-== 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
+==== 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+* BUILD_LINUX instructions are way out of date.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 ====
+* 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.
+* <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>Petunia icon on desktop
+**Window's quirk?  Sometimes I see this sometimes I don't.  The code in the installer looks solid.</s> '''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
+* <s>tpp_models: bad links to js/ resources ("/ISB/html...")</s> '''FIXED'''
+* <s>missing jquery.flot.errorbars.js.</s> '''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.
+* <s>ProtXMLViewer fails...(bad gateway)</s> '''FIXED;''
+* <s>Old ProtXMLViewer fails too: system cannot find the path specified</s> '''FIXED'''
+* <s>updatepaths does not seem to do anything, no output, even with -vv</s> '''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.
+* <s>decoyFastaGenerator.pl does not launch from Petunia</s>  '''FIXED'''
+* <s>Downloading Spectral Libs fails, yet again:  bad paths to md5sum, wget, and unzip</s> '''FIXED'''
 ==== Release 5.0.0a1 ====
 * 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
 * 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?
+* <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>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>
-* Create data/dbase/speclibs/  dir, if not present
+* <s>Create data/dbase/speclibs/  dir, if not present</s>
 * <s>PWiz -lrt issue on Windows</s>

TPP:V5Feedback

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TPP 5.0 pre-release tasks

Feedback related to TPP version 5.0 builds

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