Migrate CWL parsing from cwltool to cwl-utils

This commit replaces the cwltool parser with the faster
auto-generated parser included in cwl-utils.

.github/workflows/ci-tests.yaml

@@ -36,7 +36,7 @@ jobs:
           - commit: "6397014050177074c9ccd0d771577f7fa9f728a3"
             exclude: "docker_entrypoint,stdin_shorcut,inplace_update_on_file_content"
             version: "v1.1"
-          - commit: "ad6f77c648ae9f0eaa2fd53ba7032b0523e12de8"
+          - commit: "f79146f6b59884ecbe6445ab3cb2b8a374b0ee64"
             exclude: "docker_entrypoint,modify_file_content"
             version: "v1.2"
     steps:

requirements.txt

@@ -5,7 +5,7 @@ asyncssh==2.13.0
 bcrypt==4.0.1
 cachetools==5.3.0
 cwltool==3.1.20230127121939
-cwl-utils==0.22
+cwl-utils==0.23
 importlib_metadata==6.0.0
 Jinja2==3.1.2
 jsonref==1.1.0

streamflow/cwl/main.py

@@ -3,6 +3,7 @@
 import logging
 import os
 
+import cwl_utils.parser
 import cwltool.context
 import cwltool.load_tool
 import cwltool.loghandler
@@ -12,7 +13,7 @@
 from streamflow.config.config import WorkflowConfig
 from streamflow.core.context import StreamFlowContext
 from streamflow.cwl.translator import CWLTranslator
-from streamflow.cwl.utils import load_cwl_inputs, load_cwl_workflow
+from streamflow.cwl.utils import load_cwl_inputs
 from streamflow.log_handler import logger
 from streamflow.workflow.executor import StreamFlowExecutor
 
@@ -43,9 +44,12 @@ async def main(
         # noinspection PyProtectedMember
         cwltool.loghandler._logger.setLevel(logging.WARN)
     # Load CWL workflow definition
-    cwl_definition, loading_context = load_cwl_workflow(cwl_args[0])
+    cwl_definition = cwl_utils.parser.load_document_by_uri(cwl_args[0])
     if len(cwl_args) == 2:
-        cwl_inputs = load_cwl_inputs(loading_context, cwl_definition, cwl_args[1])
+        loading_context = cwltool.context.LoadingContext()
+        cwl_inputs = load_cwl_inputs(
+            loading_context, cwl_definition.loadingOptions, cwl_args[1]
+        )
     else:
         cwl_inputs = {}
     # Transpile CWL workflow to the StreamFlow representation
@@ -58,7 +62,6 @@ async def main(
         cwl_definition=cwl_definition,
         cwl_inputs=cwl_inputs,
         workflow_config=workflow_config,
-        loading_context=loading_context,
     )
     if logger.isEnabledFor(logging.INFO):
         logger.info("Building workflow execution plan")