Merge pull request #19 from crs4/add_orphacode_script

Creates a script to add orphacodes to directory emx file

add_orphacodes.py

@@ -0,0 +1,83 @@
+"""
+Script to add Orphacodes to collections in the BBMRI directory EMX file.
+The script gets in input the directory EMX file, the orphanet file with mappings used by OrphaCodes class and the output
+file.
+
+For every ICD-10 diagnosis in the input file, it gets the mappings and if the orphanet mapping type is BTNT or EXACT it
+adds the orphacode to the collection.
+
+NB: The script gets the mapping Orphacodes from OrphaCodes class in orphacodes.py. The class marks the mapping type
+from icd to orpha as the inverse of orpha to icd, so BTNT become NTBT. That means, that we need to check for the NTBT
+mapping level in the script.
+"""
+
+import argparse
+import os.path
+import sys
+
+import openpyxl
+from openpyxl.utils.exceptions import InvalidFileException
+
+from orphacodes import OrphaCodes
+
+DIAGNOSIS_AVAILABLE_COLUMN = 'diagnosis_available'
+COLLECTIONS_SHEET = 'eu_bbmri_eric_collections'
+
+
+def _get_diagnosis_available_column(sheet):
+    for col in sheet.iter_cols(max_row=1):
+        if col[0].value == DIAGNOSIS_AVAILABLE_COLUMN:
+            return col[0].col_idx - 1
+
+
+def add_orphacodes(directory_file, orphanet_file, output_file):
+    orphacodes = OrphaCodes(orphanet_file)
+    try:
+        wb = openpyxl.load_workbook(directory_file)
+    except InvalidFileException:
+        print("{} is not a valid Directory file".format(directory_file))
+        sys.exit(-1)
+
+    try:
+        sheet = wb.get_sheet_by_name(COLLECTIONS_SHEET)
+    except KeyError:
+        print("Missing {} sheet in file {}".format(COLLECTIONS_SHEET, directory_file))
+        sys.exit(-1)
+
+    diag_col = _get_diagnosis_available_column(sheet)
+    if diag_col is None:
+        print("Missing {} in sheet {}".format(DIAGNOSIS_AVAILABLE_COLUMN, directory_file))
+        sys.exit(-1)
+
+    for row in sheet.iter_rows(min_row=2):
+        cell_value = row[diag_col].value
+        if cell_value is not None:
+            diagnosis = cell_value.split(',')
+            for d in diagnosis[:]:
+                orpha_codes = orphacodes.icd10ToOrpha(d.split(':')[-1])
+                if orpha_codes is not None:
+                    for code in orpha_codes:
+                        # considering NTBT because OrphaCodes register the mapping as inverse from the Orphacode
+                        if code['mapping_type'] in ('NTBT', 'E'):
+                            diagnosis.append("ORPHA:{}".format(code['code']))
+
+                    row[diag_col].value = ','.join(diagnosis)
+    wb.save(output_file)
+
+
+if __name__ == '__main__':
+    def file_exist(file_argument):
+        if os.path.exists(file_argument):
+            return file_argument
+        raise argparse.ArgumentTypeError("File {} does not exist".format(file_argument))
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--directory-emx-file', '-d', dest='directory_file', type=file_exist, required=True,
+                        help='Input file with list of collections and associated icd 10 codes to map')
+    parser.add_argument('--orpha-mappings-file', '-O', dest='orphanet_file', type=file_exist, required=True,
+                        help='XML file with orphanet icd 10/orphanet mappings')
+    parser.add_argument('--output', '-o', dest='output_file', type=str, required=False,
+                        help='Output file with orpacodes', default='bbmri-directory-with-orphacodes.xlsx')
+
+    args = parser.parse_args()
+    add_orphacodes(args.directory_file, args.orphanet_file, args.output_file)