Add helper scripts used for moving guides and primers between assemblies

Author: kevinlul

src/helpers/asCSV.py

@@ -0,0 +1,18 @@
+#!/usr/bin/python3
+
+import csv, sys
+from Config3 import Config
+
+
+if __name__ == "__main__":
+  db = Config(sys.argv[1])
+  guides = db.guideCollection.find()
+  with open("guides-%s.csv" % sys.argv[1], 'w') as f:
+    writer = csv.DictWriter(f, fieldnames=list(guides[0].keys()) + ["pamLocation","org","dateAdded","commitHash","strand"])
+    writer.writeheader()
+    writer.writerows(guides)
+  primers = db.primerCollection.find()
+  with open("primers-%s.csv" % sys.argv[1], 'w') as f:
+    writer = csv.DictWriter(f, fieldnames=list(primers[0].keys()) + ["pamLocation","org","dateAdded","commitHash","strand"])
+    writer.writeheader()
+    writer.writerows(primers)

src/helpers/importCSV.py

@@ -0,0 +1,37 @@
+#!/usr/bin/python3
+
+import csv, sys
+from pprint import pprint
+from typing import Dict
+from pymongo.errors import BulkWriteError
+from Config3 import Config
+
+
+def pop(d: Dict[str, str]) -> Dict[str, str]:
+    d.pop("_id", None)
+    return d
+
+
+def reset_guides(d: Dict[str, str]) -> Dict[str, str]:
+    d["guides"] = { "rank": "manual", "ids": [] }
+    return d
+
+
+if __name__ == "__main__":
+  db = Config(sys.argv[1])
+  if sys.argv[2] == "guides":
+    with open(sys.argv[3]) as f:
+      reader = csv.DictReader(f)
+      results = [pop(d) for d in reader]
+      try:
+        db.guideCollection.insert_many(results)
+      except BulkWriteError as e:
+        pprint(e.details)
+  elif sys.argv[2] == "primers":
+    with open(sys.argv[3]) as f:
+      reader = csv.DictReader(f)
+      results = [reset_guides(pop(d)) for d in reader]
+      try:
+        db.primerCollection.insert_many(results)
+      except BulkWriteError as e:
+        pprint(e.details)