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HTML output not working in CONVERT mode #30

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Running CONVERT mode with -f html

[kmkeati2@compute-3-9 ~]$ /home/apps/iprscan/iprscan-5.44/interproscan.sh -mode 
convert -f html -i /home/a-m/kmkeati2/test_proteins_convert_mode.xml -b 
/home/a-m/kmkeati2/ 
04/10/2013 13:51:54:293 Welcome to InterProScan-5-44.0
04/10/2013 13:52:02:234 Running InterProScan v5 in CONVERT mode...
2013-10-04 13:52:04,170 
[uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesH
TMLResultWriter:217] WARN - Couldn't create temp directory 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/P22298.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/Q97R95.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A2YIW7.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A2VDN9.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A0B786.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/Q1A5X6.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
2013-10-04 13:52:12,761 [uk.ac.ebi.interpro.scan.jms.converter.Converter:258] 
ERROR - Cannot write or create result file!
java.io.IOException: This archives contains unclosed entries.
    at org.apache.commons.compress.archivers.tar.TarArchiveOutputStream.finish(TarArchiveOutputStream.java:135)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.TarArchiveBuilder.buildTarArchive(TarArchiveBuilder.java:72)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:351)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
Exception in thread "main" java.lang.NullPointerException
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:267)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)

What is the expected output? What do you see instead?
Would expect to have a HTML file that has the corresponding information from 
the input XML file. Running this command yields the file 
test_proteins_convert_mode.xml.html.tar.gz that cannot be processed by the 
command tar -zxvf. 

What version of the product are you using? On what operating system?
InterProScan 5 (version 5-44.0); RedHat Enterprise Linux 6

Linux biocluster.igb.illinois.edu 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 
23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux

Please provide any additional information below.
The cluster is set up with PBS TORQUE, not LSF or SGE.

Original issue reported on code.google.com by kthlnk...@gmail.com on 4 Oct 2013 at 8:54

GoogleCodeExporter commented 9 years ago 
Dear Kathleen,

Thanks for contacting us. We will have a look into that and keep you up-to-date 
on the progress.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 8 Oct 2013 at 8:33

GoogleCodeExporter commented 9 years ago 
Thank you for the email. I looked into this and managed to reproduce the 
problem. Convert mode is a new feature and it seems that the "-f html" 
does not work properly, we'll have to look at fixing this for a future 
release. It seems to work for all other output formats, it's just HTML 
that is affected.

There is no great workaround that I can see, but for now possible ideas 
include:

- When you run interproscan in the first place, if you need HTML output 
then ensure you pick that option (along with XML and other required 
formats) - because with the 5-44.0 version you will find that you cannot 
use convert mode to convert it to HTML later!
- Use SVG instead of HTML.

Apologies for that, we'll have to look into this - I hope this helps in 
some way, thank you for reporting the issue.

Original comment by Mr.Matth...@gmail.com on 8 Oct 2013 at 11:19

GoogleCodeExporter commented 9 years ago 
This issue is fixed in release 5.1-44.0. 

Although I just noticed that the above command (for HTML output in convert 
mode) may log a warning "Couldn't create temp directory" - when in fact it DID 
manage to create the temp directory! So if you see that message you may find 
the convert mode did work, it's just the log message that is wrong! This log 
issue will be fixed for the next release.

Original comment by Mr.Matth...@gmail.com on 1 Nov 2013 at 4:37