def shed_repository( self, trans, **kwd ):
"""
GET /api/tool_shed_repositories/shed_repository
Get details about the specified repository from its shed.
:param tsr_id: the tool_shed_repository_id
"""
tool_dependencies = dict()
tools = dict()
tool_shed_url = kwd.get( 'tool_shed_url', '' )
tsr_id = kwd.get( 'tsr_id', '' )
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app )
tool_panel_section_dict = { 'name': tool_panel_section_select_field.name,
'id': tool_panel_section_select_field.field_id,
'sections': [] }
for name, id, _ in tool_panel_section_select_field.options:
tool_panel_section_dict['sections'].append( dict( id=id, name=name ) )
repository_data = dict()
repository_data[ 'repository' ] = json.loads( util.url_get( tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id ] ) )
repository_data[ 'repository' ][ 'metadata' ] = json.loads( util.url_get( tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id, 'metadata' ] ) )
repository_data[ 'shed_conf' ] = tool_util.build_shed_tool_conf_select_field( trans.app ).get_html().replace('\n', '')
repository_data[ 'panel_section_html' ] = tool_panel_section_select_field.get_html( extra_attr={ 'style': 'width: 30em;' } ).replace( '\n', '' )
repository_data[ 'panel_section_dict' ] = tool_panel_section_dict
for changeset, metadata in repository_data[ 'repository' ][ 'metadata' ].items():
if changeset not in tool_dependencies:
tool_dependencies[ changeset ] = []
if metadata[ 'includes_tools_for_display_in_tool_panel' ]:
if changeset not in tools:
tools[ changeset ] = []
for tool_dict in metadata[ 'tools' ]:
tool_info = dict( clean=re.sub( '[^a-zA-Z0-9]+', '_', tool_dict[ 'name' ] ).lower(),
guid=tool_dict[ 'guid' ],
name=tool_dict[ 'name' ],
version=tool_dict[ 'version' ],
description=tool_dict[ 'description' ] )
if tool_info not in tools[ changeset ]:
tools[ changeset ].append( tool_info )
if metadata[ 'has_repository_dependencies' ]:
for repository_dependency in metadata[ 'repository_dependencies' ]:
tools[ changeset ] = self.__get_tools( repository_dependency, tools[ changeset ] )
repository_data[ 'tools' ] = tools
for key, dependency_dict in metadata[ 'tool_dependencies' ].items():
if 'readme' in dependency_dict:
del( dependency_dict[ 'readme' ] )
if dependency_dict not in tool_dependencies[ changeset ]:
tool_dependencies[ changeset ].append( dependency_dict )
# log.debug(tool_dependencies)
if metadata[ 'has_repository_dependencies' ]:
for repository_dependency in metadata[ 'repository_dependencies' ]:
tool_dependencies[ changeset ] = self.__get_tool_dependencies( repository_dependency, tool_dependencies[ changeset ] )
repository_data[ 'tool_dependencies' ] = tool_dependencies
return repository_data
def repository(self, trans, **kwd):
"""
GET /api/tool_shed/repository
Get details about the specified repository from its shed.
:param repository_id: the tool_shed_repository_id
:param repository_id: str
:param tool_shed_url: the URL of the toolshed whence to retrieve repository details
:param tool_shed_url: str
:param tool_ids: (optional) comma-separated list of tool IDs
:param tool_ids: str
"""
tool_dependencies = dict()
tools = dict()
tool_shed_url = urlunquote(kwd.get('tool_shed_url', ''))
log.debug(tool_shed_url)
repository_id = kwd.get('repository_id', None)
tool_ids = kwd.get('tool_ids', None)
if tool_ids is not None:
tool_ids = util.listify(tool_ids)
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
tool_panel_section_dict = {'name': tool_panel_section_select_field.name,
'id': tool_panel_section_select_field.field_id,
'sections': []}
for name, id, _ in tool_panel_section_select_field.options:
tool_panel_section_dict['sections'].append(dict(id=id, name=name))
repository_data = dict()
if tool_ids is not None:
if len(tool_shed_url) == 0:
# By design, this list should always be from the same toolshed. If
# this is ever not the case, this code will need to be updated.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_ids[0].split('/')[0])
found_repository = json.loads(util.url_get(tool_shed_url, params=dict(tool_ids=','.join(tool_ids)), pathspec=['api', 'repositories']))
fr_first_key = next(iter(found_repository.keys()))
repository_id = found_repository[fr_first_key]['repository_id']
repository_data['current_changeset'] = found_repository['current_changeset']
repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id]))
del found_repository['current_changeset']
repository_data['tool_shed_url'] = tool_shed_url
else:
repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id]))
repository_data['repository']['metadata'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id, 'metadata']))
repository_data['shed_conf'] = tool_util.build_shed_tool_conf_select_field(trans.app).to_dict()
repository_data['panel_section_dict'] = tool_panel_section_dict
for changeset, metadata in repository_data['repository']['metadata'].items():
if changeset not in tool_dependencies:
tool_dependencies[changeset] = []
if metadata['includes_tools_for_display_in_tool_panel']:
if changeset not in tools:
tools[changeset] = []
for tool_dict in metadata['tools']:
tool_info = dict(clean=re.sub('[^a-zA-Z0-9]+', '_', tool_dict['name']).lower(),
guid=tool_dict['guid'],
name=tool_dict['name'],
version=tool_dict['version'],
description=tool_dict['description'])
if tool_info not in tools[changeset]:
tools[changeset].append(tool_info)
if metadata['has_repository_dependencies']:
for repository_dependency in metadata['repository_dependencies']:
tools[changeset] = self.__get_tools(repository_dependency, tools[changeset])
repository_data['tools'] = tools
for key, dependency_dict in metadata['tool_dependencies'].items():
if 'readme' in dependency_dict:
del(dependency_dict['readme'])
if dependency_dict not in tool_dependencies[changeset]:
tool_dependencies[changeset].append(dependency_dict)
if metadata['has_repository_dependencies']:
for repository_dependency in metadata['repository_dependencies']:
tool_dependencies[changeset] = self.__get_tool_dependencies(repository_dependency, tool_dependencies[changeset])
repository_data['tool_dependencies'] = tool_dependencies
return repository_data
def shed_repository(self, trans, **kwd):
"""
GET /api/tool_shed_repositories/shed_repository
Get details about the specified repository from its shed.
:param tsr_id: the tool_shed_repository_id
"""
tool_dependencies = dict()
tools = dict()
tool_shed_url = kwd.get('tool_shed_url', '')
tsr_id = kwd.get('tsr_id', '')
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(
trans.app)
tool_panel_section_dict = {
'name': tool_panel_section_select_field.name,
'id': tool_panel_section_select_field.field_id,
'sections': []
}
for name, id, _ in tool_panel_section_select_field.options:
tool_panel_section_dict['sections'].append(dict(id=id, name=name))
repository_data = dict()
repository_data['repository'] = json.loads(
util.url_get(tool_shed_url,
pathspec=['api', 'repositories', tsr_id]))
repository_data['repository']['metadata'] = json.loads(
util.url_get(tool_shed_url,
pathspec=['api', 'repositories', tsr_id, 'metadata']))
repository_data[
'shed_conf'] = tool_util.build_shed_tool_conf_select_field(
trans.app).get_html().replace('\n', '')
repository_data[
'panel_section_html'] = tool_panel_section_select_field.get_html(
extra_attr={
'style': 'width: 30em;'
}).replace('\n', '')
repository_data['panel_section_dict'] = tool_panel_section_dict
for changeset, metadata in repository_data['repository'][
'metadata'].items():
if changeset not in tool_dependencies:
tool_dependencies[changeset] = []
if metadata['includes_tools_for_display_in_tool_panel']:
if changeset not in tools:
tools[changeset] = []
for tool_dict in metadata['tools']:
tool_info = dict(clean=re.sub('[^a-zA-Z0-9]+', '_',
tool_dict['name']).lower(),
guid=tool_dict['guid'],
name=tool_dict['name'],
version=tool_dict['version'],
description=tool_dict['description'])
if tool_info not in tools[changeset]:
tools[changeset].append(tool_info)
if metadata['has_repository_dependencies']:
for repository_dependency in metadata[
'repository_dependencies']:
tools[changeset] = self.__get_tools(
repository_dependency, tools[changeset])
repository_data['tools'] = tools
for key, dependency_dict in metadata['tool_dependencies'].items():
if 'readme' in dependency_dict:
del (dependency_dict['readme'])
if dependency_dict not in tool_dependencies[changeset]:
tool_dependencies[changeset].append(dependency_dict)
# log.debug(tool_dependencies)
if metadata['has_repository_dependencies']:
for repository_dependency in metadata[
'repository_dependencies']:
tool_dependencies[
changeset] = self.__get_tool_dependencies(
repository_dependency,
tool_dependencies[changeset])
repository_data['tool_dependencies'] = tool_dependencies
return repository_data