Merge pull request #348 from helxplatform/radx-parser

Radx parser

src/dug/core/parsers/__init__.py

@@ -13,6 +13,7 @@
 from .bacpac_parser import BACPACParser
 from .heal_dp_parser import HEALDPParser
 from .ctn_parser import CTNParser
+from .radx_parser import RADxParser
 
 
 logger = logging.getLogger('dug')
@@ -35,6 +36,7 @@ def define_parsers(parser_dict: Dict[str, Parser]):
     parser_dict["heal-studies"] = HEALDPParser(study_type="HEAL Studies")
     parser_dict["heal-research"] = HEALDPParser(study_type="HEAL Research Programs")
     parser_dict["ctn"] = CTNParser()
+    parser_dict["radx"] = RADxParser()
 
 
 

src/dug/core/parsers/radx_parser.py

@@ -0,0 +1,36 @@
+import logging
+from typing import List
+from xml.etree import ElementTree as ET
+
+from dug import utils as utils
+from ._base import DugElement, FileParser, Indexable, InputFile
+
+logger = logging.getLogger('dug')
+
+
+class RADxParser(FileParser):
+
+    def __call__(self, input_file: InputFile) -> List[Indexable]:
+        tree = ET.parse(input_file, ET.XMLParser(encoding='utf-8'))
+        root = tree.getroot()
+        study_id = root.attrib['id']        
+        # If still None, raise an error message
+        study_name = root.attrib['study_name']
+        elements = []
+        for variable in root.iter('variable'):
+            desc = variable.find('description').text if variable.find('description') is not None else ''
+            desc = desc or ''
+            elem = DugElement(elem_id=f"{variable.attrib['id']}",
+                              name=variable.find('name').text,
+                              desc=desc,
+                              elem_type=root.attrib['module'],
+                              collection_id=f"{study_id}",
+                              collection_name=study_name)
+
+            # Create DBGaP links as study/variable actions
+            elem.collection_action = utils.get_dbgap_study_link(study_id=elem.collection_id)
+            logger.debug(elem)
+            elements.append(elem)
+
+        # You don't actually create any concepts
+        return elements