remove args from utils_cwl, remove args 4/n

Author: Vasu Jaganath

src/sophios/apis/rest/api.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-# import argparse
 import copy
 import yaml
 
@@ -9,11 +8,11 @@
 from fastapi.middleware.cors import CORSMiddleware
 
 from sophios import __version__, compiler
-from sophios import run_local, input_output
+from sophios import input_output
 from sophios.utils_graphs import get_graph_reps
 from sophios.utils_yaml import wic_loader
 from sophios import utils_cwl
-from sophios.post_compile import cwl_inline_runtag, verify_container_engine_config
+from sophios.post_compile import cwl_inline_runtag
 from sophios.cli import get_args
 from sophios.wic_types import CompilerInfo, Json, Tool, Tools, StepId, YamlTree, Cwl, NodeData
 from sophios.apis.utils import converter
@@ -41,33 +40,6 @@ 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
-
-
 app = FastAPI()
 
 origins = ["*"]

src/sophios/compiler.py

@@ -213,6 +213,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
     graph_settings['graph_dark_theme'] = args.graph_dark_theme
     graph_settings['graph_inline_depth'] = args.graph_inline_depth
     graph_settings['graph_label_edges'] = args.graph_label_edges
+    graph_settings['graph_show_outputs'] = args.graph_show_outputs
 
     for i, step_key in enumerate(steps_keys):
         step_name_i = utils.step_name_str(yaml_stem, i, step_key)
@@ -827,7 +828,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
 
     vars_workflow_output_internal = list(set(vars_workflow_output_internal))  # Get uniques
     # (Why are we getting uniques?)
-    workflow_outputs = utils_cwl.get_workflow_outputs(args, namespaces, is_root, yaml_stem,
+    workflow_outputs = utils_cwl.get_workflow_outputs(graph_settings, namespaces, is_root, yaml_stem,
                                                       steps, outputs_workflow, vars_workflow_output_internal,
                                                       graph, tools_lst, step_node_name, tools)
     # Add the provided workflow outputs to the workflow outputs from each step

src/sophios/utils_cwl.py

@@ -1,4 +1,3 @@
-import argparse
 import copy
 from pathlib import Path
 from typing import Any, Dict, List
@@ -102,7 +101,7 @@ def add_yamldict_keyval_out(steps_i: Yaml, step_key: str, strs: List[str]) -> Ya
     return steps_i
 
 
-def get_workflow_outputs(args: argparse.Namespace,
+def get_workflow_outputs(graph_settings: Dict[str, Any],
                          namespaces: Namespaces,
                          is_root: bool,
                          yaml_stem: str,
@@ -116,7 +115,7 @@ def get_workflow_outputs(args: argparse.Namespace,
     """Chooses a subset of the CWL outputs: to actually output
 
     Args:
-        args (argparse.Namespace): The command line arguments
+        graph_settings (Dict[str, Any]): The settings dict for graphpviz graphs
         namespaces (Namespaces): Specifies the path in the AST of the current subworkflow
         is_root (bool): True if this is the root workflow
         yaml_stem (str): The name of the current subworkflow (stem of the yaml filepath)
@@ -148,7 +147,7 @@ def get_workflow_outputs(args: argparse.Namespace,
             out_var = f'{step_name_or_key}/{out_key}'
             # Avoid duplicating intermediate outputs in GraphViz
             out_key_no_namespace = out_key.split('___')[-1]
-            if args.graph_show_outputs:
+            if graph_settings['graph_show_outputs']:
                 vars_nss = [var.replace('/', '___') for var in vars_workflow_output_internal]
                 case1 = (tool_i['class'] == 'Workflow') and (not out_key in vars_nss)
                 # Avoid duplicating outputs from subgraphs in parent graphs.
@@ -164,8 +163,8 @@ def get_workflow_outputs(args: argparse.Namespace,
                     attrs = {'label': out_key_no_namespace, 'shape': 'box',
                              'style': 'rounded, filled', 'fillcolor': 'lightyellow'}
                     graph_gv.node(namespaced_output_name, **attrs)
-                    font_edge_color = 'black' if args.graph_dark_theme else 'white'
-                    if args.graph_label_edges:
+                    font_edge_color = 'black' if graph_settings['graph_dark_theme'] else 'white'
+                    if graph_settings['graph_label_edges']:
                         graph_gv.edge(step_node_name, namespaced_output_name, color=font_edge_color,
                                       label=out_key_no_namespace)  # Is labeling necessary?
                     else: