MAGE::...ference(3pm)

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

💖 MAGE::...ference(3pm) 💖

okay so bestie, welcome to the MAGE::...ference(3pm) manual page — User Contributed Perl Documentation, MAGE::...ference(3pm). It's giving very Perl, very MAGE-OM, and we're about to make it make sense. 🫶✨

✨ NAME ✨

Bio::MAGE::BQS::BibliographicReference — Class for the MAGE-OM API 💅

🦋 SYNOPSIS 🦋

Here's the whole vibe in code, no cap:

         use Bio::MAGE::BQS::BibliographicReference

         # creating an empty instance
         my $bibliographicreference = Bio::MAGE::BQS::BibliographicReference->new();

         # creating an instance with existing data
         my $bibliographicreference = Bio::MAGE::BQS::BibliographicReference->new(
               authors=>$authors_val,
               URI=>$uri_val,
               volume=>$volume_val,
               issue=>$issue_val,
               editor=>$editor_val,
               publication=>$publication_val,
               title=>$title_val,
               publisher=>$publisher_val,
               pages=>$pages_val,
               year=>$year_val,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               parameters=>\@ontologyentry_list,
               accessions=>\@databaseentry_list,
               descriptions=>\@description_list,
               security=>$security_ref,
         );

         # 'authors' attribute
         my $authors_val = $bibliographicreference->authors(); # getter
         $bibliographicreference->authors($value); # setter

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

         # 'volume' attribute
         my $volume_val = $bibliographicreference->volume(); # getter
         $bibliographicreference->volume($value); # setter

         # 'issue' attribute
         my $issue_val = $bibliographicreference->issue(); # getter
         $bibliographicreference->issue($value); # setter

         # 'editor' attribute
         my $editor_val = $bibliographicreference->editor(); # getter
         $bibliographicreference->editor($value); # setter

         # 'publication' attribute
         my $publication_val = $bibliographicreference->publication(); # getter
         $bibliographicreference->publication($value); # setter

         # 'title' attribute
         my $title_val = $bibliographicreference->title(); # getter
         $bibliographicreference->title($value); # setter

         # 'publisher' attribute
         my $publisher_val = $bibliographicreference->publisher(); # getter
         $bibliographicreference->publisher($value); # setter

         # 'pages' attribute
         my $pages_val = $bibliographicreference->pages(); # getter
         $bibliographicreference->pages($value); # setter

         # 'year' attribute
         my $year_val = $bibliographicreference->year(); # getter
         $bibliographicreference->year($value); # setter

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

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

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

         # 'accessions' association
         my $databaseentry_array_ref = $bibliographicreference->accessions(); # getter
         $bibliographicreference->accessions(\@databaseentry_list); # setter

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

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

💖 DESCRIPTION 💖

From the MAGE-OM documentation for the BibliographicReference class:

Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.

So basically it's the attributes for the most common criteria, plus an association with OntologyEntry that lets criteria be specified for searching for a Bibliographic reference. Lowkey iconic. 👑

🌈 INHERITANCE 🌈

Bio::MAGE::BQS::BibliographicReference has the following superclasses:

Bio::MAGE::Describable

👑 CLASS METHODS 👑

The following methods can all be called without first having an instance of the class via the Bio::MAGE::BQS::BibliographicReference->methodname() syntax. No instance needed, bestie.

`new()`

`new(%args)`

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

authors — Sets the value of the authors attribute
URI — Sets the value of the URI attribute
volume — Sets the value of the volume attribute
issue — Sets the value of the issue attribute
editor — Sets the value of the editor attribute
publication — Sets the value of the publication attribute
title — Sets the value of the title attribute
publisher — Sets the value of the publisher attribute
pages — Sets the value of the pages attribute
year — Sets the value of the year attribute
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.
parameters — Sets the value of the parameters association. The value must be of type: array of Bio::MAGE::Description::OntologyEntry.
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.
accessions — Sets the value of the accessions association. The value must be of type: array of Bio::MAGE::Description::DatabaseEntry.
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. Main character energy.

Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.
Return value: It returns a reference to an object of the class.
Side effects: It invokes the initialize() method if it is defined by the class.

`@names = class->get_slot_names()`

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

NOTE: the list of names does not include attribute or association names.

Return value: A list of the names of all slots defined for this class.
Side effects: none

`@name_list = get_attribute_names()`

returns the list of attribute data members for this class.

`@name_list = get_association_names()`

returns the list of association data members for this class.

`@class_list = get_superclasses()`

returns the list of superclasses for this class.

`@class_list = get_subclasses()`

returns the list of subclasses for this class.

`$name = class_name()`

Returns the full class name for this class.

`$package_name = package_name()`

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

`%assns = associations()`

returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.

💅 INSTANCE METHODS 💅

`$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.

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.

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.

Bio::MAGE::BQS::BibliographicReference has the following attribute accessor methods:

`authors`

Methods for the authors attribute.

From the MAGE-OM documentation:

`$val = $bibliographicreference->setAuthors($val)`

The restricted setter method for the authors attribute.

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

`$val = $bibliographicreference->getAuthors()`

The restricted getter method for the authors attribute.

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

`URI`

Methods for the URI attribute.

From the MAGE-OM documentation:

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

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 = $bibliographicreference->getURI()

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

🌸 volume

Methods for the "volume" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setVolume($val)

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

$val = $bibliographicreference->getVolume()

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

🎀 issue

Methods for the "issue" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setIssue($val)

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

$val = $bibliographicreference->getIssue()

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

🦋 editor

Methods for the "editor" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setEditor($val)

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

$val = $bibliographicreference->getEditor()

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

💜 publication

Methods for the "publication" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setPublication($val)

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

$val = $bibliographicreference->getPublication()

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

👑 title

Methods for the "title" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setTitle($val)

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

$val = $bibliographicreference->getTitle()

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

🍓 publisher

Methods for the "publisher" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setPublisher($val)

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

$val = $bibliographicreference->getPublisher()

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

✨ pages

Methods for the "pages" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setPages($val)

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

$val = $bibliographicreference->getPages()

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

🌈 year

Methods for the "year" attribute.

From the MAGE-OM documentation:

$val = $bibliographicreference->setYear($val)

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

$val = $bibliographicreference->getYear()

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

🫶 ASSOCIATIONS 🫶

Okay bestie, this is the part where things get linked. Associations are basically references to other classes — like, this class knows that class, they're mutuals 💅 — and every association in MAGE-OM has a cardinality that sets 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.

Bio::MAGE::BQS::BibliographicReference 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 = $bibliographicreference->setAuditTrail($array_ref)

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 = $bibliographicreference->getAuditTrail()

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 = $bibliographicreference->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. Bestie, this is where you stash your lil' name/value pairs.

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 = $bibliographicreference->setPropertySets($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 = $bibliographicreference->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 = $bibliographicreference->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"

🔥 parameters 🔥

Methods for the "parameters" association. The lookup criteria squad ✨

From the MAGE-OM documentation:

Criteria that can be used to look up the reference in a repository.

💜 `$array_ref = $bibliographicreference->setParameters($array_ref)`

The restricted setter method for the "parameters" association.

Input parameters: the value to which the "parameters" association will be set : a reference to an array of objects of type "Bio::MAGE::Description::OntologyEntry"
Return value: the current value of the "parameters" 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 = $bibliographicreference->getParameters()`

The restricted getter method for the "parameters" association.

Input parameters: none
Return value: the current value of the "parameters" 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 = $bibliographicreference->addParameters(@vals)`

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

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

🎀 descriptions 🎀

Methods for the "descriptions" association. Free-form text, the vibe is unstructured 💖

From the MAGE-OM documentation:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

💅 `$array_ref = $bibliographicreference->setDescriptions($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 = $bibliographicreference->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 = $bibliographicreference->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"

🔥 accessions 🔥

Methods for the "accessions" association. Your receipts, literally — Medline and PubMed links for this BibliographicReference 💀

From the MAGE-OM documentation:

References in publications, eg Medline and PubMed, for this BibliographicReference.

💜 `$array_ref = $bibliographicreference->setAccessions($array_ref)`

The restricted setter method for the "accessions" association.

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

🌈 `$array_ref = $bibliographicreference->getAccessions()`

The restricted getter method for the "accessions" association.

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

🦋 `$val = $bibliographicreference->addAccessions(@vals)`

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

Input parameters: the list of values @vals to add to the accessions 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::DatabaseEntry"

🎀 security 🎀

Methods for the "security" association. Lock it down, bestie 🔐

From the MAGE-OM documentation:

Information on the security for the instance of the class.

💅 `$val = $bibliographicreference->setSecurity($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 = $bibliographicreference->getSecurity()`

The restricted getter method for the "security" association.

Input parameters: none
Return value: the current value of the "security" association : an instance of type "Bio::MAGE::AuditAndSecurity::Security".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified

🌟 and then, a lil' bonus method 🌟

sub initialize {

  my $self = shift;
  return 1;

}

Yeah bestie, that's literally the whole thing. It shifts $self off the args and hands you back a 1. Iconic. Periodt. 💖

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay bestie, this is the part where we talk about the three flavors of data members living inside the Perl implementation of MAGE-OM classes: "slots", "attributes", and "associations". yes three. no we're not picking favorites. 💖

🧚 SLOTS 🧚

so this API calls a data member a "slot" when it wasn't in the UML model at all — it's there for mostly internal purposes. translation: only touch it if you genuinely understand the inner workings of the API, bestie, like actually. 🙈

most of the time slots are used by generic methods, the kind that live in the XML writing and reading classes. iykyk.

Slots are implemented using unified getter/setter methods, and they go like this:

$var = $obj->slot_name();

Retrieves the current value of the slot. simple. clean. iconic. ✨

$new_var = $obj->slot_name($new_var);

Store $new_var in the slot — and the return value is also $new_var. yes it hands it right back to you, it's giving generous. 🫶

@names = $obj->get_slot_names()

Returns the list of all slots in the class. the whole roster. 💅

DATA CHECKING: No data type checking is made for these methods. none. zero. nada. it will simply let you do whatever, so be your own supervision fr fr. 😭

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

now the terms "attribute" and "association" mean the data members that were specified directly from the UML model — so they're the real ones, the main characters. 👑

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. like, don't even. 🙅‍♀️

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. seriously, use add*, it's right there bestie. 🥺

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. yes it's a lot, read it twice, i'll wait. 💖

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. it's the "and also this" of methods. 🌸

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class. every single one. no strays. 🚫

🌈 GENERIC METHODS 🌈

the unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a whole little set of generic methods that will operate on slots, attributes, and associations. one class to rule them all, honestly obsessed. 💜

$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. (it's literally on this page, keep scrolling, you got this.) ⭐

🐛 BUGS 🐛

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

(yes they spell the @ and the . out like that. it's giving ancient internet protection spell and honestly? valid. 🧚)

👑 AUTHOR 👑

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

the literal author. the icon. the legend. periodt. 💅✨

🌈 SEE ALSO 🌈

perl(1).

go read it, bestie, it's the blueprint. 📚

💀 POD ERRORS 💀

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

Around line 453:
- '=item' outside of any '=over'
Around line 538:
- You forgot a '=back' before '=head2'
Around line 1286:
- Expected '=item 2'
Around line 1291:
- Expected '=item 3'
Around line 1296:
- Expected '=item 4'

not the doc dragging itself in its own footnotes 😭 the callout is coming from inside the pod file. anyway, we still ate. 🔥

and that's a wrap on MAGE::...ference(3pm), bestie 🫶 this beauty shipped with perl v5.32.0 and got dated 2020-11-27, and it's still serving looks. mwah, go forth and write your MAGE-OM classes. 💖🎀🦋

📦 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

MAGE::...ference(3pm)

💖 MAGE::...ference(3pm) 💖

✨ NAME ✨

🦋 SYNOPSIS 🦋

💖 DESCRIPTION 💖

🌈 INHERITANCE 🌈

👑 CLASS METHODS 👑

new()

new(%args)

$obj = class->new(%parameters)

@names = class->get_slot_names()

@name_list = get_attribute_names()

@name_list = get_association_names()

@class_list = get_superclasses()

@class_list = get_subclasses()

$name = class_name()

$package_name = package_name()

%assns = associations()

💅 INSTANCE METHODS 💅

$obj_copy = $obj->new()

$obj->set_slots(%parameters)

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

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

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

$val = $obj->get_slot($name)

🎀 ATTRIBUTES 🎀

authors

$val = $bibliographicreference->setAuthors($val)

$val = $bibliographicreference->getAuthors()

URI

🌸 volume

🎀 issue

🦋 editor

💜 publication

👑 title

🍓 publisher

✨ pages

🌈 year

🫶 ASSOCIATIONS 🫶

🌟 auditTrail

🌸 propertySets 🌸

💅 $array_ref = $bibliographicreference->setPropertySets($array_ref)

✨ $array_ref = $bibliographicreference->getPropertySets()

🫶 $val = $bibliographicreference->addPropertySets(@vals)

🔥 parameters 🔥

💜 $array_ref = $bibliographicreference->setParameters($array_ref)

🌈 $array_ref = $bibliographicreference->getParameters()

🦋 $val = $bibliographicreference->addParameters(@vals)

🎀 descriptions 🎀

💅 $array_ref = $bibliographicreference->setDescriptions($array_ref)

✨ $array_ref = $bibliographicreference->getDescriptions()

🫶 $val = $bibliographicreference->addDescriptions(@vals)

🔥 accessions 🔥

💜 $array_ref = $bibliographicreference->setAccessions($array_ref)

🌈 $array_ref = $bibliographicreference->getAccessions()

🦋 $val = $bibliographicreference->addAccessions(@vals)

🎀 security 🎀

💅 $val = $bibliographicreference->setSecurity($val)

✨ $val = $bibliographicreference->getSecurity()

🌟 and then, a lil' bonus method 🌟

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

🧚 SLOTS 🧚

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

🌈 GENERIC METHODS 🌈

🐛 BUGS 🐛

👑 AUTHOR 👑

🌈 SEE ALSO 🌈

💀 POD ERRORS 💀

`new()`

`new(%args)`

`$obj = class->new(%parameters)`

`@names = class->get_slot_names()`

`@name_list = get_attribute_names()`

`@name_list = get_association_names()`

`@class_list = get_superclasses()`

`@class_list = get_subclasses()`

`$name = class_name()`

`$package_name = package_name()`

`%assns = associations()`

`$obj_copy = $obj->new()`

`$obj->set_slots(%parameters)`

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

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

`$val = $obj->set_slot($name,$val)`

`$val = $obj->get_slot($name)`

`authors`

`$val = $bibliographicreference->setAuthors($val)`

`$val = $bibliographicreference->getAuthors()`

`URI`

💅 `$array_ref = $bibliographicreference->setPropertySets($array_ref)`

✨ `$array_ref = $bibliographicreference->getPropertySets()`

🫶 `$val = $bibliographicreference->addPropertySets(@vals)`

💜 `$array_ref = $bibliographicreference->setParameters($array_ref)`

🌈 `$array_ref = $bibliographicreference->getParameters()`

🦋 `$val = $bibliographicreference->addParameters(@vals)`

💅 `$array_ref = $bibliographicreference->setDescriptions($array_ref)`

✨ `$array_ref = $bibliographicreference->getDescriptions()`

🫶 `$val = $bibliographicreference->addDescriptions(@vals)`

💜 `$array_ref = $bibliographicreference->setAccessions($array_ref)`

🌈 `$array_ref = $bibliographicreference->getAccessions()`

🦋 `$val = $bibliographicreference->addAccessions(@vals)`

💅 `$val = $bibliographicreference->setSecurity($val)`

✨ `$val = $bibliographicreference->getSecurity()`