b3a0a0ff01fb854c0f93e4b1 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-20f4fdf1735aeff23a6e7ab00389781fe3f3142c latest_2014.08.11
+e8453771b1dbfe462974b63216e00752fb8c4097 latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e8453771b1db/
Changeset: e8453771b1db
Branch: stable
User: jmchilton
Date: 2014-09-03 22:05:29
Summary: Fix tool rerunning for data_collection parameters.
Bug report from takadonet - https://gist.github.com/Takadonet/ba21ca26748a459615e3. My testing shows this fixes that bug and likewise he confirmed the fix works.
Affected #: 1 file
diff -r 8b183d7571ab1180f8a82e0dfbaf57b098cc50a6 -r e8453771b1dbfe462974b63216e00752fb8c4097 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2096,6 +2096,8 @@
elif isinstance( value, basestring ):
if value.startswith( "dce:" ):
rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
+ elif value.startswith( "hdca:" ):
+ rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] )
else:
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value )
if rval and isinstance( rval, trans.app.model.HistoryDatasetCollectionAssociation ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ebbc5e725c62/
Changeset: ebbc5e725c62
User: jmchilton
Date: 2014-09-03 21:17:49
Summary: Fill out tool test for configured discovered datasets.
Add new example based on Anton's bamtools split work and label all the outputs as visible - this should likely be the default but until it is might as well demonstrate them as visible since that is how they are most useful.
Affected #: 1 file
diff -r e128330d8e78e3d2d7bbc5f60c7515fab9762626 -r ebbc5e725c62e22926e5c0141aeaa95a3da20239 test/functional/tools/multi_output_configured.xml
--- a/test/functional/tools/multi_output_configured.xml
+++ b/test/functional/tools/multi_output_configured.xml
@@ -10,6 +10,8 @@
echo "3" > subdir2/CUSTOM_3.txt;
mkdir subdir3;
echo "Foo" > subdir3/Foo;
+ echo "mapped reads" > split_bam_.MAPPED.bam;
+ echo "unmapped reads" > split_bam_.UNMAPPED.bam;
</command><inputs><param name="num_param" type="integer" value="7" />
@@ -17,9 +19,10 @@
</inputs><outputs><data format="txt" name="report">
- <discover_datasets pattern="__designation_and_ext__" directory="subdir1" />
- <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" />
- <discover_datasets pattern="__designation__" directory="subdir3" ext="input" />
+ <discover_datasets pattern="__designation_and_ext__" directory="subdir1" visible="true" />
+ <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" visible="true" />
+ <discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" />
+ <discover_datasets pattern="split_bam_\.(?P<designation>([A-Z-])\w+)\.bam" ext="txt" visible="true" /></data></outputs><tests>
@@ -45,6 +48,12 @@
<discovered_dataset designation="Foo" ftype="txt"><assert_contents><has_line line="Foo" /></assert_contents></discovered_dataset>
+ <discovered_dataset designation="MAPPED" ftype="txt">
+ <assert_contents><has_line line="mapped reads" /></assert_contents>
+ </discovered_dataset>
+ <discovered_dataset designation="UNMAPPED" ftype="txt">
+ <assert_contents><has_line line="unmapped reads" /></assert_contents>
+ </discovered_dataset></output></test></tests>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e128330d8e78/
Changeset: e128330d8e78
User: martenson
Date: 2014-09-03 17:14:42
Summary: small bugfix and new method in folder manager
Affected #: 1 file
diff -r 3180ca1c1994705a17dedb5d6c4f8373b4f5aae4 -r e128330d8e78e3d2d7bbc5f60c7515fab9762626 lib/galaxy/managers/folders.py
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -83,7 +83,7 @@
Check whether the folder is accessible to current user.
By default every folder is accessible (contents have their own permissions).
"""
- return True
+ return folder
def get_folder_dict( self, trans, folder ):
"""
@@ -156,6 +156,19 @@
add_library_item_role_list = [ ( add_role.name, trans.security.encode_id( add_role.id ) ) for add_role in add_roles ]
return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list )
+ def can_add_item( self, trans, folder ):
+ """
+ Return true if the user has permissions to add item to the given folder.
+ """
+ if trans.user_is_admin:
+ return True
+ current_user_roles = trans.get_current_user_roles()
+ add_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) )
+ for role in current_user_roles:
+ if role in add_roles:
+ return True
+ return False
+
def cut_the_prefix( self, encoded_folder_id ):
"""
Remove the prefix from the encoded folder id.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8b183d7571ab/
Changeset: 8b183d7571ab
Branch: stable
User: natefoo
Date: 2014-09-03 16:00:28
Summary: Update tag latest_2014.08.11 for changeset 20f4fdf1735a
Affected #: 1 file
diff -r 20f4fdf1735aeff23a6e7ab00389781fe3f3142c -r 8b183d7571ab1180f8a82e0dfbaf57b098cc50a6 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-ea12550fbc34260ae70bde38db59a4024f35f988 latest_2014.08.11
+20f4fdf1735aeff23a6e7ab00389781fe3f3142c latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3180ca1c1994/
Changeset: 3180ca1c1994
User: carlfeberhard
Date: 2014-09-03 15:30:27
Summary: Visualizations registry: in universe_wsgi.ini, set default value of visualization_plugins_directory to config/plugins/visualizations
Affected #: 3 files
diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r 3180ca1c1994705a17dedb5d6c4f8373b4f5aae4 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -96,11 +96,9 @@
# Load history import/export tools.
load_history_imp_exp_tools( self.toolbox )
# visualizations registry: associates resources with visualizations, controls how to render
- self.visualizations_registry = None
- if self.config.visualization_plugins_directory:
- self.visualizations_registry = VisualizationsRegistry( self,
- directories_setting=self.config.visualization_plugins_directory,
- template_cache_dir=self.config.template_cache )
+ self.visualizations_registry = VisualizationsRegistry( self,
+ directories_setting=self.config.visualization_plugins_directory,
+ template_cache_dir=self.config.template_cache )
# Load security policy.
self.security_agent = self.model.security_agent
self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions )
diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r 3180ca1c1994705a17dedb5d6c4f8373b4f5aae4 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -376,8 +376,9 @@
self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) )
self.fluent_host = kwargs.get( 'fluent_host', 'localhost' )
self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) )
- # visualization plugin framework
- self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', None )
+ # directory where the visualization/registry searches for plugins
+ self.visualization_plugins_directory = kwargs.get(
+ 'visualization_plugins_directory', 'config/plugins/visualizations' )
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
diff -r 012e6eb765684020eb597d8925e4ca5b58b9d904 -r 3180ca1c1994705a17dedb5d6c4f8373b4f5aae4 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -210,8 +210,8 @@
# Visualizations config directory: where to look for individual visualization plugins.
# The path is relative to the Galaxy root dir. To use an absolute path begin the path
-# with '/'.
-visualization_plugins_directory = config/plugins/visualizations
+# with '/'. Defaults to "config/plugins/visualizations".
+#visualization_plugins_directory = config/plugins/visualizations
# Each job is given a unique empty directory as its current working directory.
# This option defines in what parent directory those directories will be
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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