Beginning of Chado Web Service API

tripal_core/includes/tripal_core.ws_hal.inc

@@ -0,0 +1,177 @@
+<?php 
+
+
+function tripal_core_chado_hal_api() {
+  global $base_url;
+
+  // Set some initial variables.
+  $response = array();
+  $result = array();
+  $status = 'success';
+  $version = '0.1';
+  $message = '';
+  $api_url = "$base_url/ws/chado/$version";
+  
+  try {
+    $table_name = arg(3);
+    $schema = chado_get_schema($table_name);
+    if (!$schema) {
+      throw new Exception("Table $table_name is not a valid table.");
+    }
+  
+    $limit = 25;
+    $pager_id = 0;
+    
+    $options = array(
+      'return_array' => 1,
+      'pager' => array(
+        'limit' => $limit, 
+        'element' => $pager_id
+      ),
+    );
+    $values = array();
+  
+    $var = chado_generate_var($table_name, $values, $options);
+    
+    
+    // Links come first
+    $result['_links'] = array('self' => array('href' => "$api_url/$table_name"));
+    
+    if (count($var) > 1) {
+      $total = chado_pager_get_count($pager_id);
+      // Add pager links
+      $result['_links']['first'] = array('href' => "$api_url/$table_name");
+      $result['_links']['prev']  = array('href' => "$api_url/$table_name?page=2");
+      $result['_links']['next']  = array('href' => "$api_url/$table_name?page=4");
+      $result['_links']['last']  = array('href' => "$api_url/$table_name?page=12");
+      
+      $result['count'] = count($var);
+      $result['total'] = (integer) $total;
+  
+      // Collection names are always plural of the table name
+      foreach ($var as $item) {
+        $table_name = $item->tablename;
+  
+        $item = tripal_core_chado_ws_api_object_format($item, $schema, $api_url);
+        $result['_embedded'][$table_name][] = $item;
+      }
+    }
+  }
+  catch (Exception $e) {
+    watchdog('tripal_ws', $e->getMessage(), array(), WATCHDOG_ERROR);
+    $message = $e->getMessage();
+    $status = 'error';
+    $result = array();
+  }
+  
+  // The responses follow the same format as the AGAVE API with a
+  // status, message, version and all data in the "result" object.
+  $response['status']  = $status;
+  $response['message'] = $message;
+  $response['version'] = $version;
+  $response['result']  = $result;
+  print drupal_json_output($response);
+}
+
+/**
+ * 
+ * @param $object
+ * @param $schema
+ * @param $api_url
+ */
+function tripal_core_chado_ws_api_object_format($object, $schema, $api_url) {
+  global $base_url;
+  $table_name = $object->tablename;
+  $pkey = $schema['primary key'][0];
+  $id = $object->$pkey;
+
+  // Add the self link.
+  $object->_links = array('self' => array('href' => "$api_url/$table_name/$id"));
+  
+  // Add the schema link.
+  $object->_links["schema"] = array('href' => "$api_url/$table_name/schema");
+  
+  // Add links for editing, insert, delete but only if user has permission.
+  // TODO: how do we set permissions?
+  $object->_links["add"] = array('href' => "$api_url/$table_name/add");
+  $object->_links["edit"] = array('href' => "$api_url/$table_name/$id/edit");
+  $object->_links["delete"] = array('href' => "$api_url/$table_name/$id/delete");
+  
+  // Add the link to the Drupal page.
+  if ($object->nid) {
+    $object->_links["view"] = array('href' => $base_url . url("node/$object->nid"));
+  }
+  
+  // Deal with the expandable tables/fields/fkeys/nodes. Sometimes there are
+  // specified in PHP with explicit numerical indexes and sometimes not. But,
+  // the JSON converter will maintain the indexes if present which creates
+  // an inconsistent look. So, we use the array_values function to just
+  // get the list. 
+  $object->expandable_tables = array_values($object->expandable_tables);
+  $object->expandable_fields = array_values($object->expandable_fields);
+  $object->expandable_foreign_keys = array_values($object->expandable_foreign_keys);
+  $object->expandable_nodes = array_values($object->expandable_nodes);
+
+  
+  // Add the links for the expandable fields, fkeys, nodes and tables
+  if (count($object->expandable_fields) > 0) {
+    $object->_links["expand_field"] = array('href' => "$api_url/$table_name/$id?expand_field={field}");
+  }
+  else {
+    unset($object->expandable_fields);
+  }
+  if (count($object->expandable_foreign_keys) > 0) {
+    $object->_links["expand_fkey"] = array('href' => "$api_url/$table_name/$id?expand_fkey={fkey}");
+  }
+  else {
+    unset($object->expandable_foreign_keys);
+  }
+  if (count($object->expandable_nodes) > 0) {
+    $object->_links["expand_node"] = array('href' => "$api_url/$table_name/$id?expand_node={node}");
+  }
+  else {
+    unset($object->expandable_nodes);
+  }
+  if (count($object->expandable_tables) > 0) {
+    $object->_links["expand_table"] = array('href' => "$api_url/$table_name/$id?expand_table={table}");
+  }
+  else {
+    unset($object->expandable_tables);
+  }
+  
+  // iterate through the items in the object and see if they in turn are
+  // objects.  If so, then recurse.
+   foreach ($object as $key => $value) {
+     if (is_object($value)) {
+        $table_name = $value->tablename;
+        $schema = chado_get_schema($table_name);
+        if ($schema) {
+          // Replace the object with the actual value.
+          $object->$key = $value->$key;
+          // Recursively format the object.
+          $value = tripal_core_chado_ws_api_object_format($value, $schema, $api_url);
+          // Add the object as an "_embedded" object of the JSON.
+          if (array_key_exists($table_name, $object->_embedded)) {
+            // If the element is already an array then add to it, otherwise
+            // convert it into an array.
+            if (is_array($object->_embedded[$table_name])) {
+              $object->_embedded[$table_name][] = $value;
+            }
+            else {
+              $first = $object->_embedded[$table_name];
+              $object->_embedded[$table_name] = array();
+              $object->_embedded[$table_name] = $first;
+              $object->_embedded[$table_name][] = $value;
+            }
+          }
+          // This is the first time this embedded table has been seen
+          // there fore, add the value as a single element.
+          else {
+            $object->_embedded[$table_name] = $value;
+          }
+        } 
+     }
+   }
+  
+  return $object;
+}

tripal_core/tripal_core.module

@@ -376,6 +376,15 @@ function tripal_core_menu() {
     'type' => MENU_LOCAL_TASK,
     'file' => '/includes/tripal_core.toc.inc',
   );
+  
+  // Web Services API callbacks.
+  $items['ws/chado/v1.0'] = array(
+    'title' => 'Tripal Web Services API v1.0',
+    'page callback' => 'tripal_core_chado_hal_api',
+    'access arguments' => array('access content'),
+    'type' => MENU_CALLBACK,
+    'file' => '/includes/tripal_core.ws_hal.inc',
+  );
 
   return $items;
 }

tripal_organism/tripal_organism.info

@@ -9,4 +9,6 @@ configure = admin/tripal/chado/tripal_organism
 stylesheets[all][] = theme/css/tripal_organism.css
 
 dependencies[] = tripal_core
+dependencies[] = tripal_cv
+dependencies[] = tripal_db
 dependencies[] = tripal_views