remove args in rest api, removing args 3/n

Author: Vasu Jaganath

src/sophios/apis/rest/api.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-import argparse
+# import argparse
 import copy
 import yaml
 
@@ -41,31 +41,31 @@ def remove_dot_dollar(tree: Cwl) -> Cwl:
     return tree_no_dd
 
 
-def run_workflow(compiler_info: CompilerInfo, args: argparse.Namespace) -> int:
-    """
-    Get the Sophios yaml tree from incoming JSON
-    Args:
-        req (JSON): A raw JSON content of incoming JSON object
-    Returns:
-        Cwl: A Cwl document with . and $ removed from $namespaces and $schemas
-    """
-    # ========= WRITE OUT =======================
-    basepath = 'autogenerated'
-    input_output.write_to_disk(compiler_info.rose, Path(basepath), relative_run_path=True)
-    # ======== TEST RUN =========================
-    # verify container_engine install and config
-    verify_container_engine_config(args.container_engine, args.ignore_docker_install)
-    run_args_dict = {}
-    run_args_dict['container_engine'] = args.container_engine
-    run_args_dict['cwl_runner'] = args.cwl_runner
-    run_args_dict['copy_output_files'] = str(args.copy_output_files)
-    rose_tree = compiler_info.rose
-    retval = run_local.run_local(run_args_dict, False, passthrough_args=[],
-                                 workflow_name=rose_tree.data.name, basepath=basepath)
-    retval_local = 1
-    if retval:
-        retval_local = retval
-    return retval_local
+# def run_workflow(compiler_info: CompilerInfo, args: argparse.Namespace) -> int:
+#     """
+#     Get the Sophios yaml tree from incoming JSON
+#     Args:
+#         req (JSON): A raw JSON content of incoming JSON object
+#     Returns:
+#         Cwl: A Cwl document with . and $ removed from $namespaces and $schemas
+#     """
+#     # ========= WRITE OUT =======================
+#     basepath = 'autogenerated'
+#     input_output.write_to_disk(compiler_info.rose, Path(basepath), relative_run_path=True)
+#     # ======== TEST RUN =========================
+#     # verify container_engine install and config
+#     verify_container_engine_config(args.container_engine, args.ignore_docker_install)
+#     run_args_dict = {}
+#     run_args_dict['container_engine'] = args.container_engine
+#     run_args_dict['cwl_runner'] = args.cwl_runner
+#     run_args_dict['copy_output_files'] = str(args.copy_output_files)
+#     rose_tree = compiler_info.rose
+#     retval = run_local.run_local(run_args_dict, False, passthrough_args=[],
+#                                  workflow_name=rose_tree.data.name, basepath=basepath)
+#     retval_local = 1
+#     if retval:
+#         retval_local = retval
+#     return retval_local
 
 
 app = FastAPI()

src/sophios/compiler.py

@@ -320,8 +320,8 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 # Use auto-discovery mechanism (with run tag)
                 tool_i = tools[stepid_runtag]
             else:
-                msg = f"Error! Neither {stepid.stem} nor {
-                    stepid_runtag.stem} found!, check your 'search_paths_cwl' in global_config.json"
+                msg = f"Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!"
+                msg += "check your 'search_paths_cwl' in global_config.json"
                 raise Exception(msg)
             # Programmatically modify tool_i here
             graph_dummy = graph  # Just use anything here to satisfy mypy

tests/test_rest_core.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 import asyncio
 import subprocess as sub
-import sys
 import traceback
 import yaml
 
@@ -91,9 +90,7 @@ def run_cwl_local(workflow_name: str, cwl_runner: str, docker_cmd: str, use_subp
             print(f'See error_{workflow_name}.txt for detailed technical information.')
             # Do not display a nasty stack trace to the user; hide it in a file.
             with open(f'error_{workflow_name}.txt', mode='w', encoding='utf-8') as f:
-                # https://mypy.readthedocs.io/en/stable/common_issues.html#python-version-and-system-platform-checks
-                if sys.version_info >= (3, 10):
-                    traceback.print_exception(type(e), value=e, tb=None, file=f)
+                traceback.print_exception(type(e), value=e, tb=None, file=f)
             print(e)  # we are always running this on CI
     return retval