Merge pull request #269 from sameeul/v014

V014

src/sophios/cli.py

@@ -7,24 +7,33 @@
 __version__ = _version.get_versions()['version']
 
 parser = argparse.ArgumentParser(prog='main', description='Convert a high-level yaml workflow file to CWL.')
-parser.add_argument('--yaml', type=str, required=('--generate_schemas' not in sys.argv),
+
+parser.add_argument('--yaml', type=str,
+                    required=(not ('--generate_config' in sys.argv or '--generate_schemas' in sys.argv)),
                     help='Yaml workflow file')
+group_gen = parser.add_mutually_exclusive_group()
+group_gen.add_argument('--generate_schemas', default=False, action="store_true",
+                       help='Generate schemas for the files in config.json (search_paths_wic and search_paths_cwl)')
+group_gen.add_argument('--generate_config', default=False, action="store_true",
+                       help='''Generate default config in wic/global_config.json
+                       with default search_paths_wic and search_paths_cwl''')
 parser.add_argument('--inputs_file', type=str, required=False, default='',
                     help='Additional inputs Yaml file')
 parser.add_argument('--config_file', type=str, required=False, default=str(Path().home()/'wic'/'global_config.json'),
                     help='User provided (JSON) config file')
-# version action exits the parser Ref : https://github.com/python/cpython/blob/1f515e8a109204f7399d85b7fd806135166422d9/Lib/argparse.py#L1167
+# version action exits the parser
+# Ref : https://github.com/python/cpython/blob/1f515e8a109204f7399d85b7fd806135166422d9/Lib/argparse.py#L1167
 parser.add_argument('--version', action='version', version=__version__,
                     default='==SUPPRESS==', help='Current version of the Workflow Inference Compiler')
-parser.add_argument('--generate_schemas', default=False, action="store_true",
-                    help='Generate schemas for the files in config.json (search_paths_wic and search_paths_cwl)')
 parser.add_argument('--homedir', type=str, required=False, default=str(Path().home()),
-                    help='The users home directory. This is necessary because CWL clears environment variables (e.g. HOME)')
+                    help='''The users home directory.
+                    This is necessary because CWL clears environment variables (e.g. HOME)''')
 parser.add_argument('--insert_steps_automatically', default=False, action="store_true",
                     help='''Attempt to fix inference failures by speculatively
                     inserting workflow steps from a curated whitelist.''')
 parser.add_argument('--no_provenance', default=False, action="store_true",
-                    help='Do not use the --provenance feature of CWL. (You should only disable provenance if absolutely necessary.)')
+                    help='''Do not use the --provenance feature of CWL.
+                    (You should only disable provenance if absolutely necessary.)''')
 parser.add_argument('--copy_output_files', default=False, action="store_true",
                     help='Copies output files from the cachedir to outdir/ (automatically enabled with --run_local)')
 parser.add_argument('--inline_cwl_runtag', default=False, action="store_true",

src/sophios/input_output.py

@@ -186,15 +186,15 @@ def move_adapters_and_examples(config: Json) -> None:
     Args:
         config (Json): Json containing search path information
     """
-    # if the sophios installation is through pip package
-    pip_dir_name = 'sophios'
-    if str(Path(__file__).parent).endswith(pip_dir_name):
-        adapters_dir = Path(__file__).parent / 'cwl_adapters'
-        examples_dir = Path(__file__).parent / 'examples'
     # when using dev/git install
-    else:
+    paren_dir = 'src'
+    if str(Path(__file__).parent.parent).endswith(paren_dir):
         adapters_dir = Path(__file__).parent.parent.parent / 'cwl_adapters'
         examples_dir = Path(__file__).parent.parent.parent / 'docs' / 'tutorials'
+    # if the sophios installation is through pip package
+    else:
+        adapters_dir = Path(__file__).parent / 'cwl_adapters'
+        examples_dir = Path(__file__).parent / 'examples'
 
     extlist = ['*.png', '*.md', '*.rst', '*.pyc', '__pycache__', '*.json']
     # the default search paths will be the first entry in the 'global' namespace

src/sophios/main.py

@@ -23,6 +23,15 @@ def main() -> None:
 
     # User may specify a different homedir
     default_config_file = Path(args.homedir)/'wic'/'global_config.json'
+    if args.generate_config:
+        if default_config_file.exists():
+            print(f'Config already exists. To overwrite delete {default_config_file.parent} directory. Exiting')
+        else:
+            basic_config = io.get_basic_config()
+            io.write_config_to_disk(basic_config, default_config_file)
+            io.move_adapters_and_examples(basic_config)
+            print('Finished generating config. Exiting.')
+        sys.exit(0)
     global_config: Json = io.get_config(Path(args.config_file), default_config_file)
 
     tools_cwl = plugins.get_tools_cwl(global_config,

src/sophios/plugins.py

@@ -189,6 +189,9 @@ def cwl_update_inline_runtag(cwl: Cwl, path: Path, relative_run_path: bool) -> C
                 yml_path = Path(runtag_orig)  # Assume absolute path in the runtag
             with open(yml_path, mode='r', encoding='utf-8') as f:
                 runtag_raw = yaml.safe_load(f.read())
+                # local $namespace and $schema tag shouldn't be in inline cwl steps
+                runtag_raw.pop('$namespaces', None)
+                runtag_raw.pop('$schemas', None)
                 step['run'] = runtag_raw
         else:
             pass  # We only care if the runtag is a cwl filepath