MAGE::...erence(3pm)

✨ NAME ✨

Bio::MAGE::Description::ExternalReference — the class for the MAGE-OM API. 💅

Oh and hey, you're reading the MAGE::...erence(3pm) page, straight out of the User Contributed Perl Documentation. So you know it's gonna be a whole vibe. 🎀

---

🌸 SYNOPSIS 🌸

okay so here's the whole menu, bestie — copy-paste away:

use Bio::MAGE::Description::ExternalReference

# creating an empty instance
my $externalreference = Bio::MAGE::Description::ExternalReference->new();

# creating an instance with existing data
my $externalreference = Bio::MAGE::Description::ExternalReference->new(
      exportedFromDB=>$exportedfromdb_val,
      exportName=>$exportname_val,
      exportID=>$exportid_val,
      exportedFromServer=>$exportedfromserver_val,
      propertySets=>\@namevaluetype_list,
);

# 'exportedFromDB' attribute
my $exportedFromDB_val = $externalreference->exportedFromDB(); # getter
$externalreference->exportedFromDB($value); # setter

# 'exportName' attribute
my $exportName_val = $externalreference->exportName(); # getter
$externalreference->exportName($value); # setter

# 'exportID' attribute
my $exportID_val = $externalreference->exportID(); # getter
$externalreference->exportID($value); # setter

# 'exportedFromServer' attribute
my $exportedFromServer_val = $externalreference->exportedFromServer(); # getter
$externalreference->exportedFromServer($value); # setter

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

---

🦋 DESCRIPTION 🦋

So, straight from the MAGE-OM documentation for the ExternalReference class, and I quote:

A reference to the originating source for the object.

That's the whole thing. Short, sweet, iconic. It's giving "mysterious but essential." 💜

---

👑 INHERITANCE 👑

Bio::MAGE::Description::ExternalReference has the following superclasses, and yes she comes from good stock:

• Bio::MAGE::Extendable

---

💖 CLASS METHODS 💖

Okay this is the good part. All of the following methods can be called without first having an instance of the class — just use the

Bio::MAGE::Description::ExternalReference->methodname()

syntax. No object required, she's flexible like that. ✨

new()

new(%args)

The object constructor new() takes the following optional named-value style arguments, and it's lowkey obsessed with them:

• exportedFromDB — sets the value of the exportedFromDB attribute
• exportName — sets the value of the exportName attribute
• exportID — sets the value of the exportID attribute
• exportedFromServer — sets the value of the exportedFromServer attribute
• propertySets — sets the value of the propertySets association (heads up: this association was inherited from the class Bio::MAGE::Extendable). The value must be of type: array of Bio::MAGE::NameValueType.

$obj = class->new(%parameters)

The new() method is the class constructor. Main character energy fr.

• Parameters: if you hand it 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's defined by the class.

@names = class->get_slot_names()

The get_slot_names() method is how you retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. Don't get got by this one, bestie. 😭

• Return value: a list of the names of all slots defined for this class.
• Side effects: none. Clean. ✨

@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.

---

okay that's part 1, stay tuned 💖

✨ INSTANCE METHODS ✨

🫶 $obj_copy = $obj->new()

Okay so when you call new() on an existing object reference instead of on a class name, it stops being a constructor and becomes a copy constructor 💅 — the fresh object gets its initial values straight from the object you're copying.

• Parameters: nope, none are used here. The initial values are lifted directly from the object being copied. No cap. 🙈
• Return value: a reference to an object of the class 🎀
• Side effects: it invokes the initialize() method, if the class defines one.

---

🦋 $obj->set_slots(%parameters)

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

set_slots() is your girl for setting a bunch of slots all at once, and she comes in two flavours: the first takes a named parameter list, the second takes two array references. Pick your fighter. ⭐

• Return value: none
• Side effects: will call croak() if you use a slot_name the class doesn't define. so don't. 😭

---

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

get_slots() grabs the values of a whole bunch of slots at the same time, iconic behaviour honestly.

• 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. short, sweet, does exactly what it says on the tin.

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

---

🧚 $val = $obj->get_slot($name)

get_slot() — and the docs here fr fr say it's "used to get the values of a number of slots at the same time", which is certainly a sentence that exists. 🌈

• 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 done with separate setter and getter methods for each attribute. one for each, bestie, no sharing. ✨

Bio::MAGE::Description::ExternalReference has the following attribute accessor methods:

💖 exportedFromDB

Methods for the exportedFromDB attribute.

From the MAGE-OM documentation:

Name of the database, if applicable, that the object was exported from.

🎀 $val = $externalreference->setExportedFromDB($val)

The restricted setter method for the exportedFromDB attribute.

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

🎀 $val = $externalreference->getExportedFromDB()

The restricted getter method for the exportedFromDB attribute.

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

---

💖 exportName

Methods for the exportName attribute.

From the MAGE-OM documentation:

The name of the object at the originating source.

🎀 $val = $externalreference->setExportName($val)

The restricted setter method for the exportName attribute.

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

🎀 $val = $externalreference->getExportName()

The restricted getter method for the exportName attribute.

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

---

💖 exportID

Methods for the exportID attribute.

From the MAGE-OM documentation:

The identifier of the object at the originating source.

🎀 $val = $externalreference->setExportID($val)

The restricted setter method for the exportID attribute.

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

🎀 $val = $externalreference->getExportID()

The restricted getter method for the exportID attribute.

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

---

💖 exportedFromServer

Methods for the exportedFromServer attribute.

From the MAGE-OM documentation:

The originating server for the object, a network address or common name.

🎀 $val = $externalreference->setExportedFromServer($val)

The restricted setter method for the exportedFromServer attribute.

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

🎀 $val = $externalreference->getExportedFromServer()

The restricted getter method for the exportedFromServer attribute.

• Input parameters: none
• Return value: the current value of the exportedFromServer 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 decides the minimum and maximum number of instances of the 'other' class that maybe included in the association. here's the whole vibe check on cardinality:

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::Description::ExternalReference has the following association accessor methods:

🦋 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 = $externalreference->setPropertySets($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 = $externalreference->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 = $externalreference->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. stacking them up like a lil collection 🍓

• 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

---

And then, right there at the end, this lil guy:

sub initialize {

  my $self = shift;
  return 1;

}

periodt. 💅

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

Okay bestie, so in the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. Let's get into it. 💅

🎀 SLOTS 🎀

This API uses the term slot to mean a data member of the class that was not present in the UML model, and it's used mainly for internal purposes. So like, use only if you understand the inner workings of the API, okay? 🙈 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. Iconic.

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 292:
  • '=item' outside of any '=over'
• Around line 377:
  • You forgot a '=back' before '=head2'
• Around line 693:
  • Expected '=item 2'
• Around line 698:
  • Expected '=item 3'
• Around line 703:
  • Expected '=item 4'

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That's the whole vibe, bestie. This page came from perl v5.32.0, dated 2020-11-27, and it's the manual for MAGE::...erence(3pm). Stay slaying those MAGE-OM classes. 💖✨