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PDFtoXML.py
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PDFtoXML.py
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#/bin/python
#
# written by Bethany Seeger <bseeger.cs.umass.edu>
# July 2, 2014
#
# python script that will process all pdf files in a specified directory
# It will run them first through pstotext and then metatagger
# The end result will be two extra files per pdf, like this:
#
# 00007BF8CD3BCA7EB1F474EB124A06714A36EE3F.pdf <-- input
# 00007BF8CD3BCA7EB1F474EB124A06714A36EE3F.pdf.meta.xml
# 00007BF8CD3BCA7EB1F474EB124A06714A36EE3F.pdf.pstotext.xml
#
import sys, getopt
import os.path
import glob
from subprocess import call
# location of pstotext and metatagger exe's
pstotext = "/Users/bseeger/Projects/rexa-workspace/rexa1-pstotext/bin/pstotext"
metatagger_dir = "/Users/bseeger/Projects/rexa-workspace/rexa1-metatagger/"
metatagger = metatagger_dir + "/bin/runcrf"
inst_dict = "/Users/bseeger/Projects/UniversityParser/University.dict"
# AEI = Author Email Institution
analyzeAEI_dir = "/Users/bseeger/Projects/rexa-workspace/rexa1-metatagger/"
analyzeAEI = analyzeAEI_dir + "bin/runAnalyze"
csvAuthorEmail = "/Users/bseeger/Projects/dataset/goodfiles/dataset_AuthorEmailInst.csv";
csvCitation = "/Users/bseeger/Projects/dataset/anyfiles/dataset.csv"
tmpfile = "PDFtoText.tmp"
def usage():
print "PdftoXML -d <directory> -s <step>"
print " -d --dir : directory where PDF files are located"
print " -f : where to put the analysis's output "
print " default: whatever -d dir is with Analysis.txt tacked on end"
print " -s --step : skip to a starting at a specific step [1,2,3] default 1"
print " 1 is pstotext"
print " 2 is metatagger"
print " 3 is analyze results"
print " -h : usage message"
def step1_pstotext(directory):
fileobj = open(directory + tmpfile, 'w')
num_files = 0
print ("---- pstotext ----");
if directory != '':
#filename will contain path
for filename in glob.glob(os.path.join(directory, '*.pdf')):
print ("Processing file '" + filename + "'");
filename_pstotext = filename + ".pstotext.xml"
print(pstotext + " " + filename + " > " + filename_pstotext);
with open (filename_pstotext, 'w') as outfile:
call([pstotext, filename], stdout=outfile)
print ("Finished processing file '" + filename + "'");
fileobj.write(os.path.abspath(filename_pstotext) + " -> " + os.path.abspath(filename) + ".meta.xml\n");
num_files += 1
fileobj.close()
while (fileobj.closed != True) :
print("File obj not closed yet");
return num_files
def step2_metatagger(directory) :
# Now run metatager on the entire newly created dataset, versus one file at a time. More efficient use
# of resourses that way, since metatagger has a large setup cost.
# First, switch to metatagger dir so sbt dependencies work.
origdir = os.getcwd()
os.chdir(metatagger_dir)
print ("---- metatagger ----");
print ("directory: " + tmpfile)
with open (directory + tmpfile, 'r') as infile:
call([metatagger], stdin=infile)
os.chdir(origdir);
def step3_analyzeAEI(directory, csvFile, outfile) :
success = 0;
failure = 0;
origdir = os.getcwd()
os.chdir(analyzeAEI_dir)
num_files = 0
print ("---- Analyzing Author/Email/Institution Tagging ----");
retval = call([analyzeAEI, "-d", directory, "-a", csvAuthorEmail, "-c", csvCitation, "-f", outfile]);
os.chdir(origdir)
def main(argv):
try:
opts, args = getopt.getopt(argv, "d:f:hr:s:", ["dir=","step="])
except getopt.GetoptError:
usage()
sys.exit(2);
directory = ''
num_files = 0
skipto = 1
csvFile = ''
analysisFile = ''
for opt,arg in opts:
print ("opt is '" + opt + "' and arg is '" + arg + "'")
if opt in ('-d', '--dir'):
directory = arg;
if opt in ('-r') :
csvFile = arg;
if opt in ('-f') :
analysisFile = arg;
if opt in ('-h') :
usage()
sys.exit(2)
if opt in ('-s', '--step'):
skipto = int(arg)
if (directory == '') :
usage()
sys.exit(2)
if (skipto in (1,2,3) == False) :
print ("Invalid skip request: " + str(skipto));
usage()
sys.exit(2)
print ("Examining directory '" + directory + "'")
print ("Starting with Step " + str(skipto))
# unix only right now.
directory = os.path.abspath(directory);
if (not directory.endswith('/')) :
directory += '/'
print ("directory is " + directory)
if (analysisFile == '') :
analysisFile = directory + "Analysis.txt"
# This does not handle the directory equalling "." right now. Sigh.
pstotext_num = 0
successes = 0
failures = 0
# STEP ONE
if (skipto == 1) :
pstotext_num = step1_pstotext(directory)
# now run meta tagger and parser on things.
if (os.path.isfile(directory + tmpfile)) :
# STEP TWO
if (skipto <= 2) :
step2_metatagger(directory)
# STEP THREE
if (skipto <= 3) :
step3_analyzeAEI(directory, csvFile, analysisFile)
#todo - delete the tmp file, but not really necessary right now and kinda useful to see.
print ("Processing complete. Processed files in directory " + directory)
print ("\tpstotext: " + str(pstotext_num))
print("\tNumber of metatagger files parsed:")
call(["wc", "-l", directory+tmpfile])
if __name__ == "__main__":
main(sys.argv[1:])