issue #1178 - CSV quoting

snpdb/management/commands/one_off_fix_csv_quoting.py

@@ -0,0 +1,35 @@
+import csv
+import os
+import zipfile
+
+from django.core.management.base import BaseCommand
+from snpdb.models import CachedGeneratedFile
+
+
+class Command(BaseCommand):
+    """
+
+    """
+    @staticmethod
+    def fix_csv_zip(zip_filename):
+        # Move the old one to a backup
+        backup_name = zip_filename + ".backup"
+        os.rename(zip_filename, backup_name)
+
+        with zipfile.ZipFile(zip_filename, 'r') as zip_file:
+            csv_filename = os.path.splitext(os.path.basename(zip_filename))[0]
+            with zip_file.open(csv_filename) as csv_file:
+                reader = csv.reader(csv_file.read().decode('utf-8').splitlines(), dialect='excel', escapechar='\\',
+                                    quoting=csv.QUOTE_NONE)
+
+            fixed_csv_filename = os.path.splitext(zip_filename)[0]
+            with open(fixed_csv_filename, "wt") as out_csv_file:
+                writer = csv.writer(out_csv_file, dialect='excel', quoting=csv.QUOTE_MINIMAL)
+                for r in reader:
+                    writer.writerow(r)
+
+    def handle(self, *args, **options):
+        AFFECTED_GENERATORS = ["export_sample_to_downloadable_file", "export_cohort_to_downloadable_file"]
+        for cgf in CachedGeneratedFile.objects.filter(generator__in=AFFECTED_GENERATORS):
+            self.fix_csv_zip(cgf.filename)
+