Fix client request, fix dependencies, fix a bug in Makefile

Author: stxue1

Makefile

@@ -150,7 +150,7 @@ test: $(PYSOURCES) FORCE
 
 ## testcov                : run the wes-service test suite and collect coverage
 testcov: $(PYSOURCES)
-	python -m pytest -rsx --cov ${PYTEST_EXTRA}
+	python -m pytest ${PYTEST_EXTRA} -rsx --cov
 
 sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "connexion[swagger-ui] >= 3, < 4",
+    "connexion[swagger-ui,flask,uvicorn] >= 3, < 4",
     "ruamel.yaml >= 0.15.78",
     "schema-salad",
 ]

test/test_integration.py

@@ -246,7 +246,6 @@ def setUp(self) -> None:
                 "--opt",
                 "runner=cwltool",
                 "--port=8080",
-                "--debug",
             ]
         )
         time.sleep(5)
@@ -304,7 +303,6 @@ def setUp(self) -> None:
                 os.path.abspath("wes_service/wes_service_main.py"),
                 "--backend=wes_service.arvados_wes",
                 "--port=8080",
-                "--debug",
             ]
         )
         self.client.auth = {

wes_client/util.py

@@ -128,7 +128,7 @@ def fixpaths(d: Any) -> None:
 
 def build_wes_request(
     workflow_file: str, json_path: str, attachments: Optional[list[str]] = None
-) -> list[tuple[str, Any]]:
+) -> tuple[list[tuple[str, Any]], list[tuple[str, Any]]]:
     """
     :param workflow_file: Path to cwl/wdl file.  Can be http/https/file.
     :param json_path: Path to accompanying json file.
@@ -157,10 +157,12 @@ def build_wes_request(
         ("workflow_type_version", wf_version),
     ]
 
+    workflow_attachments = []
+
     if workflow_file.startswith("file://"):
         if wfbase is None:
             wfbase = os.path.dirname(workflow_file[7:])
-        parts.append(
+        workflow_attachments.append(
             (
                 "workflow_attachment",
                 (os.path.basename(workflow_file[7:]), open(workflow_file[7:], "rb")),
@@ -182,9 +184,9 @@ def build_wes_request(
                 attach_f = urlopen(attachment)  # nosec B310
                 relpath = os.path.basename(attach_f)
 
-            parts.append(("workflow_attachment", (relpath, attach_f)))
+            workflow_attachments.append(("workflow_attachment", (relpath, attach_f)))
 
-    return parts
+    return parts, workflow_attachments
 
 
 def expand_globs(attachments: Optional[Union[list[str], str]]) -> set[str]:
@@ -275,11 +277,12 @@ def run(
         :return: The body of the post result as a dictionary.
         """
         attachments = list(expand_globs(attachments))
-        parts = build_wes_request(wf, jsonyaml, attachments)
+        parts, attachments = build_wes_request(wf, jsonyaml, attachments)
         postresult = requests.post(  # nosec B113
             f"{self.proto}://{self.host}/ga4gh/wes/v1/runs",
-            files=parts,
-            headers=self.auth,
+            data=parts,
+            files=attachments,
+            # headers=self.auth,
         )
         return wes_response(postresult)