Mercurial > repos > guerler > dbkit

annotate dbkit_create.py @ 1:987e55ea29b8 draft

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"planemo upload commit ce9026535c3c6da5e97366a4f0b347b0ec572dbc-dirty"
author guerler
date Thu, 26 Nov 2020 11:05:51 +0000
parents 1914107cc967
children 81c7d4668a7e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #! /usr/bin/env python3
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2 import argparse
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3 from os import system
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4 from os.path import isfile, getsize
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6
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7 def getIdentifiers(args):
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8 entries = set()
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9 with open(args.list) as file:
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10 for line in file:
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11 entry = line.split()[0]
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12 idLength = int(args.idlength)
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13 if idLength > 0:
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14 entry = entry[:idLength]
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15 if args.idcase == "lower":
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16 entry = entry.lower()
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17 elif args.idcase == "upper":
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18 entry = entry.upper()
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19 if args.idextension is not None:
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20 entry = "%s.%s" % (entry, args.idextension)
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21 entries.add(entry)
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22 return sorted(entries)
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23
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24
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25 def main(args):
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26 entries = getIdentifiers(args)
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27 logFile = open(args.log, "w")
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28 logFile.write("Found %s entries.\n" % len(entries))
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29 outputIndex = args.index
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30 outputDatabase = args.database
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31 system("rm -f %s" % outputDatabase)
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32 indexFile = open(outputIndex, 'w')
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33 start = 0
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34 for entryId in entries:
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35 logFile.write("Loading %s.\n" % entryId)
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36 if args.url:
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37 fileName = "temp.dat"
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38 system("wget -q -O %s %s%s" % (fileName, args.url, entryId))
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39 else:
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40 pathName = args.path.rstrip("/")
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41 fileName = "%s/%s" % (pathName, entryId)
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42 if isfile(fileName):
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43 size = getsize(fileName)
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44 if size == 0:
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45 logFile.write("Entry `%s` not found.\n" % entryId)
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46 else:
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47 indexFile.write("%s\t%d\t%d\n" % (entryId, start, size))
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48 start = start + size
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49 system("cat %s >> %s" % (fileName, outputDatabase))
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50 logFile.flush()
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51 logFile.close()
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54 if __name__ == "__main__":
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55 parser = argparse.ArgumentParser(description='DBKit - Download and Merge files into a single file.')
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56 parser.add_argument('-l', '--list', help='List of entries', required=True)
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57 parser.add_argument('-u', '--url', help='Source Url', required=False)
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58 parser.add_argument('-p', '--path', help='Path to files', required=False)
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59 parser.add_argument('-il', '--idlength', help='Format Identifier Length (integer)', required=False, default="0")
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60 parser.add_argument('-ic', '--idcase', help='Format Identifier Case (lower, upper)', required=False, default=None)
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61 parser.add_argument('-ie', '--idextension', help='Format Identifier Extension', required=False, default=None)
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62 parser.add_argument('-o', '--index', help='Output Database Index', required=True)
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63 parser.add_argument('-d', '--database', help='Output Database', required=True)
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64 parser.add_argument('-g', '--log', help="Log file", required=True)
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65 args = parser.parse_args()
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66 main(args)