Mercurial > repos > guerler > dbkit

comparison dbkit_create.py @ 3:03e124ff7e26 draft

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"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author guerler
date Wed, 16 Dec 2020 13:11:35 +0000
parents 81c7d4668a7e
children
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2:81c7d4668a7e 3:03e124ff7e26
1 #! /usr/bin/env python3 1 #! /usr/bin/env python3
2 import argparse 2 import argparse
3 from os import system 3 from os import remove
4 from os.path import isfile, getsize 4 from os.path import isfile, getsize
5 import wget
6
7 from dbkit_package.DBKit import writeEntry
5 8
6 9
7 def getIdentifiers(args): 10 def getIdentifiers(args):
8 entries = set() 11 entries = set()
9 with open(args.list) as file: 12 with open(args.list) as file:
26 entries = getIdentifiers(args) 29 entries = getIdentifiers(args)
27 logFile = open(args.log, "w") 30 logFile = open(args.log, "w")
28 logFile.write("Found %s entries.\n" % len(entries)) 31 logFile.write("Found %s entries.\n" % len(entries))
29 outputIndex = args.index 32 outputIndex = args.index
30 outputDatabase = args.database 33 outputDatabase = args.database
31 system("rm -f %s" % outputDatabase) 34 if isfile(outputDatabase):
32 indexFile = open(outputIndex, 'w') 35 remove(outputDatabase)
33 start = 0
34 for entryId in entries: 36 for entryId in entries:
35 logFile.write("Loading %s.\n" % entryId) 37 logFile.write("Loading %s.\n" % entryId)
36 if args.url: 38 if args.url:
37 fileName = "temp.dat" 39 fileName = wget.download("%s%s" % (args.url, entryId))
38 system("wget -q -O %s %s%s" % (fileName, args.url, entryId))
39 else: 40 else:
40 pathName = args.path.rstrip("/") 41 pathName = args.path.rstrip("/")
41 fileName = "%s/%s" % (pathName, entryId) 42 fileName = "%s/%s" % (pathName, entryId)
42 if isfile(fileName): 43 if isfile(fileName):
43 size = getsize(fileName) 44 entrySize = getsize(fileName)
44 if size == 0: 45 if entrySize == 0:
45 logFile.write("Entry `%s` not found.\n" % entryId) 46 logFile.write("Entry `%s` not found.\n" % entryId)
46 else: 47 else:
47 indexFile.write("%s\t%d\t%d\n" % (entryId, start, size)) 48 writeEntry(entryId, fileName, outputIndex, outputDatabase)
48 start = start + size
49 system("cat %s >> %s" % (fileName, outputDatabase))
50 else: 49 else:
51 logFile.write("Content not found: %s.\n" % fileName) 50 logFile.write("Content not found: %s.\n" % fileName)
52 logFile.flush() 51 logFile.flush()
53 logFile.close() 52 logFile.close()
54 53