Damian, I'll contact you offline to see if we can figure out what's happening. Both Lorikeet and old Comet viewer access the underlying spectra in the same way. So the fact that the old viewer is having an issue means that Lorikeet will to.
- Jimmy On Mon, Apr 8, 2013 at 12:15 PM, GATTACA <[email protected]> wrote: > Hi. > > I'm running TPP 4.6.2 on RHEL 6.4 (64bit) fully patched. > Users are having problems viewing spectra in this version with lorikeet. > > It doesn't happen for all data sets but generally speaking the older the > interact XML files are, the less likely they are to be viewable in lorikeet. > > If I click on the 'Ions2' link in a pepXML file I get a grey screen with > nothing in the window. Here is the URL for the page: > > http://111.111.111.111/tpp/cgi-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=0&PepMass=1331.6054&Pep=SLRPGTAEQDEK&Dta=/tpp.data/venky/UM_2013_1308.2013_03_05.091612/UM_2013_1308_50%/UM_2013_1308_50%.00028.00028.2.dta > > Nothing gets written to the error logs. The http access logs report this: > [08/Apr/2013:15:01:53 -0400] "GET > /tpp/cgi-bin/plot-msms-js.cgi?PrecursorMassType=1&FragmentMassType=0&PepMass=1331.6054&Pep=SLRPGTAEQDEK&Dta=/tpp.data/venky/UM_2013_1308.2013_03_05.091612/UM_2013_1308_50%/UM_2013_1308_50%.00028.00028.2.dta > HTTP/1.1" 200 2138 > > Using the old Comet viewer at least generates an error on the browser: > Error - cannot get scan number from input file > /tpp.data/venky/UM_2013_1308.2013_03_05.091612/; unexpected dta name format > > The error logs for httpd also get something: > [Mon Apr 08 15:09:56 2013] [error] [client 111.111.111.111] script not > found or unable to stat: /usr/local/apps/tpp/cgi-bin/vbasrur, referer: > http://111.111.1.111/tpp/cgi-bin/PepXMLViewer.cgi?page=1&columns=Pprobability%2CGspectrum%2CSexpect%2CGions2%2CGpeptide%2CGprotein%2CGcalc_neutral_pep_mass%2CGions&displayState=columnsOptionsDiv&exportSpreadsheet=0&sortField2=Gspectrum&sortDir2=0&FmPprobability2=&FMPprobability2=&xmlFileName=%2Ftpp.data%2Fvbasrur%2FUM_2013_1308.2013_03_05.091612%2Finteract.pep.xml&perPage=50&sortField=Gspectrum&sortDir=0&highlightedPeptideText=&highlightedProteinText=&highlightedSpectrumText=&expandProteinList=condense&minimizeTableHeaders=yes&requiredAA=&requiredPeptideText=&requiredProteinText=&requiredSpectrumText=&FmGnum_tol_term=&FmShyperscore=&FMShyperscore=&FmSnextscore=&FMSnextscore=&FmSbscore=&FMSbscore=&FmSyscore=&FMSyscore=&FmSexpect=&FMSexpect=&FmPprobability=&FMPprobability=&jumpPage=1 > > > Any ideas for what's going on? > Thanks, > Damian > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
