Merge pull request #41 from jmchilton/BioComputeDev

Testing and docs update.

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -1238,7 +1238,13 @@ def _generate_invocation_bco(self, trans, invocation_id, **kwd):
     def export_invocation_bco(self, trans, invocation_id, **kwd):
         '''
         GET /api/invocations/{invocations_id}/biocompute
+
         Return a BioCompute Object for the workflow invocation.
+
+        The BioCompute Object endpoints are in beta - important details such
+        as how inputs and outputs are represented, how the workflow is encoded,
+        and how author and version information is encoded, and how URLs are
+        generated will very likely change in important ways over time.
         '''
         return self._generate_invocation_bco(trans, invocation_id, **kwd)
 
@@ -1247,8 +1253,13 @@ def download_invocation_bco(self, trans, invocation_id, **kwd):
         """
         GET /api/invocations/{invocations_id}/biocompute/download
 
-        Returns a selected BioCompute Object.
+        Returns a selected BioCompute Object as a file for download (HTTP
+        headers configured with filename and such).
 
+        The BioCompute Object endpoints are in beta - important details such
+        as how inputs and outputs are represented, how the workflow is encoded,
+        and how author and version information is encoded, and how URLs are
+        generated will very likely change in important ways over time.
         """
         ret_dict = self._generate_invocation_bco(trans, invocation_id, **kwd)
         trans.response.headers["Content-Disposition"] = 'attachment; filename="bco_%s.json"' % invocation_id

lib/galaxy_test/api/test_workflows.py

@@ -1195,6 +1195,9 @@ def test_run_subworkflow_simple(self):
             assert [step for step in subworkflow_invocation['steps'] if step['workflow_step_label'] == 'inner_input']
             assert [step for step in subworkflow_invocation['steps'] if step['workflow_step_label'] == 'random_lines']
 
+            bco = self.workflow_populator.get_biocompute_object(run_response.invocation_id)
+            self.workflow_populator.validate_biocompute_object(bco)
+
     @skip_without_tool("random_lines1")
     def test_run_subworkflow_runtime_parameters(self):
         with self.dataset_populator.test_history() as history_id:
@@ -1437,14 +1440,9 @@ def test_export_invocation_bco(self):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_jobs(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
             invocation_id = summary.invocation_id
-            bco = self._get("invocations/%s/biocompute" % invocation_id).json()
-            self._assert_has_keys(bco, "object_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
+            bco = self.workflow_populator.get_biocompute_object(invocation_id)
+            self.workflow_populator.validate_biocompute_object(bco)
             self.assertEqual(bco['provenance_domain']['name'], "Simple Workflow")
-            self._assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
-            self._assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
-            for p in bco['parametric_domain']:
-                self._assert_has_keys(p, "param", "value", "step")
-            self._assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
 
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):

lib/galaxy_test/base/populators.py

@@ -813,6 +813,21 @@ def get_invocation(self, invocation_id):
         r.raise_for_status()
         return r.json()
 
+    def get_biocompute_object(self, invocation_id):
+        bco_response = self._get("invocations/%s/biocompute" % invocation_id)
+        bco_response.raise_for_status()
+        return bco_response.json()
+
+    def validate_biocompute_object(self, bco, expected_schema_version='https://w3id.org/ieee/ieee-2791-schema/2791object.json'):
+        # TODO: actually use jsonref and jsonschema to validate this someday
+        api_asserts.assert_has_keys(bco, "object_id", "spec_version", "etag", "provenance_domain", "usability_domain", "description_domain", "execution_domain", "parametric_domain", "io_domain", "error_domain")
+        assert bco['spec_version'] == expected_schema_version
+        api_asserts.assert_has_keys(bco['description_domain'], "keywords", "xref", "platform", "pipeline_steps")
+        api_asserts.assert_has_keys(bco['execution_domain'], "script_access_type", "script", "script_driver", "software_prerequisites", "external_data_endpoints", "environment_variables")
+        for p in bco['parametric_domain']:
+            api_asserts.assert_has_keys(p, "param", "value", "step")
+        api_asserts.assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
+
     def invoke_workflow_raw(self, workflow_id, request):
         url = "workflows/%s/usage" % (workflow_id)
         invocation_response = self._post(url, data=request)