Example program for reading and manipulating the quantitation.xml file.
#!/usr/local/bin/perl
##############################################################################
# file: config_quantitation.pl #
# 'msparser' toolkit example code #
##############################################################################
# COPYRIGHT NOTICE #
# Copyright 1998-2010 Matrix Science Limited All Rights Reserved. #
# #
##############################################################################
# $Source: parser/examples/test_perl/config_quantitation.pl $ #
# $Author: villek@matrixscience.com $ #
# $Date: 2018-07-30 16:23:53 +0100 $ #
# $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords:: $ #
##############################################################################
use strict;
##############################################################################
use msparser;
if (!defined($ARGV[0])) {
print <<EOF;
The location of quantitation.xml file has to be specified as a parameter.
The location should either be the full path to the quantitation.xml file
or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi
EOF
exit 1;
}
if (!defined($ARGV[1])) {
print <<EOF;
The location of schema file quantitation_XXX.xsd has to be specified as the
second parameter. The location should only be a full or relative path to the
quantitation_XXX.xsd file.
EOF
exit 1;
}
# Note: $cs must not be lexically scoped; you need to keep it in scope
# for as long as you use $file. See "Using the toolkit from Perl, Java and
# Python" in Mascot Parser manual.
my ($file, $cs);
# A sessionID can optionally be passed as the third parameter.
# This will only be required if the 'file' is a URL.
if (defined($ARGV[2])) {
$cs = new msparser::ms_connection_settings;
$cs->setSessionID($ARGV[2]);
$file = new msparser::ms_quant_configfile($ARGV[0], $ARGV[1], $cs);
} else {
$file = new msparser::ms_quant_configfile($ARGV[0], $ARGV[1]);
}
if (!$file->isValid) {
print "There are errors. Cannot continue. The last error description:\n";
print $file->getLastErrorString(), "\n";
exit 1;
}
my $n = $file->getNumberOfMethods;
print "There are ", $n, " quantitation methods available:\n";
for my $i (0 .. $n-1) {
print $file->getMethodByNumber($i)->getName(), "\n";
}
# Validate the original document.
if (my $errs = $file->validateDocument())
{
print "Initial document validation errors:\n";
print $errs, "\n";
}
# Now try to read in the schema file.
my $schemaFile = new msparser::ms_xml_schema;
$schemaFile->setFileName($ARGV[1]);
$schemaFile->read_file;
if (!$schemaFile->isValid) {
print "Errors while reading schema-file. The last error description:\n";
print $schemaFile->getLastErrorString(), "\n";
exit 1;
}
# The document can be validated programmatically, but this is different from
# real validation against a schema. We'll validate each quantitation
# method separately.
for my $i (0 .. $n-1) {
# Shallow validation: only check the presence of required attributes and
# elements.
my $pMethod = $file->getMethodByNumber($i);
if (my $errs = $pMethod->validateShallow($schemaFile)) {
print "Shallow validation errors (method ", $pMethod->getName, "): ";
print $errs, "\n\n";
}
# Deep validation: check attributes and elements recursively applying basic
# constraints.
if (my $errs = $pMethod->validateDeep($schemaFile)) {
print "Deep validation errors (method ", $pMethod->getName, "): ";
print $errs, "\n\n";
}
}
# We can validate objects as well. First, copy the first method from the
# original file (method "null").
my $myMethodInvalid = new msparser::ms_quant_method($file->getMethodByNumber(0));
# And set an invalid name with less than allowed string length.
$myMethodInvalid->setName("");
# First way: use shallow and deep validation as above.
if (my $errs = $myMethodInvalid->validateShallow($schemaFile)) {
print "Shallow validation of a method: ", $errs, "\n";
}
if (my $errs = $myMethodInvalid->validateDeep($schemaFile)) {
print "Deep validation of a method: ", $errs, "\n";
}
# Second way: use the schema object. This is equivalent to the previous
# two-step process as long as you pass 'true' as the second parameter
# for deep validation.
if (my $errs = $schemaFile->validateComplexObject($myMethodInvalid, 1)) {
print "Deep validation using schema-object: ", $errs, "\n";
}
# Third way: validate an attribute separately. Available validation methods
# are validateSimpleInteger(), validateSimpleDouble(), validateSimpleBool()
# and validateSimpleString().
if (my $errs = $schemaFile->validateSimpleString($myMethodInvalid->getName(), $myMethodInvalid->getNameSchemaType())) {
print "Attribute validation: ", $errs, "\n";
}
# Fourth way: validate an entire document. For this, we need to create
# a new document and append the invalid method definition.
my $configFileInvalid = new msparser::ms_quant_configfile;
$configFileInvalid->appendMethod($myMethodInvalid);
if (my $errs = $configFileInvalid->validateDocument()) {
print "Document validation errors: ", $errs, "\n";
}
# The config file object itself stays valid, even if it has an invalid
# method definition.
if ( !$configFileInvalid->isValid() ) {
# Control flow never comes here!
print "Errors in config file object. The last error description:\n";
print $configFileInvalid->getLastErrorString(), "\n";
}
# The file can be saved even if it has invalid definitions.
$configFileInvalid->setFileName("quantitation_temp.xml");
$configFileInvalid->save_file();
if ( !$configFileInvalid->isValid() ) {
print "Failed to save: ", $configFileInvalid->getLastErrorString(), "\n";
}
=pod
Running the program as
perl -I../bin config_quantitation.pl ../config/quantitation.xml ../html/xmlns/schema/quantitation_2/quantitation_2.xsd
will give the following output under Mascot Server 2.3 (depending on how
quantitation methods have been configured):
There are 26 quantitation methods available:
None
iTRAQ 4plex
iTRAQ 8plex
TMT 6plex
TMT 2plex
18O multiplex
SILAC K+6 R+6 multiplex
IPTL (Succinyl and IMID) multiplex
ICPL duplex pre-digest [MD]
ICPL duplex post-digest [MD]
ICPL triplex pre-digest [MD]
18O corrected [MD]
15N Metabolic [MD]
15N + 13C Metabolic [MD]
SILAC K+6 R+10 [MD]
SILAC K+6 R+10 Arg-Pro [MD]
SILAC K+6 R+6 [MD]
SILAC R+6 R+10 [MD]
SILAC K+8 R+10 [MD]
SILAC K+4 K+8 R+6 R+10 [MD]
ICAT ABI Cleavable [MD]
ICAT D8 [MD]
Dimethylation [MD]
NBS Shimadzu [MD]
Label-free [MD]
Average [MD]
Deep validation of a method: Attribute 'name' -> String is shorter than minLength-limit
Deep validation using schema-object: Attribute 'name' -> String is shorter than minLength-limit
Attribute validation: String is shorter than minLength-limit
=cut
1.9.6