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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