MAGE::...aTuples(3pm)

MAGE::...aTuples(3pm) 💖

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

okay bestie, buckle up, we're reading a Perl manpage and honestly? it's giving ✨structured✨

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🌸 NAME 🌸

Bio::MAGE::BioAssayData::BioDataTuples — it's a Class for the MAGE-OM API, periodt 💅

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🦋 SYNOPSIS 🦋

here's the vibe, copy it exactly, no cap:

use Bio::MAGE::BioAssayData::BioDataTuples

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

# creating an instance with existing data
my $biodatatuples = Bio::MAGE::BioAssayData::BioDataTuples->new(
      propertySets=>\@namevaluetype_list,
      bioAssayTupleData=>\@bioassaydatum_list,
);

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

# 'bioAssayTupleData' association
my $bioassaydatum_array_ref = $biodatatuples->bioAssayTupleData(); # getter
$biodatatuples->bioAssayTupleData(\@bioassaydatum_list); # setter

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🎀 DESCRIPTION 🎀

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

A relational, tuple representation of the data.

that's it. that's the whole personality. lowkey iconic 🫶

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💜 INHERITANCE 💜

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

• Bio::MAGE::BioAssayData::BioDataValues

so yeah, it's got ancestors, we love a class with lineage 👑

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⭐ CLASS METHODS ⭐

all of these? you can call them without even having an instance yet, bestie. just use the Bio::MAGE::BioAssayData::BioDataTuples->methodname() syntax and you're set.

🍓 new()

new()

new(%args)

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

• 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.

• bioAssayTupleData — Sets the value of the bioAssayTupleData association.

The value must be of type: array of Bio::MAGE::BioAssayData::BioAssayDatum.

$obj = class->new(%parameters)

The new() method is the class constructor. main character energy fr fr.

• 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.

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@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 @ me, that's just how it is.

• Return value: a list of the names of all slots defined for this class.
• Side effects: none

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@name_list = get_attribute_names()

returns the list of attribute data members for this class. 💅

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@name_list = get_association_names()

returns the list of association data members for this class. 🔥

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@class_list = get_superclasses()

returns the list of superclasses for this class.

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@class_list = get_subclasses()

returns the list of subclasses for this class.

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$name = class_name()

Returns the full class name for this class. ✨

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$package_name = package_name()

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

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%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. it's giving metadata, and we're obsessed 🫶

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🌈 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 💅

• 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.

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$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:

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 be careful bestie

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@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

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$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

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$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

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🧚 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.

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

(...that's the whole list. nothing here. no attributes. silent. mysterious. 🤫)

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💫 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::BioAssayData::BioDataTuples has the following association accessor methods:

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🌸 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 = $biodatatuples->setPropertySets($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 = $biodatatuples->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 = $biodatatuples->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 is more, 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

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🦋 bioAssayTupleData 🦋

Methods for the bioAssayTupleData association.

From the MAGE-OM documentation:

The collection of BioAssayData tuples.

$array_ref = $biodatatuples->setBioAssayTupleData($array_ref)

The restricted setter method for the bioAssayTupleData association.

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

$array_ref = $biodatatuples->getBioAssayTupleData()

The restricted getter method for the bioAssayTupleData association.

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

$val = $biodatatuples->addBioAssayTupleData(@vals)

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

• Input parameters: the list of values @vals to add to the bioAssayTupleData 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::BioAssayDatum

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and finally, the lil guy itself, verbatim, don't touch it:

sub initialize {

  my $self = shift;
  return 1;

}

to be continued… 💖

💅 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💅

Okay bestie, listen up, because this is the part where the vocab gets ✨specific✨. In the Perl implementation of MAGE-OM classes, there are exactly three types of class data members: "slots", "attributes", and "associations". Three flavors, one class, iconic behavior. 🍓

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🧚 SLOTS 🧚

So in this API, the term "slot" means a data member of the class that was not present in the UML model — it's there for mainly internal purposes. Which means: use only if you understand the inner workings of the API. Like, for real, do not just start poking at slots because they looked at you funny. 🙈 Most often, slots get used by generic methods, like the ones hanging out in the XML writing and reading classes.

Slots are implemented with unified getter/setter methods, which is giving "one method, two jobs, main character energy":

• $var = $obj->slot_name(); — grabs the current value of the slot. That's it, that's the whole vibe. 🫶
• $new_var = $obj->slot_name($new_var); — stores $new_var in the slot, and the return value is also $new_var (yes, it hands it right back to you, generous queen 💖).
• @names = $obj->get_slot_names() — returns the list of all slots in the class. The whole roster, no gatekeeping. 👑

DATA CHECKING: No data type checking is made for these methods. Zero. None. She's not checking your ID at the door. 😭

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🌸 ATTRIBUTES AND ASSOCIATIONS 🌸

Now the terms "attribute" and "association" mean data members of the class that were specified directly from the UML model. So these ones are official, they're on the guest list, they have name tags. ✨

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. Out with the old, in with the new, periodt. 💅
  • 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 instead. (Like, set* is fine but it's not giving what add* is giving.)
  • 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* — the appender, the builder, the glow-up method. 🦋
  • NOTE: Only present in associations with list cardinality.
  • Appends a list of objects to any values that may already be stored in the association. It doesn't overwrite, it adds on. We love a method that respects what came before. 🥹
  • DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

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👑 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 — all three at once, she's versatile like that:

$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 — they're covered, don't worry, iykyk. 🔥

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💀 BUGS 💀

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

(Yes, spelled out with 'at' and 'dot' like that, because we're being sneaky with the spam bots. Respect the craft. 🎀)

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🫶 AUTHOR 🫶

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

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🌈 SEE ALSO 🌈

• perl(1).

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😭 POD ERRORS 😭

Hey! The above document had some coding errors, which are explained below. Not me exposing the manpage's own typos, but here we are, we keep it 💯 around here:

• 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'

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And that's the whole page, bestie! 💖 This little masterpiece is perl v5.32.0, dated 2020-11-27, and it's the MAGE::...aTuples(3pm) page from the User Contributed Perl Documentation. Now go forth and use those add* methods like the icon you are. Slay, hydrate, and always check your data types. 💅✨🌸