Protxml viewing error (not legacy) Server error 500 Bareword "endform" not allowed while "strict subs" in use

[Scott Walmsley]

Hi!

I would like to resolve this error generated using  TPP 4.8 when viewing protXml results after ProteinProphet.   Link to the protXML results produces a internal server error (500) in the browser.  This does not happen when viewing legacy view results on localhost, tested google chrome and IE.   i've checked permissions, but perhaps i missed something?   Many thanks in advance!  Below are my software versions, and the Apache error/access logs toward the bottom.   Many thanks in advance!    Scott Scott

Below is the relevant perl version(active state)

This is perl 5, version 22, subversion 1 (v5.22.1) built for MSWin32-x64-multi-thread

(with 1 registered patch, see perl -V for more detail)

My OS:

Windows 7 64bit

My TPP:

4.8.0.exe

Apache 2.2

Upgraded cometms to v.2015025 (works, tested)

And pwiz to the latest release (works, tested on Bruker, agilent and thermo)

Using mzXMLs in seacrhes.

Copyright 1987-2015, Larry Wall

Binary build 2201 [299574] provided by ActiveState http://www.ActiveState.com

Built Jan  4 2016 12:12:58

Below is the relevant server access log: 

127.0.0.1 - - [11/Mar/2016:12:54:54 -0700] "GET /tpp-bin/ProtXMLViewer.pl?file=c:/Inetpub/wwwroot/ISB/data/perm/interact.prot.xml HTTP/1.1" 500 540

127.0.0.1 - - [11/Mar/2016:12:55:01 -0700] "GET /tpp-bin/tpp_gui.pl?Action=AJAXCheckStatusUpdates&rand=0.9998256567811105 HTTP/1.1" 200 4029

127.0.0.1 - - [11/Mar/2016:12:55:12 -0700] "GET /tpp-bin/tpp_gui.pl?Action=AJAXCheckStatusUpdates&rand=0.040754614766979336 HTTP/1.1" 200 4029

127.0.0.1 - - [11/Mar/2016:12:55:22 -0700] "GET /tpp-bin/tpp_gui.pl?Action=AJAXCheckStatusUpdates&rand=0.2696647564134357 HTTP/1.1" 200 4029

 

And below is the relevant error log:

[Fri Mar 11 12:54:54 2016] [error] [client 127.0.0.1] Premature end of script headers: ProtXMLViewer.pl, referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:54:54 2016] [error] [client 127.0.0.1] Bareword "endform" not allowed while "strict subs" in use at C:\\Inetpub\\tpp-bin\\ProtXMLViewer.pl line 286., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:54:54 2016] [error] [client 127.0.0.1] Bareword "endform" not allowed while "strict subs" in use at C:\\Inetpub\\tpp-bin\\ProtXMLViewer.pl line 286., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:54:54 2016] [error] [client 127.0.0.1] Execution of C:\\Inetpub\\tpp-bin\\ProtXMLViewer.pl aborted due to compilation errors., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:01 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:01 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:12 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:12 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:22 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:22 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:33 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:32 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:43 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:43 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:55:53 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:55:53 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:56:04 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:56:03 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:56:14 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:56:14 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:56:24 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:56:24 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:56:35 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:56:34 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Fri Mar 11 12:56:45 2016] [error] [client 127.0.0.1] [Fri Mar 11 12:56:45 2016] tpp_gui.pl: CGI::Pretty is DEPRECATED and will be removed in a future release. Please see https://github.com/leejo/CGI.pm/issues/162 for more information at C:/Perl/lib/CGI/Pretty.pm line 19., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=jobs&show_job=ZXEOQKV60_20160311-122718

[Luis Mendoza]

Hello Scott,

The error that you are encountering arises from lack of backward compatibility in one of the perl modules that you are using.  We have fixed this for the next release of TPP.

In the meantime, for a quick fix: open the source code of the viewer (under C:\Inetpub\tpp-bin\ProtXMLViewer.pl ) in Notepad (or your favorite text editor), and replace all instances of "endform"  with "end_form"  -- no spaces, just place that underscore between "end" and "form".  Save it (and keep a backup) and try again.

Thanks for the detailed report, and hope this helps!

--Luis

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[Scott Walmsley]

Works!    Most excellent.  Thank you very much for your quick help!

s

[Steven Shuken]

Luis,

I had a similar problem and it was killing me for hours. This endform to end_form edit worked, much to my surprise and delight. Thanks!

-Steven