def get_workflows_list(self, trans, kwd):
"""
Displays a collection of workflows.
:param show_published: if True, show also published workflows
:type show_published: boolean
:param missing_tools: if True, include a list of missing tools per workflow
:type missing_tools: boolean
"""
missing_tools = util.string_as_bool(kwd.get('missing_tools', 'False'))
rval = []
filter1 = (trans.app.model.StoredWorkflow.user == trans.user)
user = trans.get_user()
if user is None:
show_published = util.string_as_bool(
kwd.get('show_published', 'True'))
else:
show_published = util.string_as_bool(
kwd.get('show_published', 'False'))
if show_published:
filter1 = or_(filter1,
(trans.app.model.StoredWorkflow.published == true()))
for wf in trans.sa_session.query(
trans.app.model.StoredWorkflow).options(
joinedload("latest_workflow").undefer(
"step_count").lazyload("steps")).options(
joinedload("tags")).filter(
filter1,
trans.app.model.StoredWorkflow.table.c.deleted
== false()).order_by(
desc(trans.app.model.StoredWorkflow.table.
c.update_time)).all():
item = wf.to_dict(value_mapper={'id': trans.security.encode_id})
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = wf.user.username
item['number_of_steps'] = wf.latest_workflow.step_count
item['show_in_tool_panel'] = False
if user is not None:
item['show_in_tool_panel'] = wf.show_in_tool_panel(
user_id=user.id)
rval.append(item)
for wf_sa in trans.sa_session.query(
model.StoredWorkflowUserShareAssociation
).join(
model.StoredWorkflowUserShareAssociation.stored_workflow
).options(
joinedload("stored_workflow").joinedload(
"latest_workflow").undefer("step_count").lazyload("steps")
).options(joinedload("stored_workflow").joinedload("user")).options(
joinedload("stored_workflow").joinedload("tags")).filter(
model.StoredWorkflowUserShareAssociation.user == trans.user
).filter(model.StoredWorkflow.deleted == false()).order_by(
desc(model.StoredWorkflow.update_time)).all():
item = wf_sa.stored_workflow.to_dict(
value_mapper={'id': trans.security.encode_id})
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for('workflow', id=encoded_id)
item['slug'] = wf_sa.stored_workflow.slug
item['owner'] = wf_sa.stored_workflow.user.username
item[
'number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count
item['show_in_tool_panel'] = False
if user is not None:
item[
'show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(
user_id=user.id)
rval.append(item)
if missing_tools:
workflows_missing_tools = []
workflows = []
workflows_by_toolshed = dict()
for key, value in enumerate(rval):
tool_ids = []
workflow_details = self.workflow_contents_manager.workflow_to_dict(
trans,
self.__get_stored_workflow(trans, value['id']),
style='instance')
if 'steps' in workflow_details:
for step in workflow_details['steps']:
tool_id = workflow_details['steps'][step].get(
'tool_id')
if tool_id and tool_id not in tool_ids and self.app.toolbox.is_missing_shed_tool(
tool_id):
tool_ids.append(tool_id)
if len(tool_ids) > 0:
value['missing_tools'] = tool_ids
workflows_missing_tools.append(value)
for workflow in workflows_missing_tools:
for tool_id in workflow['missing_tools']:
toolshed, _, owner, name, tool, version = tool_id.split(
'/')
shed_url = self.__get_full_shed_url(toolshed)
repo_identifier = '/'.join([toolshed, owner, name])
if repo_identifier not in workflows_by_toolshed:
workflows_by_toolshed[repo_identifier] = dict(
shed=shed_url.rstrip('/'),
repository=name,
owner=owner,
tools=[tool_id],
workflows=[workflow['name']])
else:
if tool_id not in workflows_by_toolshed[
repo_identifier]['tools']:
workflows_by_toolshed[repo_identifier][
'tools'].append(tool_id)
if workflow['name'] not in workflows_by_toolshed[
repo_identifier]['workflows']:
workflows_by_toolshed[repo_identifier][
'workflows'].append(workflow['name'])
for repo_tag in workflows_by_toolshed:
workflows.append(workflows_by_toolshed[repo_tag])
return workflows
return rval
def get_workflows_list(self, trans, kwd):
"""
Displays a collection of workflows.
:param show_published: if True, show also published workflows
:type show_published: boolean
:param missing_tools: if True, include a list of missing tools per workflow
:type missing_tools: boolean
"""
missing_tools = util.string_as_bool(kwd.get('missing_tools', 'False'))
rval = []
filter1 = (trans.app.model.StoredWorkflow.user == trans.user)
user = trans.get_user()
if user is None:
show_published = util.string_as_bool(kwd.get('show_published', 'True'))
else :
show_published = util.string_as_bool(kwd.get('show_published', 'False'))
if show_published:
filter1 = or_(filter1, (trans.app.model.StoredWorkflow.published == true()))
for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).options(
joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
joinedload("tags")).filter(
filter1, trans.app.model.StoredWorkflow.table.c.deleted == false()).order_by(
desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
item = wf.to_dict(value_mapper={'id': trans.security.encode_id})
encoded_id = trans.security.encode_id(wf.id)
item['url'] = url_for('workflow', id=encoded_id)
item['owner'] = wf.user.username
item['number_of_steps'] = wf.latest_workflow.step_count
item['show_in_tool_panel'] = False
if user is not None:
item['show_in_tool_panel'] = wf.show_in_tool_panel(user_id=user.id)
rval.append(item)
for wf_sa in trans.sa_session.query(model.StoredWorkflowUserShareAssociation).join(
model.StoredWorkflowUserShareAssociation.stored_workflow).options(
joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
joinedload("stored_workflow").joinedload("user")).options(
joinedload("stored_workflow").joinedload("tags")).filter(model.StoredWorkflowUserShareAssociation.user == trans.user).filter(
model.StoredWorkflow.deleted == false()).order_by(
desc(model.StoredWorkflow.update_time)).all():
item = wf_sa.stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
item['url'] = url_for('workflow', id=encoded_id)
item['slug'] = wf_sa.stored_workflow.slug
item['owner'] = wf_sa.stored_workflow.user.username
item['number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count
item['show_in_tool_panel'] = False
if user is not None:
item['show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id)
rval.append(item)
if missing_tools:
workflows_missing_tools = []
workflows = []
workflows_by_toolshed = dict()
for key, value in enumerate(rval):
tool_ids = []
workflow_details = self.workflow_contents_manager.workflow_to_dict(trans, self.__get_stored_workflow(trans, value['id']), style='instance')
if 'steps' in workflow_details:
for step in workflow_details['steps']:
tool_id = workflow_details['steps'][step].get('tool_id')
if tool_id and tool_id not in tool_ids and self.app.toolbox.is_missing_shed_tool(tool_id):
tool_ids.append(tool_id)
if len(tool_ids) > 0:
value['missing_tools'] = tool_ids
workflows_missing_tools.append(value)
for workflow in workflows_missing_tools:
for tool_id in workflow['missing_tools']:
toolshed, _, owner, name, tool, version = tool_id.split('/')
shed_url = self.__get_full_shed_url(toolshed)
repo_identifier = '/'.join([toolshed, owner, name])
if repo_identifier not in workflows_by_toolshed:
workflows_by_toolshed[repo_identifier] = dict(shed=shed_url.rstrip('/'), repository=name, owner=owner, tools=[tool_id], workflows=[workflow['name']])
else:
if tool_id not in workflows_by_toolshed[repo_identifier]['tools']:
workflows_by_toolshed[repo_identifier]['tools'].append(tool_id)
if workflow['name'] not in workflows_by_toolshed[repo_identifier]['workflows']:
workflows_by_toolshed[repo_identifier]['workflows'].append(workflow['name'])
for repo_tag in workflows_by_toolshed:
workflows.append(workflows_by_toolshed[repo_tag])
return workflows
return rval
