Added doc strings to functions

Also added timeouts to requests get responses

Author: alexiswl

Diff for: cwl_utils/inputs_schema_gen.py

@@ -370,6 +370,11 @@ def cwl_to_jsonschema(cwl_obj: Union[Workflow, CommandLineTool]) -> Any:
 
 # Traverse the properties and return all definitions that are used
 def _recursive_search(json_data, target_key, result=None):
+    """
+    Function for slim_definitions.
+
+    Given a target key return all instances of a key in a json object.
+    """
     if result is None:
         result = []
 
@@ -388,6 +393,11 @@ def _recursive_search(json_data, target_key, result=None):
 
 # Get all the property dependencies
 def _get_all_ref_attributes(json_object):
+    """
+    Function get slim_definitions.
+
+    Given a json object, return all the reference attributes.
+    """
     return _recursive_search(json_object, "$ref")
 
 
@@ -396,6 +406,11 @@ def get_property_dependencies(
     input_json_schema: Dict,
     existing_property_dependencies: List = None,
 ) -> List[str]:
+    """
+    Function for get slim_definitions.
+
+    Recursively collect all dependencies for a property (so we don't remove them from the schema).
+    """
     # Initialise return list
     if existing_property_dependencies is None:
         existing_property_dependencies = []
@@ -485,7 +500,7 @@ def get_cwl_url(url: str) -> str:
         return url
     else:
         # urlparse(url).scheme not in ['file']:
-        response = requests.get(url)
+        response = requests.get(url, timeout=20)
         if response.status_code != 200:
             logging.error("The CWL URL is invalid.")
             raise FileNotFoundError

Diff for: cwl_utils/utils.py

@@ -457,7 +457,7 @@ def load_schema_from_uri(uri_input: str) -> InputRecordSchema:
     else:
         # On the internet somewhere!
         file_path = temp_file_obj.name
-        response = requests.get(uri_input)
+        response = requests.get(uri_input, timeout=20)
         with open(temp_file_obj.name, "w") as file_h:
             file_h.write(response.text)