def installed_tool_list(self):
"""
gets a tool list from the toolclient
:return:
"""
tool_client = ToolClient(self.gi)
return tool_client.get_tools()
def installed_tool_list(self):
"""
gets a tool list from the toolclient
:return:
"""
tool_client = ToolClient(self.gi)
return tool_client.get_tools()
def retrieve_tools_from_instance(cls, instance):
galaxy_instance = GalaxyInstance(url=instance.url)
tool_client = ToolClient(galaxy_instance)
for element in tool_client.get_tools():
if element['model_class'] == 'Tool':
tool_name = element['id']
if '/' in tool_name:
tool_name = tool_name.split('/')[-2]
tool = Tool.query.filter_by(name=tool_name).first()
if tool is None:
tool = Tool(name=tool_name)
db.session.add(tool)
tool.description = element['description']
tool.display_name = element['name']
if 'link' in element:
link = element.get('link', None)
link_start = link.find('/tool_runner')
if link_start != -1:
tool.link = link[link_start:]
for edam_opetation_id in element.get('edam_operations', []):
edam_operation = EDAMOperation.get_from_id(
edam_opetation_id, allow_creation=True)
if edam_operation is not None and edam_operation not in tool.edam_operations:
tool.edam_operations.append(edam_operation)
if 'tool_shed_repository' in element:
tool_version = ToolVersion.query\
.filter_by(name=tool_name)\
.filter_by(changeset=element['tool_shed_repository']['changeset_revision'])\
.filter_by(tool_shed=element['tool_shed_repository']['tool_shed'])\
.filter_by(owner=element['tool_shed_repository']['owner'])\
.first()
else:
tool_version = ToolVersion.query\
.filter_by(name=tool_name)\
.filter_by(version=element['version'])\
.filter_by(tool_shed=None)\
.filter_by(owner=None)\
.first()
if tool_version is None:
tool_version = ToolVersion(name=tool_name,
version=element['version'])
db.session.add(tool_version)
if 'tool_shed_repository' in element:
tool_version.changeset = element['tool_shed_repository'][
'changeset_revision']
tool_version.tool_shed = element['tool_shed_repository'][
'tool_shed']
tool_version.owner = element['tool_shed_repository'][
'owner']
if instance not in tool_version.instances:
tool_version.instances.append(instance)
if tool_version not in tool.versions:
tool.versions.append(tool_version)
db.session.commit()
def get_tools(gi):
tool_client = ToolClient(gi)
return tool_client.get_tools()
def retrieve_tools_from_instance(cls, instance):
galaxy_instance = GalaxyInstance(url=instance.url)
tool_client = ToolClient(galaxy_instance)
for element in tool_client.get_tools():
if element['model_class'] == 'Tool':
tool_name = element['id']
if '/' in tool_name:
tool_name = tool_name.split('/')[-2]
try:
tool = Tool.objects.get(name=tool_name)
except Tool.DoesNotExist:
tool = Tool(name=tool_name)
tool.description = element['description']
tool.display_name = element['name']
for edam_opetation_id in element['edam_operations']:
edam_operation = EDAMOperation.get_from_id(
edam_opetation_id, allow_creation=True)
if edam_operation is not None and edam_operation not in tool.edam_operations:
tool.edam_operations.append(edam_operation)
try:
if 'tool_shed_repository' in element:
tool_version = ToolVersion.objects.get(
name=tool_name,
changeset=element['tool_shed_repository']
['changeset_revision'],
tool_shed=element['tool_shed_repository']
['tool_shed'],
owner=element['tool_shed_repository']['owner'])
else:
tool_version = ToolVersion.objects.get(
name=tool_name,
version=element['version'],
tool_shed=None,
owner=None)
except ToolVersion.DoesNotExist:
tool_version = ToolVersion(name=tool_name,
version=element['version'])
if 'tool_shed_repository' in element:
tool_version.changeset = element['tool_shed_repository'][
'changeset_revision']
tool_version.tool_shed = element['tool_shed_repository'][
'tool_shed']
tool_version.owner = element['tool_shed_repository'][
'owner']
if instance not in tool_version.instances:
tool_version.instances.append(instance)
tool_version.save()
if tool_version not in tool.versions:
tool.versions.append(tool_version)
tool.save()
