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__NOTOC__ | __NOTOC__ | ||
= Using | = Using The Web-Services Interface = | ||
== Synopsis == | == Synopsis == | ||
Web-services allow for interchange of structured data via the internet. EMMA provides a SOAP-based web-service layer to query for expression data. | Web-services allow for interchange of structured data via the internet. EMMA provides a SOAP-based web-service layer to query for expression data. The server has been tested with Perl SOAP::Lite and Java Axis clients. | ||
== Available Methods == | |||
EMMA | |||
WSDL location: https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl | |||
Methods: | |||
* <code><nowiki>fetchAllProjects()</nowiki></code> | |||
o Gets all available EMMA projects. | |||
o '''Input''': | |||
--none-- | |||
o Output: | |||
tns:[[ArrayOfString]] -- The projects | |||
* <code><nowiki>fetchAllExperiments()</nowiki></code> | |||
o Gets all experminents in the given project. | |||
o Input: | |||
- xsd:string -- The project | |||
o Output: | |||
tns:[[ArrayOfString]] -- The experiments | |||
* <code><nowiki>fetchAllExperimentalFactorsByExperiment()</nowiki></code> | |||
o Gets all factors associated with the given experiment in the given project. | |||
o Input: | |||
- xsd:string -- The project | |||
- xsd:string -- The experiment | |||
o Output: | |||
tns:[[ArrayOfString]] -- The factors | |||
* <code><nowiki>fetchAllExperimentalFactorValuesByFactorAndExperiment()</nowiki></code> | |||
o Gets all factor values for given project, experiment and factor. | |||
o Input: | |||
- xsd:string -- The project | |||
- xsd:string -- The experiment | |||
- xsd:string -- The factor | |||
o Output: | |||
tns:[[ArrayOfString]] -- The factor value identifiers | |||
* <code><nowiki>fetchAllReporterByName()</nowiki></code> | |||
o Gets the valid reporter names for the given gene. | |||
o Input: | |||
- xsd:string -- The project | |||
- xsd:string -- The experiment | |||
- xsd:string -- The gene name | |||
o Output: | |||
tns:[[ArrayOfString]] -- The valid reporter identifiers | |||
* <code><nowiki>fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue()</nowiki></code> | |||
o Gets the latest significant mean expression value of best quality for the given project, experiment, reporter, factor, and factor value. | |||
o Input: | |||
- xsd:string -- The project | |||
- xsd:string -- The experiment | |||
- xsd:string -- The reporter | |||
- xsd:string -- The factor | |||
- xsd:string -- The factor value | |||
o Output: | |||
xsd:double -- The M-value | |||
* <code><nowiki>fetchMultipleMvalues()</nowiki></code> | |||
o Gets the latest significant mean expression as above but can handle a list of reporters. | |||
o Input: | |||
- xsd:string -- The project | |||
- xsd:string -- The experiment | |||
- Array of xsd:string -- The list of reporter Identifiers | |||
- xsd:string -- The factor | |||
- xsd:string -- The factor value | |||
o Output: | |||
Array of [[GeneMvalueStruct]] -- A list of GeneIDs and Mvalues | |||
== Sample Perl-client == | == Sample Perl-client == | ||
| Line 25: | Line 125: | ||
print Dumper $soap->fetchAllProjects(); | print Dumper $soap->fetchAllProjects(); | ||
print Dumper $soap->fetchAllExperiments('EMMA2.Coryne-Center'); | print Dumper $soap->fetchAllExperiments('EMMA2.Coryne-Center'); | ||
print Dumper $soap->fetchAllReporterByName('EMMA2.Coryne-Center', ' | print Dumper $soap->fetchAllReporterByName('EMMA2.Coryne-Center', 'GlucoseAcetat', "cg0001"); | ||
print $soap-> fetchAllExperimentalFactorValuesByFactorAndExperiment ('EMMA2 | print Dumper $soap-> fetchAllExperimentalFactorsByExperiment ('EMMA2.Coryne-Center','GlucoseAcetat'); | ||
print Dumper $soap-> fetchAllExperimentalFactorValuesByFactorAndExperiment ('EMMA2.Coryne-Center','GlucoseAcetat','Carbon Source'); | |||
print Dumper $soap->fetchMultipleMvalues('EMMA2.Coryne-Center', 'GlucoseAcetat',['R:cg0001', 'R:cg0012'], 'Carbon Source', 'Acetat.Glucose'); | |||
</nowiki></pre> | </nowiki></pre> | ||
| Line 61: | Line 162: | ||
push @vals ,["cg$_",$wt,$hspr]; | push @vals ,["cg$_",$wt,$hspr]; | ||
$min = $wt if $wt < $min;$min = $hspr if $hspr < $min; | $min = $wt if $wt < $min;$min = $hspr if $hspr < $min; | ||
$max = $wt if $wt > $max; $max = $hspr if $hspr > $ | $max = $wt if $wt > $max; $max = $hspr if $hspr > $max; | ||
print STDERR '.'; | print STDERR '.'; | ||
| Line 95: | Line 196: | ||
And here ist the resulting output: | And here ist the resulting output: | ||
[[Media:UsingTheWSInterface$test.html]] | |||
Latest revision as of 07:17, 26 October 2011
Using The Web-Services Interface
Synopsis
Web-services allow for interchange of structured data via the internet. EMMA provides a SOAP-based web-service layer to query for expression data. The server has been tested with Perl SOAP::Lite and Java Axis clients.
Available Methods
EMMA WSDL location: https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl Methods:
fetchAllProjects()
o Gets all available EMMA projects.
o Input:
--none--
o Output:
tns:ArrayOfString -- The projects
fetchAllExperiments()
o Gets all experminents in the given project.
o Input:
- xsd:string -- The project
o Output:
tns:ArrayOfString -- The experiments
fetchAllExperimentalFactorsByExperiment()
o Gets all factors associated with the given experiment in the given project.
o Input:
- xsd:string -- The project
- xsd:string -- The experiment
o Output:
tns:ArrayOfString -- The factors
fetchAllExperimentalFactorValuesByFactorAndExperiment()
o Gets all factor values for given project, experiment and factor.
o Input:
- xsd:string -- The project
- xsd:string -- The experiment
- xsd:string -- The factor
o Output:
tns:ArrayOfString -- The factor value identifiers
fetchAllReporterByName()
o Gets the valid reporter names for the given gene.
o Input:
- xsd:string -- The project
- xsd:string -- The experiment
- xsd:string -- The gene name
o Output:
tns:ArrayOfString -- The valid reporter identifiers
fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue()
o Gets the latest significant mean expression value of best quality for the given project, experiment, reporter, factor, and factor value.
o Input:
- xsd:string -- The project
- xsd:string -- The experiment
- xsd:string -- The reporter
- xsd:string -- The factor
- xsd:string -- The factor value
o Output:
xsd:double -- The M-value
fetchMultipleMvalues()
o Gets the latest significant mean expression as above but can handle a list of reporters.
o Input:
- xsd:string -- The project
- xsd:string -- The experiment
- Array of xsd:string -- The list of reporter Identifiers
- xsd:string -- The factor
- xsd:string -- The factor value
o Output:
Array of GeneMvalueStruct -- A list of GeneIDs and Mvalues
Sample Perl-client
Have a look at the a very simple :-) SOAP::Lite client written in perl.
#!/usr/bin/env perl
use strict;
use warnings;
use SOAP::Lite;
use Data::Dumper;
my $soap = SOAP::Lite->
service('https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl');
print Dumper $soap->fetchAllProjects();
print Dumper $soap->fetchAllExperiments('EMMA2.Coryne-Center');
print Dumper $soap->fetchAllReporterByName('EMMA2.Coryne-Center', 'GlucoseAcetat', "cg0001");
print Dumper $soap-> fetchAllExperimentalFactorsByExperiment ('EMMA2.Coryne-Center','GlucoseAcetat');
print Dumper $soap-> fetchAllExperimentalFactorValuesByFactorAndExperiment ('EMMA2.Coryne-Center','GlucoseAcetat','Carbon Source');
print Dumper $soap->fetchMultipleMvalues('EMMA2.Coryne-Center', 'GlucoseAcetat',['R:cg0001', 'R:cg0012'], 'Carbon Source', 'Acetat.Glucose');
Here is a more sophisticated client, that can produce a heatmap web-page for some genes of interest:
#!/usr/bin/env perl
use strict;
use Getopt::Std;
use SOAP::Lite;
use Data::Dumper;
use CGI qw/:standard/;
my $soap = SOAP::Lite->
service('https://www.cebitec.uni-bielefeld.de/groups/brf/software/emma/web_service_emma.wsdl');
my @vals = ();
my $min = my $max = 0;
print "<html><head></head><body><table><tr><th>Gene name</th><th>WT</th><th>Delta hspR (cg3097)</th></tr>";
foreach (('0001'..'0020')) {
#print "cg$_";
my $reps = $soap->fetchAllReporterByName('EMMA2:Coryne','Heat Shock',"cg$_");
next unless ref ($reps) and scalar @$reps;
my $wt = $soap->fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue('EMMA2:Coryne','Heat Shock',$reps->[0],'Strains','WT');
my $hspr = $soap->fetchLatestSignificantMeanM1WithBestQualityByExperimentAndReporterAndFactorAndFactorValue('EMMA2:Coryne','Heat Shock',$reps->[0],'Strains','Delta hspR (cg3097)');
push @vals ,["cg$_",$wt,$hspr];
$min = $wt if $wt < $min;$min = $hspr if $hspr < $min;
$max = $wt if $wt > $max; $max = $hspr if $hspr > $max;
print STDERR '.';
};
foreach (@vals)
{
my ($v1,$v2,$v3) = (@$_);
my $red1 = my $red2 = my $green1 = my $green2 = 0;
if ($max > 0) {
$red1 = ($v2 > 0)?100*$v2 /$max : 0;
$red2 = ($v3 > 0)?100*$v3 /$max : 0;
};
if ($min < 0) {
$green1 = ($v2 < 0)? 100*$v2 / $min : 0;
$green2 = ($v3 < 0)? 100*$v3 / $min : 0;
};
print qq|
<tr> <td >$v1 </td> <td style="background-color:rgb($red1%,$green1%,0%)" > <span style="color:white">$v2 </span></td> <td style="background-color:rgb($red2%,$green2%,0%)" > <span style="color:white">$v3</span>
</td></tr> |
;
}
print "</table></body></html>\n";
__END__
And here ist the resulting output: