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[Sashimi-commit] SF.net SVN: sashimi:[4806] trunk/trans_proteomic_pipeline/CGI/tpp_gui/ tpp_gui.pl
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From: <rea...@us...> - 2009-12-23 01:28:42
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Revision: 4806
http://sashimi.svn.sourceforge.net/sashimi/?rev=4806&view=rev
Author: real_procopio
Date: 2009-12-23 01:28:35 +0000 (Wed, 23 Dec 2009)
Log Message:
-----------
Optionally authenticate against an .htpasswd entry (from J.Slagel);
Fix tabs (from 4.3 branch);
Added a variable to hold location of tpp-bin;
Refer to tpp_hostname by full path.
Modified Paths:
--------------
trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl
Modified: trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl
===================================================================
--- trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl 2009-12-23 01:18:19 UTC (rev 4805)
+++ trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl 2009-12-23 01:28:35 UTC (rev 4806)
@@ -42,6 +42,8 @@
my $debug = readconfig('debug',0); # set to 0 (zero) to suppress debug output to log file
my $doMzXMLGzip = readconfig('doMzXMLGzip',0); # set to 1 to tell converters to gzip their mzxml output
my $mascot_server = readconfig('mascot_server',"http://myserver/mascot/"); # Mascot server top-level url (if applicable)
+my $htpasswd = readconfig('htpasswd',""); # Optionally authenticate using htpasswd file
+my $tppbin = readconfig('tppbin',"/usr/bin"); # Location of TPP bin
#
# end config section
########################################################################
@@ -62,33 +64,34 @@
'wget' => '/usr/bin/wget', # full path to wget
'cygpath' => '/usr/bin/cygpath', # full path to cygpath -- cygwin only
# TPP executables
- 'readw' => '/usr/bin/ReAdW', # some Windows installations only
- 'mzwiff' => '/usr/bin/mzWiff', # some Windows installations only
- 'masswolf' => '/usr/bin/massWolf', # some Windows installations only
- 'trapper' => '/usr/bin/trapper', # some Windows installations only
- 'decoyfasta' => '/usr/bin/decoyFASTA',
- 'decoyvalpeps' => '/usr/bin/ProphetModels.pl',
- 'decoyvalprots' => '/usr/bin/ProtProphModels.pl',
- 'msconvert' => '/usr/bin/msconvert',
- 'mzxml2search'=> '/usr/bin/MzXML2Search',
- 'dta2mzxml' => '/usr/bin/dta2mzxml',
- 'out2xml' => '/usr/bin/Out2XML',
- 'mascot2xml' => '/usr/bin/Mascot2XML',
- 'comet2xml' => '/usr/bin/Comet2XML',
- 'tandem2xml' => '/usr/bin/Tandem2XML',
- 'protxml2html'=> '/usr/bin/protxml2html.pl',
- 'runsearch' => '/usr/bin/runsearch', # cygwin installations only
- 'tandem' => '/usr/bin/tandem',
- 'spectrast' => '/usr/bin/spectrast',
- 'lib2html' => '/usr/bin/Lib2HTML',
- 'downloader' => '/usr/bin/fileDownloader.pl',
- 'qualscore' => 'java -jar ' . '/usr/bin/qualscore.jar',
- 'xinteract' => '/usr/bin/xinteract',
- 'interprophet'=> '/usr/bin/InterProphetParser',
- 'runprophet' => '/usr/bin/ProteinProphet',
- 'updateallpaths'=>'/usr/bin/updateAllPaths.pl',
- 'chargefile' =>'/usr/bin/createChargeFile.pl',
- 'mergecharges'=>'/usr/bin/mergeCharges.pl',
+ 'readw' => "$tppbin/ReAdW", # some Windows installations only
+ 'mzwiff' => "$tppbin/mzWiff", # some Windows installations only
+ 'masswolf' => "$tppbin/massWolf", # some Windows installations only
+ 'trapper' => "$tppbin/trapper", # some Windows installations only
+ 'decoyfasta' => "$tppbin/decoyFASTA",
+ 'decoyvalpeps' => "$tppbin/ProphetModels.pl",
+ 'decoyvalprots' => "$tppbin/ProtProphModels.pl",
+ 'msconvert' => "$tppbin/msconvert",
+ 'mzxml2search'=> "$tppbin/MzXML2Search",
+ 'dta2mzxml' => "$tppbin/dta2mzxml",
+ 'out2xml' => "$tppbin/Out2XML",
+ 'mascot2xml' => "$tppbin/Mascot2XML",
+ 'comet2xml' => "$tppbin/Comet2XML",
+ 'tandem2xml' => "$tppbin/Tandem2XML",
+ 'protxml2html'=> "$tppbin/protxml2html.pl",
+ 'runsearch' => "$tppbin/runsearch", # cygwin installations only
+ 'tandem' => "$tppbin/tandem",
+ 'spectrast' => "$tppbin/spectrast",
+ 'lib2html' => "$tppbin/Lib2HTML",
+ 'downloader' => "$tppbin/fileDownloader.pl",
+ 'qualscore' => 'java -jar ' . "$tppbin/qualscore.jar",
+ 'xinteract' => "$tppbin/xinteract",
+ 'interprophet'=> "$tppbin/InterProphetParser",
+ 'runprophet' => "$tppbin/ProteinProphet",
+ 'updateallpaths'=>"$tppbin/updateAllPaths.pl",
+ 'chargefile' => "$tppbin/createChargeFile.pl",
+ 'mergecharges'=> "$tppbin/mergeCharges.pl",
+ 'tpp_hostname'=> "$tppbin/tpp_hostname",
);
my $in_windows = ( ($^O eq 'cygwin' )); # really this means in_cygwin, but that's a pervasive change to track
@@ -956,20 +959,38 @@
# get parameters
my $user = shift || '';
my $pswd = shift || '';
+ my $upwd = '';
+ my $ckey = '';
+
+ # get encrypted password
+ if ( $htpasswd ) { # use htpasswd to authenticate
+ &printToLog("looking in $htpasswd for password\n") if ($debug);
+ open(PWD, $htpasswd) || &fatalError('PWD_FILE',"Error verifying password!");
+ while ( <PWD> ) {
+ chop();
+ my ( $u, $p ) = split /:/;
+ $upwd = $p if ( $u eq $user );
+ }
+ close(PWD);
+ $ckey = substr( $upwd, 0, 2 );
+ } else { # use local password file in user dir
+ my $pfile = "${users_dir}$user/.password";
+ &printToLog("looking in $pfile for password\n") if ($debug);
+ if ( -e $pfile ) {
+ open(PWD, $pfile) || &fatalError('PWD_FILE',"Error verifying password!");
+ chomp($upwd = <PWD>);
+ close(PWD);
+ }
+ $ckey = $crypt_key;
+ }
+ &printToLog("stored password is: --$upwd--\n") if ($debug);
- my $pfile = "${users_dir}$user/.password";
-
if ( !($user && $pswd)) {
push @messages, "Not enough information for login. Please fill out all fields.";
- } elsif (!(-e $pfile)) {
+ } elsif (!$upwd) {
push @messages, "User $user not found. Please check your user name, or log in as guest.";
} else {
- open(PWD, $pfile) || &fatalError('PWD_FILE',"Error verifying password!");
- chomp(my $upwd = <PWD>);
- close(PWD);
- &printToLog("stored password is: --$upwd--\n") if ($debug);
-
- if (crypt($pswd, $crypt_key) eq $upwd) {
+ if (crypt($pswd, $ckey) eq $upwd) {
$retstr = 'OK';
} else {
push @messages, "Incorrect password. Please re-enter.";
@@ -1885,7 +1906,7 @@
push @messages, "Please 'Select' file(s) to process.";
return 'topepxml';
}
- my $pepxml_ext = `tpp_hostname GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
+ my $pepxml_ext = `$command{tpp_hostname} GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
# Build commands
#
@@ -2515,7 +2536,7 @@
return 'runsearch';
}
- my $pepxml_ext = `tpp_hostname GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
+ my $pepxml_ext = `$command{tpp_hostname} GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
# Perform Basic Validation
@@ -3296,7 +3317,7 @@
########################################################################
sub isMassSpecFile {
my $file_path = shift;
- my $file_test = `tpp_hostname "$file_path"`;
+ my $file_test = `$command{tpp_hostname} "$file_path"`;
return 1 if ($file_path eq $file_test);
return 0;
}
@@ -3589,11 +3610,11 @@
{ name => 'SpectraST Tools', pages=> 'spectrastlib,getspeclibs,lib2html'}
);
if ($pipeline eq 'Mascot') {
- $sections[2] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runmascot,topepxml,xinteract,iprophet,runprophet'};
+ $sections[3] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runmascot,topepxml,xinteract,iprophet,runprophet'};
} elsif ($pipeline eq 'SpectraST') {
- $sections[2] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runspectrast,xinteract,iprophet,runprophet'};
+ $sections[3] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runspectrast,xinteract,iprophet,runprophet'};
} elsif ($pipeline eq 'Tandem') {
- $sections[2] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runtandem,topepxml,xinteract,iprophet,runprophet'};
+ $sections[3] = { name => 'Analysis Pipeline', pages=> 'mzxml,msconvert,runtandem,topepxml,xinteract,iprophet,runprophet'};
}
my %tabs = (
@@ -6582,7 +6603,7 @@
sub pageXInteract {
# files to process (from session)
- my $pepxml_ext = `tpp_hostname GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
+ my $pepxml_ext = `$command{tpp_hostname} GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
my $any_files_there = &showFiles('xinteract','xinteract','xml','Select File(s) to Analyze');
@@ -7050,7 +7071,7 @@
########################################################################
sub pageInterProphet {
# files to process (from session)
- my $pepxml_ext = `tpp_hostname GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
+ my $pepxml_ext = `$command{tpp_hostname} GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
my $any_files_there = &showFiles('runprophet','iprophet','xml','Select File(s) to Analyze');
@@ -7157,7 +7178,7 @@
sub pageRunProphet {
# files to process (from session)
- my $protxml_ext = `tpp_hostname GET_PROTXML_EXT!`; # get TPP's idea of canonical protxml file ext
+ my $protxml_ext = `$command{tpp_hostname} GET_PROTXML_EXT!`; # get TPP's idea of canonical protxml file ext
my $any_files_there = &showFiles('runprophet','runprophet','xml','Select File(s) to Analyze');
@@ -7373,8 +7394,8 @@
push @outfiles, $outf; # like foo.xml, or foo.pep.xml or foo.pep.xml.gz or foo.shtml
- my $pepml_ext = `tpp_hostname GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
- my $prot_shtml_ext = `tpp_hostname GET_PROTXML_EXT!`; # get TPP's idea of canonical protxml file ext
+ my $pepml_ext = `$command{tpp_hostname} GET_PEPXML_EXT!`; # get TPP's idea of canonical pepxml file ext
+ my $prot_shtml_ext = `$command{tpp_hostname} GET_PROTXML_EXT!`; # get TPP's idea of canonical protxml file ext
$pepml_ext =~ s/\.xml(\.gz)?$/\.shtml/; # like .pep.shtml
$prot_shtml_ext =~ s/\.xml(\.gz)?$/\.shtml/; # like -prot.shtml, or .prot.shtml
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