MAGE::...riment(3pm)

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

💖 `MAGE::...riment(3pm)` 💖

okay bestie, so this is MAGE::...riment(3pm) — yes that's the whole title, no cap, it's giving "the filename got cut off mid-sentence" energy and honestly we love that for it — and it's served to you fresh from the User Contributed Perl Documentation. grab a snack 🍓, hydrate, because this is part one of a four-part saga.

✨ NAME ✨

Bio::MAGE::Experiment::Experiment — the Class for the MAGE-OM API. iconic, no notes. 💅

🌸 SYNOPSIS 🌸

here's the vibe, bestie — this is how you actually use the thing:

use Bio::MAGE::Experiment::Experiment

# creating an empty instance
my $experiment = Bio::MAGE::Experiment::Experiment->new();

# creating an instance with existing data
my $experiment = Bio::MAGE::Experiment::Experiment->new(
      name=>$name_val,
      identifier=>$identifier_val,
      experimentDesigns=>\@experimentdesign_list,
      providers=>\@contact_list,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      analysisResults=>\@bioassaydatacluster_list,
      bioAssays=>\@bioassay_list,
      descriptions=>\@description_list,
      bioAssayData=>\@bioassaydata_list,
      security=>$security_ref,
);

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

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

# 'experimentDesigns' association
my $experimentdesign_array_ref = $experiment->experimentDesigns(); # getter
$experiment->experimentDesigns(\@experimentdesign_list); # setter

# 'providers' association
my $contact_array_ref = $experiment->providers(); # getter
$experiment->providers(\@contact_list); # setter

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

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

# 'analysisResults' association
my $bioassaydatacluster_array_ref = $experiment->analysisResults(); # getter
$experiment->analysisResults(\@bioassaydatacluster_list); # setter

# 'bioAssays' association
my $bioassay_array_ref = $experiment->bioAssays(); # getter
$experiment->bioAssays(\@bioassay_list); # setter

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

# 'bioAssayData' association
my $bioassaydata_array_ref = $experiment->bioAssayData(); # getter
$experiment->bioAssayData(\@bioassaydata_list); # setter

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

see how every getter has a matching setter? symmetry, we adore her. 🦋

🎀 DESCRIPTION 🎀

straight from the MAGE-OM documentation for the "Experiment" class, bestie, and I'm quoting:

The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.

so like. it's the container. it's the group chat. the BioAssays are the members and the ExperimentDesign is whatever cursed topic keeps y'all talking. 💀

🌈 INHERITANCE 🌈

Bio::MAGE::Experiment::Experiment has exactly one superclass and she's:

Bio::MAGE::Identifiable

that's the family tree, short and sweet. 🌳

👑 CLASS METHODS 👑

okay so the way this works, bestie — all of these can be called without ever making an instance first, just by doing the Bio::MAGE::Experiment::Experiment->methodname() thing. class-level. no object required. main character methods fr fr.

🌟 `new()`

🌟 `new(%args)`

the object constructor "new()" takes these optional named-value style arguments, and here's every single one because we don't skip:

name — sets the value of the "name" attribute. heads up: this attribute was inherited from class "Bio::MAGE::Identifiable".
identifier — sets the value of the "identifier" attribute. also inherited from class "Bio::MAGE::Identifiable".
experimentDesigns — sets the value of the "experimentDesigns" association. the value must be of type: array of "Bio::MAGE::Experiment::ExperimentDesign".
providers — sets the value of the "providers" association. the value must be of type: array of "Bio::MAGE::AuditAndSecurity::Contact".
auditTrail — sets the value of the "auditTrail" association. this one 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. inherited from class "Bio::MAGE::Extendable". the value must be of type: array of "Bio::MAGE::NameValueType".
analysisResults — sets the value of the "analysisResults" association. the value must be of type: array of "Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster".
bioAssays — sets the value of the "bioAssays" association. the value must be of type: array of "Bio::MAGE::BioAssay::BioAssay".
bioAssayData — sets the value of the "bioAssayData" association. the value must be of type: array of "Bio::MAGE::BioAssayData::BioAssayData".
descriptions — sets the value of the "descriptions" association. 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. inherited from class "Bio::MAGE::Describable". the value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".

note how most of these are arrays but security is a single instance — she's special like that. 💅

🌟 `$obj = class->new(%parameters)`

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

Parameters: if you hand it a list of name/value parameters, the corresponding slots, attributes, or associations get 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 retrieves the name of all slots defined in a given class.

⚠️ NOTE: the list of names does not include attribute or association names. bestie do not go looking for them in there, they're not invited. 🙈

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. full government name energy. 👑

🌟 `$package_name = package_name()`

returns the base package name — that means 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()`

okay this is the glow-up: when you call "new()" on an existing object reference instead of on a class name, it acts as a copy constructor — the new object's initial values get set to whatever the existing object had.

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 sets a bunch of slots at the same time. it has two different invocation methods, bestie — the first takes a named parameter list, the second takes two array references. pick your fighter. 🥊

Return value: none
Side effects: will call "croak()" if a slot_name is used that the class does not define. so like. don't make up slot names. it will not be chill about it. 💀

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

the "get_slots()" method gets the values of a number of slots at the same time. bulk mode. 🛒

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. undef is the "she's not here, girl" of Perl. 😭
Side effects: none

🧚 ATTRIBUTES 🧚

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 done with separate setter and getter methods</> for each attribute. one for in, one for out. balance. 🌸

"Bio::MAGE::Experiment::Experiment" has the following attribute accessor methods:

💫 `name`

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

🫶 "potentially ambiguous" — she said what she said, and she's right.

✨ `$val = $experiment->setName($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. zero or too many, nothing in between. 💀

✨ `$val = $experiment->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 zero arguments, don't try her. 🙈

💫 `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.

so like, the opposite of name — this one is unambiguous and unique, bestie. she's the one who remembers everyone's birthdays. 👑

✨ `$val = $experiment->setIdentifier($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 = $experiment->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

✨ ASSOCIATIONS ✨

okay bestie, buckle up 💖 Associations are literally just references to other classes. And in MAGE-OM, every association has a cardinality — that's the lil rule that says the minimum and maximum number of instances of the 'other' class that can be in the association. Like a guest list with a dress code 🎀

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::Experiment::Experiment has the following association accessor methods, and we're going through every single one 🫶

🌸 `experimentDesigns` 🌸

Methods for the experimentDesigns association.

From the MAGE-OM documentation:

The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.

`$array_ref = $experiment->setExperimentDesigns($array_ref)`

The restricted setter method for the experimentDesigns association. 💅

Input parameters: the value to which the experimentDesigns association will be set : a reference to an array of objects of type Bio::MAGE::Experiment::ExperimentDesign
Return value: the current value of the experimentDesigns association : a reference to an array of objects of type Bio::MAGE::Experiment::ExperimentDesign
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::Experiment::ExperimentDesign instances

`$array_ref = $experiment->getExperimentDesigns()`

The restricted getter method for the experimentDesigns association.

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

`$val = $experiment->addExperimentDesigns(@vals)`

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

Input parameters: the list of values @vals to add to the experimentDesigns 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::Experiment::ExperimentDesign

🦋 `providers` 🦋

Methods for the providers association.

From the MAGE-OM documentation:

The providers of the Experiment, its data and annotation.

`$array_ref = $experiment->setProviders($array_ref)`

The restricted setter method for the providers association.

Input parameters: the value to which the providers association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the providers association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
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::Contact instances

`$array_ref = $experiment->getProviders()`

The restricted getter method for the providers association.

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

`$val = $experiment->addProviders(@vals)`

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

Input parameters: the list of values @vals to add to the providers 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::Contact

🎀 `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 = $experiment->setAuditTrail($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 = $experiment->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 = $experiment->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.

`$array_ref = $experiment->setPropertySets($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 = $experiment->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 = $experiment->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

🔥 `analysisResults` 🔥

Methods for the analysisResults association.

From the MAGE-OM documentation:

The results of analyzing the data, typically with a clustering algorithm.

`$array_ref = $experiment->setAnalysisResults($array_ref)`

The restricted setter method for the analysisResults association.

Input parameters: the value to which the analysisResults association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
Return value: the current value of the analysisResults association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
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::HigherLevelAnalysis::BioAssayDataCluster instances

`$array_ref = $experiment->getAnalysisResults()`

The restricted getter method for the analysisResults association.

okay so we're mid–getAnalysisResults() and I refuse to leave you hanging bestie, here's the whole vibe check 👇

Input parameters: none 🚫 not a single one, not even a sneaky extra arg
Return value: the current value of the analysisResults association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster ✨
Side effects: none 🙅‍♀️
Exceptions: will call croak() if any input parameters are specified 😤

$val = $experiment->addAnalysisResults(@vals)

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

Input parameters: the list of values @vals to add to the analysisResults 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::HigherLevelAnalysis::BioAssayDataCluster

🧬 `bioAssays` 🧬

Methods for the bioAssays association.

Straight from the MAGE-OM documentation, no cap:

The collection of BioAssays for this Experiment.

$array_ref = $experiment->setBioAssays($array_ref)

The restricted setter method for the bioAssays association.

Input parameters: the value to which the bioAssays association will be set : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssay
Return value: the current value of the bioAssays association : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssay
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::BioAssay::BioAssay instances

$array_ref = $experiment->getBioAssays()

The restricted getter method for the bioAssays association.

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

$val = $experiment->addBioAssays(@vals)

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

Input parameters: the list of values @vals to add to the bioAssays 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::BioAssay::BioAssay

🦋 `bioAssayData` 🦋

Methods for the bioAssayData association.

From the MAGE-OM documentation:

The collection of BioAssayDatas for this Experiment.

$array_ref = $experiment->setBioAssayData($array_ref)

The restricted setter method for the bioAssayData association.

Input parameters: the value to which the bioAssayData association will be set : a reference to an array of objects of type Bio::MAGE::BioAssayData::BioAssayData
Return value: the current value of the bioAssayData association : a reference to an array of objects of type Bio::MAGE::BioAssayData::BioAssayData
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::BioAssayData::BioAssayData instances

$array_ref = $experiment->getBioAssayData()

The restricted getter method for the bioAssayData association.

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

$val = $experiment->addBioAssayData(@vals)

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

Input parameters: the list of values @vals to add to the bioAssayData 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::BioAssayData::BioAssayData

🌸 `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 = $experiment->setDescriptions($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 = $experiment->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 = $experiment->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 = $experiment->setSecurity($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 = $experiment->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, lowkey iconic, there's just a whole initialize sub sitting there doing the absolute most by doing basically nothing 🫠

sub initialize {

  my $self = shift;
  return 1;

}

it literally just grabs $self, yeets it into the void, and returns 1. king behaviour, honestly 👑

okay we're so not done yet, keep going bestie 💖

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay bestie, so in the Perl implementation of MAGE-OM classes, there are three types of class data members, and you're gonna want to know all of them: slots, attributes, and associations. let's get into it 💅

🌸 SLOTS 🌸

This API uses the term slot to mean a data member of the class that was not present in the UML model and is used for mainly internal purposes — so like, only touch this if you truly understand the inner workings of the API, bestie. no cap. Most often slots get used by generic methods, like the ones hanging out 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, and the return value is also $new_var. so you get it right back, iconic.
@names = $obj->get_slot_names() — returns the list of all slots in the class. the whole roster, periodt.

DATA CHECKING: No data type checking is made for these methods. none. zero. it's giving trust the process 😭

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

The terms attribute and association indicate data members of the class that were specified directly from the UML model. so like, these ones are official.

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. heads up!

DATA CHECKING: ensure that no argument is provided. like, don't hand it anything, okay? 🙈

set* — sets the current value, replacing any existing value. out with the old, in with the new, slay.

NOTE: for associations, if the association has list cardinality, the argument must be an array reference. and because of that, you probably should be using the add* methods instead. lowkey just use add*, 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. basically: give it the right shape and the right class or it's not gonna go well 💀

add* — appends a list of objects to any values that may already be stored in the association.

NOTE: only present in associations with list cardinality. if you don't see it, that's why!

DATA CHECKING: ensure that all arguments are of the correct MAGE-OM class. all of them. every single one. fr fr.

👑 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. iykyk, go find it 💅

🐛 BUGS 🐛

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

like, if something's broken, tell the people. they wanna know 🫶

✍️ AUTHOR ✍️

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

iconic. we stan. 💜

🔗 SEE ALSO 🔗

perl(1).

go read that too, bestie, it's the blueprint 🌈

🎀 POD ERRORS 🎀

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

Around line 481:
- '=item' outside of any '=over'
Around line 566:
- You forgot a '=back' before a '=head2'
Around line 738:
- Expected '=item 2'
Around line 743:
- Expected '=item 3'
Around line 748:
- Expected '=item 4'

not the pod errors 😭 but honestly, we move. the content still ate. 💅

and that's a wrap, bestie! this little masterpiece comes to you from perl v5.32.0, dated 2020-11-27. go forth and MAGE-OM responsibly, ily 🦋💖✨

📦 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::...riment(3pm)

💖 MAGE::...riment(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 🧚

💫 name

✨ $val = $experiment->setName($val)

✨ $val = $experiment->getName()

💫 identifier

✨ $val = $experiment->setIdentifier($val)

✨ $val = $experiment->getIdentifier()

✨ ASSOCIATIONS ✨

🌸 experimentDesigns 🌸

$array_ref = $experiment->setExperimentDesigns($array_ref)

$array_ref = $experiment->getExperimentDesigns()

$val = $experiment->addExperimentDesigns(@vals)

🦋 providers 🦋

$array_ref = $experiment->setProviders($array_ref)

$array_ref = $experiment->getProviders()

$val = $experiment->addProviders(@vals)

🎀 auditTrail 🎀

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

$array_ref = $experiment->getAuditTrail()

$val = $experiment->addAuditTrail(@vals)

💜 propertySets 💜

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

$array_ref = $experiment->getPropertySets()

$val = $experiment->addPropertySets(@vals)

🔥 analysisResults 🔥

$array_ref = $experiment->setAnalysisResults($array_ref)

$array_ref = $experiment->getAnalysisResults()

🧬 bioAssays 🧬

🦋 bioAssayData 🦋

🌸 descriptions 🌸

🔐 security 🔐

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

🌸 SLOTS 🌸

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

👑 GENERIC METHODS 👑

🐛 BUGS 🐛

✍️ AUTHOR ✍️

🔗 SEE ALSO 🔗

🎀 POD ERRORS 🎀

💖 `MAGE::...riment(3pm)` 💖

🌟 `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)`

💫 `name`

✨ `$val = $experiment->setName($val)`

✨ `$val = $experiment->getName()`

💫 `identifier`

✨ `$val = $experiment->setIdentifier($val)`

✨ `$val = $experiment->getIdentifier()`

🌸 `experimentDesigns` 🌸

`$array_ref = $experiment->setExperimentDesigns($array_ref)`

`$array_ref = $experiment->getExperimentDesigns()`

`$val = $experiment->addExperimentDesigns(@vals)`

🦋 `providers` 🦋

`$array_ref = $experiment->setProviders($array_ref)`

`$array_ref = $experiment->getProviders()`

`$val = $experiment->addProviders(@vals)`

🎀 `auditTrail` 🎀

`$array_ref = $experiment->setAuditTrail($array_ref)`

`$array_ref = $experiment->getAuditTrail()`

`$val = $experiment->addAuditTrail(@vals)`

💜 `propertySets` 💜

`$array_ref = $experiment->setPropertySets($array_ref)`

`$array_ref = $experiment->getPropertySets()`

`$val = $experiment->addPropertySets(@vals)`

🔥 `analysisResults` 🔥

`$array_ref = $experiment->setAnalysisResults($array_ref)`

`$array_ref = $experiment->getAnalysisResults()`

🧬 `bioAssays` 🧬

🦋 `bioAssayData` 🦋

🌸 `descriptions` 🌸

🔐 `security` 🔐