Creates rawphenotypes germplasm field

includes/TripalFields/ncit__raw_data/ncit__raw_data.inc

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+<?php
+/**
+ * @class
+ * Purpose: Provide quick browse functionality for entity pages
+ *
+ * Data: No data.
+ * Assumptions:
+ */
+class ncit__raw_data extends TripalField {
+  // --------------------------------------------------------------------------
+  //                     EDITABLE STATIC CONSTANTS
+  //
+  // The following constants SHOULD be set for each descendant class.  They are
+  // used by the static functions to provide information to Drupal about
+  // the field and it's default widget and formatter.
+  // --------------------------------------------------------------------------
+  // The default label for this field.
+  public static $default_label = 'Germplasm Raw Phenotypes';
+  // The default description for this field.
+  public static $default_description = 'Show available raw phenotypes of a germplasm';
+  // The default widget for this field.
+  public static $default_widget = 'ncit__raw_data_widget';
+  // The default formatter for this field.
+  public static $default_formatter = 'ncit__raw_data_formatter';
+  // The module that manages this field.
+  public static $module = 'rawphenotypes';
+
+  // A list of global settings. These can be accessed within the
+  // globalSettingsForm.  When the globalSettingsForm is submitted then
+  // Drupal will automatically change these settings for all fields.
+  // Once instances exist for a field type then these settings cannot be
+  // changed.
+  public static $default_settings = array(
+    'storage' => 'tripal_no_storage',
+    // It is expected that all fields set a 'value' in the load() function.
+    // In many cases, the value may be an associative array of key/value pairs.
+    // In order for Tripal to provide context for all data, the keys should
+    // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
+    // function that are supported by the query() function should be
+    // listed here.
+    'browseable_keys' => array(),
+  );
+
+  // Provide a list of instance specific settings. These can be access within
+  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
+  // then Drupal with automatically change these settings for the instance.
+  // It is recommended to put settings at the instance level whenever possible.
+  // If you override this variable in a child class be sure to replicate the
+  // term_name, term_vocab, term_accession and term_fixed keys as these are
+  // required for all TripalFields.
+  public static $default_instance_settings = array(
+    // The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
+    'term_vocabulary' => 'NCIT',
+    // The name of the term.
+    'term_name' => 'Raw Data',
+    // The unique ID (i.e. accession) of the term.
+    'term_accession' => 'C142663',
+    // Set to TRUE if the site admin is not allowed to change the term
+    // type, otherwise the admin can change the term mapped to a field.
+    'term_fixed' => FALSE,
+    // Indicates if this field should be automatically attached to display
+    // or web services or if this field should be loaded separately. This
+    // is convenient for speed.  Fields that are slow should for loading
+    // should have auto_attach set to FALSE so tha their values can be
+    // attached asynchronously.
+    'auto_attach' => FALSE,
+    // The table where the options for this specific field are stored.
+    // This can be one of trpfancy_browse_options or trpfancy_browse_options_per_entity
+    // based on admin configuration. Default: trpfancy_browse_options.
+    'option_storage' => '',
+    // A list of browser types this field intends to provide.
+    'browser_types' => '',
+  );
+
+  // A boolean specifying that users should not be allowed to create
+  // fields and instances of this field type through the UI. Such
+  // fields can only be created programmatically with field_create_field()
+  // and field_create_instance().
+  public static $no_ui = FALSE;
+  // A boolean specifying that the field will not contain any data. This
+  // should exclude the field from web services or downloads.  An example
+  // could be a quick browse field that appears on the page that redirects
+  // the user but otherwise provides no data.
+  public static $no_data = TRUE;
+
+ /**
+   * Loads the field values from the underlying data store.
+   *
+   * @param $entity
+   *
+   * @return
+   *   An array of the following format:
+   *     $entity->{$field_name}['und'][0]['value'] = $value;
+   *   where:
+   *     - $entity is the entity object to which this field is attached.
+   *     - $field_name is the name of this field
+   *     - 'und' is the language code (in this case 'und' == undefined)
+   *     - 0 is the cardinality.  Increment by 1 when more than one item is
+   *       available.
+   *     - 'value' is the key indicating the value of this field. It should
+   *       always be set.  The value of the 'value' key will be the contents
+   *       used for web services and for downloadable content.  The value
+   *       should be of the follow format types: 1) A single value (text,
+   *       numeric, etc.) 2) An array of key value pair. 3) If multiple entries
+   *       then cardinality should incremented and format types 1 and 2 should
+   *       be used for each item.
+   *   The array may contain as many other keys at the same level as 'value'
+   *   but those keys are for internal field use and are not considered the
+   *   value of the field.
+   *
+   *
+   */
+  public function load($entity) {
+    // Arrays to hold phenotypes related to this germplasm.
+    $germplasm = array();
+    $icons = array();
+    $summary = array();
+    $current_user = array();
+    $traits = array();
+
+    // User profile.
+    global $user;
+    $current_user['id'] = $user->uid;
+
+    // User permissions.
+    $rawpheno_permission = array('access rawpheno', 'download rawpheno');
+    $count_permission = 0;
+    foreach($rawpheno_permission as $permission) {
+      if (user_access($permission, $user)) {
+        $count_permission++;
+      }
+    }
+
+    // If user has no permission to begin with, skip all and report
+    // raw phenotypes not available.
+    $field_name = $this->instance['field_name'];
+    $entity->{$field_name}['und'][0]['value'] = array();
+
+    if ($count_permission == 2 || user_is_logged_in()) {
+      // User appointed experiments.
+      // See api library in includes directory for this function definition.
+      $user_experiment = rawpheno_function_user_project($user->uid);
+      $user_experiment = array_keys($user_experiment);
+
+      // Current user.
+      $current_user['permission'] = TRUE;
+      $current_user['experiments'] = $user_experiment;
+
+      // Germplasm.
+      $germplasm['id'] = $entity->chado_record->stock_id;
+      $germplasm['name'] = $entity->chado_record->name;
+
+      // Icons.
+      $icon_path = $GLOBALS['base_url'] . '/' . drupal_get_path('module', 'rawpheno') . '/includes/TripalFields/ncit__raw_data/theme/';
+
+      $icons['leaf'] = $icon_path . 'icon-leaf.png';
+      $icons['export'] = $icon_path . 'icon-export.png';
+      $icons['raw'] = $icon_path . 'icon-raw.jpg';
+      $icons['download'] = $icon_path . 'icon-download.jpg';
+
+      $traits = [];
+      // This query is identical to the rawphenotypes download page.
+      // Get all experiments (by plant id) where germplasm was used.
+      $all_experiment_locations = chado_query("
+        SELECT p2.project_id, p2.name, value AS location
+        FROM pheno_plantprop 
+          INNER JOIN pheno_plant_project AS p1 USING (plant_id) 
+          INNER JOIN {project} AS p2 ON p1.project_id = p2.project_id
+        WHERE
+          type_id = (SELECT cvterm_id FROM {cvterm} cvt LEFT JOIN {cv} cv ON cv.cv_id = cvt.cv_id
+            WHERE cvt.name = 'Location' AND cv.name = 'phenotype_plant_property_types') AND
+          plant_id IN (SELECT plant_id FROM pheno_plant WHERE stock_id = :germplasm GROUP BY plant_id)
+        GROUP BY p2.project_id, p2.name, value
+      ", array(':germplasm' => $germplasm['id']));
+      $experiment_locations = $all_experiment_locations->fetchAll();
+
+      // All traits in experiment and location.
+      $sql_cvterm = "
+        SELECT c_j.cvterm_json->>'id', c_j.cvterm_json->>'name' FROM (
+          SELECT JSON_BUILD_OBJECT('id', cvterm_id, 'name', name) AS cvterm_json FROM {cvterm} WHERE cvterm_id = ANY ((
+            SELECT STRING_TO_ARRAY(list_id.all_traits, ',') FROM (
+              SELECT string_agg(DISTINCT all_traits, ',') AS all_traits
+              FROM {rawpheno_rawdata_mview}
+              WHERE
+                location IN(:location)
+                AND plant_id IN (SELECT plant_id FROM pheno_plant_project WHERE project_id = :project_id)
+            ) AS list_id
+          )::int[])
+        ) AS c_j
+        WHERE c_j.cvterm_json->>'name' NOT IN ('Rep', 'Entry', 'Location', 'Name', 'Plot', 'Planting Date (date)', '# of Seeds Planted (count)')
+        ORDER BY c_j.cvterm_json->>'name' ASC
+      ";
+
+      $trait_experiment_location = array();
+      $cache_exp = array();
+      $cache_loc = array();
+      foreach($experiment_locations as $item) {
+        $cache_exp[] = $item->project_id;
+        $cache_loc[] = $item->location;
+
+        $trait_set = chado_query($sql_cvterm, array(':location' => $item->location, ':project_id' => $item->project_id))
+          ->fetchAllKeyed(0, 1);
+
+        if ($trait_set) {
+          foreach($trait_set as $trait_id => $trait_name) {
+            // Trait id, project id and name + location:
+            $trait_experiment_location[ $trait_id . '_' . $trait_name ][] = $trait_id . '#' . $item->project_id . '#' . $item->name . '#' . $item->location;            
+          }
+        }
+      }
+
+      ksort($trait_experiment_location);
+
+      // Summarize.
+      $summary['traits'] = count($trait_experiment_location);
+      $summary['experiments'] = count(array_unique($cache_exp));
+      $summary['locations'] = count(array_unique($cache_loc));
+
+      $entity->{$field_name}['und'][0]['value']['NCIT:Raw Data'] = array(
+        'user' => $current_user,
+        'germplasm' => $germplasm,
+        'summary'  => $summary,
+        'traits'   => $trait_experiment_location,
+        'icons' => $icons
+      );
+    }
+  }
+
+  /**
+   * Provides a form for the 'Field Settings' of an instance of this field.
+   *
+   * This function corresponds to the hook_field_instance_settings_form()
+   * function of the Drupal Field API.
+   *
+   * Validation of the instance settings form is not supported by Drupal, but
+   * the TripalField class does provide a mechanism for supporting validation.
+   * To allow for validation of your setting form you must call the parent
+   * in your child class:
+   *
+   * @code
+   *   $element = parent::instanceSettingsForm();
+   * @endcode
+   *
+   * Please note, the form generated with this function does not easily
+   * support AJAX calls in the same way that other Drupal forms do.  If you
+   * need to use AJAX you must manually alter the $form in your ajax call.
+   * The typical way to handle updating the form via an AJAX call is to make
+   * the changes in the form function itself but that doesn't work here.
+   */
+  public function instanceSettingsForm() {
+
+    // Retrieve the current settings.
+    // If this field was just created these will contain the default values.
+    $settings = $this->instance['settings'];
+
+    // Allow the parent Tripal Field to set up the form element for us.
+    $element = parent::instanceSettingsForm();
+
+    return $element;
+  }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
+}