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annotate bin/plinks.py @ 11:b0d9fe66ce8a

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give up on mpiexec_mpt
author Henry S. Thompson <ht@inf.ed.ac.uk>
date Tue, 25 Feb 2020 18:33:22 +0000
parents a33db8e3f51c
children 3bc1d24363a1
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65a56c0d1c1f bolting the barn door...
Henry S. Thompson <ht@inf.ed.ac.uk>
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1 #!/lustre/sw/miniconda3/bin/python3
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25ca3505b4d7 more logging
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2 import sys,pdfx,traceback,os
25ca3505b4d7 more logging
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3 from datetime import datetime
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a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
Henry Thompson <ht@markup.co.uk>
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4 from os import path
a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
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5
a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
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6 def run(file):
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65a56c0d1c1f bolting the barn door...
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7 global pdf
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a33db8e3f51c bigger run, longer limit
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8 pdf=pdfx.PDFx(file,limit=60)
a33db8e3f51c bigger run, longer limit
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9 return (pdf.get_references_as_dict(),pdf.limited)
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65a56c0d1c1f bolting the barn door...
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10
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0f494c76a887 refactor to address tarred-up pdfs
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11 tarnum=sys.argv[1]
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12 print(tarnum, sys.argv, os.getcwd(),file=sys.stderr)
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13 gf=0
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14 with open('badpdfs_%s'%tarnum,'w') as bf:
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a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
Henry Thompson <ht@markup.co.uk>
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15 for l in sys.stdin:
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0f494c76a887 refactor to address tarred-up pdfs
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16 (fno,f)=l.split()
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a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
Henry Thompson <ht@markup.co.uk>
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17 try:
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a33db8e3f51c bigger run, longer limit
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18 (links,limited)=run(f)
a33db8e3f51c bigger run, longer limit
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19 if limited:
a33db8e3f51c bigger run, longer limit
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20 print("%s\t%s\tProcessing limited after timeout"%(
a33db8e3f51c bigger run, longer limit
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21 datetime.now().isoformat(),fno),file=bf)
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b0d9fe66ce8a give up on mpiexec_mpt
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22 bf.flush()
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462179da7dc2 try harder not to write empty links files
Henry S. Thompson <ht@inf.ed.ac.uk>
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23 if bool(links) and (links.get('scrape',False) or
462179da7dc2 try harder not to write empty links files
Henry S. Thompson <ht@inf.ed.ac.uk>
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24 links.get('annot',False)):
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25 gf+=1
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0f494c76a887 refactor to address tarred-up pdfs
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26 with open('links_%s_%s'%(tarnum,fno),'w') as of:
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cbd13beb0922 only create links file if there are some
Henry Thompson <ht@markup.co.uk>
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27 for k in links.keys():
cbd13beb0922 only create links file if there are some
Henry Thompson <ht@markup.co.uk>
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28 for l in links[k]:
cbd13beb0922 only create links file if there are some
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29 print("%s\t%s"%(k,l),file=of)
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a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
Henry Thompson <ht@markup.co.uk>
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30 except Exception as e:
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0f494c76a887 refactor to address tarred-up pdfs
Henry S. Thompson <ht@inf.ed.ac.uk>
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31 if str(e)=='Unexpected EOF':
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25ca3505b4d7 more logging
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32 print("%s:\t%s\t%s\t%s"%(datetime.now().isoformat(),
25ca3505b4d7 more logging
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33 tarnum,fno,e),file=bf)
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b0d9fe66ce8a give up on mpiexec_mpt
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34 bf.flush()
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35 else:
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36 print("%s: "%(datetime.now().isoformat()),end='',file=bf)
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37 traceback.print_exc(file=bf)
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b0d9fe66ce8a give up on mpiexec_mpt
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38 bf.flush()
b0d9fe66ce8a give up on mpiexec_mpt
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39 if path.exists('stopJob'):
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40 print("%s: Quiting early: %s %s"%(datetime.now().isoformat(),tarnum,fno),
25ca3505b4d7 more logging
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41 file=sys.stderr)
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b0d9fe66ce8a give up on mpiexec_mpt
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42 sys.stderr.flush()
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a4b0359456bc switch to file loop inside python, assume file index integer in pipe as well as filename, check /dev/shm/stopJob
Henry Thompson <ht@markup.co.uk>
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43 exit(1)
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44 now=datetime.now().isoformat()
25ca3505b4d7 more logging
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45 print('%s: exiting from %s having found %s files with links out of %s'%(now,
25ca3505b4d7 more logging
Henry S. Thompson <ht@inf.ed.ac.uk>
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46 tarnum,
25ca3505b4d7 more logging
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47 gf,
25ca3505b4d7 more logging
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48 fno))