TPP:V5Feedback
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| Revision as of 05:50, 3 September 2015 JoeS (Talk | contribs) (→Release 5.0.0a3) ← Previous diff |
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| ** ''Joe: now urlencode the cgi parameters so it won't crash. But it also doesn't find the protein'' | ** ''Joe: now urlencode the cgi parameters so it won't crash. But it also doesn't find the protein'' | ||
| - | * Issue with extracted ion current, launched from pepxmlviewer on spectrast results | + | * <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" | + | ** May be that d3.js is not found "localhost/ISB//html/js/d3.js"</s> |
| + | ** ''Joe: fixed multiple issues'' | ||
| * Same gnuplot error as before, on pepxmlviewer when viewing peptideprophet results of spectrast results | * Same gnuplot error as before, on pepxmlviewer when viewing peptideprophet results of spectrast results | ||
Revision as of 07:10, 3 September 2015
Contents |
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 5.0.0a3
- 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.
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Haven't merged DDS/Luis changes from today in.
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New batch of DDS changes have to be merged
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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
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comet-fastadb.cgi crashes if database doesn't exist (or for that matter if no cgi options are provided).
- 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
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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
- Extra '/' in link for Additional Analysis Info on pepxmlviewer
- Can't remove mzML files from spectrast 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"
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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
-
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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
- 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
- ASAPRatioPeptideCGIDisplayParser.cgi, call to unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, int inbuflen, char *spectrumName) 'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file.
- ProteinProphet spits this error:
'gnuplot.exe' is not recognized as an internal or external command, operable program or batch file. command "gnuplot.exe "C:/tmp/interact.prot.png.script.tmp.a06012"" failed: Operation not permitted command "gnuplot.exe "C:/tmp/interact.prot.png.script.tmp.a06012"" failed with exit code 1 ProteinProphet: png file c:/TPP/data/interact.prot.png not written, error code 1 INFO: mu=2.491e-005, db_size=6222892
- 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
- legacy proteinprophet results: prot_wt_xml.pl: "The system cannot find the path specified."
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.
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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 desktopFIXED- Window's quirk? Sometimes I see this sometimes I don't. The code in the installer looks solid.
- 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
- 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.
- Joe: not sure what this means.
Release 5.0.0a1
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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
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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?
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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.
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Create data/dbase/speclibs/ dir, if not present
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PWiz -lrt issue on Windows
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Upgrade comet
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Upgrade pwiz-win32
