def build_workflow_from_dict(
self,
trans,
data,
source=None,
add_to_menu=False,
publish=False,
create_stored_workflow=True,
exact_tools=False,
):
# Put parameters in workflow mode
trans.workflow_building_mode = True
# If there's a source, put it in the workflow name.
if source:
name = "%s (imported from %s)" % (data['name'], source)
else:
name = data['name']
workflow, missing_tool_tups = self._workflow_from_dict(
trans,
data,
name=name,
exact_tools=exact_tools,
)
if 'uuid' in data:
workflow.uuid = data['uuid']
if create_stored_workflow:
# Connect up
stored = model.StoredWorkflow()
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
stored.published = publish
if data['annotation']:
annotation = sanitize_html(data['annotation'], 'utf-8',
'text/html')
self.add_item_annotation(trans.sa_session, stored.user, stored,
annotation)
# Persist
trans.sa_session.add(stored)
if add_to_menu:
if trans.user.stored_workflow_menu_entries is None:
trans.user.stored_workflow_menu_entries = []
menuEntry = model.StoredWorkflowMenuEntry()
menuEntry.stored_workflow = stored
trans.user.stored_workflow_menu_entries.append(menuEntry)
else:
stored = None
# Persist
trans.sa_session.add(workflow)
trans.sa_session.flush()
return CreatedWorkflow(stored_workflow=stored,
workflow=workflow,
missing_tools=missing_tool_tups)
def update( self, trans, id, payload, **kwds ):
"""
* PUT /api/workflows/{id}
updates the workflow stored with ``id``
:type id: str
:param id: the encoded id of the workflow to update
:type payload: dict
:param payload: a dictionary containing any or all the
* workflow the json description of the workflow as would be
produced by GET workflows/<id>/download or
given to `POST workflows`
The workflow contents will be updated to target
this.
* name optional string name for the workflow, if not present in payload,
name defaults to existing name
* annotation optional string annotation for the workflow, if not present in payload,
annotation defaults to existing annotation
* menu_entry optional boolean marking if the workflow should appear in the user's menu,
if not present, workflow menu entries are not modified
:rtype: dict
:returns: serialized version of the workflow
"""
stored_workflow = self.__get_stored_workflow( trans, id )
if 'workflow' in payload:
stored_workflow.name = sanitize_html(payload['name']) if ('name' in payload) else stored_workflow.name
if 'annotation' in payload:
newAnnotation = sanitize_html(payload['annotation'])
self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation)
if 'menu_entry' in payload:
if payload['menu_entry']:
menuEntry = model.StoredWorkflowMenuEntry()
menuEntry.stored_workflow = stored_workflow
trans.get_user().stored_workflow_menu_entries.append(menuEntry)
else:
# remove if in list
entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries}
if (trans.security.decode_id(id) in entries):
trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
try:
workflow, errors = self.workflow_contents_manager.update_workflow_from_dict(
trans,
stored_workflow,
payload[ 'workflow' ],
)
except workflows.MissingToolsException:
raise exceptions.MessageException( "This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed." )
else:
message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
raise exceptions.RequestParameterInvalidException( message )
return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" )
def set_workflow_menu(self, trans, **kwd):
"""
Save workflow menu to be shown in the tool panel
PUT /api/workflows/menu
"""
payload = kwd.get('payload')
user = trans.get_user()
workflow_ids = payload.get('workflow_ids')
if workflow_ids is None:
workflow_ids = []
elif type(workflow_ids) != list:
workflow_ids = [workflow_ids]
workflow_ids_decoded = []
# Decode the encoded workflow ids
for ids in workflow_ids:
workflow_ids_decoded.append(trans.security.decode_id(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 wf_id in workflow_ids_decoded:
if wf_id in seen_workflow_ids:
continue
else:
seen_workflow_ids.add(wf_id)
m = model.StoredWorkflowMenuEntry()
m.stored_workflow = q.get(wf_id)
user.stored_workflow_menu_entries.append(m)
sess.flush()
message = "Menu updated."
trans.set_message(message)
return {'message': message, 'status': 'done'}
def update(self, trans, id, payload, **kwds):
"""
* PUT /api/workflows/{id}
updates the workflow stored with ``id``
:type id: str
:param id: the encoded id of the workflow to update
:type payload: dict
:param payload: a dictionary containing any or all the
* workflow the json description of the workflow as would be
produced by GET workflows/<id>/download or
given to `POST workflows`
The workflow contents will be updated to target
this.
* name optional string name for the workflow, if not present in payload,
name defaults to existing name
* annotation optional string annotation for the workflow, if not present in payload,
annotation defaults to existing annotation
* menu_entry optional boolean marking if the workflow should appear in the user's menu,
if not present, workflow menu entries are not modified
:rtype: dict
:returns: serialized version of the workflow
"""
stored_workflow = self.__get_stored_workflow(trans, id)
workflow_dict = payload.get('workflow') or payload
if workflow_dict:
raw_workflow_description = self.__normalize_workflow(
trans, workflow_dict)
workflow_dict = raw_workflow_description.as_dict
new_workflow_name = workflow_dict.get('name') or workflow_dict.get(
'name')
if new_workflow_name and new_workflow_name != stored_workflow.name:
sanitized_name = sanitize_html(new_workflow_name)
workflow = stored_workflow.latest_workflow.copy()
workflow.stored_workflow = stored_workflow
workflow.name = sanitized_name
stored_workflow.name = sanitized_name
stored_workflow.latest_workflow = workflow
trans.sa_session.add(workflow, stored_workflow)
trans.sa_session.flush()
if 'annotation' in workflow_dict:
newAnnotation = sanitize_html(workflow_dict['annotation'])
self.add_item_annotation(trans.sa_session, trans.get_user(),
stored_workflow, newAnnotation)
if 'menu_entry' in workflow_dict or 'show_in_tool_panel' in workflow_dict:
if workflow_dict.get('menu_entry') or workflow_dict.get(
'show_in_tool_panel'):
menuEntry = model.StoredWorkflowMenuEntry()
menuEntry.stored_workflow = stored_workflow
trans.get_user().stored_workflow_menu_entries.append(
menuEntry)
else:
# remove if in list
entries = {
x.stored_workflow_id: x
for x in trans.get_user().stored_workflow_menu_entries
}
if (trans.security.decode_id(id) in entries):
trans.get_user().stored_workflow_menu_entries.remove(
entries[trans.security.decode_id(id)])
# set tags
trans.app.tag_handler.set_tags_from_list(
user=trans.user,
item=stored_workflow,
new_tags_list=workflow_dict.get('tags', []))
if 'steps' in workflow_dict:
try:
from_dict_kwds = self.__import_or_update_kwds(payload)
workflow, errors = self.workflow_contents_manager.update_workflow_from_raw_description(
trans, stored_workflow, raw_workflow_description,
**from_dict_kwds)
except workflows.MissingToolsException:
raise exceptions.MessageException(
"This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed."
)
else:
# We only adjusted tags and menu entry
return payload
else:
message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
raise exceptions.RequestParameterInvalidException(message)
return self.workflow_contents_manager.workflow_to_dict(
trans, stored_workflow, style="instance")
def build_workflow_from_dict(self,
trans,
data,
source=None,
add_to_menu=False,
publish=False):
# Put parameters in workflow mode
trans.workflow_building_mode = True
# Create new workflow from incoming dict
workflow = model.Workflow()
# If there's a source, put it in the workflow name.
if source:
name = "%s (imported from %s)" % (data['name'], source)
else:
name = data['name']
workflow.name = name
if 'uuid' in data:
workflow.uuid = data['uuid']
# Assume no errors until we find a step that has some
workflow.has_errors = False
# Create each step
steps = []
# The editor will provide ids for each step that we don't need to save,
# but do need to use to make connections
steps_by_external_id = {}
# Keep track of tools required by the workflow that are not available in
# the local Galaxy instance. Each tuple in the list of missing_tool_tups
# will be ( tool_id, tool_name, tool_version ).
missing_tool_tups = []
for step_dict in self.__walk_step_dicts(data):
module, step = self.__module_from_dict(trans,
step_dict,
secure=False)
steps.append(step)
steps_by_external_id[step_dict['id']] = step
if module.type == 'tool' and module.tool is None:
# A required tool is not available in the local Galaxy instance.
missing_tool_tup = (step_dict['tool_id'], step_dict['name'],
step_dict['tool_version'])
if missing_tool_tup not in missing_tool_tups:
missing_tool_tups.append(missing_tool_tup)
# Save the entire step_dict in the unused config field, be parsed later
# when we do have the tool
step.config = json.dumps(step_dict)
if step.tool_errors:
workflow.has_errors = True
# Second pass to deal with connections between steps
self.__connect_workflow_steps(steps, steps_by_external_id)
# Order the steps if possible
attach_ordered_steps(workflow, steps)
# Connect up
stored = model.StoredWorkflow()
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
stored.published = publish
if data['annotation']:
annotation = sanitize_html(data['annotation'], 'utf-8',
'text/html')
self.add_item_annotation(trans.sa_session, stored.user, stored,
annotation)
# Persist
trans.sa_session.add(stored)
trans.sa_session.flush()
if add_to_menu:
if trans.user.stored_workflow_menu_entries is None:
trans.user.stored_workflow_menu_entries = []
menuEntry = model.StoredWorkflowMenuEntry()
menuEntry.stored_workflow = stored
trans.user.stored_workflow_menu_entries.append(menuEntry)
trans.sa_session.flush()
return CreatedWorkflow(stored_workflow=stored,
missing_tools=missing_tool_tups)
