Merge pull request #187 from tripal/deal-with-blastdb

Add exception to remove blast database nodes

docker-compose.yml

@@ -11,4 +11,4 @@ services:
   elasticsearch:
     image: 'elasticsearch:5'
     ports:
-      - "9200:9200"
+      - "9201:9200"

includes/Elasticsearch/ESInstance.php

@@ -293,18 +293,25 @@ public function setIndexParams($index_name, $shards = 5, $replicas = 0,
    * Perform the actual search.
    * Use this function after setting the search params.
    *
+   * @param bool $return_source whether to format the results or not.
+   *
    * @see \ESInstance::setTableSearchParams()
    * @see \ESInstance::setWebsiteSearchParams()
    *
    * @return array
    * @throws \Exception
    */
-  public function search() {
+  public function search($return_source = false) {
     if (empty($this->searchParams)) {
       throw new Exception('Please build search parameters before attempting to search.');
     }
 
     $hits = $this->client->search($this->searchParams);
+
+    if($return_source) {
+      return $hits;
+    }
+
     $results = [];
     foreach ($hits['hits']['hits'] as $hit) {
       if (isset($hit['highlight'])) {

includes/Jobs/NodesIndexJob.php

@@ -194,6 +194,7 @@ public function total() {
    * @return int
    */
   public function count() {
-    return db_query('SELECT COUNT(nid) FROM {node} WHERE status=1')->fetchField();
+    return db_query('SELECT COUNT(nid) FROM {node} N
+                      WHERE status=1 AND type != :type', [':type' => 'blastdb'])->fetchField();
   }
 }

tripal_elasticsearch.install

@@ -134,13 +134,13 @@ function tripal_elasticsearch_uninstall() {
 
   // Auto drop anything in the schema
   foreach ($schema as $table => $fields) {
-    if(db_table_exists($table)) {
+    if (db_table_exists($table)) {
       db_drop_table($table);
     }
   }
 
   // Drop tables that are created in the update functions
-  if(db_table_exists('tripal_elasticsearch_indices')) {
+  if (db_table_exists('tripal_elasticsearch_indices')) {
     db_drop_table('tripal_elasticsearch_indices');
   }
 }
@@ -380,3 +380,49 @@ function tripal_elasticsearch_update_7209() {
     throw $exception;
   }
 }
+
+/**
+ * Remove blast database content type from website index.
+ *
+ * @throws \Exception
+ */
+function tripal_elasticsearch_update_7210() {
+  try {
+    $es = new ESInstance();
+    $count = $es->setWebsiteSearchParams('*', 'Blast Database', 'website')
+      ->count();
+    $client = $es->client;
+
+    if ($count === 0) {
+      print "No blast database content was found\n";
+      return;
+    }
+
+    for ($i = 0; $i < $count; $i += 100) {
+      $results = $es->setWebsiteSearchParams('*', 'Blast Database', 'website', 'website', [
+        $i,
+        100,
+      ])->search(FALSE);
+      foreach ($results as $result) {
+        $client->deleteByQuery([
+          'index' => 'website',
+          'type' => 'website',
+          'body' => [
+            'query' => [
+              'match' => [
+                'nid' => $result['nid'],
+              ],
+            ],
+          ],
+        ]);
+      }
+    }
+
+    print "Successfully removed all blast database nodes from website index.\n";
+  } catch (Exception $exception) {
+    print "ERROR: failed to remove blast database nodes from website index due to the following exception\n";
+    print $exception->getMessage();
+
+    throw $exception;
+  }
+}