Begin of functions for support APIs for programmatically creating entities

tripal/api/tripal.entities.api.inc

@@ -1121,3 +1121,169 @@ function tripal_entity_label($entity) {
   }
   return NULL;
 }
+
+function tripal_get_bundle_details($bundle_name) {
+  global $user;
+
+  $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
+  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
+  $vocab = $term->vocab;
+  $instances = field_info_instances('TripalEntity', $bundle->name);
+
+  $details = array(
+    'name' => $bundle->name,
+    'label' => $bundle->label,
+    'term' => array(
+      'accession' => $vocab->vocabulary . ':' . $term->accession,
+      'name' => $term->name,
+      'definition' => $term->definition,
+      'url' => $term->url
+    ),
+    'fields' => array(),
+  );
+
+  // Iterate through each feild and provide a discription of it and
+  // it's sub elements.
+  foreach ($instances as $instance) {
+    // Skip deleted fields.
+    if ($instance['deleted']) {
+      continue;
+    }
+
+    $field_name = $instance['field_name'];
+    $field = field_info_field($field_name);
+
+    $field_class = $field['type'];
+    $term_vocab = $instance['settings']['term_vocabulary'];
+    $term_accession = $instance['settings']['term_accession'];
+    $field_term = tripal_get_term_details($term_vocab, $term_accession);
+    $field_details = array(
+      'name' => $field_name,
+      'label' => $instance['label'],
+      'term' => array(
+        'accession' => $term_vocab . ":" . $term_accession,
+        'name' => $field_term['name'],
+        'definition' => $field_term['definition'],
+        'url' => $field_term['url'],
+      ),
+      // These items can be overridden by the element_info array that
+      // is present in a TripalField instance.  Here we set defaults.
+      'required' => $instance['required'] ? TRUE : FALSE,
+      'type' => 'xs:string',
+      'readonly' => TRUE,
+      // The cardinatlity value always comes from the field.
+      'cardinality' => $field['cardinality'],
+    );
+
+    if (tripal_load_include_field_class($field_class)) {
+      $field_obj = new $field_class($field, $instance);
+      $element_info = $field_obj->elementInfo();
+      $element_info = $element_info[$term_vocab . ':' . $term_accession];
+
+      // If the element info for this field sets required, type and readonly
+      // attributes then set those.
+      $field_details['required'] = array_key_exists('required', $element_info) ? $element_info['required'] : FALSE;
+      $field_details['type'] = array_key_exists('type', $element_info) ? $element_info['type'] : 'xs:string';
+      $field_details['readonly'] = array_key_exists('readonly', $element_info) ? $element_info['readonly'] : TRUE;
+      $field_details['label'] = array_key_exists('label', $element_info) ? $element_info['label'] : $field_details['label'];
+      $field_details['help'] = array_key_exists('help', $element_info) ? $element_info['help'] : '';
+
+      // If this field is an 'xs:complexType' then it will have sub elements.
+      // we need to add those as well.
+      if (array_key_exists('elements', $element_info) and is_array($element_info['elements'])) {
+        _tripal_get_bundle_field_element_details($element_info['elements'], $field_details);
+      }
+      $details['fields'][] = $field_details;
+    }
+
+  }
+  return $details;
+}
+/**
+ * A recursive helper function for the tripal_get_bundle_details.
+ *
+ * @param $elementInfo
+ */
+function _tripal_get_bundle_field_element_details($elements, &$field_details) {
+   $field_details['elements'] = array();
+   foreach ($elements as $element_key => $element_info) {
+     // Handle the entity element differnetly.
+     if ($element_key == 'entity') {
+       continue;
+     }
+     list($term_vocab, $term_accession) = explode(':', $element_key);
+     $term = tripal_get_term_details($term_vocab, $term_accession);
+
+     $element_details = array(
+       'name' => $element_info['name'],
+       'label' => array_key_exists('label', $element_info) ? $element_info['label'] : ucfirst(preg_replace('/_/', ' ', $term['name'])),
+       'help' => array_key_exists('help', $element_info) ? $element_info['help'] : '',
+       'term' => array(
+         'accession' => $term_vocab . ':' . $term_accession,
+         'name' => $term['name'],
+         'definition' => $term['definition'],
+         'url' => $term['url'],
+       ),
+       'required' => array_key_exists('required', $element_info) ? $element_info['required'] : FALSE,
+       'type' => array_key_exists('type', $element_info) ? $element_info['type'] : 'xs:string',
+       'readonly' => array_key_exists('readonly', $element_info) ? $element_info['readonly'] : TRUE,
+     );
+     if (array_key_exists('elements', $element_info) and is_array($element_info['elements'])) {
+       _tripal_get_bundle_field_element_details($element_info['elements'], $element_details);
+     }
+     $field_details['elements'][] = $element_details;
+   }
+}
+
+function tripal_insert_entity($bundle_name, $values){
+  global $user;
+
+  $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
+
+  // Get the fields associated with this content type.
+  $instances = field_info_instances('TripalEntity', $bundle->name);
+
+  foreach ($instances as $instance) {
+    $field_name = $instance['field_name'];
+    $field = field_info_field($field_name);
+    $field_type = $field['type'];
+    $field_settings = $field['settings'];
+    $instance_settings = $instance['settings'];
+    $field_name = $field['field_name'];
+    $vocabulary = $instance['settings']['term_vocabulary'];
+    $accession = $instance['settings']['term_accession'];
+    $field_accession = $vocabulary . ':' . $accession;
+    $field_term = tripal_get_term_details($vocabulary, $accession);
+    $field_key = $field_term['name'];
+    $field_key = strtolower(preg_replace('/ /', '_', $key));
+
+    // There are three ways that a field value can be specified. Those
+    // are as the controlled vocabulary accession (e.g. GO:0000134), sa
+    // the field name or as the field key which is the term name with
+    // spaces replaced with underscores.
+    // First make sure that required fields are present.
+    if ($instance['required'] == TRUE) {
+      if (!array_key_exists($field_key, $values) and
+          !array_key_exists($field_accession, $values) and
+          !array_key_exists($field_name, $values)) {
+        throw new Exception(t('Cannot insert the record. Missing the required field "%missing".',
+          array('%missing' => $field_name)));
+      }
+    }
+  }
+
+  // Make sure that all required fields are presnet
+
+  // TODO: make sure the user has permission to do this.
+  $ec = entity_get_controller('TripalEntity');
+  $entity = $ec->create(array(
+    'bundle' => $bundle_name,
+    'term_id' => $bundle->term_id,
+  ));
+  $entity = $entity->save();
+}
+
+function tripal_update_entity($bundle_name, $values) {
+
+
+}

tripal_chado/includes/TripalFields/chado_linker__contact/chado_linker__contact.inc

@@ -72,7 +72,8 @@ class chado_linker__contact extends ChadoField {
         'operations' => array('eq', 'contains', 'starts'),
         'sortable' => TRUE,
         'searchable' => TRUE,
-        'type' => 'string',
+        'type' => 'xs:complexType',
+        'readonly' => FALSE,
         'elements' => array(
           $type_term => array(
             'searchable' => TRUE,
@@ -80,6 +81,9 @@ class chado_linker__contact extends ChadoField {
             'help' => 'The type of contact',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $name_term => array(
             'searchable' => TRUE,
@@ -87,6 +91,9 @@ class chado_linker__contact extends ChadoField {
             'help' => 'The name of the contact.',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $description_term => array(
             'searchable' => TRUE,
@@ -94,6 +101,9 @@ class chado_linker__contact extends ChadoField {
             'help' => 'A descriptoin of the contact.',
             'operations' => array('contains'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'entity' => array(
             'searchable' => FALSE,

tripal_chado/includes/TripalFields/data__protein_sequence/data__protein_sequence.inc

@@ -62,6 +62,8 @@ class data__protein_sequence extends ChadoField {
         'help' => 'The polypeptide sequence derived from mRNA',
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => FALSE,
       ),
     );
     return $info;

tripal_chado/includes/TripalFields/data__sequence/data__sequence.inc

@@ -61,6 +61,8 @@ class data__sequence extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => FALSE,
       ),
     );
   }

tripal_chado/includes/TripalFields/data__sequence_checksum/data__sequence_checksum.inc

@@ -64,6 +64,9 @@ class data__sequence_checksum extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
+        'required' => FALSE,
       ),
     );
   }

tripal_chado/includes/TripalFields/data__sequence_coordinates/data__sequence_coordinates.inc

@@ -74,6 +74,8 @@ class data__sequence_coordinates extends ChadoField {
         'searchable' => FALSE,
         'label' => 'Location Coordinates',
         'help' => 'The locations on other genomic sequences where this record has been aligned.',
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           $reference_term => array(
             'searchable' => TRUE,
@@ -81,6 +83,9 @@ class data__sequence_coordinates extends ChadoField {
             'help' => 'The genomic feature on which this feature is localized.',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $fmin_term => array(
             'searchable' => TRUE,
@@ -89,6 +94,9 @@ class data__sequence_coordinates extends ChadoField {
             'type' => 'numeric',
             'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
             'sortable' => TRUE,
+            'type' => 'xs:integer',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $fmax_term => array(
             'searchable' => TRUE,
@@ -97,6 +105,9 @@ class data__sequence_coordinates extends ChadoField {
             'type' => 'numeric',
             'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
             'sortable' => TRUE,
+            'type' => 'xs:integer',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $phase_term => array(
             'searchable' => TRUE,
@@ -105,6 +116,9 @@ class data__sequence_coordinates extends ChadoField {
             'help' => 'The phase of the feature (applicable only to coding sequences).',
             'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
             'sortable' => TRUE,
+            'type' => 'xs:integer',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $strand_term => array(
             'searchable' => TRUE,
@@ -112,6 +126,9 @@ class data__sequence_coordinates extends ChadoField {
             'help' => 'The orientation of this feature where it is localized',
             'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         ),
       ),

tripal_chado/includes/TripalFields/data__sequence_length/data__sequence_length.inc

@@ -65,7 +65,8 @@ class data__sequence_length extends ChadoField {
         'operations' => array('eq', 'gt', 'lt', 'gte', 'lte'),
         'sortable' => TRUE,
         'searchable' => TRUE,
-        'type' => 'numeric',
+        'type' => 'xs:integer',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/go__gene_expression/go__gene_expression.inc

@@ -70,6 +70,8 @@ class go__gene_expression extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/local__contact/local__contact.inc

@@ -70,7 +70,8 @@ class local__contact extends ChadoField {
         'operations' => array('eq', 'contains', 'starts'),
         'sortable' => TRUE,
         'searchable' => TRUE,
-        'type' => 'string',
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           $type_term => array(
             'searchable' => TRUE,
@@ -78,6 +79,9 @@ class local__contact extends ChadoField {
             'help' => 'The type of contact',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $name_term => array(
             'searchable' => TRUE,
@@ -85,6 +89,9 @@ class local__contact extends ChadoField {
             'help' => 'The name of the contact.',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $description_term => array(
             'searchable' => TRUE,
@@ -92,6 +99,9 @@ class local__contact extends ChadoField {
             'help' => 'A descriptoin of the contact.',
             'operations' => array('contains'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => FALSE,
           ),
           'entity' => array(
             'searchable' => FALSE,

tripal_chado/includes/TripalFields/local__source_data/local__source_data.inc

@@ -70,24 +70,35 @@ class local__source_data extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           $sourcename_term => array(
             'searchable' => TRUE,
             'label' => 'Data Source Name',
             'help' => 'The name of the data source used for the analysis.',
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $sourceversion_term => array(
             'searchable' => TRUE,
             'label' => 'Data Source Version',
             'help' => 'If applicable, the version number of the source data used for the analysis.',
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $sourceuri_term => array(
             'searchable' => FALSE,
             'label' => 'Data Source URI',
             'help' => 'If applicable, the universal resource indicator (e.g. URL) of the source data used for the analysis.',
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         ),
       ),

tripal_chado/includes/TripalFields/obi__organism/obi__organism.inc

@@ -221,37 +221,53 @@ class obi__organism extends ChadoField {
         'operations' => array('eq', 'contains', 'starts'),
         'sortable' => TRUE,
         'searchable' => TRUE,
-        'type' => 'string',
+        'readonly' => FALSE,
+        'type' => 'xs:complexType',
         'elements' => array(
           'rdfs:label' => array(
             'searchable' => TRUE,
             'name' => 'scientfic_name',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
-            'sortable' => FALSE,
+            'sortable' => FALSE),
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $genus_term => array(
             'searchable' => TRUE,
             'name' => 'genus',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'readonly' => FALSE,
+            'type' => 'xs:string',
+            'required' => TRUE,
           ),
           $species_term => array(
             'searchable' => TRUE,
             'name' => 'species',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'readonly' => FALSE,
+            'type' => 'xs:string',
+            'required' => TRUE,
           ),
           $infraspecific_name_term => array(
             'searchable' => TRUE,
             'name' => 'infraspecies',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'readonly' => FALSE,
+            'type' => 'xs:string',
+            'required' => FALSE,
           ),
           $infraspecific_type_term => array(
             'searchable' => TRUE,
             'name' => 'infraspecific_type',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'readonly' => FALSE,
+            'type' => 'xs:integer',
+            'required' => FALSE,
           ),
           'entity' => array(
             'searchable' => FALSE,

tripal_chado/includes/TripalFields/ogi__location_on_map/ogi__location_on_map.inc

@@ -73,22 +73,33 @@ class ogi__location_on_map extends ChadoField {
       $field_term => array(
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           $map_term => array(
             'searchable' => FALSE,
             'sortable' => FALSE,
+            'type' => 'xs:complexType',
+            'readonly' => TRUE,
+            'required' => FALSE,
             'elements' => array(
               $name_term => array(
                 'label' => 'Map Name',
                 'help' => 'The name of the map.',
                 'searchable' => TRUE,
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => TRUE,
+                'required' => FALSE,
               ),
               $description_term => array(
                 'label' => 'Map Description',
                 'help' => 'A description of the map.',
                 'searchable' => TRUE,
                 'sortable' => FALSE,
+                'type' => 'xs:string',
+                'readonly' => TRUE,
+                'required' => FALSE,
               ),
               'entity' => array(
                 'searchable' => FALSE,
@@ -99,24 +110,36 @@ class ogi__location_on_map extends ChadoField {
           $ref_feature_term => array(
             'searchable' => FALSE,
             'sortable' => FALSE,
+            'type' => 'xs:complexType',
+            'readonly' => TRUE,
+            'required' => FALSE,
             'elements' => array(
               $ref_feature_name => array(
                 'label' => 'Map Reference Feature Name',
                 'help' => 'The genomic or genetic feature Nameof the map on which this feature is mapped.',
                 'searchable' => TRUE,
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => TRUE,
+                'required' => FALSE,
               ),
               $ref_feature_id=> array(
                 'label' => 'Map Reference Feature Identifier',
                 'help' => 'The genomic or genetic feature of the map on which this feature is mapped.',
                 'searchable' => TRUE,
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => TRUE,
+                'required' => FALSE,
               ),
               $ref_feature_type=> array(
                 'label' => 'Map Reference Feature Type',
                 'help' => 'The type of genomic or genetic feature of the map on which this feature is mapped.',
                 'searchable' => TRUE,
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => TRUE,
+                'required' => FALSE,
               ),
             ),
           ),
@@ -125,6 +148,9 @@ class ogi__location_on_map extends ChadoField {
             'help' => 'Maps may use different coordinate systems. This indicates the type of coordinate.',
             'searchable' => TRUE,
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         ),
       ),

tripal_chado/includes/TripalFields/operation__phylotree_vis/operation__phylotree_vis.inc

@@ -94,9 +94,14 @@ class operation__phylotree_vis extends ChadoField {
         'sortable' => FALSE,
         'searchable' => FALSE,
         'type' => 'string',
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           'schema:url' => array(
             'searchabel' => FALSE,
+            'type' => 'xs:anyURI',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         ),
       )

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference.inc

@@ -73,24 +73,35 @@ class sbo__database_cross_reference extends ChadoField {
         'label' => 'Cross Reference',
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:complexType',
+        'readonly' => FALSE,
         'elements' => array(
           $dbname_term => array(
             'searchable' => TRUE,
             'label' => 'Cross Reference Database Name',
             'help' => 'The name of the remote database that houses the cross reference.',
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $accession_term => array(
             'searchable' => TRUE,
             'label' => 'Cross Reference Database Accession',
             'help' => 'The unique accession (identifier) in the database that houses the cross reference.',
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $dburl_term => array(
             'searchable' => FALSE,
             'label' => 'Cross Reference Database URL',
             'help' => 'The URL of the database that houses the cross reference.',
             'sortable' => FALSE,
+            'type' => 'xs:anyURI',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         ),
       ),

tripal_chado/includes/TripalFields/sbo__phenotype/sbo__phenotype.inc

@@ -67,6 +67,8 @@ class sbo__phenotype extends ChadoField {
         'operations' => array('eq', 'ne', 'contains', 'starts'),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/sbo__relationship/sbo__relationship.inc

@@ -82,33 +82,49 @@ class sbo__relationship extends ChadoField {
         'operations' => array('eq', 'contains', 'starts'),
         'sortable' => FALSE,
         'searchable' => FALSE,
-        'type' => 'string',
+        'type' => 'xs:complexType',
+        'readonly' => FALSE,
         'elements' => array(
           'SIO:000493' => array(
             'searchable' => FALSE,
+            'name' => 'relationship_clause',
             'label' => 'Relationship Clause',
             'help' => 'An English phrase describing the relationships.',
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'local:relationship_subject' => array(
             'searchable' => FALSE,
             'name' => 'relationship_subject',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:complexType',
+            'readonly' => FALSE,
+            'required' => TRUE,
             'elements' => array(
               'rdfs:type' => array(
+                'name' => 'type',
                 'searchable' => TRUE,
                 'label' => 'Relationship Subject Type',
                 'help' => 'The subject\'s data type in a relationship clause',
                 'operations' => array('eq', 'ne', 'contains', 'starts'),
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => FALSE,
+                'required' => TRUE,
               ),
               'schema:name' => array(
+                'name' => 'name',
                 'searchable' => TRUE,
                 'label' => 'Relationship Subject Name',
                 'help' => 'The subject\'s name in a relationship clause',
                 'operations' => array('eq', 'ne', 'contains', 'starts'),
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => FALSE,
+                'required' => TRUE,
               ),
               'entity' => array(
                 'searchable' => FALSE,
@@ -121,12 +137,18 @@ class sbo__relationship extends ChadoField {
             'name' => 'relationship_type',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => TRUE,
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           'local:relationship_object' => array(
             'searchable' => FALSE,
-            'name' => 'species',
+            'name' => 'relationship_object',
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:complexType',
+            'readonly' => FALSE,
+            'required' => TRUE,
             'elements' => array(
               'rdfs:type' => array(
                 'searchable' => TRUE,
@@ -135,6 +157,9 @@ class sbo__relationship extends ChadoField {
                 'help' => 'The objects\'s data type in a relationship clause',
                 'operations' => array('eq', 'ne', 'contains', 'starts'),
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => FALSE,
+                'required' => TRUE,
               ),
               'schema:name' => array(
                 'searchable' => TRUE,
@@ -143,6 +168,9 @@ class sbo__relationship extends ChadoField {
                 'help' => 'The objects\'s name in a relationship clause',
                 'operations' => array('eq', 'ne', 'contains', 'starts'),
                 'sortable' => TRUE,
+                'type' => 'xs:string',
+                'readonly' => FALSE,
+                'required' => TRUE,
               ),
               'entity' => array(
                 'searchable' => FALSE,

tripal_chado/includes/TripalFields/schema__publication/schema__publication.inc

@@ -66,6 +66,8 @@ class schema__publication extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/sio__annotation/sio__annotation.inc

@@ -102,22 +102,32 @@ class sio__annotation extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
-        'type' => 'array',
+        'type' => 'xs:complexType',
+        'readonly' => FALSE,
         'elements' => array(
           $vocabulary_term => array(
             'sortable' => TRUE,
             'searchable' => TRUE,
             'label' => 'Annotation Term Vocabulary',
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $accession_term => array(
             'sortable' => TRUE,
             'searchable' => TRUE,
             'label' => 'Annotation Term Accession',
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $definition_term => array(
             'sortable' => TRUE,
             'searchable' => TRUE,
             'label' => 'Annotation Term Description',
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => FALSE,
           ),
         ),
       ),
@@ -129,6 +139,9 @@ class sio__annotation extends ChadoField {
         'sortable' => FALSE,
         'searchable' => FALSE,
         'label' => 'Annotation Term Negates',
+        'type' => 'xs:boolean',
+        'readonly' => FALSE,
+        'required' => FALSE,
       );
     }
     if (array_key_exists('rank', $schema['fields'])) {
@@ -137,7 +150,9 @@ class sio__annotation extends ChadoField {
         'sortable' => FALSE,
         'searchable' => FALSE,
         'label' => 'Annotation Term Rank',
-        'type' => 'numeric'
+        'type' => 'xs:integer',
+        'readonly' => FALSE,
+        'required' => FALSE,
       );
     }
     if (array_key_exists('pub_id', $schema['fields'])) {

tripal_chado/includes/TripalFields/sio__references/sio__references.inc

@@ -66,6 +66,8 @@ class sio__references extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/so__cds/so__cds.inc

@@ -53,6 +53,8 @@ class so__cds extends ChadoField {
       $field_term => array(
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:string',
+        'readonly' => TRUE,
       ),
     );
   }

tripal_chado/includes/TripalFields/so__genotype/so__genotype.inc

@@ -65,24 +65,35 @@ class so__genotype extends ChadoField {
       $field_term => array(
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           'rdfs:type' => array(
             'searchable' => FALSE,
             'label' => 'Genotype Type',
             'help' => 'The type of genotype.',
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'schema:name' => array(
             'label' => 'Genotype Name',
             'help' => 'The name of the genotype.',
             'searchable' => FALSE,
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'schema:description' => array(
             'label' => 'Genotype Description',
             'help' => 'A description of the genotype.',
             'searchable' => FALSE,
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
         )
       ),

tripal_chado/includes/TripalFields/so__transcript/so__transcript.inc

@@ -64,6 +64,8 @@ class so__transcript extends ChadoField {
         'operations' => array(),
         'sortable' => FALSE,
         'searchable' => FALSE,
+        'type' => 'xs:complexType',
+        'readonly' => TRUE,
         'elements' => array(
           'rdfs:type' => array(
             'name' => 'transcript_type',
@@ -72,6 +74,9 @@ class so__transcript extends ChadoField {
             'searchable' => FALSE,
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'schema:name' => array(
             'name' => 'transcript_name',
@@ -80,6 +85,9 @@ class so__transcript extends ChadoField {
             'searchable' => FALSE,
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'data:0842' => array(
             'name' => 'transcript_uniquename',
@@ -88,6 +96,9 @@ class so__transcript extends ChadoField {
             'searchable' => FALSE,
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'SO:0000735' => array(
             'name' => 'loc',
@@ -96,6 +107,9 @@ class so__transcript extends ChadoField {
             'searchable' => FALSE,
             'operations' => array('eq', 'ne', 'contains', 'starts'),
             'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           'entity' => array(
             'searchable' => FALSE,

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon.inc

@@ -68,24 +68,38 @@ class taxrank__infraspecific_taxon extends ChadoField {
       $field_term => array(
         'sortable' => FALSE,
         'searchable' => TRUE,
+        'readonly' => FALSE,
+        'type' => 'xs:complexType',
         'elements' => array(
           $label_term => array(
+            'name' => 'label',
             'sortable' => FALSE,
             'searchable' => TRUE,
             'label' => 'Infraspecific Full Name',
             'help' => 'The full infraspecific name including the rank and name.',
+            'type' => 'xsstring',
+            'readonly' => TRUE,
+            'required' => FALSE,
           ),
           $infraspecific_name_term => array(
+            'name' => 'infraspecific_name',
             'sortable' => TRUE,
             'searchable' => TRUE,
             'label' => 'Infrasepcies Name',
             'help' => 'The infraspecific name of the organism below the rank of species.',
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
           $infraspecific_type_term => array(
+            'name' => 'infraspecific_rank',
             'sortable' => TRUE,
             'searchable' => TRUE,
             'label' => 'Infraspecific Rank',
             'help' => 'The infraspecific rank of the organism below the rank of species.',
+            'type' => 'xs:string',
+            'readonly' => FALSE,
+            'required' => TRUE,
           ),
         )
       ),