Bacpac fix

src/dug/config.py

@@ -71,12 +71,17 @@ class Config:
             # Parse nodes matching criteria in kg
             "node_type": "biolink:Publication",
             "curie_prefix": "HEALCDE",
+            # list of attributes that are lists to be casted to strings 
+            "list_field_choose_first": [
+                "files"
+            ],
             "attribute_mapping": {
                 # "DugElement Attribute" : "KG Node attribute"
                 "name": "name",
                 "desc": "summary",
                 "collection_name": "cde_category",
-                "collection_id":  "cde_category"
+                "collection_id":  "cde_category",
+                "collection_action": "files"
             }
         }
     })

src/dug/core/crawler.py

@@ -208,6 +208,7 @@ def expand_to_dug_element(self,
         target_node_type = casting_config["node_type"]
         curie_filter = casting_config["curie_prefix"]
         attribute_mapping = casting_config["attribute_mapping"]
+        array_to_string = casting_config["list_field_choose_first"]
         target_node_type_snake_case = biolink_snake_case(target_node_type.replace("biolink:", ""))
         for ident_id, identifier in concept.identifiers.items():
 
@@ -248,9 +249,12 @@ def expand_to_dug_element(self,
                         if target_node_type in node["category"]:
                             if node['id'].startswith(curie_filter):
                                 element_attribute_args = {"elem_id": node_id, "elem_type": dug_element_type}
-                                element_attribute_args.update({key: node.get(attribute_mapping[key], "")
-                                                               for key in attribute_mapping
-                                                               })
+                                for key in attribute_mapping:
+                                    mapped_value = node.get(attribute_mapping[key], "")
+                                    # treat all attributes as strings 
+                                    if key in array_to_string and isinstance(mapped_value, list) and len(mapped_value) > 0:
+                                        mapped_value = mapped_value[0]
+                                    element_attribute_args.update({key: mapped_value})
                                 element = DugElement(
                                     **element_attribute_args
                                 )

src/dug/core/factory.py

@@ -104,7 +104,8 @@ def build_element_extraction_parameters(self, source=None):
                 "casting_config": {
                     "node_type": queries[dug_type]["node_type"],
                     "curie_prefix": queries[dug_type]["curie_prefix"],
-                    "attribute_mapping": queries[dug_type]["attribute_mapping"]
+                    "attribute_mapping": queries[dug_type]["attribute_mapping"],
+                    "list_field_choose_first": queries[dug_type]["list_field_choose_first"]
                     # CDE's are only ones
                     # but if we had two biolink:Publication nodes we want to conditionally
                     # cast to other output_dug_type, we could extend this config

src/dug/core/parsers/_base.py

@@ -10,16 +10,16 @@ class DugElement:
     # Basic class for holding information for an object you want to make searchable via Dug
     # Could be a DbGaP variable, DICOM image, App, or really anything
     # Optionally can hold information pertaining to a containing collection (e.g. dbgap study or dicom image series)
-    def __init__(self, elem_id, name, desc, elem_type, collection_id="", collection_name="", collection_desc=""):
+    def __init__(self, elem_id, name, desc, elem_type, collection_id="", collection_name="", collection_desc="", action="", collection_action=""):
         self.id = elem_id
         self.name = name
         self.description = desc
         self.type = elem_type
         self.collection_id = collection_id
         self.collection_name = collection_name
         self.collection_desc = collection_desc
-        self.action = ""
-        self.collection_action = ""
+        self.action = action
+        self.collection_action = collection_action
         self.concepts = {}
         self.ml_ready_desc = desc
         self.search_terms = []

src/dug/core/parsers/bacpac_parser.py

@@ -12,18 +12,18 @@ class BACPACParser(FileParser):
     # Class for parsing BACPAC data dictionaries in dbGaP XML format into a set of Dug Elements.
 
     @staticmethod
-    def parse_study_name_from_filename(filename: str):
+    def get_study_file_name():
         # Parse the form name from the xml filename
-        return filename.split('/')[-1].replace('.xml', '')
+        return "Back Pain Consortium (BACPAC) Minimum Dataset"
 
     def __call__(self, input_file: InputFile) -> List[Indexable]:
         logger.debug(input_file)
         tree = ET.parse(input_file)
         root = tree.getroot()
-        study_id = root.attrib['study_id']
+        study_id = "HEALPLATFORM:HDP00692"
 
         # Parse study name from file handle
-        study_name = self.parse_study_name_from_filename(str(input_file))
+        study_name = self.get_study_file_name()
 
         if study_name is None:
             err_msg = f"Unable to parse BACPAC Form name from data dictionary: {input_file}!"
@@ -38,8 +38,10 @@ def __call__(self, input_file: InputFile) -> List[Indexable]:
                               desc=description.lower(),
                               elem_type="BACPAC",
                               collection_id=f"{study_id}",
-                              collection_name=study_name)
-
+                              collection_name=study_name
+            )
+            elem.action = "https://healdata.org/portal/discovery/HDP00692"      
+            elem.collection_action = "https://healdata.org/portal/discovery/HDP00692"
             # Add to set of variables
             logger.debug(elem)
             elements.append(elem)

tests/unit/test_crawler.py

@@ -92,7 +92,8 @@ def test_expand_to_dug_element(crawler):
                 "desc": "summary",
                 "collection_name": "cde_category",
                 "collection_id":  "cde_category"
-            }
+            },
+            "list_field_choose_first": []
         },
         dug_element_type="test-element",
         tranql_source="test:graph"