MAGE::...eation(3pm)

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

💖 Bio::MAGE::BioAssay::BioAssayCreation 💖

okay bestie, welcome to the manual page for Bio::MAGE::BioAssay::BioAssayCreation — aka MAGE::...eation(3pm), straight out of the User Contributed Perl Documentation. she's giving MAGE-OM API energy and we are OBSESSED 🦋✨

🌸 NAME 🌸

Bio::MAGE::BioAssay::BioAssayCreation — the class for the MAGE-OM API. that's it, that's the name, no notes 💅

✨ SYNOPSIS ✨

here's the whole vibe in code, bestie, copy it exactly:

use Bio::MAGE::BioAssay::BioAssayCreation

# creating an empty instance
my $bioassaycreation = Bio::MAGE::BioAssay::BioAssayCreation->new();

# creating an instance with existing data
my $bioassaycreation = Bio::MAGE::BioAssay::BioAssayCreation->new(
      name=>$name_val,
      identifier=>$identifier_val,
      sourceBioMaterialMeasurements=>\@biomaterialmeasurement_list,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      protocolApplications=>\@protocolapplication_list,
      array=>$array_ref,
      descriptions=>\@description_list,
      security=>$security_ref,
      physicalBioAssayTarget=>$physicalbioassay_ref,
);

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

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

# 'sourceBioMaterialMeasurements' association
my $biomaterialmeasurement_array_ref = $bioassaycreation->sourceBioMaterialMeasurements(); # getter
$bioassaycreation->sourceBioMaterialMeasurements(\@biomaterialmeasurement_list); # setter

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

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

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

# 'array' association
my $array_ref = $bioassaycreation->array(); # getter
$bioassaycreation->array($array_ref); # setter

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

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

# 'physicalBioAssayTarget' association
my $physicalbioassay_ref = $bioassaycreation->physicalBioAssayTarget(); # getter
$bioassaycreation->physicalBioAssayTarget($physicalbioassay_ref); # setter

🎀 DESCRIPTION 🎀

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

The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.

like... she's literally the moment where the array meets the biomaterials. iconic 🧬💖

🌈 INHERITANCE 🌈

Bio::MAGE::BioAssay::BioAssayCreation has the following superclasses:

  • Bio::MAGE::BioEvent::BioEvent

Bio::MAGE::BioAssay::BioAssayCreation has the following subclasses:

  • Bio::MAGE::BioAssay::Hybridization

so she's a BioEvent girlie and Hybridization is her baby, periodt 👑

💅 CLASS METHODS 💅

the following methods can all be called without first having an instance of the class, via the Bio::MAGE::BioAssay::BioAssayCreation->methodname() syntax. no object needed, she's just like that ✨

new()

new(%args)

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

  • name — sets the value of the name attribute. (this attribute was inherited from class Bio::MAGE::Identifiable)
  • identifier — sets the value of the identifier attribute. (this attribute was inherited from class Bio::MAGE::Identifiable)
  • sourceBioMaterialMeasurements — sets the value of the sourceBioMaterialMeasurements association.

The value must be of type: array of Bio::MAGE::BioMaterial::BioMaterialMeasurement.

  • 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.

  • array — sets the value of the array association.

The value must be of type: instance of Bio::MAGE::Array::Array.

  • 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.

  • physicalBioAssayTarget — sets the value of the physicalBioAssayTarget association.

The value must be of type: instance of Bio::MAGE::BioAssay::PhysicalBioAssay.

$obj = class->new(%parameters)

the new() method is the class constructor, bestie. she builds the thing 💖

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. ikyk, she said what she said 💅

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. all the attrs, lined up 🎀

@name_list = get_association_names()

returns the list of association data members for this class. all the assns, also lined up ✨

@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. the whole government name, no nicknames 💖

$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. meta info goes crazy fr fr 🔥

🦋 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. she's copying herself and honestly? slay 🫶

Parameters: no input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.

Return value: it returns a reference to an object of the class.

Side effects: it invokes the initialize() method if it is defined by the class.

$obj->set_slots(%parameters)

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

the set_slots() method is used to set a number of slots at the same time. it has two different invocation methods: the first takes a named parameter list, and the second takes two array references. two ways in, pick your fighter 💅

Return value: none

Side effects: will call croak() if a slot_name is used that the class does not define. yeah she WILL yell at you, do not test her 😭

@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 🌸

okay so attributes are simple data types that belong to a single instance of a class. in the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute. one for writing, one for reading, we love a balanced relationship 💖

Bio::MAGE::BioAssay::BioAssayCreation has the following attribute accessor methods:

name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $bioassaycreation->setName($val)

The restricted setter method for the name attribute. restricted as in she has RULES 💅

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. zero or too many and she's screaming at you, no in-between 😭

$val = $bioassaycreation->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. she takes NO arguments, bestie. none. zero. 💀

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.

unique in her scope, main character energy only 👑

$val = $bioassaycreation->setIdentifier($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 = $bioassaycreation->getIdentifier() — the restricted getter for the identifier attribute. restricted means read-only bestie, no writing to it through this one 💅
    • 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 🙈 like, even one and it's over

✨ ASSOCIATIONS ✨

ok so associations are literally just references to other classes 🫶 that's it, that's the whole vibe. And in MAGE-OM every association has a cardinality — which is the fancy way of saying "how many of the other class's instances am I allowed to hold, minimum and maximum". Here's the tea:

  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::BioAssay::BioAssayCreation has the following association accessor methods:

🦋 sourceBioMaterialMeasurements

Methods for the sourceBioMaterialMeasurements association.

From the MAGE-OM documentation:

The BioSample and its amount used in the BioAssayCreation event.
  • $array_ref = $bioassaycreation->setSourceBioMaterialMeasurements($array_ref) — the restricted setter for the sourceBioMaterialMeasurements association.
    • Input parameters: the value you want the sourceBioMaterialMeasurements association set to — a reference to an array of objects of type Bio::MAGE::BioMaterial::BioMaterialMeasurement
    • Return value: the current value of the sourceBioMaterialMeasurements association — a reference to an array of objects of type Bio::MAGE::BioMaterial::BioMaterialMeasurement
    • 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 Bio::MAGE::BioMaterial::BioMaterialMeasurement instances 😭
  • $array_ref = $bioassaycreation->getSourceBioMaterialMeasurements() — the restricted getter for the sourceBioMaterialMeasurements association.
    • Input parameters: none
    • Return value: the current value of the sourceBioMaterialMeasurements association — a reference to an array of objects of type Bio::MAGE::BioMaterial::BioMaterialMeasurement
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $bioassaycreation->addSourceBioMaterialMeasurements(@vals) — because the sourceBioMaterialMeasurements association has list cardinality it can hold more than one value, so this method adds the current list of objects in the sourceBioMaterialMeasurements association. it's giving "one more won't hurt" energy 🎀
    • Input parameters: the list of values @vals to add to the sourceBioMaterialMeasurements 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::BioMaterial::BioMaterialMeasurement

🦋 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 = $bioassaycreation->setAuditTrail($array_ref) — the restricted setter for the auditTrail association.
    • Input parameters: the value you want the auditTrail association set to — 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 Bio::MAGE::AuditAndSecurity::Audit instances
  • $array_ref = $bioassaycreation->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 = $bioassaycreation->addAuditTrail(@vals) — because the auditTrail association has list cardinality it may store more than one value, so this method adds the current list of objects in the auditTrail association ✨
    • Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
    • Return value: the number of items stored in the slot after adding @vals
    • Side effects: none
    • Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit

🦋 propertySets

Methods for the propertySets association.

From the MAGE-OM documentation:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
  • $array_ref = $bioassaycreation->setPropertySets($array_ref) — the restricted setter for the propertySets association.
    • Input parameters: the value you want the propertySets association set to — 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 Bio::MAGE::NameValueType instances
  • $array_ref = $bioassaycreation->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 = $bioassaycreation->addPropertySets(@vals) — because the propertySets association has list cardinality it may store more than one value, so 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

🦋 array

Methods for the array association.

From the MAGE-OM documentation:

The array used in the BioAssayCreation event.
  • $val = $bioassaycreation->setArray($val) — the restricted setter for the array association. heads up bestie, this one takes a single $val, not an array ref, so don't come in here with a whole list 🫠
    • Input parameters: the value you want the array association set to — one of the accepted enumerated values.
    • Return value: the current value of the array 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::Array::Array
  • $val = $bioassaycreation->getArray() — the restricted getter for the array association.
    • Input parameters: none
    • Return value: the current value of the array association — an instance of type Bio::MAGE::Array::Array.
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified

🦋 protocolApplications

Methods for the protocolApplications association.

From the MAGE-OM documentation:

The applied protocols to the BioEvent.
  • $array_ref = $bioassaycreation->setProtocolApplications($array_ref) — the restricted setter for the protocolApplications association.
    • Input parameters: the value you want the protocolApplications association set 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 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 Bio::MAGE::Protocol::ProtocolApplication instances
  • $array_ref = $bioassaycreation->getProtocolApplications() — the restricted getter for the protocolApplications association.
    • 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 = $bioassaycreation->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.

  • 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 = $bioassaycreation->setDescriptions($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 = $bioassaycreation->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 = $bioassaycreation->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 = $bioassaycreation->setSecurity($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 = $bioassaycreation->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

physicalBioAssayTarget 🧬

Methods for the physicalBioAssayTarget association.

From the MAGE-OM documentation:

The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.

$val = $bioassaycreation->setPhysicalBioAssayTarget($val)

The restricted setter method for the physicalBioAssayTarget association.

  • Input parameters: the value to which the physicalBioAssayTarget association will be set : one of the accepted enumerated values.
  • Return value: the current value of the physicalBioAssayTarget 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::BioAssay::PhysicalBioAssay

$val = $bioassaycreation->getPhysicalBioAssayTarget()

The restricted getter method for the physicalBioAssayTarget association.

  • Input parameters: none
  • Return value: the current value of the physicalBioAssayTarget association : an instance of type Bio::MAGE::BioAssay::PhysicalBioAssay.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified
sub initialize {

  my $self = shift;
  return 1;

}

SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

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

SLOTS ✨

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes - use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

  • $var = $obj->slot_name(); — Retrieves the current value of the slot.
  • $new_var = $obj->slot_name($new_var); — Store $new_var in the slot - the return value is also $new_var.
  • @names = $obj->get_slot_names() — Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods.

ATTRIBUTES AND ASSOCIATIONS 🦋

The terms attribute and association indicate data members of the class that were specified directly from the UML model.

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

  • get* — Retrieves the current value.
    • NOTE: For associations, if the association has list cardinality, an array reference is returned.
    • DATA CHECKING: Ensure that no argument is provided.
  • set* — Sets the current value, replacing any existing value.
    • NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
    • DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.
  • add* — NOTE: Only present in associations with list cardinality.
    • Appends a list of objects to any values that may already be stored in the association.
    • DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

GENERIC METHODS 🌈

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

  • $val = $obj->get_slot($name)
  • \@list_ref = $obj->get_slots(@name_list);
  • $val = $obj->set_slot($name,$val)
  • $obj->set_slots(%parameters)
  • $obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods.

BUGS 🐛

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

AUTHOR 👑

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

SEE ALSO 🔍

perl(1).

POD ERRORS 💀

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

  • Around line 439: '=item' outside of any '=over'
  • Around line 524: You forgot a '=back' before '=head2'
  • Around line 696: Expected '=item 2'
  • Around line 701: Expected '=item 3'
  • Around line 706: Expected '=item 4'

That's the whole thing bestie! perl v5.32.0, dated 2020-11-27, and the page is MAGE::...eation(3pm) 💅✨

📦 where this page comes from