TPP:V5Feedback

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* ERROR in Petunia. CGI::multi_param is not a valid subroutine (new version of CGI.pm) * ERROR in Petunia. CGI::multi_param is not a valid subroutine (new version of CGI.pm)
** Joe: This again?!?! So if you use ActivePerl you'll need to update CGI, I sent along instructions in a email to Luis. Otherwise yes, there still are places where parm() is called in a array context and needs to be replaced with multi_param(). I did another pass looking for these occurrences, but there are many. Someone other than me should do a grep 'param(' and check them out. ** Joe: This again?!?! So if you use ActivePerl you'll need to update CGI, I sent along instructions in a email to Luis. Otherwise yes, there still are places where parm() is called in a array context and needs to be replaced with multi_param(). I did another pass looking for these occurrences, but there are many. Someone other than me should do a grep 'param(' and check them out.
-* <s>Adjust web timeout!?? Seemed to have pooped at 2 minutes...?</s> '''FIXED. No long takes a poop break.'''+* <s>Adjust web timeout!?? Seemed to have pooped at 2 minutes...?</s> '''FIXED. No longer takes a poop break.'''
* <s>PepXMLViewer: BAD link to SpectraST ("ST")</s> '''FIXED''' (I think. Is it now doing what its suppose to) * <s>PepXMLViewer: BAD link to SpectraST ("ST")</s> '''FIXED''' (I think. Is it now doing what its suppose to)
* <s>Petunia icon on desktop * <s>Petunia icon on desktop

Revision as of 06:04, 28 July 2015

Feedback related to releasing TPP version 5.0

This page here is to record feedback/issues found with the development builds of 5.0.0

Release 5.0.0a2

  • Uninstall leaves cmd.exe, and data/ log/ users/ dirs. (by design?)
    • Joe: Yes. Well at least data/, log/. Don't think you'd want to remove TPP and lose all your data. The users/ directory could get removed, and I guess the log directory if you guys think so. The cmd.exe file, is that in bin? If so it should have been removed.
    • Joe: Just retested and it only left data/ behind.
  • ERROR in Petunia. CGI::multi_param is not a valid subroutine (new version of CGI.pm)
    • Joe: This again?!?! So if you use ActivePerl you'll need to update CGI, I sent along instructions in a email to Luis. Otherwise yes, there still are places where parm() is called in a array context and needs to be replaced with multi_param(). I did another pass looking for these occurrences, but there are many. Someone other than me should do a grep 'param(' and check them out.
  • Adjust web timeout!?? Seemed to have pooped at 2 minutes...? FIXED. No longer takes a poop break.
  • PepXMLViewer: BAD link to SpectraST ("ST") FIXED (I think. Is it now doing what its suppose to)
  • Petunia icon on desktop
    • Window's quirk? Sometimes I see this sometimes I don't. The code in the installer looks solid. FIXED
  • Petunia favico in browser tab is missing on some pages
    • Joe: as far as I can tell, Petunia is the only one that actually supplies a favico. Otherwise it defaults to what the browser provides. On regis its that regis icon. I don't know what it is on windows. I looked but didn't see where we might have setup an favico in the apache config file. Can you check on a older TPP windows installation? Oh, and I didn't see a way to configure one for Appweb in the documentation however if you do place a favicon.ico file at the document level it seems to work, though your browser caching may hide this fact.
  • tpp_models: bad links to js/ resources ("/ISB/html...") FIXED
  • missing jquery.flot.errorbars.js. FIXED
    • Joe: as far as I can tell this was never a part of TPP. However the file was being copied into the TPP installation on regis by lmendoza. So I added it to the distribution.
  • ProtXMLViewer fails...(bad gateway) 'FIXED;
  • Old ProtXMLViewer fails too: system cannot find the path specified FIXED
  • updatepaths does not seem to do anything, no output, even with -vv FIXED
  • mzIdent conversion fails Potentially fixed with the perl script fix?
  • Petunia::Issue when selecting a directory from quick-select drop-down
    • Joe: not sure what this means.
  • decoyFastaGenerator.pl does not launch from Petunia FIXED
  • Downloading Spectral Libs fails, yet again: bad paths to md5sum, wget, and unzip FIXED

Release 5.0.0a1

  • Merge last set of trunk changes into branch
  • Review one last time what's in external. Ditch unneeded stuff.
  • Add instructions on wiki on how to use your own Perl/Apache
    • (Joe) warn users if they choose not to install perl or appweb
  • Luis says the TPP icon is ugly and use the purple flower instead
  • Update linux scripts in installer_linux
  • Update BUILD_LINUX. Especially Apache instructions
  • Luis says msconvert fails.
    • Luis is right<\s>
  • <s>README opens poorly in Notepad (needs DOS line endings)
  • Move tools params from /conf to data/param(eter)s/
    • They need to be accessible from Petunia/web browser
    • Which files? taxonomy.xml and tandem_params.xml only? or more?
  • Attempted to access forbidden directory error when selecting files and adding them. It's comparing $data_dir with param('workingdir'). One has a '/' on it and one doesn't.
  • Keep an eye out for "this page failed" in Petunia when submitting forms. If prompted resend try it a couple of times. If the page appears check the bottom of the page out. There may be a message about security and the params() function. If so note the line #. I've gone through tpp_gui.pl trying to fix all of these calls but apparently have missed some.
  • Create data/dbase/speclibs/ dir, if not present
  • PWiz -lrt issue on Windows
  • Upgrade comet
  • Upgrade pwiz-win32
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