Added a Transcripts field for the gene bundle

tripal_chado/includes/fields/chado_gene__transcripts.inc

@@ -0,0 +1,244 @@
+<?php
+
+/**
+ * Implements hook_info() for fields.
+ *
+ * This is a hook provided by the tripal_chado module for offloading the
+ * hook_field_info() hook for each field to specify.
+ */
+function chado_gene__transcripts_info() {
+  return array(
+    'label' => t('Transcripts'),
+    'description' => t('Transcripts of genes.'),
+    'default_widget' => 'chado_gene__transcripts_widget',
+    'default_formatter' => 'chado_gene__transcripts_formatter',
+    'settings' => array(),
+    'storage' => array(
+      'type' => 'field_chado_storage',
+      'module' => 'tripal_chado',
+      'active' => TRUE
+    ),
+  );
+}
+/**
+ * Implements hook_attach_info().
+ *
+ * This is a hook provided by the tripal_Chado module. It allows the field
+ * to specify which bundles it will attach to and to specify thee settings.
+ *
+ * @param $entity_type
+ * @param $entity
+ * @param $term
+ *
+ * @return
+ *   A field array
+ */
+function chado_gene__transcripts_attach_info($entity_type, $bundle, $target) {
+  $field_info = array();
+
+  $table_name = $target['data_table'];
+  $type_table = $target['type_table'];
+  $type_field = $target['field'];
+  $cv_id      = $target['cv_id'];
+  $cvterm_id  = $target['cvterm_id'];
+
+  // If the linker table does not exists or this is not a gene then we don't want to add attach.
+  $rel_table = $table_name . '_relationship';
+  if (!chado_table_exists($rel_table) || $bundle->label != 'gene') {
+    return $field_info;
+  }
+
+  $schema = chado_get_schema($rel_table);
+  $pkey = $schema['primary key'][0];
+
+  // Initialize the field array.
+  $field_info = array(
+    'field_name' => 'gene__transcripts',
+    'field_type' => 'chado_gene__transcripts',
+    'widget_type' => 'chado_gene__transcripts_widget',
+    'widget_settings' => array('display_label' => 1),
+    'description' => '',
+    'label' => 'Transcripts',
+    'is_required' => 0,
+    'cardinality' => FIELD_CARDINALITY_UNLIMITED,
+    'storage' => 'field_chado_storage',
+    'field_settings' => array(
+      'chado_table' => $rel_table,
+      'chado_column' => $pkey,
+      'base_table' => $table_name,
+      'semantic_web' => array(
+        'type' => '',
+        'ns' => '',
+        'nsurl' => '',
+      ),
+    ),
+  );
+
+  return $field_info;
+
+}
+/**
+ * Implements hook_widget_info.
+ *
+ * This is a hook provided by the tripal_chado module for offloading
+ * the hook_field_widget_info() hook for each field to specify.
+ */
+function chado_gene__transcripts_widget_info() {
+  return array(
+    'label' => t('Transcripts Settings'),
+    'field types' => array('chado_gene__transcripts')
+  );
+}
+/**
+ * Implements hook_formatter_info.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_info() for each field
+ * to specify.
+ *
+ */
+function chado_gene__transcripts_formatter_info() {
+  return array(
+    'label' => t('Transcripts'),
+    'field types' => array('chado_gene__transcripts'),
+    'settings' => array(
+    ),
+  );
+}
+
+/**
+ * Implements hook_formatter_settings_summary.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_settings_summary() for each field
+ * to specify.
+ *
+ */
+function chado_gene__transcripts_formatter_settings_summary($field, $instance,
+    $view_mode) {
+
+}
+
+/**
+ * Provides a settings form for the formatter.
+ *
+ * This is a hook provided by the tripal_chado module for
+ * offloading the hook_field_formatter_settings_form() for each field
+ * to specify.
+ */
+function chado_gene__transcripts_formatter_settings_form($field, $instance,
+    $view_mode, $form, &$form_state) {
+
+
+
+}
+
+/**
+ * Validation function for the chado_gene_featureloc_formatter_settings_form.
+ */
+function chado_gene__transcripts_formatter_settings_form_validate(&$form, &$form_state) {
+
+  // Place here as an example for validating the settings form.
+}
+
+/**
+ * TODO: because this field is meant to handle any xxxxx_transcripts table
+ * then feature hard-coding needs to be replaced as it won't work for
+ * stocks, etc.
+ */
+function chado_gene__transcripts_formatter(&$element, $entity_type, $entity,
+    $field, $instance, $langcode, $items, $display) {
+
+  // Get the settings
+  $settings = $display['settings'];
+  $record = $entity->chado_record;
+
+  foreach ($items as $delta => $item) {
+
+    $all_transcripts = key_exists('part of', $item['all_transcripts']['object'])  && 
+    key_exists('mRNA', $item['all_transcripts']['object']['part of']) ? 
+    $item['all_transcripts']['object']['part of']['mRNA'] : array();   
+    
+    $headers = array('Feature Name' ,'Unique Name', 'Location');
+    $rows = array();
+
+    foreach ($all_transcripts AS $transcript) {
+      // link the feature to it's node
+      $feature_name = $transcript->record->subject_id->name;
+      $entity_id = $transcript->record->subject_id->entity_id;
+      if ($entity_id) {
+        $feature_name = l($feature_name, "bio_data/" . $entity_id, array('attributes' => array('target' => "_blank")));
+      }
+      $locations = $transcript->child_featurelocs;
+      $loc = "";
+      foreach ($locations AS $location) {
+        $loc .= $location->srcfeature_name . ":" . $location->fmin . ".." . $location->fmax . "<br>";
+      }
+      $rows[] = array(
+        array('data' => $feature_name, 'width' => '30%'),
+        array('data' => $transcript->record->subject_id->uniquename, 'width' => '30%'),
+        array('data' => $loc, 'width' => '30%'),
+      );
+    }
+    $table = array(
+      'header' => $headers,
+      'rows' => $rows,
+      'attributes' => array(
+        'id' => 'tripal_feature-table-transcripts-object',
+        'class' => 'tripal-data-table'
+      ),
+      'sticky' => FALSE,
+      'caption' => "",
+      'colgroups' => array(),
+      'empty' => '',
+    );
+
+    $content = theme_table($table);
+  }
+
+  // once we have our table array structure defined, we call Drupal's theme_table()
+  // function to generate the table.
+  $element[$delta] = array(
+    '#type' => 'markup',
+    '#markup' => $content,
+  ); 
+}
+
+/**
+ * Loads the field values with appropriate data.
+ *
+ * This function is called by the tripal_chado_field_storage_load() for
+ * each property managed by the field_chado_storage storage type.  This is
+ * an optional hook function that is only needed if the field has
+ * multiple form elements.
+ */
+function chado_gene__transcripts_load($field, $entity, $base_table, $record) {
+  $field_name = $field['field_name'];
+
+
+  $entity->{$field_name}['und'][0]['all_transcripts'] = tripal_get_feature_relationships($record);
+}
+
+/**
+ * Implements hook_ws_formatter().
+ */
+// function chado_gene__transcripts_ws_formatter(&$element, $entity_type, $entity,
+//     $field, $instance, $items) {
+
+//   foreach ($items as $delta => $item) {
+
+//   }
+// }
+
+/**
+ *  Implements hook_widget().
+ */
+function chado_gene__transcripts_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+
+}
+/**
+ * Callback function for validating the chado_gene_featureloc_widget.
+ */
+function chado_gene__transcripts_widget_validate($element, &$form_state) {
+
+}