MAGE::...ribable(3pm)

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

✨ NAME ✨

okay bestie, this is the MAGE::...ribable(3pm) manual page from the User Contributed Perl Documentation, and the star of the show is:

Bio::MAGE::Describable — Class for the MAGE-OM API 💅

🦋 SYNOPSIS 🦋

Here’s the code vibe, fr fr:

use Bio::MAGE::Describable

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

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

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

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

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

🌸 DESCRIPTION 🌸

The MAGE-OM documentation for the Describable class says it’s an abstract class that lets subclasses inherit the association to Description — for detailed annotations such as Ontology entries and Database references — plus the association to Audit for tracking changes, and the association to Security for indicating permissions. 🫶

Bio::MAGE::Describable is an abstract base class and should not be directly instantiated. Instead it serves as an interface definition for its subclasses. No cap. 🚫

👑 INHERITANCE 👑

Bio::MAGE::Describable has the following superclasses:

  • Bio::MAGE::Extendable

Bio::MAGE::Describable has the following subclasses:

  • Bio::MAGE::HigherLevelAnalysis::Node
  • Bio::MAGE::HigherLevelAnalysis::NodeContents
  • Bio::MAGE::Description::Description
  • Bio::MAGE::AuditAndSecurity::Audit
  • Bio::MAGE::Identifiable
  • Bio::MAGE::Array::Fiducial
  • Bio::MAGE::BQS::BibliographicReference
  • Bio::MAGE::Experiment::ExperimentDesign
  • Bio::MAGE::Array::ManufactureLIMS
  • Bio::MAGE::BioSequence::SeqFeature
  • Bio::MAGE::Protocol::ParameterizableApplication

⭐ CLASS METHODS ⭐

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

new()

new(%args)

Bio::MAGE::Describable 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:

  • auditTrail — Sets the value of the auditTrail association. 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. The value must be of type: array of Bio::MAGE::Description::Description. 💖
  • security — Sets the value of the security association. 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 🎀

okay bestie, these are the ones you actually call on a thing you already made. let's go 💅

✨ $obj_copy = $obj->new() ✨

When you call this on an existing object reference instead of on a class name, new() moonlights as a copy constructor — the new object's initial values get set to be exactly those of the existing object. it's giving clone arc, no cap 🦋

  • 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) ✨

set_slots() is your "set a bunch of slots at once" bestie. She 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. so like… don't do that 🙈

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

get_slots() grabs the values of a bunch of slots all at once. efficiency queen 👑

  • Return value: a list of instance objects
  • Side effects: none

✨ $val = $obj->set_slot($name,$val) ✨

set_slot() sets the slot $name to the value $val. one slot, one value, simple as 🌸

  • Return value: the new value of the slot, i.e. $val
  • Side effects: none

✨ $val = $obj->get_slot($name) ✨

get_slot() is used to get the values of a number of slots at the same time. (that's what the docs say, bestie, I'm just the messenger 🫶)

  • 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. so like, one method to put a value in, one method to get it out. balanced. iconic. ✨

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

💜 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 maybe included in the association:

  1. There must be exactly one item in the association, i.e. this is a mandatory data field.
  2. 0..1 There may be one item in the association, i.e. this is an optional data field.
  3. 1..N There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
  4. 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::Describable has the following association accessor methods:

🦋 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 = $describable->setAuditTrail($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 = $describable->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 = $describable->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.

$array_ref = $describable->setPropertySets($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 = $describable->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 = $describable->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 = $describable->setDescriptions($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 = $describable->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 = $describable->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 = $describable->setSecurity($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 = $describable->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, bestie, this little guy just… lives at the bottom of the section. no explanation. he's just there. respect. 💀

sub initialize {

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

}
ngl, that carp is the class itself telling you "girl, you are NOT supposed to instantiate an abstract base class." listen to her. 🙈

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

okay bestie so here's the tea on how MAGE-OM classes in Perl hold their data. There are three whole flavors of class data members, and you gotta know which is which: "slots", "attributes", and "associations". ✨

🎀 SLOTS 🎀

So in this API, the word "slot" means a data member of the class that wasn't in the UML model at all — it's there mostly for internal purposes. Translation: only touch these if you actually understand the inner workings of the API, fr fr. 💅

Most of the time, slots are the ones getting used by generic methods — like the ones hanging out in the XML writing and reading classes. iykyk.

Slots get implemented with unified getter/setter methods, and here's the whole set:

  • $var = $obj->slot_name(); — grabs the current value of the slot. 💖
  • $new_var = $obj->slot_name($new_var); — stores $new_var in the slot, and the return value is also $new_var. cute, right?
  • @names = $obj->get_slot_names() — hands you back the list of all the slots in the class. the whole roster.
DATA CHECKING: literally none. No data type checking is made for these methods. 🫣 so be careful, bestie.

🌸 ATTRIBUTES AND ASSOCIATIONS 🌸

Okay so the terms "attribute" and "association" both mean data members of the class that came directly from the UML model. so like, officially specified, not internal sneaky stuff.

In the Perl implementation of MAGE-OM classes, association and attribute accessors get implemented using three separate methods — and yes, you have to keep track of all three. 👑

  • 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. (not me warning you in advance 💀)
    • 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, is out here providing a whole set of generic methods that operate on slots, attributes, and associations. main character energy, honestly. 💜

$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. (yes, go look, it's all there 👀)

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net). they wanna hear from you, fr.

👑 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:

  • Around line 400:
    • '=item' outside of any '=over'
  • Around line 485:
    • You forgot a '=back' before a '=head2'
  • Around line 513:
    • Expected '=item 2'
  • Around line 518:
    • Expected '=item 3'
  • Around line 523:
    • Expected '=item 4'

and that's a wrap on the whole page, bestie!! 🫶 this was perl v5.32.0, dated 2020-11-27, from the MAGE::...ribable(3pm) era — slay, go forth and build your MAGE-OM objects responsibly 💅✨

📦 where this page comes from