Advanced Search

docker-compose.yml

@@ -9,6 +9,20 @@ services:
       - .:/modules/tripal_elasticsearch
       - ./vendor:/var/www/html/sites/all/libraries/elasticsearch-php
   elasticsearch:
-    image: 'elasticsearch:6.5.4'
+    image: 'elasticsearch:6.6.1'
     ports:
       - "9201:9200"
+    volumes:
+      - es_data:/usr/share/elasticsearch/data
+      - ./synonyms:/usr/share/elasticsearch/config/analysis
+  kibana:
+    image: 'kibana:6.6.1'
+    ports:
+      - "5601:5601"
+    environment:
+      ELASTICSEARCH_URL: "http://elasticsearch:9200"
+      ELASTICSEARCH_HOSTS: "http://elasticsearch:9200"
+      SERVER_HOST: "0.0.0.0"
+
+volumes:
+  es_data:

docs/cross-site-search.md

@@ -31,4 +31,4 @@ to provide the url path to the block.
 
 **Next section: [Elasticsearch Daemon](/docs/daemon.md)**
 
-**[Return to Handbook Index](/docs)**
+'**[Return to Handbook Index](README.md)**

docs/custom-indices.md

@@ -25,4 +25,4 @@ For a custom index, you will need to:
 
 **Next section: [Building Search Forms](/docs/forms.md)**
 
-**[Return to Handbook Index](/docs)**
+'**[Return to Handbook Index](README.md)**

docs/default-indices.md

@@ -16,6 +16,10 @@ Next, you'll need to activate the `Tripal Elasticsearch website search box` bloc
 Tripal Elasticsearch also provides a default index for Tripal 3 entities. To activate the index, follow the same procedure
 as the website nodes index above, selecting "Entities" from the dropdown list when creating the index.
 
+# Warning!
+
+Before running the indexer, please make sure that your content types have the correct permissions. The indexer is only allowed to access content as an anonymous user. This prevents it from indexing private content that only administrators or authenticated users should be able to access.
+
 ### Create, Update and Delete Pages
 
 Whenever you create a new page, update existing pages or delete pages, indexing jobs will automatically 
@@ -41,4 +45,4 @@ If this setup is satisfied, you can run the indexing job in the same manner as o
 
 **Next section: [Building Custom Indices](/docs/custom-indices.md)**
 
-**[Return to Handbook Index](/docs)**
+'**[Return to Handbook Index](README.md)**

docs/forms.md

@@ -28,4 +28,4 @@ If you choose a `select` field type, you must provide **key|value** pairs to bui
 
 **Next section: [Cross Site Searching](/docs/cross-site-search.md)**
 
-**[Return to Handbook Index](/docs)**
+'**[Return to Handbook Index](README.md)**

docs/indexing.md

@@ -10,4 +10,6 @@ For details about indexing operations, please visit [Elasticsearch's documentati
 - [Building Custom Indices](custom-indices.md)
 
 
-**[Return to Handbook Index](/docs)**
+**Next Section: [Running Indexing Queues](queues.md)**
+
+'**[Return to Handbook Index](README.md)**

docs/installation.md

@@ -57,4 +57,4 @@ After connecting a remote server, it will be displayed in the remote server heal
 
 **Next section: [What Is Indexing?](/docs/indexing.md)**
 
-**[Return to Handbook Index](/docs)**
+'**[Return to Handbook Index](README.md)**

docs/queues.md

@@ -30,3 +30,5 @@ right of each cron queue. At the bottom of the page, the URL will display. The c
 the URL. For example, the cron job name is `queue_elasticsearch_queue_1` in the example below:
 
 ![cron job name](../images/get-cron-name.png)
+
+**Next Section: [Indexing](indexing.md)**

includes/Common/BundleHelper.php

@@ -0,0 +1,186 @@
+<?php
+
+namespace ES\Common;
+
+class BundleHelper{
+
+  /**
+   * Gets a list of bundles with their associated cv terms and accessions.
+   *
+   * @return array
+   *   An array of bundles.
+   */
+  public function getBundles() {
+    $query = db_query(
+      'SELECT tb.name AS name,
+            tb.label AS label,
+            tb.type AS type,
+            tb.term_id AS term_id,
+            tv.vocabulary AS cv_name,
+            tt.accession AS accession
+      FROM tripal_bundle tb
+      INNER JOIN tripal_term tt ON tb.term_id = tt.id
+      INNER JOIN tripal_vocab tv ON tt.vocab_id = tv.id'
+    );
+    return $query->fetchAll();
+  }
+
+  /**
+   * @param $name
+   *
+   * @return mixed
+   */
+  public function getBundleByName($name) {
+    $query = db_query(
+      'SELECT tb.name AS name,
+            tb.label AS label,
+            tb.type AS type,
+            tb.term_id AS term_id,
+            tv.vocabulary AS cv_name,
+            tt.accession AS accession
+      FROM tripal_bundle tb
+      INNER JOIN tripal_term tt ON tb.term_id = tt.id
+      INNER JOIN tripal_vocab tv ON tt.vocab_id = tv.id
+      WHERE tb.name = :name',
+      [
+        ':name' => $name,
+      ]
+    );
+    return $query->fetchObject();
+  }
+
+  /**
+   * Given a term and accession, get all bundles.
+   *
+   * @param string $cv_name The vocabulary name such as NCIT.
+   * @param string $accession The accession such as 0000044.
+   *
+   * @return array|null
+   *    An array of bundles. Null if no bundles exist.
+   */
+  public function getBundleByTerm($cv_name, $accession) {
+    // Get the bundle
+    $bundles = db_query(
+      'SELECT tb.name AS name,
+              tb.label AS label,
+              tb.type AS type,
+              tb.term_id AS term_id,
+              tv.vocabulary AS cv_name,
+              tt.accession AS accession
+      FROM tripal_bundle tb
+      INNER JOIN tripal_term tt ON tb.term_id = tt.id
+      INNER JOIN tripal_vocab tv ON tt.vocab_id = tv.id
+      WHERE tv.vocabulary = :cv_name 
+            AND tt.accession = :accession',
+      [
+        ':cv_name' => $cv_name,
+        ':accession' => $accession,
+      ]
+    )->fetchAll();
+
+    if (count($bundles) === 0) {
+      return NULL;
+    }
+
+    return $bundles;
+  }
+
+  /**
+   * Given a bundle, get all available fields.
+   *
+   * @param object $bundle The bundle object as returned from the db
+   *   (tripal_bundle table).
+   *
+   * @return array|mixed
+   */
+  public function getFieldsByBundle($bundle) {
+    $fields = field_info_instances($bundle->type, $bundle->name);
+
+    // Format the results into a simple low-memory array
+    $formatted = [];
+    foreach ($fields as $field => $data) {
+      $formatted[] = (object) [
+        'id' => $data['id'],
+        'name' => $field,
+        'label' => $data['label'],
+      ];
+    }
+
+    return $formatted;
+  }
+
+  /**
+   * Get a list of fields for all bundles that match the given term.
+   *
+   * @param string $cv_name The vocabulary name.
+   * @param string $accession The term accesstion.
+   *
+   * @return array|null
+   *   The list of array as ['id', 'name', 'label']. Null if no bundle exists.
+   */
+  public function getFieldsByBundleTerm($cv_name, $accession) {
+    $bundles = $this->getBundleByTerm($cv_name, $accession);
+
+    if (is_null($bundles)) {
+      return NULL;
+    }
+
+    // It is likely that this loop will run only once since the possibility of
+    // having multiple bundles matching a single term is extra rare. We have to
+    // do this since there is no DB constraint on the aforementioned assertion.
+    $fields = [];
+    foreach ($bundles as $bundle) {
+      $fields = $fields + $this->getFieldsByBundle($bundle);
+    }
+
+    return $fields;
+  }
+
+  /**
+   * Gets node types in the same format as bundles.
+   *
+   * @return array
+   *    A list of node types.
+   */
+  public function getNodeTypes() {
+    $node_types = db_select('node_type', 'nt')
+      ->fields('nt', ['type', 'name'])
+      ->execute()
+      ->fetchAll();
+
+    $categories = [];
+
+    foreach ($node_types as $node_type) {
+      $categories[] = [
+        'name' => $node_type->type,
+        'label' => $node_type->name,
+        'type' => 'node',
+        'term_id' => NULL,
+        'cv_term' => NULL,
+        'accession' => NULL,
+        'fields' => [],
+      ];
+    }
+
+    return $categories;
+  }
+
+  /**
+   * Get a list of bundles and attach fields.
+   *
+   * @return array
+   *   A list of bundles with fields attached.
+   */
+  public function getBundlesWithFields() {
+    $bundles = $this->getBundles();
+
+    $categories = [];
+    foreach ($bundles as $bundle) {
+      $fields = $this->getFieldsByBundle($bundle);
+      $bundle->fields = $fields;
+      $categories[] = $bundle;
+    }
+
+    return $categories;
+  }
+}