MAGE::...atabase(3pm)

✨ NAME ✨

okay so bestie, this page is from the User Contributed Perl Documentation, and the manual you've got open is MAGE::...atabase(3pm). What's actually in it? It's Bio::MAGE::Description::Database — a Class for the MAGE-OM API. That's the whole vibe. 💅

---

🎀 SYNOPSIS 🎀

here's the tea, straight up, no edits:

use Bio::MAGE::Description::Database

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

# creating an instance with existing data
my $database = Bio::MAGE::Description::Database->new(
      URI=>$uri_val,
      version=>$version_val,
      name=>$name_val,
      identifier=>$identifier_val,
      contacts=>\@contact_list,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

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

# 'version' attribute
my $version_val = $database->version(); # getter
$database->version($value); # setter

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

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

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

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

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

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

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

---

🌸 DESCRIPTION 🌸

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

An address to a repository.

that's it. that's the whole description. iconic, honestly ✨

---

🦋 INHERITANCE 🦋

Bio::MAGE::Description::Database has the following superclasses — aka its ancestors, its lineage, its nepo-baby situation 💅:

• Bio::MAGE::Identifiable

---

👑 CLASS METHODS 👑

okay so here's the thing — all of these methods can be called without first having an instance of the class. You just hit them with the Bio::MAGE::Description::Database->methodname() syntax. no object required, she's independent like that 🫶

new()

new(%args)

The object constructor "new()" accepts the following optional named-value style arguments — feed her whatever she needs, she'll take it from there:

• URI — Sets the value of the "URI" attribute
• version — Sets the value of the "version" attribute
• name — Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• identifier — Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• contacts — Sets the value of the "contacts" 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".
• 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".
• 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".

$obj = class->new(%parameters)

The "new()" method is the class constructor. the main character, 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. (yes, really. don't @ me.)

• 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. short king of a method fr fr 🍓

@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()

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. it's giving 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.

$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 — pick 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.

⚠️ heads up bestie, croak() is coming for you if you make up a slot name that doesn't exist. she does not play.

@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. so one method to put the thing in, one method to get the thing out. balanced. 💅

"Bio::MAGE::Description::Database" has the following attribute accessor methods:

URI

Methods for the "URI" attribute.

From the MAGE-OM documentation:

The location of the Database.

$val = $database->setURI($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 = $database->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

version

Methods for the "version" attribute.

From the MAGE-OM documentation:

The version for which a DatabaseReference applies.

$val = $database->setVersion($val)

The restricted setter method for the "version" attribute.

• Input parameters: the value to which the "version" attribute will be set
• Return value: the current value of the "version" attribute
• Side effects: none
• Exceptions: will call "croak()" if no input parameters are specified, or if too many input parameters are specified

$val = $database->getVersion()

The restricted getter method for the "version" attribute.

• Input parameters: none
• Return value: the current value of the "version" 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 = $database->setName($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 = $database->getName()

The restricted getter method for the "name" attribute.

• 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

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 = $database->setIdentifier($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, bestie, literally nothing happens
• Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified 😤

$val = $database->getIdentifier()

The restricted getter method for the identifier attribute. Read-only queen 👑

• 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 — like, why are you passing args to a getter, girlie 😭

---

🌈 ASSOCIATIONS 🌈

okay so associations are references to other classes 🦋. Every association in MAGE-OM has a cardinality, and that cardinality tells you 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::Database has the following association accessor methods:

contacts

Methods for the contacts association.

From the MAGE-OM documentation:

Information on the contacts for the database

$array_ref = $database->setContacts($array_ref)

The restricted setter method for the contacts association.

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

The restricted getter method for the contacts association.

• Input parameters: none
• Return value: the current value of the contacts 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 = $database->addContacts(@vals)

Because the contacts association has list cardinality, it may store more than one value. This method adds the current list of objects in the contacts association. she's a collector, she collects 🎀

• Input parameters: the list of values @vals to add to the contacts association. NOTE: submitting a single value is permitted. yes bestie, one is fine, she's not gonna judge you ✨
• 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 = $database->setAuditTrail($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 = $database->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 = $database->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. the receipts are being kept 📝

• 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 = $database->setPropertySets($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 = $database->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 = $database->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

---

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 = $database->setDescriptions($array_ref)

The restricted setter method 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 = $database->getDescriptions()

The restricted getter method for the descriptions association.

• 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 = $database->addDescriptions(@vals)

Because the descriptions association has list cardinality, it may store more than one value. 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

---

security

Methods for the security association. 🔐

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $database->setSecurity($val)

The restricted setter method 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 = $database->getSecurity() — bestie, this is 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. 💀

And here's the initialize method, short and sweet:

sub initialize {

  my $self = shift;
  return 1;

}

---

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. Periodt.

🎀 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. iykyk.

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. ✨
• @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. No cap.

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* — 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. 👑

💀 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 367: '=item' outside of any '=over'
• Around line 452: You forgot a '=back' before '=head2'
• Around line 768: Expected '=item 2'
• Around line 773: Expected '=item 3'
• Around line 778: Expected '=item 4'

💖 That's the whole page, bestie! This was perl v5.32.0, dated 2020-11-27, from MAGE::...atabase(3pm). Stay iconic. 💖