Repository: common-workflow-language/workflow-service

Issue:
No support for Connexion 3, so a vulnerable Werkzeug is required
The `wes-service` PyPI package at 4.0 depends on `connexion` <3.

But the latest `connexion` 2, 2.14.2, depends on `werkzeug<2.3`.

But only Werkzeug 3.0.3+ has the [patch](https://github.com/pallets/werkzeug/commit/3386395b24c7371db11a5b8eaac0c91da5362692) for [CVE-2024-34069](https://cve.circl.lu/cve/CVE-2024-34069)

So it's not possible to install `wes-service` with a fully patched Werkzeug, which makes it difficult to use securely.

`wes-service` should be updated to work with `connexion` 3.

Hints from issue comments:

Solution patch:
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 4dfacc5..9fbd8f6 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -3,3 +3,4 @@ types-PyYAML
 types-requests
 types-setuptools
 arvados-cwl-runner
+flask
diff --git a/pyproject.toml b/pyproject.toml
index 7ed17a1..96b4578 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "wes-service"
-version = "4.0"
+version = "5.0"
 authors = [{name = "GA4GH Containers and Workflows task team", email = "common-workflow-language@googlegroups.com"}]
 description = "GA4GH Workflow Execution Service reference implementation"
 classifiers = [
@@ -23,7 +23,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "connexion[swagger-ui] >= 2.0.2, < 3",
+    "connexion[swagger-ui,flask,uvicorn] >= 3, < 4",
     "ruamel.yaml >= 0.15.78",
     "schema-salad",
 ]
diff --git a/wes_client/util.py b/wes_client/util.py
index 3e9672d..862ec57 100644
--- a/wes_client/util.py
+++ b/wes_client/util.py
@@ -128,7 +128,7 @@ def modify_jsonyaml_paths(jsonyaml_file: str) -> str:
 
 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 @@ class WESClient:
         :return: The body of the post result as a dictionary.
         """
         attachments = list(expand_globs(attachments))
-        parts = build_wes_request(wf, jsonyaml, attachments)
+        parts, files = 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=files,
+            # headers=self.auth,
         )
         return wes_response(postresult)
 
diff --git a/wes_service/arvados_wes.py b/wes_service/arvados_wes.py
index e2369cc..7f1ecf6 100644
--- a/wes_service/arvados_wes.py
+++ b/wes_service/arvados_wes.py
@@ -298,7 +298,7 @@ class ArvadosBackend(WESBackend):
         )
 
         try:
-            tempdir, body = self.collect_attachments(cr["uuid"])
+            tempdir, body = self.collect_attachments(args, cr["uuid"])
 
             workflow_engine_parameters = cast(
                 dict[str, Any], body.get("workflow_engine_parameters", {})
diff --git a/wes_service/cwl_runner.py b/wes_service/cwl_runner.py
index 9fc31a6..af3400d 100644
--- a/wes_service/cwl_runner.py
+++ b/wes_service/cwl_runner.py
@@ -198,7 +198,7 @@ class CWLRunnerBackend(WESBackend):
 
     def RunWorkflow(self, **args: str) -> dict[str, str]:
         """Submit the workflow run request."""
-        tempdir, body = self.collect_attachments()
+        tempdir, body = self.collect_attachments(args)
 
         run_id = uuid.uuid4().hex
         job = Workflow(run_id)
diff --git a/wes_service/toil_wes.py b/wes_service/toil_wes.py
index 1461d04..f6cbde6 100644
--- a/wes_service/toil_wes.py
+++ b/wes_service/toil_wes.py
@@ -1,3 +1,6 @@
+"""Toil backed for the WES service."""
+
+import errno
 import json
 import logging
 import os
@@ -294,18 +297,41 @@ class ToilWorkflow:
                     logging.info("Workflow " + self.run_id + ": EXECUTOR_ERROR")
                     open(self.staterrorfile, "a").close()
                     return "EXECUTOR_ERROR", 255
+
+        # get the jobstore
+        with open(self.jobstorefile, "r") as f:
+            jobstore = f.read().rstrip()
         if (
             subprocess.run(  # nosec B603
                 [
                     shutil.which("toil") or "toil",
                     "status",
                     "--failIfNotComplete",
-                    self.jobstorefile,
+                    jobstore,
                 ]
             ).returncode
             == 0
         ):
-            completed = True
+            # Get the PID of the running process
+            with open(self.pidfile, "r") as f:
+                pid = int(f.read())
+            try:
+                os.kill(pid, 0)
+            except OSError as e:
+                if e.errno == errno.ESRCH:
+                    # Process is no longer running, could be completed
+                    completed = True
+                    # Reap zombie child processes in a non-blocking manner
+                    # os.WNOHANG still raises an error if no child processes exist
+                    try:
+                        os.waitpid(pid, os.WNOHANG)
+                    except OSError as e:
+                        if e.errno != errno.ECHILD:
+                            raise
+                else:
+                    raise
+            # If no exception, process is still running
+            # We can't rely on toil status as the process may not have created the jobstore yet
         if completed:
             logging.info("Workflow " + self.run_id + ": COMPLETE")
             open(self.statcompletefile, "a").close()
@@ -354,9 +380,9 @@ class ToilBackend(WESBackend):
         workflows = [{"run_id": w.run_id, "state": w.getstate()[0]} for w in wf]  # NOQA
         return {"workflows": workflows, "next_page_token": ""}
 
-    def RunWorkflow(self) -> dict[str, str]:
+    def RunWorkflow(self, **args: str) -> dict[str, str]:
         """Submit the workflow run request."""
-        tempdir, body = self.collect_attachments()
+        tempdir, body = self.collect_attachments(args)
 
         run_id = uuid.uuid4().hex
         job = ToilWorkflow(run_id)
diff --git a/wes_service/util.py b/wes_service/util.py
index b710db5..b687490 100644
--- a/wes_service/util.py
+++ b/wes_service/util.py
@@ -4,7 +4,6 @@ import os
 import tempfile
 from typing import Any, Callable, Optional
 
-import connexion  # type: ignore[import-untyped]
 from werkzeug.utils import secure_filename
 
 
@@ -49,52 +48,37 @@ class WESBackend:
         logging.info("Workflow %s: %s", run_id, message)
 
     def collect_attachments(
-        self, run_id: Optional[str] = None
+        self, args: dict[str, Any], run_id: Optional[str] = None
     ) -> tuple[str, dict[str, str]]:
         """Stage all attachments to a temporary directory."""
         tempdir = tempfile.mkdtemp()
         body: dict[str, str] = {}
         has_attachments = False
-        for k, ls in connexion.request.files.lists():
-            try:
-                for v in ls:
-                    if k == "workflow_attachment":
-                        sp = v.filename.split("/")
-                        fn = []
-                        for p in sp:
-                            if p not in ("", ".", ".."):
-                                fn.append(secure_filename(p))
-                        dest = os.path.join(tempdir, *fn)
-                        if not os.path.isdir(os.path.dirname(dest)):
-                            os.makedirs(os.path.dirname(dest))
-                        self.log_for_run(
-                            run_id,
-                            f"Staging attachment {v.filename!r} to {dest!r}",
-                        )
-                        v.save(dest)
-                        has_attachments = True
-                        body[k] = (
-                            "file://%s" % tempdir
-                        )  # Reference to temp working dir.
-                    elif k in ("workflow_params", "tags", "workflow_engine_parameters"):
-                        content = v.read()
-                        body[k] = json.loads(content.decode("utf-8"))
-                    else:
-                        body[k] = v.read().decode()
-            except Exception as e:
-                raise ValueError(f"Error reading parameter {k!r}: {e}") from e
-        for k, ls in connexion.request.form.lists():
-            try:
-                for v in ls:
-                    if not v:
-                        continue
-                    if k in ("workflow_params", "tags", "workflow_engine_parameters"):
-                        body[k] = json.loads(v)
-                    else:
-                        body[k] = v
-            except Exception as e:
-                raise ValueError(f"Error reading parameter {k!r}: {e}") from e
-
+        for k, v in args.items():
+            if k == "workflow_attachment":
+                for file in v or []:
+                    sp = file.filename.split("/")
+                    fn = []
+                    for p in sp:
+                        if p not in ("", ".", ".."):
+                            fn.append(secure_filename(p))
+                    dest = os.path.join(tempdir, *fn)
+                    if not os.path.isdir(os.path.dirname(dest)):
+                        os.makedirs(os.path.dirname(dest))
+                    self.log_for_run(
+                        run_id,
+                        f"Staging attachment {file.filename!r} to {dest!r}",
+                    )
+                    file.save(dest)
+                    has_attachments = True
+                    body["workflow_attachment"] = (
+                        "file://%s" % tempdir
+                    )  # Reference to temp working dir.
+            elif k in ("workflow_params", "tags", "workflow_engine_parameters"):
+                if v is not None:
+                    body[k] = json.loads(v)
+            else:
+                body[k] = v
         if "workflow_url" in body:
             if ":" not in body["workflow_url"]:
                 if not has_attachments:
diff --git a/wes_service/wes_service_main.py b/wes_service/wes_service_main.py
index fa81888..6ef50b1 100644
--- a/wes_service/wes_service_main.py
+++ b/wes_service/wes_service_main.py
@@ -63,7 +63,6 @@ def get_parser() -> argparse.ArgumentParser:
         help="Example: '--opt runner=cwltoil --opt extra=--logLevel=CRITICAL' "
         "or '--opt extra=--workDir=/'.  Accepts multiple values.",
     )
-    parser.add_argument("--debug", action="store_true", default=False)
     parser.add_argument("--version", action="store_true", default=False)
     return parser
 
@@ -78,7 +77,7 @@ def main(argv: list[str] = sys.argv[1:]) -> None:
 
     app = setup(args)
 
-    app.run(port=args.port, debug=args.debug)
+    app.run(port=args.port)
 
 
 if __name__ == "__main__":


Test patch:
diff --git a/test/test_integration.py b/test/test_integration.py
index 0d6fd17..5929666 100644
--- a/test/test_integration.py
+++ b/test/test_integration.py
@@ -246,7 +246,6 @@ class CwltoolTest(IntegrationTest):
                 "--opt",
                 "runner=cwltool",
                 "--port=8080",
-                "--debug",
             ]
         )
         time.sleep(5)
@@ -304,7 +303,6 @@ class ArvadosTest(IntegrationTest):
                 os.path.abspath("wes_service/wes_service_main.py"),
                 "--backend=wes_service.arvados_wes",
                 "--port=8080",
-                "--debug",
             ]
         )
         self.client.auth = {