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