MAGE::...eEntry(3pm)

💖 NAME 💖

okay so bestie, welcome to MAGE::...eEntry(3pm) — yes that's the user-contributed Perl documentation section, we're fancy like that ✨ — and this whole page is about Bio::MAGE::Description::DatabaseEntry, the class for the MAGE-OM API. it's giving "reference to a database record" realness, and we're gonna get into every single detail, no cap 💅

---

✨ SYNOPSIS ✨

like, here's the vibe of how you actually use it:

use Bio::MAGE::Description::DatabaseEntry

# creating an empty instance
my $databaseentry = Bio::MAGE::Description::DatabaseEntry->new();

# creating an instance with existing data
my $databaseentry = Bio::MAGE::Description::DatabaseEntry->new(
      URI=>$uri_val,
      accession=>$accession_val,
      accessionVersion=>$accessionversion_val,
      propertySets=>\@namevaluetype_list,
      database=>$database_ref,
      type=>$ontologyentry_ref,
);

# 'URI' attribute
my $URI_val = $databaseentry->URI(); # getter
$databaseentry->URI($value); # setter

# 'accession' attribute
my $accession_val = $databaseentry->accession(); # getter
$databaseentry->accession($value); # setter

# 'accessionVersion' attribute
my $accessionVersion_val = $databaseentry->accessionVersion(); # getter
$databaseentry->accessionVersion($value); # setter

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

# 'database' association
my $database_ref = $databaseentry->database(); # getter
$databaseentry->database($database_ref); # setter

# 'type' association
my $ontologyentry_ref = $databaseentry->type(); # getter
$databaseentry->type($ontologyentry_ref); # setter

---

🦋 DESCRIPTION 🦋

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

A reference to a record in a database.

that's it. that's the whole thing. iconic, honestly 🎀

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🌸 INHERITANCE 🌸

Bio::MAGE::Description::DatabaseEntry has the following superclasses:

• Bio::MAGE::Extendable

so it's lowkey part of the family tree, and that matters for the inherited bits below 👑

---

👑 CLASS METHODS 👑

the following methods can all be called without first having an instance of the class, via the Bio::MAGE::Description::DatabaseEntry->methodname() syntax. yes bestie, class methods, we love to see it ✨

new()

new(%args)

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

• URI — sets the value of the URI attribute 💖
• accession — sets the value of the accession attribute 🎀
• accessionVersion — sets the value of the accessionVersion attribute 🦋
• 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.

• database — sets the value of the database association

the value must be of type: instance of Bio::MAGE::Description::Database.

• type — sets the value of the type association

the value must be of type: instance of Bio::MAGE::Description::OntologyEntry.

---

$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.

---

@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 come for me, that's just how it is 😭

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. 🔥

---

more parts coming bestie, don't go anywhere 🫶

💫 INSTANCE METHODS 💫

$obj_copy = $obj->new()

Okay so when you call new() on an existing object reference instead of a class name, it's giving copy constructor — the new object starts out with all the same values as the one you copied. Bestie, it's literally a clone. 👯

• Parameters: nope, zero input parameters get used here. The initial values are just taken straight from the object you're copying.
• 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) and $obj->set_slots(\@name_list, \@value_list)

The set_slots() method is how you set a whole bunch of slots at once, and it's got two whole ways to be called:

1. the first one takes a named parameter list (%parameters), and
2. the second one takes two array references (\@name_list and \@value_list).

• Return value: none. 🫥
• Side effects: it will call croak() if you use a slot_name that the class doesn't define. So don't be out here making up slots, bestie. 💀

---

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

get_slots() is the grab-a-bunch-at-once move — you use it 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.

Bio::MAGE::Description::DatabaseEntry has the following attribute accessor methods:

URI

Methods for the URI attribute.

From the MAGE-OM documentation:

The location of the record. 📍

• $val = $databaseentry->setURI($val) — the restricted setter method for the URI attribute.
  • Input parameters: the value to which the URI attribute will be set.
  • Return value: the current value of the URI attribute.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified. 😭
• $val = $databaseentry->getURI() — the restricted getter method for the URI attribute.
  • Input parameters: none.
  • Return value: the current value of the URI attribute.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

accession

Methods for the accession attribute.

From the MAGE-OM documentation:

The identifier used to look up the record. 🔍

• $val = $databaseentry->setAccession($val) — the restricted setter method for the accession attribute.
  • Input parameters: the value to which the accession attribute will be set.
  • Return value: the current value of the accession attribute.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified.
• $val = $databaseentry->getAccession() — the restricted getter method for the accession attribute.
  • Input parameters: none.
  • Return value: the current value of the accession attribute.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

accessionVersion

Methods for the accessionVersion attribute.

From the MAGE-OM documentation:

The appropriate version of the accession (if applicable). 🏷️

• $val = $databaseentry->setAccessionVersion($val) — the restricted setter method for the accessionVersion attribute.
  • Input parameters: the value to which the accessionVersion attribute will be set.
  • Return value: the current value of the accessionVersion attribute.
  • Side effects: none.
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified.
• $val = $databaseentry->getAccessionVersion() — the restricted getter method for the accessionVersion attribute.
  • Input parameters: none.
  • Return value: the current value of the accessionVersion attribute.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

---

🔗 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::Description::DatabaseEntry 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. 🧾

• $array_ref = $databaseentry->setPropertySets($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 = $databaseentry->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 = $databaseentry->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.

database

Methods for the database association.

From the MAGE-OM documentation:

Reference to the database where the DataEntry instance can be found. 🗄️

• $val = $databaseentry->setDatabase($val) — the restricted setter method for the database association.
  • Input parameters: the value to which the database association will be set : one of the accepted enumerated values.
  • Return value: the current value of the database 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::Database. 💀
• $val = $databaseentry->getDatabase() — the restricted getter method for the database association.
  • Input parameters: none.
  • Return value: the current value of the database association : an instance of type Bio::MAGE::Description::Database.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

type

Methods for the type association.

From the MAGE-OM documentation:

The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD). 🧬

• $val = $databaseentry->setType($val) — the restricted setter method for the type association.
  • Input parameters: the value to which the type association will be set : one of the accepted enumerated values.
  • Return value: the current value of the type 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 = $databaseentry->getType() — the restricted getter method for the type association.
  • Input parameters: none.
  • Return value: the current value of the type association : an instance of type Bio::MAGE::Description::OntologyEntry.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

And last but not least, this lil guy is just vibing at the end of the section, exactly as written:

sub initialize {

  my $self = shift;
  return 1;

}

to be continued, bestie… 💜

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

ok so in the Perl version of MAGE-OM classes, there are literally three kinds of class data members, and you gotta know the difference bestie: slots, attributes, and associations. 🫶

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💅 SLOTS

so this API uses the word "slot" for a data member that wasn't in the UML model — it's mostly there for internal stuff, so like… only touch it if you genuinely understand the inner workings of the API, no cap. most of the time slots get used by generic methods, like the ones in the XML writing and reading classes. 🎀

slots are implemented with unified getter/setter methods, and they go like this:

• $var = $obj->slot_name(); — grabs 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. (yes it gives you back what you just put in, iconic behaviour tbh)
• @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. 💀 like, zero, none, she does not check. be careful.

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🦋 ATTRIBUTES AND ASSOCIATIONS

"attribute" and "association" mean a data member of the class that was specified directly from the UML model. so these are the real ones, the main characters. 👑

in the Perl implementation of MAGE-OM classes, association and attribute accessors get implemented with three separate methods, and here's the whole tea:

• 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. (just. no arguments. don't. 🙈)

• 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.

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🌈 GENERIC METHODS

the unified base class of all MAGE-OM classes, Bio::MAGE::Base, hooks you up with a whole set of generic methods that operate on slots, attributes, and associations. it's giving very generous of her. 🎁

• $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, bestie — the receipts are all here, iykyk. 📜

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🐛 BUGS

found a bug? 😭 please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) — she's waiting for your letters, fr fr.

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👑 AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org) — the author, the moment, the legend. 🫶

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🌈 SEE ALSO

• perl(1). that's it, that's the list. go read your perl manpage bestie. 💜

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💀 POD ERRORS

hey! 🙈 the above document had some coding errors, which are explained below:

• Around line 350:
  • '=item' outside of any '=over' — not her going rogue with an =item and no =over to hold it 💀
• Around line 435:
  • You forgot a '=back' before '=head2' — ma'am. the =back. you forgot it. 😭
• Around line 679:
  • Expected '=item 2'
• Around line 684:
  • Expected '=item 3'
• Around line 689:
  • Expected '=item 4'

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and that's a wrap on the whole page, bestie!! 🎀✨ this was perl v5.32.0, dated 2020-11-27, and honestly? she ate. now go forth and slay your MAGE-OM classes. 💅🦋💖