Mercurial > repos > guerler > dbkit

annotate dbkit_merge.py @ 5:184b00847620 draft default tip

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"planemo upload commit 49504c53e0cdd7b98908b064fad4c0b8baeaa317"
author guerler
date Thu, 11 Mar 2021 19:31:37 +0000
parents 03e124ff7e26
children
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1 #! /usr/bin/env python3
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2 import argparse
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3 from os.path import getsize
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4 from shutil import copyfile
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5
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6 from dbkit_package.DBKit import DBKit, writeEntry
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9 def main(args):
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10 logFile = open(args.log, "w")
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11 outputIndex = args.outputindex
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12 outputDatabase = args.outputdatabase
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13 if getsize(args.firstindex) > getsize(args.secondindex):
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14 firstIndex = args.firstindex
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15 firstData = args.firstdata
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16 secondIndex = args.secondindex
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17 secondData = args.seconddata
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18 else:
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19 firstIndex = args.secondindex
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20 firstData = args.seconddata
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21 secondIndex = args.firstindex
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22 secondData = args.firstdata
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23 copyfile(firstIndex, outputIndex)
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24 copyfile(firstData, outputDatabase)
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25 firstEntries = set()
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26 with open(firstIndex, "r") as f:
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27 for line in f:
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28 name = line.split()[0]
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29 firstEntries.add(name)
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30 logFile.write("Detected %s entries.\n" % len(firstEntries))
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31 secondEntries = list()
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32 with open(secondIndex, "r") as f:
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33 for line in f:
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34 name = line.split()[0]
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35 secondEntries.append(name)
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36 fileName = "temp.dat"
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37 count = 0
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38 dbkit = DBKit(secondIndex, secondData)
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39 for secondKey in secondEntries:
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40 if secondKey not in firstEntries:
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41 dbkit.createFile(secondKey, fileName)
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42 writeEntry(secondKey, fileName, outputIndex, outputDatabase)
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43 count = count + 1
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44 else:
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45 logFile.write("Skipping existing entry %s.\n" % secondKey)
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46 logFile.write("Added %s entries.\n" % count)
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47 logFile.close()
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49
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50 if __name__ == "__main__":
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51 parser = argparse.ArgumentParser(description='DBKit - Merge database pair.')
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52 parser.add_argument('-fi', '--firstindex', help='First Index file', required=True)
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53 parser.add_argument('-fd', '--firstdata', help='First Data file', required=True)
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54 parser.add_argument('-si', '--secondindex', help='Second Index file', required=True)
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55 parser.add_argument('-sd', '--seconddata', help='Second Data file', required=True)
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56 parser.add_argument('-oi', '--outputindex', help='Output Index file', required=True)
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57 parser.add_argument('-od', '--outputdatabase', help='Output Data file', required=True)
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58 parser.add_argument('-log', '--log', help='Log file', required=True)
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59 args = parser.parse_args()
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60 main(args)