MAGE::...zation(3pm)

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

💖 MAGE::...zation(3pm) 💖

okay so welcome to the manpage for MAGE::...zation(3pm), straight outta the User Contributed Perl Documentation collection. it's giving extremely specific bioinformatics, and honestly? we're obsessed. buckle up bestie 🎀

✨ NAME ✨

Bio::MAGE::AuditAndSecurity::Organization — the Class for the MAGE-OM API. yeah. that's the whole vibe. 💅

🌸 SYNOPSIS 🌸

okay so here's literally everything you can do, no cap:

use Bio::MAGE::AuditAndSecurity::Organization

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

# creating an instance with existing data
my $organization = Bio::MAGE::AuditAndSecurity::Organization->new(
      URI=>$uri_val,
      name=>$name_val,
      phone=>$phone_val,
      email=>$email_val,
      identifier=>$identifier_val,
      tollFreePhone=>$tollfreephone_val,
      fax=>$fax_val,
      address=>$address_val,
      roles=>\@ontologyentry_list,
      parent=>$organization_ref,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

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

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

# 'phone' attribute
my $phone_val = $organization->phone(); # getter
$organization->phone($value); # setter

# 'email' attribute
my $email_val = $organization->email(); # getter
$organization->email($value); # setter

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

# 'tollFreePhone' attribute
my $tollFreePhone_val = $organization->tollFreePhone(); # getter
$organization->tollFreePhone($value); # setter

# 'fax' attribute
my $fax_val = $organization->fax(); # getter
$organization->fax($value); # setter

# 'address' attribute
my $address_val = $organization->address(); # getter
$organization->address($value); # setter

# 'roles' association
my $ontologyentry_array_ref = $organization->roles(); # getter
$organization->roles(\@ontologyentry_list); # setter

# 'parent' association
my $organization_ref = $organization->parent(); # getter
$organization->parent($organization_ref); # setter

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

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

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

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

🦋 DESCRIPTION 🦋

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

Organizations are entities like companies, universities, government agencies for which the attributes are self describing.

fr fr. companies, unis, government agencies — the whole roster. and the attributes just describe themselves. main character energy tbh 👑

💜 INHERITANCE 💜

Bio::MAGE::AuditAndSecurity::Organization has the following superclasses:

Bio::MAGE::AuditAndSecurity::Contact

that's the family tree, bestie. it inherits. as one does. 🌈

🔥 CLASS METHODS 🔥

the way that all of these can be called without having an instance first — you just use the Bio::MAGE::AuditAndSecurity::Organization->methodname() syntax. iconic. no object required, we're just built different. ✨

`new()`

`new(%args)`

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

URI — sets the value of the "URI" attribute. heads up: this attribute was inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
name — sets the value of the "name" attribute. this one was inherited from class "Bio::MAGE::Identifiable".
phone — sets the value of the "phone" attribute. inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
email — sets the value of the "email" attribute. inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
identifier — sets the value of the "identifier" attribute. inherited from class "Bio::MAGE::Identifiable".
tollFreePhone — sets the value of the "tollFreePhone" attribute. inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
fax — sets the value of the "fax" attribute. inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
address — sets the value of the "address" attribute. inherited from class "Bio::MAGE::AuditAndSecurity::Contact".
roles — sets the value of the "roles" association. inherited from class "Bio::MAGE::AuditAndSecurity::Contact". the value must be of type: array of Bio::MAGE::Description::OntologyEntry.
parent — sets the value of the "parent" association. the value must be of type: instance of Bio::MAGE::AuditAndSecurity::Organization.
auditTrail — sets the value of the "auditTrail" association. 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. 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. 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. 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 whole moment. 💅

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. periodt.

`@name_list = get_association_names()`

returns the list of association data members for this class. also periodt.

`@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. iykyk 🧚

💀 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. it's giving clone era. 💅

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 ways to do the same slay. ✨

Return value: none
Side effects: will call "croak()" if a slot_name is used that the class does not define.

bestie that croak() is real. use a slot name the class doesn't define and it's over for you. 😭

`@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 for reading, one for writing, no crossover. very demure. 💅

"Bio::MAGE::AuditAndSecurity::Organization" has the following attribute accessor methods:

`URI`

methods for the "URI" attribute.

from the MAGE-OM documentation:

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

the restricted setter method for the "URI" attribute.
Input parameters: the value to which the "URI" attribute will be set
Return value: the current value of the "URI" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getURI()

the restricted getter method for the "URI" attribute.
Input parameters: none
Return value: the current value of the "URI" attribute
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified

`name`

methods for the "name" attribute.

from the MAGE-OM documentation:

the potentially ambiguous common identifier.

Okay so for the name attribute — it's giving classic getter/setter energy, no drama, just vibes. 🎀

$val = $organization->setName($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 = $organization->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

📞 phone

Methods for the "phone" attribute.

From the MAGE-OM documentation:

$val = $organization->setPhone($val)

The restricted setter method for the "phone" attribute.

Input parameters: the value to which the "phone" attribute will be set
Return value: the current value of the "phone" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getPhone()

The restricted getter method for the "phone" attribute.

Input parameters: none
Return value: the current value of the "phone" attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

💌 email

Methods for the "email" attribute.

From the MAGE-OM documentation:

$val = $organization->setEmail($val)

The restricted setter method for the "email" attribute.

Input parameters: the value to which the "email" attribute will be set
Return value: the current value of the "email" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getEmail()

The restricted getter method for the "email" attribute.

Input parameters: none
Return value: the current value of the "email" 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 = $organization->setIdentifier($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 = $organization->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

☎️ tollFreePhone

Methods for the "tollFreePhone" attribute.

From the MAGE-OM documentation:

$val = $organization->setTollFreePhone($val)

The restricted setter method for the "tollFreePhone" attribute.

Input parameters: the value to which the "tollFreePhone" attribute will be set
Return value: the current value of the "tollFreePhone" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getTollFreePhone()

The restricted getter method for the "tollFreePhone" attribute.

Input parameters: none
Return value: the current value of the "tollFreePhone" attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

📠 fax

Methods for the "fax" attribute.

From the MAGE-OM documentation:

$val = $organization->setFax($val)

The restricted setter method for the "fax" attribute.

Input parameters: the value to which the "fax" attribute will be set
Return value: the current value of the "fax" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getFax()

The restricted getter method for the "fax" attribute.

Input parameters: none
Return value: the current value of the "fax" attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

🏠 address

Methods for the "address" attribute.

From the MAGE-OM documentation:

$val = $organization->setAddress($val)

The restricted setter method for the "address" attribute.

Input parameters: the value to which the "address" attribute will be set
Return value: the current value of the "address" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $organization->getAddress()

The restricted getter method for the "address" attribute.

Input parameters: none
Return value: the current value of the "address" attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

🔗 ASSOCIATIONS

Okay bestie, now we're getting into the networking part of the codebase. 💅 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:

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.

So Bio::MAGE::AuditAndSecurity::Organization has the following association accessor methods:

🎭 roles

Methods for the "roles" association.

From the MAGE-OM documentation:

The roles (lab equipment sales, contractor, etc.) the contact fills.

$array_ref = $organization->setRoles($array_ref)

The restricted setter method for the "roles" association.

Input parameters: the value to which the "roles" association will be set : a reference to an array of objects of type "Bio::MAGE::Description::OntologyEntry"
Return value: the current value of the "roles" association : a reference to an array of objects of type "Bio::MAGE::Description::OntologyEntry"
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::OntologyEntry" instances

$array_ref = $organization->getRoles()

The restricted getter method for the "roles" association.

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

$val = $organization->addRoles(@vals)

Because the roles association has list cardinality, it may store more than one value. This method adds the current list of objects in the roles association. (yesss, stack 'em up 🫶)

Input parameters: the list of values @vals to add to the roles 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::OntologyEntry"

🧬 parent

Methods for the "parent" association.

From the MAGE-OM documentation:

The containing organization (the university or business which a lab belongs to, etc.)

$val = $organization->setParent($val)

The restricted setter method for the "parent" association.

Input parameters: the value to which the "parent" association will be set : one of the accepted enumerated values.
Return value: the current value of the "parent" 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::Organization"

$val = $organization->getParent()

The restricted getter method for the "parent" association.

Input parameters: none
Return value: the current value of the "parent" association : an instance of type "Bio::MAGE::AuditAndSecurity::Organization".
Side effects: none
Exceptions: 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 = $organization->setAuditTrail($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 = $organization->getAuditTrail()`

The restricted getter method for the auditTrail association. It's giving "just hand over the array ref, bestie" 💅

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 = $organization->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 = $organization->setPropertySets($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 = $organization->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 = $organization->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 = $organization->setDescriptions($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 = $organization->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 = $organization->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 = $organization->setSecurity($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 = $organization->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, looking all cute and simple:

sub initialize {

  my $self = shift;
  return 1;

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

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

✨ 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:

$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 422: '=item' outside of any '=over'

Around line 507: You forgot a '=back' before '=head2'

Around line 1111: Expected '=item 2'

Around line 1116: Expected '=item 3'

Around line 1121: Expected '=item 4'

This whole vibe was brought to you by perl v5.32.0, dated 2020-11-27, and the page is MAGE::...zation(3pm). Stay slaying, bestie 💖✨🦋

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