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Correctly update TS repo status

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Execute build_dependency_cache() only if using a cached dependency
manager.
Set tool versions only if the TS repo contains tools.
Raise exception if fetch_tool_versions() fails, previously the
error message never reached the UI.
This commit is contained in:
Nicola Soranzo
2016-12-11 20:31:38 +00:00
committed by Nicola Soranzo
parent 879e3d6960
commit 5a7f9e876e
1 changed files with 19 additions and 31 deletions
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lib/tool_shed/galaxy_install/install_manager.py
+19 -31
View File
@@ -26,8 +26,6 @@ from tool_shed.util import tool_util, xml_util
log = logging.getLogger( __name__ )
FAILED_TO_FETCH_VERSIONS = object()
class InstallToolDependencyManager( object ):
@@ -494,7 +492,7 @@ class InstallRepositoryManager( object ):
def __handle_repository_contents( self, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir,
tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False,
tool_versions_response=None, tool_panel_section_mapping={} ):
tool_panel_section_mapping={} ):
"""
Generate the metadata for the installed tool shed repository, among other things.
This method is called when an administrator is installing a new repository or
@@ -522,10 +520,6 @@ class InstallRepositoryManager( object ):
tool_shed_repository.tool_shed_status = tool_shed_status_dict
self.install_model.context.add( tool_shed_repository )
self.install_model.context.flush()
if tool_versions_response and tool_versions_response is not FAILED_TO_FETCH_VERSIONS:
tool_version_dicts = tool_versions_response
tvm = tool_version_manager.ToolVersionManager( self.app )
tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository )
if 'tool_dependencies' in irmm_metadata_dict and not reinstalling:
tool_dependency_util.create_tool_dependency_objects( self.app,
tool_shed_repository,
@@ -542,6 +536,12 @@ class InstallRepositoryManager( object ):
self.app.config.shed_tool_data_table_config,
persist=True )
if 'tools' in irmm_metadata_dict:
# Get the tool_versions from the Tool Shed for each tool in the installed change set.
self.update_tool_shed_repository_status( tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
tool_version_dicts = fetch_tool_versions( self.app, tool_shed_repository )
tvm = tool_version_manager.ToolVersionManager( self.app )
tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository )
tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section )
sample_files = irmm_metadata_dict.get( 'sample_files', [] )
tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files )
@@ -583,7 +583,8 @@ class InstallRepositoryManager( object ):
tool_shed_repository,
repository_tools_tups )
if 'datatypes' in irmm_metadata_dict:
tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
self.update_tool_shed_repository_status( tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES )
if not tool_shed_repository.includes_datatypes:
tool_shed_repository.includes_datatypes = True
self.install_model.context.add( tool_shed_repository )
@@ -866,7 +867,7 @@ class InstallRepositoryManager( object ):
tool_section = None
if isinstance( repo_info_dict, string_types ):
repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict )
# Clone each repository to the configured location.
# Clone the repository to the configured location.
self.update_tool_shed_repository_status( tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.CLONING )
repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
@@ -890,7 +891,6 @@ class InstallRepositoryManager( object ):
create=False )
hg_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
hg_util.update_repository( repo, ctx_rev=current_ctx_rev )
tool_versions_response = fetch_tool_versions( self.app, tool_shed_repository )
self.__handle_repository_contents( tool_shed_repository=tool_shed_repository,
tool_path=tool_path,
repository_clone_url=repository_clone_url,
@@ -898,30 +898,22 @@ class InstallRepositoryManager( object ):
tool_shed=tool_shed_repository.tool_shed,
tool_section=tool_section,
shed_tool_conf=shed_tool_conf,
tool_versions_response=tool_versions_response,
reinstalling=reinstalling,
tool_panel_section_mapping=tool_panel_section_mapping )
self.install_model.context.refresh( tool_shed_repository )
metadata = tool_shed_repository.metadata
if 'tools' in metadata:
if install_resolver_dependencies:
requirements = suc.get_unique_requirements_from_repository(tool_shed_repository)
[self._view.install_dependency(id=None, **req) for req in requirements]
if 'tools' in metadata and install_resolver_dependencies:
self.update_tool_shed_repository_status( tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
requirements = suc.get_unique_requirements_from_repository(tool_shed_repository)
[self._view.install_dependency(id=None, **req) for req in requirements]
if self.app.config.use_cached_dependency_manager:
cached_requirements = []
for tool_d in metadata['tools']:
tool = self.app.toolbox._tools_by_id.get(tool_d['guid'], None)
if tool and tool.requirements not in cached_requirements:
cached_requirements.append(tool.requirements)
tool.build_dependency_cache()
# Get the tool_versions from the tool shed for each tool in the installed change set.
self.update_tool_shed_repository_status( tool_shed_repository,
self.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
if tool_versions_response is FAILED_TO_FETCH_VERSIONS:
if not error_message:
error_message = ""
error_message += "Version information for the tools included in the <b>%s</b> repository is missing. " % tool_shed_repository.name
error_message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions "
error_message += "from the installed repository's <b>Repository Actions</b> menu. "
if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itsr" )
# Install tool dependencies.
@@ -1029,7 +1021,6 @@ def fetch_tool_versions( app, tool_shed_repository ):
""" Fetch a data structure describing tool shed versions from the tool shed
corresponding to a tool_shed_repository object.
"""
failed_to_fetch = False
try:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( tool_shed_repository.tool_shed ) )
params = dict( name=str( tool_shed_repository.name ),
@@ -1041,10 +1032,7 @@ def fetch_tool_versions( app, tool_shed_repository ):
if text:
return json.loads( text )
else:
log.error("No content returned from tool shed repository version request to %s", url)
failed_to_fetch = True
raise Exception("No content returned from Tool Shed repository version request to %s" % url)
except Exception:
failed_to_fetch = True
log.exception("Failed to fetch tool shed repository version information.")
if failed_to_fetch:
return FAILED_TO_FETCH_VERSIONS
log.exception("Failed to fetch tool version information for Tool Shed repository.")
raise