TPP:V5Feedback

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-== Feedback related to releasing TPP version 5.0 ==+== TPP 5.0 pre-release tasks ==
 + 
 +* Update the TPP wiki tutorial
 +* Update the TPP wiki installation instructions
 +* Update the TPP wiki build instructions
 +* I'd recommend finishing the new wiki/replace old wiki project
 +** go through the current pages and update/remove them
 + 
 +== Feedback related to TPP version 5.0 builds ==
This page here is to record feedback/issues found with the development builds of 5.0.0 This page here is to record feedback/issues found with the development builds of 5.0.0
 +
 +==== Release 5.0.0a5 ====
 +
 +* nothing yet
 +
 +==== Release 5.0.0a4 ====
 +
 +* <s>Uninstall reports error when tpptray is running and in system tray. Should shut down executable before deleting</s>
 +** ''Joe: only an issue with TPP's "make uninstall". Works as expected when run from command shell or add/remove programs.''
 +
 +* <s>Possible bug with the tpp data directory. When you have install over TPP 4.8, it sets the default tpp data directory to the old directory under Inetpub. But I don't think it's updating it everywhere as it seemed the web interface was looking in the new area.</s>
 +** ''Joe: changed priority of default TPP_DATA environment variable, if that doesn't exist then old ISB directory, if that isn't there then {app}/data.''
 +
 +* <s>Launching TPP Tray pops up a command window, despite using wperl.exe. Largely because we associate .pl with perl.exe instead of wperl.exe. Not a big deal as TPP tray should be launched at startup when you log in. Could turn this into a .bat file and get rid of this problem.</s>
 +
 +* Like to include tpp tray in the startup menu but that then screws up the order.
 +
 +* On my system seems to keep trying to install the VS 2005 runtime every install.
 +
 +* BUILD_LINUX instructions are way out of date. Also take a look at the BUILD_OSX
 +** mention (or otherwise notify users) that make install only works in top directory because of dependencies
 +
 +* <s>Interesting issue -- when shutting down appweb, any jobs continue to run. Can't restart appweb (port 80 in use) until jobs finish or are killed in taskmanager</s>
 +
 +* Any call to gnuplot.exe results in "Fontconfig error: Cannot load default config file"
 +
 +* <s>Seems to be a limit to post/put forms found by deleting 25+ files in petunia</s>
 +** ''Joe: doesn't seem to be a limit as I tested by setting available directives to high settings. Also seen situation where it seems to forget the login session''
 +** ''Joe: reported as an appweb bug: https://github.com/embedthis/appweb/issues/530. They say they won't fix it.''
 +
 +* <s>legacy proteinprophet results: prot_wt_xml.pl: "The system cannot find the path specified."</s>
 +** ASAPRatio link to ASAPCGIDisplay.cgi on the resulting page crashes
 +** pvalue link to interact-pval.png is broken. (look in PValueModel.cxx)
 +
 +* <s>ASAPRatioPeptideCGIDisplayParser.cgi, call to unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName)</s>
 +** <s>Also reports 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.</s>
 +
 +* <s>Clicking on the ions2 link to view the spectrum in comet results in the pepxmlviewer results in a bad url error</s>
 +
 +* <s>Clicking on the ions link in the comet pepxml view of the top 5 matching peptides results in a bad url error</s>
 +
 +* <s>Clicking on the 'st' in the pepxmlviewer to view the spectrast results at peptideatlas is broken</s>
 +
 +==== Release 5.0.0a3 ====
 +
 +* <s>Haven't merged DDS/Luis changes from today in.</s>
 +
 +* <s>New batch of DDS changes have to be merged</s>
 +
 +* <s>PWiz Window's runtime dependencies can fail to install causing TPP installer to fail. Other than not installing pwiz no way to get past this.</s>
 +** <s>Joe: Made it an option</s>
 +
 +* <s>comet-fastadb.cgi crashes if database doesn't exist (or for that matter if no cgi options are provided).</s>
 +
 +* <s>multi_parm() calls in protxmlviewer</s>
 +
 +* <s>Links are bad in pep3d save as html document. Resulting page has a bad link (windows path) to the image. Opening the html file also doesn't link to image</s>
 +
 +* <s>Export spreadsheet from pepxmlviewer doesn't seem to do anything ''Joe: nevermind seems to work''</s>
 +
 +* <s>Extra '/' in link for Additional Analysis Info on pepxmlviewer</s>
 +
 +* <s>Can't remove mzML files from processing search form</s>
 +
 +* <s>Clicking on spectrum id in the pepxmlviewer when viewing results of a spectrast search result in:
 +** command "gnuplot.exe c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.gp" failed: Operation not permitted command "gnuplot.exe c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.gp" failed with exit code 1 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.
 +** URL is plotspectrast.cgi?LibFile=c:/TPP/data/dbase/speclibs/NIST_yeast_IT_v2.0_2008-07-11.splib&LibFileOffset=413954123&QueryFile=c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.mzML&QueryScanNum=00417</s>
 +
 +* <s>Lumping these all together under "protein identifiers don't seem to be parsed correctly. Contain '|' NCBI field seperators"</s>
 +** <s>Clicking on the protein link in the pepxmlviewer when viewing spectrast results causes an cgi crash with "400 - Bad Request, Bad URL"
 +*** url: comet-fastadb.cgi?Ref=gi|6321631|ref|NP_011708.1|&Db=c:/TPP/data/yeast_orfs_all_REV.20060126.short.fasta&Pep=YDSTHGR&MassType=1&sample_enzyme=trypsin&min_ntt=0
 +*** It really looks like the Ref isn't escaped. Clicking on a ref with a plain text string works
 +** Clicking on the protein link in the pepxmlviewer when viewing peptideprophet results of spectrast results causes an cgi crash with "400 - Bad Request, Bad URL" (see above)</s>
 +** ''Joe: now urlencode the cgi parameters so it won't crash. But it also doesn't find the protein''
 +** ''Joe: update -- luis says this is the way its always worked''
 +
 +* <s>Issue with extracted ion current, launched from pepxmlviewer on spectrast results
 +** May be that d3.js is not found "localhost/ISB//html/js/d3.js"
 +** ''Joe: fixed multiple issues''</s>
 +
 +* <s>Same gnuplot error as before, on pepxmlviewer when viewing peptideprophet results of spectrast results</s>. Displayed when selecting the spectrum inthe pepxmlviewer on spectrast results.
 +
 +* <s>plotspectrast.cgi has bad image link in it (http://maserati/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.png) Seen when clicking on a spectrum in the pepxmlviewer on spectrast results.</s>
 +
 +*<s>ProteinProphet spits this error:
 +**'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.</s>
 +
 +*<s>proteinprophet results: new viewer doesn't display anything in pepxmlviewer when a peptide is clicked on (no peptides shown in view)</s>
 +
 +*<s>proteinprophet results: saving to JSON in new viewer reported error "Service Unavailable"</s>
 +
 +* <s>legacy proteinprophet results: sensitivity/error info has broken image/page with error "The system cannot find the path specified."</s>
 +
 +* <s>legacy proteinprophet results: more analysis info reports error "The system cannot find the path specified."</s>
 +
 +* <s>legacy proteinprophet results: help link has page that's missing images</s>
 +
==== Release 5.0.0a2 ==== ==== Release 5.0.0a2 ====
Line 10: Line 115:
* 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
Line 16: Line 121:
* Petunia favico in browser tab is missing on some pages * 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. ** 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.
 +** Joe: also, keep in mind that the browser will stubbornly cache the icon and display it. http://stackoverflow.com/questions/2208933/how-do-i-force-a-favicon-refresh
* <s>tpp_models: bad links to js/ resources ("/ISB/html...")</s> '''FIXED''' * <s>tpp_models: bad links to js/ resources ("/ISB/html...")</s> '''FIXED'''
* <s>missing jquery.flot.errorbars.js.</s> '''FIXED''' * <s>missing jquery.flot.errorbars.js.</s> '''FIXED'''
Line 35: Line 141:
* Add instructions on wiki on how to use your own Perl/Apache * Add instructions on wiki on how to use your own Perl/Apache
-** (Joe) warn users if they choose not to install perl or appweb+** (Joe) warn users if they choose not to install perl or <s>appweb</s> Apache
* Luis says the TPP icon is ugly and use the purple flower instead * Luis says the TPP icon is ugly and use the purple flower instead
Line 53: Line 159:
* <s>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. </s> * <s>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. </s>
-* 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.+* <s>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.</s>
* <s>Create data/dbase/speclibs/ dir, if not present</s> * <s>Create data/dbase/speclibs/ dir, if not present</s>

Current revision

Contents

[edit]

TPP 5.0 pre-release tasks

  • Update the TPP wiki tutorial
  • Update the TPP wiki installation instructions
  • Update the TPP wiki build instructions
  • I'd recommend finishing the new wiki/replace old wiki project
    • go through the current pages and update/remove them
[edit]

Feedback related to TPP version 5.0 builds

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

[edit]

Release 5.0.0a5

  • nothing yet
[edit]

Release 5.0.0a4

  • Uninstall reports error when tpptray is running and in system tray. Should shut down executable before deleting
    • Joe: only an issue with TPP's "make uninstall". Works as expected when run from command shell or add/remove programs.
  • Possible bug with the tpp data directory. When you have install over TPP 4.8, it sets the default tpp data directory to the old directory under Inetpub. But I don't think it's updating it everywhere as it seemed the web interface was looking in the new area.
    • Joe: changed priority of default TPP_DATA environment variable, if that doesn't exist then old ISB directory, if that isn't there then {app}/data.
  • Launching TPP Tray pops up a command window, despite using wperl.exe. Largely because we associate .pl with perl.exe instead of wperl.exe. Not a big deal as TPP tray should be launched at startup when you log in. Could turn this into a .bat file and get rid of this problem.
  • Like to include tpp tray in the startup menu but that then screws up the order.
  • On my system seems to keep trying to install the VS 2005 runtime every install.
  • BUILD_LINUX instructions are way out of date. Also take a look at the BUILD_OSX
    • mention (or otherwise notify users) that make install only works in top directory because of dependencies
  • Interesting issue -- when shutting down appweb, any jobs continue to run. Can't restart appweb (port 80 in use) until jobs finish or are killed in taskmanager
  • Any call to gnuplot.exe results in "Fontconfig error: Cannot load default config file"
  • Seems to be a limit to post/put forms found by deleting 25+ files in petunia
    • Joe: doesn't seem to be a limit as I tested by setting available directives to high settings. Also seen situation where it seems to forget the login session
    • Joe: reported as an appweb bug: https://github.com/embedthis/appweb/issues/530. They say they won't fix it.
  • legacy proteinprophet results: prot_wt_xml.pl: "The system cannot find the path specified."
    • ASAPRatio link to ASAPCGIDisplay.cgi on the resulting page crashes
    • pvalue link to interact-pval.png is broken. (look in PValueModel.cxx)
  • ASAPRatioPeptideCGIDisplayParser.cgi, call to unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName)
    • Also reports 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.
  • Clicking on the ions2 link to view the spectrum in comet results in the pepxmlviewer results in a bad url error
  • Clicking on the ions link in the comet pepxml view of the top 5 matching peptides results in a bad url error
  • Clicking on the 'st' in the pepxmlviewer to view the spectrast results at peptideatlas is broken
[edit]

Release 5.0.0a3

  • Haven't merged DDS/Luis changes from today in.
  • New batch of DDS changes have to be merged
  • PWiz Window's runtime dependencies can fail to install causing TPP installer to fail. Other than not installing pwiz no way to get past this.
    • Joe: Made it an option
  • comet-fastadb.cgi crashes if database doesn't exist (or for that matter if no cgi options are provided).
  • multi_parm() calls in protxmlviewer
  • Links are bad in pep3d save as html document. Resulting page has a bad link (windows path) to the image. Opening the html file also doesn't link to image
  • Export spreadsheet from pepxmlviewer doesn't seem to do anything Joe: nevermind seems to work
  • Extra '/' in link for Additional Analysis Info on pepxmlviewer
  • Can't remove mzML files from processing search form
  • Clicking on spectrum id in the pepxmlviewer when viewing results of a spectrast search result in:
    • command "gnuplot.exe c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.gp" failed: Operation not permitted command "gnuplot.exe c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.gp" failed with exit code 1 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.
    • URL is plotspectrast.cgi?LibFile=c:/TPP/data/dbase/speclibs/NIST_yeast_IT_v2.0_2008-07-11.splib&LibFileOffset=413954123&QueryFile=c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.mzML&QueryScanNum=00417
  • Lumping these all together under "protein identifiers don't seem to be parsed correctly. Contain '|' NCBI field seperators"
    • Clicking on the protein link in the pepxmlviewer when viewing spectrast results causes an cgi crash with "400 - Bad Request, Bad URL"
      • url: comet-fastadb.cgi?Ref=gi|6321631|ref|NP_011708.1|&Db=c:/TPP/data/yeast_orfs_all_REV.20060126.short.fasta&Pep=YDSTHGR&MassType=1&sample_enzyme=trypsin&min_ntt=0
      • It really looks like the Ref isn't escaped. Clicking on a ref with a plain text string works
    • Clicking on the protein link in the pepxmlviewer when viewing peptideprophet results of spectrast results causes an cgi crash with "400 - Bad Request, Bad URL" (see above)
    • Joe: now urlencode the cgi parameters so it won't crash. But it also doesn't find the protein
    • Joe: update -- luis says this is the way its always worked
  • Issue with extracted ion current, launched from pepxmlviewer on spectrast results
    • May be that d3.js is not found "localhost/ISB//html/js/d3.js"
    • Joe: fixed multiple issues
  • Same gnuplot error as before, on pepxmlviewer when viewing peptideprophet results of spectrast results. Displayed when selecting the spectrum inthe pepxmlviewer on spectrast results.
  • plotspectrast.cgi has bad image link in it (OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.png) Seen when clicking on a spectrum in the pepxmlviewer on spectrast results.
  • ProteinProphet spits this error:
    • 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.
  • proteinprophet results: new viewer doesn't display anything in pepxmlviewer when a peptide is clicked on (no peptides shown in view)
  • proteinprophet results: saving to JSON in new viewer reported error "Service Unavailable"
  • legacy proteinprophet results: sensitivity/error info has broken image/page with error "The system cannot find the path specified."
  • legacy proteinprophet results: more analysis info reports error "The system cannot find the path specified."
  • legacy proteinprophet results: help link has page that's missing images


[edit]

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.
    • Joe: also, keep in mind that the browser will stubbornly cache the icon and display it. http://stackoverflow.com/questions/2208933/how-do-i-force-a-favicon-refresh
  • 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
[edit]

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 Apache
  • 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
Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:V5Feedback"
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