semi-fix the inline_cwl when using stock CLT names with REST API

src/sophios/api/http/restapi.py

@@ -130,9 +130,13 @@ async def compile_wf(request: Request) -> Json:
     compiler_info: CompilerInfo = compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, {}, {},
                                                             tools_cwl, True, relative_run_path=True, testing=False)
 
+    rose_tree = compiler_info.rose
+    if args.inline_cwl_runtag:
+        input_output.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+        rose_tree = plugins.cwl_update_inline_runtag_rosetree(rose_tree, Path('autogenerated/'), True)
     # ======== OUTPUT PROCESSING ================
     # ========= PROCESS COMPILED OBJECT =========
-    sub_node_data: NodeData = compiler_info.rose.data
+    sub_node_data: NodeData = rose_tree.data
     yaml_stem = sub_node_data.name
     cwl_tree = sub_node_data.compiled_cwl
     yaml_inputs = sub_node_data.workflow_inputs_file

src/sophios/compiler.py

@@ -880,14 +880,15 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 newval['format'] = in_format
             new_keyval = {key: newval}
         elif 'Directory' == in_dict['type']:
-            if in_dict['value'].startswith('/'):
-                print("Warning! directory can not start with '/'")
-                print("It is most likely an incorrect path! Treating it as './' relative path")
-                in_dict['value'] = '.' + in_dict['value']
-            ldir = Path(in_dict['value'])
-            if not ldir.is_absolute():
-                ldir = Path('autogenerated') / ldir
-            ldir.mkdir(parents=True, exist_ok=True)
+            if not args.ignore_dir_path:
+                if in_dict['value'].startswith('/'):
+                    print("Warning! directory can not start with '/'")
+                    print("It is most likely an incorrect path! Can't create directories!")
+                    sys.exit(1)
+                ldir = Path(in_dict['value'])
+                if not ldir.is_absolute():
+                    ldir = Path('autogenerated') / ldir
+                ldir.mkdir(parents=True, exist_ok=True)
             newval = {'class': 'Directory', 'location': in_dict['value']}
             new_keyval = {key: newval}
         # TODO: Check for all valid types?

tests/test_rest_core.py

@@ -144,7 +144,7 @@ async def receive() -> Json:
 
 
 @pytest.mark.fast
-def test_rest_core_multi_node() -> None:
+def test_rest_core_multi_node_file() -> None:
     """A simple multi node sophios/restapi test"""
     inp_file = "multi_node.json"
     inp: Json = {}