Initial commit

Lts/Tests/DatabaseInitialisation/update_barcode_se.py

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+#!/usr/bin/python
+# This Python file uses the following encoding: utf-8
+
+import sys
+from collections import OrderedDict
+
+
+def readBarcodes(filename):
+  """Create a dictionary { name, MSE-name : barcode }."""
+  ret = OrderedDict()
+
+  with open(filename, "r") as f:
+    lines = f.read().split("\n")
+    cols = lines[0].strip().split(',')
+
+    assert cols[1].lower() == "name"
+    #assert cols[2].lower() == "main_structure_element_id"
+    assert cols[3].lower() == "main_name"
+    assert cols[4].lower() == "barcode"
+
+    rows = [line.strip() for line in lines[1:] if line.strip() != ""]
+    for row in rows:
+      items = row.split(",")
+      ret[items[1], items[3]] = items[4]
+
+  return ret
+
+
+def appendBarcodeUpdates(outputFile, barcodes):
+  """Append an SQL UPDATE statement for barcodes."""
+  lines = []
+  for key in barcodes.keys():
+    name, main_name = key
+    update = "UPDATE ism.ism_structure_element SET barcode = '%s' WHERE main_structure_element_id = (SELECT id FROM ism.ism_main_structure_element WHERE name = '%s') AND name = '%s';" % (barcodes[key], main_name, name)
+    lines.append(update)
+
+  with open(outputFile, "w") as f:
+    for line in lines:
+      f.write(line + "\n")
+
+
+if __name__ == "__main__":
+  barcodeFile = sys.argv[1]
+  barcodes = readBarcodes(barcodeFile)
+
+  sqlOutputFile = sys.argv[2]
+  appendBarcodeUpdates(sqlOutputFile, barcodes)