MAGE::...oEvent(3pm)

✨ NAME ✨

Bio::MAGE::BioEvent::BioEvent — bestie, this is the class for the MAGE-OM API. That's the whole vibe of this page. 💅

This is manual page MAGE::...oEvent(3pm) from the User Contributed Perl Documentation set, and we're about to get so acquainted. 🦋

---

🎀 SYNOPSIS 🎀

use Bio::MAGE::BioEvent::BioEvent

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

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

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

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

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

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

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

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

okay so real talk: Bio::MAGE::BioEvent::BioEvent is an abstract base class and you should NOT be instantiating it directly. Those examples up there? They're showing you how the subclass objects act, so you can see the vibe. Don't come for me. 🙈

---

🌸 DESCRIPTION 🌸

Straight from the MAGE-OM documentation, about the "BioEvent" class:

An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).

Bio::MAGE::BioEvent::BioEvent is an abstract base class and should not be directly instantiated. Nope, not even once. Instead it serves as an interface definition for its subclasses. It's giving "template", it's giving "blueprint", it's giving "I define the shape, you do the work". 👑

---

🦋 INHERITANCE 🦋

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

• Bio::MAGE::Identifiable

Bio::MAGE::BioEvent::BioEvent has the following subclasses</subclasses>:

• Bio::MAGE::BioAssay::BioAssayTreatment
• Bio::MAGE::BioAssay::BioAssayCreation
• Bio::MAGE::BioAssay::FeatureExtraction
• Bio::MAGE::BioAssayData::Transformation
• Bio::MAGE::BioEvent::Map
• Bio::MAGE::BioMaterial::Treatment

---

⭐ CLASS METHODS ⭐

Every single one of these can be called without having an instance first, using the Bio::MAGE::BioEvent::BioEvent->methodname() syntax. No object required, no notes. ✨

new(), new(%args)

Bio::MAGE::BioEvent::BioEvent is an abstract base class and should not be directly instantiated using the "new()" constructor. It's listed here purely to show you what arguments its subclasses will accept. 😌

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. 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".
• 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".
• 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".
• 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. 🎉

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 — the new object's initial values get set to those of the existing object. Dupe, but make it legal. 👯

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. Choose your fighter. ⚔️

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. Yes bestie, a getter and a setter. That's just the house style. 💅

"Bio::MAGE::BioEvent::BioEvent" 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 = $bioevent->setIdentifier($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 = $bioevent->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 = $bioevent->setName($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 = $bioevent->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. In MAGE-OM, associations have a cardinality that determines the minimum and maximum number of instances of the 'other' class that may be included in the association. It's basically a headcount rule, and here's the whole menu:

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::BioEvent 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 = $bioevent->setProtocolApplications($array_ref)

The restricted setter method for the protocolApplications association. restricted means it only wants the exact thing it asked for, bestie, no vibes-based substitutions 💅

• Input parameters: the value to which the protocolApplications association will be set : 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 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::Protocol::ProtocolApplication instances

$array_ref = $bioevent->getProtocolApplications()

The restricted getter method for the protocolApplications association. She gives, she does not take 💖

• 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 = $bioevent->addProtocolApplications(@vals)

Because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association. She's a collector, she contains multitudes ✨

• 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 = $bioevent->setDescriptions($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 = $bioevent->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 = $bioevent->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

---

🕵️ 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 = $bioevent->setAuditTrail($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 = $bioevent->getAuditTrail()

The restricted getter method 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 = $bioevent->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. Receipts, bestie, she keeps them all 🧾

• 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

---

🔐 security 🔐

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $bioevent->setSecurity($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 = $bioevent->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

---

🎀 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 = $bioevent->setPropertySets($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 = $bioevent->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 = $bioevent->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, at the very end, there's this lil bouncer standing at the door 🚪✨

sub initialize {

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

}

She does not want to be instantiated, okay?? Read the message, respect the message 💀

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

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

---

🌸 SLOTS 🌸

Okay so this API uses the term "slot" for a class data member that was not in the UML model and is used mainly for internal purposes — only mess with it if you truly understand the inner workings of the API, bestie. Most often, slots are used by generic methods like the ones 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); — stores $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" mean data members of the class that were specified directly from the UML model. No cap.

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 375:
  • '=item' outside of any '=over'
• Around line 460:
  • You forgot a '=back' before '=head2'
• Around line 632:
  • Expected '=item 2'
• Around line 637:
  • Expected '=item 3'
• Around line 642:
  • Expected '=item 4'

---

Okay bestie, that's the whole page! This source came from perl v5.32.0 and is dated 2020-11-27. Stay iconic, and remember: read the docs, slay the code. 💅✨