Continued work on web services

tripal/api/tripal.entities.api.inc

@@ -792,6 +792,7 @@ function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL)
 
   // Now that all necessary fields are attached process the tokens.
   foreach($used_tokens as $token) {
+    $field_name = str_replace(array('.','[',']'), array('__','',''), $token);
     $value = '';
     if (isset($entity->{$field_name})) {
 

tripal/includes/TripalField.inc

@@ -92,6 +92,7 @@ class TripalField {
     return $this->field_name;
   }
 
+
   /**
    * A helper function to determine if this field wants to attach to a bundle.
    *

tripal/includes/TripalFieldQuery.inc

@@ -22,7 +22,8 @@ class TripalFieldQuery {
   /**
    *
    * @param $field_name
-   *   The name of the field.
+   *   The name of the field.  Or, the name of the field with a subfield
+   *   concatenated using a '.' as a delimter.
    * @param $value
    *   The value to use for filtering.
    * @param $operator
@@ -32,11 +33,21 @@ class TripalFieldQuery {
    *   be an array of literals of the same type as the column.
    */
   public function fieldCondition($field_name, $value, $operator = '=') {
-    $field = field_info_field($field_name);
+
+    // See if there is a subfield as part of the field_name.
+    $subfields = explode('.', $field_name);
+    if ($subfields > 1) {
+      $field = field_info_field($subfields[0]);
+    }
+    else {
+      $field = field_info_field($field_name);
+    }
+
     if ($field) {
       $field_storage_type = $field['storage']['type'];
       $this->conditions[$field_storage_type][] = array(
         'field' => $field,
+        'filter' => $field_name,
         'value' => $value,
         'operator' => $operator,
       );

tripal/includes/tripal.entity.inc

@@ -304,17 +304,19 @@ function tripal_entity_view($entity, $type, $view_mode, $langcode) {
         $entity->content[$child_name]['#suffix'] .= '</div>';
       }
 
-      // Add a tooltip to the field.
+      // Add a tooltip to the field for the term.
       $field = field_info_field($child_name);
       if (array_key_exists('settings', $field) and
           array_key_exists('semantic_web', $field['settings'])) {
         list($vocabulary, $accession) = explode(':', $field['settings']['semantic_web']);
         $term = tripal_get_term_details($vocabulary, $accession);
         if ($term) {
+          $tooltip_img = url(drupal_get_path('module', 'tripal') . '/theme/images/info.gif');
+          $tooltip_text = $term['definition'] ? $term['definition'] : $term['name'];
           $entity->content[$child_name]['#prefix'] .= '' .
             '<div class="tripal-tooltip">' .
-              '<img src="' . url(drupal_get_path('module', 'tripal') . '/theme/images/info.gif') . '">' .
-              '<div class="tripal-tooltiptext">' . $term['definition'] . '</div>' .
+              '<img src="' . $tooltip_img . '">' .
+              '<div class="tripal-tooltiptext">' . $tooltip_text . '</div>' .
             '</div>';
         }
       }

tripal/includes/tripal.field_storage.inc

@@ -85,9 +85,13 @@ function tripal_field_storage_tquery($conditions) {
 
   $filter = array();
   $entity_ids = array();
+
   foreach ($conditions as $index => $condition) {
 
     $field = $condition['field'];
+    if ($field['storage']['type'] != 'tripal_no_storage') {
+      continue;
+    }
     $field_type = $field['type'];
     $field_module = $field['module'];
     $settings = $field['settings'];

tripal_chado/api/tripal_chado.query.api.inc

@@ -1240,7 +1240,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
       $new_values = array();
       $new_columns = array();
       $new_options = array();
-      $uq_sname = "uq_" . $table . "_";
       $has_pkey = 0;
 
       // include the primary key in the results returned
@@ -1256,7 +1255,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
       foreach ($fields as $field) {
         if (array_key_exists($field, $values)) {
           $new_values[$field] = $values[$field];
-          $uq_sname .= substr($field, 0, 2);
           // if there is no primary key then use the unique contraint fields
           if (!$has_pkey) {
             array_push($new_columns, $field);
@@ -1266,7 +1264,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
         // substitute any default values
         elseif (array_key_exists('default', $table_desc['fields'][$field])) {
           $new_values[$field] = $table_desc['fields'][$field]['default'];
-          $uq_sname .= substr($field, 0, 2);
           if (!$has_pkey) {
             array_push($new_columns, $field);
           }
@@ -1275,7 +1272,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
         // allowed to be null
         elseif (!$table_desc['fields'][$field]['not null']) {
           $new_values[$field] = NULL;
-          $uq_sname .= "n" . substr($field, 0, 2);
           if (!$has_pkey) {
             array_push($new_columns, $field);
           }

tripal_chado/api/tripal_chado.semweb.api.inc

@@ -191,5 +191,4 @@ function tripal_get_chado_semweb_term($chado_table, $chado_column, $options = ar
 
     return $cvterm->dbxref_id->db_id->name . ':' . $cvterm->dbxref_id->accession;
   }
-
-}
+}

tripal_chado/includes/fields/chado_base__organism_id.inc

@@ -275,6 +275,8 @@ class chado_base__organism_id extends TripalField {
         $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $fk_entity_id;
       }
 
+      // Add in the semantic web settings.  This array is expected by
+      // other Tripal modules that handle semantic web for fields.
       $entity->{$field_name}['und'][0]['semantic_web'] = array(
         'label' => 'rdfs:label',
         'genus' => tripal_get_chado_semweb_term('organism', 'genus'),
@@ -282,6 +284,17 @@ class chado_base__organism_id extends TripalField {
         'infraspecific_name' => tripal_get_chado_semweb_term('organism', 'infraspecific_name'),
         'infraspecific_type' => tripal_get_chado_semweb_term('organism', 'type_id'),
       );
+
+      // Add in subfield mapping to Chado tables. This is used by the
+      // chado_field_storage for performing queries on sub element values.
+      // It should be a comma-separated list (no spacing) of the field names
+      // as foreign keys are followed.
+      $entity->{$field_name}['und'][0]['chado_mapping'] = array(
+        'genus' => 'organism_id,genus',
+        'species' => 'organism_id,genus',
+        'infraspecific_name' => 'organism_id,infraspecific_name',
+        'infraspecific_type' => 'organism_id,infraspecific_type',
+      );
     }
   }
 

tripal_chado/includes/fields/chado_linker__contact.inc

@@ -271,11 +271,23 @@ class chado_linker__contact extends TripalField {
             'name' => $contact->name,
             'description' => $contact->description,
           ),
+          // Add in the semantic web settings.  This array is expected by
+          // other Tripal modules that handle semantic web for fields.
           'semantic_web' => array(
             'type' => $contact->type_id->dbxref_id->db_id->name . ':' . $contact->type_id->dbxref_id->accession,
             'name' => tripal_get_chado_semweb_term('contact', 'name'),
             'description' => tripal_get_chado_semweb_term('contact', 'description'),
           ),
+          // Add in subfield mapping to Chado tables. This is used by the
+          // chado_field_storage for performing queries on sub element values.
+          // It should be a comma-separated list (no spacing) of the field names
+          // as foreign keys are followed starting from the Chado table to which
+          // this field maps.
+          'chado_mapping' => array(
+            'type' => 'type_id,name',
+            'name' => 'contact_id,name',
+            'description' => 'contact_id,name'
+          ),
           $field_table . '__' . $pkey => $contact_linker->$pkey,
           $field_table . '__' . $fkey_lcolumn => $contact_linker->$fkey_lcolumn->$fkey_lcolumn,
           $field_table . '__' . 'contact_id' => $contact->contact_id

tripal_chado/includes/fields/chado_linker__dbxref.inc

@@ -183,6 +183,12 @@ class chado_linker__dbxref extends TripalField {
         );
       }
     }
+    if (count($items) > 0) {
+      $element[$delta] = array(
+        '#type' => 'markup',
+        '#markup' => '',
+      );
+    }
   }
 
   /**

tripal_chado/includes/tripal_chado.entity.inc

@@ -264,12 +264,8 @@ function tripal_chado_entity_access($op, $entity = NULL, $account = NULL) {
 function tripal_chado_tripal_default_title_format($entity, $available_tokens) {
   $format = array();
 
-  // Load the term associated with this Tripal Content type.
-  $term = entity_load('TripalTerm', array('id' => $entity->term_id));
-  $term = reset($term);
-
   // Load the bundle
-  $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
+  $bundle = tripal_load_bundle_entity(array('term_id' => $entity->term_id));
   $bundle_id = $bundle->id;
   $table = tripal_get_bundle_variable('chado_table', $bundle_id);
   $column = tripal_get_bundle_variable('chado_column', $bundle_id);

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -427,58 +427,69 @@ function tripal_chado_field_storage_query($query) {
  * @param $conditions
  */
 function tripal_chado_field_storage_tquery($conditions) {
-  $filter = array();
+  $filters = array();
+  $entity_ids = array();
+
   foreach ($conditions as $index => $condition) {
     $field = $condition['field'];
+    $filter = $condition['filter'];
+
+    if ($field['storage']['type'] != 'field_chado_storage') {
+      continue;
+    }
     $field_type = $field['type'];
     $field_module = $field['module'];
     $settings = $field['settings'];
     $chado_table = $settings['chado_table'];
     $chado_column = $settings['chado_column'];
 
-    // Allow the creating module to alter the value if desired.
-    $value = '';
-    module_load_include('inc', $field_module, 'includes/fields/' . $field_type);
-    if (preg_match('/^chado/', $field_type) and class_exists($field_type)) {
-      $field_obj = new $field_type();
-      if (method_exists($field_obj, 'query')) {
-        $value = $field_obj->query($condition);
-      }
+    // Set the value for this field search.
+    $value = NULL;
+    $subfields = explode('.', $filter);
+    if (count($subfields) > 1) {
+      // Get the term for this field's column and replace the field_name with
+      // the term.  We need to do this for the recursive function to work.
+      // We must lowercase the term and underscore it because that's how we
+      // can support case-insensitivity and lack of spacing such as for
+      // web services.
+      $subfield1 = tripal_get_chado_semweb_term($chado_table, $chado_column, array('return_object' => TRUE));
+      $subfields[0] = strtolower(preg_replace('/ /', '_', $subfield1->name));
+      $value = tripal_chado_field_storage_recurse_subfilters($chado_table, $subfields, $condition['value']);
+      $value = array_shift($value);
     }
-    // If there is no field to rewrite the value then use defaults.
     else {
       $value = $condition['value'];
     }
 
-    // use the appropriate operator.
+    // Use the appropriate operator.
     $operator = $condition['operator'];
     switch ($operator) {
       case '=':
-        $filter[$chado_table][$chado_column] = $condition['value'];
+        $filters[$chado_table][$chado_column] = $value;
         break;
       case '>':
       case '>=':
       case '<':
       case '<=':
-        $filter[$chado_table][$chado_column] = array(
+        $filters[$chado_table][$chado_column] = array(
           'op' => $operator,
           'data' => $value,
         );
         break;
       case '<>':
-        $filter[$chado_table][$chado_column] = array(
+        $filters[$chado_table][$chado_column] = array(
           'op' => 'NOT',
           'data' => $value,
         );
         break;
       case 'CONTAINS':
-        break;
-        $filter[$chado_table][$chado_column] = array(
+        $filters[$chado_table][$chado_column] = array(
           'op' => 'LIKE',
           'data' => '%' . $value . '%',
         );
+        break;
       case 'STARTS WITH':
-        $filter[$chado_table][$chado_column] = array(
+        $filters[$chado_table][$chado_column] = array(
           'op' => 'LIKE',
           'data' => $value . '%',
         );
@@ -491,7 +502,7 @@ function tripal_chado_field_storage_tquery($conditions) {
 
   // Iterate through the filters and perform the query
   $entity_ids = array();
-  foreach ($filter as $chado_table => $values) {
+  foreach ($filters as $chado_table => $values) {
     // First get the matching record IDs from the Chado table.
     $schema = chado_get_schema($chado_table);
     $pkey = $schema['primary key'][0];
@@ -523,4 +534,59 @@ function tripal_chado_field_storage_tquery($conditions) {
   }
 
   return $entity_ids;
-}
+}
+
+/**
+ *
+ * @param $subfields
+ * @param $value
+ */
+function tripal_chado_field_storage_recurse_subfilters($chado_table, $subfields, $value) {
+   $sub_value = array();
+
+   // Get the subvalue for this iteration
+   $subfield = array_shift($subfields);
+
+   // Get the cvterms mapped to this table.
+   $columns = db_select('chado_semweb', 'CS')
+     ->fields('CS', array('chado_column', 'cvterm_id'))
+     ->condition('chado_table', $chado_table)
+     ->execute();
+
+   // Iterate through the columns and find the one with cvterm that matches
+   // the subfield name.
+   $chado_column = '';
+   while($column = $columns->fetchObject()) {
+     $cvterm_id = $column->cvterm_id;
+     $cvterm = tripal_get_cvterm(array('cvterm_id' => $cvterm_id));
+     // Convert the term name to lower-case and replace spaces with underscores
+     // so we can perform case insensitive comparisions and ingore spacing.
+     $term_name = strtolower(preg_replace('/ /', '_', $cvterm->name));
+     if ($subfield == $term_name) {
+       $chado_column = $column->chado_column;
+     }
+   }
+
+
+   // If we have more subfields then this should be a foreign key and we should
+   // recurse.
+   if (count($subfields) > 0) {
+
+    // Get the foreign keys for this Chado table.
+     $schema = chado_get_schema($chado_table);
+     $fkeys = $schema['foreign keys'];
+
+     // Iterate through the FKs to find the one that matches this Chado field.
+     foreach ($fkeys as $fk_table => $details) {
+       foreach ($details['columns'] as $lkey => $rkey) {
+         if ($lkey == $chado_column) {
+           $sub_value = tripal_chado_field_storage_recurse_subfilters($fk_table, $subfields, $value);
+           return array($chado_column => $sub_value);
+         }
+       }
+     }
+   }
+   return array($chado_column => $value);
+}
+
+

tripal_chado/includes/tripal_chado.semweb.inc

@@ -1,4 +1,5 @@
 <?php
+
 /**
  * Adds defaults to the chado_semweb table.
  */
@@ -10,6 +11,13 @@ function tripal_chado_populate_chado_semweb_table() {
     tripal_add_chado_semweb_table($chado_table);
   }
 
+  // TODO: should this code be in the tripal_chado module? Some of these terms
+  // are used solely by web services (e.g. rdfs:label) and are not used to
+  // map chado terms to vocabularies.
+
+  // Perhaps we should have an API for working with terms where these can be
+  // inserted.
+
   // Now set defaults!
   tripal_chado_populate_vocab_EDAM();
   tripal_chado_populate_vocab_FOAF();
@@ -57,6 +65,12 @@ function tripal_chado_populate_vocab_RDFS() {
     'cv_name' => 'rdfs',
     'definition' => 'The type of resource.',
   ));
+  $name = tripal_insert_cvterm(array(
+    'id' => 'rdfs:label',
+    'name' => 'type',
+    'cv_name' => 'rdfs',
+    'definition' => 'A human-readable version of a resource\'s name.',
+  ));
 }
 /**
  * Adds the Schema.org database and terms.
@@ -612,7 +626,7 @@ function tripal_chado_semweb_edit_form($form, &$form_state, $table = NULL, $colu
          '#title' =>  $term->name,
          '#default_value' => $default,
          '#attributes' => $attrs,
-         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name .
+         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
              '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
              '<br><b>Definition:</b>  ' . $term->definition,
        );

tripal_chado/includes/tripal_chado.vocab_storage.inc

@@ -81,6 +81,9 @@ function tripal_chado_vocab_import_form_submit($form, &$form_state) {
 }
 /**
  * Implements hook_vocab_select_term_form().
+ *
+ * TODO: can't this be moved over to the tripal module and remove the
+ *  Chado specific parts???
  */
 function tripal_chado_vocab_select_term_form($form, &$form_state) {
   $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
@@ -138,7 +141,7 @@ function tripal_chado_vocab_select_term_form($form, &$form_state) {
          '#title' =>  $term->name,
          '#default_value' => $default,
          '#attributes' => $attrs,
-         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name .
+         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
              '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
              '<br><b>Definition:</b>  ' . $term->definition,
        );

tripal_ws/includes/tripal_ws.rest.inc → tripal_ws/includes/tripal_ws.rest_v0.1.inc

@@ -1,26 +1,16 @@
 <?php
 
-/**
- *_a
- */
-function tripal_ws_rest() {
 
-  global $base_url;
-  $ws_path = func_get_args();
-  $params = $_GET;
-  unset($params['q']);
 
-  // The web services should never be cached.
-  drupal_page_is_cacheable(FALSE);
+/**
+ *
+ */
+function tripal_ws_services_v0_1($api_url, $ws_path, $params) {
 
   // Set some initial variables.
   $response = array();
-  $status = 'success';
   $version = 'v0.1';
-  $message = '';
-  $api_url = $base_url . '/ws/' . $version;
-  $page_limit = 25;
-  $pager_id = 0;
+
 
   // Set some defaults for the response.
   $response['@context'] =  array();
@@ -34,40 +24,26 @@ function tripal_ws_rest() {
 
     switch ($service) {
       case 'doc':
-        tripal_ws_handle_doc_service($api_url, $response);
+        tripal_ws_services_v0_1_handle_doc_service($api_url, $response);
         break;
       case 'content':
-        tripal_ws_handle_content_service($api_url, $response, $ws_path, $params);
+        tripal_ws_services_v0_1_handle_content_service($api_url, $response, $ws_path, $params);
         break;
       case 'vocab':
-        tripal_ws_handle_vocab_service($api_url, $response, $ws_path);
+        tripal_ws_services_v0_1_handle_vocab_service($api_url, $response, $ws_path);
         break;
       default:
-        tripal_ws_handle_no_service($api_url, $response);
+        tripal_ws_services_v0_1_handle_no_service($api_url, $response);
     }
   }
   catch (Exception $e) {
     watchdog('tripal_ws', $e->getMessage(), array(), WATCHDOG_ERROR);
     $message = $e->getMessage();
-    $status = 'error';
+    drupal_add_http_header('Status', '400 Bad Request');
+
   }
 
-  // The responses follow a similar format as the AGAVE API with a
-  // status, message, version and all data in the 'result' object.
-/*   $response['status']  = $status;
-  $response['message'] = $message;
-  $response['api_version'] = $version;
-  $response['source'] = array(
-    'site_name' => variable_get('site_name', 'Unspecified'),
-    'site_url' => $base_url,
-    'site_slogan' => variable_get('site_slogan', 'Unspecified'),
-    'site_email' =>  variable_get('site_mail', 'Unspecified'),
-  ); */
-
-  // Rather than use the drupal_json_output() funciton we manually specify
-  // content type because we want it to be 'ld+json'.
-  drupal_add_http_header('Content-Type', 'application/ld+json');
-  print drupal_json_encode($response);
+  return $response;
 }
 
 
@@ -77,7 +53,7 @@ function tripal_ws_rest() {
  * @param $response
  * @param $ws_path
  */
-function tripal_ws_handle_content_service($api_url, &$response, $ws_path, $params) {
+function tripal_ws_services_v0_1_handle_content_service($api_url, &$response, $ws_path, $params) {
 
   // Get the content type.
   $ctype     = (count($ws_path) > 1) ? $ws_path[1] : '';
@@ -85,25 +61,25 @@ function tripal_ws_handle_content_service($api_url, &$response, $ws_path, $param
 
   // If we have no content type then list all of the available content types.
   if (!$ctype) {
-    tripal_ws_get_content_types($api_url, $response);
+    tripal_ws_services_v0_1_get_content_types($api_url, $response);
   }
   // If we don't have an entity ID then show a paged list of entities with
   // the given type.
   else if ($ctype and !$entity_id) {
-    tripal_ws_get_content_type($api_url, $response, $ws_path, $ctype, $params);
+   tripal_ws_services_v0_1_get_content_type($api_url, $response, $ws_path, $ctype, $params);
   }
   // If we have a content type and an entity ID then show the entity
   else {
-    tripal_ws_get_content($api_url, $response, $ws_path, $ctype, $entity_id, $params);
+    tripal_ws_services_v0_1_get_content($api_url, $response, $ws_path, $ctype, $entity_id, $params);
   }
 }
 /**
- *
- * @param $api_url
- * @param $response
- * @param $ws_path
- */
-function tripal_ws_handle_vocab_service($api_url, &$response, $ws_path) {
+*
+* @param $api_url
+* @param $response
+* @param $ws_path
+*/
+function tripal_ws_services_v0_1_handle_vocab_service($api_url, &$response, $ws_path) {
 
   // Get the vocab name.
   $vocabulary = (count($ws_path) > 1) ? $ws_path[1] : '';
@@ -111,15 +87,15 @@ function tripal_ws_handle_vocab_service($api_url, &$response, $ws_path) {
 
   // If we have no $vocabulary type then list all of the available vocabs.
   if (!$vocabulary) {
-    tripal_ws_get_vocabs($api_url, $response);
+    tripal_ws_services_v0_1_get_vocabs($api_url, $response);
   }
   // If we don't have a $vocabulary then show a paged list of terms.
   else if ($vocabulary and !$accession) {
-    tripal_ws_get_vocab($api_url, $response, $ws_path, $vocabulary);
+    tripal_ws_services_v0_1_get_vocab($api_url, $response, $ws_path, $vocabulary);
   }
   // If we have a content type and an entity ID then show the entity
   else if ($vocabulary and $accession) {
-    tripal_ws_get_term($api_url, $response, $ws_path, $vocabulary, $accession);
+    tripal_ws_services_v0_1_get_term($api_url, $response, $ws_path, $vocabulary, $accession);
   }
 }
 
@@ -128,13 +104,13 @@ function tripal_ws_handle_vocab_service($api_url, &$response, $ws_path) {
  * @param $api_url
  * @param $response
  */
-function tripal_ws_get_vocabs($api_url, &$response) {
+function tripal_ws_services_v0_1_get_vocabs($api_url, &$response) {
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
   $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
 
   // Next add in the ID for tihs resource.
-  $response['@id'] = $api_url . '/vocab';
+  $response['@id'] = url($api_url . '/vocab', array('absolute' => TRUE));
 
   // Start the list.
   $response['@type'] = 'Collection';
@@ -148,10 +124,9 @@ function tripal_ws_get_vocabs($api_url, &$response) {
   // Iterate through the vocabularies and add an entry in the collection.
   $i = 0;
   while ($vocab = $vocabs->fetchObject()) {
-    $term =
     // Add the bundle as a content type.
     $response['member'][] = array(
-      '@id' => $api_url . '/vocab/' . urlencode($vocab->vocabulary),
+      '@id' => url($api_url . '/vocab/' . urlencode($vocab->vocabulary), array('absolute' => TRUE)),
       '@type' => 'vocabulary',
       'vocabulary' => $vocab->vocabulary,
     );
@@ -159,8 +134,6 @@ function tripal_ws_get_vocabs($api_url, &$response) {
   }
   $response['totalItems'] = $i;
 
-  //$response['totalItems'] = $i;
-
   // Lastly, add in the terms used into the @context section.
   $response['@context']['Collection'] = 'hydra:Collection';
   $response['@context']['totalItems'] = 'hydra:totalItems';
@@ -175,7 +148,7 @@ function tripal_ws_get_vocabs($api_url, &$response) {
  * @param $response
  * @param $ws_path
  */
-function tripal_ws_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
+function tripal_ws_services_v0_1_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
 
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
@@ -183,7 +156,7 @@ function tripal_ws_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
   $response['@context']['schema'] = 'https://schema.org/';
 
   // Next add in the ID for tihs resource.
-  $response['@id'] = $api_url . '/vocab/' . $vocabulary;
+  $response['@id'] = url($api_url . '/vocab/' . $vocabulary, array('absolute' => TRUE));
 
   // Get the vocabulary
   $vocab = tripal_load_vocab_entity(array('vocabulary' => $vocabulary));
@@ -193,8 +166,8 @@ function tripal_ws_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
   $response['totalItems'] = 0;
   $response['label'] = vocabulary . " vocabulary collection";
   $response['comment'] = 'The following list of terms may not be the full ' .
-    'list for the vocabulary.  The terms listed here are only those ' .
-    'that have associated content on this site.';
+      'list for the vocabulary.  The terms listed here are only those ' .
+      'that have associated content on this site.';
 
   // Get the list of terms for this vocab.
   $query = db_select('tripal_term', 'tt')
@@ -208,7 +181,7 @@ function tripal_ws_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
   while($term = $terms->fetchObject()) {
     $term = tripal_load_term_entity(array('term_id' => $term->id));
     $response['member'][] = array(
-      '@id' => $api_url . '/vocab/' . urlencode($vocabulary) . '/' .  urlencode($term->accession),
+      '@id' => url($api_url . '/vocab/' . urlencode($vocabulary) . '/' .  urlencode($term->accession), array('absolute' => TRUE)),
       '@type' => 'vocabulary_term',
       'vocabulary' => $vocab->vocabulary,
       'accession' => $term->accession,
@@ -235,7 +208,7 @@ function tripal_ws_get_vocab($api_url, &$response, $ws_path, $vocabulary) {
  * @param $response
  * @param $ws_path
  */
-function tripal_ws_get_term($api_url, &$response, $ws_path, $vocabulary, $accession) {
+function tripal_ws_services_v0_1_get_term($api_url, &$response, $ws_path, $vocabulary, $accession) {
 
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
@@ -246,7 +219,7 @@ function tripal_ws_get_term($api_url, &$response, $ws_path, $vocabulary, $access
   $term = tripal_load_term_entity(array('vocabulary' => $vocabulary, 'accession' => $accession));
 
   // Next add in the ID and Type for this resources.
-  $response['@id'] = $api_url . '/vocab/' . urlencode($vocabulary) . '/' . urlencode($accession);
+  $response['@id'] = url($api_url . '/vocab/' . urlencode($vocabulary) . '/' . urlencode($accession), array('absolute' => TRUE));
   $response['@type'] = 'vocabulary_term';
   $response['label'] = $term->name;
   $response['vocabulary'] = $vocabulary;
@@ -268,14 +241,14 @@ function tripal_ws_get_term($api_url, &$response, $ws_path, $vocabulary, $access
  * @param $api_url
  * @param $response
  */
-function tripal_ws_get_content_types($api_url, &$response) {
+function tripal_ws_services_v0_1_get_content_types($api_url, &$response) {
 
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
   $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
 
   // Next add in the ID for tihs resource.
-  $response['@id'] = $api_url . '/content';
+  $response['@id'] = url($api_url . '/content', array('absolute' => TRUE));
 
   // Start the list.
   $response['@type'] = 'Collection';
@@ -288,7 +261,6 @@ function tripal_ws_get_content_types($api_url, &$response) {
     ->fields('tb')
     ->orderBy('tb.label', 'ASC')
     ->execute();
-  $terms = array();
 
   // Iterate through the terms and add an entry in the collection.
   $i = 0;
@@ -297,15 +269,8 @@ function tripal_ws_get_content_types($api_url, &$response) {
     $term = reset($entity);
     $vocab = $term->vocab;
 
-    if (!array_key_exists($vocab->vocabulary, $response['@context'])) {
-      // If there is no URL prefix then use this API's vocabulary API
-      if ($term->urlprefix) {
-        $response['@context'][$vocab->vocabulary] = $term->urlprefix;
-      }
-      else {
-        $response['@context'][$vocab->vocabulary] = $api_url . '/vocab/' . $vocab->vocabulary . '/';
-      }
-    }
+    $response['@context'][$term->name] = $term->url;
+
     // Get the bundle description. If no description is provided then
     // use the term definition
     $description = tripal_get_bundle_variable('description', $bundle->id);
@@ -314,8 +279,8 @@ function tripal_ws_get_content_types($api_url, &$response) {
     }
     // Add the bundle as a content type.
     $response['member'][] = array(
-      '@id' => $api_url . '/content/' . urlencode($bundle->label),
-      '@type' => $vocab->vocabulary . ':' . $term->accession,
+      '@id' => url($api_url . '/content/' . urlencode($bundle->label), array('absolute' => TRUE)),
+      '@type' => $term->name,
       'label' => $bundle->label,
       'description' => $description,
     );
@@ -337,71 +302,135 @@ function tripal_ws_get_content_types($api_url, &$response) {
  * @param $response
  * @param $ws_path
  */
-function tripal_ws_get_content_type($api_url, &$response, $ws_path, $ctype, $params) {
+function tripal_ws_services_v0_1_get_content_type($api_url, &$response, $ws_path, $ctype, $params) {
 
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
   $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
-  $response['@context']['schema'] = 'https://schema.org/';
 
   // Next add in the ID for tihs resource.
-  $response['@id'] = $api_url . '/content/' . $ctype;
+  $response['@id'] = url($api_url . '/content/' . $ctype, array('absolute' => TRUE));
 
   // Get the TripalBundle, TripalTerm and TripalVocab type for this type.
   $bundle = tripal_load_bundle_entity(array('label' => $ctype));
   $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
   $term = reset($term);
-  $vocab = $term->vocab;
-
-  if (!array_key_exists($vocab->vocabulary, $response['@context'])) {
-    // If there is no URL prefix then use this API's vocabulary API
-    if ($term->urlprefix) {
-      $response['@context'][$vocab->vocabulary] = $term->urlprefix;
-    }
-    else {
-      $response['@context'][$vocab->vocabulary] = $api_url . '/vocab/' . $vocab->vocabulary . '/';
-    }
-  }
+  $response['@context'][$term->name] = $term->url;
 
   // Start the list.
   $response['@type'] = 'Collection';
   $response['totalItems'] = 0;
   $response['label'] = $bundle->label . " collection";
 
-  // Organize the fields by their web service names.
+  // Iterate through the fields and create a $field_mapping array that makes
+  // it easier to determine which filter criteria belongs to which field.
+  $field_mapping = array();
   $fields = field_info_fields();
-  $field_ws_names = array();
-  foreach ($fields as $field_name => $details) {
-    if (array_key_exists('settings', $details) and
-         array_key_exists('semantic_web', $details['settings'])) {
-      $sw_name = $details['settings']['semantic_web']['name'];
-      $field_ws_names[$sw_name][] = $field_name;
+  foreach ($fields as $field) {
+    if (array_key_exists('TripalEntity', $field['bundles'])) {
+      foreach ($field['bundles']['TripalEntity'] as $bundle_name) {
+        if ($bundle_name == $bundle->name) {
+          if (array_key_exists('semantic_web', $field['settings'])) {
+            list($vocabulary, $accession) = explode(':', $field['settings']['semantic_web']);
+            $term = tripal_get_term_details($vocabulary, $accession);
+            $key = $term['name'];
+            $key = strtolower(preg_replace('/ /', '_', $key));
+            $field_mapping[$key] = $field['field_name'];
+          }
+        }
+      }
+    }
+  }
+
+  // Convert the filters to their field names
+  $new_params = array();
+  foreach ($params as $param => $value) {
+
+    // Break apart any operators
+    $key = $param;
+    $op = '=';
+    $matches = array();
+    if (preg_match('/^(.+);(.+)$/', $key, $matches)) {
+      $key = $matches[1];
+      $op = $matches[2];
+    }
+
+    // Break apart any subkeys and pull the first one out for the term name key.
+    $subkeys = explode(',', $key);
+    if (count($subkeys) > 0) {
+      $key = array_shift($subkeys);
+    }
+
+    // Map the values in the filters to their appropriate field names.
+    if (array_key_exists($key, $field_mapping)) {
+      $field_name = $field_mapping[$key];
+      if (count($subkeys) > 0) {
+        $field_name .= '.' . implode('.', $subkeys);
+      }
+      $new_params[$field_name]['value'] = $value;
+      $new_params[$field_name]['op'] = $op;
+    }
+    else {
+      throw new Exception("The filter term, '$key', is not available for use.");
     }
   }
 
   // Get the list of entities for this bundle.
   $query = new TripalFieldQuery();
-  $query->fieldCondition('content_type', $term->id);
-  foreach($params as $key => $value) {
-    foreach ($field_ws_names[$key] as $field_name) {
-      $query->fieldCondition($field_name, $value);
+  $query->fieldCondition('content_type', $bundle->id);
+  foreach($new_params as $field_name => $details) {
+    $value = $details['value'];
+    switch ($details['op']) {
+      case 'eq':
+        $op = '=';
+        break;
+      case 'gt':
+        $op = '>';
+        break;
+      case 'gte':
+        $op = '>=';
+        break;
+      case 'lt':
+        $op = '<';
+        break;
+      case 'lte':
+        $op = '<=';
+        break;
+      case 'ne':
+        $op = '<>';
+        break;
+      case 'contains':
+        $op = 'CONTAINS';
+        break;
+      case 'starts':
+        $op = 'STARTS WITH';
+        break;
+      default:
+        $op = '=';
     }
+    $query->fieldCondition($field_name, $value, $op);
   }
   $results = $query->execute();
 
-  // Get the entities from the above search.  We do a direct query of the
-  // table because the load_entity() function is too slow.
-  $query = db_select('tripal_entity', 'TE');
-  $query->fields('TE');
-  $query->condition('id', array_keys($results['TripalEntity']));
-  $results = $query->execute();
-
   // Iterate through the entities and add them to the list.
   $i = 0;
-  while($entity = $results->fetchObject()) {
+  foreach ($results['TripalEntity'] as $entity_id => $stub) {
+   $vocabulary = '';
+   $term_name = '';
+
+   // We don't need all of the attached fields for an entity so, we'll
+   // not use the entity_load() function.  Instead just pull it from the
+   // database table.
+   $entity = db_select('tripal_entity', 'TE')
+     ->fields('TE')
+     ->condition('TE.id', $entity_id)
+     ->execute()
+     ->fetchObject();
+
+    //$entity = tripal_load_entity('TripalEntity', array($entity->id));
     $response['member'][] = array(
-      '@id' => $api_url . '/content/' . urlencode($ctype) . '/' .  $entity->id,
-      '@type' => $vocab->vocabulary . ':' . $term->accession,
+      '@id' => url($api_url . '/content/' . urlencode($ctype) . '/' .  $entity->id, array('absolute' => TRUE)),
+      '@type' => $ctype,
       'label' => $entity->title,
       'itemPage' => url('/bio_data/' . $entity->id, array('absolute' => TRUE)),
     );
@@ -416,22 +445,22 @@ function tripal_ws_get_content_type($api_url, &$response, $ws_path, $ctype, $par
   $response['@context']['label'] = 'rdfs:label';
   $response['@context']['itemPage'] = 'schema:itemPage';
 
-  $response['operation'][] = array(
-    '@type' => 'hydra:CreateResourceOperation',
-    'hydra:method' => 'PUT'
-  );
-
-  $response['query'] = array(
-    '@id' => $response['@id'],
-    '@type' => 'IriTemplate',
-    "template" => $response['@id'] . "{?name,}",
-    "mapping" => array(
-      array(
-        "hydra:variable" => 'name',
-        "hydra:property" => 'name',
-      )
-    )
-  );
+//   $response['operation'][] = array(
+//     '@type' => 'hydra:CreateResourceOperation',
+//     'hydra:method' => 'PUT'
+//   );
+
+//   $response['query'] = array(
+//     '@id' => $response['@id'],
+//     '@type' => 'IriTemplate',
+//     "template" => $response['@id'] . "{?name,}",
+//     "mapping" => array(
+//       array(
+//         "hydra:variable" => 'name',
+//         "hydra:property" => 'name',
+//       )
+//     )
+//   );
 }
 
 /**
@@ -442,7 +471,7 @@ function tripal_ws_get_content_type($api_url, &$response, $ws_path, $ctype, $par
  * @param unknown $entity_id
  * @param unknown $params
  */
-function tripal_ws_get_content_add_fields($entity, $bundle, $api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
+function tripal_ws_services_v0_1_get_content_add_fields($entity, $bundle, $api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
 
 
   // Get information about the fields attached to this bundle and sort them
@@ -485,13 +514,14 @@ function tripal_ws_get_content_add_fields($entity, $bundle, $api_url, &$response
     $field_name = $instance['field_name'];
     $field_settings = $field['settings'];
     $key = $field_name;
-    //$key = strtolower(preg_replace('/ /', '_', $key));
+    $key_adj = strtolower(preg_replace('/ /', '_', $key));
     if (array_key_exists('semantic_web', $field_settings) and $field_settings['semantic_web']) {
       list($vocabulary, $accession) = explode(':', $field_settings['semantic_web']);
       $term = tripal_get_term_details($vocabulary, $accession);
       if ($term) {
         $key = $term['name'];
-        $response['@context'][$key] = array(
+        $key_adj = strtolower(preg_replace('/ /', '_', $key));
+        $response['@context'][$key_adj] = array(
           '@id' => $term['url'],
         );
       }
@@ -502,14 +532,13 @@ function tripal_ws_get_content_add_fields($entity, $bundle, $api_url, &$response
     $instance_settings = $instance['settings'];
     if (array_key_exists('auto_attach', $instance_settings) and
         $instance_settings['auto_attach'] != TRUE) {
-      $response['@context'][$key]['@type'] = '@id';
-      $response[$key] = $api_url . '/content/' . $ctype . '/' . $entity->id . '/' . urlencode($key);
+      $response['@context'][$key_adj]['@type'] = '@id';
+      $response[$key_adj] = url($api_url . '/content/' . $ctype . '/' . $entity->id . '/' . urlencode($key), array('absolute' => TRUE));
       continue;
     }
 
     // Get the details for this field for the JSON-LD response.
-    tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_url, $response);
-
+    tripal_ws_services_v0_1_get_content_add_field($key_adj, $entity, $field, $instance, $api_url, $response);
   }
 
   // Lastly, add in the terms used into the @context section.
@@ -535,7 +564,7 @@ function tripal_ws_get_content_add_fields($entity, $bundle, $api_url, &$response
  * @param unknown $entity_id
  * @param unknown $params
  */
-function tripal_ws_get_content_find_field($field_arg, $ctype, $entity_id) {
+function tripal_ws_services_v0_1_get_content_find_field($field_arg, $ctype, $entity_id) {
 
   $bundle = tripal_load_bundle_entity(array('label' => $ctype));
   $entity = tripal_load_entity('TripalEntity', array('id' => $entity_id));
@@ -551,12 +580,12 @@ function tripal_ws_get_content_find_field($field_arg, $ctype, $entity_id) {
     $field_settings = $field['settings'];
     if (array_key_exists('semantic_web', $field_settings) and
         $field_settings['semantic_web']) {
-      list($vocabulary, $accession) = explode(':', $field_settings['semantic_web']);
-      $temp_term = tripal_get_term_details($vocabulary, $accession);
-      if ($temp_term['name'] == $field_arg) {
-        return array($entity, $bundle, $field, $instance, $temp_term);
-      }
-    }
+          list($vocabulary, $accession) = explode(':', $field_settings['semantic_web']);
+          $temp_term = tripal_get_term_details($vocabulary, $accession);
+          if ($temp_term['name'] == $field_arg) {
+            return array($entity, $bundle, $field, $instance, $temp_term);
+          }
+        }
   }
 }
 /**
@@ -569,7 +598,7 @@ function tripal_ws_get_content_find_field($field_arg, $ctype, $entity_id) {
  * @param unknown $params
  * @return number
  */
-function tripal_ws_get_content($api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
+function tripal_ws_services_v0_1_get_content($api_url, &$response, $ws_path, $ctype, $entity_id, $params) {
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
   $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
@@ -581,7 +610,7 @@ function tripal_ws_get_content($api_url, &$response, $ws_path, $ctype, $entity_i
   if (array_key_exists(3, $ws_path)) {
 
     $field_arg = $ws_path[3];
-    list($entity, $bundle, $field, $instance, $term) = tripal_ws_get_content_find_field($field_arg, $ctype, $entity_id);
+    list($entity, $bundle, $field, $instance, $term) = tripal_ws_services_v0_1_get_content_find_field($field_arg, $ctype, $entity_id);
 
     // Next add in the ID and Type for this resources.
     $key = $term['name'];
@@ -592,7 +621,7 @@ function tripal_ws_get_content($api_url, &$response, $ws_path, $ctype, $entity_i
     field_attach_load($entity->type, array($entity->id => $entity), FIELD_LOAD_CURRENT,
         array('field_id' => $field['id']));
 
-    tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_url, $response, TRUE);
+    tripal_ws_services_v0_1_get_content_add_field($key, $entity, $field, $instance, $api_url, $response, TRUE);
 
     return;
   }
@@ -611,7 +640,7 @@ function tripal_ws_get_content($api_url, &$response, $ws_path, $ctype, $entity_i
       $response['@context'][$vocab->vocabulary] = $term->urlprefix;
     }
     else {
-      $response['@context'][$vocab->vocabulary] = $api_url . '/vocab/' . $vocab->vocabulary . '/';
+      $response['@context'][$vocab->vocabulary] = url($api_url . '/vocab/' . $vocab->vocabulary . '/', array('absolute' => TRUE));
     }
   }
 
@@ -620,20 +649,50 @@ function tripal_ws_get_content($api_url, &$response, $ws_path, $ctype, $entity_i
   $entity = reset($entity);
 
   // Next add in the ID and Type for this resources.
-  $response['@id'] = $api_url . '/content/' . $ctype . '/' . $entity_id;
+  $response['@id'] = url($api_url . '/content/' . $ctype . '/' . $entity_id, array('absolute' => TRUE));
   $response['@type'] = $term->name;
   $response['@context'][$term->name] = $term->url;
   $response['label'] = $entity->title;
   $response['itemPage'] = url('/bio_data/' . $entity->id, array('absolute' => TRUE));
 
-  tripal_ws_get_content_add_fields($entity, $bundle, $api_url, $response, $ws_path, $ctype, $entity_id, $params);
+  tripal_ws_services_v0_1_get_content_add_fields($entity, $bundle, $api_url, $response, $ws_path, $ctype, $entity_id, $params);
 
+  //tripal_ws_services_v0_1_write_context($response, $ctype);
 }
 
 /**
  *
+ * @param $response
+ * @param $ctype
  */
-function tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_url, &$response, $is_field_page = NULL) {
+function tripal_ws_services_v0_1_write_context(&$response, $ctype) {
+  // We want to write the context to a file. Try to open the lock file. if we
+  // can't then just leave the context in the response.
+  $context_uri = file_build_uri("ws.v0_1.$ctype.context.jsonld");
+  $context_file = drupal_realpath($context_uri);
+  $context_URL = file_create_url($context_uri);
+  $lock_fp = fopen("$context_file.lock", "w");
+  if (flock($lock_fp, LOCK_EX|LOCK_NB)) {
+    $fp = fopen("$context_file", "w");
+    if ($fp) {
+      $context = array('@context' => $response['@context']);
+      fwrite($fp, json_encode($context));
+      fflush($fp);
+      // Release the lock.
+      flock($lock_fp, LOCK_UN);
+      // Close the files.
+      fclose($lock_fp);
+      fclose($fp);
+      // Change the context to point to the file
+      $response['@context'] = $context_URL;
+    }
+  }
+}
+
+/**
+*
+*/
+function tripal_ws_services_v0_1_get_content_add_field($key, $entity, $field, $instance, $api_url, &$response, $is_field_page = NULL) {
   // Get the field  settings.
   $field_name = $field['field_name'];
   $field_settings = $field['settings'];
@@ -662,11 +721,10 @@ function tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_
 
     // Recurse through the values array and set the entity elemtns
     // and add the fields to the context.
-    tripal_ws_get_content_add_field_context($items[$i], $response, $api_url);
+    tripal_ws_services_v0_1_get_content_add_field_context($items[$i], $response, $api_url);
 
     // Add the remaining values to the $values array.
     $values[] = $items[$i]['value'];
-
   }
 
   // If we only have one value then set the response with just the value.
@@ -693,13 +751,13 @@ function tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_
   // If we have more than one value then set the response to be a collection.
   if (count($values) > 1) {
 
-    // If this is the field page then the Collection is added directly to the
+  // If this is the field page then the Collection is added directly to the
     // response, otherwise, it's added under the field $key.
     if ($is_field_page) {
-      $response['@type'] = 'Collection';
-      $response['totalItems'] = count($values);
-      $response['label'] = $instance['label'];
-      $response['member'] = $values;
+    $response['@type'] = 'Collection';
+        $response['totalItems'] = count($values);
+        $response['label'] = $instance['label'];
+        $response['member'] = $values;
     }
     else {
       $response[$key] = array(
@@ -715,11 +773,11 @@ function tripal_ws_get_content_add_field($key, $entity, $field, $instance, $api_
 /**
  *
  */
-function tripal_ws_get_content_add_field_context(&$items, &$response, $api_url) {
+function tripal_ws_services_v0_1_get_content_add_field_context(&$items, &$response, $api_url) {
 
   foreach ($items as $key => $value) {
     if (is_array($value)) {
-      tripal_ws_get_content_add_field_context($items[$key], $response, $api_url);
+      tripal_ws_services_v0_1_get_content_add_field_context($items[$key], $response, $api_url);
       continue;
     }
 
@@ -729,7 +787,7 @@ function tripal_ws_get_content_add_field_context(&$items, &$response, $api_url)
         $item_entity = tripal_load_entity($item_etype, array($item_eid));
         $item_entity = reset($item_entity);
         $item_term = tripal_load_term_entity(array('term_id' => $item_entity->term_id));
-        $items['@id'] = $api_url . '/content/' . $item_term->name . '/' . $item_eid;
+        $items['@id'] = url($api_url . '/content/' . $item_term->name . '/' . $item_eid, array('absolute' => TRUE));
       }
       unset($items['entity']);
     }
@@ -742,16 +800,16 @@ function tripal_ws_get_content_add_field_context(&$items, &$response, $api_url)
  * @param $api_url
  * @param $response
  */
-function tripal_ws_handle_doc_service($api_url, &$response) {
+function tripal_ws_services_v0_1_handle_doc_service($api_url, &$response) {
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
   $response['@context']['hydra'] = 'http://www.w3.org/ns/hydra/core#';
 
   // Next add in the ID for tihs resource.
   $site_name = variable_get('site_name', '');
-  $response['@id'] = $api_url . '/doc/';
+  $response['@id'] = url($api_url . '/doc/', array('absolute' => TRUE));
   $response['title'] =  $site_name . ": RESTful Web Services API";
-  $response['entrypoint'] = $api_url;
+  $response['entrypoint'] = url($api_url, array('absolute' => TRUE));
   $response['description'] = "A fully queryable REST API using JSON-LD and " .
       "discoverable using the WC3 Hydra specification.";
 
@@ -771,7 +829,7 @@ function tripal_ws_handle_doc_service($api_url, &$response) {
  * @param $response
  * @param $ws_path
  */
-function tripal_ws_handle_no_service($api_url, &$response) {
+function tripal_ws_services_v0_1_handle_no_service($api_url, &$response) {
 
   // First, add the vocabularies used into the @context section.
   $response['@context']['rdfs'] = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
@@ -780,8 +838,7 @@ function tripal_ws_handle_no_service($api_url, &$response) {
   $response['@context']['schema'] = 'https://schema.org/';
 
   // Next add in the ID for tihs resource.
-  $response['@id'] = $api_url;
-
+  $response['@id'] = url($api_url, array('absolute' => TRUE));
 
   // Start the list.
   $response['@type'] = 'Collection';
@@ -791,28 +848,28 @@ function tripal_ws_handle_no_service($api_url, &$response) {
 
   // Start the list.
   $response['member'][] = array(
-    '@id' => $api_url . '/content/',
+    '@id' => url($api_url . '/content/', array('absolute' => TRUE)),
     '@type' => 'Service',
     'label' => 'Content Types',
     'description' => 'Provides acesss to the biological and ' .
-      'ancilliary data available on this site. Each content type ' .
-      'represents biological data that is defined in a controlled vocabulary '.
-      '(e.g. Sequence Ontology term: gene (SO:0000704)).',
+    'ancilliary data available on this site. Each content type ' .
+    'represents biological data that is defined in a controlled vocabulary '.
+    '(e.g. Sequence Ontology term: gene (SO:0000704)).',
   );
   $response['member'][] = array(
-    '@id' => $api_url . '/doc/',
+    '@id' => url($api_url . '/doc/', array('absolute' => TRUE)),
     '@type' => 'Service',
     'label' => 'API Documentation',
     'description' => 'The WC3 Hydra compatible documentation for this API.',
   );
   $response['member'][] = array(
-    '@id' => $api_url . '/vocab/',
+    '@id' => url($api_url . '/vocab/', array('absolute' => TRUE)),
     '@type' => 'Service',
     'label' => 'Vocabulary',
     'description' => 'Defines in-house locally defined vocabulary terms that ' .
-      'have been added specifically for this site.  These terms are typically ' .
-      'added because no other appropriate term exists in another community-vetted '.
-      'controlled vocabulary.',
+    'have been added specifically for this site.  These terms are typically ' .
+    'added because no other appropriate term exists in another community-vetted '.
+    'controlled vocabulary.',
   );
 
   $response['totalItems'] = count($response['member']);

tripal_ws/tripal_ws.module

@@ -29,11 +29,10 @@ function tripal_ws_init() {
 function tripal_ws_menu() {
 
   // Web Services API callbacks.
-  $items['ws/v0.1'] = array(
-    'title' => 'Tripal Entities Web Services API v0.1',
-    'page callback' => 'tripal_ws_rest',
+  $items['ws'] = array(
+    'title' => 'Tripal Web Services API',
+    'page callback' => 'tripal_ws_services',
     'access arguments' => array('access content'),
-    'file' => '/includes/tripal_ws.rest.inc',
     'type' => MENU_CALLBACK,
   );
 
@@ -63,6 +62,38 @@ function tripal_ws_menu() {
   return $items;
 }
 
-function tripal_ws_test() {
-  print "Blah!!!!\n";
+/**
+ * The callback function for all RESTful web services.
+ *
+ */
+function tripal_ws_services() {
+  $ws_path = func_get_args();
+  $params = $_GET;
+  unset($params['q']);
+
+  // The web services should never be cached.
+  drupal_page_is_cacheable(FALSE);
+
+  // Using the provided version number, determine which web services
+  // verion to call.
+  $version = array_shift($ws_path);
+  if ($version and preg_match('/v\d+\.\d+/', $version)) {
+
+    $api_url = 'ws/' . $version;
+
+    // Add the file with the appropriate web services.
+    module_load_include('inc', 'tripal_ws', 'includes/tripal_ws.rest_' . $version);
+    $version = preg_replace('/\./', '_', $version);
+    $function = 'tripal_ws_services_' . $version;
+    $response = array();
+    if (function_exists($function)) {
+      $response = $function($api_url, $ws_path, $params);
+    }
+  }
+  else {
+    // TODO: What do we do if no version is provided?
+  }
+
+  drupal_add_http_header('Content-Type', 'application/ld+json');
+  print drupal_json_encode($response);
 }