Improvements to to yaml_to_workflow for Kyle.

Add UUID to workflows (his contribution) - add shortcuts for rename an hide actions with tests (his request, my implementation).

test/api/test_workflow_extraction.py

@@ -182,68 +182,6 @@ test_data:
         collection_step_state = loads( collection_step[ "tool_state" ] )
         self.assertEquals( collection_step_state[ "collection_type" ], u"list:paired" )
 
-    def _run_jobs( self, jobs_yaml ):
-        history_id = self.history_id
-        workflow_id = self._upload_yaml_workflow(
-            jobs_yaml
-        )
-        jobs_descriptions = yaml.load( jobs_yaml )
-        test_data = jobs_descriptions["test_data"]
-
-        label_map = {}
-        inputs = {}
-        for key, value in test_data.items():
-            if isinstance( value, dict ):
-                elements_data = value.get( "elements", [] )
-                elements = []
-                for element_data in elements_data:
-                    identifier = element_data[ "identifier" ]
-                    content = element_data["content"]
-                    elements.append( ( identifier, content ) )
-                collection_type = value["type"]
-                if collection_type == "list:paired":
-                    hdca = self.dataset_collection_populator.create_list_of_pairs_in_history( history_id ).json()
-                elif collection_type == "list":
-                    hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=elements ).json()
-                else:
-                    hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=elements ).json()
-                label_map[key] = self._ds_entry( hdca )
-                inputs[key] = hdca
-            else:
-                hda = self.dataset_populator.new_dataset( history_id, content=value )
-                label_map[key] = self._ds_entry( hda )
-                inputs[key] = hda
-        workflow_request = dict(
-            history="hist_id=%s" % history_id,
-            workflow_id=workflow_id,
-        )
-        workflow_request[ "inputs" ] = dumps( label_map )
-        workflow_request[ "inputs_by" ] = 'name'
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        url = "workflows/%s/usage" % ( workflow_id )
-        invocation_response = self._post( url, data=workflow_request )
-        self._assert_status_code_is( invocation_response, 200 )
-        invocation = invocation_response.json()
-        invocation_id = invocation[ "id" ]
-        # Wait for workflow to become fully scheduled and then for all jobs
-        # complete.
-        self.wait_for_invocation( workflow_id, invocation_id )
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        jobs = self._history_jobs( history_id )
-        return RunJobsSummary(
-            history_id=history_id,
-            workflow_id=workflow_id,
-            inputs=inputs,
-            jobs=jobs,
-        )
-
-    def wait_for_invocation( self, workflow_id, invocation_id ):
-        url = "workflows/%s/usage/%s" % ( workflow_id, invocation_id )
-        return wait_on_state( lambda: self._get( url )  )
-
-    def _history_jobs( self, history_id ):
-        return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json()
-
     def _job_id_for_tool( self, jobs, tool_id ):
         return self._job_for_tool( jobs, tool_id )[ "id" ]
 

test/api/test_workflows.py

@@ -1,6 +1,12 @@
+from .helpers import wait_on_state
+
 from base import api
 from json import dumps
+from collections import namedtuple
+
 import time
+
+import yaml
 from .helpers import WorkflowPopulator
 from .helpers import DatasetPopulator
 from .helpers import DatasetCollectionPopulator
@@ -101,6 +107,69 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase ):
         invocation_details = invocation_details_response.json()
         return invocation_details
 
+    def _run_jobs( self, jobs_yaml, history_id=None ):
+        if history_id is None:
+            history_id = self.history_id
+        workflow_id = self._upload_yaml_workflow(
+            jobs_yaml
+        )
+        jobs_descriptions = yaml.load( jobs_yaml )
+        test_data = jobs_descriptions["test_data"]
+
+        label_map = {}
+        inputs = {}
+        for key, value in test_data.items():
+            if isinstance( value, dict ):
+                elements_data = value.get( "elements", [] )
+                elements = []
+                for element_data in elements_data:
+                    identifier = element_data[ "identifier" ]
+                    content = element_data["content"]
+                    elements.append( ( identifier, content ) )
+                collection_type = value["type"]
+                if collection_type == "list:paired":
+                    hdca = self.dataset_collection_populator.create_list_of_pairs_in_history( history_id ).json()
+                elif collection_type == "list":
+                    hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=elements ).json()
+                else:
+                    hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=elements ).json()
+                label_map[key] = self._ds_entry( hdca )
+                inputs[key] = hdca
+            else:
+                hda = self.dataset_populator.new_dataset( history_id, content=value )
+                label_map[key] = self._ds_entry( hda )
+                inputs[key] = hda
+        workflow_request = dict(
+            history="hist_id=%s" % history_id,
+            workflow_id=workflow_id,
+        )
+        workflow_request[ "inputs" ] = dumps( label_map )
+        workflow_request[ "inputs_by" ] = 'name'
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        url = "workflows/%s/usage" % ( workflow_id )
+        invocation_response = self._post( url, data=workflow_request )
+        self._assert_status_code_is( invocation_response, 200 )
+        invocation = invocation_response.json()
+        invocation_id = invocation[ "id" ]
+        # Wait for workflow to become fully scheduled and then for all jobs
+        # complete.
+        self.wait_for_invocation( workflow_id, invocation_id )
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        jobs = self._history_jobs( history_id )
+        return RunJobsSummary(
+            history_id=history_id,
+            workflow_id=workflow_id,
+            inputs=inputs,
+            jobs=jobs,
+        )
+
+    def wait_for_invocation( self, workflow_id, invocation_id ):
+        url = "workflows/%s/usage/%s" % ( workflow_id, invocation_id )
+        return wait_on_state( lambda: self._get( url )  )
+
+    def _history_jobs( self, history_id ):
+        return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json()
+
 
 # Workflow API TODO:
 # - Allow history_id as param to workflow run action. (hist_id)
@@ -641,3 +710,7 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
                 shared_workflow_id=workflow_id,
             )
         return self._post( route, import_data )
+
+
+RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
+

test/api/test_workflows_from_yaml.py

@@ -1,4 +1,3 @@
-import json
 
 from .test_workflows import BaseWorkflowsApiTestCase
 
@@ -30,3 +29,33 @@ class WorkflowsFromYamlApiTestCase( BaseWorkflowsApiTestCase ):
       __current_case__: 1
 """)
         self._get("workflows/%s/download" % workflow_id).content
+
+    def test_simple_output_actions( self ):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+steps:
+  - type: input
+    label: input1
+  - tool_id: cat1
+    label: first_cat
+    state:
+      input1:
+        $link: 0
+    outputs:
+       out_file1:
+         hide: true
+         rename: "the new value"
+  - tool_id: cat1
+    state:
+      input1:
+        $link: first_cat#out_file1
+test_data:
+  input1: "hello world"
+""", history_id=history_id)
+
+        details1 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
+        assert not details1["visible"]
+        assert details1["name"] == "the new value", details1
+        details2 = self.dataset_populator.get_history_dataset_details(history_id, hid=3)
+        assert details2["visible"]
+        assert False

test/api/yaml_to_workflow.py

@@ -2,6 +2,7 @@ import sys
 
 import yaml
 import json
+import uuid
 
 try:
     from collections import OrderedDict
@@ -25,7 +26,8 @@ def yaml_to_workflow(has_yaml):
         "a_galaxy_workflow": "true",
         "format-version": "0.1",
         "annotation": "",
-        "name": "Workflow"
+        "name": "Workflow",
+        "uuid": str(uuid.uuid4()),
     })
 
     steps = as_python["steps"]
@@ -107,8 +109,10 @@ def transform_tool(context, step):
 
     __ensure_defaults( step, {
         "annotation": "",
+        "post_job_actions": {},
     } )
     __ensure_inputs_connections(step)
+    post_job_actions = step["post_job_actions"]
 
     tool_state = {
         # TODO: Galaxy should not require tool state actually specify a __page__.
@@ -178,6 +182,30 @@ def transform_tool(context, step):
 
     __populate_tool_state(step, tool_state)
 
+    # Handle outputs.
+    if "outputs" in step:
+        for name, output in step.get("outputs", {}).items():
+            if output.get("hide", False):
+                action_name = "HideDatasetAction%s" % name
+                action = __action(
+                    "HideDatasetAction",
+                    name,
+                )
+                post_job_actions[action_name] = action
+
+            if output.get("rename", None):
+                new_name = output.get("rename")
+                action_name = "RenameDatasetAction%s" % name
+                arguments = dict(newname=new_name)
+                action = __action(
+                    "RenameDatasetAction",
+                    name,
+                    arguments,
+                )
+                post_job_actions[action_name] = action
+
+        del step["outputs"]
+
 
 class ConversionContext(object):
 
@@ -185,6 +213,14 @@ class ConversionContext(object):
         self.labels = {}
 
 
+def __action(type, name, arguments={}):
+    return {
+        "action_arguments": arguments,
+        "action_type": type,
+        "output_name": name,
+    }
+
+
 def __is_link(value):
     return isinstance(value, dict) and "$link" in value