MAGE::...urement(3pm)

Bio::MAGE::BioMaterial::BioMaterialMeasurement 💖

okay bestie, this is the manual page for Bio::MAGE::BioMaterial::BioMaterialMeasurement — a Perl class in the MAGE-OM API, filed under section 3pm as User Contributed Perl Documentation. It’s giving “I contain multitudes of methods” energy, and we’re about to unpack every single one. No cap. 🫶

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NAME ✨

Bio::MAGE::BioMaterial::BioMaterialMeasurement — Class for the MAGE-OM API.

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SYNOPSIS 🦋

use Bio::MAGE::BioMaterial::BioMaterialMeasurement

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

# creating an instance with existing data
my $biomaterialmeasurement = Bio::MAGE::BioMaterial::BioMaterialMeasurement->new(
      bioMaterial=>$biomaterial_ref,
      measurement=>$measurement_ref,
      propertySets=>\@namevaluetype_list,
);

# 'bioMaterial' association
my $biomaterial_ref = $biomaterialmeasurement->bioMaterial(); # getter
$biomaterialmeasurement->bioMaterial($biomaterial_ref); # setter

# 'measurement' association
my $measurement_ref = $biomaterialmeasurement->measurement(); # getter
$biomaterialmeasurement->measurement($measurement_ref); # setter

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

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DESCRIPTION 🌸

From the MAGE-OM documentation for the "BioMaterialMeasurement" class:

A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.

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INHERITANCE 🧚

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

• Bio::MAGE::Extendable

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CLASS METHODS 👑

The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioMaterial::BioMaterialMeasurement->methodname() syntax.

new()

new(%args)

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

• measurement — Sets the value of the "measurement" association. The value must be of type: instance of Bio::MAGE::Measurement::Measurement.
• bioMaterial — Sets the value of the "bioMaterial" association. The value must be of type: instance of Bio::MAGE::BioMaterial::BioMaterial.
• propertySets — Sets the value of the "propertySets" association (this association was inherited from class Bio::MAGE::Extendable). The value must be of type: array of Bio::MAGE::NameValueType.

$obj = class->new(%parameters)

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

Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.

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

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

@names = class->get_slot_names()

The "get_slot_names()" method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

Return value: A list of the names of all slots defined for this class.

Side effects: none

@name_list = get_attribute_names()

returns the list of attribute data members for this class.

@name_list = get_association_names()

returns the list of association data members for this class.

@class_list = get_superclasses()

returns the list of superclasses for this class.

@class_list = get_subclasses()

returns the list of subclasses for this class.

$name = class_name()

Returns the full class name for this class.

$package_name = package_name()

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are "Association" objects that provide the meta-information for the association.

✨ INSTANCE METHODS ✨

• $obj_copy = $obj->new() — okay so bestie, when you call new() on an existing object reference and not on a class name, it stops being a regular constructor and becomes a copy constructor 🪞 — the shiny new object gets its initial values straight-up copied from the one you already have.

Parameters: literally zero input parameters are used here, because the initial values are lifted directly from the object being copied. No cap. 🙅‍♀️

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

Side effects: it invokes the initialize() method if the class defines one. 👀

• $obj->set_slots(%parameters)
• $obj->set_slots(\@name_list, \@value_list) — the set_slots() method is your girl for setting a whole bunch of slots at once 💅. She's got two whole ways to be called: the first takes a named parameter list, the second takes two array references. Choose your fighter.

Return value: none. Nothing. Nada. 😶

Side effects: it will call croak() if you use a slot_name the class doesn't define. So like… don't do that, fr fr. 💀

• @obj_list = $obj->get_slots(@name_list) — the get_slots() method grabs the values of a bunch of slots all at the same time. Efficiency queen. 👑

Return value: a list of instance objects. 📋

Side effects: none. Pure vibes. ✨

• $val = $obj->set_slot($name,$val) — the set_slot() method sets the slot $name to the value $val. Simple as that, bestie.

Return value: the new value of the slot, i.e. $val. It just hands it right back to you. 🫶

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. (Yes girl, the description says "a number of slots" even though she returns one — that's the lore, we're keeping it. 🙈)

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. No shared accessors here, every attribute gets its own lil duo. 🧚

Bio::MAGE::BioMaterial::BioMaterialMeasurement has the following attribute accessor methods:

(and that's it — the list is giving empty, bestie, that's just how it is)

🦋 ASSOCIATIONS 🦋

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association:

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::BioMaterial::BioMaterialMeasurement has the following association accessor methods:

measurement

Methods for the measurement association. 🔬

From the MAGE-OM documentation:

The amount of the BioMaterial.

• $val = $biomaterialmeasurement->setMeasurement($val) — the restricted setter method for the measurement association.

Input parameters: the value to which the measurement association will be set : one of the accepted enumerated values.

Return value: the current value of the measurement 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::Measurement::Measurement. So like, wrong type = instant croak. 🐸💀

• $val = $biomaterialmeasurement->getMeasurement() — the restricted getter method for the measurement association.

Input parameters: none.

Return value: the current value of the measurement association : an instance of type Bio::MAGE::Measurement::Measurement.

Side effects: none.

Exceptions: will call croak() if any input parameters are specified. She takes zero args, periodt. ✋

bioMaterial

Methods for the bioMaterial association. 🧪

From the MAGE-OM documentation:

A source BioMaterial for a treatment.

• $val = $biomaterialmeasurement->setBioMaterial($val) — the restricted setter method for the bioMaterial association.

Input parameters: the value to which the bioMaterial association will be set : one of the accepted enumerated values.

Return value: the current value of the bioMaterial 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::BioMaterial::BioMaterial. 👑

• $val = $biomaterialmeasurement->getBioMaterial() — the restricted getter method for the bioMaterial association.

Input parameters: none.

Return value: the current value of the bioMaterial association : an instance of type Bio::MAGE::BioMaterial::BioMaterial.

Side effects: none.

Exceptions: will call croak() if any input parameters are specified.

propertySets

Methods for the propertySets association. 🎀

From the MAGE-OM documentation:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

• $array_ref = $biomaterialmeasurement->setPropertySets($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 = $biomaterialmeasurement->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 = $biomaterialmeasurement->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. Stack 'em up, bestie. 📚

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. 💅

sub initialize {

  my $self = shift;
  return 1;

}

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🌈 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌈

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. Three whole categories, we love a structured queen. 👑

💜 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. Two-for-one, iconic. ✨
• @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. She simply does not check. Free-spirited. 🦋

🌸 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. (She's telling you nicely, bestie — take the hint. 🫶)

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. 👀

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💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) — do it, bestie, they wanna hear from you. 📬

👑 AUTHOR 👑

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

🎀 SEE ALSO 🎀

perl(1).

💀 POD ERRORS 💀

Okay bestie, so the doc itself had a lil moment. POD — that's Plain Old Documentation, the stuff Perl reads to build man pages — flagged some coding errors, and they're all spelled out right here. It's giving "the author was typing fast and the linter was typing faster" 🙈 Not a single one of these changes how the module runs, but they're part of the page, so we're reporting them. No skipping, no summarising, that's the rule.

Here's the full list, exactly as the parser yelled them:

• Around line 323:

'=item' outside of any '=over'

• Around line 408:

You forgot a '=back' before '=head2'

• Around line 436:

Expected '=item 2'

• Around line 441:

Expected '=item 3'

• Around line 446:

Expected '=item 4'

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Real talk: the =over / =item / =back situation is the POD way of saying "start a list, here's an entry, end the list". An =item with no =over above it is like starting a group chat with zero members 🫠, and a missing =back before an =head2 means the list never got closed out before the next big heading rolled up. The Expected '=item 2' trio is the parser going "girl, you numbered one and then just… stopped?" Numbered lists need their numbers, periodt.

⭐ These are documentation formatting hiccups only. Nothing here is a runtime bug, nothing here changes an option, a slot or a method. Your code is fine, the prose markup just needed a vibe check. 💅

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And that's a wrap on the whole page, bestie!! 🎀 You made it all the way to the bottom of MAGE::...urement(3pm) — the User Contributed Perl Documentation version — which is perl v5.32.0, dated 2020-11-27. Slay. Now go write some gloriously well-formed =over blocks and make the parser proud of you. 🦋✨👑