def editor(self, trans, id=None, version=None):
"""
Render the main workflow editor interface. The canvas is embedded as
an iframe (necessary for scrolling to work properly), which is
rendered by `editor_canvas`.
"""
if not id:
error("Invalid workflow id")
stored = self.get_stored_workflow(trans, id)
# The following query loads all user-owned workflows,
# So that they can be copied or inserted in the workflow editor.
workflows = trans.sa_session.query(model.StoredWorkflow) \
.filter_by(user=trans.user, deleted=False) \
.order_by(desc(model.StoredWorkflow.table.c.update_time)) \
.options(joinedload('latest_workflow').joinedload('steps')) \
.all()
if version is None:
version = len(stored.workflows) - 1
else:
version = int(version)
return trans.fill_template("workflow/editor.mako",
workflows=workflows,
stored=stored,
version=version,
annotation=self.get_item_annotation_str(
trans.sa_session, trans.user, stored))
def editor(self, trans, id=None, version=None):
"""
Render the main workflow editor interface. The canvas is embedded as
an iframe (necessary for scrolling to work properly), which is
rendered by `editor_canvas`.
"""
if not id:
error("Invalid workflow id")
stored = self.get_stored_workflow(trans, id)
# The following query loads all user-owned workflows,
# So that they can be copied or inserted in the workflow editor.
workflows = trans.sa_session.query(model.StoredWorkflow) \
.filter_by(user=trans.user, deleted=False) \
.order_by(desc(model.StoredWorkflow.table.c.update_time)) \
.options(joinedload('latest_workflow').joinedload('steps')) \
.all()
if version is None:
version = len(stored.workflows) - 1
else:
version = int(version)
return trans.fill_template("workflow/editor.mako",
workflows=workflows,
stored=stored,
version=version,
annotation=self.get_item_annotation_str(trans.sa_session, trans.user, stored))
def list_for_run(self, trans):
"""
Render workflow list for analysis view (just allows running workflow
or switching to management view)
"""
user = trans.get_user()
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.filter( model.StoredWorkflow.deleted == False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
return trans.fill_template("workflow/list_for_run.mako",
workflows=workflows,
shared_by_others=shared_by_others)
def list(self, trans):
"""
Render workflow main page (management of existing workflows)
"""
user = trans.get_user()
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.join( 'stored_workflow' ) \
.filter( model.StoredWorkflow.deleted == False ) \
.order_by( desc( model.StoredWorkflow.update_time ) ) \
.all()
return trans.fill_template("workflow/list.mako",
workflows=workflows,
shared_by_others=shared_by_others)
def list_for_run( self, trans ):
"""
Render workflow list for analysis view (just allows running workflow
or switching to management view)
"""
user = trans.get_user()
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.filter( model.StoredWorkflow.deleted == False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
return trans.fill_template( "workflow/list_for_run.mako",
workflows = workflows,
shared_by_others = shared_by_others )
def list( self, trans ):
"""
Render workflow main page (management of existing workflows)
"""
user = trans.get_user()
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.join( 'stored_workflow' ) \
.filter( model.StoredWorkflow.deleted == False ) \
.order_by( desc( model.StoredWorkflow.update_time ) ) \
.all()
return trans.fill_template( "workflow/list.mako",
workflows = workflows,
shared_by_others = shared_by_others )
def configure_menu(self, trans, workflow_ids=None):
user = trans.get_user()
if trans.request.method == "POST":
if workflow_ids is None:
workflow_ids = []
elif type(workflow_ids) != list:
workflow_ids = [workflow_ids]
sess = trans.sa_session
# This explicit remove seems like a hack, need to figure out
# how to make the association do it automatically.
for m in user.stored_workflow_menu_entries:
sess.delete(m)
user.stored_workflow_menu_entries = []
q = sess.query(model.StoredWorkflow)
# To ensure id list is unique
seen_workflow_ids = set()
for id in workflow_ids:
if id in seen_workflow_ids:
continue
else:
seen_workflow_ids.add(id)
m = model.StoredWorkflowMenuEntry()
m.stored_workflow = q.get(id)
user.stored_workflow_menu_entries.append(m)
sess.flush()
return trans.show_message("Menu updated", refresh_frames=['tools'])
else:
user = trans.get_user()
ids_in_menu = set([
x.stored_workflow_id for x in user.stored_workflow_menu_entries
])
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.filter( model.StoredWorkflow.deleted == False ) \
.all()
return trans.fill_template("workflow/configure_menu.mako",
workflows=workflows,
shared_by_others=shared_by_others,
ids_in_menu=ids_in_menu)
def configure_menu( self, trans, workflow_ids=None ):
user = trans.get_user()
if trans.request.method == "POST":
if workflow_ids is None:
workflow_ids = []
elif type( workflow_ids ) != list:
workflow_ids = [ workflow_ids ]
sess = trans.sa_session
# This explicit remove seems like a hack, need to figure out
# how to make the association do it automatically.
for m in user.stored_workflow_menu_entries:
sess.delete( m )
user.stored_workflow_menu_entries = []
q = sess.query( model.StoredWorkflow )
# To ensure id list is unique
seen_workflow_ids = set()
for id in workflow_ids:
if id in seen_workflow_ids:
continue
else:
seen_workflow_ids.add( id )
m = model.StoredWorkflowMenuEntry()
m.stored_workflow = q.get( id )
user.stored_workflow_menu_entries.append( m )
sess.flush()
return trans.show_message( "Menu updated", refresh_frames=['tools'] )
else:
user = trans.get_user()
ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] )
workflows = trans.sa_session.query( model.StoredWorkflow ) \
.filter_by( user=user, deleted=False ) \
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
.all()
shared_by_others = trans.sa_session \
.query( model.StoredWorkflowUserShareAssociation ) \
.filter_by( user=user ) \
.filter( model.StoredWorkflow.deleted == False ) \
.all()
return trans.fill_template( "workflow/configure_menu.mako",
workflows=workflows,
shared_by_others=shared_by_others,
ids_in_menu=ids_in_menu )
def editor(self, trans, id=None, workflow_id=None, version=None):
"""
Render the main workflow editor interface. The canvas is embedded as
an iframe (necessary for scrolling to work properly), which is
rendered by `editor_canvas`.
"""
if not id:
if workflow_id:
workflow = trans.sa_session.query(model.Workflow).get(trans.security.decode_id(workflow_id))
stored_workflow = workflow.stored_workflow
self.security_check(trans, stored_workflow, True, False)
stored_workflow_id = trans.security.encode_id(stored_workflow.id)
return trans.response.send_redirect(f'{url_for("/")}workflow/editor?id={stored_workflow_id}')
error("Invalid workflow id")
stored = self.get_stored_workflow(trans, id)
# The following query loads all user-owned workflows,
# So that they can be copied or inserted in the workflow editor.
workflows = trans.sa_session.query(model.StoredWorkflow) \
.filter_by(user=trans.user, deleted=False, hidden=False) \
.order_by(desc(model.StoredWorkflow.table.c.update_time)) \
.options(joinedload('latest_workflow').joinedload('steps')) \
.all()
if version is None:
version = len(stored.workflows) - 1
else:
version = int(version)
# create workflow module models
module_sections = []
for module_section in load_module_sections(trans).values():
module_sections.append({
"title": module_section.get("title"),
"name": module_section.get("name"),
"elems": [{
"name": elem.get("name"),
"title": elem.get("title"),
"description": elem.get("description")
} for elem in module_section.get("modules")]
})
# create data manager tool models
data_managers = []
if trans.user_is_admin and trans.app.data_managers.data_managers:
for data_manager_val in trans.app.data_managers.data_managers.values():
tool = data_manager_val.tool
if not tool.hidden:
data_managers.append({
"id": tool.id,
"name": tool.name,
"hidden": tool.hidden,
"description": tool.description,
"is_workflow_compatible": tool.is_workflow_compatible
})
# create workflow models
workflows = [{
'id': trans.security.encode_id(workflow.id),
'latest_id': trans.security.encode_id(workflow.latest_workflow.id),
'step_count': len(workflow.latest_workflow.steps),
'name': workflow.name
} for workflow in workflows if workflow.id != stored.id]
# identify item tags
item_tags = [tag for tag in stored.tags if tag.user == trans.user]
item_tag_names = []
for ta in item_tags:
item_tag_names.append(escape(ta.tag.name))
# build workflow editor model
editor_config = {
'id': trans.security.encode_id(stored.id),
'name': stored.name,
'tags': item_tag_names,
'initialVersion': version,
'annotation': self.get_item_annotation_str(trans.sa_session, trans.user, stored),
'toolbox': trans.app.toolbox.to_dict(trans),
'moduleSections': module_sections,
'dataManagers': data_managers,
'workflows': workflows
}
# parse to mako
return trans.fill_template("workflow/editor.mako", editor_config=editor_config)