1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/870ed2858703/
Changeset: 870ed2858703
User: guerler
Date: 2013-06-25 20:09:50
Summary: Fix Galaxy CSS utility
Affected #: 1 file
diff -r 75bc22eefbd917b15d118ebbbe01cb2e01864c0d -r 870ed28587032d80fd955ca31c94bf0977f86165 static/scripts/utils/galaxy.css.js
--- a/static/scripts/utils/galaxy.css.js
+++ b/static/scripts/utils/galaxy.css.js
@@ -28,7 +28,7 @@
function load_file (url)
{
// check if css is already available
- if (!$('link[href="' + url + '"]').length)
+ if (!$('link[href^="' + url + '"]').length)
$('<link href="' + url + '" rel="stylesheet">').appendTo('head');
};
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/75bc22eefbd9/
Changeset: 75bc22eefbd9
User: guerler
Date: 2013-06-25 16:52:30
Summary: Update Galaxy Frames CSS
Affected #: 1 file
diff -r f51a4898866a51cfe93c26cf36346a4678a4ca59 -r 75bc22eefbd917b15d118ebbbe01cb2e01864c0d static/style/blue/galaxy.frame.css
--- a/static/style/blue/galaxy.frame.css
+++ b/static/style/blue/galaxy.frame.css
@@ -1,4 +1,7 @@
-body {background: #000000}
+/*
+ galaxy-frames generic styles
+*/
+
.f-corner
{
-moz-border-radius: 4px;
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/f51a4898866a/
Changeset: f51a4898866a
User: Dave Bouvier
Date: 2013-06-25 16:44:27
Summary: Fix issue with change_directory action where the target folder would be appended to the full path twice.
Affected #: 1 file
diff -r e4a8cdf0b3722bbce79a55e5ed7e70306f39885a -r f51a4898866a51cfe93c26cf36346a4678a4ca59 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -313,9 +313,8 @@
extract = action_dict.get( 'extract', False )
common_util.url_download( current_dir, filename, url, extract=extract )
elif action_type == 'change_directory':
- target_directory = os.path.realpath( os.path.join( current_dir, dir, action_dict[ 'directory' ] ) )
- current_working_dir = os.path.realpath( dir )
- if target_directory.startswith( current_working_dir ) and os.path.exists( target_directory ):
+ target_directory = os.path.realpath( os.path.join( current_dir, action_dict[ 'directory' ] ) )
+ if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ):
dir = target_directory
else:
log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory )
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/e4a8cdf0b372/
Changeset: e4a8cdf0b372
User: greg
Date: 2013-06-25 15:51:26
Summary: Fix the Galaxy API for installing tool shed repositories when attempting to install a repository that was previously installed but is not longer in the installed state.
Affected #: 1 file
diff -r 1cbd7fb4e7e1350a489534779545534d82607db7 -r e4a8cdf0b3722bbce79a55e5ed7e70306f39885a lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -266,11 +266,7 @@
action='show',
id=trans.security.encode_id( tool_shed_repository.id ) )
installed_tool_shed_repositories.append( tool_shed_repository_dict )
- elif message:
- log.error( message, exc_info=True )
- trans.response.status = 500
- return dict( status='error', error=message )
- elif not created_or_updated_tool_shed_repositories and not message:
+ else:
# We're attempting to install more than 1 repository, and all of them have already been installed.
return dict( status='error', error='All repositories that you are attempting to install have been previously installed.' )
# Display the list of installed repositories.
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/1cbd7fb4e7e1/
Changeset: 1cbd7fb4e7e1
User: greg
Date: 2013-06-25 14:56:23
Summary: Fix recently introduced bug when the download_file action tag implementation was enhanced. This is related to installing tool dependencies along with a tool shed repository.
Affected #: 1 file
diff -r 05528b8aa8a1decc291f582b34265918c68f798e -r 1cbd7fb4e7e1350a489534779545534d82607db7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -194,7 +194,7 @@
# Download a single file to the working directory.
filtered_actions = actions[ 1: ]
url = action_dict[ 'url' ]
- if action_dict[ 'target_filename' ]:
+ if 'target_filename' in action_dict:
# Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this
# attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction.
filename = action_dict[ 'target_filename' ]
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/80dcf7e41b4a/
Changeset: 80dcf7e41b4a
User: carlfeberhard
Date: 2013-06-24 23:47:29
Summary: Visualizations registry: decompose get_visualzations into both single vis check and all registered check
Affected #: 1 file
diff -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 -r 80dcf7e41b4aec1d5608c05c870a634651af2924 lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -98,11 +98,44 @@
"""
self.listings = VisualizationsConfigParser.parse( self.configuration_filepath )
- #TODO: def get_visualization( self, trans, visualization_name, target_object ):
- # """
- # Is the visualization with the given `visualization_name` applicable
- # to the `target_object`?
- # """
+ def get_visualization( self, trans, visualization_name, target_object ):
+ """
+ Return data to build a url to the visualization with the given
+ `visualization_name` if it's applicable to `target_object` or
+ `None` if it's not.
+ """
+ # a little weird to pass trans because this registry is part of the trans.app
+ listing_data = self.listings.get( visualization_name, None )
+ if not listing_data:
+ return None
+
+ data_sources = listing_data[ 'data_sources' ]
+ for data_source in data_sources:
+ # currently a model class is required
+ model_class = data_source[ 'model_class' ]
+ if not isinstance( target_object, model_class ):
+ continue
+
+ # tests are optional - default is the above class test
+ tests = data_source[ 'tests' ]
+ if tests and not self.is_object_applicable( trans, target_object, tests ):
+ continue
+
+ param_data = data_source[ 'to_params' ]
+ url = self.get_visualization_url( trans, target_object, visualization_name, param_data )
+ link_text = listing_data.get( 'link_text', None )
+ if not link_text:
+ # default to visualization name, titlecase, and replace underscores
+ link_text = visualization_name.title().replace( '_', ' ' )
+ render_location = listing_data.get( 'render_location' )
+ # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html)
+ return {
+ 'href' : url,
+ 'html' : link_text,
+ 'target': render_location
+ }
+
+ return None
# -- building links to visualizations from objects --
def get_visualizations( self, trans, target_object ):
@@ -111,36 +144,11 @@
the urls to call in order to render the visualizations.
"""
#TODO:?? a list of objects? YAGNI?
- # a little weird to pass trans because this registry is part of the trans.app
applicable_visualizations = []
- for vis_name, listing_data in self.listings.items():
-
- data_sources = listing_data[ 'data_sources' ]
- for data_source in data_sources:
- # currently a model class is required
- model_class = data_source[ 'model_class' ]
- if not isinstance( target_object, model_class ):
- continue
-
- # tests are optional - default is the above class test
- tests = data_source[ 'tests' ]
- if tests and not self.is_object_applicable( trans, target_object, tests ):
- continue
-
- param_data = data_source[ 'to_params' ]
- url = self.get_visualization_url( trans, target_object, vis_name, param_data )
- link_text = listing_data.get( 'link_text', None )
- if not link_text:
- # default to visualization name, titlecase, and replace underscores
- link_text = vis_name.title().replace( '_', ' ' )
- render_location = listing_data.get( 'render_location' )
- # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html)
- applicable_visualizations.append({
- 'href' : url,
- 'html' : link_text,
- 'target': render_location
- })
-
+ for vis_name in self.listings:
+ url_data = self.get_visualization( trans, vis_name, target_object )
+ if url_data:
+ applicable_visualizations.append( url_data )
return applicable_visualizations
def is_object_applicable( self, trans, target_object, data_source_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/208bb69cae38/
Changeset: 208bb69cae38
User: greg
Date: 2013-06-24 22:50:05
Summary: Clean up support for installing a tool shed repository that is not in the installed state.
Affected #: 4 files
diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -216,13 +216,8 @@
tool_path=tool_path,
tool_shed_url=tool_shed_url )
# Create the tool_shed_repository database records and gather additional information for repository installation.
- created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \
+ created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=True )
- if message and len( repo_info_dicts ) == 1:
- # We're attempting to install a single repository that has already been installed into this Galaxy instance.
- log.error( message, exc_info=True )
- trans.response.status = 500
- return dict( status='error', error=message )
if created_or_updated_tool_shed_repositories:
# Build the dictionary of information necessary for installing the repositories.
installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -884,15 +884,8 @@
tool_panel_section=tool_panel_section,
tool_path=tool_path,
tool_shed_url=tool_shed_url )
- created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \
+ created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
repository_util.handle_tool_shed_repositories( trans, installation_dict, using_api=False )
- if message and len( repo_info_dicts ) == 1:
- # We're undoubtedly attempting to install a repository that has been previously installed.
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='browse_repositories',
- message=message,
- status='error' ) )
-
if created_or_updated_tool_shed_repositories:
installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
filtered_repo_info_dicts=filtered_repo_info_dicts,
@@ -1126,7 +1119,7 @@
repository_dependencies=repository_dependencies )
repo_info_dicts.append( repo_info_dict )
# Make sure all tool_shed_repository records exist.
- created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \
+ created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
repository_dependency_util.create_repository_dependency_objects( trans=trans,
tool_path=tool_path,
tool_shed_url=tool_shed_url,
diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -358,7 +358,7 @@
tool_panel_section = installation_dict[ 'tool_panel_section' ]
tool_path = installation_dict[ 'tool_path' ]
tool_shed_url = installation_dict[ 'tool_shed_url' ]
- created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \
+ created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
repository_dependency_util.create_repository_dependency_objects( trans=trans,
tool_path=tool_path,
tool_shed_url=tool_shed_url,
@@ -368,11 +368,7 @@
no_changes_checked=no_changes_checked,
tool_panel_section=tool_panel_section,
new_tool_panel_section=new_tool_panel_section )
- if message and len( repo_info_dicts ) == 1 and not using_api:
- installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ]
- message += 'Click <a href="%s">here</a> to manage the repository. ' % \
- ( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) )
- return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message
+ return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts
def initiate_repository_installation( trans, installation_dict ):
# The following installation_dict entries are all required.
diff -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 -r 208bb69cae38e31f60ae9650c3cc261bfda7b079 lib/tool_shed/util/repository_dependency_util.py
--- a/lib/tool_shed/util/repository_dependency_util.py
+++ b/lib/tool_shed/util/repository_dependency_util.py
@@ -103,7 +103,6 @@
the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy
instance and when uninstalled repositories are being reinstalled.
"""
- message = ''
# The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository dependencies
# that may not be installed.
all_created_or_updated_tool_shed_repositories = []
@@ -241,7 +240,7 @@
filtered_repo_info_dicts.append( repo_info_dict )
# Build repository dependency relationships even if the user chose to not install repository dependencies.
build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories )
- return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message
+ return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
def generate_message_for_invalid_repository_dependencies( metadata_dict ):
"""Return the error message associated with an invalid repository dependency for display in the caller."""
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/93e9f520616c/
Changeset: 93e9f520616c
User: Dave Bouvier
Date: 2013-06-24 22:30:23
Summary: Fix bug with installing tool dependencies when new_file_path is not set in the Galaxy configuration file.
Affected #: 1 file
diff -r be547fe12a1e1b02bc4c7e79834739c590797526 -r 93e9f520616ce9bc066c5e43a0e4d9d977a94192 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -240,13 +240,13 @@
if istar( file_path ):
# <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action>
extract_tar( file_path, install_dir )
- dir = tar_extraction_directory( install_dir, file_path )
+ dir = tar_extraction_directory( install_dir, downloaded_file_name )
elif isjar( file_path ):
dir = os.path.curdir
elif iszip( file_path ):
# <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action>
zip_archive_extracted = extract_zip( file_path, install_dir )
- dir = zip_extraction_directory( install_dir, file_path )
+ dir = zip_extraction_directory( install_dir, downloaded_file_name )
else:
dir = install_dir
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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