Bio::Genex::ExperimentSet - Methods for processing data from the GeneX DB table: ExperimentSet

- NAME
- SYNOPSIS
- DESCRIPTION
- ATTRIBUTES
- CLASS VARIABLES
- DELAYED FETCH
- CLASS METHODS
- INSTANCE METHODS
- FOREIGN KEY ACCESSOR METHODS
- ATTRIBUTE METHODS
- IMPLEMENTATION DETAILS
- BUGS
- LAST UPDATED
- AUTHOR
- SEE ALSO

# NAME

Bio::Genex::ExperimentSet - Methods for processing data from the GeneX DB table: ExperimentSet

# SYNOPSIS

      use Bio::Genex::ExperimentSet;

      # instantiating an instance
      my $ExperimentSet = Bio::Genex::ExperimentSet->new(id=>47);

      # retrieve data from the DB for all columns
      $ExperimentSet->fetch();

      # creating an instance, without pre-fetching all columns
      my $ExperimentSet = new Bio::Genex::ExperimentSet(id=>47);

      # creating an instance with pre-fetched data
      my $ExperimentSet = new Bio::Genex::ExperimentSet(id=>47, 'fetch_all'=>1);

      # retrieving multiple instances via primary keys
      my @objects = Bio::Genex::ExperimentSet->get_objects(23,57,98)

      # retrieving all instances from a table
      my @objects = Bio::Genex::ExperimentSet->get_objects('ALL');

      # retrieving the primary key for an object, generically
      my $primary_key = $ExperimentSet->id();

      # or specifically
      my $es_pk_val = $ExperimentSet->es_pk();

      # retreving other DB column attributes
      my $name_val = $ExperimentSet->name();
      $ExperimentSet->name($value);

      my $gs_fk_val = $ExperimentSet->gs_fk();
      $ExperimentSet->gs_fk($value);

      my $us_fk_val = $ExperimentSet->us_fk();
      $ExperimentSet->us_fk($value);

      my $cit_fk_val = $ExperimentSet->cit_fk();
      $ExperimentSet->cit_fk($value);

      my $group_can_update_val = $ExperimentSet->group_can_update();
      $ExperimentSet->group_can_update($value);

      my $biology_description_val = $ExperimentSet->biology_description();
      $ExperimentSet->biology_description($value);

      my $analysis_description_val = $ExperimentSet->analysis_description();
      $ExperimentSet->analysis_description($value);

      my $treatment_type_val = $ExperimentSet->treatment_type();
      $ExperimentSet->treatment_type($value);

      my $quantity_series_type_val = $ExperimentSet->quantity_series_type();
      $ExperimentSet->quantity_series_type($value);

      my $is_public_val = $ExperimentSet->is_public();
      $ExperimentSet->is_public($value);

      my $release_date_val = $ExperimentSet->release_date();
      $ExperimentSet->release_date($value);

      my $submission_date_val = $ExperimentSet->submission_date();
      $ExperimentSet->submission_date($value);

      my $local_accession_val = $ExperimentSet->local_accession();
      $ExperimentSet->local_accession($value);

      my $archive_bundle_ref_val = $ExperimentSet->archive_bundle_ref();
      $ExperimentSet->archive_bundle_ref($value);

# DESCRIPTION

Each Genex class has a one to one correspondence with a GeneX DB table of the same name (i.e. the corresponding table for Bio::Genex::ExperimentSet is ExperimentSet).

Most applications will first create an instance of Bio::Genex::ExperimentSet and then fetch the data for the object from the DB by invoking `fetch()`. However, in cases where you may only be accessing a single value from an object the built-in delayed fetch mechanism can be used. All objects are created without pre-fetching any data from the DB. Whenever an attribute of the object is accessed via a getter method, the data for that attribute will be fetched from the DB if it has not already been. Delayed fetching happens transparently without the user needing to enable or disable any features.

Since data is not be fetched from the DB until it is accessed by the calling application, it could presumably save a lot of access time for large complicated objects when only a few attribute values are needed.

# ATTRIBUTES

There are three different types of attributes which instances of Bio::Genex::ExperimentSet can access: raw foreign key attributes, Obect-Oriented foreign key attributes, and simple column attributes.

Raw Foreign Keys Attributes
Object Oriented Foreign Key Attributes
  This mode presents foreign key attributes in a special way, with all non-foreign key attributes presented normally. Foreign keys are first retrieved from the DB, and then objects of the appropriate classes are created and stored in slots. This mode is useful for applications that want to process information from the DB because it automates looking up information.

  Specifying the '`recursive_fetch`' parameter when calling `new()`, modifies the behavior of this mode. The value given specifies the number of levels deep that fetch will be invoked on sub-objects created.

Simple Column Attributes

# CLASS VARIABLES

Class Bio::Genex::ExperimentSet defines the following utility variables for assisting programmers to access the ExperimentSet table.

$Bio::Genex::ExperimentSet::LIMIT
  If defined, $LIMIT will set a limit on any select statements that can return multiple instances of this class (for example `get_objects()` or any call to a `ONE_TO_MANY` or `LOOKUP_TABLE` foreign key accessor method).

$Bio::Genex::ExperimentSet::USE_CACHE
  This variable controls whether the class will cache any objects created in calls to `new()`. Objects are cached by primary key. The caching is very simple, and no effort is made to track whether different invocations of `new()` are being made for an object with the same primary key value, but with different options set. If you desire to reinstantiate an object with a different set of parameters, you would need to undefine `$USE_CACHE` first.

WARNING: variables other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.

# DELAYED FETCH

It is possible to retrieve only the subset of attributes one chooses by simply creating an object instance and then calling the appropriate getter function. The object will automatically fetch the value from the DB when requested. This can potentially save time for large complicated objects. This triggers a separate DB query for each attribute that is accessed, whereas calling `fetch()` will retrieve all fields of the object with a single query.

For example:

      my $ExperimentSet = Bio::Genex::ExperimentSet->new(id=>47);
      my $val = $ExperimentSet->es_pk();

The attribute's value is then cached in the object so any further calls to that attribute's getter method do not trigger a DB query.

NOTE: Methods may still return `undef` if their value in the DB is `NULL`.

# CLASS METHODS

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

`new(%args)`
  `new()` accepts the following arguments:
  id
    Numeric or string value. The value of the primary key for looking up the object in the DB.

`linking_table()`
  Used by generic functions to determine if a specified class is a linking table class. For Bio::Genex::ExperimentSet it returns 0, since it is not a linking table class.

`pkey_name()`
  This method returns the name of the column which is used as the primary key for this DB table. This method only exists for non-linking table classes, and for Bio::Genex::ExperimentSet it returns the value 'es_pk';

`table_name()`
  Returns the name of the DB table represented by this class. For Bio::Genex::ExperimentSet it returns 'ExperimentSet';

`column2name()`
  This method returns a hashref that translates DB column names into human readable format.

`name2column()`
  This method returns a hashref that is a reverse lookup table to translate the human readable version of a DB column name back into the column_name. This is useful for preparing table output in CGI scripts:

          %column2name = %{$class->column2name()};
          if (exists $column2name{$_}) {
            push(@column_copy,$column2name{$_});
          }

          # now that we've translated the names, we sort them
          @column_copy = sort @column_copy;

          # make a header element.
          push(@rows,th(\@column_copy));

`fkeys()`
  This method returns a hashref that holds all the foreign key entries for the ExperimentSet table.

`column_names()`
  This method returns an array ref which holds the names of all the columns in table ExperimentSet.

          # first retrieve the data from the DB
          $object = $full_module_name->new(id=>$id);
          $object->fetch();

          # now extract the data from the object
          foreach (@{$class->column_names}) {
          # we use this to temporarily relax the strict pragma
          # to use symbolic references
            no strict 'refs';
            $tmp_values{$_} = $object->$_;

          # back to our regularily scheduled strictness
          }

`insert_db($dbh)`
  This method inserts the data for the object into the database specified by the DB handle $dbh. To use this method, create a blank object with `new()`, set the attributes that you want, and then call `insert_db()`.

        my $dbh = Bio::Genex::current_connection(USER=>$SU_USERNAME,
                                            PASSWORD=>$SU_PASSWORD);
        my ExperimentSet = Bio::Genex::ExperimentSet->new();
        ExperimentSet->name('some_value');
        ExperimentSet->insert_db($dbh);

  NOTE: You must log into the DB with a user/password that has INSERT priveleges in the DB, otherwise you will get a DBI error.

  WARNING: `fetch()` will not be called, so if you are using this method to insert a copy of an existing DB object, then it is up to you to call `fetch()`, otherwise, only the attributes that are currently set in the object will be inserted.

`update_db($dbh)`
  This method update the data for an object already in the database specified by the DB handle $dbh. To use this method, fetch an object from the DB, change the attributes that you want, and then call `update_db()`.

        my $dbh = Bio::Genex::current_connection(USER=>$SU_USERNAME,
                                            PASSWORD=>$SU_PASSWORD);
        my ExperimentSet = Bio::Genex::ExperimentSet->new(id=>43);
        ExperimentSet->name('some_value');
        ExperimentSet->update_db($dbh);

  NOTE: You must log into the DB with a user/password that has INSERT priveleges in the DB, otherwise you will get a DBI error.

  NOTE: Any modification of the primary key value will be discarded ('es_pk' for module Bio::Genex::ExperimentSet).

`get_objects(@id_list)`
`get_objects('ALL')`
get_objects({column=>'col_name',value=>'val'})
  This method is used to retrieve multiple instances of class Bio::Genex::ExperimentSet simultaneously. There are three different ways to invoke this method.

  By passing in an `@id_list`, `get_objects()` uses each element of the list as a primary key for the ExperimentSet table and returns a single instance for each entry.

  WARNING: Passing incorrect id values to `get_objects()` will cause a warning from `Bio::Genex::ExperimentSet::initialize()`. Objects will be created for other correct id values in the list.

  By passing the 'ALL' parameter, `get_objects()` returns an instance for every entry in the table.

  By passing an anonymous hash reference that contains the 'column' and 'name' keys, the method will return all objects from the DB whose that have the specified value in the specified column.

NOTE: All objects must have the 'id' parameter set before attempting to use `fetch()` or any of the objects getter functions.

# INSTANCE METHODS

The following methods can only be called by first having valid instance of class Bio::Genex::ExperimentSet.

`fetch()`
  This method triggers a DB query to retrieve ALL columns from the DB associated with this object.

WARNING: methods other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.

# FOREIGN KEY ACCESSOR METHODS

There are two major categories of foreign key accessor methods: Object Oriented foreign key methods, and raw foreign key methods.

Each foreign key column in the table is represented by two methods, one OO method and one raw method. The raw method enables fethcing the exact numeric or string values stored in the DB. The OO method creates objects of the class the fkey column refers to. The idea is that if only the numeric fkey value is desired, the raw fkey method can be used. If it is necessary to get attributes from the table referred to by the fkey column, then the OO method should be invoked, and the necessary methods on that object can be queried.

The names of the raw fkey methods is the same as the fkey columns in the DB table they represent (all fkey columns end in the suffix '_fk'). The OO methods have the same names as the column they represent, with the difference that they have the suffix '_obj' instead of '_fk'.

So for example, in class Bio::Genex::ArrayMeasurement the '`primary_es_fk`' column is represented by two methods, the raw method `primary_es_fk()`, and the OO method `primary_es_obj`.

The following foreign key accessors are defined for class Bio::Genex::ExperimentSet:

@id_list = `experimentfactors_fk()`
@obj_list = `experimentfactors_obj()`
  This is an attribute of type ONE_TO_MANY and refers to class the Bio::Genex::ExperimentFactors manpage. The raw accessor method, `experimentfactors_fk()` returns a list of foreign key ids. The OO accessor method, `experimentfactors_obj()` returns a list of objects of class Bio::Genex::ExperimentFactors.

@id_list = `hotspots_fk()`
@obj_list = `hotspots_obj()`
  This is an attribute of type ONE_TO_MANY_LINK and refers to class the Bio::Genex::HotSpots manpage. The raw accessor method, `hotspots_fk()` returns a list of foreign key ids. The OO accessor method, `hotspots_obj()` returns a list of objects of class Bio::Genex::HotSpots.

@id_list = `arraymeasurement_fk()`
@obj_list = `arraymeasurement_obj()`
  This is an attribute of type ONE_TO_MANY and refers to class the Bio::Genex::ArrayMeasurement manpage. The raw accessor method, `arraymeasurement_fk()` returns a list of foreign key ids. The OO accessor method, `arraymeasurement_obj()` returns a list of objects of class Bio::Genex::ArrayMeasurement.

@id_list = `treatmentlevel_fk()`
@obj_list = `treatmentlevel_obj()`
  This is an attribute of type ONE_TO_MANY and refers to class the Bio::Genex::TreatmentLevel manpage. The raw accessor method, `treatmentlevel_fk()` returns a list of foreign key ids. The OO accessor method, `treatmentlevel_obj()` returns a list of objects of class Bio::Genex::TreatmentLevel.

@id_list = `citationlink_fk()`
@obj_list = `citationlink_obj()`
  This is an attribute of type ONE_TO_MANY_LINK and refers to class the Bio::Genex::CitationLink manpage. The raw accessor method, `citationlink_fk()` returns a list of foreign key ids. The OO accessor method, `citationlink_obj()` returns a list of objects of class Bio::Genex::CitationLink.

Every foreign key in a DB table belongs to a certain class of foreign keys. Each type of foreign key confers a different behavior on the class that contains it. The classifications used in Genex.pm are:

- MANY_TO_ONE

  If a class contains a foreign key of this type it will not be visible to the API of that class, but instead it confers a special method to the class that it references.

  For example, the Chromosome table has a MANY_TO_ONE foreign key, spc_fk, that refers to the species table. Class the Bio::Genex::Chromosome manpage, has it\'s normal `spc_fk()` attribute method, but no special foreign key accessor method. However, class the Bio::Genex::Species manpage is given a special foreign key accessor method, `chromosome_fk()` of type ONE_TO_MANY. When invoked, this method returns a list of objects of class the Bio::Genex::Species manpage.

- ONE_TO_MANY

  The inverse of type MANY_TO_ONE. It is not an attribute inherent to a given foreign key in any DB table, but instead is created by the existence of a MANY_TO_ONE foreign key in another table. See the above discussion about MANY_TO_ONE foreign keys.

- LOOKUP_TABLE

  This type of key is similar to type ONE_TO_MANY. However, However the API will never retrieve an object of this type. Instead it retrieves a matrix of values, that represent the list of objects. It is used in only two places in the API: the Bio::Genex::ArrayMeasurement manpage and the Bio::Genex::ArrayLayout manpage classes with the `am_spots()` and `al_spots()` accessor functions.

- LINKING_TABLE

  Foreign keys of this type appear in tables without primary keys. The foreign keys are each of type LINKING_TABLE, and when invoked return an object of the class referred to by the foreign key.

- FKEY

  A generic foreign key with no special properties. When invoked it returns an object of the class referred to by the foreign key.

# ATTRIBUTE METHODS

These are the setter and getter methods for attributes in class Bio::Genex::ExperimentSet.

NOTE: To use the getter methods, you may either invoke the `fetch()` method to retrieve all the values for an object, or else rely on delayed fetching to retrieve the attributes as needed.

`id()`
  `id()` is a special attribute method that is common to all the Genex classes. This method returns the primary key of the given instance (and for class Bio::Genex::ExperimentSet it is synonomous with the `es_pk()`method). The `id()` method can be useful in writing generic methods because it avoids having to know the name of the primary key column.

`es_pk()`
  This is the primary key attribute for Bio::Genex::ExperimentSet. It has no setter method.

$value = name();
name($value);
  Methods for the name attribute.

$value = gs_fk();
gs_fk($value);
  Methods for the gs_fk attribute.

$value = us_fk();
us_fk($value);
  Methods for the us_fk attribute.

$value = cit_fk();
cit_fk($value);
  Methods for the cit_fk attribute.

$value = group_can_update();
group_can_update($value);
  Methods for the group_can_update attribute.

$value = biology_description();
biology_description($value);
  Methods for the biology_description attribute.

$value = analysis_description();
analysis_description($value);
  Methods for the analysis_description attribute.

$value = treatment_type();
treatment_type($value);
  Methods for the treatment_type attribute.

$value = quantity_series_type();
quantity_series_type($value);
  Methods for the quantity_series_type attribute.

$value = is_public();
is_public($value);
  Methods for the is_public attribute.

$value = release_date();
release_date($value);
  Methods for the release_date attribute.

$value = submission_date();
submission_date($value);
  Methods for the submission_date attribute.

$value = local_accession();
local_accession($value);
  Methods for the local_accession attribute.

$value = archive_bundle_ref();
archive_bundle_ref($value);
  Methods for the archive_bundle_ref attribute.

WARNING: methods other than those listed here are for internal use only and are subject to change without notice. Use them at your own risk.

# IMPLEMENTATION DETAILS

These classes are automatically generated by the create_genex_classes.pl script. Each class is a subclass of the ObjectTemplate class (written by Sriram Srinivasan, described in Advanced Perl Programming, and heavily modified by Jason Stewart). ObjectTemplate implements automatic class creation in perl (there exist other options such as `Class::Struct` and `Class::MethodMaker` by Damian Conway) via an `attributes()` method call at class creation time.

# BUGS

Please send bug reports to genex@ncgr.org

# LAST UPDATED

on Thu Dec 7 18:35:39 2000 by /home/jasons/Genex/scripts/create_genex_class.pl --target=ExperimentSet --support=ArrayMeasurement --support=HotSpots --support=TreatmentLevel --support=CitationLink --support=ExperimentFactors

# AUTHOR

Jason E. Stewart (jes@ncgr.org)

# SEE ALSO

perl(1).