1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4f4f7bd74074/
Changeset: 4f4f7bd74074
User: greg
Date: 2013-03-29 16:22:10
Summary: Minor fixes to the questionable install_repository_revisions method in
Galaxy's tool_shed_repositories API controller.
Affected #: 1 file
diff -r 93f069f8325ca3bd7aff1cfd8673efdb3b61b4d5 -r
4f4f7bd74074090bd0192e76e361d42d9db70060
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
@@ -271,11 +271,13 @@
It's questionable whether this method is needed as the above method for
installing a single repository can probably cover all
desired scenarios. We'll keep this one around just in case...
+ :param key: the current Galaxy admin user's API key
+
+ The following parameters are included in the payload.
:param tool_shed_urls: the base URLs of the Tool Sheds from which to install a
specified Repository
:param names: the names of the Repositories to be installed
:param owners: the owners of the Repositories to be installed
:param changset_revisions: the changset_revisions of each RepositoryMetadata
object associated with each Repository to be installed
- :param key: the current Galaxy admin user's API key
:param new_tool_panel_section_label: optional label of a new section to be added
to the Galaxy tool panel in which to load
tools contained in the Repository. Either
this parameter must be an empty string or
the tool_panel_section_id parameter must be
an empty string, as both cannot be used.
@@ -283,6 +285,16 @@
If not set, tools will be loaded outside of any
sections in the tool panel. Either this
parameter must be an empty string or the
tool_panel_section_id parameter must be an empty string,
as both cannot be used.
+ :param install_repository_dependencies (optional): Set to True if you want to
install repository dependencies defined for the specified
+ repository being installed.
The default setting is False.
+ :param install_tool_dependencies (optional): Set to True if you want to install
tool dependencies defined for the specified repository being
+ installed. The default setting is
False.
+ :param shed_tool_conf (optional): The shed-related tool panel configuration file
configured in the "tool_config_file" setting in the Galaxy config file
+ (e.g., universe_wsgi.ini). At least one
shed-related tool panel config file is required to be configured. Setting
+ this parameter to a specific file enables you
to choose where the specified repository will be installed because
+ the tool_path attribute of the <toolbox>
from the specified file is used as the installation location
+ (e.g., <toolbox
tool_path="../shed_tools">). If this parameter is not set, a shed-related
tool panel configuration
+ file will be selected automatically.
"""
if not suc.have_shed_tool_conf_for_install( trans ):
# This Galaxy instance is not configured with a shed-related tool panel
configuration file.
@@ -312,7 +324,7 @@
# forcing all repositories to use the same settings.
install_repository_dependencies = payload.get(
'install_repository_dependencies', False )
install_tool_dependencies = payload.get( 'install_tool_dependencies',
False )
- new_tool_panel_section = payload.get( 'new_tool_panel_section_label',
'' )
+ new_tool_panel_section_label = payload.get(
'new_tool_panel_section_label', '' )
shed_tool_conf = payload.get( 'shed_tool_conf', None )
tool_path = payload.get( 'tool_path', None )
tool_panel_section_id = payload.get( 'tool_panel_section_id', ''
)
@@ -323,12 +335,11 @@
current_payload[ 'name' ] = names[ index ]
current_payload[ 'owner' ] = owners[ index ]
current_payload[ 'changeset_revision' ] = changeset_revisions[ index
]
+ current_payload[ 'new_tool_panel_section_label' ] =
new_tool_panel_section_label
+ current_payload[ 'tool_panel_section_id' ] = tool_panel_section_id
current_payload[ 'install_repository_dependencies' ] =
install_repository_dependencies
current_payload[ 'install_tool_dependencies' ] =
install_tool_dependencies
- current_payload[ 'new_tool_panel_section' ] = new_tool_panel_section
current_payload[ 'shed_tool_conf' ] = shed_tool_conf
- current_payload[ 'tool_path' ] = tool_path
- current_payload[ 'tool_panel_section_id' ] = tool_panel_section_id
installed_tool_shed_repositories = self.install_repository_revision( trans,
**current_payload )
if isinstance( installed_tool_shed_repositories, dict ):
# We encountered an error.
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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