v0.7.0

README.md

@@ -13,6 +13,14 @@ including support for additional endpoints defined in [ELIXIR Cloud &
 AAI's][res-elixir-cloud] generic [TRS-Filer][res-elixir-cloud-trs-filer] TRS
 implementation.
 
+The TRS API version underlying the client can be found
+[here][res-ga4gh-trs-version].
+
+TRS-cli has so far been succesfully tested with the
+[TRS-Filer][res-elixir-cloud-trs-filer] and
+[WorkflowHub][res-eosc-workflow-hub] TRS implementations. WorkflowHub's public
+TRS API endpoint can be found here: <https://dev.workflowhub.eu/ga4gh/trs/v2>
+
 ## Table of Contents
 
 * [Usage](#usage)
@@ -41,20 +49,23 @@ from trs_cli import TRSClient
 ### Configure client class
 
 It is possible to configure the `TRSClient` class with the `.config()` class
-method. Currently there is only a single configuration parameter available,
-the `debug` flag. Setting it to `True` (default: False) will have the exception
-handler print tracebacks for every exception encountered.
+method. The following configuration parameters are available:
+
+| Parameter | Type | Default | Description |
+| --- | --- | ---- | --- |
+| `debug` | `bool` | `False` | If set, the exception handler prints tracebacks for every exception encountered. |
+| `no_validate` | `bool` | `False` | If set, responses JSON are not validated against the TRS API schemas. In that case, unserialized `response` objects are returned. Set this flag if the TRS implementation you are working with is not fully compliant with the TRS API specification. |
 
 Example:
 
 ```py
 from trs_cli import TRSClient
 
-TRSClient.config(debug=True)
+TRSClient.config(debug=True, no_validate=True)
 ```
 
 > Note that as a _class method_, the `.config()` method will affect _all_
-> client instances.
+> client instances, including existing ones.
 
 ### Create client instance
 
@@ -171,15 +182,6 @@ methods for additional endpoints implemented in
 | [`.delete_version()`][docs-api-delete_version] | `DELETE ​/tools​/{id}​/versions​/{version_id}` | Delete a tool version |
 | [`.post_service_info()`][docs-api-post_service_info] | `POST ​/service-info` | Register service info |
 
-#### Convenience methods
-
-Finally, TRS-cli tries to provide convenience methods for common operations
-that involve multiple API calls.  Currently there is one such method defined:
-
-| Method | Description |
-| --- | --- |
-| [`.retrieve_files()`][docs-api-retrieve_files] | Retrieve all files associated with a given tool version and descriptor type. Useful for downloading workflows. |
-
 ### Authorization
 
 Authorization [bearer tokens][res-bearer-token] can be provided either during
@@ -306,8 +308,10 @@ question etc.
 [res-elixir-cloud-coc]: <https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/CODE_OF_CONDUCT.md>
 [res-elixir-cloud-contributing]: <https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/CONTRIBUTING.md>
 [res-elixir-cloud-trs-filer]: <https://github.com/elixir-cloud-aai/trs-filer>
+[res-eosc-workflow-hub]: <https://workflowhub.eu/>
 [res-ga4gh]: <https://www.ga4gh.org/>
 [res-ga4gh-trs]: <https://github.com/ga4gh/tool-registry-service-schemas>
+[res-ga4gh-trs-version]: <https://github.com/ga4gh/tool-registry-service-schemas/blob/91a57cd93caf380019d4952c0c74bb7e343e647b/openapi/openapi.yaml>
 [res-ga4gh-trs-uri]: <https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs_uris>
 [res-pydantic]: <https://pydantic-docs.helpmanual.io/>
 [res-pydantic-docs-export]: <https://pydantic-docs.helpmanual.io/usage/exporting_models/>

tests/test_client.py

@@ -32,8 +32,9 @@
 MOCK_API = f"{MOCK_HOST}:{MOCK_PORT}/{MOCK_BASE_PATH}"
 MOCK_ID = "123456"
 MOCK_ID_INVALID = "N0T VAL!D"
+MOCK_TEXT_PLAIN = "SOME TEXT"
 MOCK_TRS_URI = f"trs://{MOCK_DOMAIN}/{MOCK_ID}"
-MOCK_TRS_URI_VERSIONED = f"trs://{MOCK_DOMAIN}/{MOCK_ID}/versions/{MOCK_ID}"
+MOCK_TRS_URI_VERSIONED = f"trs://{MOCK_DOMAIN}/{MOCK_ID}/{MOCK_ID}"
 MOCK_TOKEN = "MyT0k3n"
 MOCK_DESCRIPTOR = "CWL"
 MOCK_RESPONSE_INVALID = {"not": "valid"}
@@ -489,7 +490,7 @@ class TestDeleteVersion:
         f"{cli.uri}/tools/{MOCK_ID}/versions/{MOCK_ID}"
     )
 
-    def test_success(self, monkeypatch, requests_mock):
+    def test_success(self, requests_mock):
         """Returns 200 response."""
         requests_mock.delete(self.endpoint, json=MOCK_ID)
         r = self.cli.delete_version(
@@ -665,6 +666,10 @@ class TestGetDescriptorByPath:
         f"{cli.uri}/tools/{MOCK_ID}/versions/{MOCK_ID}/{MOCK_DESCRIPTOR}"
         f"/descriptor/{MOCK_ID}"
     )
+    endpoint_plain = (
+        f"{cli.uri}/tools/{MOCK_ID}/versions/{MOCK_ID}/PLAIN_{MOCK_DESCRIPTOR}"
+        f"/descriptor/{MOCK_ID}"
+    )
 
     def test_success(self, requests_mock):
         """Returns 200 response."""
@@ -677,6 +682,17 @@ def test_success(self, requests_mock):
         )
         assert r.dict() == MOCK_FILE_WRAPPER
 
+    def test_success_plain(self, requests_mock):
+        """Returns 200 response."""
+        requests_mock.get(self.endpoint_plain, text=MOCK_TEXT_PLAIN)
+        r = self.cli.get_descriptor_by_path(
+            type=f"PLAIN_{MOCK_DESCRIPTOR}",
+            id=MOCK_ID,
+            version_id=MOCK_ID,
+            path=MOCK_ID,
+        )
+        assert r.text == MOCK_TEXT_PLAIN
+
 
 class TestGetFiles:
     """Test getter for files of a given descriptor type."""
@@ -713,17 +729,85 @@ def test_ContentTypeUnavailable(self, requests_mock):
                 format=MOCK_ID,
             )
 
-    def test_success_trs_uri_zip(self, requests_mock):
+    def test_success_trs_uri_zip(self, requests_mock, tmpdir):
         """Returns 200 ZIP response with TRS URI."""
-        requests_mock.get(self.endpoint, json=[MOCK_TOOL_FILE])
+        outfile = tmpdir / 'test.zip'
+        requests_mock.get(self.endpoint)
         r = self.cli.get_files(
             type=MOCK_DESCRIPTOR,
             id=MOCK_TRS_URI_VERSIONED,
             format='zip',
+            outfile=outfile,
         )
-        if not isinstance(r, Error):
-            assert r[0].file_type.value == MOCK_TOOL_FILE['file_type']
-            assert r[0].path == MOCK_TOOL_FILE['path']
+        assert r == outfile
+
+    def test_success_trs_uri_zip_default_filename(
+                self,
+                requests_mock,
+                monkeypatch,
+            ):
+        """Returns 200 ZIP response with default filename."""
+        requests_mock.get(self.endpoint)
+        monkeypatch.setattr(
+            'builtins.open',
+            lambda *args, **kwargs: _raise(Exception)
+        )
+        with pytest.raises(Exception):
+            self.cli.get_files(
+                type=MOCK_DESCRIPTOR,
+                id=MOCK_TRS_URI_VERSIONED,
+                format='zip',
+            )
+
+    def test_zip_content_type(self, requests_mock, tmpdir):
+        """Test wrong content type."""
+        outfile = tmpdir / 'test.zip'
+        requests_mock.get(
+            self.endpoint,
+            headers={'Content-Type': 'text/plain'},
+        )
+        r = self.cli.get_files(
+            type=MOCK_DESCRIPTOR,
+            id=MOCK_TRS_URI_VERSIONED,
+            format='zip',
+            outfile=outfile,
+        )
+        print(r)
+        print(type(r))
+        print(dir(r))
+        print(r.headers)
+        assert isinstance(r, requests.models.Response)
+
+    def test_zip_io_error(self, monkeypatch, requests_mock, tmpdir):
+        """Test I/O error."""
+        outfile = tmpdir / 'test.zip'
+        requests_mock.get(self.endpoint)
+        monkeypatch.setattr(
+            'builtins.open',
+            lambda *args, **kwargs: _raise(IOError)
+        )
+        r = self.cli.get_files(
+            type=MOCK_DESCRIPTOR,
+            id=MOCK_TRS_URI_VERSIONED,
+            format='zip',
+            outfile=outfile,
+        )
+        assert isinstance(r, requests.models.Response)
+
+    def test_zip_connection_error(self, monkeypatch, tmpdir):
+        """Test connection error."""
+        outfile = tmpdir / 'test.zip'
+        monkeypatch.setattr(
+            'requests.get',
+            lambda *args, **kwargs: _raise(requests.exceptions.ConnectionError)
+        )
+        with pytest.raises(requests.exceptions.ConnectionError):
+            self.cli.get_files(
+                type=MOCK_DESCRIPTOR,
+                id=MOCK_TRS_URI_VERSIONED,
+                format='zip',
+                outfile=outfile,
+            )
 
 
 class TestGetTests:
@@ -1108,6 +1192,9 @@ class TestSendRequestAndValidateRespose:
     """Test request sending and response validation."""
 
     cli = TRSClient(uri=MOCK_TRS_URI)
+    cli.headers = {
+        'Accept': 'application/json'
+    }
     endpoint = MOCK_API
     payload = {}
 
@@ -1122,12 +1209,21 @@ def test_connection_error(self, monkeypatch):
                 url=MOCK_API,
             )
 
+    def test_no_validation(self, requests_mock):
+        TRSClient.config(no_validate=True)
+        requests_mock.get(self.endpoint, text=MOCK_ID)
+        response = self.cli._send_request_and_validate_response(
+            url=MOCK_API,
+        )
+        assert response.text == MOCK_ID
+        TRSClient.config(no_validate=False)
+
     def test_get_str_validation(self, requests_mock):
         """Test for getter with string response."""
         requests_mock.get(self.endpoint, json=MOCK_ID)
         response = self.cli._send_request_and_validate_response(
             url=MOCK_API,
-            validation_class_ok=str,
+            json_validation_class=str,
         )
         assert response == MOCK_ID
 
@@ -1136,7 +1232,7 @@ def test_get_none_validation(self, requests_mock):
         requests_mock.get(self.endpoint, json=MOCK_ID)
         response = self.cli._send_request_and_validate_response(
             url=MOCK_API,
-            validation_class_ok=None,
+            json_validation_class=None,
         )
         assert response is None
 
@@ -1145,7 +1241,7 @@ def test_get_model_validation(self, requests_mock):
         requests_mock.get(self.endpoint, json=MOCK_TOOL)
         response = self.cli._send_request_and_validate_response(
             url=MOCK_API,
-            validation_class_ok=Tool,
+            json_validation_class=Tool,
         )
         assert response == MOCK_TOOL
 
@@ -1154,7 +1250,7 @@ def test_get_list_validation(self, requests_mock):
         requests_mock.get(self.endpoint, json=[MOCK_TOOL])
         response = self.cli._send_request_and_validate_response(
             url=MOCK_API,
-            validation_class_ok=(Tool, ),
+            json_validation_class=(Tool, ),
         )
         assert response == [MOCK_TOOL]
 
@@ -1165,7 +1261,7 @@ def test_post_validation(self, requests_mock):
             url=MOCK_API,
             method='post',
             payload=self.payload,
-            validation_class_ok=str,
+            json_validation_class=str,
         )
         assert response == MOCK_ID
 
@@ -1175,7 +1271,7 @@ def test_get_success_invalid(self, requests_mock):
         with pytest.raises(InvalidResponseError):
             self.cli._send_request_and_validate_response(
                 url=MOCK_API,
-                validation_class_ok=Error,
+                json_validation_class=Error,
             )
 
     def test_error_response(self, requests_mock):
@@ -1188,12 +1284,12 @@ def test_error_response(self, requests_mock):
 
     def test_error_response_invalid(self, requests_mock):
         """Test for error response that fails validation."""
-        requests_mock.get(self.endpoint, json=MOCK_ERROR, status_code=400)
+        requests_mock.get(self.endpoint, json=MOCK_TOOL, status_code=400)
         with pytest.raises(InvalidResponseError):
-            self.cli._send_request_and_validate_response(
+            bla = self.cli._send_request_and_validate_response(
                 url=MOCK_API,
-                validation_class_error=Tool,
             )
+            print(bla)
 
     def test_invalid_http_method(self, requests_mock):
         """Test for invalid HTTP method."""
@@ -1204,3 +1300,17 @@ def test_invalid_http_method(self, requests_mock):
                 method='non_existing',
                 payload=self.payload,
             )
+
+    def test_text_plain_responses(self, requests_mock):
+        """Test for invalid HTTP method."""
+        requests_mock.get(
+            self.endpoint,
+            text=MOCK_TEXT_PLAIN,
+            headers={'Content-Type': 'text/plain'},
+        )
+        self.cli.headers['Accept'] = 'text/plain'
+        r = self.cli._send_request_and_validate_response(
+            url=MOCK_API,
+        )
+        assert r == MOCK_TEXT_PLAIN
+        self.cli.headers['Accept'] = 'application/json'

trs_cli/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '0.6.1'
+__version__ = '0.7.0'
 
 from trs_cli.client import TRSClient  # noqa: F401