MAGE::...ayData(3pm)

📦 version 20030502.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 MAGE::...ayData(3pm) 💖

okay bestie, this is the MAGE::...ayData(3pm) page from the User Contributed Perl Documentation. It's part 1, and it's lowkey iconic. Let's go. ✨

✨ NAME ✨

Bio::MAGE::BioAssayData::BioAssayData — Class for the MAGE-OM API.

🌸 SYNOPSIS 🌸

okay so real talk: Bio::MAGE::BioAssayData::BioAssayData is an abstract base class and should not be directly instantiated. These examples show how subclass objects will behave. 💅

         use Bio::MAGE::BioAssayData::BioAssayData

         # Bio::MAGE::BioAssayData::BioAssayData is an abstract base class and should not
         # be directly instantiated. These examples indicate how subclass
         # objects will behave

         # 'name' attribute
         my $name_val = $bioassaydata->name(); # getter
         $bioassaydata->name($value); # setter

         # 'identifier' attribute
         my $identifier_val = $bioassaydata->identifier(); # getter
         $bioassaydata->identifier($value); # setter

         # 'bioAssayDimension' association
         my $bioassaydimension_ref = $bioassaydata->bioAssayDimension(); # getter
         $bioassaydata->bioAssayDimension($bioassaydimension_ref); # setter

         # 'auditTrail' association
         my $audit_array_ref = $bioassaydata->auditTrail(); # getter
         $bioassaydata->auditTrail(\@audit_list); # setter

         # 'propertySets' association
         my $namevaluetype_array_ref = $bioassaydata->propertySets(); # getter
         $bioassaydata->propertySets(\@namevaluetype_list); # setter

         # 'summaryStatistics' association
         my $namevaluetype_array_ref = $bioassaydata->summaryStatistics(); # getter
         $bioassaydata->summaryStatistics(\@namevaluetype_list); # setter

         # 'descriptions' association
         my $description_array_ref = $bioassaydata->descriptions(); # getter
         $bioassaydata->descriptions(\@description_list); # setter

         # 'designElementDimension' association
         my $designelementdimension_ref = $bioassaydata->designElementDimension(); # getter
         $bioassaydata->designElementDimension($designelementdimension_ref); # setter

         # 'security' association
         my $security_ref = $bioassaydata->security(); # getter
         $bioassaydata->security($security_ref); # setter

         # 'bioDataValues' association
         my $biodatavalues_ref = $bioassaydata->bioDataValues(); # getter
         $bioassaydata->bioDataValues($biodatavalues_ref); # setter

         # 'quantitationTypeDimension' association
         my $quantitationtypedimension_ref = $bioassaydata->quantitationTypeDimension(); # getter
         $bioassaydata->quantitationTypeDimension($quantitationtypedimension_ref); # setter

💜 DESCRIPTION 💜

From the MAGE-OM documentation for the "BioAssayData" class: it represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data. 🌈

Bio::MAGE::BioAssayData::BioAssayData is an abstract base class and should not be directly instantiated. Instead it serves as an interface definition for its subclasses.

🦋 INHERITANCE 🦋

Bio::MAGE::BioAssayData::BioAssayData has the following superclasses:

Bio::MAGE::Identifiable

Bio::MAGE::BioAssayData::BioAssayData has the following subclasses:

Bio::MAGE::BioAssayData::DerivedBioAssayData
Bio::MAGE::BioAssayData::MeasuredBioAssayData

🔥 CLASS METHODS 🔥

The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioAssayData::BioAssayData->methodname() syntax.

`new()`

`new(%args)`

Bio::MAGE::BioAssayData::BioAssayData is an abstract base class and should not be directly instantiated using the "new()" constructor. It is listed here to indicate what arguments will be accepted for its subclasses. 😌

The object constructor "new()" accepts the following optional named-value style arguments:

name — Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
identifier — Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
bioAssayDimension — Sets the value of the "bioAssayDimension" association. The value must be of type: instance of "Bio::MAGE::BioAssayData::BioAssayDimension".
auditTrail — Sets the value of the "auditTrail" association (this association was inherited from class "Bio::MAGE::Describable"). The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Audit".
propertySets — Sets the value of the "propertySets" association (this association was inherited from class "Bio::MAGE::Extendable"). The value must be of type: array of "Bio::MAGE::NameValueType".
summaryStatistics — Sets the value of the "summaryStatistics" association. The value must be of type: array of "Bio::MAGE::NameValueType".
designElementDimension — Sets the value of the "designElementDimension" association. The value must be of type: instance of "Bio::MAGE::BioAssayData::DesignElementDimension".
descriptions — Sets the value of the "descriptions" association (this association was inherited from class "Bio::MAGE::Describable"). The value must be of type: array of "Bio::MAGE::Description::Description".
quantitationTypeDimension — Sets the value of the "quantitationTypeDimension" association. The value must be of type: instance of "Bio::MAGE::BioAssayData::QuantitationTypeDimension".
bioDataValues — Sets the value of the "bioDataValues" association. The value must be of type: instance of "Bio::MAGE::BioAssayData::BioDataValues".
security — Sets the value of the "security" association (this association was inherited from class "Bio::MAGE::Describable"). The value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".

`$obj = class->new(%parameters)`

The "new()" method is the class constructor.

Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the "initialize()" method if it is defined by the class.

`@names = class->get_slot_names()`

The "get_slot_names()" method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

Return value: A list of the names of all slots defined for this class.

Side effects: none

`@name_list = get_attribute_names()`

returns the list of attribute data members for this class.

`@name_list = get_association_names()`

returns the list of association data members for this class.

`@class_list = get_superclasses()`

returns the list of superclasses for this class.

`@class_list = get_subclasses()`

returns the list of subclasses for this class.

`$name = class_name()`

Returns the full class name for this class.

`$package_name = package_name()`

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

`%assns = associations()`

returns the association meta-information in a hash where the keys are the association names and the values are "Association" objects that provide the meta-information for the association.

👑 INSTANCE METHODS 👑

`$obj_copy = $obj->new()`

When invoked with an existing object reference and not a class name, the "new()" method acts as a copy constructor - with the new object's initial values set to be those of the existing object.

Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.

Return value: It returns a reference to an object of the class.

Side effects: It invokes the "initialize()" method if it is defined by the class.

`$obj->set_slots(%parameters)`

`$obj->set_slots(\@name_list, \@value_list)`

The "set_slots()" method is used to set a number of slots at the same time. It has two different invocation methods. The first takes a named parameter list, and the second takes two array references.

Return value: none

Side effects: will call "croak()" if a slot_name is used that the class does not define.

`@obj_list = $obj->get_slots(@name_list)`

The "get_slots()" method is used to get the values of a number of slots at the same time.

Return value: a list of instance objects

Side effects: none

`$val = $obj->set_slot($name,$val)`

The "set_slot()" method sets the slot $name to the value $val

Return value: the new value of the slot, i.e. $val

Side effects: none

`$val = $obj->get_slot($name)`

The "get_slot()" method is used to get the values of a number of slots at the same time.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

🎀 ATTRIBUTES 🎀

Attributes are simple data types that belong to a single instance of a class. In the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute.

"Bio::MAGE::BioAssayData::BioAssayData" has the following attribute accessor methods:

`name`

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

`$val = $bioassaydata->setName($val)`

The restricted setter method for the "name" attribute.

Input parameters: the value to which the "name" attribute will be set

Return value: the current value of the "name" attribute

Side effects: none

Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified

`$val = $bioassaydata->getName()`

The restricted getter method for the "name" attribute.

Input parameters: none

Return value: the current value of the "name" attribute

Side effects: none

Exceptions: will call "croak()" if any input parameters are specified

`identifier`

Methods for the "identifier" attribute.

From the MAGE-OM documentation:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

`$val = $bioassaydata->setIdentifier($val)`

The restricted setter method for the "identifier" attribute.

the setter for the identifier attribute — you hand it the value you want identifier to be. It hands you back the current value of identifier. Side effects? literally none, it's so chill. But bestie, it will call croak() if you pass no input parameters, or if you pass too many input parameters. Pick a number and stick to it. 💅
$val = $bioassaydata->getIdentifier() — the restricted getter for the identifier attribute. Takes no input parameters. Returns the current value of identifier. Side effects: none. Exceptions: it will call croak() if you pass any input parameters, so keep your hands to yourself. 🙈

🔗 ASSOCIATIONS 🔗

okay so associations are refs to other classes. 🦋 In MAGE-OM every association has a cardinality, and that cardinality decides the minimum and maximum number of instances of the 'other' class that can be in the association. The vibe check:

There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1

There may be one item in the association, i.e. this is an optional data field.

1..N

There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.

0..N

There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::BioAssayData::BioAssayData has the following association accessor methods, and yes we're doing all of them, no skipping, no cap:

`bioAssayDimension`

Methods for the bioAssayDimension association.

From the MAGE-OM documentation:

The BioAssays of the BioAssayData.

$val = $bioassaydata->setBioAssayDimension($val) — the restricted setter for the bioAssayDimension association. Input parameters: the value to which the bioAssayDimension association will be set : one of the accepted enumerated values. Return value: the current value of the bioAssayDimension association : one of the accepted enumerated values. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::BioAssayData::BioAssayDimension. 🫶
$val = $bioassaydata->getBioAssayDimension() — the restricted getter for the bioAssayDimension association. Input parameters: none. Return value: the current value of the bioAssayDimension association : an instance of type Bio::MAGE::BioAssayData::BioAssayDimension. Side effects: none. Exceptions: it will call croak() if any input parameters are specified.

`auditTrail`

Methods for the auditTrail association.

From the MAGE-OM documentation:

A list of Audit instances that track changes to the instance of Describable.

$array_ref = $bioassaydata->setAuditTrail($array_ref) — the restricted setter for the auditTrail association. Input parameters: the value to which the auditTrail association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit. Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit instances. 💀
$array_ref = $bioassaydata->getAuditTrail() — the restricted getter for the auditTrail association. Input parameters: none. Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit. Side effects: none. Exceptions: it will call croak() if any input parameters are specified.
$val = $bioassaydata->addAuditTrail(@vals) — because the auditTrail association has list cardinality, it can hold more than one value, she's got range. ✨ This method adds the current list of objects in the auditTrail association. Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted. Return value: the number of items stored in the slot after adding @vals. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit.

`propertySets`

Methods for the propertySets association.

From the MAGE-OM documentation:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

$array_ref = $bioassaydata->setPropertySets($array_ref) — the restricted setter for the propertySets association. Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType. Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances. 🎀
$array_ref = $bioassaydata->getPropertySets() — the restricted getter for the propertySets association. Input parameters: none. Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType. Side effects: none. Exceptions: it will call croak() if any input parameters are specified.
$val = $bioassaydata->addPropertySets(@vals) — because the propertySets association has list cardinality, it can store more than one value. This method adds the current list of objects in the propertySets association. Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted. Return value: the number of items stored in the slot after adding @vals. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType.

`summaryStatistics`

Methods for the summaryStatistics association.

From the MAGE-OM documentation:

Statistics on the Quality of the BioAssayData.

$array_ref = $bioassaydata->setSummaryStatistics($array_ref) — the restricted setter for the summaryStatistics association. Input parameters: the value to which the summaryStatistics association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType. Return value: the current value of the summaryStatistics association : a reference to an array of objects of type Bio::MAGE::NameValueType. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances. 🌸
$array_ref = $bioassaydata->getSummaryStatistics() — the restricted getter for the summaryStatistics association. Input parameters: none. Return value: the current value of the summaryStatistics association : a reference to an array of objects of type Bio::MAGE::NameValueType. Side effects: none. Exceptions: it will call croak() if any input parameters are specified.
$val = $bioassaydata->addSummaryStatistics(@vals) — because the summaryStatistics association has list cardinality, it can store more than one value. This method adds the current list of objects in the summaryStatistics association. Input parameters: the list of values @vals to add to the summaryStatistics association. NOTE: submitting a single value is permitted. Return value: the number of items stored in the slot after adding @vals. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType.

`designElementDimension`

Methods for the designElementDimension association.

From the MAGE-OM documentation:

The DesignElements of the BioAssayData.

$val = $bioassaydata->setDesignElementDimension($val) — the restricted setter for the designElementDimension association. Input parameters: the value to which the designElementDimension association will be set : one of the accepted enumerated values. Return value: the current value of the designElementDimension association : one of the accepted enumerated values. Side effects: none. Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::BioAssayData::DesignElementDimension. 🦋
$val = $bioassaydata->getDesignElementDimension() — the restricted getter for the designElementDimension association. Input parameters: none. Return value: the current value of the designElementDimension association : an instance of type Bio::MAGE::BioAssayData::DesignElementDimension. Side effects: none. Exceptions: it will call croak() if any input parameters are specified.

`descriptions`

Methods for the descriptions association.

From the MAGE-OM documentation:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable. 💖

$array_ref = $bioassaydata->setDescriptions($array_ref) — the restricted setter for the descriptions association, bestie. 🔒

Input parameters: the value to which the descriptions association will be set — a reference to an array of objects of type Bio::MAGE::Description::Description
Return value: the current value of the descriptions association — a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances

$array_ref = $bioassaydata->getDescriptions() — the restricted getter for the descriptions association. peek but don't touch 💅

Input parameters: none
Return value: the current value of the descriptions association — a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified

$val = $bioassaydata->addDescriptions(@vals) — okay so because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association. it's giving collector energy 🎀

Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description

🌈 quantitationTypeDimension 🌈

Methods for the quantitationTypeDimension association.

From the MAGE-OM documentation:

The QuantitationTypes of the BioAssayData.

$val = $bioassaydata->setQuantitationTypeDimension($val) — the restricted setter for the quantitationTypeDimension association.

Input parameters: the value to which the quantitationTypeDimension association will be set — one of the accepted enumerated values.
Return value: the current value of the quantitationTypeDimension association — one of the accepted enumerated values.
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::BioAssayData::QuantitationTypeDimension

$val = $bioassaydata->getQuantitationTypeDimension() — the restricted getter for the quantitationTypeDimension association.

Input parameters: none
Return value: the current value of the quantitationTypeDimension association — an instance of type Bio::MAGE::BioAssayData::QuantitationTypeDimension.
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified

🦋 bioDataValues 🦋

Methods for the bioDataValues association.

From the MAGE-OM documentation:

The data values of the BioAssayData.

$val = $bioassaydata->setBioDataValues($val) — the restricted setter for the bioDataValues association.

Input parameters: the value to which the bioDataValues association will be set — one of the accepted enumerated values.
Return value: the current value of the bioDataValues association — one of the accepted enumerated values.
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::BioAssayData::BioDataValues

$val = $bioassaydata->getBioDataValues() — the restricted getter for the bioDataValues association.

Input parameters: none
Return value: the current value of the bioDataValues association — an instance of type Bio::MAGE::BioAssayData::BioDataValues.
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified

🎀 security 🎀

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $bioassaydata->setSecurity($val) — the restricted setter for the security association.

Input parameters: the value to which the security association will be set — one of the accepted enumerated values.
Return value: the current value of the security association — one of the accepted enumerated values.
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security

$val = $bioassaydata->getSecurity() — the restricted getter for the security association.

Input parameters: none
Return value: the current value of the security association — an instance of type Bio::MAGE::AuditAndSecurity::Security.
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified

And then, real talk, this one is just sitting right there in the middle of everything like a lil warning sign 🚨:

sub initialize {

  carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. 🫶

💜 SLOTS

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes — use only if you understand the inner workings of the API, bestie. no casual touching 🔥 Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

$var = $obj->slot_name(); — retrieves the current value of the slot.
$new_var = $obj->slot_name($new_var); — store $new_var in the slot — the return value is also $new_var.
@names = $obj->get_slot_names() — returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods. 💀

🌸 ATTRIBUTES AND ASSOCIATIONS

The terms attribute and association indicate data members of the class that were specified directly from the UML model. like, the real ones 💅

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

get* — retrieves the current value.
- NOTE: for associations, if the association has list cardinality, an array reference is returned.
- DATA CHECKING: ensure that no argument is provided.
set* — sets the current value, replacing any existing value.
- NOTE: for associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
- DATA CHECKING: for attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.
add* — NOTE: only present in associations with list cardinality.
- Appends a list of objects to any values that may already be stored in the association.
- DATA CHECKING: ensure that all arguments are of the correct MAGE-OM class.

🌈 GENERIC METHODS 🌈

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. 👀

🐛 BUGS

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

👑 AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org)

🔗 SEE ALSO

perl(1).

💀 POD ERRORS

Hey! The above document had some coding errors, which are explained below. not me getting caught in 4k 🙈

Around line 491:
- '=item' outside of any '=over'
Around line 576:
- You forgot a '=back' before '=head2'
Around line 748:
- Expected '=item 2'
Around line 753:
- Expected '=item 3'
Around line 758:
- Expected '=item 4'

And that's a wrap, bestie 🎬✨ this lil page is perl v5.32.0, dated 2020-11-27, and it goes by MAGE::...ayData(3pm). you ate that, fr fr 💅🫶

📦 where this page comes from

debian bookworm: libbio-mage-perl 20030502.3-6 · MIT
debian trixie: libbio-mage-perl 20030502.3-6 · MIT
ubuntu jammy: libbio-mage-perl 20030502.3-6 · MIT
ubuntu noble: libbio-mage-perl 20030502.3-6 · MIT
ubuntu resolute: libbio-mage-perl 20030502.3-6 · MIT
ubuntu stonking: libbio-mage-perl 20030502.3-6 · MIT
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms