MAGE::...Mapping(3pm)

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

💖 MAGE::...Mapping(3pm) — User Contributed Perl Documentation 💖

okay bestie, welcome to Bio::MAGE::BioAssayData::BioAssayMapping, a whole class in the MAGE-OM API, and honestly? she's giving container-of-mappings energy and I'm obsessed. this is part 1 so don't go anywhere, there's more coming 🫶

✨ NAME ✨

Bio::MAGE::BioAssayData::BioAssayMapping — a whole Class for the MAGE-OM API. that's the whole name, no notes 💅

🌸 SYNOPSIS 🌸

so here's how you'd actually use her, no cap:

use Bio::MAGE::BioAssayData::BioAssayMapping

# creating an empty instance
my $bioassaymapping = Bio::MAGE::BioAssayData::BioAssayMapping->new();

# creating an instance with existing data
my $bioassaymapping = Bio::MAGE::BioAssayData::BioAssayMapping->new(
      propertySets=>\@namevaluetype_list,
      bioAssayMaps=>\@bioassaymap_list,
);

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

# 'bioAssayMaps' association
my $bioassaymap_array_ref = $bioassaymapping->bioAssayMaps(); # getter
$bioassaymapping->bioAssayMaps(\@bioassaymap_list); # setter

like, getter, setter, getter, setter. she's symmetrical, she's tidy, she's iconic ✨

🦋 DESCRIPTION 🦋

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

Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.

literally that's her job. she maps input BioAssay dimensions → output BioAssay dimension. a whole matchmaker fr fr 🎀

💜 INHERITANCE 💜

Bio::MAGE::BioAssayData::BioAssayMapping has the following superclasses:

  • Bio::MAGE::Extendable

so yes, she inherits from Bio::MAGE::Extendable, and that's gonna matter in a sec when we talk about propertySets 👀

⭐ CLASS METHODS ⭐

okay so the way that these work: you can call all of the following without even having an instance of the class yet, using the Bio::MAGE::BioAssayData::BioAssayMapping->methodname() syntax. class methods, bestie. no object required. periodt.

🎀 new() 🎀

🎀 new(%args) 🎀

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

  • propertySets — sets the value of the propertySets association. fun fact: this association was inherited from class Bio::MAGE::Extendable. The value must be of type: array of Bio::MAGE::NameValueType.
  • bioAssayMaps — sets the value of the bioAssayMaps association. The value must be of type: array of Bio::MAGE::BioAssayData::BioAssayMap.

🎀 $obj = class->new(%parameters) 🎀

The new() method is the class constructor. she builds the thing. main character energy 🌟

  • 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. so don't come for her about that, she's just being precise 💅
  • 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 💅

now we're in object territory, bestie. these ones need an actual instance, iykyk.

🍓 $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 her, she's that good 😭

  • 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. She has two different invocation methods, choose your fighter:

  1. the first takes a named parameter list
  2. 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. so like. don't make up slot names. she WILL notice 🙈

🍓 @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. so no sneaky two-in-one, bestie, you get a whole pair 💖

Bio::MAGE::BioAssayData::BioAssayMapping has the following attribute accessor methods:

...and that's it. that's the list. empty. she has no attributes of her own. and honestly? that's valid. minimal queen 👑

🧚 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. so like, how many friends can she bring to the function:

  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::BioAssayData::BioAssayMapping has the following association accessor methods:

💜 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.

like, a lil side pocket for your non-spec extra values. she's thoughtful like that 🎀

🌸 $array_ref = $bioassaymapping->setPropertySets($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 = $bioassaymapping->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 = $bioassaymapping->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. more friends, more vibes ✨

  • 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

💜 bioAssayMaps 💜

Methods for the bioAssayMaps association.

From the MAGE-OM documentation:

The maps for the BioAssays.

short. sweet. to the point. she said what she said 💅

🌸 $array_ref = $bioassaymapping->setBioAssayMaps($array_ref) 🌸

The restricted setter method for the bioAssayMaps association.

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

🌸 $array_ref = $bioassaymapping->getBioAssayMaps() 🌸

The restricted getter method for the bioAssayMaps association.

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

🌸 $val = $bioassaymapping->addBioAssayMaps(@vals) 🌸

Because the bioAssayMaps association has list cardinality, it may store more than one value. This method adds the current list of objects in the bioAssayMaps association. stack 'em up bestie 🫶

  • Input parameters: the list of values @vals to add to the bioAssayMaps 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::BioAssayMap

and then, just sitting there at the bottom of the association methods, there's this whole lil subroutine, and yes we're keeping it exactly as-is:

sub initialize {

  my $self = shift;
  return 1;

}

she returns 1. always. she's just like that. iconic. 💖

okay bestie, that's the end of part 1 — more is coming, don't go anywhere 🌈

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

So in the Perl implementation of MAGE-OM classes, there are literally three types of class data members: slots, attributes, and associations. That's the whole vibe. 🫶

✨ 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); — stores $new_var in the slot; the return value is also $new_var. 🔁
  • @names = $obj->get_slot_names() — returns the list of all slots in the class. 📋
DATA CHECKING: No data type checking is made for these methods. 💀

💅 ATTRIBUTES AND ASSOCIATIONS 💅

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

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* — appends a list of objects to any values that may already be stored in the association.
NOTE: Only present in associations with list cardinality. 🌈 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 290: '=item' outside of any '=over'
  • Around line 375: You forgot a '=back' before '=head2'
  • Around line 403: Expected '=item 2'
  • Around line 408: Expected '=item 3'
  • Around line 413: Expected '=item 4'

— and that's the tea ☕: this page is MAGE::...Mapping(3pm), from perl v5.32.0, dated 2020-11-27. mwah 💅✨

📦 where this page comes from