mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
157939aa8f
Details: - Add a new workflow module describing subworkflows. - Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node. - Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution. - Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language. - Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow). - Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation. - Extend workflow import and export code to allow a nested representation of workflows. - Update format 2 workflow description to allow testing nested workflows. Most relevant new and modified test cases can be run using the following commands: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs nosetests test/unit/test_galaxy_mapping.py nosetests test/unit/workflows/test_workflow_progress.py ```
127 lines
3.9 KiB
Python
127 lines
3.9 KiB
Python
from functools import partial
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import yaml
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from galaxy.util import bunch
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from galaxy import model
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from galaxy.model import mapping
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from galaxy.web.security import SecurityHelper
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class MockTrans( object ):
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def __init__( self ):
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self.app = TestApp()
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self.sa_session = self.app.model.context
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self._user = None
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def save_workflow(self, workflow):
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stored_workflow = model.StoredWorkflow()
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stored_workflow.latest_workflow = workflow
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stored_workflow.user = self.user
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self.sa_session.add( stored_workflow )
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self.sa_session.flush()
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return stored_workflow
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@property
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def user(self):
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if self._user is None:
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self._user = model.User(
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email="testworkflows@bx.psu.edu",
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password="password"
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)
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return self._user
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class TestApp( object ):
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def __init__( self ):
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self.config = bunch.Bunch(
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tool_secret="awesome_secret",
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)
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self.model = mapping.init(
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"/tmp",
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"sqlite:///:memory:",
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create_tables=True
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)
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self.toolbox = TestToolbox()
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self.datatypes_registry = TestDatatypesRegistry()
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self.security = SecurityHelper(id_secret="testing")
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class TestDatatypesRegistry( object ):
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def __init__( self ):
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pass
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def get_datatype_by_extension( self, ext ):
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return ext
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class TestToolbox( object ):
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def __init__( self ):
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self.tools = {}
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def get_tool( self, tool_id, tool_version=None ):
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# Real tool box returns None of missing tool also
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return self.tools.get( tool_id, None )
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def get_tool_id( self, tool_id ):
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tool = self.get_tool( tool_id )
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return tool and tool.id
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def yaml_to_model(has_dict, id_offset=100):
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if isinstance(has_dict, str):
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has_dict = yaml.load(has_dict)
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workflow = model.Workflow()
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workflow.steps = []
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for i, step in enumerate(has_dict.get("steps", [])):
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workflow_step = model.WorkflowStep()
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if "order_index" not in step:
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step["order_index"] = i
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if "id" not in step:
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# Fixed Offset ids just to test against assuption order_index != id
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step["id"] = id_offset
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id_offset += 1
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step_type = step.get("type", None)
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assert step_type is not None
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if step_type == "subworkflow":
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subworkflow_dict = step["subworkflow"]
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del step["subworkflow"]
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subworkflow = yaml_to_model(subworkflow_dict, id_offset=id_offset)
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step["subworkflow"] = subworkflow
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id_offset += len(subworkflow.steps)
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for key, value in step.iteritems():
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if key == "input_connections":
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connections = []
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for conn_dict in value:
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conn = model.WorkflowStepConnection()
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for conn_key, conn_value in conn_dict.iteritems():
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if conn_key == "@output_step":
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target_step = workflow.steps[conn_value]
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conn_value = target_step
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conn_key = "output_step"
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if conn_key == "@input_subworkflow_step":
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conn_value = step["subworkflow"].step_by_index(conn_value)
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conn_key = "input_subworkflow_step"
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setattr(conn, conn_key, conn_value)
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connections.append(conn)
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value = connections
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if key == "workflow_outputs":
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value = map(partial(_dict_to_workflow_output, workflow_step), value)
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setattr(workflow_step, key, value)
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workflow.steps.append( workflow_step )
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return workflow
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def _dict_to_workflow_output(workflow_step, as_dict):
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output = model.WorkflowOutput(workflow_step)
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for key, value in as_dict.iteritems():
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setattr(output, key, value)
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return output
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