Merge pull request #7556 from jmchilton/expression_tools

Implement expression tools and non-data tool outputs.

test/api/test_tools.py

@@ -2130,6 +2130,48 @@ class ToolsTestCase(api.ApiTestCase):
         output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
         self.assertEqual(output_content.strip(), "123\n456\n456\n0ab")
 
+    @skip_without_tool("expression_forty_two")
+    def test_galaxy_expression_tool_simplest(self):
+        history_id = self.dataset_populator.new_history()
+        inputs = {
+        }
+        run_response = self._run(
+            "expression_forty_two", history_id, inputs
+        )
+        self._assert_status_code_is(run_response, 200)
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        output_content = self.dataset_populator.get_history_dataset_content(history_id)
+        self.assertEqual(output_content, "42")
+
+    @skip_without_tool("expression_parse_int")
+    def test_galaxy_expression_tool_simple(self):
+        history_id = self.dataset_populator.new_history()
+        inputs = {
+            'input1': '7',
+        }
+        run_response = self._run(
+            "expression_parse_int", history_id, inputs
+        )
+        self._assert_status_code_is(run_response, 200)
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        output_content = self.dataset_populator.get_history_dataset_content(history_id)
+        self.assertEqual(output_content, "7")
+
+    @skip_without_tool("expression_log_line_count")
+    def test_galaxy_expression_metadata(self):
+        history_id = self.dataset_populator.new_history()
+        new_dataset1 = self.dataset_populator.new_dataset(history_id, content='1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14')
+        inputs = {
+            'input1': dataset_to_param(new_dataset1),
+        }
+        run_response = self._run(
+            "expression_log_line_count", history_id, inputs
+        )
+        self._assert_status_code_is(run_response, 200)
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        output_content = self.dataset_populator.get_history_dataset_content(history_id)
+        self.assertEqual(output_content, "3")
+
     def __build_group_list(self, history_id):
         response = self.dataset_collection_populator.upload_collection(history_id, "list", elements=[
             {

test/api/test_workflows.py

@@ -822,12 +822,14 @@ test_data:
 """, history_id=history_id, assert_ok=False, wait=False)
             self.wait_for_invocation_and_jobs(history_id, job_summary.workflow_id, job_summary.invocation_id, assert_ok=False)
             history_contents = self.dataset_populator._get_contents_request(history_id=history_id).json()
+            first_input = history_contents[1]
+            assert first_input['history_content_type'] == 'dataset'
             paused_dataset = history_contents[-1]
             failed_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, assert_ok=False)
             assert paused_dataset['state'] == 'paused', paused_dataset
             assert failed_dataset['state'] == 'error', failed_dataset
             inputs = {"input1": {'values': [{'src': 'hda',
-                                             'id': history_contents[0]['id']}]
+                                             'id': first_input['id']}]
                                  },
                       "failbool": "false",
                       "rerun_remap_job_id": failed_dataset['creating_job']}
@@ -1996,7 +1998,7 @@ text_input:
   type: raw
 """, history_id=history_id, wait=True, assert_ok=False)
 
-    def test_run_with_text_connection(self):
+    def test_run_with_text_input_connection(self):
         with self.dataset_populator.test_history() as history_id:
             self._run_jobs("""
 class: GalaxyWorkflow
@@ -2027,6 +2029,27 @@ text_input:
             content = self.dataset_populator.get_history_dataset_content(history_id)
             self.assertEqual("chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", content)
 
+    def test_run_with_numeric_input_connection(self):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+steps:
+- label: forty_two
+  tool_id: expression_forty_two
+  state: {}
+- label: consume_expression_parameter
+  tool_id: cheetah_casting
+  state:
+    floattest: 3.14
+    inttest:
+      $link: forty_two#out1
+test_data: {}
+""", history_id=history_id)
+
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        content = self.dataset_populator.get_history_dataset_content(history_id)
+        self.assertEquals("43\n4.14\n", content)
+
     @skip_without_tool('cat1')
     def test_workflow_rerun_with_use_cached_job(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_run")