mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
7e45ca2a72
How to use: 1.) Place multiple tools with different IDs in your tool conf. 2.) ... ummm ... no step 2 - just use the tools. Implementation: The Tool Shed allows tool lineages by assigning each tool version a GUID and tracking versions in a database. This implementation works by simply allowing the ToolBox to contain multiple tools with the same ID and orders them by the version specified by the tool author. To track enable this a second tool lineage has been introduced that just uses tool versions instead of a database (non-toolshed installed tools are not longer placed into the Tool Shed install database). The ToolBox has been updated to allow multiple versions per tool id (defaulting to the 'latest' version for all operations which do not specify a version). Both jobs and workflow steps would track tool versions but did not use that version when fetching tools from the Toolbox - these components have been updated to try to use the tool version. Unit tests working through most of the ToolBox and tool panel have been added, as well as functional tests exercising the tools API and to ensure workflows now at least attempt to respect tool versions (still kind of silently switches versions in some cases). Manual tests against the new tool form seem to demonstrate the tool switching and tool re-running work with only minor changes to the tools API and the job handler.
1000 lines
47 KiB
Python
1000 lines
47 KiB
Python
from .helpers import wait_on_state
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from base import api
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from json import dumps
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from collections import namedtuple
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from uuid import uuid4
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import time
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import yaml
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from .helpers import WorkflowPopulator
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from .helpers import DatasetPopulator
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from .helpers import DatasetCollectionPopulator
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from .helpers import skip_without_tool
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from .yaml_to_workflow import yaml_to_workflow
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from requests import delete
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from requests import put
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from galaxy.exceptions import error_codes
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class BaseWorkflowsApiTestCase( api.ApiTestCase ):
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# TODO: Find a new file for this class.
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def setUp( self ):
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super( BaseWorkflowsApiTestCase, self ).setUp()
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self.workflow_populator = WorkflowPopulator( self.galaxy_interactor )
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self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
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self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
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def _assert_user_has_workflow_with_name( self, name ):
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names = self._workflow_names()
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assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names )
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def _workflow_names( self ):
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index_response = self._get( "workflows" )
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self._assert_status_code_is( index_response, 200 )
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names = map( lambda w: w[ "name" ], index_response.json() )
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return names
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def _upload_yaml_workflow(self, has_yaml):
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workflow = yaml_to_workflow(has_yaml)
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workflow_str = dumps(workflow, indent=4)
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data = {
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'workflow': workflow_str
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}
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upload_response = self._post( "workflows", data=data )
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self._assert_status_code_is( upload_response, 200 )
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self._assert_user_has_workflow_with_name( "%s (imported from API)" % ( workflow[ "name" ] ) )
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return upload_response.json()[ "id" ]
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def _setup_workflow_run( self, workflow, inputs_by='step_id', history_id=None ):
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uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
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if not history_id:
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history_id = self.dataset_populator.new_history()
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hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
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hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" )
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workflow_request = dict(
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history="hist_id=%s" % history_id,
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workflow_id=uploaded_workflow_id,
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)
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label_map = {
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'WorkflowInput1': self._ds_entry(hda1),
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'WorkflowInput2': self._ds_entry(hda2)
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}
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if inputs_by == 'step_id':
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ds_map = self._build_ds_map( uploaded_workflow_id, label_map )
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workflow_request[ "ds_map" ] = ds_map
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elif inputs_by == "step_index":
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index_map = {
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'0': self._ds_entry(hda1),
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'1': self._ds_entry(hda2)
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}
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workflow_request[ "inputs" ] = dumps( index_map )
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workflow_request[ "inputs_by" ] = 'step_index'
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elif inputs_by == "name":
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workflow_request[ "inputs" ] = dumps( label_map )
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workflow_request[ "inputs_by" ] = 'name'
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elif inputs_by in [ "step_uuid", "uuid_implicitly" ]:
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uuid_map = {
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workflow["steps"]["0"]["uuid"]: self._ds_entry(hda1),
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workflow["steps"]["1"]["uuid"]: self._ds_entry(hda2),
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}
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workflow_request[ "inputs" ] = dumps( uuid_map )
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if inputs_by == "step_uuid":
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workflow_request[ "inputs_by" ] = "step_uuid"
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return workflow_request, history_id
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def _build_ds_map( self, workflow_id, label_map ):
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workflow_inputs = self._workflow_inputs( workflow_id )
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ds_map = {}
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for key, value in workflow_inputs.iteritems():
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label = value[ "label" ]
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if label in label_map:
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ds_map[ key ] = label_map[ label ]
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return dumps( ds_map )
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def _ds_entry( self, hda ):
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src = 'hda'
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if 'history_content_type' in hda and hda[ 'history_content_type' ] == "dataset_collection":
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src = 'hdca'
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return dict( src=src, id=hda[ "id" ] )
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def _workflow_inputs( self, uploaded_workflow_id ):
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workflow_show_resposne = self._get( "workflows/%s" % uploaded_workflow_id )
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self._assert_status_code_is( workflow_show_resposne, 200 )
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workflow_inputs = workflow_show_resposne.json()[ "inputs" ]
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return workflow_inputs
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def _invocation_details( self, workflow_id, invocation_id ):
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invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) )
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self._assert_status_code_is( invocation_details_response, 200 )
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invocation_details = invocation_details_response.json()
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return invocation_details
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def _run_jobs( self, jobs_yaml, history_id=None, wait=True ):
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if history_id is None:
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history_id = self.history_id
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workflow_id = self._upload_yaml_workflow(
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jobs_yaml
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)
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jobs_descriptions = yaml.load( jobs_yaml )
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test_data = jobs_descriptions["test_data"]
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label_map = {}
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inputs = {}
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for key, value in test_data.items():
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if isinstance( value, dict ):
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elements_data = value.get( "elements", [] )
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elements = []
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for element_data in elements_data:
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identifier = element_data[ "identifier" ]
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content = element_data["content"]
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elements.append( ( identifier, content ) )
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collection_type = value["type"]
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if collection_type == "list:paired":
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hdca = self.dataset_collection_populator.create_list_of_pairs_in_history( history_id ).json()
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elif collection_type == "list":
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hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=elements ).json()
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else:
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hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=elements ).json()
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label_map[key] = self._ds_entry( hdca )
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inputs[key] = hdca
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else:
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hda = self.dataset_populator.new_dataset( history_id, content=value )
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label_map[key] = self._ds_entry( hda )
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inputs[key] = hda
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workflow_request = dict(
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history="hist_id=%s" % history_id,
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workflow_id=workflow_id,
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)
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workflow_request[ "inputs" ] = dumps( label_map )
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workflow_request[ "inputs_by" ] = 'name'
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self.dataset_populator.wait_for_history( history_id, assert_ok=True )
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url = "workflows/%s/usage" % ( workflow_id )
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invocation_response = self._post( url, data=workflow_request )
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self._assert_status_code_is( invocation_response, 200 )
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invocation = invocation_response.json()
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invocation_id = invocation[ "id" ]
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# Wait for workflow to become fully scheduled and then for all jobs
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# complete.
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if wait:
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self.wait_for_invocation( workflow_id, invocation_id )
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self.dataset_populator.wait_for_history( history_id, assert_ok=True )
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jobs = self._history_jobs( history_id )
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return RunJobsSummary(
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history_id=history_id,
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workflow_id=workflow_id,
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inputs=inputs,
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jobs=jobs,
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)
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def wait_for_invocation( self, workflow_id, invocation_id ):
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url = "workflows/%s/usage/%s" % ( workflow_id, invocation_id )
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return wait_on_state( lambda: self._get( url ) )
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def _history_jobs( self, history_id ):
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return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json()
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# Workflow API TODO:
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# - Allow history_id as param to workflow run action. (hist_id)
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# - Allow post to workflows/<workflow_id>/run in addition to posting to
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# /workflows with id in payload.
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# - Much more testing obviously, always more testing.
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class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
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def setUp( self ):
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super( WorkflowsApiTestCase, self ).setUp()
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def test_show_valid( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_regular" )
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show_response = self._get( "workflows/%s" % workflow_id )
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workflow = show_response.json()
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self._assert_looks_like_instance_workflow_representation( workflow )
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assert len(workflow["steps"]) == 3
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def test_show_invalid_key_is_400( self ):
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show_response = self._get( "workflows/%s" % self._random_key() )
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self._assert_status_code_is( show_response, 400 )
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def test_cannot_show_private_workflow( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" )
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with self._different_user():
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show_response = self._get( "workflows/%s" % workflow_id )
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self._assert_status_code_is( show_response, 403 )
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def test_delete( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_delete" )
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workflow_name = "test_delete (imported from API)"
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self._assert_user_has_workflow_with_name( workflow_name )
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workflow_url = self._api_url( "workflows/%s" % workflow_id, use_key=True )
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delete_response = delete( workflow_url )
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self._assert_status_code_is( delete_response, 200 )
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# Make sure workflow is no longer in index by default.
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assert workflow_name not in self._workflow_names()
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def test_other_cannot_delete( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_other_delete" )
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with self._different_user():
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workflow_url = self._api_url( "workflows/%s" % workflow_id, use_key=True )
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delete_response = delete( workflow_url )
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self._assert_status_code_is( delete_response, 403 )
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def test_index( self ):
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index_response = self._get( "workflows" )
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self._assert_status_code_is( index_response, 200 )
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assert isinstance( index_response.json(), list )
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def test_upload( self ):
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self.__test_upload( use_deprecated_route=False )
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def test_upload_deprecated( self ):
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self.__test_upload( use_deprecated_route=True )
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def __test_upload( self, use_deprecated_route=False, name="test_import", workflow=None ):
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if workflow is None:
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workflow = self.workflow_populator.load_workflow( name=name )
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data = dict(
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workflow=dumps( workflow ),
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)
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if use_deprecated_route:
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route = "workflows/upload"
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else:
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route = "workflows"
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upload_response = self._post( route, data=data )
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self._assert_status_code_is( upload_response, 200 )
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self._assert_user_has_workflow_with_name( "%s (imported from API)" % name )
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return upload_response
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def test_update( self ):
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original_workflow = self.workflow_populator.load_workflow( name="test_import" )
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uuids = {}
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labels = {}
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for order_index, step_dict in original_workflow["steps"].iteritems():
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uuid = str(uuid4())
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step_dict["uuid"] = uuid
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uuids[order_index] = uuid
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label = "label_%s" % order_index
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step_dict["label"] = label
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labels[order_index] = label
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def check_label_and_uuid(order_index, step_dict):
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assert order_index in uuids
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assert order_index in labels
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self.assertEquals(uuids[order_index], step_dict["uuid"])
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self.assertEquals(labels[order_index], step_dict["label"])
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upload_response = self.__test_upload( workflow=original_workflow )
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workflow_id = upload_response.json()["id"]
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def update(workflow_object):
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data = dict(
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workflow=workflow_object
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)
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raw_url = 'workflows/%s' % workflow_id
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url = self._api_url( raw_url, use_key=True )
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put_response = put( url, data=dumps(data) )
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self._assert_status_code_is( put_response, 200 )
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return put_response
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workflow_content = self._download_workflow(workflow_id)
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steps = workflow_content["steps"]
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def tweak_step(step):
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order_index, step_dict = step
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check_label_and_uuid( order_index, step_dict)
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assert step_dict['position']['top'] != 1
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assert step_dict['position']['left'] != 1
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step_dict['position'] = {'top': 1, 'left': 1}
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map(tweak_step, steps.iteritems())
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update(workflow_content)
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def check_step(step):
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order_index, step_dict = step
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check_label_and_uuid(order_index, step_dict)
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assert step_dict['position']['top'] == 1
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assert step_dict['position']['left'] == 1
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updated_workflow_content = self._download_workflow(workflow_id)
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map(check_step, updated_workflow_content['steps'].iteritems())
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# Re-update against original worklfow...
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update(original_workflow)
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updated_workflow_content = self._download_workflow(workflow_id)
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# Make sure the positions have been updated.
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map(tweak_step, updated_workflow_content['steps'].iteritems())
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def test_require_unique_step_uuids( self ):
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workflow_dup_uuids = self.workflow_populator.load_workflow( name="test_import" )
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uuid0 = str(uuid4())
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for step_dict in workflow_dup_uuids["steps"].values():
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step_dict["uuid"] = uuid0
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response = self.workflow_populator.create_workflow_response( workflow_dup_uuids )
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self._assert_status_code_is( response, 400 )
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def test_require_unique_step_labels( self ):
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workflow_dup_label = self.workflow_populator.load_workflow( name="test_import" )
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for step_dict in workflow_dup_label["steps"].values():
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step_dict["label"] = "my duplicated label"
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response = self.workflow_populator.create_workflow_response( workflow_dup_label )
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self._assert_status_code_is( response, 400 )
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def test_import_deprecated( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True )
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with self._different_user():
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other_import_response = self.__import_workflow( workflow_id )
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self._assert_status_code_is( other_import_response, 200 )
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self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)")
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def test_import_annotations( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_import_annotations", publish=True )
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with self._different_user():
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other_import_response = self.__import_workflow( workflow_id )
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self._assert_status_code_is( other_import_response, 200 )
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# Test annotations preserved during upload and copied over during
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# import.
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other_id = other_import_response.json()["id"]
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imported_workflow = self._show_workflow( other_id )
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assert imported_workflow["annotation"] == "simple workflow"
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step_annotations = set(map(lambda step: step["annotation"], imported_workflow["steps"].values()))
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assert "input1 description" in step_annotations
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def test_not_importable_prevents_import( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" )
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with self._different_user():
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other_import_response = self.__import_workflow( workflow_id )
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self._assert_status_code_is( other_import_response, 403 )
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def test_import_published( self ):
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workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True )
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with self._different_user():
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other_import_response = self.__import_workflow( workflow_id, deprecated_route=True )
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self._assert_status_code_is( other_import_response, 200 )
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self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)")
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def test_export( self ):
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uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" )
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downloaded_workflow = self._download_workflow( uploaded_workflow_id )
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assert downloaded_workflow[ "name" ] == "test_for_export (imported from API)"
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assert len( downloaded_workflow[ "steps" ] ) == 3
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first_input = downloaded_workflow[ "steps" ][ "0" ][ "inputs" ][ 0 ]
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assert first_input[ "name" ] == "WorkflowInput1"
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assert first_input[ "description" ] == "input1 description"
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self._assert_has_keys( downloaded_workflow, "a_galaxy_workflow", "format-version", "annotation", "uuid", "steps" )
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for step in downloaded_workflow["steps"].values():
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self._assert_has_keys(
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step,
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'id',
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'type',
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'tool_id',
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'tool_version',
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'name',
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'tool_state',
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'tool_errors',
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'annotation',
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'inputs',
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'user_outputs',
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'outputs'
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)
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if step['type'] == "tool":
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self._assert_has_keys( step, "post_job_actions" )
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def test_export_editor( self ):
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uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" )
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downloaded_workflow = self._download_workflow( uploaded_workflow_id, style="editor" )
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self._assert_has_keys( downloaded_workflow, "name", "steps", "upgrade_messages" )
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for step in downloaded_workflow["steps"].values():
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self._assert_has_keys(
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step,
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'id',
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'type',
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'tool_id',
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'name',
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'tool_state',
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'tooltip',
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'tool_errors',
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'data_inputs',
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'data_outputs',
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'form_html',
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'annotation',
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'post_job_actions',
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'workflow_outputs',
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'uuid',
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'label',
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)
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def test_import_export_with_runtime_inputs( self ):
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workflow = self.workflow_populator.load_workflow_from_resource( name="test_workflow_with_runtime_input" )
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workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
downloaded_workflow = self._download_workflow( workflow_id )
|
|
assert len( downloaded_workflow[ "steps" ] ) == 2
|
|
runtime_input = downloaded_workflow[ "steps" ][ "1" ][ "inputs" ][ 0 ]
|
|
assert runtime_input[ "description" ].startswith( "runtime parameter for tool" )
|
|
assert runtime_input[ "name" ] == "num_lines"
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_workflow_by_index( self ):
|
|
self.__run_cat_workflow( inputs_by='step_index' )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_workflow_by_uuid( self ):
|
|
self.__run_cat_workflow( inputs_by='step_uuid' )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_workflow_by_uuid_implicitly( self ):
|
|
self.__run_cat_workflow( inputs_by='uuid_implicitly' )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_workflow_by_name( self ):
|
|
self.__run_cat_workflow( inputs_by='name' )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_workflow( self ):
|
|
self.__run_cat_workflow( inputs_by='step_id' )
|
|
|
|
@skip_without_tool( "multiple_versions" )
|
|
def test_run_versioned_tools( self ):
|
|
history_01_id = self.dataset_populator.new_history()
|
|
workflow_version_01 = self._upload_yaml_workflow( """
|
|
- tool_id: multiple_versions
|
|
tool_version: "0.1"
|
|
state:
|
|
inttest: 0
|
|
""" )
|
|
self.__invoke_workflow( history_01_id, workflow_version_01 )
|
|
self.dataset_populator.wait_for_history( history_01_id, assert_ok=True )
|
|
|
|
history_02_id = self.dataset_populator.new_history()
|
|
workflow_version_02 = self._upload_yaml_workflow( """
|
|
- tool_id: multiple_versions
|
|
tool_version: "0.2"
|
|
state:
|
|
inttest: 1
|
|
""" )
|
|
self.__invoke_workflow( history_02_id, workflow_version_02 )
|
|
self.dataset_populator.wait_for_history( history_02_id, assert_ok=True )
|
|
|
|
def __run_cat_workflow( self, inputs_by ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_run" )
|
|
workflow["steps"]["0"]["uuid"] = str(uuid4())
|
|
workflow["steps"]["1"]["uuid"] = str(uuid4())
|
|
workflow_request, history_id = self._setup_workflow_run( workflow, inputs_by=inputs_by )
|
|
# TODO: This should really be a post to workflows/<workflow_id>/run or
|
|
# something like that.
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
invocation_id = run_workflow_response.json()[ "id" ]
|
|
invocation = self._invocation_details( workflow_request[ "workflow_id" ], invocation_id )
|
|
assert invocation[ "state" ] == "scheduled", invocation
|
|
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
def test_workflow_request( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow )
|
|
url = "workflows/%s/usage" % ( workflow_request[ "workflow_id" ] )
|
|
del workflow_request[ "workflow_id" ]
|
|
run_workflow_response = self._post( url, data=workflow_request )
|
|
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
# Give some time for workflow to get scheduled before scanning the history.
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
def test_workflow_pause( self ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
|
|
index_map = {
|
|
'0': self._ds_entry(hda1),
|
|
}
|
|
invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
|
|
# Give some time for workflow to get scheduled before scanning the history.
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
# Wait for all the datasets to complete, make sure the workflow invocation
|
|
# is not complete.
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] != 'scheduled', invocation
|
|
|
|
self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=2, action=True )
|
|
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] == 'scheduled', invocation
|
|
|
|
def test_workflow_pause_cancel( self ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
|
|
index_map = {
|
|
'0': self._ds_entry(hda1),
|
|
}
|
|
invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
|
|
# Give some time for workflow to get scheduled before scanning the history.
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
# Wait for all the datasets to complete, make sure the workflow invocation
|
|
# is not complete.
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] != 'scheduled'
|
|
|
|
self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=2, action=False )
|
|
# Not immediately cancelled, must wait until workflow scheduled again.
|
|
time.sleep( 4 )
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] == 'cancelled', invocation
|
|
|
|
def test_workflow_map_reduce_pause( self ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_map_reduce_pause" )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
hda1 = self.dataset_populator.new_dataset( history_id, content="reviewed\nunreviewed" )
|
|
hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=["1\n2\n3", "4\n5\n6"] ).json()
|
|
index_map = {
|
|
'0': self._ds_entry(hda1),
|
|
'1': self._ds_entry(hdca1),
|
|
}
|
|
invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
|
|
# Give some time for workflow to get scheduled before scanning the history.
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
# Wait for all the datasets to complete, make sure the workflow invocation
|
|
# is not complete.
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] != 'scheduled'
|
|
|
|
self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=4, action=True )
|
|
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] == 'scheduled'
|
|
self.assertEquals("reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content( history_id ) )
|
|
|
|
def test_cancel_workflow_invocation( self ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
|
|
index_map = {
|
|
'0': self._ds_entry(hda1),
|
|
}
|
|
invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
|
|
# Give some time for workflow to get scheduled before scanning the history.
|
|
time.sleep( 5 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
|
|
# Wait for all the datasets to complete, make sure the workflow invocation
|
|
# is not complete.
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] != 'scheduled'
|
|
|
|
invocation_url = self._api_url( "workflows/%s/usage/%s" % (uploaded_workflow_id, invocation_id), use_key=True )
|
|
delete_response = delete( invocation_url )
|
|
self._assert_status_code_is( delete_response, 200 )
|
|
|
|
# Wait for all the datasets to complete, make sure the workflow invocation
|
|
# is not complete.
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] == 'cancelled'
|
|
|
|
def test_run_with_implicit_connection( self ):
|
|
history_id = self.dataset_populator.new_history()
|
|
run_summary = self._run_jobs("""
|
|
steps:
|
|
- label: test_input
|
|
type: input
|
|
- label: first_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: test_input
|
|
- label: the_pause
|
|
type: pause
|
|
connect:
|
|
input:
|
|
- first_cat#out_file1
|
|
- label: second_cat
|
|
tool_id: cat1
|
|
state:
|
|
input1:
|
|
$link: the_pause
|
|
- label: third_cat
|
|
tool_id: random_lines1
|
|
connect:
|
|
$step: second_cat
|
|
state:
|
|
num_lines: 1
|
|
input:
|
|
$link: test_input
|
|
seed_source:
|
|
seed_source_selector: set_seed
|
|
seed: asdf
|
|
__current_case__: 1
|
|
test_data:
|
|
test_input: "hello world"
|
|
""", history_id=history_id, wait=False)
|
|
time.sleep( 2 )
|
|
history_id = run_summary.history_id
|
|
workflow_id = run_summary.workflow_id
|
|
invocation_id = run_summary.workflow_id
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
invocation = self._invocation_details( workflow_id, invocation_id )
|
|
assert invocation[ 'state' ] != 'scheduled'
|
|
# Expect two jobs - the upload and first cat. randomlines shouldn't run
|
|
# it is implicitly dependent on second cat.
|
|
assert len( self._history_jobs( history_id ) ) == 2
|
|
|
|
self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True )
|
|
self.wait_for_invocation( workflow_id, invocation_id )
|
|
time.sleep(1)
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
time.sleep(1)
|
|
assert len( self._history_jobs( history_id ) ) == 4
|
|
|
|
def test_cannot_run_inaccessible_workflow( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow )
|
|
with self._different_user():
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 403 )
|
|
|
|
def test_400_on_invalid_workflow_id( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow )
|
|
workflow_request[ "workflow_id" ] = self._random_key()
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 400 )
|
|
|
|
def test_cannot_run_against_other_users_history( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow )
|
|
with self._different_user():
|
|
other_history_id = self.dataset_populator.new_history()
|
|
workflow_request[ "history" ] = "hist_id=%s" % other_history_id
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 403 )
|
|
|
|
@skip_without_tool( "cat" )
|
|
@skip_without_tool( "cat_list" )
|
|
def test_workflow_run_with_matching_lists( self ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_matching_lists" )
|
|
workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=[("sample1-1", "1 2 3"), ("sample2-1", "7 8 9")] ).json()
|
|
hdca2 = self.dataset_collection_populator.create_list_in_history( history_id, contents=[("sample1-2", "4 5 6"), ("sample2-2", "0 a b")] ).json()
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
label_map = { "list1": self._ds_entry( hdca1 ), "list2": self._ds_entry( hdca2 ) }
|
|
workflow_request = dict(
|
|
history="hist_id=%s" % history_id,
|
|
workflow_id=workflow_id,
|
|
ds_map=self._build_ds_map( workflow_id, label_map ),
|
|
)
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
self.assertEquals("1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content( history_id ) )
|
|
|
|
def test_workflow_stability( self ):
|
|
# Run this index stability test with following command:
|
|
# ./run_tests.sh test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_stability
|
|
from pkg_resources import resource_string
|
|
num_tests = 1
|
|
for workflow_file in [ "test_workflow_topoambigouity.ga", "test_workflow_topoambigouity_auto_laidout.ga" ]:
|
|
workflow_str = resource_string( __name__, workflow_file )
|
|
workflow = self.workflow_populator.load_workflow( "test1", content=workflow_str )
|
|
last_step_map = self._step_map( workflow )
|
|
for i in range(num_tests):
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
downloaded_workflow = self._download_workflow( uploaded_workflow_id )
|
|
step_map = self._step_map(downloaded_workflow)
|
|
assert step_map == last_step_map
|
|
last_step_map = step_map
|
|
|
|
def _step_map(self, workflow):
|
|
# Build dict mapping 'tep index to input name.
|
|
step_map = {}
|
|
for step_index, step in workflow["steps"].iteritems():
|
|
if step[ "type" ] == "data_input":
|
|
step_map[step_index] = step["inputs"][0]["name"]
|
|
return step_map
|
|
|
|
def test_empty_create( self ):
|
|
response = self._post( "workflows" )
|
|
self._assert_status_code_is( response, 400 )
|
|
self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER )
|
|
|
|
def test_invalid_create_multiple_types( self ):
|
|
data = {
|
|
'shared_workflow_id': '1234567890abcdef',
|
|
'from_history_id': '1234567890abcdef'
|
|
}
|
|
response = self._post( "workflows", data )
|
|
self._assert_status_code_is( response, 400 )
|
|
self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_run_with_pja( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow, inputs_by='step_index' )
|
|
workflow_request[ "replacement_params" ] = dumps( dict( replaceme="was replaced" ) )
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
|
|
assert content[ "name" ] == "foo was replaced"
|
|
|
|
@skip_without_tool( "random_lines1" )
|
|
def test_run_replace_params_by_tool( self ):
|
|
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" )
|
|
workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) )
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
# Would be 8 and 6 without modification
|
|
self.__assert_lines_hid_line_count_is( history_id, 2, 5 )
|
|
self.__assert_lines_hid_line_count_is( history_id, 3, 5 )
|
|
|
|
@skip_without_tool( "random_lines1" )
|
|
def test_run_replace_params_by_uuid( self ):
|
|
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" )
|
|
workflow_request[ "parameters" ] = dumps( {
|
|
"58dffcc9-bcb7-4117-a0e1-61513524b3b1": dict( num_lines=4 ),
|
|
"58dffcc9-bcb7-4117-a0e1-61513524b3b2": dict( num_lines=3 ),
|
|
} )
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
# Would be 8 and 6 without modification
|
|
self.__assert_lines_hid_line_count_is( history_id, 2, 4 )
|
|
self.__assert_lines_hid_line_count_is( history_id, 3, 3 )
|
|
|
|
@skip_without_tool( "validation_default" )
|
|
def test_parameter_substitution_validation( self ):
|
|
substitions = dict( input1="\" ; echo \"moo" )
|
|
run_workflow_response, history_id = self._run_validation_workflow_with_substitions( substitions )
|
|
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
self.assertEquals("__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content( history_id, hid=1 ) )
|
|
|
|
@skip_without_tool( "validation_default" )
|
|
def test_parameter_substitution_validation_value_errors_1( self ):
|
|
substitions = dict( select_param="\" ; echo \"moo" )
|
|
run_workflow_response, history_id = self._run_validation_workflow_with_substitions( substitions )
|
|
|
|
self._assert_status_code_is( run_workflow_response, 400 )
|
|
|
|
def _run_validation_workflow_with_substitions( self, substitions ):
|
|
workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_validation_1" )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
history_id = self.dataset_populator.new_history()
|
|
workflow_request = dict(
|
|
history="hist_id=%s" % history_id,
|
|
workflow_id=uploaded_workflow_id,
|
|
parameters=dumps( dict( validation_default=substitions ) )
|
|
)
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
return run_workflow_response, history_id
|
|
|
|
@skip_without_tool( "random_lines1" )
|
|
def test_run_replace_params_by_steps( self ):
|
|
workflow_request, history_id, steps = self._setup_random_x2_workflow_steps( "test_for_replace_step_params" )
|
|
params = dumps( { str(steps[1]["id"]): dict( num_lines=5 ) } )
|
|
workflow_request[ "parameters" ] = params
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
# Would be 8 and 6 without modification
|
|
self.__assert_lines_hid_line_count_is( history_id, 2, 8 )
|
|
self.__assert_lines_hid_line_count_is( history_id, 3, 5 )
|
|
|
|
@skip_without_tool( "random_lines1" )
|
|
def test_run_replace_params_nested( self ):
|
|
workflow_request, history_id, steps = self._setup_random_x2_workflow_steps( "test_for_replace_step_params_nested" )
|
|
seed_source = dict(
|
|
seed_source_selector="set_seed",
|
|
seed="moo",
|
|
)
|
|
params = dumps( { str(steps[0]["id"]): dict( num_lines=1, seed_source=seed_source ),
|
|
str(steps[1]["id"]): dict( num_lines=1, seed_source=seed_source ) } )
|
|
workflow_request[ "parameters" ] = params
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
|
self.assertEquals("3\n", self.dataset_populator.get_history_dataset_content( history_id ) )
|
|
|
|
def test_pja_import_export( self ):
|
|
workflow = self.workflow_populator.load_workflow( name="test_for_pja_import", add_pja=True )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
downloaded_workflow = self._download_workflow( uploaded_workflow_id )
|
|
self._assert_has_keys( downloaded_workflow[ "steps" ], "0", "1", "2" )
|
|
pjas = downloaded_workflow[ "steps" ][ "2" ][ "post_job_actions" ].values()
|
|
assert len( pjas ) == 1, len( pjas )
|
|
pja = pjas[ 0 ]
|
|
self._assert_has_keys( pja, "action_type", "output_name", "action_arguments" )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_only_own_invocations_accessible( self ):
|
|
workflow_id, usage = self._run_workflow_once_get_invocation( "test_usage")
|
|
with self._different_user():
|
|
usage_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, usage[ "id" ] ) )
|
|
self._assert_status_code_is( usage_details_response, 403 )
|
|
|
|
@skip_without_tool( "cat1" )
|
|
def test_invocation_usage( self ):
|
|
workflow_id, usage = self._run_workflow_once_get_invocation( "test_usage")
|
|
invocation_id = usage[ "id" ]
|
|
usage_details = self._invocation_details( workflow_id, invocation_id )
|
|
# Assert some high-level things about the structure of data returned.
|
|
self._assert_has_keys( usage_details, "inputs", "steps" )
|
|
invocation_steps = usage_details[ "steps" ]
|
|
for step in invocation_steps:
|
|
self._assert_has_keys( step, "workflow_step_id", "order_index", "id" )
|
|
an_invocation_step = invocation_steps[ 0 ]
|
|
step_id = an_invocation_step[ "id" ]
|
|
step_response = self._get( "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id ) )
|
|
self._assert_status_code_is( step_response, 200 )
|
|
self._assert_has_keys( step_response.json(), "id", "order_index" )
|
|
|
|
def _invocation_step_details( self, workflow_id, invocation_id, step_id ):
|
|
invocation_step_response = self._get( "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id ) )
|
|
self._assert_status_code_is( invocation_step_response, 200 )
|
|
invocation_step_details = invocation_step_response.json()
|
|
return invocation_step_details
|
|
|
|
def _execute_invocation_step_action( self, workflow_id, invocation_id, step_id, action ):
|
|
raw_url = "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id )
|
|
url = self._api_url( raw_url, use_key=True )
|
|
payload = dumps( dict( action=action ) )
|
|
action_response = put( url, data=payload )
|
|
self._assert_status_code_is( action_response, 200 )
|
|
invocation_step_details = action_response.json()
|
|
return invocation_step_details
|
|
|
|
def _run_workflow_once_get_invocation( self, name ):
|
|
workflow = self.workflow_populator.load_workflow( name=name )
|
|
workflow_request, history_id = self._setup_workflow_run( workflow )
|
|
workflow_id = workflow_request[ "workflow_id" ]
|
|
response = self._get( "workflows/%s/usage" % workflow_id )
|
|
self._assert_status_code_is( response, 200 )
|
|
assert len( response.json() ) == 0
|
|
run_workflow_response = self._post( "workflows", data=workflow_request )
|
|
self._assert_status_code_is( run_workflow_response, 200 )
|
|
|
|
response = self._get( "workflows/%s/usage" % workflow_id )
|
|
self._assert_status_code_is( response, 200 )
|
|
usages = response.json()
|
|
assert len( usages ) == 1
|
|
return workflow_id, usages[ 0 ]
|
|
|
|
def _setup_random_x2_workflow_steps( self, name ):
|
|
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" )
|
|
random_line_steps = self._random_lines_steps( workflow_request )
|
|
return workflow_request, history_id, random_line_steps
|
|
|
|
def _random_lines_steps( self, workflow_request ):
|
|
workflow_summary_response = self._get( "workflows/%s" % workflow_request[ "workflow_id" ] )
|
|
self._assert_status_code_is( workflow_summary_response, 200 )
|
|
steps = workflow_summary_response.json()[ "steps" ]
|
|
return sorted( filter(lambda step: step["tool_id"] == "random_lines1", steps.values()), key=lambda step: step["id"] )
|
|
|
|
def _setup_random_x2_workflow( self, name ):
|
|
workflow = self.workflow_populator.load_random_x2_workflow( name )
|
|
uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
|
|
workflow_inputs = self._workflow_inputs( uploaded_workflow_id )
|
|
key = workflow_inputs.keys()[ 0 ]
|
|
history_id = self.dataset_populator.new_history()
|
|
ten_lines = "\n".join( map( str, range( 10 ) ) )
|
|
hda1 = self.dataset_populator.new_dataset( history_id, content=ten_lines )
|
|
workflow_request = dict(
|
|
history="hist_id=%s" % history_id,
|
|
workflow_id=uploaded_workflow_id,
|
|
ds_map=dumps( {
|
|
key: self._ds_entry(hda1),
|
|
} ),
|
|
)
|
|
return workflow_request, history_id
|
|
|
|
def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ):
|
|
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
|
|
invocation_steps = invocation[ "steps" ]
|
|
pause_steps = [ s for s in invocation_steps if s[ 'order_index' ] == order_index ]
|
|
for pause_step in pause_steps:
|
|
pause_step_id = pause_step[ 'id' ]
|
|
|
|
self._execute_invocation_step_action( uploaded_workflow_id, invocation_id, pause_step_id, action=action )
|
|
|
|
def __assert_lines_hid_line_count_is( self, history, hid, lines ):
|
|
contents_url = "histories/%s/contents" % history
|
|
history_contents_response = self._get( contents_url )
|
|
self._assert_status_code_is( history_contents_response, 200 )
|
|
hda_summary = filter( lambda hc: hc[ "hid" ] == hid, history_contents_response.json() )[ 0 ]
|
|
hda_info_response = self._get( "%s/%s" % ( contents_url, hda_summary[ "id" ] ) )
|
|
self._assert_status_code_is( hda_info_response, 200 )
|
|
self.assertEquals( hda_info_response.json()[ "metadata_data_lines" ], lines )
|
|
|
|
def __invoke_workflow( self, history_id, workflow_id, inputs={}, assert_ok=True ):
|
|
workflow_request = dict(
|
|
history="hist_id=%s" % history_id,
|
|
)
|
|
workflow_request[ "inputs" ] = dumps( inputs )
|
|
workflow_request[ "inputs_by" ] = 'step_index'
|
|
url = "workflows/%s/usage" % ( workflow_id )
|
|
|
|
invocation_response = self._post( url, data=workflow_request )
|
|
if assert_ok:
|
|
self._assert_status_code_is( invocation_response, 200 )
|
|
invocation_id = invocation_response.json()[ "id" ]
|
|
return invocation_id
|
|
else:
|
|
return invocation_response
|
|
|
|
def __import_workflow( self, workflow_id, deprecated_route=False ):
|
|
if deprecated_route:
|
|
route = "workflows/import"
|
|
import_data = dict(
|
|
workflow_id=workflow_id,
|
|
)
|
|
else:
|
|
route = "workflows"
|
|
import_data = dict(
|
|
shared_workflow_id=workflow_id,
|
|
)
|
|
return self._post( route, import_data )
|
|
|
|
def _download_workflow(self, workflow_id, style=None):
|
|
params = {}
|
|
if style:
|
|
params = {"style": style}
|
|
download_response = self._get( "workflows/%s/download" % workflow_id, params )
|
|
self._assert_status_code_is( download_response, 200 )
|
|
downloaded_workflow = download_response.json()
|
|
return downloaded_workflow
|
|
|
|
def _show_workflow(self, workflow_id):
|
|
show_response = self._get( "workflows/%s" % workflow_id )
|
|
self._assert_status_code_is( show_response, 200 )
|
|
return show_response.json()
|
|
|
|
def _assert_looks_like_instance_workflow_representation(self, workflow):
|
|
self._assert_has_keys(
|
|
workflow,
|
|
'url',
|
|
'owner',
|
|
'inputs',
|
|
'annotation',
|
|
'steps'
|
|
)
|
|
for step in workflow["steps"].values():
|
|
self._assert_has_keys(
|
|
step,
|
|
'id',
|
|
'type',
|
|
'tool_id',
|
|
'tool_version',
|
|
'annotation',
|
|
'tool_inputs',
|
|
'input_steps',
|
|
)
|
|
|
|
RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
|