MAGE::...tyGroup(3pm)

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

💖 NAME 💖

Bio::MAGE::AuditAndSecurity::SecurityGroup — Class for the MAGE-OM API

okay so bestie, welcome to MAGE::...tyGroup(3pm) 💅 that's the one, that's the page, it's from the User Contributed Perl Documentation collection and it's giving very much "niche Perl module that runs your whole lab pipeline". let's get into it 🦋

✨ SYNOPSIS ✨

use Bio::MAGE::AuditAndSecurity::SecurityGroup

# creating an empty instance
my $securitygroup = Bio::MAGE::AuditAndSecurity::SecurityGroup->new();

# creating an instance with existing data
my $securitygroup = Bio::MAGE::AuditAndSecurity::SecurityGroup->new(
      name=>$name_val,
      identifier=>$identifier_val,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      members=>\@contact_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

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

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

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

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

# 'members' association
my $contact_array_ref = $securitygroup->members(); # getter
$securitygroup->members(\@contact_list); # setter

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

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

🌸 DESCRIPTION 🌸

so straight from the MAGE-OM documentation for the SecurityGroup class, and I quote:

Groups contacts together based on their security privileges.

that's it, that's the whole vibe. a group. of contacts. sorted by what they're allowed to do. security privileges 💅

🎀 INHERITANCE 🎀

Bio::MAGE::AuditAndSecurity::SecurityGroup has the following superclasses (its whole ancestry, its bloodline, its main character lineage):

Bio::MAGE::Identifiable

👑 CLASS METHODS 👑

the following methods can all be called without first having an instance of the class, using the syntax:

Bio::MAGE::AuditAndSecurity::SecurityGroup->methodname()

like, you don't need an object to call these. they live at the class level. iconic behaviour fr fr ✨

💜 new()

💜 new(%args)

The object constructor new() accepts the following optional named-value style arguments — all of them optional, none of them required, she's flexible:

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).
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.

members — Sets the value of the members association

The value must be of type: array of Bio::MAGE::AuditAndSecurity::Contact.

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 blueprint. the origin story.

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. just so we're clear, bestie 🙈

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. like a clone, but make it fashion 💅

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. two doors, same room, pick your fave 🚪✨

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. one to put the value in, one to get the value out. balanced. symmetrical. chi 🧚

Bio::MAGE::AuditAndSecurity::SecurityGroup has the following attribute accessor methods:

💖 name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $securitygroup->setName($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 = $securitygroup->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 = $securitygroup->setIdentifier($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 = $securitygroup->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 maybe included in the association. so basically: how many of the other thing are we legally allowed to link up in here 🔗

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::AuditAndSecurity::SecurityGroup 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 = $securitygroup->setAuditTrail($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

okay so that's the setter, now let's get into the getter and adder, bestie. 💖

`$array_ref = $securitygroup->getAuditTrail()`

The restricted getter method for the auditTrail association. It's giving just give me the goods, no questions asked. 🫶

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 = $securitygroup->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

So you can add a whole squad or just one, we don't judge. periodt. 👑

✨ propertySets ✨

Methods for the propertySets association.

From the MAGE-OM documentation: This lets you specify name/value pairs. It's mainly for helping in-house pipeline processing of instances by giving you a spot for values that aren't part of the spec proper. 💅

`$array_ref = $securitygroup->setPropertySets($array_ref)`

The restricted setter method for the propertySets association. Slay.

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 = $securitygroup->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 = $securitygroup->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

🎀 members 🎀

Methods for the members association.

From the MAGE-OM documentation: The members of the Security Group, periodt. 💜

`$array_ref = $securitygroup->setMembers($array_ref)`

The restricted setter method for the members association.

Input parameters: the value to which the members association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the members association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
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::Contact instances

`$array_ref = $securitygroup->getMembers()`

The restricted getter method for the members association.

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

`$val = $securitygroup->addMembers(@vals)`

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

Input parameters: the list of values @vals to add to the members 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::Contact

🦋 descriptions 🦋

Methods for the descriptions association.

From the MAGE-OM documentation: Free hand text descriptions. It makes available the associations of Description to an instance of Describable. 🌈

`$array_ref = $securitygroup->setDescriptions($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 = $securitygroup->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 = $securitygroup->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: Info on the security for the instance of the class. 🔥

`$val = $securitygroup->setSecurity($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 = $securitygroup->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 here's the initialize sub, just in case you need it:

sub initialize {

  my $self = shift;
  return 1;

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

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

🌸 SLOTS 🌸

This API uses the term "slot" to mean 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:

$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:

Around line 349:
- '=item' outside of any '=over'
Around line 434:
- You forgot a '=back' before '=head2'
Around line 606:
- Expected '=item 2'
Around line 611:
- Expected '=item 3'
Around line 616:
- Expected '=item 4'

And that's the whole vibe, bestie — this page is from perl v5.32.0, dated 2020-11-27, and it's the MAGE::...tyGroup(3pm) manpage. Slay. 💅✨

📦 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