Fixed a few bugs, pager is now working for base collection

tripal_core/api/tripal_core.chado_variables.api.inc

@@ -55,7 +55,7 @@
  *     should specify the number of records to return and 'element' is a
  *     unique integer to differentiate between pagers when more than one
  *     appear on a page.  The 'element' should start with zero and increment by
- *     one for each pager.  This only works when type is a 'table'.
+ *     one for each pager.
  * @return
  *   Either an object (if only one record was selected from the base table)
  *   or an array of objects (if more than one record was selected from the base table).

tripal_core/includes/tripal_core.ws_hal.inc

@@ -14,10 +14,13 @@ function tripal_core_chado_hal_api() {
   $page_limit = 25;
   $pager_id = 0;
   
+  // Lump everything ito a try block so that if there is a problem we can
+  // throw an error and have that returned in the response.
   try {
     $id = 0;
     $action = '';
     
+    // GET THE BASE TABLE TO QUERY
     // The table name is always specifid as the 3rd argument in the 
     // current Drupal path.
     $table_name = arg(3);
@@ -27,11 +30,15 @@ function tripal_core_chado_hal_api() {
     $schema = chado_get_schema($table_name);
     $pkey = $schema['primary key'][0];
     
+    // GET THE RECORD AND THE ACTION TO PERFORM
     // If the fourth argument is numeric then the user is requesting a
     // record from the table.  Otherwise the users is specifying an
     // action to perform on the table.
     if (is_numeric(arg(4))) {
       $id = arg(4);
+      if (arg(5)) {
+        $action = arg(5);
+      }
     }
     else {
       $action = arg(4);
@@ -40,60 +47,93 @@ function tripal_core_chado_hal_api() {
     // Get any URL query arguments
     $query = drupal_get_query_parameters();
     
-    // Specify the options for retrieving data.
-    $options = array(
-      'return_array' => 1,
-      'pager' => array(
-        'limit' => $page_limit, 
-        'element' => $pager_id
-      ),
-    );
-    
-    // Specify the values for selecing records.
-    $values = array();
-    if ($id) {
-      $values[$pkey] = $id;
-    }
-  
-    // Generate the chado variable.
-    $var = chado_generate_var($table_name, $values, $options);
+    switch ($action) {
+      case 'schema':
+        $result = $schema;
+        break;
+      case 'add':
+        $message = "Action, '$action', is currently not supported.";
+        $result = array();
+        break;
+      default: 
+        // Specify the values for selecing records.
+        $values = array();
+        if ($id) {
+          $values[$pkey] = $id;
+        }
 
-    // Links come first
-    $result['_links'] = array('self' => array('href' => "$api_url/$table_name"));
-    
-    // If we have more than one record returned then this is a collection and
-    // we should create the appropriate JSON for a collection.
-    if (count($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;
-      
-      // Do any expansion requested.
-      $var = tripal_core_chado_ws_api_expand_object($var, $query);
+        // Specify the options for retrieving data.
+        $options = array(
+          'return_array' => 1,
+          'pager' => array(
+            'limit' => $page_limit,
+            'element' => $pager_id
+          ),
+        );
+        
+        // Generate the chado variable.
+        $var = chado_generate_var($table_name, $values, $options);
   
-      // 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, $query);
-        $result['_embedded'][$table_name][] = $item;
-      }
-    }
-    // If we only have one record then add it as a single record to the JSON.
-    else {
-
-      // Do any expansion requested.
-      $var = tripal_core_chado_ws_api_expand_object($var, $query);
+        // If we have more than one record returned then this is a collection and
+        // we should create the appropriate JSON for a collection.
+        if (count($var) > 1) {
+          
+          // Get the total number of records
+          $total = chado_pager_get_count($pager_id);
+          $curr_page = array_key_exists('page', $query) ? $query['page'] : 0;
+          
+          $first_page = '0';
+          $last_page = ceil($total / $page_limit) - 1;
+          $result['_links']['first'] = array('href' => "$api_url/$table_name");
+          if ($curr_page > 0) {
+            $prev_page = $curr_page - 1;
+            if ($prev_page != $first_page) {
+              $result['_links']['previous'] = array('href' => "$api_url/$table_name?page=$prev_page");
+            }
+            else {
+              $result['_links']['previous'] = $result['_links']['first'];
+            }
+          }
+          if ($curr_page < $last_page) { 
+            $next_page = $curr_page + 1;
+            $result['_links']['next'] = array('href' => "$api_url/$table_name?page=$next_page");
+          }
+          if ($last_page > $first_page) {
+            $result['_links']['last'] = array('href' => "$api_url/$table_name?page=$last_page");
+          }
 
-      $table_name = $item->tablename;
-      $item = tripal_core_chado_ws_api_object_format($var, $schema, $api_url, $query);
-      $result = $item;
+          // Add the number of elements for this collection
+          $result['count'] = count($var);
+          $result['total'] = (integer) $total;
+          $result['current_page'] = (integer) $curr_page;
+          $result['items_per_page'] = $page_limit;
+          
+          // Do any expansion requested.
+          if ($action == 'expand') {
+            $var = tripal_core_chado_ws_api_expand_object($var, $query);
+          }
+    
+          // recursively reformat the expanded objects to match HAL requirements.
+          foreach ($var as $item) {
+            $table_name = $item->tablename;
+    
+            $item = tripal_core_chado_ws_api_object_format($item, $schema, $api_url, $query);
+            $result['_embedded'][$table_name][] = $item;
+          }
+        }
+        // If we only have one record then add it as a single record to the JSON.
+        else {
+          $item = $var[0];
+          
+          // Do any expansion requested.
+          if ($action == 'expand') {
+            $item = tripal_core_chado_ws_api_expand_object($item, $query);
+          }
+    
+          // recursively reformat the expanded objects to match HAL requirements.
+          $item = tripal_core_chado_ws_api_object_format($item, $schema, $api_url, $query);
+          $result = $item;
+        }
     }
   }
   catch (Exception $e) {
@@ -118,6 +158,7 @@ function tripal_core_chado_hal_api() {
  * @param unknown $query
  */
 function tripal_core_chado_ws_api_expand_object($var, $query) {
+
   $page_limit = 25;
   $pager_id = 0;
   $options = array(
@@ -127,10 +168,10 @@ function tripal_core_chado_ws_api_expand_object($var, $query) {
       'element' => $pager_id
     ),
   );
-  
+
   // If the user has requested to expand any fields then do that
-  if ($query['expand_table']) {
-    $expand_tables = explode(',', $query['expand_table']);
+  if ($query['table']) {
+    $expand_tables = explode(',', $query['table']);
     foreach($expand_tables as $table) {
       // Does the table exist?
       if(!chado_table_exists($table)) {
@@ -151,26 +192,20 @@ function tripal_core_chado_ws_api_expand_object($var, $query) {
       }
     }
   }
-  if ($query['expand_field']) {
-    $expand_fields = explode(',', $query['expand_field']);
+  if ($query['field']) {
+    $expand_fields = explode(',', $query['field']);
     foreach($expand_fields as $field) {
       // TODO: check to make sure the field exists
       $var = chado_expand_var($var, 'field', $field);
     }
   }
-  if ($query['expand_fkey']) {
-    $expand_fkeys = explode(',', $query['expand_fkey']);
+  if ($query['fkey']) {
+    $expand_fkeys = explode(',', $query['fkey']);
     foreach($expand_fkeys as $fkey) {
       // TODO: check to make sure the fkey exists
       $var = chado_expand_var($var, 'foreign_key', $fkey);
     }
   }
-  if ($query['expand_node']) {
-    $node_types = explode(',', $query['expand_node']);
-    foreach($node_types as $node_type) {
-      $var = chado_expand_var($var, 'node', $node_type);
-    }
-  }
   return $var;
 }
 
@@ -181,6 +216,7 @@ function tripal_core_chado_ws_api_expand_object($var, $query) {
  * @param $api_url
  */
 function tripal_core_chado_ws_api_object_format($object, $schema, $api_url, $query) {
+
   global $base_url;
   $table_name = $object->tablename;
   $pkey = $schema['primary key'][0];
@@ -202,9 +238,24 @@ function tripal_core_chado_ws_api_object_format($object, $schema, $api_url, $que
     $object->_links["delete"] = array('href' => "$api_url/$table_name/$id/delete");
   }
     
-  // Add the link to the Drupal page.
-  if ($object->nid) {
+  // Add the link to the Drupal page if a node exists.
+  if (property_exists($object, 'nid')) {
     $object->_links["view"] = array('href' => $base_url . url("node/$object->nid"));
+    // Unset the node ID because it's really only needed within the context
+    // of the local Drupal site.
+    unset($object->nid);
+  }
+  
+  // It doesn't make sense to allow expansion of node information outside
+  // of the context of the local Drupal site so remove this object.
+  unset($object->expandable_nodes);
+  
+  // Only include links for expanding if the option to exclude them has not
+  // been passed.
+  if (array_key_exists('no_expansion_details', $query)) {
+     unset($object->expandable_fields);
+     unset($object->expandable_foreign_keys);
+     unset($object->expandable_tables);
   }
   
   // Deal with the expandable tables/fields/fkeys/nodes. Sometimes there are
@@ -212,48 +263,44 @@ function tripal_core_chado_ws_api_object_format($object, $schema, $api_url, $que
   // 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
-  // TODO: making a single key be an array may not be correct for HAL. check this out.
-  if (count($object->expandable_fields) > 0) {
-    $object->_links["expand_field"][] = array('href' => "$api_url/$table_name?expand_field={field}[,{field}...]");
-    $object->_links["expand_field"][] = array('href' => "$api_url/$table_name/$id?expand_field={field}[,{field}...]");
-  }
-  else {
-    unset($object->expandable_fields);
-  }
-  if (count($object->expandable_foreign_keys) > 0) {
-    $object->_links["expand_fkey"][] = array('href' => "$api_url/$table_name?expand_fkey={fkey}[,{fkey}...]");
-    $object->_links["expand_fkey"][] = array('href' => "$api_url/$table_name/$id?expand_fkey={fkey}[,{fkey}...]");
-  }
-  else {
-    unset($object->expandable_foreign_keys);
-  }
-  if (count($object->expandable_nodes) > 0) {
-    $object->_links["expand_node"][] = array('href' => "$api_url/$table_name?expand_node={node}[,{node}...]");
-    $object->_links["expand_node"][] = array('href' => "$api_url/$table_name/$id?expand_node={node}[,{node}...]");
-  }
-  else {
-    unset($object->expandable_nodes);
+  if (array_key_exists('expandable_tables', $object)) {
+    $object->expandable_tables = array_values($object->expandable_tables);
+    if (count($object->expandable_tables) > 0) {
+      $object->_links["expand_table"][] = array('href' => "$api_url/$table_name/expand?table={table}[,{table}...]");
+      $object->_links["expand_table"][] = array('href' => "$api_url/$table_name/$id/expand?table={table}[,{table}...]");
+    }
+    else {
+      unset($object->expandable_tables);
+    }
   }
-  if (count($object->expandable_tables) > 0) {
-    $object->_links["expand_table"][] = array('href' => "$api_url/$table_name?expand_table={table}[,{table}...]");
-    $object->_links["expand_table"][] = array('href' => "$api_url/$table_name/$id?expand_table={table}[,{table}...]");
+  if (array_key_exists('expandable_fields', $object)) {
+    $object->expandable_fields = array_values($object->expandable_fields);
+    if (count($object->expandable_fields) > 0) {
+      $object->_links["expand_field"][] = array('href' => "$api_url/$table_name/expand?field={field}[,{field}...]");
+      $object->_links["expand_field"][] = array('href' => "$api_url/$table_name/$id/expand?field={field}[,{field}...]");
+    }
+    else {
+      unset($object->expandable_fields);
+    }
   }
-  else {
-    unset($object->expandable_tables);
+  if (array_key_exists('expandable_foreign_keys', $object)) {
+    $object->expandable_foreign_keys = array_values($object->expandable_foreign_keys);
+    if (count($object->expandable_foreign_keys) > 0) {
+      $object->_links["expand_fkey"][] = array('href' => "$api_url/$table_name/expand?fkey={fkey}[,{fkey}...]");
+      $object->_links["expand_fkey"][] = array('href' => "$api_url/$table_name/$id/expand?fkey={fkey}[,{fkey}...]");
+    }
+    else {
+      unset($object->expandable_foreign_keys);
+    }
   }
   
   // iterate through the items in the object and see if they in turn are
   // objects.  If so, then recurse.
   foreach ($object as $key => $value) {
+    
     // If any values are objects then recurse and format them correctly.
     if (is_object($value)) {
+
       $table_name = $value->tablename;
       $schema = chado_get_schema($table_name);
       if ($schema) {
@@ -263,12 +310,13 @@ function tripal_core_chado_ws_api_object_format($object, $schema, $api_url, $que
           $object->$key = $value->$key;
         }
         else {
-          unset($object->key);
+          unset($object->$key);
         }
         // Recursively format the object.
         $value = tripal_core_chado_ws_api_object_format($value, $schema, $api_url, $query);
         // Add the object as an "_embedded" object of the JSON.
-        if (array_key_exists($table_name, $object->_embedded)) {
+        if (property_exists($object,'_embedded') and 
+            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[$table_name])) {
@@ -293,5 +341,9 @@ function tripal_core_chado_ws_api_object_format($object, $schema, $api_url, $que
     }
   }
   
+  if (array_key_exists('no_links', $query)) {
+    unset($object->_links);
+  }
+  
   return $object;
 }