Merge branch '7.x-3.x' of github.com:tripal/tripal into 7.x-3.x

tripal_chado/api/modules/tripal_chado.pub.api.inc

@@ -105,7 +105,7 @@ function chado_get_publication($identifiers, $options = []) {
     }
     else {
       tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
-        "chado_get_publication: The dbxref identifier is not correctly formatted.",
+        "chado_get_publication: The dbxref identifier is not correctly formatted. Identifiers passed: %identifier.",
         ['%identifier' => print_r($identifiers, TRUE)]
       );
     }
@@ -1169,6 +1169,47 @@ function chado_pub_create_citation($pub) {
   return $citation;
 }
 
+/**
+ * Retrieves an array with all database cross references
+ *
+ * Implemented as SQL for performance reasons because chado_expand_var
+ * can take too long as it loads more information than needed
+ *
+ * @param $pub_id
+ *   A pub_id from the 'chado.pub' table
+ *
+ * @return
+ *   An array of records with the following keys:  'accession', 'version',
+ *   'description', 'name', 'url', 'urlprefix'.
+ *   These are the column names from the 'dbxref' and 'db' tables
+ *
+ * @ingroup tripal_pub_api
+ */
+function chado_get_pub_dbxrefs($pub_id) {
+  $fkey = 'pub_id';  // Should this be looked up in the schema?
+  $options = ['return_array' => 1];
+  $sql = "SELECT REF.accession, REF.version, REF.description, DB.name, DB.url, DB.urlprefix "
+       . "FROM {pub_dbxref} LINK "
+       . "INNER JOIN {dbxref} REF on LINK.dbxref_id = REF.dbxref_id "
+       . "INNER JOIN {db} DB on REF.db_id = DB.db_id "
+       . "WHERE LINK.$fkey = :pub_id";
+  $args = [':pub_id' => $pub_id];
+  $records = chado_query($sql, $args);
+
+  $results = [];
+  $delta = 0;
+  while($record = $records->fetchObject()) {
+    $results[$delta]['accession'] = $record->accession;
+    $results[$delta]['version'] = $record->version;
+    $results[$delta]['description'] = $record->description;
+    $results[$delta]['name'] = $record->name;
+    $results[$delta]['url'] = $record->url;
+    $results[$delta]['urlprefix'] = $record->urlprefix;
+    $delta++;
+  }
+  return $results;
+}
+
 /**
  * Retrieves the minimal information to uniquely describe any publication.
  *
@@ -1238,17 +1279,24 @@ function chado_get_minimal_pub_info($pub) {
     }
   }
 
+  // Load all database cross references.
+  $pub_dbxrefs = chado_get_pub_dbxrefs($pub->pub_id);
+
   // Get the first database cross-reference with a url.
-  $options = ['return_array' => 1];
-  $pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);
-  $dbxref = NULL;
-  if ($pub->pub_dbxref) {
-    foreach ($pub->pub_dbxref as $index => $pub_dbxref) {
-      if ($pub_dbxref->dbxref_id->db_id->urlprefix) {
-        $dbxref = $pub_dbxref->dbxref_id;
-      }
-    }
-  }
+// it is not clear what this was doing, it would have retrieved the last not the first
+// dbxref with a url, but the variable $dbxref is not referenced later. It could have
+// added information to $pub, but that does not appear to be referenced later.
+// chado_expand_var() can sometimes take a long time to execute, so just remove it?
+//  $options = ['return_array' => 1];
+//  $pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);
+//  $dbxref = NULL;
+//  if ($pub->pub_dbxref) {
+//    foreach ($pub->pub_dbxref as $index => $pub_dbxref) {
+//      if ($pub_dbxref->dbxref_id->db_id->urlprefix) {
+//        $dbxref = $pub_dbxref->dbxref_id;
+//      }
+//    }
+//  }
 
   // Get the URL.
   $values = [
@@ -1270,17 +1318,10 @@ function chado_get_minimal_pub_info($pub) {
     }
   }
 
-  // Get the list of database cross references.
-  $values = [
-    'pub_id' => $pub->pub_id,
-  ];
-  $options = [
-    'return_array' => 1,
-  ];
-  $pub_dbxrefs = chado_generate_var('pub_dbxref', $values, $options);
+  // Generate a list of database cross references formatted as "DB:accession".
   $dbxrefs = [];
   foreach ($pub_dbxrefs as $pub_dbxref) {
-    $dbxrefs[] = $pub_dbxref->dbxref_id->db_id->name . ':' . $pub_dbxref->dbxref_id->accession;
+    $dbxrefs[] = $pub_dbxref['name'] . ':' . $pub_dbxref['accession'];
   }
 
   // Get the citation.

tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record.inc

@@ -98,6 +98,12 @@ class data__sequence_record extends ChadoField {
     else {
       $this->addGenericReference($entity, $feature, $field_name);
     }
+
+    // The field should always return a 'value' key so even if we don't
+    // have a sequence we still need to add it
+    if (count(array_keys($entity->{$field_name}['und'])) == 0) {
+      $entity->{$field_name}['und'][0]['value'] = '';
+    }
   }
 
   /**

tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record_formatter.inc

@@ -28,10 +28,8 @@ class data__sequence_record_formatter extends ChadoFieldFormatter {
     $phase_term = chado_get_semweb_term('featureloc', 'phase');
     $fasta_defline = 'local:fasta_definition';
 
-    $content = [];
-
     foreach ($items as $delta => $item) {
-      if (empty($item['value'])) {
+      if (!$item['value']) {
         continue;
       }
 
@@ -41,24 +39,19 @@ class data__sequence_record_formatter extends ChadoFieldFormatter {
       $residues .= wordwrap($item['value'][$sequence_term], $num_bases, "<br>", TRUE);
       $residues .= '</pre>';
 
-      $content[] = [
+      $element[$delta] = [
         '#type' => 'item',
         '#title' => $item['value'][$label_term],
         '#description' => $item['value'][$description_term],
         '#markup' => $residues,
       ];
-
-
     }
 
-    if (empty($content)) {
+    if (count($element) == 0) {
       $element[0] = [
         '#type' => 'markup',
-        '#markup' => '',
+        '#markup' => 'There are no sequences for this feature.',
       ];
-      return;
     }
-
-    $element[0] = $content;
   }
 }

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference.inc

@@ -37,6 +37,10 @@ class sbo__database_cross_reference extends ChadoField {
     // type. This will create form elements when editing the field instance
     // to allow the site admin to change the term settings above.
     'term_fixed' => FALSE,
+    // The number of items to show on a page.
+    'items_per_page' => 10,
+    // Limit to the number of items to show in cases of large number of cross references.
+    'max_items' => 10000,
   ];
 
   // The default widget for this field.
@@ -138,33 +142,39 @@ class sbo__database_cross_reference extends ChadoField {
 
     $linker_table = $base_table . '_dbxref';
     $options = ['return_array' => 1];
-    $record = chado_expand_var($record, 'table', $linker_table, $options);
-    if (property_exists($record, $linker_table) and is_array($record->$linker_table) and count($record->$linker_table) > 0) {
-      $i = 0;
-      foreach ($record->$linker_table as $index => $linker) {
-        $dbxref = $linker->dbxref_id;
-
-        // Ignore the GFF_source database. This is a weird thing required by
-        // GBrowse and is added by the GFF loader. We don't want to show it.
-        if ($dbxref->db_id->name == 'GFF_source') {
-          continue;
-        }
-
-        $URL = chado_get_dbxref_url($dbxref);
-        $entity->{$field_name}['und'][$i] = [
-          'value' => [
-            $dbname_term => $dbxref->db_id->name,
-            $accession_term => $dbxref->accession,
-            $dburl_term => $URL,
-          ],
-          'chado-' . $field_table . '__' . $pkey => $linker->$pkey,
-          'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
-          'chado-' . $field_table . '__dbxref_id' => $dbxref->dbxref_id,
-          'db_id' => $dbxref->db_id->db_id,
-          'accession' => $dbxref->accession,
-        ];
-        $i++;
+
+    // Build the SQL to find records associated with this publication.
+    $max_items = array_key_exists('max_items', $this->instance['settings']) ? $this->instance['settings']['max_items'] : 10000;
+    $sql = "SELECT REF.accession, DB.name, DB.urlprefix "
+         . "FROM {".$linker_table."} LINK "
+         . "INNER JOIN {dbxref} REF on LINK.dbxref_id = REF.dbxref_id "
+         . "INNER JOIN {db} DB on REF.db_id = DB.db_id "
+         . "WHERE LINK.$fkey_lcolumn = :id "
+         // Ignore the GFF_source database. This is a weird thing required by
+         // GBrowse and is added by the GFF loader. We don't want to show it.
+         . "AND NOT DB.name = 'GFF_source' "
+         . "ORDER BY REF.accession "  // if we hit the limit, the subset should be consistent
+         . "LIMIT :limit";
+    $args = [':id' => $entity->{'chado_record_id'},
+             ':limit' => $max_items + 1];
+    $records = chado_query($sql, $args);
+
+    // Store the query results
+    $delta = 0;
+    while($record = $records->fetchObject()) {
+      // Need this check to detect the case where the limit exactly equals the number of records
+      if ($delta < $max_items) {
+        $entity->{$field_name}['und'][$delta] = [];
+        $entity->{$field_name}['und'][$delta]['value'][$dbname_term] = $record->name;
+        $entity->{$field_name}['und'][$delta]['value'][$accession_term] = $record->accession;
+        $entity->{$field_name}['und'][$delta]['value'][$dburl_term] = $record->urlprefix;
       }
+      $delta++;
+    }
+    // Display a warning if we have exceeded the maximum number of cross references
+    if ( $delta > $max_items ) {
+      $entity->{$field_name}['und'][$delta]['value'][$dbname_term] = 'Note';
+      $entity->{$field_name}['und'][$delta]['value'][$accession_term] = "Only the first $max_items cross references are shown";
     }
   }
 

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference_formatter.inc

@@ -15,6 +15,11 @@ class sbo__database_cross_reference_formatter extends ChadoFieldFormatter {
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
     $content = '';
 
+    // Do we have an empty list? If so, just return.
+    if (!$items[0]['value']) {
+      return;
+    }
+
     $field_name = $this->field['field_name'];
     $field_type = $this->field['type'];
     $field_table = $this->instance['settings']['chado_table'];
@@ -26,27 +31,83 @@ class sbo__database_cross_reference_formatter extends ChadoFieldFormatter {
     $accession_term = chado_get_semweb_term('dbxref', 'accession');
     $dburl_term = chado_get_semweb_term('db', 'url');
 
+    // First, organize the values by their databases.
+    $ordered_items = [];
     foreach ($items as $delta => $item) {
-      if (!$item['value']) {
-        continue;
+      $db = $item['value'][$dbname_term];
+      $accession = $item['value'][$accession_term];
+      // It is possible that a database does not have a url, in which case no link can be generated.
+      if (array_key_exists($dburl_term, $item['value']) and $item['value'][$dburl_term]) {
+        $url = $item['value'][$dburl_term];
+
+        // This emulates chado_get_dbxref_url() but implemented inline here for better performance.
+        $db_count = 0;
+        $acc_count = 0;
+        $url = preg_replace('/\{db\}/', $db, $url, -1, $acc_count);
+        $url = preg_replace('/\{accession\}/', $accession, $url, -1, $acc_count);
+
+        $content = l($accession, $url, ['attributes' => ['target' => '_blank']]);
       }
-      $content = $item['value'][$dbname_term] . ':' . $item['value'][$accession_term];
-      if ($item['value'][$dburl_term]) {
-        $dbxref = chado_get_dbxref(['dbxref_id' => $item['chado-' . $linker_table . '__dbxref_id']]);
-        $url = chado_get_dbxref_url($dbxref);
-        $content = l($content, $url, ['attributes' => ['target' => '_blank']]);
+      else {
+        $content = $accession;
       }
-      $element[$delta] = [
-        '#type' => 'markup',
-        '#markup' => $content,
-      ];
+      $ordered_items[ucfirst($db)][] = $content;
     }
 
-    if (count($element) == 0) {
-      $element[0] = [
-        '#type' => 'markup',
-        '#markup' => 'There are no cross references.',
+    // Reorder the list so it's compatible with theming a list.
+    ksort($ordered_items);
+
+    // Generate the pagers for each type.
+    $list_items = [];
+    $headers = [];
+    $rows = [];
+    foreach ($ordered_items as $type => $children) {
+      $items_per_page = array_key_exists('items_per_page', $this->instance['settings']) ? $this->instance['settings']['items_per_page'] : 10;
+      $total_records = count($children);
+      $total_pages = (int) ($total_records / $items_per_page) + 1;
+      $pelement = 0;
+      $current_page = pager_default_initialize($total_records, $items_per_page, $pelement);
+      $pager = theme('pager', [
+        'tags' => [],
+        'element' => $pelement,
+        'parameters' => [],
+        'quantity' => 5,
+      ]);
+      $pager = $this->ajaxifyPager($pager, $entity);
+      $page_items = array_chunk($children, $items_per_page);
+
+      $rows[] = [
+        [
+          'data' => ucfirst($type),
+          'header' => TRUE,
+          'width' => '20%',
+        ],
+        theme_item_list([
+          'items' => $page_items[$current_page],
+          'title' => '',
+          'type' => 'ul',
+          'attributes' => [],
+        ]) . $pager,
       ];
     }
+
+    $table = [
+      'header' => [],
+      'rows' => $rows,
+      'attributes' => [
+        'id' => 'sbo__database_cross_reference',
+        'class' => 'tripal-data-table',
+      ],
+      'sticky' => FALSE,
+      'caption' => "",
+      'colgroups' => [],
+      'empty' => 'There are no cross references.',
+    ];
+    $content = theme_table($table);
+    $element[0] = [
+      '#type' => 'markup',
+      '#markup' => $content,
+    ];
+
   }
 }

tripal_ds/api/tripal_ds.pane.api.inc

@@ -39,7 +39,7 @@ function tripal_ds_create_field($field_label, $field_name, $bundle_name) {
   //Build the rest of the passes parameters.
   $group_field_name = 'gp_' . $field_name;
   //Create the field groups.
-  tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name);
+  tripal_ds_add_generic_field_group($bundle_name, $field_label, $group_field_name, $field_name);
   //Place the field groups in the layout.
   tripal_ds_update_ds_layout($bundle_name, $field_name, $group_field_name);
 }

tripal_ds/includes/tripal_ds.ds.inc

@@ -41,117 +41,113 @@ function _ds_layout_settings_info($bundle_name, $instances) {
   $region_left = [];
   $prop_fields = [];
   $summary_fields = [];
-  $data_sequence_fields = [];
-  $all_other_fields = [];
+  $unhandled_fields = [];
   $fields_with_regions = [];
   $i = 0;
-  $all_fields = [];
+
 
   try {
+
     // Get the bundle and term objects.
     $bundle = tripal_load_bundle_entity(['name' => $bundle_name]);
     $term = tripal_load_term_entity(['term_id' => $bundle->term_id]);
 
-    // Build one large multidimensional array of all instances to sort in alpha
-    // order to display fields in label alpha order.
+    // Get the list of fields and sort them by label.
+    $sorted_instances = [];
     foreach ($instances as $key => $instance) {
-      $all_fields[$i] = $instance;
+      $sorted_instances[$i] = $instance;
       $i++;
     }
-    usort($all_fields, tripal_ds_sort_array('label'));
+    usort($sorted_instances, tripal_ds_sort_array('label'));
 
-    // Iterate through the fields of this bundle.
-    foreach ($all_fields as $key => $instance) {
+    // Iterate through the fields of this bundle and put them into appropriate
+    // field groups.
+    foreach ($sorted_instances as $key => $instance) {
+      $base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
+      $chado_table = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
       $instance_name = $instance['field_name'];
+
+      // Add the bundle type to the summary fields.
       if ($instance_name == "rdfs__type") {
         array_push($summary_fields, $instance_name);
+        continue;
       }
-      else {
-        //TODO: How do we handle non-chado dbs, placement of fields within
-        // tripal panes might need to be done in a hook.
-        $instance_base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
-        $instance_base_chado = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
-        $prop_table = strpos($instance_base_chado, 'prop');
-        $data_sequence_record = strpos($instance_name, 'data__sequence_record');
-        $data_sequence = strpos($instance_name, 'data__sequence');
-        if ($instance_base_chado && $instance_base_table) {
-
-          if ($instance_base_chado == $instance_base_table) {
-            if ($data_sequence_record !== FALSE) {
-              array_push($data_sequence_fields, $instance_name);
-            }
-            elseif ($data_sequence !== FALSE or $instance_name == 'so__cds' or $instance_name == 'data__protein_sequence') {
-              // Do nothing as these chado column sequence fields
-              // should be hidden by default.
-            }
-            elseif ($prop_table !== FALSE) {
-              array_push($prop_fields, $instance_name);
-            }
-            else {
-              array_push($summary_fields, $instance_name);
-            }
 
-          }
-          elseif ($instance_base_chado != $instance_base_table) {
-            if ($data_sequence_record !== FALSE) {
-              array_push($data_sequence_fields, $instance_name);
-            }
-            elseif ($data_sequence !== FALSE or $instance_name == 'so__cds' or $instance_name == 'data__protein_sequence') {
-              // Do nothing as these chado column sequence fields
-              // should be hidden by default.
-            }
-            elseif ($prop_table !== FALSE) {
-              array_push($prop_fields, $instance_name);
-            }
-            else {
-              array_push($all_other_fields, $instance);
+      // The tripal_chado module adds an image to the organism content
+      // type so we want to make sure that image goes in the summary.
+      // It is not a TripalField so it won't have a chado table.
+      if ($instance_name == 'data__image' and $term->name == 'organism') {
+        array_push($summary_fields, $instance_name);
+        continue;
+      }
 
-              // Update the display settings so that the title is hidden.
-              $instance['display']['default']['label'] = 'hidden';
-              field_update_instance($instance);
-            }
-          }
-        }
-        else {
-          // The tripal_chado module adds an image to the organism content
-          // type so we want to make sure that image goes in the summary.
-          // It is not a TripalField so it won't have a chado table.
-          if ($instance_name == 'data__image' and $term->name == 'organism') {
-            array_push($summary_fields, $instance_name);
-          }
+      // For fields that have a data__sequence prefix we want to hide these
+      // unless it's the data__sequence_record field which displays all of the
+      // sequence data and should be in it's own fieldset.
+      if (preg_match('/data__sequence/', $instance_name)) {
+        if ($instance_name == 'data__sequence_record') {
+          $instance['display']['default']['label'] = 'hidden';
+          field_update_instance($instance);
+          array_push($unhandled_fields, $instance);
         }
+        continue;
+      }
+
+      // For the same reason, hide the CDS and protein fields
+      if ($instance_name == 'so__cds' or $instance_name == 'data__protein_sequence'){
+        continue;
+      }
+
+      // If this field holds a value from the prop table then add it to the
+      // properties field group.
+      if (preg_match('/_prop$/', $chado_table)) {
+        array_push($prop_fields, $instance_name);
+        continue;
       }
-    }
 
-    // Consolidate the field sets.
+      // Put all fields from the base table in the summary and all other
+      // fields that were not handled above into a different array for
+      // handling later.
+      if ($base_table == $chado_table) {
+        array_push($summary_fields, $instance_name);
+        continue;
+      }
+      else {
+        // Update the display settings so that the title is hidden.
+        $instance['display']['default']['label'] = 'hidden';
+        field_update_instance($instance);
+        array_push($unhandled_fields, $instance);
+      }
+    } // end looping over fields.
+
+    // Create the summary and properties field groups.
     if (!empty($summary_fields)) {
-      _summary_field_group_info($bundle_name, $summary_fields);
+      tripal_ds_add_summary_field_group($bundle_name, $summary_fields);
     }
     if (!empty($prop_fields)) {
-      _prop_field_group_info($bundle_name, $prop_fields);
-    }
-    if (!empty($data_sequence_fields)) {
-      _data_sequence_field_group_info($bundle_name, $data_sequence_fields);
+      tripal_ds_add_prop_field_group($bundle_name, $prop_fields);
     }
-    if (!empty($all_other_fields)) {
-      foreach ($all_other_fields as $key => $other_field) {
-        $group_field_name = 'gp_' . $other_field['field_name'];
-
-        // Need to truncate the names because of database field size restrictions,
-        // updating fields here to ensure name consistency.
-        $group_field_name = substr($group_field_name, 0, 27);
-
-        // Add random numbers to ensure the field name is unique within the 32
-        // character limit of the field.
-        $group_field_name = $group_field_name . rand(0, 99999);
-        tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
-      }
+
+    // All other fields get their own field group (i.e. Tripal Pane).
+    foreach ($unhandled_fields as $key => $other_field) {
+      $group_field_name = 'gp_' . $other_field['field_name'];
+
+      // Need to truncate the names because of database field size restrictions,
+      // updating fields here to ensure name consistency.
+      $group_field_name = substr($group_field_name, 0, 27);
+
+      // Add random numbers to ensure the field name is unique within the 32
+      // character limit of the field.
+      $group_field_name = $group_field_name . rand(0, 99999);
+
+      // Now add a generic field group for this field.
+      tripal_ds_add_generic_field_group($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
     }
 
-    // Build one large multidimensional array of all instances to sort in alpha
-    // order to display fields in label alpha order.
+    // Build one large multidimensional array of all field groups to sort
+    // in alpha order to display fields in label alpha order.
     $right_fields = [];
-    $all_field_groups = field_group_info_groups('TripalEntity', $bundle_name);
+    $all_field_groups = field_group_info_groups('TripalEntity', $bundle_name, NULL, TRUE);
 
     if (!empty($all_field_groups)) {
       if (is_array($all_field_groups)) {
@@ -164,31 +160,6 @@ function _ds_layout_settings_info($bundle_name, $instances) {
         usort($right_fields, tripal_ds_sort_object('label'));
       }
     }
-    elseif (empty($all_field_groups)) {
-      //Add the original instances that were passed and the field_groups that
-      //were created.
-      $field_group_fields = db_select('field_group', 'fg')
-        ->fields('fg', ['group_name', 'data'])
-        ->condition('bundle', $bundle_name, '=')
-        ->execute()
-        ->fetchAll();
-
-      $instance_names = [];
-      $field_group_names = [];
-      foreach ($all_fields as $key => $instance) {
-        $instance_names[$key]['field_name'] = $instance['field_name'];
-        $instance_names[$key]['label'] = $instance['label'];
-
-      }
-      foreach ($field_group_fields as $key => $field_group_name) {
-        $data = unserialize($field_group_name->data);
-        $field_group_names[$key]['field_name'] = $field_group_name->group_name;
-        $field_group_names[$key]['label'] = $data['format_settings']['label'];
-
-      }
-      $all_field_groups = array_merge($instance_names, $field_group_names);
-      usort($all_field_groups, tripal_ds_sort_array('label'));
-    }
 
     // Now build the $region_right array and the fields array.
     $i = 0;
@@ -337,7 +308,7 @@ function _ds_layout_pub_settings_info($bundle_name, $instances) {
       $group_field_name = $group_field_name . rand(0, 99999);
 
       // Build the field group.
-      tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
+      tripal_ds_add_generic_field_group($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
 
       // Update arrays.
       array_push($temporary_field, $group_field_name, $other_field['field_name']);

tripal_ds/includes/tripal_ds.field_group.inc

@@ -7,7 +7,7 @@
  * @param $fields
  *  Array of the machine names of the children of the field group being created.
  */
-function _summary_field_group_info($bundle_name, $fields) {
+function tripal_ds_add_summary_field_group($bundle_name, $fields) {
   //Tripal pane to nest the summary fieldset within.
   $field_group_tripalpane = new stdClass();
   $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
@@ -80,7 +80,7 @@ function _summary_field_group_info($bundle_name, $fields) {
  * @param $fields
  *  Array of the machine names of the children of the field group being created.
  */
-function _prop_field_group_info($bundle_name, $fields) {
+function tripal_ds_add_prop_field_group($bundle_name, $fields) {
   //Tripal pane  to nest the fieldset within.
   $field_group_tripalpane = new stdClass();
   $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
@@ -152,7 +152,7 @@ function _prop_field_group_info($bundle_name, $fields) {
  * @param $fields
  *  Array of the machine names of the children of the field group being created.
  */
-function _data_sequence_field_group_info($bundle_name, $fields) {
+function tripal_ds_add_sequences_field_group($bundle_name, $fields) {
   //Tripal pane  to nest the fieldset within.
   $field_group_tripalpane = new stdClass();
   $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
@@ -182,7 +182,7 @@ function _data_sequence_field_group_info($bundle_name, $fields) {
   ];
   drupal_write_record('field_group', $field_group_tripalpane);
   //Write to the tripal_ds table to record the new tripal pane.
-  tripal_ds_bundle_menu_item($bundle_name, 'Sequence', 'group_sequence_tripalpane', 'TripalEntity');
+  tripal_ds_bundle_menu_item($bundle_name, 'Sequences', 'group_sequence_tripalpane', 'TripalEntity');
 
   //Table of fields.
   $field_group = new stdClass();
@@ -230,7 +230,7 @@ function _data_sequence_field_group_info($bundle_name, $fields) {
  * @param $field_name
  *  Machine name of the child element.
  */
-function tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name) {
+function tripal_ds_add_generic_field_group($bundle_name, $field_label, $group_field_name, $field_name) {
   //Write to the tripal_ds table to record the new tripal pane.
   tripal_ds_bundle_menu_item($bundle_name, $field_label, $group_field_name, 'TripalEntity');