MAGE::...fiable(3pm)

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

✨ MAGE::...fiable — the `Bio::MAGE::Identifiable` page 💖

(that's the MAGE::...fiable(3pm) page from your User Contributed Perl Documentation, bestie 🫶)

🌸 NAME 🌸

Bio::MAGE::Identifiable — it's the class for the MAGE-OM API, periodt.

✨ SYNOPSIS ✨

use Bio::MAGE::Identifiable

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

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

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

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

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

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

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

💅 DESCRIPTION 💅

Straight from the MAGE-OM documentation for the Identifiable class, no cap:

An Identifiable class is one that has an unambiguous reference within the scope. It also has a potentially ambiguous name.

So here's the tea, bestie: Bio::MAGE::Identifiable is an abstract base class and you should not instantiate it directly. Nope. Not the vibe. Instead it just sits there being an interface definition for all its subclasses. It's giving "I don't do the work, I define the work" energy. 👑

🦋 INHERITANCE 🦋

Bio::MAGE::Identifiable has these superclasses (aka its parents, its ancestry, its bloodline 💜):

Bio::MAGE::Describable

And these are all its subclasses (the lil baby classes that inherit from it, so many, iconic honestly):

Bio::MAGE::QuantitationType::QuantitationType
Bio::MAGE::ArrayDesign::ArrayDesign
Bio::MAGE::Description::Database
Bio::MAGE::BioAssay::Image
Bio::MAGE::BioAssay::BioAssay
Bio::MAGE::BioAssay::Channel
Bio::MAGE::AuditAndSecurity::Security
Bio::MAGE::DesignElement::DesignElement
Bio::MAGE::ArrayDesign::Zone
Bio::MAGE::AuditAndSecurity::SecurityGroup
Bio::MAGE::AuditAndSecurity::Contact
Bio::MAGE::ArrayDesign::DesignElementGroup
Bio::MAGE::BioAssayData::BioAssayData
Bio::MAGE::BioAssayData::QuantitationTypeDimension
Bio::MAGE::BioAssayData::DesignElementDimension
Bio::MAGE::Array::Array
Bio::MAGE::Array::ArrayGroup
Bio::MAGE::BioAssayData::BioAssayDimension
Bio::MAGE::Array::ArrayManufacture
Bio::MAGE::BioEvent::BioEvent
Bio::MAGE::Experiment::Experiment
Bio::MAGE::Experiment::ExperimentalFactor
Bio::MAGE::Experiment::FactorValue
Bio::MAGE::Protocol::Parameter
Bio::MAGE::BioMaterial::BioMaterial
Bio::MAGE::BioMaterial::Compound
Bio::MAGE::BioSequence::BioSequence
Bio::MAGE::Protocol::Parameterizable
Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster

👑 CLASS METHODS 👑

Okay so all of these methods can be called without having an instance first, using the Bio::MAGE::Identifiable->methodname() syntax. Class-level slay. ✨

`new()`

`new(%args)`

Bio::MAGE::Identifiable is an abstract base class so do NOT directly instantiate it with the new() constructor. It's listed here just to show you what arguments its subclasses will accept. It's a preview, not an invitation, bestie. 🙈

The object constructor new() accepts these optional named-value style arguments:

name — sets the value of the name attribute.
identifier — sets the value of the identifier attribute.
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.
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.
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. The main character of constructors, honestly.

Parameters: if you hand it a list of name/value parameters, the corresponding slots, attributes, or associations get 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's defined by the class.

`@names = class->get_slot_names()`

The get_slot_names() method grabs the name of all the slots defined in a given class.

NOTE: the list of names does not include attribute or association names. Just slots. Don't get it twisted. 💅

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

Side effects: none. (so chill)

`@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 you invoke it with an existing object reference and not a class name, the new() method acts as a copy constructor — the new object's initial values get set to be those of the existing object. It's a clone, it's a twin, it's a copy-paste glow-up. 👯‍♀️

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's defined by the class.

`$obj->set_slots(%parameters)`

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

The set_slots() method is used to set a bunch 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. Pick your fighter. 🥊

Return value: none.

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

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

The get_slots() method is used to get the values of a bunch 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 bunch 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. One for setting, one for getting, they don't share, they're independent. ✨

Bio::MAGE::Identifiable has the following attribute accessor methods:

name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

`$val = $identifiable->setName($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 = $identifiable->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 = $identifiable->setIdentifier($val)`

The restricted setter method for the identifier attribute.

Input parameters: the value to which the identifier attribute will be set.

Return value: the current value of the identifier attribute.

Side effects: none.

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

`$val = $identifiable->getIdentifier()`

The restricted getter method for the identifier attribute.

Input parameters: none.

Return value: the current value of the identifier attribute.

Side effects: none.

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

🎀 ASSOCIATIONS 🎀

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that may be included in the association:

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::Identifiable` has the following association accessor methods 💅

🎀 `auditTrail`

Methods for the "auditTrail" association, bestie.

From the MAGE-OM documentation:

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

$array_ref = $identifiable->setAuditTrail($array_ref) — the restricted setter method 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: 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 = $identifiable->getAuditTrail() — the restricted getter method 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: will call croak() if any input parameters are specified
$val = $identifiable->addAuditTrail(@vals) — because the auditTrail association has list cardinality, it may store more than one value. 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: 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. iykyk 💅

$array_ref = $identifiable->setPropertySets($array_ref) — the restricted setter method 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: 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 = $identifiable->getPropertySets() — the restricted getter method 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: will call croak() if any input parameters are specified
$val = $identifiable->addPropertySets(@vals) — because the propertySets association has list cardinality, it may 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: 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

💜 `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 = $identifiable->setDescriptions($array_ref) — the restricted setter method for the "descriptions" association.
- 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 = $identifiable->getDescriptions() — the restricted getter method for the "descriptions" association.
- 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 = $identifiable->addDescriptions(@vals) — 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. 📝
- 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

👑 `security`

Methods for the "security" association.

From the MAGE-OM documentation:

Information on the security for the instance of the class. 🔐

$val = $identifiable->setSecurity($val) — the restricted setter method 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 = $identifiable->getSecurity() — the restricted getter method 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 there's this lil guy, no cap:

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". Three whole vibes. 🫶

⭐ 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. 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.

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. Main character energy fr fr. 👑

$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 🐛

okay so if you find a bug (and bestie, you will, that's just how it goes 💀) do not just scream into the void about it. Slide into the project mailing list instead:

mged-mage 'at' lists 'dot' sf 'dot' net — that's the address, and yes you have to do the little 'at' and 'dot' dance yourself, they wrote it that way on purpose to dodge the spam bots 🫶

👑 AUTHOR 👑

this whole thing was written by Jason E. Stewart, reachable at jasons 'at' cpan 'dot' org — same deal with the 'at' and 'dot', you know the drill 💅

🌈 SEE ALSO 🌈

perl(1) — literally the blueprint, the source, the mother of us all. go read it if you wanna know how any of this is even possible ✨

💀 POD ERRORS 💀

okay so not me having to tell you this, but the documentation itself came with receipts 📜 and the receipts say the docs had some coding errors. like, the docs about the docs. it's giving meta. here's what the parser was screaming about, in order:

Around line 409:
- '=item' outside of any '=over' — bestie put an item where there was no list to be in 😭
Around line 494:
- You forgot a '=back' before '=head2' — left a list open, walked away, never closed it. classic 🙈
Around line 666:
- Expected '=item 2' — the numbering said 2 was coming and 2 did not show up
Around line 671:
- Expected '=item 3' — same energy, now it's 3 ghosting us
Around line 676:
- Expected '=item 4' — and 4 also just… never arrived. the whole numbered list stood them up 💀

ngl these are cosmetic problems in the POD markup, not in the actual code, so like. the vibes are off but the ship still sails 🚢 but still — if you're editing the docs, close your lists, bestie, it costs nothing 🌸

and that's a wrap on this whole page, fr fr 🎀 this version is from perl v5.32.0, dated 2020-11-27, and it's the user-contributed Perl documentation for MAGE::...fiable(3pm) — go forth and automate, you absolute icon 👑💖✨

📦 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

MAGE::...fiable(3pm)

✨ MAGE::...fiable — the Bio::MAGE::Identifiable page 💖

🌸 NAME 🌸

✨ SYNOPSIS ✨

💅 DESCRIPTION 💅

🦋 INHERITANCE 🦋

👑 CLASS METHODS 👑

new()

new(%args)

$obj = class->new(%parameters)

@names = class->get_slot_names()

@name_list = get_attribute_names()

@name_list = get_association_names()

@class_list = get_superclasses()

@class_list = get_subclasses()

$name = class_name()

$package_name = package_name()

%assns = associations()

💜 INSTANCE METHODS 💜

$obj_copy = $obj->new()

$obj->set_slots(%parameters)

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

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

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

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

🌈 ATTRIBUTES 🌈

name

$val = $identifiable->setName($val)

$val = $identifiable->getName()

identifier

$val = $identifiable->setIdentifier($val)

$val = $identifiable->getIdentifier()

🎀 ASSOCIATIONS 🎀

✨ Bio::MAGE::Identifiable has the following association accessor methods 💅

🎀 auditTrail

🦋 propertySets

💜 descriptions

👑 security

🌈 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌈

⭐ SLOTS

🎀 ATTRIBUTES AND ASSOCIATIONS

💖 GENERIC METHODS

🐛 BUGS 🐛

👑 AUTHOR 👑

🌈 SEE ALSO 🌈

💀 POD ERRORS 💀

✨ MAGE::...fiable — the `Bio::MAGE::Identifiable` page 💖

`new()`

`new(%args)`

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

`@names = class->get_slot_names()`

`@name_list = get_attribute_names()`

`@name_list = get_association_names()`

`@class_list = get_superclasses()`

`@class_list = get_subclasses()`

`$name = class_name()`

`$package_name = package_name()`

`%assns = associations()`

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

`$obj->set_slots(%parameters)`

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

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

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

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

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

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

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

`$val = $identifiable->getIdentifier()`

✨ `Bio::MAGE::Identifiable` has the following association accessor methods 💅

🎀 `auditTrail`

🦋 `propertySets`

💜 `descriptions`

👑 `security`