def __init__(self, trans, repository_id, changeset_revision, tools_metadata, tool_id):
self.trans = trans
self.tools_metadata = tools_metadata
self.tool_id = tool_id
self.tool = None
self.errors = None
self.tool_version = None
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
with ValidationContext.from_app(trans.app) as validation_context:
tv = tool_validator.ToolValidator(validation_context)
for tool_dict in tools_metadata:
if self.tool_id in [tool_dict['id'], tool_dict['guid']]:
repository, self.tool, message = tv.load_tool_from_changeset_revision(repository_id,
changeset_revision,
tool_dict['tool_config'])
if message and self.tool is None:
self.errors = 'unavailable'
break
else:
# We're in Galaxy.
self.tool = trans.app.toolbox.get_tool(self.tool_id, tool_version=self.tool_version)
if self.tool is None:
self.errors = 'unavailable'
self.post_job_actions = {}
self.workflow_outputs = []
self.state = None
def __init__(self, trans, repository_id, changeset_revision, tools_metadata, tool_id):
self.trans = trans
self.tools_metadata = tools_metadata
self.tool_id = tool_id
self.tool = None
self.errors = None
self.tool_version = None
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
with ValidationContext.from_app(trans.app) as validation_context:
tv = tool_validator.ToolValidator(validation_context)
for tool_dict in tools_metadata:
if self.tool_id in [tool_dict['id'], tool_dict['guid']]:
repository, self.tool, valid, message = tv.load_tool_from_changeset_revision(repository_id,
changeset_revision,
tool_dict['tool_config'])
if self.tool is None and message or not valid:
self.errors = 'unavailable'
break
else:
# We're in Galaxy.
self.tool = trans.app.toolbox.get_tool(self.tool_id, tool_version=self.tool_version)
if self.tool is None:
self.errors = 'unavailable'
self.post_job_actions = {}
self.workflow_outputs = []
self.state = None
def get_tool_validator():
app = MockApp()
with ValidationContext.from_app(app) as validation_context:
yield ToolValidator(validation_context)
def json(self, trans, **kwd):
"""
GET /api/tools/json
Get the tool form JSON for a tool in a repository.
:param guid: the GUID of the tool
:param guid: str
:param tsr_id: the ID of the repository
:param tsr_id: str
:param changeset: the changeset at which to load the tool json
:param changeset: str
"""
guid = kwd.get('guid', None)
tsr_id = kwd.get('tsr_id', None)
changeset = kwd.get('changeset', None)
if None in [changeset, tsr_id, guid]:
message = 'Changeset, repository ID, and tool GUID are all required parameters.'
trans.response.status = 400
return {'status': 'error', 'message': message}
tsucm = ToolShedUtilityContainerManager(trans.app)
repository = repository_util.get_repository_in_tool_shed(self.app, tsr_id)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(repository.user, repository)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(trans.app, tsr_id, changeset)
toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
rb = relation_builder.RelationBuilder(trans.app, repository, repository_metadata, toolshed_base_url)
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
containers_dict = tsucm.build_repository_containers(repository,
changeset,
repository_dependencies,
repository_metadata)
found_tool = None
for folder in containers_dict['valid_tools'].folders:
if hasattr(folder, 'valid_tools'):
for tool in folder.valid_tools:
tool.id = tool.tool_id
tool_guid = suc.generate_tool_guid(repository_clone_url, tool)
if tool_guid == guid:
found_tool = tool
break
if found_tool is None:
message = 'Unable to find tool with guid %s in repository %s.' % (guid, repository.name)
trans.response.status = 404
return {'status': 'error', 'message': message}
with ValidationContext.from_app(trans.app) as validation_context:
tv = tool_validator.ToolValidator(validation_context)
repository, tool, message = tv.load_tool_from_changeset_revision(tsr_id,
changeset,
found_tool.tool_config)
if message:
status = 'error'
return dict(message=message, status=status)
tool_help = ''
if tool.help:
tool_help = tool.help.render(static_path=web.url_for('/static'), host_url=web.url_for('/', qualified=True))
tool_help = util.unicodify(tool_help, 'utf-8')
tool_dict = tool.to_dict(trans)
tool_dict['inputs'] = {}
tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
tool_dict.update({
'help' : tool_help,
'citations' : bool(tool.citations),
'biostar_url' : trans.app.config.biostar_url,
'requirements' : [{'name' : r.name, 'version' : r.version} for r in tool.requirements],
'state_inputs' : params_to_strings(tool.inputs, {}, trans.app),
'display' : tool.display_interface,
'action' : web.url_for(tool.action),
'method' : tool.method,
'enctype' : tool.enctype
})
return json.dumps(tool_dict)
def json(self, trans, **kwd):
"""
GET /api/tools/json
Get the tool form JSON for a tool in a repository.
:param guid: the GUID of the tool
:param guid: str
:param tsr_id: the ID of the repository
:param tsr_id: str
:param changeset: the changeset at which to load the tool json
:param changeset: str
"""
guid = kwd.get('guid', None)
tsr_id = kwd.get('tsr_id', None)
changeset = kwd.get('changeset', None)
if None in [changeset, tsr_id, guid]:
message = 'Changeset, repository ID, and tool GUID are all required parameters.'
trans.response.status = 400
return {'status': 'error', 'message': message}
tsucm = ToolShedUtilityContainerManager(trans.app)
repository = repository_util.get_repository_in_tool_shed(
self.app, tsr_id)
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed(
repository.user, repository)
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
trans.app, tsr_id, changeset)
toolshed_base_url = str(web.url_for('/', qualified=True)).rstrip('/')
rb = relation_builder.RelationBuilder(trans.app, repository,
repository_metadata,
toolshed_base_url)
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision(
)
containers_dict = tsucm.build_repository_containers(
repository, changeset, repository_dependencies,
repository_metadata)
found_tool = None
for folder in containers_dict['valid_tools'].folders:
if hasattr(folder, 'valid_tools'):
for tool in folder.valid_tools:
tool.id = tool.tool_id
tool_guid = suc.generate_tool_guid(repository_clone_url,
tool)
if tool_guid == guid:
found_tool = tool
break
if found_tool is None:
message = f'Unable to find tool with guid {guid} in repository {repository.name}.'
trans.response.status = 404
return {'status': 'error', 'message': message}
with ValidationContext.from_app(trans.app) as validation_context:
tv = tool_validator.ToolValidator(validation_context)
repository, tool, valid, message = tv.load_tool_from_changeset_revision(
tsr_id, changeset, found_tool.tool_config)
if message or not valid:
status = 'error'
return dict(message=message, status=status)
tool_help = ''
if tool.help:
tool_help = tool.help.render(static_path=web.url_for('/static'),
host_url=web.url_for('/',
qualified=True))
tool_help = util.unicodify(tool_help, 'utf-8')
tool_dict = tool.to_dict(trans)
tool_dict['inputs'] = {}
tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
tool_dict.update({
'help':
tool_help,
'citations':
bool(tool.citations),
'requirements': [{
'name': r.name,
'version': r.version
} for r in tool.requirements],
'state_inputs':
params_to_strings(tool.inputs, {}, trans.app),
'display':
tool.display_interface,
'action':
web.url_for(tool.action),
'method':
tool.method,
'enctype':
tool.enctype
})
return json.dumps(tool_dict)
def get_tool_validator():
app = MockApp()
with ValidationContext.from_app(app) as validation_context:
yield ToolValidator(validation_context)