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writerUnion.py
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import os
from variablesWriter import nameFiles_Classes, nameFiles_Rels
##########################
# NAMES OF FILES TO JOIN #
##########################
def getInfiles_Classes(folderClasses):
infiles = ["{}{}{}".format(folderClasses, nameFiles_Classes['patient'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['episode'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['death'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['hospitalization'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['testMicro'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['microorganism'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['uh'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['service'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['bed'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['room'], '.nt'),
"{}{}{}".format(folderClasses, nameFiles_Classes['corridor'], '.nt')]
return infiles
def getInfiles_Relations(folderRels):
infiles = ["{}{}{}".format(folderRels, nameFiles_Rels['ep_pat'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_ep'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['test_micro'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_bed'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_uh'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['serv_uh'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_room'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_corridor'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_nt'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_ot'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_nt'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_ot'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['corridor_nt'], '.nt')]
return infiles
def getInfiles_Relations_star(folderRels):
infiles = ["{}{}{}".format(folderRels, nameFiles_Rels['ep_pat'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_ep'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['test_micro'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_bed'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['ev_uh'], '.nt'),
"{}{}{}".format(folderRels, nameFiles_Rels['serv_uh'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_room'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_corridor'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_nt'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['bed_ot'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_nt'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['room_ot'], '.ttl'),
"{}{}{}".format(folderRels, nameFiles_Rels['corridor_nt'], '.ttl')]
return infiles
##############
# FILE UNION #
##############
def unionNTFiles_Classes(folderClasses, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000):
infiles = getInfiles_Classes(folderClasses)
outfileName = folderClasses + "\\Classes_complete_{}-{}__{}-{}_{}.nt".format(minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
with open(outfileName, "w") as outfile:
for infileName in infiles:
copyFileWithChunks(infileName, outfile)
outfile.close()
print("\t- {} : Complete".format(outfileName))
def unionNTFiles_Relations(folderRels, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000, star):
if star:
infiles = getInfiles_Relations_star(folderRels)
outfileName = folderRels + "\\Relations_complete_{}-{}__{}-{}_{}.ttl".format(minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
else:
infiles = getInfiles_Relations(folderRels)
outfileName = folderRels + "\\Relations_complete_{}-{}__{}-{}_{}.nt".format(minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
with open(outfileName, "w") as outfile:
for infileName in infiles:
copyFileWithChunks(infileName, outfile)
outfile.close()
print("\t- {} : Complete".format(outfileName))
def unionNTFiles_Full(folder, folderClasses, folderRels, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000, star):
infiles_Classes = getInfiles_Classes(folderClasses)
if star:
infiles_Rels = getInfiles_Relations_star(folderRels)
outfileName = folder + "\\data_complete_{}-{}__{}-{}_{}.ttl".format(minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
else:
infiles_Rels = getInfiles_Relations(folderRels)
outfileName = folder + "\\data_complete_{}-{}__{}-{}_{}.nt".format(minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
with open(outfileName, "w") as outfile:
for infileName in infiles_Classes:
copyFileWithChunks(infileName, outfile)
for infileName in infiles_Rels:
copyFileWithChunks(infileName, outfile)
outfile.close()
print("\t- {} : Complete".format(outfileName))
#############
# COPY FILE #
#############
def copyFileWithChunks(infileName, outfile):
chunk_size = 1024 * 1024 * 10 # 10 MB
with open(infileName, "r") as infile:
infileSizeBytes = getFileSize(infileName)
if infileSizeBytes < chunk_size:
outfile.write(infile.read())
outfile.write('\n')
infile.close()
else:
nChunks = infileSizeBytes // chunk_size
ultChunkSize = infileSizeBytes % chunk_size
for i in range(nChunks+1):
if i==nChunks: #lastChunk
chunk_size = ultChunkSize
chunk = infile.read(chunk_size)
outfile.write(chunk)
infile.close()
def getFileSize(fileName):
file_stats = os.stat(fileName)
sizeBytes = file_stats.st_size
return sizeBytes
########
# MAIN #
########
def unionFiles(folder, folderClasses, folderRels, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000, star):
unionNTFiles_Classes(folderClasses, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000)
unionNTFiles_Relations(folderRels, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000, star)
unionNTFiles_Full(folder, folderClasses, folderRels, minYearN_2digits, maxYearN_2digits, minYear_2digits, maxYear_2digits, maxEvents_div1000, star)