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Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository.

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Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py .
This commit is contained in:
Nicola Soranzo
2015-12-03 20:05:50 +00:00
parent c9abc2bc97
commit 2b697e3c1a
1 changed files with 2 additions and 17 deletions
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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+2 -17
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@@ -1488,7 +1488,7 @@ class AdminToolshed( AdminGalaxy ):
repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
metadata = tool_shed_repository.metadata
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) )
tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app )
tool_path = tool_shed_repository.get_tool_relative_path( trans.app )[0]
if latest_changeset_revision and latest_ctx_rev:
# There are updates available in the tool shed for the repository, so use the received
# dependency information which was retrieved from the tool shed.
@@ -1497,20 +1497,14 @@ class AdminToolshed( AdminGalaxy ):
readme_files_dict = updated_repo_info_dict.get( 'readme_files_dict', None )
includes_data_managers = updated_repo_info_dict.get( 'includes_data_managers', False )
includes_datatypes = updated_repo_info_dict.get( 'includes_datatypes', False )
includes_tools = updated_repo_info_dict.get( 'includes_tools', False )
includes_tools_for_display_in_tool_panel = updated_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
includes_workflows = updated_repo_info_dict.get( 'includes_workflows', False )
has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False )
includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False )
repo_info_dict = updated_repo_info_dict[ 'repo_info_dict' ]
else:
# There are no updates available from the tool shed for the repository, so use its locally stored metadata.
has_repository_dependencies = False
includes_data_managers = False
includes_datatypes = False
includes_tool_dependencies = False
includes_tools = False
includes_tools_for_display_in_tool_panel = False
includes_workflows = False
readme_files_dict = None
tool_dependencies = None
@@ -1519,14 +1513,6 @@ class AdminToolshed( AdminGalaxy ):
includes_data_managers = True
if 'datatypes' in metadata:
includes_datatypes = True
if 'tools' in metadata:
includes_tools = True
# Handle includes_tools_for_display_in_tool_panel.
tool_dicts = metadata[ 'tools' ]
for tool_dict in tool_dicts:
if tool_dict.get( 'add_to_tool_panel', True ):
includes_tools_for_display_in_tool_panel = True
break
if 'tool_dependencies' in metadata:
includes_tool_dependencies = True
if 'workflows' in metadata:
@@ -1555,8 +1541,7 @@ class AdminToolshed( AdminGalaxy ):
dependencies_for_repository_dict = irm.get_dependencies_for_repository( tool_shed_url,
repo_info_dict,
includes_tool_dependencies,
updating=False )
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
updating=True )
includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False )
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )