revert #979

Author: linglp

tests/conftest.py

@@ -72,13 +72,6 @@ def get_python_version(self):
 
         return base_version
 
-    @staticmethod
-    def clean_up_file(self, file_name):
-        try:
-            os.remove(self.get_data_path(file_name))
-        except FileNotFoundError:
-            pass
-
 @pytest.fixture
 def helpers():
     yield Helpers

tests/test_cli.py

@@ -7,7 +7,7 @@
 # from schematic import init
 from schematic.schemas.commands import schema
 from schematic.utils.google_api_utils import download_creds_file
-from schematic.manifest.commands import manifest
+
 
 @pytest.fixture
 def runner() -> CliRunner:
@@ -16,75 +16,21 @@ def runner() -> CliRunner:
     return CliRunner()
 
 
-@pytest.fixture
-def data_model_jsonld(helpers):
-    data_model_jsonld =helpers.get_data_path("example.model.jsonld")
-    yield data_model_jsonld
-
-
 class TestSchemaCli:
-    def test_schema_convert_cli(self, runner, helpers, data_model_jsonld):
+    def test_schema_convert_cli(self, runner, config_path, helpers):
 
         data_model_csv_path = helpers.get_data_path("example.model.csv")
 
+        output_path = helpers.get_data_path("example.model.jsonld")
+
         result = runner.invoke(
-            schema, ["convert", data_model_csv_path, "--output_jsonld", data_model_jsonld]
+            schema, ["convert", data_model_csv_path, "--output_jsonld", output_path]
         )
 
         assert result.exit_code == 0
 
         expected_substr = (
-            "The Data Model was created and saved to " f"'{data_model_jsonld}' location."
+            "The Data Model was created and saved to " f"'{output_path}' location."
         )
 
         assert expected_substr in result.output
-
-    # get manifest by default
-    @pytest.mark.google_credentials_needed
-    def test_get_manifest_cli(self, runner, helpers, config, data_model_jsonld):
-        output_path = helpers.get_data_path("example.Patient.manifest.csv")
-
-        result = runner.invoke(
-            manifest, ["--config", config.CONFIG_PATH, "get",  "--data_type", "Patient", "--jsonld", data_model_jsonld]
-        )
-
-
-        assert result.exit_code == 0
-
-        expected_substr_one = "Find the manifest template using this CSV file path:" 
-
-        assert expected_substr_one in result.output
-        assert output_path in result.output
-
-        # clean up
-        helpers.clean_up_file(helpers, file_name=output_path)
-    
-    # get manifest as a csv
-    # use google drive to export
-    @pytest.mark.google_credentials_needed
-    def test_get_manifest_csv(self, runner, helpers, config, data_model_jsonld):
-        output_path = helpers.get_data_path("test.csv")
-
-        result = runner.invoke(
-            manifest, ["--config", config.CONFIG_PATH, "get",  "--data_type", "Patient", "--jsonld", data_model_jsonld, "--output_csv", output_path]
-        )
-        assert result.exit_code == 0
-        assert output_path in result.output
-
-        # clean up
-        helpers.clean_up_file(helpers, file_name=output_path)
-
-    # get manifest as an excel spreadsheet
-    @pytest.mark.google_credentials_needed
-    def test_get_manifest_excel(self, runner, helpers, config, data_model_jsonld):
-        output_path = helpers.get_data_path("test.xlsx")
-
-        result = runner.invoke(
-            manifest, ["--config", config.CONFIG_PATH,  "get",  "--data_type", "Patient", "--jsonld", data_model_jsonld, "--output_xlsx", output_path]
-        )
-
-        assert result.exit_code == 0
-        assert output_path in result.output
-
-        # clean up
-        helpers.clean_up_file(helpers, file_name=output_path)

tests/test_metadata.py

@@ -38,4 +38,4 @@ def test_get_component_requirements(self, metadata_model, as_graph):
         else:
             assert "Biospecimen" in output
             assert "Patient" in output
-            assert "BulkRNA-seqAssay" in output
+            assert "BulkRNA-seqAssay" in output