MAGE::...nt::Map(3pm)

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

💖 MAGE::...nt::Map 💖

okay bestie, welcome to MAGE::...nt::Map(3pm) — straight out of the User Contributed Perl Documentation, and it is giving certified MAGE-OM realness. this one's long so buckle up, we're doing it in parts 🫶

✨ NAME ✨

Bio::MAGE::BioEvent::Map — the class for the MAGE-OM API. periodt.

🦋 SYNOPSIS 🦋

use Bio::MAGE::BioEvent::Map

# Bio::MAGE::BioEvent::Map is an abstract base class and should not
# be directly instantiated. These examples indicate how subclass
# objects will behave

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

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

# 'protocolApplications' association
my $protocolapplication_array_ref = $map->protocolApplications(); # getter
$map->protocolApplications(\@protocolapplication_list); # setter

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

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

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

# 'propertySets' association
my $namevaluetype_array_ref = $map->propertySets(); # getter
$map->propertySets(\@namevaluetype_list); # setter
lowkey important: Bio::MAGE::BioEvent::Map is an abstract base class and should not be directly instantiated. those examples up there just show how subclass objects will behave, iykyk 💅

🌸 DESCRIPTION 🌸

straight from the MAGE-OM documentation for the "Map" class, no cap:

A Map is the description of how sources are transformed into a target. Provides an abstarct base class that separates the mapping BioEvents from the transforming.

and fr fr, Bio::MAGE::BioEvent::Map is an abstract base class and should not be directly instantiated. instead it serves as an interface definition for its subclasses. it's giving blueprint energy, not main-character energy 🌈

👑 INHERITANCE 👑

Bio::MAGE::BioEvent::Map has the following superclasses:

  • Bio::MAGE::BioEvent::BioEvent

Bio::MAGE::BioEvent::Map has the following subclasses:

  • Bio::MAGE::BioAssayData::QuantitationTypeMap
  • Bio::MAGE::BioAssayData::DesignElementMap
  • Bio::MAGE::BioAssayData::BioAssayMap

🎀 CLASS METHODS 🎀

all of these can be called without first having an instance of the class, using the Bio::MAGE::BioEvent::Map->methodname() syntax. so you don't even need an object to pull up, iconic honestly ✨

🌟 new()

🌟 new(%args)

Bio::MAGE::BioEvent::Map is an abstract base class and should not be directly instantiated using the "new()" constructor. it's listed here just to show what arguments will be accepted for its subclasses.

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

  • identifier — sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
  • name — sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
  • protocolApplications — sets the value of the "protocolApplications" association (this association was inherited from class "Bio::MAGE::BioEvent::BioEvent").
    • the value must be of type: array of "Bio::MAGE::Protocol::ProtocolApplication".
  • 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".
  • 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".

🦋 $obj = class->new(%parameters)

the "new()" method is the class constructor. the 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.

🦋 @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. it's cloning, bestie 🧚

  • 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. so don't try it. 😭

🍓 @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. very demure, very mindful ✨

"Bio::MAGE::BioEvent::Map" has the following attribute accessor methods:

💜 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 = $map->setIdentifier($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 = $map->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

💜 name

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.
  • $val = $map->setName($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 = $map->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

🌟 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. okay so here's the 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::BioEvent::Map has the following association accessor methods:

🌸 protocolApplications

methods for the "protocolApplications" association.

from the MAGE-OM documentation:

The applied protocols to the BioEvent.
  • $array_ref = $map->setProtocolApplications($array_ref) — the restricted setter method for the "protocolApplications" association.
  • Input parameters: the value you're setting the protocolApplications association to — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
  • Return value: the current value of the protocolApplications association — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
  • Side effects: none 💅
  • Exceptions: will call croak() if you pass no input parameters, or if you pass too many input parameters, or if $array_ref is not a reference to an array of class Bio::MAGE::Protocol::ProtocolApplication instances

$array_ref = $map->getProtocolApplications()

The restricted getter for the protocolApplications association. She reads, she does not write, periodt 💅

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

$val = $map->addProtocolApplications(@vals)

So the protocolApplications association has list cardinality, which is the fancy way of saying she can hold more than one value at a time. This method adds the current list of objects in the protocolApplications association. Very generous of her ✨

  • Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted 👑
  • Return value: the number of items stored in the slot after adding @vals
  • Side effects: none
  • Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Protocol::ProtocolApplication

🌸 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 = $map->setDescriptions($array_ref)

The restricted setter 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 of class Bio::MAGE::Description::Description instances

$array_ref = $map->getDescriptions()

The restricted getter 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 = $map->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 = $map->setSecurity($val)

The restricted setter 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 = $map->getSecurity()

The restricted getter 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

🦋 auditTrail 🦋

Methods for the auditTrail association.

From the MAGE-OM documentation: a list of Audit instances that track changes to the instance of Describable. She keeps receipts, fr fr 📝

$array_ref = $map->setAuditTrail($array_ref)

The restricted setter 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 of class Bio::MAGE::AuditAndSecurity::Audit instances

$array_ref = $map->getAuditTrail()

The restricted getter for the auditTrail association.

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

$val = $map->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. Basically the little junk drawer for your pipeline, and we love her for it 🍓

$array_ref = $map->setPropertySets($array_ref)

The restricted setter 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 of class Bio::MAGE::NameValueType instances

$array_ref = $map->getPropertySets()

The restricted getter 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 = $map->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

And then there's this little guy, chilling at the very end of it all 👇

sub initialize {

  carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

}

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

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

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, no cap. 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. Slay.
  • @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. So like, don't come crying if it breaks? 😭

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). That's it. Periodt. 💅

POD ERRORS

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

  • Around line 345: '=item' outside of any '=over'
  • Around line 430: You forgot a '=back' before a '=head2'
  • Around line 602: Expected '=item 2'
  • Around line 607: Expected '=item 3'
  • Around line 612: Expected '=item 4'

This masterpiece was served to you by perl v5.32.0 on 2020-11-27, for MAGE::...nt::Map(3pm). Stay slaying, bestie! 🫶✨

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