Merge pull request #308 from helxplatform/gapexchange-study-name

Try to pull study name from GapExchange file first

src/dug/core/parsers/dbgap_parser.py

@@ -1,9 +1,10 @@
 import logging
-import re
+import re, os
 from typing import List
 from xml.etree import ElementTree as ET
 
 from dug import utils as utils
+from pathlib import Path
 from ._base import DugElement, FileParser, Indexable, InputFile
 
 logger = logging.getLogger('dug')
@@ -13,27 +14,49 @@ class DbGaPParser(FileParser):
     # Class for parsers DBGaP Data dictionary into a set of Dug Elements
 
     @staticmethod
-    def parse_study_name_from_filename(filename: str):
+    def parse_study_name_from_filename(filename: str) -> str:
         # Parse the study name from the xml filename if it exists. Return None if filename isn't right format to get id from
         dbgap_file_pattern = re.compile(r'.*/*phs[0-9]+\.v[0-9]+\.pht[0-9]+\.v[0-9]+\.(.+)\.data_dict.*')
         match = re.match(dbgap_file_pattern, filename)
         if match is not None:
             return match.group(1)
         return None
+
+    @staticmethod
+    def parse_study_name_from_gap_exchange_file(filepath: Path) -> str:
+        # Parse the study name from the GapExchange file adjacent to the file passed in
+        parent_dir = filepath.parent.absolute()
+        gap_exchange_filename_str = "GapExchange_" + parent_dir.name
+        gap_exchange_filepath = None
+        for item in os.scandir(parent_dir):
+            if item.is_file and gap_exchange_filename_str in item.name:
+                gap_exchange_filepath = item.path
+        if gap_exchange_filepath is None:
+            return None
+        tree = ET.parse(gap_exchange_filepath, ET.XMLParser(encoding='iso-8859-5'))
+        tree_root = tree.getroot()
+        return tree_root.find("./Studies/Study/Configuration/StudyNameEntrez").text
+
 
     def _get_element_type(self):
         return "DbGaP"
 
     def __call__(self, input_file: InputFile) -> List[Indexable]:
         logger.debug(input_file)
+        if "GapExchange" in str(input_file).split("/")[-1]:
+            msg = f"Skipping parsing for GapExchange file: {input_file}!"
+            logger.info(msg)
+            return []
         tree = ET.parse(input_file, ET.XMLParser(encoding='iso-8859-5'))
         root = tree.getroot()
         study_id = root.attrib['study_id']
         participant_set = root.get('participant_set','0')
 
-        # Parse study name from file handle
-        study_name = self.parse_study_name_from_filename(str(input_file))
-
+        # Parse study name from GapExchange file, and if that fails try from file handle
+        # If still None, raise an error message
+        study_name = self.parse_study_name_from_gap_exchange_file(Path(input_file))
+        if study_name is None:
+            study_name = self.parse_study_name_from_filename(str(input_file))
         if study_name is None:
             err_msg = f"Unable to parse DbGaP study name from data dictionary: {input_file}!"
             logger.error(err_msg)