CaCORE
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lib/CaCORE/CaBIO.pm view on Meta::CPAN
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the SNP object
# returns: a SNP object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new SNP\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this SNP intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":SNP\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" . ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# DBSNPID;
if( defined( $self->getDBSNPID ) ) {
$tmpstr = "<DBSNPID xsi:type=\"xsd:string\">" . $self->getDBSNPID . "</DBSNPID>";
} else {
$tmpstr = "<DBSNPID xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# alleleA;
if( defined( $self->getAlleleA ) ) {
$tmpstr = "<alleleA xsi:type=\"xsd:string\">" . $self->getAlleleA . "</alleleA>";
} else {
$tmpstr = "<alleleA xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# alleleB;
if( defined( $self->getAlleleB ) ) {
$tmpstr = "<alleleB xsi:type=\"xsd:string\">" . $self->getAlleleB . "</alleleB>";
} else {
$tmpstr = "<alleleB xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# validationStatus;
if( defined( $self->getValidationStatus ) ) {
$tmpstr = "<validationStatus xsi:type=\"xsd:string\">" . $self->getValidationStatus . "</validationStatus>";
} else {
$tmpstr = "<validationStatus xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of SNP objects
# param: xml doc
# returns: list of SNP objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of SNP objects
# param: xml node
# returns: a list of SNP objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one SNP object
# param: xml node
# returns: one SNP object
sub fromWSXMLNode {
my $SNPNode = $_[1];
## begin ELEMENT_NODE children ##
my $DBSNPID;
my $alleleA;
my $alleleB;
my $bigid;
my $id;
my $validationStatus;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($SNPNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "DBSNPID") {
$DBSNPID=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "alleleA") {
$alleleA=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "alleleB") {
$alleleB=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "validationStatus") {
$validationStatus=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::SNP;
## begin set attr ##
$newobj->setDBSNPID($DBSNPID);
$newobj->setAlleleA($alleleA);
$newobj->setAlleleB($alleleB);
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setValidationStatus($validationStatus);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getDBSNPID {
my $self = shift;
return $self->{DBSNPID};
}
sub setDBSNPID {
my $self = shift;
$self->{DBSNPID} = shift;
}
sub getAlleleA {
my $self = shift;
return $self->{alleleA};
}
sub setAlleleA {
my $self = shift;
$self->{alleleA} = shift;
}
sub getAlleleB {
my $self = shift;
return $self->{alleleB};
}
sub setAlleleB {
my $self = shift;
$self->{alleleB} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getValidationStatus {
my $self = shift;
return $self->{validationStatus};
}
sub setValidationStatus {
my $self = shift;
$self->{validationStatus} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getDatabaseCrossReferenceCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::Common::DatabaseCrossReference", $self);
return @results;
}
sub getGeneRelativeLocationCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GeneRelativeLocation", $self);
return @results;
}
sub getLocationCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Location", $self);
return @results;
}
sub getPopulationFrequencyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::PopulationFrequency", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Taxon;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Taxon object
# returns: a Taxon object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Taxon\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Taxon intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Taxon\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# abbreviation;
if( defined( $self->getAbbreviation ) ) {
$tmpstr = "<abbreviation xsi:type=\"xsd:string\">" . $self->getAbbreviation . "</abbreviation>";
} else {
$tmpstr = "<abbreviation xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# commonName;
if( defined( $self->getCommonName ) ) {
$tmpstr = "<commonName xsi:type=\"xsd:string\">" . $self->getCommonName . "</commonName>";
} else {
$tmpstr = "<commonName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# ethnicityStrain;
if( defined( $self->getEthnicityStrain ) ) {
$tmpstr = "<ethnicityStrain xsi:type=\"xsd:string\">" . $self->getEthnicityStrain . "</ethnicityStrain>";
} else {
$tmpstr = "<ethnicityStrain xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# scientificName;
if( defined( $self->getScientificName ) ) {
$tmpstr = "<scientificName xsi:type=\"xsd:string\">" . $self->getScientificName . "</scientificName>";
} else {
$tmpstr = "<scientificName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Taxon objects
# param: xml doc
# returns: list of Taxon objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Taxon objects
# param: xml node
# returns: a list of Taxon objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Taxon object
# param: xml node
# returns: one Taxon object
sub fromWSXMLNode {
my $TaxonNode = $_[1];
## begin ELEMENT_NODE children ##
my $abbreviation;
my $bigid;
my $commonName;
my $ethnicityStrain;
my $id;
my $scientificName;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($TaxonNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "abbreviation") {
$abbreviation=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "commonName") {
$commonName=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "ethnicityStrain") {
$ethnicityStrain=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "scientificName") {
$scientificName=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Taxon;
## begin set attr ##
$newobj->setAbbreviation($abbreviation);
$newobj->setBigid($bigid);
$newobj->setCommonName($commonName);
$newobj->setEthnicityStrain($ethnicityStrain);
$newobj->setId($id);
$newobj->setScientificName($scientificName);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getAbbreviation {
my $self = shift;
return $self->{abbreviation};
}
sub setAbbreviation {
my $self = shift;
$self->{abbreviation} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCommonName {
my $self = shift;
return $self->{commonName};
}
sub setCommonName {
my $self = shift;
$self->{commonName} = shift;
}
sub getEthnicityStrain {
my $self = shift;
return $self->{ethnicityStrain};
}
sub setEthnicityStrain {
my $self = shift;
$self->{ethnicityStrain} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getScientificName {
my $self = shift;
return $self->{scientificName};
}
sub setScientificName {
my $self = shift;
$self->{scientificName} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChromosomeCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Chromosome", $self);
return @results;
}
sub getCloneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Clone", $self);
return @results;
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Chromosome;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Chromosome object
# returns: a Chromosome object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Chromosome\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Chromosome intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Chromosome\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# number;
if( defined( $self->getNumber ) ) {
$tmpstr = "<number xsi:type=\"xsd:string\">" . $self->getNumber . "</number>";
} else {
$tmpstr = "<number xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Chromosome objects
# param: xml doc
# returns: list of Chromosome objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Chromosome objects
# param: xml node
# returns: a list of Chromosome objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Chromosome object
# param: xml node
# returns: one Chromosome object
sub fromWSXMLNode {
my $ChromosomeNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $number;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ChromosomeNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "number") {
$number=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Chromosome;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setNumber($number);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getNumber {
my $self = shift;
return $self->{number};
}
sub setNumber {
my $self = shift;
$self->{number} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return @results;
}
sub getLocationCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Location", $self);
return @results;
}
sub getTaxon {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Taxon", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Gene;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Gene object
# returns: a Gene object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Gene\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Gene intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Gene\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ....
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# clusterId;
if( defined( $self->getClusterId ) ) {
$tmpstr = "<clusterId xsi:type=\"xsd:long\">" . $self->getClusterId . "</clusterId>";
} else {
$tmpstr = "<clusterId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# fullName;
if( defined( $self->getFullName ) ) {
$tmpstr = "<fullName xsi:type=\"xsd:string\">" . $self->getFullName . "</fullName>";
} else {
$tmpstr = "<fullName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# symbol;
if( defined( $self->getSymbol ) ) {
$tmpstr = "<symbol xsi:type=\"xsd:string\">" . $self->getSymbol . "</symbol>";
} else {
$tmpstr = "<symbol xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Gene objects
# param: xml doc
# returns: list of Gene objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Gene objects
# param: xml node
# returns: a list of Gene objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Gene object
# param: xml node
# returns: one Gene object
sub fromWSXMLNode {
my $GeneNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $clusterId;
my $fullName;
my $id;
my $symbol;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GeneNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "clusterId") {
$clusterId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "fullName") {
$fullName=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "symbol") {
$symbol=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Gene;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setClusterId($clusterId);
$newobj->setFullName($fullName);
$newobj->setId($id);
$newobj->setSymbol($symbol);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getClusterId {
my $self = shift;
return $self->{clusterId};
}
sub setClusterId {
my $self = shift;
$self->{clusterId} = shift;
}
sub getFullName {
my $self = shift;
return $self->{fullName};
}
sub setFullName {
my $self = shift;
$self->{fullName} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getSymbol {
my $self = shift;
return $self->{symbol};
}
sub setSymbol {
my $self = shift;
$self->{symbol} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChromosome {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Chromosome", $self);
return $results[0];
}
sub getDatabaseCrossReferenceCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::Common::DatabaseCrossReference", $self);
return @results;
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Protocol;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Protocol object
# returns: a Protocol object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Protocol\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Protocol intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Protocol\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:n...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# description;
if( defined( $self->getDescription ) ) {
$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
} else {
$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Protocol objects
# param: xml doc
# returns: list of Protocol objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Protocol objects
# param: xml node
# returns: a list of Protocol objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Protocol object
# param: xml node
# returns: one Protocol object
sub fromWSXMLNode {
my $ProtocolNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $description;
my $id;
my $name;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ProtocolNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "description") {
$description=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Protocol;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setDescription($description);
$newobj->setId($id);
$newobj->setName($name);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getDescription {
my $self = shift;
return $self->{description};
}
sub setDescription {
my $self = shift;
$self->{description} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getLibraryCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Library", $self);
return @results;
}
sub getTissueCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Tissue", $self);
return @results;
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Library;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Library object
# returns: a Library object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Library\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Library intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Library\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# cloneProducer;
if( defined( $self->getCloneProducer ) ) {
$tmpstr = "<cloneProducer xsi:type=\"xsd:string\">" . $self->getCloneProducer . "</cloneProducer>";
} else {
$tmpstr = "<cloneProducer xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# cloneVector;
if( defined( $self->getCloneVector ) ) {
$tmpstr = "<cloneVector xsi:type=\"xsd:string\">" . $self->getCloneVector . "</cloneVector>";
} else {
$tmpstr = "<cloneVector xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# cloneVectorType;
if( defined( $self->getCloneVectorType ) ) {
$tmpstr = "<cloneVectorType xsi:type=\"xsd:string\">" . $self->getCloneVectorType . "</cloneVectorType>";
} else {
$tmpstr = "<cloneVectorType xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# clonesToDate;
if( defined( $self->getClonesToDate ) ) {
$tmpstr = "<clonesToDate xsi:type=\"xsd:long\">" . $self->getClonesToDate . "</clonesToDate>";
} else {
$tmpstr = "<clonesToDate xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# creationDate;
if( defined( $self->getCreationDate ) ) {
$tmpstr = "<creationDate xsi:type=\"xsd:dateTime\">" . $self->getCreationDate . "</creationDate>";
} else {
$tmpstr = "<creationDate xsi:type=\"xsd:dateTime\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# description;
if( defined( $self->getDescription ) ) {
$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
} else {
$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# keyword;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
$result .= $tmpstr;
# uniGeneId;
if( defined( $self->getUniGeneId ) ) {
$tmpstr = "<uniGeneId xsi:type=\"xsd:long\">" . $self->getUniGeneId . "</uniGeneId>";
} else {
$tmpstr = "<uniGeneId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Library objects
# param: xml doc
# returns: list of Library objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Library objects
# param: xml node
# returns: a list of Library objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Library object
# param: xml node
# returns: one Library object
sub fromWSXMLNode {
my $LibraryNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $cloneProducer;
my $cloneVector;
my $cloneVectorType;
my $clonesToDate;
my $creationDate;
my $description;
my $id;
my $keyword;
my $labHost;
my $name;
my $rsite1;
my $rsite2;
my $sequencesToDate;
my $type;
my $uniGeneId;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($LibraryNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "cloneProducer") {
$cloneProducer=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "cloneVector") {
$cloneVector=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "cloneVectorType") {
$cloneVectorType=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "clonesToDate") {
$clonesToDate=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "creationDate") {
$creationDate=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "description") {
$description=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "keyword") {
$keyword=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "labHost") {
$labHost=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "rsite1") {
$rsite1=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "rsite2") {
$rsite2=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "sequencesToDate") {
$sequencesToDate=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "uniGeneId") {
$uniGeneId=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Library;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setCloneProducer($cloneProducer);
$newobj->setCloneVector($cloneVector);
$newobj->setCloneVectorType($cloneVectorType);
$newobj->setClonesToDate($clonesToDate);
$newobj->setCreationDate($creationDate);
$newobj->setDescription($description);
$newobj->setId($id);
$newobj->setKeyword($keyword);
$newobj->setLabHost($labHost);
$newobj->setName($name);
$newobj->setRsite1($rsite1);
$newobj->setRsite2($rsite2);
$newobj->setSequencesToDate($sequencesToDate);
$newobj->setType($type);
$newobj->setUniGeneId($uniGeneId);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCloneProducer {
my $self = shift;
return $self->{cloneProducer};
}
sub setCloneProducer {
my $self = shift;
$self->{cloneProducer} = shift;
}
sub getCloneVector {
my $self = shift;
return $self->{cloneVector};
}
sub setCloneVector {
my $self = shift;
$self->{cloneVector} = shift;
}
sub getCloneVectorType {
my $self = shift;
return $self->{cloneVectorType};
}
sub setCloneVectorType {
my $self = shift;
$self->{cloneVectorType} = shift;
}
sub getClonesToDate {
my $self = shift;
return $self->{clonesToDate};
}
sub setClonesToDate {
my $self = shift;
$self->{clonesToDate} = shift;
}
sub getCreationDate {
my $self = shift;
return $self->{creationDate};
}
sub setCreationDate {
my $self = shift;
$self->{creationDate} = shift;
}
sub getDescription {
my $self = shift;
return $self->{description};
}
sub setDescription {
my $self = shift;
$self->{description} = shift;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Clone;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Clone object
# returns: a Clone object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Clone\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Clone intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Clone\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# insertSize;
if( defined( $self->getInsertSize ) ) {
$tmpstr = "<insertSize xsi:type=\"xsd:long\">" . $self->getInsertSize . "</insertSize>";
} else {
$tmpstr = "<insertSize xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Clone objects
# param: xml doc
# returns: list of Clone objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Clone objects
# param: xml node
# returns: a list of Clone objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Clone object
# param: xml node
# returns: one Clone object
sub fromWSXMLNode {
my $CloneNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $insertSize;
my $name;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($CloneNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "insertSize") {
$insertSize=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Clone;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setInsertSize($insertSize);
$newobj->setName($name);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getInsertSize {
my $self = shift;
return $self->{insertSize};
}
sub setInsertSize {
my $self = shift;
$self->{insertSize} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getCloneRelativeLocationCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::CloneRelativeLocation", $self);
return @results;
}
sub getLibrary {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Library", $self);
return $results[0];
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::CloneRelativeLocation;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the CloneRelativeLocation object
# returns: a CloneRelativeLocation object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new CloneRelativeLocation\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this CloneRelativeLocation intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":CloneRelativeLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodi...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of CloneRelativeLocation objects
# param: xml doc
# returns: list of CloneRelativeLocation objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of CloneRelativeLocation objects
# param: xml node
# returns: a list of CloneRelativeLocation objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one CloneRelativeLocation object
# param: xml node
# returns: one CloneRelativeLocation object
sub fromWSXMLNode {
my $CloneRelativeLocationNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($CloneRelativeLocationNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::CloneRelativeLocation;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getClone {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Clone", $self);
return $results[0];
}
sub getNucleicAcidSequence {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::NucleicAcidSequence", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::NucleicAcidSequence;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the NucleicAcidSequence object
# returns: a NucleicAcidSequence object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new NucleicAcidSequence\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this NucleicAcidSequence intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":NucleicAcidSequence\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# accessionNumber;
if( defined( $self->getAccessionNumber ) ) {
$tmpstr = "<accessionNumber xsi:type=\"xsd:string\">" . $self->getAccessionNumber . "</accessionNumber>";
} else {
$tmpstr = "<accessionNumber xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# accessionNumberVersion;
if( defined( $self->getAccessionNumberVersion ) ) {
$tmpstr = "<accessionNumberVersion xsi:type=\"xsd:string\">" . $self->getAccessionNumberVersion . "</accessionNumberVersion>";
} else {
$tmpstr = "<accessionNumberVersion xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# length;
if( defined( $self->getLength ) ) {
$tmpstr = "<length xsi:type=\"xsd:long\">" . $self->getLength . "</length>";
} else {
$tmpstr = "<length xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# value;
if( defined( $self->getValue ) ) {
$tmpstr = "<value xsi:type=\"xsd:string\">" . $self->getValue . "</value>";
} else {
$tmpstr = "<value xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of NucleicAcidSequence objects
# param: xml doc
# returns: list of NucleicAcidSequence objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of NucleicAcidSequence objects
# param: xml node
# returns: a list of NucleicAcidSequence objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one NucleicAcidSequence object
# param: xml node
# returns: one NucleicAcidSequence object
sub fromWSXMLNode {
my $NucleicAcidSequenceNode = $_[1];
## begin ELEMENT_NODE children ##
my $accessionNumber;
my $accessionNumberVersion;
my $bigid;
my $id;
my $length;
my $type;
my $value;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($NucleicAcidSequenceNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "accessionNumber") {
$accessionNumber=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "accessionNumberVersion") {
$accessionNumberVersion=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "length") {
$length=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "value") {
$value=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::NucleicAcidSequence;
## begin set attr ##
$newobj->setAccessionNumber($accessionNumber);
$newobj->setAccessionNumberVersion($accessionNumberVersion);
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setLength($length);
$newobj->setType($type);
$newobj->setValue($value);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getAccessionNumber {
my $self = shift;
return $self->{accessionNumber};
}
sub setAccessionNumber {
my $self = shift;
$self->{accessionNumber} = shift;
}
sub getAccessionNumberVersion {
my $self = shift;
return $self->{accessionNumberVersion};
}
sub setAccessionNumberVersion {
my $self = shift;
$self->{accessionNumberVersion} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getLength {
my $self = shift;
return $self->{length};
}
sub setLength {
my $self = shift;
$self->{length} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
sub getValue {
my $self = shift;
return $self->{value};
}
sub setValue {
my $self = shift;
$self->{value} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getCloneRelativeLocation {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::CloneRelativeLocation", $self);
return $results[0];
}
sub getDatabaseCrossReferenceCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::Common::DatabaseCrossReference", $self);
return @results;
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::DiseaseOntology;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the DiseaseOntology object
# returns: a DiseaseOntology object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new DiseaseOntology\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this DiseaseOntology intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":DiseaseOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of DiseaseOntology objects
# param: xml doc
# returns: list of DiseaseOntology objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of DiseaseOntology objects
# param: xml node
# returns: a list of DiseaseOntology objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one DiseaseOntology object
# param: xml node
# returns: one DiseaseOntology object
sub fromWSXMLNode {
my $DiseaseOntologyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($DiseaseOntologyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::DiseaseOntology;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChildDiseaseOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::DiseaseOntologyRelationship", $self);
return @results;
}
sub getClinicalTrialProtocolCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::ClinicalTrialProtocol", $self);
return @results;
}
sub getHistopathologyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Histopathology", $self);
return @results;
}
sub getParentDiseaseOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::DiseaseOntologyRelationship", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GeneRelativeLocation;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GeneRelativeLocation object
# returns: a GeneRelativeLocation object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GeneRelativeLocation\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GeneRelativeLocation intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneRelativeLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodin...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GeneRelativeLocation objects
# param: xml doc
# returns: list of GeneRelativeLocation objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GeneRelativeLocation objects
# param: xml node
# returns: a list of GeneRelativeLocation objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GeneRelativeLocation object
# param: xml node
# returns: one GeneRelativeLocation object
sub fromWSXMLNode {
my $GeneRelativeLocationNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GeneRelativeLocationNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GeneRelativeLocation;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::PopulationFrequency;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the PopulationFrequency object
# returns: a PopulationFrequency object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new PopulationFrequency\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this PopulationFrequency intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":PopulationFrequency\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# ethnicity;
if( defined( $self->getEthnicity ) ) {
$tmpstr = "<ethnicity xsi:type=\"xsd:string\">" . $self->getEthnicity . "</ethnicity>";
} else {
$tmpstr = "<ethnicity xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# majorAllele;
if( defined( $self->getMajorAllele ) ) {
$tmpstr = "<majorAllele xsi:type=\"xsd:string\">" . $self->getMajorAllele . "</majorAllele>";
} else {
$tmpstr = "<majorAllele xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# majorFrequency;
if( defined( $self->getMajorFrequency ) ) {
$tmpstr = "<majorFrequency xsi:type=\"xsd:double\">" . $self->getMajorFrequency . "</majorFrequency>";
} else {
$tmpstr = "<majorFrequency xsi:type=\"xsd:double\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# minorAllele;
if( defined( $self->getMinorAllele ) ) {
$tmpstr = "<minorAllele xsi:type=\"xsd:string\">" . $self->getMinorAllele . "</minorAllele>";
} else {
$tmpstr = "<minorAllele xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# minorFrequency;
if( defined( $self->getMinorFrequency ) ) {
$tmpstr = "<minorFrequency xsi:type=\"xsd:double\">" . $self->getMinorFrequency . "</minorFrequency>";
} else {
$tmpstr = "<minorFrequency xsi:type=\"xsd:double\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of PopulationFrequency objects
# param: xml doc
# returns: list of PopulationFrequency objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of PopulationFrequency objects
# param: xml node
# returns: a list of PopulationFrequency objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one PopulationFrequency object
# param: xml node
# returns: one PopulationFrequency object
sub fromWSXMLNode {
my $PopulationFrequencyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $ethnicity;
my $id;
my $majorAllele;
my $majorFrequency;
my $minorAllele;
my $minorFrequency;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($PopulationFrequencyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "ethnicity") {
$ethnicity=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "majorAllele") {
$majorAllele=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "majorFrequency") {
$majorFrequency=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "minorAllele") {
$minorAllele=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "minorFrequency") {
$minorFrequency=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::PopulationFrequency;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setEthnicity($ethnicity);
$newobj->setId($id);
$newobj->setMajorAllele($majorAllele);
$newobj->setMajorFrequency($majorFrequency);
$newobj->setMinorAllele($minorAllele);
$newobj->setMinorFrequency($minorFrequency);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getEthnicity {
my $self = shift;
return $self->{ethnicity};
}
sub setEthnicity {
my $self = shift;
$self->{ethnicity} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getMajorAllele {
my $self = shift;
return $self->{majorAllele};
}
sub setMajorAllele {
my $self = shift;
$self->{majorAllele} = shift;
}
sub getMajorFrequency {
my $self = shift;
return $self->{majorFrequency};
}
sub setMajorFrequency {
my $self = shift;
$self->{majorFrequency} = shift;
}
sub getMinorAllele {
my $self = shift;
return $self->{minorAllele};
}
sub setMinorAllele {
my $self = shift;
$self->{minorAllele} = shift;
}
sub getMinorFrequency {
my $self = shift;
return $self->{minorFrequency};
}
sub setMinorFrequency {
my $self = shift;
$self->{minorFrequency} = shift;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::HomologousAssociation;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the HomologousAssociation object
# returns: a HomologousAssociation object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new HomologousAssociation\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this HomologousAssociation intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":HomologousAssociation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodi...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# homologousId;
if( defined( $self->getHomologousId ) ) {
$tmpstr = "<homologousId xsi:type=\"xsd:long\">" . $self->getHomologousId . "</homologousId>";
} else {
$tmpstr = "<homologousId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# similarityPercentage;
if( defined( $self->getSimilarityPercentage ) ) {
$tmpstr = "<similarityPercentage xsi:type=\"xsd:float\">" . $self->getSimilarityPercentage . "</similarityPercentage>";
} else {
$tmpstr = "<similarityPercentage xsi:type=\"xsd:float\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of HomologousAssociation objects
# param: xml doc
# returns: list of HomologousAssociation objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of HomologousAssociation objects
# param: xml node
# returns: a list of HomologousAssociation objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one HomologousAssociation object
# param: xml node
# returns: one HomologousAssociation object
sub fromWSXMLNode {
my $HomologousAssociationNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $homologousId;
my $id;
my $similarityPercentage;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($HomologousAssociationNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "homologousId") {
$homologousId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "similarityPercentage") {
$similarityPercentage=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::HomologousAssociation;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setHomologousId($homologousId);
$newobj->setId($id);
$newobj->setSimilarityPercentage($similarityPercentage);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getHomologousId {
my $self = shift;
return $self->{homologousId};
}
sub setHomologousId {
my $self = shift;
$self->{homologousId} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getSimilarityPercentage {
my $self = shift;
return $self->{similarityPercentage};
}
sub setSimilarityPercentage {
my $self = shift;
$self->{similarityPercentage} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getHomologousGene {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Cytoband;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Cytoband object
# returns: a Cytoband object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Cytoband\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Cytoband intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Cytoband\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:n...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Cytoband objects
# param: xml doc
# returns: list of Cytoband objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Cytoband objects
# param: xml node
# returns: a list of Cytoband objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Cytoband object
# param: xml node
# returns: one Cytoband object
sub fromWSXMLNode {
my $CytobandNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($CytobandNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Cytoband;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getPhysicalLocation {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::PhysicalLocation", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GeneOntology;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GeneOntology object
# returns: a GeneOntology object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GeneOntology\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GeneOntology intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xml...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GeneOntology objects
# param: xml doc
# returns: list of GeneOntology objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GeneOntology objects
# param: xml node
# returns: a list of GeneOntology objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GeneOntology object
# param: xml node
# returns: one GeneOntology object
sub fromWSXMLNode {
my $GeneOntologyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GeneOntologyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GeneOntology;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChildGeneOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GeneOntologyRelationship", $self);
return @results;
}
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return @results;
}
sub getParentGeneOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GeneOntologyRelationship", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::OrganOntology;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the OrganOntology object
# returns: a OrganOntology object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new OrganOntology\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this OrganOntology intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":OrganOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xm...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of OrganOntology objects
# param: xml doc
# returns: list of OrganOntology objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of OrganOntology objects
# param: xml node
# returns: a list of OrganOntology objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one OrganOntology object
# param: xml node
# returns: one OrganOntology object
sub fromWSXMLNode {
my $OrganOntologyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($OrganOntologyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::OrganOntology;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getAnomalyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Anomaly", $self);
return @results;
}
sub getChildOrganOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::OrganOntologyRelationship", $self);
return @results;
}
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return @results;
}
sub getHistopathologyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Histopathology", $self);
return @results;
}
sub getParentOrganOntologyRelationshipCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::OrganOntologyRelationship", $self);
return @results;
}
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::ProteinSequence;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the ProteinSequence object
# returns: a ProteinSequence object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new ProteinSequence\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this ProteinSequence intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ProteinSequence\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# checkSum;
if( defined( $self->getCheckSum ) ) {
$tmpstr = "<checkSum xsi:type=\"xsd:string\">" . $self->getCheckSum . "</checkSum>";
} else {
$tmpstr = "<checkSum xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# length;
if( defined( $self->getLength ) ) {
$tmpstr = "<length xsi:type=\"xsd:long\">" . $self->getLength . "</length>";
} else {
$tmpstr = "<length xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# molecularWeightInDaltons;
if( defined( $self->getMolecularWeightInDaltons ) ) {
$tmpstr = "<molecularWeightInDaltons xsi:type=\"xsd:double\">" . $self->getMolecularWeightInDaltons . "</molecularWeightInDaltons>";
} else {
$tmpstr = "<molecularWeightInDaltons xsi:type=\"xsd:double\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# value;
if( defined( $self->getValue ) ) {
$tmpstr = "<value xsi:type=\"xsd:string\">" . $self->getValue . "</value>";
} else {
$tmpstr = "<value xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of ProteinSequence objects
# param: xml doc
# returns: list of ProteinSequence objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of ProteinSequence objects
# param: xml node
# returns: a list of ProteinSequence objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one ProteinSequence object
# param: xml node
# returns: one ProteinSequence object
sub fromWSXMLNode {
my $ProteinSequenceNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $checkSum;
my $id;
my $length;
my $molecularWeightInDaltons;
my $value;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ProteinSequenceNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "checkSum") {
$checkSum=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "length") {
$length=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "molecularWeightInDaltons") {
$molecularWeightInDaltons=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "value") {
$value=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::ProteinSequence;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setCheckSum($checkSum);
$newobj->setId($id);
$newobj->setLength($length);
$newobj->setMolecularWeightInDaltons($molecularWeightInDaltons);
$newobj->setValue($value);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCheckSum {
my $self = shift;
return $self->{checkSum};
}
sub setCheckSum {
my $self = shift;
$self->{checkSum} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getLength {
my $self = shift;
return $self->{length};
}
sub setLength {
my $self = shift;
$self->{length} = shift;
}
sub getMolecularWeightInDaltons {
my $self = shift;
return $self->{molecularWeightInDaltons};
}
sub setMolecularWeightInDaltons {
my $self = shift;
$self->{molecularWeightInDaltons} = shift;
}
sub getValue {
my $self = shift;
return $self->{value};
}
sub setValue {
my $self = shift;
$self->{value} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getProtein {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Protein", $self);
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Protein;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Protein object
# returns: a Protein object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Protein\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Protein intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Protein\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# copyrightStatement;
if( defined( $self->getCopyrightStatement ) ) {
$tmpstr = "<copyrightStatement xsi:type=\"xsd:string\">" . $self->getCopyrightStatement . "</copyrightStatement>";
} else {
$tmpstr = "<copyrightStatement xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# primaryAccession;
if( defined( $self->getPrimaryAccession ) ) {
$tmpstr = "<primaryAccession xsi:type=\"xsd:string\">" . $self->getPrimaryAccession . "</primaryAccession>";
} else {
$tmpstr = "<primaryAccession xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# uniProtCode;
if( defined( $self->getUniProtCode ) ) {
$tmpstr = "<uniProtCode xsi:type=\"xsd:string\">" . $self->getUniProtCode . "</uniProtCode>";
} else {
$tmpstr = "<uniProtCode xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
# KeywordsCollection;
if( defined( $self->getKeywordsCollection ) ) {
my @assoclist = $self->getKeywordsCollection;
if( $#assoclist >= 0 ) {
$result .= "<keywordsCollection>";
foreach my $node ($self->getKeywordsCollection) {
$result .= "<keywordsCollection xsi:type=\"xsd:string\"> . $node . </keywordsCollection>";
}
$result .= "</keywordsCollection>";
}
}
# SecondaryAccessionCollection;
if( defined( $self->getSecondaryAccessionCollection ) ) {
my @assoclist = $self->getSecondaryAccessionCollection;
if( $#assoclist >= 0 ) {
$result .= "<secondaryAccessionCollection>";
foreach my $node ($self->getSecondaryAccessionCollection) {
$result .= "<secondaryAccessionCollection xsi:type=\"xsd:string\"> . $node . </secondaryAccessionCollection>";
}
$result .= "</secondaryAccessionCollection>";
}
}
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Protein objects
# param: xml doc
# returns: list of Protein objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Protein objects
# param: xml node
# returns: a list of Protein objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Protein object
# param: xml node
# returns: one Protein object
sub fromWSXMLNode {
my $ProteinNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $copyrightStatement;
my $id;
my $name;
my $primaryAccession;
my $uniProtCode;
my @keywords = ();
my @secondaryAccession = ();
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ProteinNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "copyrightStatement") {
$copyrightStatement=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "primaryAccession") {
$primaryAccession=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "uniProtCode") {
$uniProtCode=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "keywords") {
for my $node ($childrenNode->getChildNodes) {
if( $node->getNodeName eq "empty" ){ next; };
if( ! defined($node->getFirstChild) ){ next; };
my $txnode = $node->getFirstChild;
push @keywords, $txnode->getNodeValue;
}
}
elsif ($childrenNode->getNodeName eq "secondaryAccession") {
for my $node ($childrenNode->getChildNodes) {
if( $node->getNodeName eq "empty" ){ next; };
if( ! defined($node->getFirstChild) ){ next; };
my $txnode = $node->getFirstChild;
push @secondaryAccession, $txnode->getNodeValue;
}
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Protein;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setCopyrightStatement($copyrightStatement);
$newobj->setId($id);
$newobj->setName($name);
$newobj->setPrimaryAccession($primaryAccession);
$newobj->setUniProtCode($uniProtCode);
$newobj->setKeywordsCollection(@keywords);
$newobj->setSecondaryAccessionCollection(@secondaryAccession);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCopyrightStatement {
my $self = shift;
return $self->{copyrightStatement};
}
sub setCopyrightStatement {
my $self = shift;
$self->{copyrightStatement} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getPrimaryAccession {
my $self = shift;
return $self->{primaryAccession};
}
sub setPrimaryAccession {
my $self = shift;
$self->{primaryAccession} = shift;
}
sub getUniProtCode {
my $self = shift;
return $self->{uniProtCode};
}
sub setUniProtCode {
my $self = shift;
$self->{uniProtCode} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::ProteinAlias;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the ProteinAlias object
# returns: a ProteinAlias object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new ProteinAlias\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this ProteinAlias intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ProteinAlias\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xml...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of ProteinAlias objects
# param: xml doc
# returns: list of ProteinAlias objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of ProteinAlias objects
# param: xml node
# returns: a list of ProteinAlias objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one ProteinAlias object
# param: xml node
# returns: one ProteinAlias object
sub fromWSXMLNode {
my $ProteinAliasNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ProteinAliasNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::ProteinAlias;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getProteinCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Protein", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Target;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Target object
# returns: a Target object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Target\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Target intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Target\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns"...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Target objects
# param: xml doc
# returns: list of Target objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Target objects
# param: xml node
# returns: a list of Target objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Target object
# param: xml node
# returns: one Target object
sub fromWSXMLNode {
my $TargetNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($TargetNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Target;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getAgentCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Agent", $self);
return @results;
}
sub getAnomalyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Anomaly", $self);
return @results;
}
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GeneAlias;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GeneAlias object
# returns: a GeneAlias object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GeneAlias\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GeneAlias intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneAlias\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GeneAlias objects
# param: xml doc
# returns: list of GeneAlias objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GeneAlias objects
# param: xml node
# returns: a list of GeneAlias objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GeneAlias object
# param: xml node
# returns: one GeneAlias object
sub fromWSXMLNode {
my $GeneAliasNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GeneAliasNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GeneAlias;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GenericArray;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GenericArray object
# returns: a GenericArray object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GenericArray\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GenericArray intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GenericArray\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xml...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# arrayName;
if( defined( $self->getArrayName ) ) {
$tmpstr = "<arrayName xsi:type=\"xsd:string\">" . $self->getArrayName . "</arrayName>";
} else {
$tmpstr = "<arrayName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# platform;
if( defined( $self->getPlatform ) ) {
$tmpstr = "<platform xsi:type=\"xsd:string\">" . $self->getPlatform . "</platform>";
} else {
$tmpstr = "<platform xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GenericArray objects
# param: xml doc
# returns: list of GenericArray objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GenericArray objects
# param: xml node
# returns: a list of GenericArray objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GenericArray object
# param: xml node
# returns: one GenericArray object
sub fromWSXMLNode {
my $GenericArrayNode = $_[1];
## begin ELEMENT_NODE children ##
my $arrayName;
my $bigid;
my $id;
my $platform;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GenericArrayNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "arrayName") {
$arrayName=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "platform") {
$platform=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GenericArray;
## begin set attr ##
$newobj->setArrayName($arrayName);
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setPlatform($platform);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getArrayName {
my $self = shift;
return $self->{arrayName};
}
sub setArrayName {
my $self = shift;
$self->{arrayName} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getPlatform {
my $self = shift;
return $self->{platform};
}
sub setPlatform {
my $self = shift;
$self->{platform} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGenericReporterCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GenericReporter", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Vocabulary;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Vocabulary object
# returns: a Vocabulary object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Vocabulary\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Vocabulary intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Vocabulary\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# coreTerm;
if( defined( $self->getCoreTerm ) ) {
$tmpstr = "<coreTerm xsi:type=\"xsd:string\">" . $self->getCoreTerm . "</coreTerm>";
} else {
$tmpstr = "<coreTerm xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# generalTerm;
if( defined( $self->getGeneralTerm ) ) {
$tmpstr = "<generalTerm xsi:type=\"xsd:string\">" . $self->getGeneralTerm . "</generalTerm>";
} else {
$tmpstr = "<generalTerm xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Vocabulary objects
# param: xml doc
# returns: list of Vocabulary objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Vocabulary objects
# param: xml node
# returns: a list of Vocabulary objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Vocabulary object
# param: xml node
# returns: one Vocabulary object
sub fromWSXMLNode {
my $VocabularyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $coreTerm;
my $generalTerm;
my $id;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($VocabularyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "coreTerm") {
$coreTerm=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "generalTerm") {
$generalTerm=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Vocabulary;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setCoreTerm($coreTerm);
$newobj->setGeneralTerm($generalTerm);
$newobj->setId($id);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCoreTerm {
my $self = shift;
return $self->{coreTerm};
}
sub setCoreTerm {
my $self = shift;
$self->{coreTerm} = shift;
}
sub getGeneralTerm {
my $self = shift;
return $self->{generalTerm};
}
sub setGeneralTerm {
my $self = shift;
$self->{generalTerm} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getAnomalyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Anomaly", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::OrganOntologyRelationship;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the OrganOntologyRelationship object
# returns: a OrganOntologyRelationship object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new OrganOntologyRelationship\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this OrganOntologyRelationship intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":OrganOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/en...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of OrganOntologyRelationship objects
# param: xml doc
# returns: list of OrganOntologyRelationship objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of OrganOntologyRelationship objects
# param: xml node
# returns: a list of OrganOntologyRelationship objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one OrganOntologyRelationship object
# param: xml node
# returns: one OrganOntologyRelationship object
sub fromWSXMLNode {
my $OrganOntologyRelationshipNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($OrganOntologyRelationshipNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::OrganOntologyRelationship;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChildOrganOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::OrganOntology", $self);
return $results[0];
}
sub getParentOrganOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::OrganOntology", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Anomaly;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Anomaly object
# returns: a Anomaly object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Anomaly\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Anomaly intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Anomaly\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# description;
if( defined( $self->getDescription ) ) {
$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
} else {
$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Anomaly objects
# param: xml doc
# returns: list of Anomaly objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Anomaly objects
# param: xml node
# returns: a list of Anomaly objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Anomaly object
# param: xml node
# returns: one Anomaly object
sub fromWSXMLNode {
my $AnomalyNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $description;
my $id;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($AnomalyNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "description") {
$description=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Anomaly;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setDescription($description);
$newobj->setId($id);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getDescription {
my $self = shift;
return $self->{description};
}
sub setDescription {
my $self = shift;
$self->{description} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getHistopathology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Histopathology", $self);
return $results[0];
}
sub getOrganOntologyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::OrganOntology", $self);
return @results;
}
sub getVocabularyCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Vocabulary", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Agent;
use 5.005;
#use strict;
use warnings;
require Exporter;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Agent object
# returns: a Agent object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Agent\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Agent intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Agent\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# EVSId;
if( defined( $self->getEVSId ) ) {
$tmpstr = "<EVSId xsi:type=\"xsd:string\">" . $self->getEVSId . "</EVSId>";
} else {
$tmpstr = "<EVSId xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# NSCNumber;
if( defined( $self->getNSCNumber ) ) {
$tmpstr = "<NSCNumber xsi:type=\"xsd:long\">" . $self->getNSCNumber . "</NSCNumber>";
} else {
$tmpstr = "<NSCNumber xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# comment;
if( defined( $self->getComment ) ) {
$tmpstr = "<comment xsi:type=\"xsd:string\">" . $self->getComment . "</comment>";
} else {
$tmpstr = "<comment xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# isCMAPAgent;
if( defined( $self->getIsCMAPAgent ) ) {
$tmpstr = "<isCMAPAgent xsi:type=\"xsd:boolean\">" . $self->getIsCMAPAgent . "</isCMAPAgent>";
} else {
$tmpstr = "<isCMAPAgent xsi:type=\"xsd:boolean\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# source;
if( defined( $self->getSource ) ) {
$tmpstr = "<source xsi:type=\"xsd:string\">" . $self->getSource . "</source>";
} else {
$tmpstr = "<source xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Agent objects
# param: xml doc
# returns: list of Agent objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Agent objects
# param: xml node
# returns: a list of Agent objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Agent object
# param: xml node
# returns: one Agent object
sub fromWSXMLNode {
my $AgentNode = $_[1];
## begin ELEMENT_NODE children ##
my $EVSId;
my $NSCNumber;
my $bigid;
my $comment;
my $id;
my $isCMAPAgent;
my $name;
my $source;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($AgentNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "EVSId") {
$EVSId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "NSCNumber") {
$NSCNumber=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "comment") {
$comment=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "isCMAPAgent") {
$isCMAPAgent=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "source") {
$source=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Agent;
## begin set attr ##
$newobj->setEVSId($EVSId);
$newobj->setNSCNumber($NSCNumber);
$newobj->setBigid($bigid);
$newobj->setComment($comment);
$newobj->setId($id);
$newobj->setIsCMAPAgent($isCMAPAgent);
$newobj->setName($name);
$newobj->setSource($source);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getEVSId {
my $self = shift;
return $self->{EVSId};
}
sub setEVSId {
my $self = shift;
$self->{EVSId} = shift;
}
sub getNSCNumber {
my $self = shift;
return $self->{NSCNumber};
}
sub setNSCNumber {
my $self = shift;
$self->{NSCNumber} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getComment {
my $self = shift;
return $self->{comment};
}
sub setComment {
my $self = shift;
$self->{comment} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getIsCMAPAgent {
my $self = shift;
return $self->{isCMAPAgent};
}
sub setIsCMAPAgent {
my $self = shift;
$self->{isCMAPAgent} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getSource {
my $self = shift;
return $self->{source};
}
sub setSource {
my $self = shift;
$self->{source} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getClinicalTrialProtocolCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::ClinicalTrialProtocol", $self);
lib/CaCORE/CaBIO.pm view on Meta::CPAN
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the ClinicalTrialProtocol object
# returns: a ClinicalTrialProtocol object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new ClinicalTrialProtocol\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this ClinicalTrialProtocol intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ClinicalTrialProtocol\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodi...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# NIHAdminCode;
if( defined( $self->getNIHAdminCode ) ) {
$tmpstr = "<NIHAdminCode xsi:type=\"xsd:string\">" . $self->getNIHAdminCode . "</NIHAdminCode>";
} else {
$tmpstr = "<NIHAdminCode xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# PDQIdentifier;
if( defined( $self->getPDQIdentifier ) ) {
$tmpstr = "<PDQIdentifier xsi:type=\"xsd:string\">" . $self->getPDQIdentifier . "</PDQIdentifier>";
} else {
$tmpstr = "<PDQIdentifier xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# PIName;
if( defined( $self->getPIName ) ) {
$tmpstr = "<PIName xsi:type=\"xsd:string\">" . $self->getPIName . "</PIName>";
} else {
$tmpstr = "<PIName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# currentStatus;
if( defined( $self->getCurrentStatus ) ) {
$tmpstr = "<currentStatus xsi:type=\"xsd:string\">" . $self->getCurrentStatus . "</currentStatus>";
} else {
$tmpstr = "<currentStatus xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# currentStatusDate;
if( defined( $self->getCurrentStatusDate ) ) {
$tmpstr = "<currentStatusDate xsi:type=\"xsd:dateTime\">" . $self->getCurrentStatusDate . "</currentStatusDate>";
} else {
$tmpstr = "<currentStatusDate xsi:type=\"xsd:dateTime\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# documentNumber;
if( defined( $self->getDocumentNumber ) ) {
$tmpstr = "<documentNumber xsi:type=\"xsd:string\">" . $self->getDocumentNumber . "</documentNumber>";
} else {
$tmpstr = "<documentNumber xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# leadOrganizationId;
if( defined( $self->getLeadOrganizationId ) ) {
$tmpstr = "<leadOrganizationId xsi:type=\"xsd:string\">" . $self->getLeadOrganizationId . "</leadOrganizationId>";
} else {
$tmpstr = "<leadOrganizationId xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# leadOrganizationName;
if( defined( $self->getLeadOrganizationName ) ) {
$tmpstr = "<leadOrganizationName xsi:type=\"xsd:string\">" . $self->getLeadOrganizationName . "</leadOrganizationName>";
} else {
$tmpstr = "<leadOrganizationName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# participationType;
if( defined( $self->getParticipationType ) ) {
$tmpstr = "<participationType xsi:type=\"xsd:string\">" . $self->getParticipationType . "</participationType>";
} else {
$tmpstr = "<participationType xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# phase;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
# treatmentFlag;
if( defined( $self->getTreatmentFlag ) ) {
$tmpstr = "<treatmentFlag xsi:type=\"xsd:string\">" . $self->getTreatmentFlag . "</treatmentFlag>";
} else {
$tmpstr = "<treatmentFlag xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of ClinicalTrialProtocol objects
# param: xml doc
# returns: list of ClinicalTrialProtocol objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of ClinicalTrialProtocol objects
# param: xml node
# returns: a list of ClinicalTrialProtocol objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one ClinicalTrialProtocol object
# param: xml node
# returns: one ClinicalTrialProtocol object
sub fromWSXMLNode {
my $ClinicalTrialProtocolNode = $_[1];
## begin ELEMENT_NODE children ##
my $NIHAdminCode;
my $PDQIdentifier;
my $PIName;
my $bigid;
my $currentStatus;
my $currentStatusDate;
my $documentNumber;
my $id;
my $leadOrganizationId;
my $leadOrganizationName;
my $participationType;
my $phase;
my $title;
my $treatmentFlag;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ClinicalTrialProtocolNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "NIHAdminCode") {
$NIHAdminCode=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "PDQIdentifier") {
$PDQIdentifier=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "PIName") {
$PIName=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "currentStatus") {
$currentStatus=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "currentStatusDate") {
$currentStatusDate=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "documentNumber") {
$documentNumber=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "leadOrganizationId") {
$leadOrganizationId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "leadOrganizationName") {
$leadOrganizationName=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "participationType") {
$participationType=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "phase") {
$phase=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "title") {
$title=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "treatmentFlag") {
$treatmentFlag=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::ClinicalTrialProtocol;
## begin set attr ##
$newobj->setNIHAdminCode($NIHAdminCode);
$newobj->setPDQIdentifier($PDQIdentifier);
$newobj->setPIName($PIName);
$newobj->setBigid($bigid);
$newobj->setCurrentStatus($currentStatus);
$newobj->setCurrentStatusDate($currentStatusDate);
$newobj->setDocumentNumber($documentNumber);
$newobj->setId($id);
$newobj->setLeadOrganizationId($leadOrganizationId);
$newobj->setLeadOrganizationName($leadOrganizationName);
$newobj->setParticipationType($participationType);
$newobj->setPhase($phase);
$newobj->setTitle($title);
$newobj->setTreatmentFlag($treatmentFlag);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getNIHAdminCode {
my $self = shift;
return $self->{NIHAdminCode};
}
sub setNIHAdminCode {
my $self = shift;
$self->{NIHAdminCode} = shift;
}
sub getPDQIdentifier {
my $self = shift;
return $self->{PDQIdentifier};
}
sub setPDQIdentifier {
my $self = shift;
$self->{PDQIdentifier} = shift;
}
sub getPIName {
my $self = shift;
return $self->{PIName};
}
sub setPIName {
my $self = shift;
$self->{PIName} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getCurrentStatus {
my $self = shift;
return $self->{currentStatus};
}
sub setCurrentStatus {
my $self = shift;
$self->{currentStatus} = shift;
}
sub getCurrentStatusDate {
my $self = shift;
return $self->{currentStatusDate};
}
sub setCurrentStatusDate {
my $self = shift;
$self->{currentStatusDate} = shift;
}
sub getDocumentNumber {
my $self = shift;
return $self->{documentNumber};
}
sub setDocumentNumber {
my $self = shift;
$self->{documentNumber} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getLeadOrganizationId {
my $self = shift;
return $self->{leadOrganizationId};
}
sub setLeadOrganizationId {
my $self = shift;
$self->{leadOrganizationId} = shift;
}
sub getLeadOrganizationName {
my $self = shift;
return $self->{leadOrganizationName};
}
sub setLeadOrganizationName {
my $self = shift;
$self->{leadOrganizationName} = shift;
lib/CaCORE/CaBIO.pm view on Meta::CPAN
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the ProtocolAssociation object
# returns: a ProtocolAssociation object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new ProtocolAssociation\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this ProtocolAssociation intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ProtocolAssociation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# CTEPNAME;
if( defined( $self->getCTEPNAME ) ) {
$tmpstr = "<CTEPNAME xsi:type=\"xsd:string\">" . $self->getCTEPNAME . "</CTEPNAME>";
} else {
$tmpstr = "<CTEPNAME xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# IMTCODE;
if( defined( $self->getIMTCODE ) ) {
$tmpstr = "<IMTCODE xsi:type=\"xsd:long\">" . $self->getIMTCODE . "</IMTCODE>";
} else {
$tmpstr = "<IMTCODE xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# diseaseCategory;
if( defined( $self->getDiseaseCategory ) ) {
$tmpstr = "<diseaseCategory xsi:type=\"xsd:string\">" . $self->getDiseaseCategory . "</diseaseCategory>";
} else {
$tmpstr = "<diseaseCategory xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# diseaseSubCategory;
if( defined( $self->getDiseaseSubCategory ) ) {
$tmpstr = "<diseaseSubCategory xsi:type=\"xsd:string\">" . $self->getDiseaseSubCategory . "</diseaseSubCategory>";
} else {
$tmpstr = "<diseaseSubCategory xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of ProtocolAssociation objects
# param: xml doc
# returns: list of ProtocolAssociation objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of ProtocolAssociation objects
# param: xml node
# returns: a list of ProtocolAssociation objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one ProtocolAssociation object
# param: xml node
# returns: one ProtocolAssociation object
sub fromWSXMLNode {
my $ProtocolAssociationNode = $_[1];
## begin ELEMENT_NODE children ##
my $CTEPNAME;
my $IMTCODE;
my $bigid;
my $diseaseCategory;
my $diseaseSubCategory;
my $id;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($ProtocolAssociationNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "CTEPNAME") {
$CTEPNAME=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "IMTCODE") {
$IMTCODE=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "diseaseCategory") {
$diseaseCategory=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "diseaseSubCategory") {
$diseaseSubCategory=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::ProtocolAssociation;
## begin set attr ##
$newobj->setCTEPNAME($CTEPNAME);
$newobj->setIMTCODE($IMTCODE);
$newobj->setBigid($bigid);
$newobj->setDiseaseCategory($diseaseCategory);
$newobj->setDiseaseSubCategory($diseaseSubCategory);
$newobj->setId($id);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getCTEPNAME {
my $self = shift;
return $self->{CTEPNAME};
}
sub setCTEPNAME {
my $self = shift;
$self->{CTEPNAME} = shift;
}
sub getIMTCODE {
my $self = shift;
return $self->{IMTCODE};
}
sub setIMTCODE {
my $self = shift;
$self->{IMTCODE} = shift;
}
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getDiseaseCategory {
my $self = shift;
return $self->{diseaseCategory};
}
sub setDiseaseCategory {
my $self = shift;
$self->{diseaseCategory} = shift;
}
sub getDiseaseSubCategory {
my $self = shift;
return $self->{diseaseSubCategory};
}
sub setDiseaseSubCategory {
my $self = shift;
$self->{diseaseSubCategory} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getClinicalTrialProtocol {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::ClinicalTrialProtocol", $self);
return $results[0];
}
sub getDiseaseOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::DiseaseOntology", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GeneOntologyRelationship;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GeneOntologyRelationship object
# returns: a GeneOntologyRelationship object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GeneOntologyRelationship\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GeneOntologyRelationship intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/enc...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# relationshipType;
if( defined( $self->getRelationshipType ) ) {
$tmpstr = "<relationshipType xsi:type=\"xsd:string\">" . $self->getRelationshipType . "</relationshipType>";
} else {
$tmpstr = "<relationshipType xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GeneOntologyRelationship objects
# param: xml doc
# returns: list of GeneOntologyRelationship objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GeneOntologyRelationship objects
# param: xml node
# returns: a list of GeneOntologyRelationship objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GeneOntologyRelationship object
# param: xml node
# returns: one GeneOntologyRelationship object
sub fromWSXMLNode {
my $GeneOntologyRelationshipNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $relationshipType;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GeneOntologyRelationshipNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "relationshipType") {
$relationshipType=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GeneOntologyRelationship;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setRelationshipType($relationshipType);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getRelationshipType {
my $self = shift;
return $self->{relationshipType};
}
sub setRelationshipType {
my $self = shift;
$self->{relationshipType} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChildGeneOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GeneOntology", $self);
return $results[0];
}
sub getParentGeneOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GeneOntology", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::GenericReporter;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the GenericReporter object
# returns: a GenericReporter object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new GenericReporter\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this GenericReporter intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GenericReporter\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of GenericReporter objects
# param: xml doc
# returns: list of GenericReporter objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of GenericReporter objects
# param: xml node
# returns: a list of GenericReporter objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one GenericReporter object
# param: xml node
# returns: one GenericReporter object
sub fromWSXMLNode {
my $GenericReporterNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $name;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($GenericReporterNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::GenericReporter;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setName($name);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGene {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return $results[0];
}
sub getGenericArrayCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::GenericArray", $self);
return @results;
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::Pathway;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the Pathway object
# returns: a Pathway object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new Pathway\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this Pathway intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Pathway\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# description;
if( defined( $self->getDescription ) ) {
$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
} else {
$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# diagram;
if( defined( $self->getDiagram ) ) {
$tmpstr = "<diagram xsi:type=\"xsd:string\">" . $self->getDiagram . "</diagram>";
} else {
$tmpstr = "<diagram xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# displayValue;
if( defined( $self->getDisplayValue ) ) {
$tmpstr = "<displayValue xsi:type=\"xsd:string\">" . $self->getDisplayValue . "</displayValue>";
} else {
$tmpstr = "<displayValue xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# name;
if( defined( $self->getName ) ) {
$tmpstr = "<name xsi:type=\"xsd:string\">" . $self->getName . "</name>";
} else {
$tmpstr = "<name xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of Pathway objects
# param: xml doc
# returns: list of Pathway objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of Pathway objects
# param: xml node
# returns: a list of Pathway objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one Pathway object
# param: xml node
# returns: one Pathway object
sub fromWSXMLNode {
my $PathwayNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $description;
my $diagram;
my $displayValue;
my $id;
my $name;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($PathwayNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "description") {
$description=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "diagram") {
$diagram=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "displayValue") {
$displayValue=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "name") {
$name=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::Pathway;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setDescription($description);
$newobj->setDiagram($diagram);
$newobj->setDisplayValue($displayValue);
$newobj->setId($id);
$newobj->setName($name);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getDescription {
my $self = shift;
return $self->{description};
}
sub setDescription {
my $self = shift;
$self->{description} = shift;
}
sub getDiagram {
my $self = shift;
return $self->{diagram};
}
sub setDiagram {
my $self = shift;
$self->{diagram} = shift;
}
sub getDisplayValue {
my $self = shift;
return $self->{displayValue};
}
sub setDisplayValue {
my $self = shift;
$self->{displayValue} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getName {
my $self = shift;
return $self->{name};
}
sub setName {
my $self = shift;
$self->{name} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getGeneCollection {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
lib/CaCORE/CaBIO.pm view on Meta::CPAN
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::DiseaseOntologyRelationship;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::DomainObjectI);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the DiseaseOntologyRelationship object
# returns: a DiseaseOntologyRelationship object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new DiseaseOntologyRelationship\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this DiseaseOntologyRelationship intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":DiseaseOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# type;
if( defined( $self->getType ) ) {
$tmpstr = "<type xsi:type=\"xsd:string\">" . $self->getType . "</type>";
} else {
$tmpstr = "<type xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of DiseaseOntologyRelationship objects
# param: xml doc
# returns: list of DiseaseOntologyRelationship objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of DiseaseOntologyRelationship objects
# param: xml node
# returns: a list of DiseaseOntologyRelationship objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one DiseaseOntologyRelationship object
# param: xml node
# returns: one DiseaseOntologyRelationship object
sub fromWSXMLNode {
my $DiseaseOntologyRelationshipNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $id;
my $type;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($DiseaseOntologyRelationshipNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "type") {
$type=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::DiseaseOntologyRelationship;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setId($id);
$newobj->setType($type);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
sub getType {
my $self = shift;
return $self->{type};
}
sub setType {
my $self = shift;
$self->{type} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getChildDiseaseOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::DiseaseOntology", $self);
return $results[0];
}
sub getParentDiseaseOntology {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::DiseaseOntology", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# ------------------------------------------------------------------------------------------
package CaCORE::CaBIO::CytogeneticLocation;
use 5.005;
#use strict;
use warnings;
require Exporter;
use XML::DOM;
## begin import objects ##
use CaCORE::ApplicationService;
## end import objects ##
@ISA = qw(CaCORE::CaBIO::Location);
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
# create an instance of the CytogeneticLocation object
# returns: a CytogeneticLocation object
sub new {
my $class = shift;
my $self = {};
bless($self, $class);
#print "new CytogeneticLocation\n";
return $self;
}
# Construct the specific section of the WSDL request corresponding
# to this CytogeneticLocation intance
# returns: XML in string format
sub toWebserviceXML {
my $self = shift;
my $result = shift;
my $assigned_id = shift;
my $current_id = shift;
my $l = shift;
my %worklist = %$l;
# prefix portion of the xml
$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":CytogeneticLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
my $tmpstr = "";
$current_id ++;
## begin attribute to XML ##
# bigid;
if( defined( $self->getBigid ) ) {
$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
} else {
$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# endCytobandLocId;
if( defined( $self->getEndCytobandLocId ) ) {
$tmpstr = "<endCytobandLocId xsi:type=\"xsd:long\">" . $self->getEndCytobandLocId . "</endCytobandLocId>";
} else {
$tmpstr = "<endCytobandLocId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# startCytobandLocId;
if( defined( $self->getStartCytobandLocId ) ) {
$tmpstr = "<startCytobandLocId xsi:type=\"xsd:long\">" . $self->getStartCytobandLocId . "</startCytobandLocId>";
} else {
$tmpstr = "<startCytobandLocId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
# id;
if( defined( $self->getId ) ) {
$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
} else {
$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
}
$result .= $tmpstr;
## end attribute to XML ##
## begin association to XML ##
## end association to XML ##
# add trailing close tags
$result .= "</multiRef>";
return ($result, $current_id, %worklist);
}
# parse a given webservice response xml, construct a list of CytogeneticLocation objects
# param: xml doc
# returns: list of CytogeneticLocation objects
sub fromWebserviceXML {
my $self = shift;
my $parser = new XML::DOM::Parser;
my $docnode = $parser->parse(shift);
my $root = $docnode->getFirstChild->getFirstChild->getFirstChild->getFirstChild;
return $self->fromWSXMLListNode($root);
}
# parse a given xml node, construct a list of CytogeneticLocation objects
# param: xml node
# returns: a list of CytogeneticLocation objects
sub fromWSXMLListNode {
my $self = shift;
my $listNode = shift;
my @obj_list = ();
# get all children for this node
for my $childrenNode ($listNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
my $newobj = $self->fromWSXMLNode($childrenNode);
push @obj_list, $newobj;
}
}
return @obj_list;
}
# parse a given xml node, construct one CytogeneticLocation object
# param: xml node
# returns: one CytogeneticLocation object
sub fromWSXMLNode {
my $CytogeneticLocationNode = $_[1];
## begin ELEMENT_NODE children ##
my $bigid;
my $endCytobandLocId;
my $startCytobandLocId;
my $id;
## end ELEMENT_NODE children ##
# get all children for this node
for my $childrenNode ($CytogeneticLocationNode->getChildNodes) {
if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
if( ! defined($childrenNode->getFirstChild) ){ next; };
my $textNode = $childrenNode->getFirstChild;
## begin iterate ELEMENT_NODE ##
if (0) {
# do nothing, just a place holder for "if" component
}
elsif ($childrenNode->getNodeName eq "bigid") {
$bigid=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "endCytobandLocId") {
$endCytobandLocId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "startCytobandLocId") {
$startCytobandLocId=$textNode->getNodeValue;
}
elsif ($childrenNode->getNodeName eq "id") {
$id=$textNode->getNodeValue;
}
## end iterate ELEMENT_NODE ##
}
}
my $newobj = new CaCORE::CaBIO::CytogeneticLocation;
## begin set attr ##
$newobj->setBigid($bigid);
$newobj->setEndCytobandLocId($endCytobandLocId);
$newobj->setStartCytobandLocId($startCytobandLocId);
$newobj->setId($id);
## end set attr ##
return $newobj;
}
## begin getters and setters ##
sub getBigid {
my $self = shift;
return $self->{bigid};
}
sub setBigid {
my $self = shift;
$self->{bigid} = shift;
}
sub getEndCytobandLocId {
my $self = shift;
return $self->{endCytobandLocId};
}
sub setEndCytobandLocId {
my $self = shift;
$self->{endCytobandLocId} = shift;
}
sub getStartCytobandLocId {
my $self = shift;
return $self->{startCytobandLocId};
}
sub setStartCytobandLocId {
my $self = shift;
$self->{startCytobandLocId} = shift;
}
sub getId {
my $self = shift;
return $self->{id};
}
sub setId {
my $self = shift;
$self->{id} = shift;
}
## end getters and setters ##
## begin bean association methods ##
sub getEndCytoband {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Cytoband", $self);
return $results[0];
}
sub getStartCytoband {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Cytoband", $self);
return $results[0];
}
sub getSNP {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::SNP", $self);
return $results[0];
}
sub getChromosome {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Chromosome", $self);
return $results[0];
}
sub getGene {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::Gene", $self);
return $results[0];
}
sub getNucleicAcidSequence {
my $self = shift;
my $appSvc = CaCORE::ApplicationService->instance();
my @results = $appSvc->queryObject("CaCORE::CaBIO::NucleicAcidSequence", $self);
return $results[0];
}
## end bean association methods ##
1;
#end
# Below is module documentation for Agent
=pod
=head1 Agent
CaCORE::CaBIO::Agent - Perl extension for Agent.
=head2 ABSTRACT
The CaCORE::CaBIO::Agent is a Perl object representation of the
CaCORE Agent object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Agent
The following are all the attributes of the Agent object and their data types:
=over 4
=item EVSId
data type: C<string>
=item NSCNumber
data type: C<long>
=item bigid
data type: C<string>
=item comment
data type: C<string>
=item id
data type: C<long>
=item isCMAPAgent
data type: C<boolean>
=item name
data type: C<string>
=item source
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Agent
The following are all the objects that are associated with the Agent:
=over 4
=item Instance of L</ClinicalTrialProtocol>:
One to many assoication, use C<getClinicalTrialProtocolCollection> to get a collection of associated ClinicalTrialProtocol.
=item Instance of L</Target>:
One to many assoication, use C<getTargetCollection> to get a collection of associated Target.
=back
=cut
# Below is module documentation for Anomaly
=pod
=head1 Anomaly
CaCORE::CaBIO::Anomaly - Perl extension for Anomaly.
=head2 ABSTRACT
The CaCORE::CaBIO::Anomaly is a Perl object representation of the
CaCORE Anomaly object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Anomaly
The following are all the attributes of the Anomaly object and their data types:
=over 4
=item bigid
data type: C<string>
=item description
data type: C<string>
=item id
data type: C<long>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Anomaly
The following are all the objects that are associated with the Anomaly:
=over 4
=item Collection of L</Histopathology>:
Many to one assoication, use C<getHistopathology> to get the associated Histopathology.
=item Instance of L</OrganOntology>:
One to many assoication, use C<getOrganOntologyCollection> to get a collection of associated OrganOntology.
=item Instance of L</Vocabulary>:
One to many assoication, use C<getVocabularyCollection> to get a collection of associated Vocabulary.
=back
=cut
# Below is module documentation for Chromosome
=pod
=head1 Chromosome
CaCORE::CaBIO::Chromosome - Perl extension for Chromosome.
=head2 ABSTRACT
The CaCORE::CaBIO::Chromosome is a Perl object representation of the
CaCORE Chromosome object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Chromosome
The following are all the attributes of the Chromosome object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item number
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Chromosome
The following are all the objects that are associated with the Chromosome:
=over 4
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Location>:
One to many assoication, use C<getLocationCollection> to get a collection of associated Location.
=item Collection of L</Taxon>:
Many to one assoication, use C<getTaxon> to get the associated Taxon.
=back
=cut
# Below is module documentation for ClinicalTrialProtocol
=pod
=head1 ClinicalTrialProtocol
CaCORE::CaBIO::ClinicalTrialProtocol - Perl extension for ClinicalTrialProtocol.
=head2 ABSTRACT
The CaCORE::CaBIO::ClinicalTrialProtocol is a Perl object representation of the
CaCORE ClinicalTrialProtocol object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of ClinicalTrialProtocol
The following are all the attributes of the ClinicalTrialProtocol object and their data types:
=over 4
=item NIHAdminCode
data type: C<string>
=item PDQIdentifier
data type: C<string>
=item PIName
data type: C<string>
=item bigid
data type: C<string>
=item currentStatus
data type: C<string>
=item currentStatusDate
data type: C<dateTime>
=item documentNumber
data type: C<string>
=item id
data type: C<long>
=item leadOrganizationId
data type: C<string>
=item leadOrganizationName
data type: C<string>
=item participationType
data type: C<string>
=item phase
data type: C<string>
=item title
data type: C<string>
=item treatmentFlag
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of ClinicalTrialProtocol
The following are all the objects that are associated with the ClinicalTrialProtocol:
=over 4
=item Instance of L</Agent>:
One to many assoication, use C<getAgentCollection> to get a collection of associated Agent.
=item Instance of L</DiseaseOntology>:
One to many assoication, use C<getDiseaseOntologyCollection> to get a collection of associated DiseaseOntology.
=item Instance of L</Histopathology>:
One to many assoication, use C<getHistopathologyCollection> to get a collection of associated Histopathology.
=item Instance of L</ProtocolAssociation>:
One to many assoication, use C<getProtocolAssociationCollection> to get a collection of associated ProtocolAssociation.
=back
=cut
# Below is module documentation for Clone
=pod
=head1 Clone
CaCORE::CaBIO::Clone - Perl extension for Clone.
=head2 ABSTRACT
The CaCORE::CaBIO::Clone is a Perl object representation of the
CaCORE Clone object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Clone
The following are all the attributes of the Clone object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item insertSize
data type: C<long>
=item name
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Clone
The following are all the objects that are associated with the Clone:
=over 4
=item Instance of L</CloneRelativeLocation>:
One to many assoication, use C<getCloneRelativeLocationCollection> to get a collection of associated CloneRelativeLocation.
=item Collection of L</Library>:
Many to one assoication, use C<getLibrary> to get the associated Library.
=item Instance of L</NucleicAcidSequence>:
One to many assoication, use C<getNucleicAcidSequenceCollection> to get a collection of associated NucleicAcidSequence.
=item Instance of L</Taxon>:
One to many assoication, use C<getTaxonCollection> to get a collection of associated Taxon.
=back
=cut
# Below is module documentation for CloneRelativeLocation
=pod
=head1 CloneRelativeLocation
CaCORE::CaBIO::CloneRelativeLocation - Perl extension for CloneRelativeLocation.
=head2 ABSTRACT
The CaCORE::CaBIO::CloneRelativeLocation is a Perl object representation of the
CaCORE CloneRelativeLocation object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of CloneRelativeLocation
The following are all the attributes of the CloneRelativeLocation object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of CloneRelativeLocation
The following are all the objects that are associated with the CloneRelativeLocation:
=over 4
=item Collection of L</Clone>:
Many to one assoication, use C<getClone> to get the associated Clone.
=item Collection of L</NucleicAcidSequence>:
Many to one assoication, use C<getNucleicAcidSequence> to get the associated NucleicAcidSequence.
=back
=cut
# Below is module documentation for Cytoband
=pod
=head1 Cytoband
CaCORE::CaBIO::Cytoband - Perl extension for Cytoband.
=head2 ABSTRACT
The CaCORE::CaBIO::Cytoband is a Perl object representation of the
CaCORE Cytoband object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Cytoband
The following are all the attributes of the Cytoband object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Cytoband
The following are all the objects that are associated with the Cytoband:
=over 4
=item Collection of L</PhysicalLocation>:
Many to one assoication, use C<getPhysicalLocation> to get the associated PhysicalLocation.
=back
=cut
# Below is module documentation for CytogeneticLocation
=pod
=head1 CytogeneticLocation
CaCORE::CaBIO::CytogeneticLocation - Perl extension for CytogeneticLocation.
=head2 ABSTRACT
The CaCORE::CaBIO::CytogeneticLocation is a Perl object representation of the
CaCORE CytogeneticLocation object.
CytogeneticLocation extends from domain object L<"Location">.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of CytogeneticLocation
The following are all the attributes of the CytogeneticLocation object and their data types:
=over 4
=item bigid
data type: C<string>
=item endCytobandLocId
data type: C<long>
=item startCytobandLocId
data type: C<long>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of CytogeneticLocation
The following are all the objects that are associated with the CytogeneticLocation:
=over 4
=item Collection of L</EndCytoband>:
Many to one assoication, use C<getEndCytoband> to get the associated EndCytoband.
=item Collection of L</StartCytoband>:
Many to one assoication, use C<getStartCytoband> to get the associated StartCytoband.
=back
=cut
# Below is module documentation for DiseaseOntology
=pod
=head1 DiseaseOntology
CaCORE::CaBIO::DiseaseOntology - Perl extension for DiseaseOntology.
=head2 ABSTRACT
The CaCORE::CaBIO::DiseaseOntology is a Perl object representation of the
CaCORE DiseaseOntology object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of DiseaseOntology
The following are all the attributes of the DiseaseOntology object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of DiseaseOntology
The following are all the objects that are associated with the DiseaseOntology:
=over 4
=item Instance of L</ChildDiseaseOntologyRelationship>:
One to many assoication, use C<getChildDiseaseOntologyRelationshipCollection> to get a collection of associated ChildDiseaseOntologyRelationship.
=item Instance of L</ClinicalTrialProtocol>:
One to many assoication, use C<getClinicalTrialProtocolCollection> to get a collection of associated ClinicalTrialProtocol.
=item Instance of L</Histopathology>:
One to many assoication, use C<getHistopathologyCollection> to get a collection of associated Histopathology.
=item Instance of L</ParentDiseaseOntologyRelationship>:
One to many assoication, use C<getParentDiseaseOntologyRelationshipCollection> to get a collection of associated ParentDiseaseOntologyRelationship.
=back
=cut
# Below is module documentation for DiseaseOntologyRelationship
=pod
=head1 DiseaseOntologyRelationship
CaCORE::CaBIO::DiseaseOntologyRelationship - Perl extension for DiseaseOntologyRelationship.
=head2 ABSTRACT
The CaCORE::CaBIO::DiseaseOntologyRelationship is a Perl object representation of the
CaCORE DiseaseOntologyRelationship object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of DiseaseOntologyRelationship
The following are all the attributes of the DiseaseOntologyRelationship object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of DiseaseOntologyRelationship
The following are all the objects that are associated with the DiseaseOntologyRelationship:
=over 4
=item Collection of L</ChildDiseaseOntology>:
Many to one assoication, use C<getChildDiseaseOntology> to get the associated ChildDiseaseOntology.
=item Collection of L</ParentDiseaseOntology>:
Many to one assoication, use C<getParentDiseaseOntology> to get the associated ParentDiseaseOntology.
=back
=cut
# Below is module documentation for Gene
=pod
=head1 Gene
CaCORE::CaBIO::Gene - Perl extension for Gene.
=head2 ABSTRACT
The CaCORE::CaBIO::Gene is a Perl object representation of the
CaCORE Gene object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Gene
The following are all the attributes of the Gene object and their data types:
=over 4
=item bigid
data type: C<string>
=item clusterId
data type: C<long>
=item fullName
data type: C<string>
=item id
data type: C<long>
=item symbol
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Gene
The following are all the objects that are associated with the Gene:
=over 4
=item Collection of L</Chromosome>:
Many to one assoication, use C<getChromosome> to get the associated Chromosome.
=item Instance of L</DatabaseCrossReference>:
One to many assoication, use C<getDatabaseCrossReferenceCollection> to get a collection of associated DatabaseCrossReference.
=item Instance of L</GeneAlias>:
One to many assoication, use C<getGeneAliasCollection> to get a collection of associated GeneAlias.
=item Instance of L</GeneOntology>:
One to many assoication, use C<getGeneOntologyCollection> to get a collection of associated GeneOntology.
=item Instance of L</GeneRelativeLocation>:
One to many assoication, use C<getGeneRelativeLocationCollection> to get a collection of associated GeneRelativeLocation.
=item Instance of L</GenericReporter>:
One to many assoication, use C<getGenericReporterCollection> to get a collection of associated GenericReporter.
=item Instance of L</Histopathology>:
One to many assoication, use C<getHistopathologyCollection> to get a collection of associated Histopathology.
lib/CaCORE/CaBIO.pm view on Meta::CPAN
One to many assoication, use C<getLocationCollection> to get a collection of associated Location.
=item Instance of L</NucleicAcidSequence>:
One to many assoication, use C<getNucleicAcidSequenceCollection> to get a collection of associated NucleicAcidSequence.
=item Instance of L</OrganOntology>:
One to many assoication, use C<getOrganOntologyCollection> to get a collection of associated OrganOntology.
=item Instance of L</Pathway>:
One to many assoication, use C<getPathwayCollection> to get a collection of associated Pathway.
=item Instance of L</Protein>:
One to many assoication, use C<getProteinCollection> to get a collection of associated Protein.
=item Instance of L</Target>:
One to many assoication, use C<getTargetCollection> to get a collection of associated Target.
=item Collection of L</Taxon>:
Many to one assoication, use C<getTaxon> to get the associated Taxon.
=back
=cut
# Below is module documentation for GeneAlias
=pod
=head1 GeneAlias
CaCORE::CaBIO::GeneAlias - Perl extension for GeneAlias.
=head2 ABSTRACT
The CaCORE::CaBIO::GeneAlias is a Perl object representation of the
CaCORE GeneAlias object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GeneAlias
The following are all the attributes of the GeneAlias object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GeneAlias
The following are all the objects that are associated with the GeneAlias:
=over 4
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=back
=cut
# Below is module documentation for GeneOntology
=pod
=head1 GeneOntology
CaCORE::CaBIO::GeneOntology - Perl extension for GeneOntology.
=head2 ABSTRACT
The CaCORE::CaBIO::GeneOntology is a Perl object representation of the
CaCORE GeneOntology object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GeneOntology
The following are all the attributes of the GeneOntology object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GeneOntology
The following are all the objects that are associated with the GeneOntology:
=over 4
=item Instance of L</ChildGeneOntologyRelationship>:
One to many assoication, use C<getChildGeneOntologyRelationshipCollection> to get a collection of associated ChildGeneOntologyRelationship.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</ParentGeneOntologyRelationship>:
One to many assoication, use C<getParentGeneOntologyRelationshipCollection> to get a collection of associated ParentGeneOntologyRelationship.
=back
=cut
# Below is module documentation for GeneOntologyRelationship
=pod
=head1 GeneOntologyRelationship
CaCORE::CaBIO::GeneOntologyRelationship - Perl extension for GeneOntologyRelationship.
=head2 ABSTRACT
The CaCORE::CaBIO::GeneOntologyRelationship is a Perl object representation of the
CaCORE GeneOntologyRelationship object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GeneOntologyRelationship
The following are all the attributes of the GeneOntologyRelationship object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item relationshipType
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GeneOntologyRelationship
The following are all the objects that are associated with the GeneOntologyRelationship:
=over 4
=item Collection of L</ChildGeneOntology>:
Many to one assoication, use C<getChildGeneOntology> to get the associated ChildGeneOntology.
=item Collection of L</ParentGeneOntology>:
Many to one assoication, use C<getParentGeneOntology> to get the associated ParentGeneOntology.
=back
=cut
# Below is module documentation for GeneRelativeLocation
=pod
=head1 GeneRelativeLocation
CaCORE::CaBIO::GeneRelativeLocation - Perl extension for GeneRelativeLocation.
=head2 ABSTRACT
The CaCORE::CaBIO::GeneRelativeLocation is a Perl object representation of the
CaCORE GeneRelativeLocation object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GeneRelativeLocation
The following are all the attributes of the GeneRelativeLocation object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GeneRelativeLocation
The following are all the objects that are associated with the GeneRelativeLocation:
=over 4
=back
=cut
# Below is module documentation for GenericArray
=pod
=head1 GenericArray
CaCORE::CaBIO::GenericArray - Perl extension for GenericArray.
=head2 ABSTRACT
The CaCORE::CaBIO::GenericArray is a Perl object representation of the
CaCORE GenericArray object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GenericArray
The following are all the attributes of the GenericArray object and their data types:
=over 4
=item arrayName
data type: C<string>
=item bigid
data type: C<string>
=item id
data type: C<long>
=item platform
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GenericArray
The following are all the objects that are associated with the GenericArray:
=over 4
=item Instance of L</GenericReporter>:
One to many assoication, use C<getGenericReporterCollection> to get a collection of associated GenericReporter.
=back
=cut
# Below is module documentation for GenericReporter
=pod
=head1 GenericReporter
CaCORE::CaBIO::GenericReporter - Perl extension for GenericReporter.
=head2 ABSTRACT
The CaCORE::CaBIO::GenericReporter is a Perl object representation of the
CaCORE GenericReporter object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of GenericReporter
The following are all the attributes of the GenericReporter object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of GenericReporter
The following are all the objects that are associated with the GenericReporter:
=over 4
=item Collection of L</Gene>:
Many to one assoication, use C<getGene> to get the associated Gene.
=item Instance of L</GenericArray>:
One to many assoication, use C<getGenericArrayCollection> to get a collection of associated GenericArray.
=back
=cut
# Below is module documentation for Histopathology
=pod
=head1 Histopathology
CaCORE::CaBIO::Histopathology - Perl extension for Histopathology.
=head2 ABSTRACT
The CaCORE::CaBIO::Histopathology is a Perl object representation of the
CaCORE Histopathology object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
lib/CaCORE/CaBIO.pm view on Meta::CPAN
One to many assoication, use C<getAnomalyCollection> to get a collection of associated Anomaly.
=item Instance of L</ClinicalTrialProtocol>:
One to many assoication, use C<getClinicalTrialProtocolCollection> to get a collection of associated ClinicalTrialProtocol.
=item Collection of L</DiseaseOntology>:
Many to one assoication, use C<getDiseaseOntology> to get the associated DiseaseOntology.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Library>:
One to many assoication, use C<getLibraryCollection> to get a collection of associated Library.
=item Instance of L</Metastasis>:
One to many assoication, use C<getMetastasisCollection> to get a collection of associated Metastasis.
=item Collection of L</OrganOntology>:
Many to one assoication, use C<getOrganOntology> to get the associated OrganOntology.
=back
=cut
# Below is module documentation for HomologousAssociation
=pod
=head1 HomologousAssociation
CaCORE::CaBIO::HomologousAssociation - Perl extension for HomologousAssociation.
=head2 ABSTRACT
The CaCORE::CaBIO::HomologousAssociation is a Perl object representation of the
CaCORE HomologousAssociation object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of HomologousAssociation
The following are all the attributes of the HomologousAssociation object and their data types:
=over 4
=item bigid
data type: C<string>
=item homologousId
data type: C<long>
=item id
data type: C<long>
=item similarityPercentage
data type: C<float>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of HomologousAssociation
The following are all the objects that are associated with the HomologousAssociation:
=over 4
=item Collection of L</HomologousGene>:
Many to one assoication, use C<getHomologousGene> to get the associated HomologousGene.
=back
=cut
# Below is module documentation for Library
=pod
=head1 Library
CaCORE::CaBIO::Library - Perl extension for Library.
=head2 ABSTRACT
The CaCORE::CaBIO::Library is a Perl object representation of the
CaCORE Library object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Library
The following are all the attributes of the Library object and their data types:
=over 4
=item bigid
data type: C<string>
=item cloneProducer
data type: C<string>
=item cloneVector
data type: C<string>
=item cloneVectorType
data type: C<string>
=item clonesToDate
data type: C<long>
=item creationDate
data type: C<dateTime>
=item description
data type: C<string>
=item id
data type: C<long>
=item keyword
data type: C<string>
=item labHost
data type: C<string>
=item name
data type: C<string>
=item rsite1
data type: C<string>
=item rsite2
data type: C<string>
=item sequencesToDate
data type: C<long>
=item type
data type: C<string>
=item uniGeneId
lib/CaCORE/CaBIO.pm view on Meta::CPAN
=over 4
=item Collection of L</SNP>:
Many to one assoication, use C<getSNP> to get the associated SNP.
=item Collection of L</Chromosome>:
Many to one assoication, use C<getChromosome> to get the associated Chromosome.
=item Collection of L</Gene>:
Many to one assoication, use C<getGene> to get the associated Gene.
=item Collection of L</NucleicAcidSequence>:
Many to one assoication, use C<getNucleicAcidSequence> to get the associated NucleicAcidSequence.
=back
=cut
# Below is module documentation for NucleicAcidSequence
=pod
=head1 NucleicAcidSequence
CaCORE::CaBIO::NucleicAcidSequence - Perl extension for NucleicAcidSequence.
=head2 ABSTRACT
The CaCORE::CaBIO::NucleicAcidSequence is a Perl object representation of the
CaCORE NucleicAcidSequence object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of NucleicAcidSequence
The following are all the attributes of the NucleicAcidSequence object and their data types:
=over 4
=item accessionNumber
data type: C<string>
=item accessionNumberVersion
data type: C<string>
=item bigid
data type: C<string>
=item id
data type: C<long>
=item length
data type: C<long>
=item type
data type: C<string>
=item value
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of NucleicAcidSequence
The following are all the objects that are associated with the NucleicAcidSequence:
=over 4
=item Collection of L</CloneRelativeLocation>:
Many to one assoication, use C<getCloneRelativeLocation> to get the associated CloneRelativeLocation.
=item Instance of L</DatabaseCrossReference>:
One to many assoication, use C<getDatabaseCrossReferenceCollection> to get a collection of associated DatabaseCrossReference.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Location>:
One to many assoication, use C<getLocationCollection> to get a collection of associated Location.
=back
=cut
# Below is module documentation for OrganOntology
=pod
=head1 OrganOntology
CaCORE::CaBIO::OrganOntology - Perl extension for OrganOntology.
=head2 ABSTRACT
The CaCORE::CaBIO::OrganOntology is a Perl object representation of the
CaCORE OrganOntology object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of OrganOntology
The following are all the attributes of the OrganOntology object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of OrganOntology
The following are all the objects that are associated with the OrganOntology:
=over 4
=item Instance of L</Anomaly>:
One to many assoication, use C<getAnomalyCollection> to get a collection of associated Anomaly.
=item Instance of L</ChildOrganOntologyRelationship>:
One to many assoication, use C<getChildOrganOntologyRelationshipCollection> to get a collection of associated ChildOrganOntologyRelationship.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Histopathology>:
One to many assoication, use C<getHistopathologyCollection> to get a collection of associated Histopathology.
=item Instance of L</ParentOrganOntologyRelationship>:
One to many assoication, use C<getParentOrganOntologyRelationshipCollection> to get a collection of associated ParentOrganOntologyRelationship.
=back
=cut
# Below is module documentation for OrganOntologyRelationship
=pod
=head1 OrganOntologyRelationship
CaCORE::CaBIO::OrganOntologyRelationship - Perl extension for OrganOntologyRelationship.
=head2 ABSTRACT
The CaCORE::CaBIO::OrganOntologyRelationship is a Perl object representation of the
CaCORE OrganOntologyRelationship object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of OrganOntologyRelationship
The following are all the attributes of the OrganOntologyRelationship object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of OrganOntologyRelationship
The following are all the objects that are associated with the OrganOntologyRelationship:
=over 4
=item Collection of L</ChildOrganOntology>:
Many to one assoication, use C<getChildOrganOntology> to get the associated ChildOrganOntology.
=item Collection of L</ParentOrganOntology>:
Many to one assoication, use C<getParentOrganOntology> to get the associated ParentOrganOntology.
=back
=cut
# Below is module documentation for Pathway
=pod
=head1 Pathway
CaCORE::CaBIO::Pathway - Perl extension for Pathway.
=head2 ABSTRACT
The CaCORE::CaBIO::Pathway is a Perl object representation of the
CaCORE Pathway object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Pathway
The following are all the attributes of the Pathway object and their data types:
=over 4
=item bigid
data type: C<string>
=item description
data type: C<string>
=item diagram
data type: C<string>
=item displayValue
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Pathway
The following are all the objects that are associated with the Pathway:
=over 4
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Histopathology>:
One to many assoication, use C<getHistopathologyCollection> to get a collection of associated Histopathology.
=item Collection of L</Taxon>:
Many to one assoication, use C<getTaxon> to get the associated Taxon.
=back
=cut
# Below is module documentation for PhysicalLocation
=pod
=head1 PhysicalLocation
CaCORE::CaBIO::PhysicalLocation - Perl extension for PhysicalLocation.
lib/CaCORE/CaBIO.pm view on Meta::CPAN
=over 4
=item chromosomalEndPosition
data type: C<long>
=item chromosomalStartPosition
data type: C<long>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of PhysicalLocation
The following are all the objects that are associated with the PhysicalLocation:
=over 4
=item Instance of L</Cytoband>:
One to many assoication, use C<getCytobandCollection> to get a collection of associated Cytoband.
=back
=cut
# Below is module documentation for PopulationFrequency
=pod
=head1 PopulationFrequency
CaCORE::CaBIO::PopulationFrequency - Perl extension for PopulationFrequency.
=head2 ABSTRACT
The CaCORE::CaBIO::PopulationFrequency is a Perl object representation of the
CaCORE PopulationFrequency object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of PopulationFrequency
The following are all the attributes of the PopulationFrequency object and their data types:
=over 4
=item bigid
data type: C<string>
=item ethnicity
data type: C<string>
=item id
data type: C<long>
=item majorAllele
data type: C<string>
=item majorFrequency
data type: C<double>
=item minorAllele
data type: C<string>
=item minorFrequency
data type: C<double>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of PopulationFrequency
The following are all the objects that are associated with the PopulationFrequency:
=over 4
=item Collection of L</SNP>:
Many to one assoication, use C<getSNP> to get the associated SNP.
=back
=cut
# Below is module documentation for Protein
=pod
=head1 Protein
CaCORE::CaBIO::Protein - Perl extension for Protein.
=head2 ABSTRACT
The CaCORE::CaBIO::Protein is a Perl object representation of the
CaCORE Protein object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Protein
The following are all the attributes of the Protein object and their data types:
=over 4
=item bigid
data type: C<string>
=item copyrightStatement
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=item primaryAccession
data type: C<string>
=item uniProtCode
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Protein
The following are all the objects that are associated with the Protein:
=over 4
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Keywords>:
One to many assoication, use C<getKeywordsCollection> to get a collection of associated Keywords.
=item Instance of L</ProteinAlias>:
One to many assoication, use C<getProteinAliasCollection> to get a collection of associated ProteinAlias.
=item Collection of L</ProteinSequence>:
Many to one assoication, use C<getProteinSequence> to get the associated ProteinSequence.
=item Instance of L</SecondaryAccession>:
One to many assoication, use C<getSecondaryAccessionCollection> to get a collection of associated SecondaryAccession.
=item Instance of L</Taxon>:
One to many assoication, use C<getTaxonCollection> to get a collection of associated Taxon.
=back
=cut
# Below is module documentation for ProteinAlias
=pod
=head1 ProteinAlias
CaCORE::CaBIO::ProteinAlias - Perl extension for ProteinAlias.
=head2 ABSTRACT
The CaCORE::CaBIO::ProteinAlias is a Perl object representation of the
CaCORE ProteinAlias object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of ProteinAlias
The following are all the attributes of the ProteinAlias object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of ProteinAlias
The following are all the objects that are associated with the ProteinAlias:
=over 4
=item Instance of L</Protein>:
One to many assoication, use C<getProteinCollection> to get a collection of associated Protein.
=back
=cut
# Below is module documentation for ProteinSequence
=pod
=head1 ProteinSequence
CaCORE::CaBIO::ProteinSequence - Perl extension for ProteinSequence.
=head2 ABSTRACT
The CaCORE::CaBIO::ProteinSequence is a Perl object representation of the
CaCORE ProteinSequence object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of ProteinSequence
The following are all the attributes of the ProteinSequence object and their data types:
=over 4
=item bigid
data type: C<string>
=item checkSum
data type: C<string>
=item id
data type: C<long>
=item length
data type: C<long>
=item molecularWeightInDaltons
data type: C<double>
=item value
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of ProteinSequence
The following are all the objects that are associated with the ProteinSequence:
=over 4
=item Collection of L</Protein>:
Many to one assoication, use C<getProtein> to get the associated Protein.
=back
=cut
# Below is module documentation for Protocol
=pod
=head1 Protocol
CaCORE::CaBIO::Protocol - Perl extension for Protocol.
=head2 ABSTRACT
The CaCORE::CaBIO::Protocol is a Perl object representation of the
CaCORE Protocol object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Protocol
The following are all the attributes of the Protocol object and their data types:
=over 4
=item bigid
data type: C<string>
=item description
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Protocol
The following are all the objects that are associated with the Protocol:
=over 4
=item Instance of L</Library>:
One to many assoication, use C<getLibraryCollection> to get a collection of associated Library.
=item Instance of L</Tissue>:
One to many assoication, use C<getTissueCollection> to get a collection of associated Tissue.
=back
=cut
# Below is module documentation for ProtocolAssociation
=pod
=head1 ProtocolAssociation
CaCORE::CaBIO::ProtocolAssociation - Perl extension for ProtocolAssociation.
=head2 ABSTRACT
The CaCORE::CaBIO::ProtocolAssociation is a Perl object representation of the
CaCORE ProtocolAssociation object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of ProtocolAssociation
The following are all the attributes of the ProtocolAssociation object and their data types:
=over 4
=item CTEPNAME
data type: C<string>
=item IMTCODE
data type: C<long>
=item bigid
data type: C<string>
=item diseaseCategory
data type: C<string>
=item diseaseSubCategory
data type: C<string>
=item id
data type: C<long>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of ProtocolAssociation
The following are all the objects that are associated with the ProtocolAssociation:
=over 4
=item Collection of L</ClinicalTrialProtocol>:
Many to one assoication, use C<getClinicalTrialProtocol> to get the associated ClinicalTrialProtocol.
=item Collection of L</DiseaseOntology>:
Many to one assoication, use C<getDiseaseOntology> to get the associated DiseaseOntology.
=back
=cut
# Below is module documentation for SNP
=pod
=head1 SNP
CaCORE::CaBIO::SNP - Perl extension for SNP.
=head2 ABSTRACT
The CaCORE::CaBIO::SNP is a Perl object representation of the
CaCORE SNP object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of SNP
The following are all the attributes of the SNP object and their data types:
=over 4
=item DBSNPID
data type: C<string>
=item alleleA
data type: C<string>
=item alleleB
data type: C<string>
=item bigid
data type: C<string>
=item id
data type: C<long>
=item validationStatus
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of SNP
The following are all the objects that are associated with the SNP:
=over 4
=item Instance of L</DatabaseCrossReference>:
One to many assoication, use C<getDatabaseCrossReferenceCollection> to get a collection of associated DatabaseCrossReference.
=item Instance of L</GeneRelativeLocation>:
One to many assoication, use C<getGeneRelativeLocationCollection> to get a collection of associated GeneRelativeLocation.
=item Instance of L</Location>:
One to many assoication, use C<getLocationCollection> to get a collection of associated Location.
=item Instance of L</PopulationFrequency>:
One to many assoication, use C<getPopulationFrequencyCollection> to get a collection of associated PopulationFrequency.
=back
=cut
# Below is module documentation for Target
=pod
=head1 Target
CaCORE::CaBIO::Target - Perl extension for Target.
=head2 ABSTRACT
The CaCORE::CaBIO::Target is a Perl object representation of the
CaCORE Target object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Target
The following are all the attributes of the Target object and their data types:
=over 4
=item bigid
data type: C<string>
=item id
data type: C<long>
=item name
data type: C<string>
=item type
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Target
The following are all the objects that are associated with the Target:
=over 4
=item Instance of L</Agent>:
One to many assoication, use C<getAgentCollection> to get a collection of associated Agent.
=item Instance of L</Anomaly>:
One to many assoication, use C<getAnomalyCollection> to get a collection of associated Anomaly.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=back
=cut
# Below is module documentation for Taxon
=pod
=head1 Taxon
CaCORE::CaBIO::Taxon - Perl extension for Taxon.
=head2 ABSTRACT
The CaCORE::CaBIO::Taxon is a Perl object representation of the
CaCORE Taxon object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Taxon
The following are all the attributes of the Taxon object and their data types:
=over 4
=item abbreviation
data type: C<string>
=item bigid
data type: C<string>
=item commonName
data type: C<string>
=item ethnicityStrain
data type: C<string>
=item id
data type: C<long>
=item scientificName
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Taxon
The following are all the objects that are associated with the Taxon:
=over 4
=item Instance of L</Chromosome>:
One to many assoication, use C<getChromosomeCollection> to get a collection of associated Chromosome.
=item Instance of L</Clone>:
One to many assoication, use C<getCloneCollection> to get a collection of associated Clone.
=item Instance of L</Gene>:
One to many assoication, use C<getGeneCollection> to get a collection of associated Gene.
=item Instance of L</Pathway>:
One to many assoication, use C<getPathwayCollection> to get a collection of associated Pathway.
=item Instance of L</Protein>:
One to many assoication, use C<getProteinCollection> to get a collection of associated Protein.
=item Instance of L</Tissue>:
One to many assoication, use C<getTissueCollection> to get a collection of associated Tissue.
=back
=cut
lib/CaCORE/CaBIO.pm view on Meta::CPAN
data type: C<string>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Tissue
The following are all the objects that are associated with the Tissue:
=over 4
=item Instance of L</Library>:
One to many assoication, use C<getLibraryCollection> to get a collection of associated Library.
=item Collection of L</Protocol>:
Many to one assoication, use C<getProtocol> to get the associated Protocol.
=item Collection of L</Taxon>:
Many to one assoication, use C<getTaxon> to get the associated Taxon.
=back
=cut
# Below is module documentation for Vocabulary
=pod
=head1 Vocabulary
CaCORE::CaBIO::Vocabulary - Perl extension for Vocabulary.
=head2 ABSTRACT
The CaCORE::CaBIO::Vocabulary is a Perl object representation of the
CaCORE Vocabulary object.
=head2 SYNOPSIS
See L<CaCORE::ApplicationService>.
=head2 DESCRIPTION
=head2 ATTRIBUTES of Vocabulary
The following are all the attributes of the Vocabulary object and their data types:
=over 4
=item bigid
data type: C<string>
=item coreTerm
data type: C<string>
=item generalTerm
data type: C<string>
=item id
data type: C<long>
=back
Note: Although you can also use the corresponding setter methods to set the
attribute values, it is not recommended to do so unless you absolutely have
to change the object's attributes.
=head2 ASSOCIATIONS of Vocabulary
The following are all the objects that are associated with the Vocabulary:
=over 4
=item Instance of L</Anomaly>:
One to many assoication, use C<getAnomalyCollection> to get a collection of associated Anomaly.
=back
=cut
=pod
=head1 SUPPORT
Please do not contact author directly. Send email to ncicb@pop.nci.nih.gov to request
support or report a bug.
=head1 AUTHOR
Shan Jiang <jiangs@mail.nih.gov>
=head1 COPYRIGHT AND LICENSE
The CaCORE Software License, Version 1.0
Copyright 2001-2005 SAIC. This software was developed in conjunction with the National Cancer Institute, and so to the extent government employees are co-authors, any rights in such works shall be subject to Title 17 of the United States Code, sectio...
=over 1
=item 1
Redistributions of source code must retain the above copyright notice, this list of conditions and the disclaimer of Article 5, below. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the disclaime...
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