ogi__location_on_map.inc

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tripal_chado/includes/TripalFields/ogi__location_on_map/ogi__location_on_map.inc
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  1. <?php

  2. 

  3. class ogi__location_on_map extends ChadoField {

  4. 

  5. 

  6.   // --------------------------------------------------------------------------

  7.   //                     EDITABLE STATIC CONSTANTS

  8.   //

  9.   // The following constants SHOULD be set for each descendent class.  They are

  10.   // used by the static functions to provide information to Drupal about

  11.   // the field and it's default widget and formatter.

  12.   // --------------------------------------------------------------------------

  13. 

  14.   // The default lable for this field.

  15.   public static $default_label = 'Location on Map';

  16. 

  17.   // The default description for this field.

  18.   public static $description = 'Map position of a sequence.';

  19. 

  20.   // Provide a list of instance specific settings. These can be access within

  21.   // the instanceSettingsForm.  When the instanceSettingsForm is submitted

  22.   // then Drupal with automatically change these settings for the instnace.

  23.   // It is recommended to put settings at the instance level whenever possible.

  24.   // If you override this variable in a child class be sure to replicate the

  25.   // term_name, term_vocab, term_accession and term_fixed keys as these are

  26.   // required for all TripalFields.

  27.   public static $default_instance_settings  = array(

  28.     // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).

  29.     'term_vocabulary' => 'OGI',

  30.     // The name of the term.

  31.     'term_name' => 'location on map',

  32.     // The unique ID (i.e. accession) of the term.

  33.     'term_accession' => '0000021',

  34.     // Set to TRUE if the site admin is allowed to change the term

  35.     // type. This will create form elements when editing the field instance

  36.     // to allow the site admin to change the term settings above.

  37.     'term_fixed' => FALSE,

  38.   );

  39. 

  40.   // The default widget for this field.

  41.   public static $default_widget = 'ogi__location_on_map_widget';

  42. 

  43.   // The default formatter for this field.

  44.   public static $default_formatter = 'ogi__location_on_map_formatter';

  45. 

  46.   // --------------------------------------------------------------------------

  47.   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

  48.   // --------------------------------------------------------------------------

  49.   // An array containing details about the field. The format of this array

  50.   // is the same as that returned by field_info_fields()

  51.   protected $field;

  52.   // An array containing details about an instance of the field. A field does

  53.   // not have to have an instance.  But if dealing with an instance (such as

  54.   // when using the widgetForm, formatterSettingsForm, etc.) it should be set.

  55.   protected $instance;

  56. 

  57.   /**

  58.    * @see TripalField::elementInfo()

  59.    */

  60.   public function elementInfo() {

  61.     $field_term = $this->getFieldTermID();

  62. 

  63.     $map_term = 'data:1274';

  64.     $name_term = chado_get_semweb_term('featuremap', 'name');

  65.     $description_term = chado_get_semweb_term('featuremap', 'description');

  66.     $mappos_term = chado_get_semweb_term('featurepos', 'mappos');

  67.     $ref_feature_term = chado_get_semweb_term('featurepos', 'map_feature_id');

  68.     $ref_feature_name = chado_get_semweb_term('feature', 'name');

  69.     $ref_feature_id = chado_get_semweb_term('feature', 'uniquename');

  70.     $ref_feature_type = 'rdfs:type';

  71. 

  72.     return array(

  73.       $field_term => array(

  74.         'sortable' => FALSE,

  75.         'searchable' => FALSE,

  76.         'type' => 'xs:complexType',

  77.         'readonly' => TRUE,

  78.         'elements' => array(

  79.           $map_term => array(

  80.             'searchable' => FALSE,

  81.             'sortable' => FALSE,

  82.             'type' => 'xs:complexType',

  83.             'readonly' => TRUE,

  84.             'required' => FALSE,

  85.             'elements' => array(

  86.               $name_term => array(

  87.                 'label' => 'Map Name',

  88.                 'help' => 'The name of the map.',

  89.                 'searchable' => TRUE,

  90.                 'sortable' => TRUE,

  91.                 'type' => 'xs:string',

  92.                 'readonly' => TRUE,

  93.                 'required' => FALSE,

  94.               ),

  95.               $description_term => array(

  96.                 'label' => 'Map Description',

  97.                 'help' => 'A description of the map.',

  98.                 'searchable' => TRUE,

  99.                 'sortable' => FALSE,

  100.                 'type' => 'xs:string',

  101.                 'readonly' => TRUE,

  102.                 'required' => FALSE,

  103.               ),

  104.               'entity' => array(

  105.                 'searchable' => FALSE,

  106.                 'sortable' => FALSE,

  107.               ),

  108.             ),

  109.           ),

  110.           $ref_feature_term => array(

  111.             'searchable' => FALSE,

  112.             'sortable' => FALSE,

  113.             'type' => 'xs:complexType',

  114.             'readonly' => TRUE,

  115.             'required' => FALSE,

  116.             'elements' => array(

  117.               $ref_feature_name => array(

  118.                 'label' => 'Map Reference Feature Name',

  119.                 'help' => 'The genomic or genetic feature Nameof the map on which this feature is mapped.',

  120.                 'searchable' => TRUE,

  121.                 'sortable' => TRUE,

  122.                 'type' => 'xs:string',

  123.                 'readonly' => TRUE,

  124.                 'required' => FALSE,

  125.               ),

  126.               $ref_feature_id=> array(

  127.                 'label' => 'Map Reference Feature Identifier',

  128.                 'help' => 'The genomic or genetic feature of the map on which this feature is mapped.',

  129.                 'searchable' => TRUE,

  130.                 'sortable' => TRUE,

  131.                 'type' => 'xs:string',

  132.                 'readonly' => TRUE,

  133.                 'required' => FALSE,

  134.               ),

  135.               $ref_feature_type=> array(

  136.                 'label' => 'Map Reference Feature Type',

  137.                 'help' => 'The type of genomic or genetic feature of the map on which this feature is mapped.',

  138.                 'searchable' => TRUE,

  139.                 'sortable' => TRUE,

  140.                 'type' => 'xs:string',

  141.                 'readonly' => TRUE,

  142.                 'required' => FALSE,

  143.               ),

  144.             ),

  145.           ),

  146.           $mappos_term => array(

  147.             'label' => 'Map Reference Position',

  148.             'help' => 'Maps may use different coordinate systems. This indicates the type of coordinate.',

  149.             'searchable' => TRUE,

  150.             'sortable' => TRUE,

  151.             'type' => 'xs:string',

  152.             'readonly' => TRUE,

  153.             'required' => FALSE,

  154.           ),

  155.         ),

  156.       ),

  157.     );

  158.   }

  159. 

  160.   /**

  161.    * @see ChadoField::query()

  162.    */

  163.   public function query($query, $condition) {

  164.     $alias = $this->field['field_name'];

  165.     $operator = $condition['operator'];

  166. 

  167.     // Map details.

  168.     $field_term_id = $this->getFieldTermID();

  169.     $map_term = 'data:1274';

  170.     $name_term = $field_term_id . ',' . $map_term . ',' . chado_get_semweb_term('featuremap', 'name');

  171.     $description_term = $field_term_id . ',' . $map_term . ',' . chado_get_semweb_term('featuremap', 'description');

  172.     $mappos_term = $field_term_id . ',' . chado_get_semweb_term('featurepos', 'mappos');

  173. 

  174.     // Reference sequence details.

  175.     $ref_feature_term = chado_get_semweb_term('featurepos', 'map_feature_id');

  176.     $ref_feature_name = $field_term_id . ',' . $ref_feature_term . ',' .chado_get_semweb_term('feature', 'name');

  177.     $ref_feature_id = $field_term_id . ',' . $ref_feature_term . ',' .chado_get_semweb_term('feature', 'uniquename');

  178.     $ref_feature_type = $field_term_id . ',' . $ref_feature_term . ',' .'rdfs:type';

  179. 

  180.     $this->queryJoinOnce($query, 'featurepos', $alias, "base.feature_id = $alias.feature_id");

  181. 

  182.     if ($condition['column'] == $name_term) {

  183.       $this->queryJoinOnce($query, 'featuremap', $alias . '_map', $alias . '_map.featuremap_id = ' . $alias . '.featuremap_id');

  184.       $query->condition($alias . '_map.name', $condition['value'], $operator);

  185.     }

  186.     if ($condition['column'] == $description_term) {

  187.       $this->queryJoinOnce($query, 'featuremap', $alias . '_map', $alias . '_map.featuremap_id = ' . $alias . '.featuremap_id');

  188.       $query->condition($alias . '_map.description', $condition['value'], $operator);

  189.     }

  190.     if ($condition['column'] == $mappos_term) {

  191.       $query->condition($alias . '.mappos', $condition['value'], $operator);

  192.     }

  193. 

  194.     if ($condition['column'] == $ref_feature_name) {

  195.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id');

  196.       $query->condition($alias . '_mapref.name', $condition['value'], $operator);

  197.     }

  198.     if ($condition['column'] == $ref_feature_id) {

  199.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id');

  200.       $query->condition($alias . '_mapref.uniquename', $condition['value'], $operator);

  201.     }

  202.     if ($condition['column'] == $ref_feature_type) {

  203.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id');

  204.       $this->queryJoinOnce($query, 'cvterm', $alias . '_mapref_cvterm', $alias . '_mapref_cvterm.cvterm_id = ' . $alias . '_mapref.type_id');

  205.       $query->condition($alias . '_mapref_cvterm.name', $condition['value'], $operator);

  206.     }

  207.   }

  208.   /**

  209.    * @see ChadoField::queryOrder()

  210.    */

  211.   public function queryOrder($query, $order) {

  212.     $alias = $this->field['field_name'];

  213. 

  214.     // Map details.

  215.     $field_term_id = $this->getFieldTermID();

  216.     $map_term = 'data:1274';

  217.     $name_term = $field_term_id . ',' . $map_term . ',' . chado_get_semweb_term('featuremap', 'name');

  218.     $description_term = $field_term_id . ',' . $map_term . ',' . chado_get_semweb_term('featuremap', 'description');

  219.     $mappos_term = $field_term_id . ',' . chado_get_semweb_term('featurepos', 'mappos');

  220. 

  221.     // Reference sequence details.

  222.     $ref_feature_term = chado_get_semweb_term('featurepos', 'map_feature_id');

  223.     $ref_feature_name = $field_term_id . ',' . $ref_feature_term . ',' .chado_get_semweb_term('feature', 'name');

  224.     $ref_feature_id = $field_term_id . ',' . $ref_feature_term . ',' .chado_get_semweb_term('feature', 'uniquename');

  225.     $ref_feature_type = $field_term_id . ',' . $ref_feature_term . ',' .'rdfs:type';

  226. 

  227.     $this->queryJoinOnce($query, 'featurepos', $alias, "base.feature_id = $alias.feature_id", 'LEFT OUTER');

  228. 

  229.     if ($order['column'] == $name_term) {

  230.       $this->queryJoinOnce($query, 'featuremap', $alias . '_map', $alias . '_map.featuremap_id = ' . $alias . '.featuremap_id', 'LEFT OUTER');

  231.       $query->orderBy($alias . '_map.name', $order['direction']);

  232.     }

  233.     if ($order['column'] == $description_term) {

  234.       $this->queryJoinOnce($query, 'featuremap', $alias . '_map', $alias . '_map.featuremap_id = ' . $alias . '.featuremap_id', 'LEFT OUTER');

  235.       $query->orderBy($alias . '_map.description', $order['direction']);

  236.     }

  237.     if ($order['column'] == $mappos_term) {

  238.       $query->orderBy($alias . '.mappos', $order['direction']);

  239.     }

  240. 

  241.     if ($order['column'] == $ref_feature_name) {

  242.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id', 'LEFT OUTER');

  243.       $query->orderBy($alias . '_mapref.name', $order['direction']);

  244.     }

  245.     if ($order['column'] == $ref_feature_id) {

  246.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id', 'LEFT OUTER');

  247.       $query->orderBy($alias . '_mapref.uniquename', $order['direction']);

  248.     }

  249.     if ($order['column'] == $ref_feature_type) {

  250.       $this->queryJoinOnce($query, 'feature', $alias . '_mapref', $alias . '_mapref.feature_id = ' . $alias . '.map_feature_id', 'LEFT OUTER');

  251.       $this->queryJoinOnce($query, 'cvterm', $alias . '_mapref_cvterm', $alias . '_mapref_cvterm.cvterm_id = ' . $alias . '_mapref.type_id', 'LEFT OUTER');

  252.       $query->orderBy($alias . '_mapref_cvterm.name', $order['direction']);

  253.     }

  254.   }

  255.   /**

  256.    *

  257.    * @see TripalField::load()

  258.    */

  259.   public function load($entity) {

  260. 

  261.     $record = $entity->chado_record;

  262.     $settings = $this->field['settings'];

  263.     $field_name = $this->field['field_name'];

  264.     $field_type = $this->field['type'];

  265. 

  266.     // Map details

  267.     $map_term = 'data:1274';

  268.     $name_term = chado_get_semweb_term('featuremap', 'name');

  269.     $description_term = chado_get_semweb_term('featuremap', 'description');

  270.     $mappos_term = chado_get_semweb_term('featurepos', 'mappos');

  271. 

  272.     // Reference sequence details.

  273.     $ref_feature_term = chado_get_semweb_term('featurepos', 'map_feature_id');

  274.     $ref_feature_name = chado_get_semweb_term('feature', 'name');

  275.     $ref_feature_id = chado_get_semweb_term('feature', 'uniquename');

  276.     $ref_feature_type = 'rdfs:type';

  277. 

  278.     // Set some defaults for the empty record.

  279.     $entity->{$field_name}['und'][0] = array(

  280.       'value' => array(),

  281.     );

  282. 

  283.     // Add the featurepos records to our $record.

  284.     $options = array('return_array' => TRUE,

  285.       'include_fk' => array(

  286.         'map_feature_id' => array(

  287.           'type_id' => 1,

  288.         ),

  289.         'feature_id' => array(

  290.           'type_id' => 1

  291.         ),

  292.       ),

  293.     );

  294.     $feature = chado_expand_var($record, 'table', 'featurepos', $options);

  295. 

  296.     // Iterate through the positions and add them to our values.

  297.     $i = 0;

  298.     if (isset($feature->featurepos->feature_id)) {

  299.       foreach ($feature->featurepos->feature_id AS $featurepos) {

  300.         // Get details about the map

  301.         $featuremap = chado_generate_var('featuremap', array('featuremap_id' => $featurepos->featuremap_id));

  302.         $entity->{$field_name}['und'][$i]['value'] = array (

  303.           // Map.

  304.           $map_term => array(

  305.             $name_term => $featuremap->name,

  306.             $description_term => $featuremap->description,

  307.           ),

  308.           $ref_feature_term => array(

  309.             $ref_feature_name => $featurepos->map_feature_id->name,

  310.             $ref_feature_id => $featurepos->map_feature_id->uniquename,

  311.             $ref_feature_type => $featurepos->map_feature_id->type_id->name,

  312.           ),

  313.           $mappos_term => $featurepos->mappos

  314.         );

  315.         if (property_exists($featuremap, 'entity_id')) {

  316.           $entity->{$field_name}['und'][$i]['value'][$map_term]['entity'] = 'TripalEntity:' . $featuremap->entity_id;

  317.         }

  318.         if (property_exists($featurepos->map_feature_id, 'entity_id')) {

  319.           $entity->{$field_name}['und'][$i]['value'][$map_term]['entity'] = 'TripalEntity:' . $featurepos->map_feature_id->entity_id;

  320.         }

  321.         $i++;

  322.       }

  323.     }

  324.   }

  325. 

  326. }