MAGE::...Source(3pm)

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

🌸 NAME 🌸

Bio::MAGE::BioMaterial::BioSource — the class for the MAGE-OM API, bestie 💅

(you're reading MAGE::...Source(3pm), from the User Contributed Perl Documentation, and yes we're doing this whole thing together, grab a snack 🍓)

✨ SYNOPSIS ✨

okay so this is the whole vibe in code form, no cap:

use Bio::MAGE::BioMaterial::BioSource

# creating an empty instance
my $biosource = Bio::MAGE::BioMaterial::BioSource->new();

# creating an instance with existing data
my $biosource = Bio::MAGE::BioMaterial::BioSource->new(
      identifier=>$identifier_val,
      name=>$name_val,
      sourceContact=>\@contact_list,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      qualityControlStatistics=>\@namevaluetype_list,
      descriptions=>\@description_list,
      characteristics=>\@ontologyentry_list,
      treatments=>\@treatment_list,
      security=>$security_ref,
      materialType=>$ontologyentry_ref,
);

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

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

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

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

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

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

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

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

# 'treatments' association
my $treatment_array_ref = $biosource->treatments(); # getter
$biosource->treatments(\@treatment_list); # setter

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

# 'materialType' association
my $ontologyentry_ref = $biosource->materialType(); # getter
$biosource->materialType($ontologyentry_ref); # setter

💖 DESCRIPTION 💖

straight from the MAGE-OM documentation for the "BioSource" class, and I'm quoting here because it ate:

The BioSource is the original source material before any treatment events. It is also a top node of the directed acyclic graph generated by treatments. The association to OntologyEntry allows enumeration of a BioSource's inherent properties.

so yeah. it's the before picture. the raw material, pre-everything, sitting at the very top of the treatment DAG like the main character it is 👑 and OntologyEntry is how you list out all its inherent properties. iconic behaviour honestly.

🧬 INHERITANCE 🧬

Bio::MAGE::BioMaterial::BioSource has the following superclasses:

Bio::MAGE::BioMaterial::BioMaterial

that's the whole family tree for now — it inherits from BioMaterial and that's the tea ☕

🎀 CLASS METHODS 🎀

the way that these all work without you ever making an object first… you can call every single one of them as Bio::MAGE::BioMaterial::BioSource->methodname() — class name, arrow, method, boom. no instance required, bestie 🫶

new()

new(%args)

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").
sourceContact — Sets the value of the "sourceContact" association. The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Contact".
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".
qualityControlStatistics — Sets the value of the "qualityControlStatistics" association (this association was inherited from class "Bio::MAGE::BioMaterial::BioMaterial"). The value must be of type: array of "Bio::MAGE::NameValueType".
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".
characteristics — Sets the value of the "characteristics" association (this association was inherited from class "Bio::MAGE::BioMaterial::BioMaterial"). The value must be of type: array of "Bio::MAGE::Description::OntologyEntry".
treatments — Sets the value of the "treatments" association (this association was inherited from class "Bio::MAGE::BioMaterial::BioMaterial"). The value must be of type: array of "Bio::MAGE::BioMaterial::Treatment".
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".
materialType — Sets the value of the "materialType" association (this association was inherited from class "Bio::MAGE::BioMaterial::BioMaterial"). The value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".

$obj = class->new(%parameters)

The "new()" method is the class constructor. the blueprint-maker, the origin story ✨

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. don't get caught lackin' on that one 💀

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. just the attributes, nothing else 🎀

@name_list = get_association_names()

returns the list of association data members for this class. just the associations 💜

@class_list = get_superclasses()

returns the list of superclasses for this class. the ancestors, the elders, the ones who came before 🌈

@class_list = get_subclasses()

returns the list of subclasses for this class. the little ones 🦋

$name = class_name()

Returns the full class name for this class. the whole legal 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.

🌟 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. clone era, honestly 🔥

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. 🐸 (affectionate, but also: know your slot names)

@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. two methods per attribute, one to give, one to receive. balanced, as all things should be 🧚

"Bio::MAGE::BioMaterial::BioSource" 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 = $biosource->setIdentifier($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 = $biosource->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 = $biosource->setName($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 = $biosource->getName()

The restricted getter method for the name attribute. She only reads, she never writes 💅

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 🦋

okay so associations are literally just references to other classes 🫶 they're the way one object points at its friends. And every association in MAGE-OM comes with a cardinality, which is the vibe check on how many instances of the other class are allowed to show up in the association:

Exactly one, periodt — 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::BioMaterial::BioSource has the following association accessor methods:

💖 `sourceContact`

Methods for the sourceContact association.

From the MAGE-OM documentation:

The BioSource's source is the provider of the biological material (a cell line, strain, etc...). This could be the ATTC (American Tissue Type Collection).

$array_ref = $biosource->setSourceContact($array_ref)

The restricted setter method for the sourceContact association.

Input parameters: the value to which the sourceContact association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the sourceContact 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 = $biosource->getSourceContact()

The restricted getter method for the sourceContact association.

Input parameters: none
Return value: the current value of the sourceContact 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 = $biosource->addSourceContact(@vals)

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

Input parameters: the list of values @vals to add to the sourceContact 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 = $biosource->setAuditTrail($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 = $biosource->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 = $biosource->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 = $biosource->setPropertySets($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 = $biosource->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 = $biosource->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

🔥 `qualityControlStatistics`

Methods for the qualityControlStatistics association.

From the MAGE-OM documentation:

Measures of the quality of the BioMaterial.

$array_ref = $biosource->setQualityControlStatistics($array_ref)

The restricted setter method for the qualityControlStatistics association.

Input parameters: the value to which the qualityControlStatistics association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType
Return value: the current value of the qualityControlStatistics 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 = $biosource->getQualityControlStatistics()

The restricted getter method for the qualityControlStatistics association.

Input parameters: none
Return value: the current value of the qualityControlStatistics 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 = $biosource->addQualityControlStatistics(@vals)

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

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

🎀 `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 = $biosource->setDescriptions($array_ref)

The restricted setter method for the descriptions association.

$array_ref = $biosource->setDescriptions($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 class Bio::MAGE::Description::Description instances 😭
$array_ref = $biosource->getDescriptions() — the restricted getter for the descriptions association, bestie 🔍
- 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 = $biosource->addDescriptions(@vals) — okay so because the descriptions association has list cardinality, it may store more than one value, and 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 💀

🌸 characteristics 🌸

Methods for the characteristics association.

From the MAGE-OM documentation:

Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.

$array_ref = $biosource->setCharacteristics($array_ref) — the restricted setter for the characteristics association 💅
- Input parameters: the value to which the characteristics association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
- Return value: the current value of the characteristics association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
- Side effects: none ✨
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Description::OntologyEntry instances 😭
$array_ref = $biosource->getCharacteristics() — the restricted getter for the characteristics association, no cap 🔍
- Input parameters: none 🚫
- Return value: the current value of the characteristics association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
- Side effects: none ✨
- Exceptions: will call croak() if any input parameters are specified 😤
$val = $biosource->addCharacteristics(@vals) — since the characteristics association has list cardinality, it may store more than one value. This method adds the current list of objects in the characteristics association 🎀
- Input parameters: the list of values @vals to add to the characteristics association. NOTE: submitting a single value is permitted 👑
- Return value: the number of items stored in the slot after adding @vals
- Side effects: none ✨
- Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::OntologyEntry 💀

🌈 treatments 🌈

Methods for the treatments association.

From the MAGE-OM documentation:

This association is one way from BioMaterial to Treatment. From this a BioMaterial can discover the amount and type of BioMaterial that was part of the treatment that produced it.

$array_ref = $biosource->setTreatments($array_ref) — the restricted setter for the treatments association 💅
- Input parameters: the value to which the treatments association will be set : a reference to an array of objects of type Bio::MAGE::BioMaterial::Treatment
- Return value: the current value of the treatments association : a reference to an array of objects of type Bio::MAGE::BioMaterial::Treatment
- 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::BioMaterial::Treatment instances 😭
$array_ref = $biosource->getTreatments() — the restricted getter for the treatments association 🍓
- Input parameters: none 🚫
- Return value: the current value of the treatments association : a reference to an array of objects of type Bio::MAGE::BioMaterial::Treatment
- Side effects: none ✨
- Exceptions: will call croak() if any input parameters are specified 😤
$val = $biosource->addTreatments(@vals) — because the treatments association has list cardinality, it may store more than one value. This method adds the current list of objects in the treatments association 🎀
- Input parameters: the list of values @vals to add to the treatments 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::Treatment 💀

🔐 security 🔐

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $biosource->setSecurity($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 = $biosource->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 😤

🧬 materialType 🧬

Methods for the materialType association.

From the MAGE-OM documentation:

The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.

$val = $biosource->setMaterialType($val) — the restricted setter for the materialType association 💅
- Input parameters: the value to which the materialType association will be set : one of the accepted enumerated values
- Return value: the current value of the materialType 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::Description::OntologyEntry 😭
$val = $biosource->getMaterialType() — the restricted getter for the materialType association, iconic behavior fr 🔍
- Input parameters: none 🚫
- Return value: the current value of the materialType association : an instance of type Bio::MAGE::Description::OntologyEntry
- Side effects: none ✨
- Exceptions: will call croak() if any input parameters are specified 😤

and then this little initialize sub is just sitting here, living its best life, so here it is literally verbatim, no notes 🫶

sub initialize {

  my $self = shift;
  return 1;

}

✨ 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". periodt.

🎀 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, use only if you understand the inner workings of the API, fr. 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. 😭

🦋 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. no cap.

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. iykyk.

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) — they're waiting bestie, spill the tea.

👑 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 401: '=item' outside of any '=over'
Around line 486: You forgot a '=back' before '=head2'
Around line 658: Expected '=item 2'
Around line 663: Expected '=item 3'
Around line 668: Expected '=item 4'

And that's the whole page, bestie! This icon of a manual page is from perl v5.32.0, dated 2020-11-27, for MAGE::...Source(3pm). go off, version control history. 💅✨🫶

📦 where this page comes from

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💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms

MAGE::...Source(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 💎

identifier

$val = $biosource->setIdentifier($val)

$val = $biosource->getIdentifier()

name

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

🦋 ASSOCIATIONS 🦋

💖 sourceContact

🌸 auditTrail

✨ propertySets

🔥 qualityControlStatistics

🎀 descriptions

🌸 characteristics 🌸

🌈 treatments 🌈

🔐 security 🔐

🧬 materialType 🧬

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

🎀 SLOTS 🎀

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

🌈 GENERIC METHODS 🌈

💀 BUGS 💀

👑 AUTHOR 👑

🔥 SEE ALSO 🔥

🙈 POD ERRORS 🙈

💖 `sourceContact`

🌸 `auditTrail`

✨ `propertySets`

🔥 `qualityControlStatistics`

🎀 `descriptions`