♻️ SSOT preconfig_yaml

CPAC/utils/configuration/configuration.py

@@ -118,8 +118,8 @@ def __init__(self, config_map=None):
             config_map = update_nested_dict(base_config.dict(), config_map)
         else:
             # base everything on blank pipeline for unspecified keys
-            with open(preconfig_yaml('blank'), 'r', encoding='utf-8') as _f:
-                config_map = update_nested_dict(yaml.safe_load(_f), config_map)
+            config_map = update_nested_dict(
+                preconfig_yaml('blank', load=True), config_map)
 
         config_map = self._nonestr_to_None(config_map)
 
@@ -636,9 +636,9 @@ def preconfig_yaml(preconfig_name='default', load=False):
     from CPAC.pipeline import ALL_PIPELINE_CONFIGS, AVAILABLE_PIPELINE_CONFIGS
     if preconfig_name not in ALL_PIPELINE_CONFIGS:
         raise BadParameter(
-            "The pre-configured pipeline name '{0}' you provided is not one "
-            "of the available pipelines.\n\nAvailable pipelines:\n"
-            f"{1}\n".format(preconfig_name, str(AVAILABLE_PIPELINE_CONFIGS)),
+            f"The pre-configured pipeline name '{preconfig_name}' you "
+            "provided is not one of the available pipelines.\n\nAvailable "
+            f"pipelines:\n{str(AVAILABLE_PIPELINE_CONFIGS)}\n",
             param='preconfig')
     if load:
         with open(preconfig_yaml(preconfig_name), 'r', encoding='utf-8') as _f:

CPAC/utils/configuration/yaml_template.py

@@ -20,6 +20,7 @@
 import re
 from datetime import datetime
 from hashlib import sha1
+from click import BadParameter
 import yaml
 
 from CPAC.utils.configuration import Configuration, Preconfiguration, \
@@ -58,16 +59,20 @@ def __init__(self, original_yaml, base_config=None):
 
         base_config : Configuration, optional
         """
-        preconfig_path = preconfig_yaml(original_yaml)
-        if os.path.exists(preconfig_path):
-            original_yaml = preconfig_path
+        try:
+            original_yaml = preconfig_yaml(original_yaml)
+        except BadParameter:
+            pass
         if os.path.exists(original_yaml):
             with open(original_yaml, 'r', encoding='utf-8') as _f:
                 original_yaml = _f.read()
         self.comments = {}
         self.template = original_yaml
         if base_config is None:
-            self._dict = yaml.safe_load(self.template)
+            if isinstance(self.template, dict):
+                self._dict = self.template
+            if isinstance(self.template, str):
+                self._dict = yaml.safe_load(self.template)
         else:
             self._dict = base_config.dict()
         self._parse_comments()

CPAC/utils/tests/test_yaml.py

@@ -50,8 +50,7 @@ def test_yaml_template():
     # Create a new YAML configuration file based on the default pipeline
     # YAML file.
     pipeline_file = preconfig_yaml('default')
-    with open(pipeline_file, 'r', encoding='utf-8') as f:
-        config = yaml.safe_load(f)
+    config = preconfig_yaml('default', load=True)
     new_config = create_yaml_from_template(config, pipeline_file)
     with open(config_file, 'w', encoding='utf-8') as f:
         f.write(new_config)

dev/docker_data/run.py

@@ -460,11 +460,14 @@ def run_main():
                 run(f"bids-validator {bids_dir}")
 
         if args.preconfig:
-            args.pipeline_file = preconfig_yaml(args.preconfig, load=True)
+            args.pipeline_file = preconfig_yaml(args.preconfig)
 
         # otherwise, if we are running group, participant, or dry run we
         # begin by conforming the configuration
-        c = load_yaml_config(args.pipeline_file, args.aws_input_creds)
+        if isinstance(args.pipeline_file, dict):
+            c = args.pipeline_file
+        else:
+            c = load_yaml_config(args.pipeline_file, args.aws_input_creds)
 
         if 'pipeline_setup' not in c:
             _url = (f'{DOCS_URL_PREFIX}/user/pipelines/'