Merge pull request #197 from pbashyal-nmdp/3130_rename_to_3131

Special case 3130->3131 version of allelelist.txt

Author: mmaiers-nmdp

api-spec.yaml

@@ -2,7 +2,7 @@ openapi: 3.0.3
 info:
   title: ARD Reduction
   description: Reduce to ARD Level
-  version: "0.9.0"
+  version: "0.9.1"
 servers:
   - url: 'http://localhost:8080'
 tags:

pyard/__init__.py

@@ -25,4 +25,4 @@
 from .blender import blender as dr_blender
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = "0.9.0"
+__version__ = "0.9.1"

pyard/data_repository.py

@@ -20,10 +20,13 @@
 #    > http://www.fsf.org/licensing/licenses/lgpl.html
 #    > http://www.opensource.org/licenses/lgpl-license.php
 #
+import sys
 import copy
 from collections import namedtuple
 import functools
 import sqlite3
+from urllib.error import HTTPError
+
 import pandas as pd
 
 from . import db
@@ -334,10 +337,21 @@ def generate_alleles_and_xx_codes_and_who(
     if imgt_version == "Latest":
         allele_list_url = f"{IMGT_HLA_URL}Latest/Allelelist.txt"
     else:
+        if imgt_version == "3130":
+            # 3130 was renamed to 3131 for Allelelist file only 🤷🏾‍
+            imgt_version = "3131"
         allele_list_url = (
             f"{IMGT_HLA_URL}Latest/allelelist/Allelelist.{imgt_version}.txt"
         )
-    allele_df = pd.read_csv(allele_list_url, header=6, usecols=["Allele"])
+
+    try:
+        allele_df = pd.read_csv(allele_list_url, header=6, usecols=["Allele"])
+    except HTTPError as e:
+        print(
+            f"Failed importing alleles for version {imgt_version} from {allele_list_url}",
+            file=sys.stderr,
+        )
+        sys.exit(1)
 
     # Create a set of valid alleles
     # All 2-field, 3-field and the original Alleles are considered valid alleles

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.0
+current_version = 0.9.1
 commit = True
 tag = True
 
@@ -19,10 +19,4 @@ replace = version: "{new_version}"
 universal = 1
 
 [flake8]
-exclude =
-	venv,
-	.git,
-	__pycache__,
-	build,
-	dist,
-	docs
+exclude = venv, .git, __pycache__, build, dist, docs

setup.py

@@ -39,7 +39,7 @@
 
 setup(
     name="py-ard",
-    version="0.9.0",
+    version="0.9.1",
     description="ARD reduction for HLA with Python",
     long_description=readme + "\n\n" + history,
     long_description_content_type="text/markdown",