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Create a new ToolShedRepository record only if necessary - if one already exists for the installed repository but is marked deleted, mark the exisint record undeleted.

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This commit is contained in:
Greg Von Kuster
2011-10-27 15:08:07 -04:00
parent e988c4ee63
commit 690dc8fd92
2 changed files with 27 additions and 14 deletions
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lib/galaxy/web/base/controller.py
+7
View File
@@ -2443,6 +2443,13 @@ def get_quota( trans, id ):
id = trans.security.decode_id( id )
quota = trans.sa_session.query( trans.model.Quota ).get( id )
return quota
def get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ):
return trans.sa_session.query( trans.model.ToolShedRepository ) \
.filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed,
trans.model.ToolShedRepository.table.c.name == name,
trans.model.ToolShedRepository.table.c.owner == owner,
trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
def handle_sample_tool_data_table_conf_file( trans, filename ):
"""
Parse the incoming filename and add new entries to the in-memory
lib/galaxy/web/controllers/admin.py
+20 -14
View File
@@ -766,12 +766,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
os.chdir( current_working_dir )
tmp_stderr.close()
if returncode == 0:
# Add a new record to the tool_shed_repository table.
tool_shed_repository = self.__create_tool_shed_repository( trans,
name,
description,
changeset_revision,
repository_clone_url )
# Add a new record to the tool_shed_repository table if one doesn't
# already exist. If one exists but is marked deleted, undelete it.
self.__create_or_undelete_tool_shed_repository( trans, name, description, changeset_revision, repository_clone_url )
# Update the cloned repository to changeset_revision.
repo_files_dir = os.path.join( clone_dir, name )
log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision )
@@ -1055,17 +1052,26 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
# We have an invalid .xml file, so not a tool config.
log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) )
return sample_files, repository_tools_tups
def __create_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ):
def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ):
tmp_url = self.__clean_repository_clone_url( repository_clone_url )
tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
owner = self.__get_repository_owner( tmp_url )
tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
name=name,
description=description,
owner=owner,
changeset_revision=changeset_revision )
trans.sa_session.add( tool_shed_repository )
trans.sa_session.flush()
flush_needed = False
tool_shed_repository = get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision )
if tool_shed_repository:
if tool_shed_repository.deleted:
tool_shed_repository.deleted = False
flush_needed = True
else:
tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed,
name=name,
description=description,
owner=owner,
changeset_revision=changeset_revision )
flush_needed = True
if flush_needed:
trans.sa_session.add( tool_shed_repository )
trans.sa_session.flush()
def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ):
# Add an entry in the shed_tool_conf file. An entry looks something like:
# <section name="Filter and Sort" id="filter">