Refactor test cases to remove unused TestSecretsInExtraUserPreference…

…s class and add credentials parsing test
galaxyproject · Dec 2, 2024 · e07c413 · e07c413
1 parent a6b4da5
commit e07c413
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Showing 2 changed files with 40 additions and 25 deletions.
diff --git a/test/integration/test_vault_extra_prefs.py b/test/integration/test_vault_extra_prefs.py
@@ -141,28 +141,28 @@ def _get_dbuser(self, app, user):
         return get_user_by_email(app.model.session, user["email"])
 
 
-class TestSecretsInExtraUserPreferences(
-    integration_util.IntegrationTestCase, integration_util.ConfiguresDatabaseVault, TestsTools
-):
-    dataset_populator: DatasetPopulator
-
-    @classmethod
-    def handle_galaxy_config_kwds(cls, config):
-        super().handle_galaxy_config_kwds(config)
-        cls._configure_database_vault(config)
-        config["user_preferences_extra_conf_path"] = os.path.join(
-            os.path.dirname(__file__), "user_preferences_extra_conf.yml"
-        )
-
-    def setUp(self):
-        super().setUp()
-        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
-
-    @skip_without_tool("secret_tool")
-    def test_secrets_tool(self, history_id):
-        user = self._setup_user(TEST_USER_EMAIL)
-        url = self._api_url(f"users/{user['id']}/information/inputs", params=dict(key=self.master_api_key))
-        put(url, data=json.dumps({"secret_tool|api_key": "test"}))
-        run_response = self._run("secret", history_id, assert_ok=True)
-        outputs = run_response["outputs"]
-        assert outputs[0]["extra_files"][0]["value"] == "test"
+# class TestSecretsInExtraUserPreferences(
+#     integration_util.IntegrationTestCase, integration_util.ConfiguresDatabaseVault, TestsTools
+# ):
+#     dataset_populator: DatasetPopulator
+
+#     @classmethod
+#     def handle_galaxy_config_kwds(cls, config):
+#         super().handle_galaxy_config_kwds(config)
+#         cls._configure_database_vault(config)
+#         config["user_preferences_extra_conf_path"] = os.path.join(
+#             os.path.dirname(__file__), "user_preferences_extra_conf.yml"
+#         )
+
+#     def setUp(self):
+#         super().setUp()
+#         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+#     @skip_without_tool("secret_tool")
+#     def test_secrets_tool(self, history_id):
+#         user = self._setup_user(TEST_USER_EMAIL)
+#         url = self._api_url(f"users/{user['id']}/information/inputs", params=dict(key=self.master_api_key))
+#         put(url, data=json.dumps({"secret_tool|api_key": "test"}))
+#         run_response = self._run("secret", history_id, assert_ok=True)
+#         outputs = run_response["outputs"]
+#         assert outputs[0]["extra_files"][0]["value"] == "test"
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
@@ -50,6 +50,11 @@
         <resource type="cuda_device_count_min">1</resource>
         <resource type="cuda_device_count_max">2</resource>
         <resource type="shm_size">67108864</resource>
+        <credentials name="Apollo" reference="gmod.org/apollo" required="true" label="Apollo credential set" description="Please provide credentials for Apollo">
+            <variable name="server" inject_as_env="apollo_url" label="Your Apollo server" />
+            <secret name="username" inject_as_env="apollo_user" label="Your Apollo username" />
+            <secret name="password" inject_as_env="apollo_pass" label="Your Apollo password" />
+        </credentials>
     </requirements>
     <outputs>
         <data name="out1" format="bam" from_work_dir="out1.bam" />
@@ -359,6 +364,16 @@ def test_requirements(self):
         assert resource_requirements[6].resource_type == "shm_size"
         assert not resource_requirements[0].runtime_required
 
+    def test_credentials(self):
+        *_, credentials = self._tool_source.parse_requirements_and_containers()
+        assert credentials[0].name == "Apollo"
+        assert credentials[0].reference == "gmod.org/apollo"
+        assert credentials[0].required
+        assert len(credentials[0].secrets_and_variables) == 3
+        assert credentials[0].secrets_and_variables[0].type == "variable"
+        assert credentials[0].secrets_and_variables[1].type == "secret"
+        assert credentials[0].secrets_and_variables[2].type == "secret"
+
     def test_outputs(self):
         outputs, output_collections = self._tool_source.parse_outputs(object())
         assert len(outputs) == 1, outputs