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Bad parse of XPLOR data with many quotes #275

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Process entry
assign (resid 20 and name H7#)  (resid 19 and name H2"'') 3.916 1.019 1.1
assign (resid 20 and name H7#)  (resid 20 and name H1') 5.080 1.239 1.1
assign (resid 20 and name H2"')  (resid 20 and name H7#) 4.966 1.444 1.1
assign (resid 20 and name H2"'')  (resid 20 and name H7#) 5.215 1.337 1.1
assign (resid 20 and name H3')  (resid 20 and name H7#) 5.731 1.228 1.1
assign (resid 23 and name H7#)  (resid 22 and name H1') 5.121 1.115 1.1

Reading file: /raid/mr_anno_progress/2rrr.mr as a textual file.
Read 6815 lines.
Doing: splitToBlocks
Number of lines in block: 22
Number of lines in block: 400
Number of lines in block: 6381
Checks successful.
Moving the MR file to the database.
Trying to convert block: 0 of type: MR format, comment, n/a, n/a
Trying to convert block: 1 of type: XPLOR/CNS, distance, NOE, simple
ERROR:
Wattos.Converters.Xplor.TokenMgrError: Lexical error at line 401,
column 0.  Encountered: <EOF> after : "\") (resid 3 and name H3) 5.0
3.2 0.0\nassign (resid 24 and name H1) (resid 23 and name H3) 5.0 3.2
0.0\nassign (resid 16 and name H1) (resid 13 and name H5) 5.0 3.2
0.0\nassign (resid 23 and name H3) (resid 7 and name H3) 5.0 3.2
0.0\n\n"
       at Wattos.Converters.Xplor.XplorParserAllTokenManager.getNextToken(XplorParserAllTokenManager.java:1179)
       at Wattos.Converters.Xplor.XplorParserAll.jj_consume_token(XplorParserAll.java:1044)
       at Wattos.Converters.Xplor.XplorParserAll.TermTail(XplorParserAll.java:703)
       at Wattos.Converters.Xplor.XplorParserAll.TermTail(XplorParserAll.java:705)
       at Wattos.Converters.Xplor.XplorParserAll.Term(XplorParserAll.java:690)
       at Wattos.Converters.Xplor.XplorParserAll.SelExpr(XplorParserAll.java:657)
       at Wattos.Converters.Xplor.XplorParserAll.Selection(XplorParserAll.java:642)
       at Wattos.Converters.Xplor.XplorParserAll.AssiStateDistance(XplorParserAll.java:212)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:181)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)
       at Wattos.Converters.Xplor.XplorParserAll.AssiListDistance(XplorParserAll.java:182)

Original issue reported on code.google.com by jurge...@gmail.com on 14 Jun 2011 at 2:19

GoogleCodeExporter commented 9 years ago 
Chris, please reclassify this block as something else than XPLOR and reprocess.

The Wattos parser should be debugged on this but it's unfeasible to make the 
effort now.

Original comment by jurge...@gmail.com on 24 Feb 2012 at 10:07

GoogleCodeExporter commented 9 years ago 
Done - the change should show up next week.

Original comment by schulte....@gmail.com on 24 Feb 2012 at 4:08

GoogleCodeExporter commented 9 years ago 
Change didn't get pushed to production yet. 
Should I simply wait a bit longer?

Original comment by jurge...@gmail.com on 27 Feb 2012 at 8:48

GoogleCodeExporter commented 9 years ago 
It takes a long time to synchronize and chokes the bandwidth on grunt, so I was 
just going to do the weekly update on Tuesday afternoon.

Original comment by schulte....@gmail.com on 27 Feb 2012 at 3:00

GoogleCodeExporter commented 9 years ago 
Thanks, I'll check again on Thu when we meet.

Original comment by jurge...@gmail.com on 27 Feb 2012 at 3:35

GoogleCodeExporter commented 9 years ago 
I think 2rrr still needs to be pushed to production.

Original comment by jurge...@gmail.com on 2 Mar 2012 at 9:56

GoogleCodeExporter commented 9 years ago 
With the new CCPN install this works on development for other entries as per 
email from Chris.

Original comment by jurge...@gmail.com on 2 Mar 2012 at 9:57

GoogleCodeExporter commented 9 years ago 
2rrr has been fully processed with the new ccpn.  The data are still set to 
'unknown' because of parse errors. It will show up on the public site next week.

Original comment by schulte....@gmail.com on 2 Mar 2012 at 2:57