Merge pull request #770 from jmchilton/workflow_fixes_2

Add a native Galaxy workflow (.ga) testing test.

Author: jmchilton

tests/data/wf2-job.yml

@@ -0,0 +1,6 @@
+WorkflowInput1:
+  class: File
+  path: hello.txt
+WorkflowInput2:
+  class: File
+  path: hello.txt

tests/data/wf2-test.yml

@@ -0,0 +1,6 @@
+- doc: Simple concat workflow test
+  job: wf2-job.yml
+  outputs:
+    wf_output_1:
+      checksum: 'sha1$7bd92c6cd84285e4fc7215d506bbabfe328acb8f'
+

tests/data/wf2.ga

@@ -0,0 +1,90 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "simple workflow",
+    "format-version": "0.1", 
+    "name": "TestWorkflow1", 
+    "steps": {
+        "0": {
+            "annotation": "input1 description", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "input1 description", 
+                    "name": "WorkflowInput1"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 199.55555772781372, 
+                "top": 200.66666460037231
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"WorkflowInput1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "WorkflowInput2"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 206.22221422195435, 
+                "top": 327.33335161209106
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"WorkflowInput2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input1": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "queries_0|input2": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Concatenate datasets", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 419.33335876464844, 
+                "top": 200.44446563720703
+            }, 
+            "workflow_outputs": [
+                {"output_name": "out_file1", "label": "wf_output_1"}
+            ],
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "cat",
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/john/workspace/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}

tests/test_cmd_serve.py

@@ -109,6 +109,7 @@ def _run(self, serve_args=[]):
         test_cmd = [
             "serve",
             "--install_galaxy",
+            "--no_dependency_resolution",
             "--port",
             str(self._port),
             self._serve_artifact,

tests/test_cmd_test.py

@@ -16,8 +16,8 @@ class CmdTestTestCase(CliTestCase):
     """Integration tests for the ``test`` command."""
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    def test_workflow_test_simple(self):
-        """Test testing a simple workflow with Galaxy."""
+    def test_workflow_test_simple_yaml(self):
+        """Test testing a simple YAML workflow with Galaxy."""
         with self._isolate():
             random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
             cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
@@ -28,12 +28,36 @@ def test_workflow_test_simple(self):
             ]
             test_command = self.append_profile_argument_if_needed(test_command)
             test_command += [
+                "--no_dependency_resolution",
                 "--extra_tools", random_lines,
                 "--extra_tools", cat,
                 test_artifact,
             ]
             self._check_exit_code(test_command, exit_code=0)
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_workflow_test_simple_ga(self):
+        """Test testing a simple GA workflow with Galaxy."""
+        with self._isolate():
+            cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
+            test_artifact = os.path.join(TEST_DATA_DIR, "wf2.ga")
+            test_command = [
+                "--verbose",
+                "test"
+            ]
+            test_command = self.append_profile_argument_if_needed(test_command)
+            test_command += [
+                "--no_dependency_resolution",
+                "--extra_tools", cat,
+                test_artifact,
+            ]
+            # try:
+            self._check_exit_code(test_command, exit_code=0)
+            # except Exception:
+            #    with open(os.path.join(f, "tool_test_output.json"), "r") as o:
+            #        print(o.read())
+            #    raise
+
     @skip_unless_python_2_7()
     @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
     def test_cwltool_tool_test(self):

tests/test_galaxy_serve.py

@@ -32,6 +32,7 @@ def test_serve_daemon(self):
             install_galaxy=True,
             port=port,
             daemon=True,
+            no_dependency_resolution=True,
         )
 
         assert network_util.wait_net_service(
@@ -63,6 +64,7 @@ def test_serve_workflow(self):
             port=port,
             daemon=True,
             extra_tools=extra_tools,
+            no_dependency_resolution=True,
         )
         user_gi = config.user_gi
         assert user_gi.tools.get_tools(tool_id="random_lines1")

tests/test_run.py

@@ -59,6 +59,7 @@ def test_run_gxtool_randomlines(self):
             test_cmd = [
                 "--verbose",
                 "run",
+                "--no_dependency_resolution",
                 tool_path,
                 job_path,
             ]
@@ -73,6 +74,7 @@ def test_run_cat(self):
             job_path = _cwl_file("cat-job.json")
             test_cmd = [
                 "run",
+                "--no_dependency_resolution",
                 tool_path,
                 job_path,
             ]
@@ -88,6 +90,7 @@ def test_run_output_directory(self):
             test_cmd = [
                 "--verbose",
                 "run",
+                "--no_dependency_resolution",
                 "--output_directory",
                 f,
                 tool_path,