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Eliminate the use of trans in the tool shed's tool_dependency_util.py module.

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This commit is contained in:
Greg Von Kuster
2014-07-17 15:49:48 -04:00
parent 6ee8b83fbb
commit 8cc9558aba
2 changed files with 9 additions and 9 deletions
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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+7 -7
View File
@@ -169,7 +169,7 @@ class AdminToolshed( AdminGalaxy ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
if tool_dependency.in_error_state:
message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). "
message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems "
@@ -806,7 +806,7 @@ class AdminToolshed( AdminGalaxy ):
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
if tool_dependency_ids:
# We need a tool_shed_repository, so get it from one of the tool_dependencies.
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
tool_shed_repository = tool_dependency.tool_shed_repository
else:
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
@@ -830,7 +830,7 @@ class AdminToolshed( AdminGalaxy ):
elif operation == 'uninstall':
tool_dependencies_for_uninstallation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.INSTALLED,
trans.install_model.ToolDependency.installation_status.ERROR ]:
tool_dependencies_for_uninstallation.append( tool_dependency )
@@ -845,7 +845,7 @@ class AdminToolshed( AdminGalaxy ):
if trans.app.config.tool_dependency_dir:
tool_dependencies_for_installation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
@@ -889,7 +889,7 @@ class AdminToolshed( AdminGalaxy ):
repository_id = kwd.get( 'repository_id', None )
if tool_dependency_ids:
# We need a tool_shed_repository, so get it from one of the tool_dependencies.
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
tool_shed_repository = tool_dependency.tool_shed_repository
else:
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
@@ -914,7 +914,7 @@ class AdminToolshed( AdminGalaxy ):
if trans.app.config.tool_dependency_dir:
tool_dependencies_for_installation = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
@@ -1849,7 +1849,7 @@ class AdminToolshed( AdminGalaxy ):
tool_dependency_ids = util.listify( kwd.get( 'id', None ) )
tool_dependencies = []
for tool_dependency_id in tool_dependency_ids:
tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id )
tool_dependencies.append( tool_dependency )
tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
if kwd.get( 'uninstall_tool_dependencies_button', False ):
lib/tool_shed/util/tool_dependency_util.py
+2 -2
View File
@@ -128,9 +128,9 @@ def get_platform_info_dict():
platform_dict[ 'architecture' ] = machine.lower()
return platform_dict
def get_tool_dependency( trans, id ):
def get_tool_dependency( app, id ):
"""Get a tool_dependency from the database via id"""
return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) )
return app.install_model.context.query( app.install_model.ToolDependency ).get( app.security.decode_id( id ) )
def get_tool_dependency_by_name_type_repository( app, repository, name, type ):
context = app.install_model.context