Merge pull request #1350 from lldelisle/make_test_run

Make test dockstore init with creator run and pass
galaxyproject · Feb 16, 2023 · ef68fb3 · ef68fb3
2 parents da2c58b + 7cc16d3
commit ef68fb3
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Showing 3 changed files with 20 additions and 5 deletions.
diff --git a/planemo/workflow_lint.py b/planemo/workflow_lint.py
@@ -99,7 +99,7 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
                                 requests.get(
                                     f"https://orcid.org/{orcid[0]}",
                                     headers={"Accept": "application/xml"},
-                                    allow_redirects=False,
+                                    allow_redirects=True,
                                 ).status_code
                                 == 200
                             ):

diff --git a/tests/test_cmd_dockstore_init.py b/tests/test_cmd_dockstore_init.py
@@ -17,6 +17,9 @@ def test_init_publish_true(self):
     def test_init_publish_false(self):
         self.run_dockstore_init(False)
 
+    def test_init_with_creator(self):
+        self.run_dockstore_init_with_creator()
+
     def run_dockstore_init(self, publish: Optional[bool] = None):
         with self._isolate_with_test_data("wf_repos/from_format2/0_basic_native") as f:
             init_cmd = ["dockstore_init"]
@@ -38,15 +41,17 @@ def run_dockstore_init(self, publish: Optional[bool] = None):
             self._check_exit_code(workflow_lint_cmd)
 
     def run_dockstore_init_with_creator(self):
-        with self._isolate_with_test_data("wf_repos/autoupdate_tests/workflow_with_unexisting_version_of_tool.ga") as f:
-            init_cmd = ["dockstore_init", f]
+        with self._isolate_workflow("wf_repos/autoupdate_tests/workflow_with_unexisting_tool.ga") as f:
+            init_cmd = ["dockstore_init"]
             self._check_exit_code(init_cmd)
+            assert os.path.exists(".dockstore.yml")
             with open(".dockstore.yml") as fh:
                 dockstore_config = yaml.safe_load(fh)
             assert str(dockstore_config["version"]) == "1.2"
             assert "workflows" in dockstore_config
             assert len(dockstore_config["workflows"]) == 1
-            assert "authors" in dockstore_config["workflows"]
-            assert dockstore_config["workflows"]["authors"]["orcid"] == "0000-0002-1964-4960"
+            workflow = dockstore_config["workflows"][0]
+            assert "authors" in workflow
+            assert workflow["authors"][0]["orcid"] == "0000-0002-1964-4960"
             workflow_lint_cmd = ["workflow_lint", "--skip", "tool_ids", "--fail_level", "error", f]
             self._check_exit_code(workflow_lint_cmd)
diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -115,6 +115,12 @@ def _isolate_repo(self, name):
             self._copy_repo(name, f)
             yield f
 
+    @contextlib.contextmanager
+    def _isolate_workflow(self, name):
+        with self._isolate() as f:
+            self._copy_workflow(name, f)
+            yield f
+
     @contextlib.contextmanager
     def _isolate_with_test_data(self, relative_path):
         with self._isolate() as f:
@@ -126,6 +132,10 @@ def _copy_repo(self, name, dest):
         repo = os.path.join(TEST_REPOS_DIR, name)
         self._copy_directory(repo, dest)
 
+    def _copy_workflow(self, name, dest):
+        workflow = os.path.join(TEST_DATA_DIR, name)
+        io.shell(["cp", workflow, dest])
+
     def _copy_directory(self, path, dest):
         io.shell(["cp", "-r", f"{path}/.", dest])