MAGE::...rizable(3pm)

πŸ’– Bio::MAGE::Protocol::Parameterizable πŸ’–

okay so bestie, welcome to the manual page for Bio::MAGE::Protocol::Parameterizable β€” it's a 3pm page from the User Contributed Perl Documentation, and we're about to make it make sense fr fr. ✨


🌸 NAME 🌸

Bio::MAGE::Protocol::Parameterizable β€” the class for the MAGE-OM API. that's it, that's the name, she's an icon, no cap. πŸ’…


✨ SYNOPSIS ✨

okay so here's the vibe. first you pull her in:

use Bio::MAGE::Protocol::Parameterizable

but lowkey β€” and this is important bestie β€” Bio::MAGE::Protocol::Parameterizable is an abstract base class and should not be directly instantiated. so like, these examples are just showing you how subclass objects will behave. she's giving main character energy but she's not the one you actually talk to, iykyk. 🫢

# 'URI' attribute
my $URI_val = $parameterizable->URI(); # getter
$parameterizable->URI($value); # setter

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

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

# 'parameterTypes' association
my $parameter_array_ref = $parameterizable->parameterTypes(); # getter
$parameterizable->parameterTypes(\@parameter_list); # setter

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

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

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

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

🌈 DESCRIPTION 🌈

straight from the MAGE-OM documentation for the "Parameterizable" class, and I quote:

The Parameterizable interface encapsulates the association of Parameters with ParameterValues. πŸ’œ

and like, that's the whole point of her. but also β€” Bio::MAGE::Protocol::Parameterizable is an abstract base class and should not be directly instantiated. instead, she serves as an interface definition for her subclasses. she's the blueprint, not the building. ✨


πŸ¦‹ INHERITANCE πŸ¦‹

so who does she come from? Bio::MAGE::Protocol::Parameterizable has the following superclasses:

  • Bio::MAGE::Identifiable

and who's in her family tree coming after her? Bio::MAGE::Protocol::Parameterizable has the following subclasses:

  • Bio::MAGE::Protocol::Protocol
  • Bio::MAGE::Protocol::Software
  • Bio::MAGE::Protocol::Hardware

she's literally the mother of them all. iconic. πŸ‘‘


⭐ CLASS METHODS ⭐

okay so these methods? you can call all of them without even having an instance of the class first β€” just use the Bio::MAGE::Protocol::Parameterizable->methodname() syntax and you're good. πŸ’…

πŸŽ€ new()

πŸŽ€ new(%args)

so Bio::MAGE::Protocol::Parameterizable is an abstract base class and should not be directly instantiated using the "new()" constructor β€” she said don't do it. but she's listed here anyway so you can see what arguments her subclasses will accept. 🫢

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

  • URI β€” sets the value of the "URI" attribute ✨
  • name β€” sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable"). πŸ’–
  • identifier β€” sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable"). πŸ’–
  • parameterTypes β€” sets the value of the "parameterTypes" association. The value must be of type: array of "Bio::MAGE::Protocol::Parameter". 🌸
  • auditTrail β€” 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 β€” 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 β€” 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 β€” 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". 🌸

πŸŽ€ $obj = class->new(%parameters)

the "new()" method is the class constructor, bestie. the moment of creation. πŸ’«

  • Parameters: if you give her 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. πŸŽ€
  • Side effects: it invokes the "initialize()" method if it's defined by the class. πŸ‘€

πŸŽ€ @names = class->get_slot_names()

the "get_slot_names()" method is how you retrieve the name of all slots defined in a given class. get you a method that can do both. πŸ’…

NOTE: the list of names does not include attribute or association names. okay so don't come for her about it. πŸ™ˆ
  • Return value: a list of the names of all slots defined for this class. ✨
  • Side effects: none. she's chill. πŸ¦‹

πŸŽ€ @name_list = get_attribute_names()

returns the list of attribute data members for this class. slay. πŸ’–


πŸŽ€ @name_list = get_association_names()

returns the list of association data members for this class. also slay. πŸ’–


πŸŽ€ @class_list = get_superclasses()

returns the list of superclasses for this class. family reunion energy. πŸ‘‘


πŸŽ€ @class_list = get_subclasses()

returns the list of subclasses for this class. the children!! πŸ₯Ή


πŸŽ€ $name = class_name()

returns the full class name for this class. the whole government name. πŸ’…


πŸŽ€ $package_name = package_name()

returns the base package name (i.e. no 'namespace::') of the package that contains this class. just the first name, no last name energy. πŸŽ€


πŸŽ€ %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. very meta of her. ✨


πŸ’œ INSTANCE METHODS πŸ’œ

πŸŽ€ $obj_copy = $obj->new()

when you invoke this with an existing object reference instead of a class name, the "new()" method acts as a copy constructor β€” with the new object's initial values set to be those of the existing object. twin energy fr fr. πŸ‘―

  • 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. πŸ‘€

πŸŽ€ $obj->set_slots(%parameters)

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

the "set_slots()" method is for setting a bunch of slots at the same time, and she's flexible like that β€” she's got two different invocation methods. the first takes a named parameter list, and the second takes two array references. pick your fighter. πŸ’…

  • Return value: none. πŸ¦‹
  • Side effects: will call "croak()" if a slot_name is used that the class does not define. so like, don't try it. 😭

πŸŽ€ @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. efficiency queen. ✨

  • Return value: a list of instance objects. πŸŽ€
  • Side effects: none. πŸ’–

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

the "set_slot()" method sets the slot $name to the value $val. one slot, one value, no drama. πŸ’…

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

πŸŽ€ $val = $obj->get_slot($name)

the "get_slot()" method is used to get the values of a number of slots at the same time. (yes, that's what the docs say, we're not editing her.) πŸ“

  • Return value: a single slot value, or undef if the slot has not been initialized. πŸ™ˆ
  • Side effects: none. πŸ’œ

🌸 ATTRIBUTES 🌸

okay so 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. very demure, very mindful. πŸŽ€

"Bio::MAGE::Protocol::Parameterizable" has the following attribute accessor methods:

πŸŽ€ URI

methods for the "URI" attribute. ✨

from the MAGE-OM documentation:

Where an instantiated Parameterizable is located. πŸ’œ

$val = $parameterizable->setURI($val)

the restricted setter method for the "URI" attribute. πŸ”’

  • Input parameters: the value to which the "URI" attribute will be set. ✨
  • Return value: the current value of the "URI" attribute. πŸŽ€
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified. 😭

$val = $parameterizable->getURI()

the restricted getter method for the "URI" attribute. πŸ”’

  • Input parameters: none. πŸ™…
  • Return value: the current value of the "URI" attribute. ✨
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if any input parameters are specified. 😭

πŸŽ€ name

methods for the "name" attribute. πŸ’–

from the MAGE-OM documentation:

The potentially ambiguous common identifier. πŸ’œ

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

the restricted setter method for the "name" attribute. πŸ”’

  • Input parameters: the value to which the "name" attribute will be set. ✨
  • Return value: the current value of the "name" attribute. πŸŽ€
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified. 😭

$val = $parameterizable->getName()

the restricted getter method for the "name" attribute. πŸ”’

  • Input parameters: none. πŸ™…
  • Return value: the current value of the "name" attribute. ✨
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if any input parameters are specified. 😭

πŸŽ€ identifier

methods for the "identifier" attribute. πŸ’–

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. πŸ’œ

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

the restricted setter method for the "identifier" attribute. πŸ”’

  • Input parameters: the value to which the "identifier" attribute will be set. ✨
  • Return value: the current value of the "identifier" attribute. πŸŽ€
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified. 😭

$val = $parameterizable->getIdentifier()

the restricted getter method for the "identifier" attribute. πŸ”’

  • Input parameters: none. πŸ™…
  • Return value: the current value of the "identifier" attribute. ✨
  • Side effects: none. πŸ¦‹
  • Exceptions: will call "croak()" if any input parameters are specified. 😭

and that's part 1 bestie, there's more coming so don't go anywhere πŸ’–βœ¨

πŸ¦‹ ASSOCIATIONS

okay bestie, this is the part where it gets good. Associations are basically references to other classes β€” like, the little red string connecting one object to another πŸ”—. Every association in MAGE-OM comes with a cardinality, which is just a fancy way of saying "how many of the other class's instances are allowed to be in here β€” minimum and maximum, no more no less":

  1. There must be exactly one item in the association, i.e. this is a mandatory data field.
  2. 0..1 β€” There may be one item in the association, i.e. this is an optional data field.
  3. 1..N β€” There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
  4. 0..N β€” There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::Protocol::Parameterizable has the following association accessor methods:


🌸 parameterTypes

Methods for the parameterTypes association.

From the MAGE-OM documentation:

The description of the parameters for the Parameterizable class instance.

$array_ref = $parameterizable->setParameterTypes($array_ref)

The restricted setter method for the parameterTypes association.

  • Input parameters: the value to which the parameterTypes association will be set : a reference to an array of objects of type Bio::MAGE::Protocol::Parameter
  • Return value: the current value of the parameterTypes association : a reference to an array of objects of type Bio::MAGE::Protocol::Parameter
  • 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::Protocol::Parameter instances

$array_ref = $parameterizable->getParameterTypes()

The restricted getter method for the parameterTypes association.

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

$val = $parameterizable->addParameterTypes(@vals)

Because the parameterTypes association has list cardinality, it may store more than one value. This method adds the current list of objects in the parameterTypes association.

  • Input parameters: the list of values @vals to add to the parameterTypes 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::Protocol::Parameter

πŸ¦‹ 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 = $parameterizable->setAuditTrail($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 = $parameterizable->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 = $parameterizable->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

πŸŽ€ 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 = $parameterizable->setPropertySets($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 = $parameterizable->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 = $parameterizable->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 = $parameterizable->setDescriptions($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 = $parameterizable->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 = $parameterizable->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

πŸ”’ security

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $parameterizable->setSecurity($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 = $parameterizable->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
sub initialize {
             carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

           }

so yeah, that's the carp at the end of initialize β€” it complains at whoever called it, not at the module itself, and then the block just... closes. πŸ’€ classic.


🌸 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌸

okay so in the Perl implementation of MAGE-OM classes, there are three whole flavors of class data members, and you will be expected to know which one you're dealing with:

  • slots
  • attributes
  • associations

✨ SLOTS ✨

bestie, listen. This API uses the term "slot" to mean a data member of the class that was not present in the UML model β€” it's there for mainly internal purposes. So: use only if you understand the inner workings of the API. πŸ™ˆ Most often, slots get used by generic methods like the ones in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

  • $var = $obj->slot_name(); β€” grabs the current value of the slot.
  • $new_var = $obj->slot_name($new_var); β€” stores $new_var in the slot, and the return value is also $new_var. (yes, it gives you back exactly what you handed it. iconic behavior. πŸ’…)
  • @names = $obj->get_slot_names() β€” returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods. 🫠 none. zero. nada.

🌈 ATTRIBUTES AND ASSOCIATIONS 🌈

The terms "attribute" and "association" mean data members of the class that were specified directly from the UML model. so like, the real ones, not the internal ones.

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

  • get* β€” 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* β€” 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 instead. (fr fr, just use add*.)
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* β€” appends a list of objects to any values that may already be stored in the association.
NOTE: Only present in associations with list cardinality.
DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

πŸ¦‹ GENERIC METHODS πŸ¦‹

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. one class to rule them all, truly:

$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. πŸ‘€ (iykyk)


πŸ’€ BUGS πŸ’€

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

yes the email is written out with 'at' and 'dot' because we are all collectively avoiding spam bots. respect the craft. πŸŽ€


πŸ‘‘ AUTHOR πŸ‘‘

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


⭐ SEE ALSO ⭐

that's it. that's the whole list. go read perl(1). it's giving required reading. πŸ“š


πŸ™ˆ POD ERRORS πŸ™ˆ

Hey! The above document had some coding errors, which are explained below:

  • Around line 374:
    • '=item' outside of any '=over'
  • Around line 459:
    • You forgot a '=back' before '=head2'
  • Around line 703:
    • Expected '=item 2'
  • Around line 708:
    • Expected '=item 3'
  • Around line 713:
    • Expected '=item 4'

not the POD errors exposing the whole doc 😭 but honestly? relatable. we've all forgotten a =back.


and that's a wrap on this page, bestie πŸ’– this was perl v5.32.0, dated 2020-11-27, for MAGE::...rizable(3pm). go forth and instantiate responsibly βœ¨πŸ¦‹πŸŒΈ