Merge pull request #1585 from tripal/tv4g2-1571-cvtermAutocompleteFilter

Cvterm autocomplete needs filter by cv

tripal_chado/src/Controller/ChadoCVTermAutocompleteController.php

@@ -11,51 +11,61 @@
  */
 class ChadoCVTermAutocompleteController extends ControllerBase {
   /**
-   * Contoller method, autocomplete cvterm name.
-   * 
+   * Controller method, autocomplete cvterm name.
+   *
    * @param Request request
-   * @param int $cv
-   *   @TODO: Limit the match of term to a CV.
+   *
    * @param int $count
    *   Desired number of matching names to suggest.
    *   Default to 5 items.
-   * 
+   *   Zero will disable autocomplete.
+   *
+   * @param int $cv_id
+   *   Limit the match of term to the CV with this cv_id.
+   *   Zero, the default, will return matches to any CV.
+   *
    * @return Json Object
    *   Matching cvterm rows where each row is formatted as string:
    *   cvterm.name (db.name:dbxref.accession) and is the value for
    *   the object keys label and value.
    */
-  public function handleAutocomplete(Request $request, int $count = 5) {
+  public function handleAutocomplete(Request $request, int $count = 5, int $cv_id = 0) {
     // Array to hold matching cvterm names.
     $response = [];
-    
+
     if ($request->query->get('q')) {
       // Get typed in string input from the URL.
       $string = trim($request->query->get('q'));
-      
+
       if (strlen($string) > 0 && $count > 0) {
         // Proceed to autocomplete when string is at least a character
         // long and result count is set to a value greater than 0.
 
-        // Transform string as a search keyword pattern.
-        $keyword = '%' . strtolower($string) . '%';
+        // Transform string as a case-insensitive search keyword pattern.
+        $keyword = strtolower($string) . '%';
 
-        // Query cvterm (joins: dbxref - accession and db - dn name) for names matching 
-        // the keyword pattern and return each row in the format specified. 
+        // Query cvterm (joins: dbxref - accession and db - dn name) for names matching
+        // the keyword pattern and return each row in the format specified.
         // Tables indicate schema sequence number #1 to use default schema.
-        $sql = sprintf("
+        $sql = "
           SELECT ct.name AS term, db.name AS dbname, dx.accession
-          FROM {1:cvterm} AS ct 
-            LEFT JOIN {1:dbxref} AS dx USING(dbxref_id) 
+          FROM {1:cvterm} AS ct
+            LEFT JOIN {1:dbxref} AS dx USING(dbxref_id)
             LEFT JOIN {1:db} USING(db_id)
-          WHERE LOWER(ct.name) LIKE :keyword ORDER BY ct.name ASC LIMIT %d
-        ", $count);
+          WHERE LOWER(ct.name) LIKE :keyword";
+        $args = [':keyword' => $keyword, ':limit' => $count];
+        // Limit terms to selected CV when this is specified.
+        if ($cv_id) {
+          $sql .= " AND ct.cv_id = :cv_id";
+          $args[':cv_id'] = $cv_id;
+        }
+        $sql .= " ORDER BY ct.name ASC LIMIT :limit";
 
-        // Prepare Chado database connection and execute sql query by providing value 
+        // Prepare Chado database connection and execute sql query by providing value
         // for :keyword placeholder text.
         $connection = \Drupal::service('tripal_chado.database');
-        $results = $connection->query($sql, [':keyword' => $keyword]);  
-        
+        $results = $connection->query($sql, $args);
+
         // Compose response result.
         if ($results) {
           foreach ($results as $record) {
@@ -68,65 +78,89 @@ public function handleAutocomplete(Request $request, int $count = 5) {
         }
       }
     }
-    
+
     return new JsonResponse($response);
   }
 
   /**
    * Fetch the cvterm.cvterm_id given a cvterm name (db.name:dbxref.accession)
    * value returned by the handler method above.
-   * 
+   *
    * @param string $term
-   *   String value returned by authocomplete handler method. 
-   * 
+   *   String value returned by autocomplete handler method.
+   *
+   * @param string $cv_name
+   *   Optional name of a controlled vocabulary. Can be used if user
+   *   bypassed autocomplete and entered just a CV term name manually.
+   *
    * @return integer
    *   Id number corresponding to chado.cvterm_id field of the matching term
    *   or 0 if no match was found.
    */
-  public static function getCVtermId(string $term): int {
+  public static function getCVtermId(string $term, $cv_name = ''): int {
     $id = 0;
 
     if (strlen($term) > 0) {
       $sql = "
-        SELECT ct.cvterm_id FROM {1:cvterm} AS ct 
-          LEFT JOIN {1:dbxref} AS dx USING(dbxref_id) 
+        SELECT ct.cvterm_id FROM {1:cvterm} AS ct
+          LEFT JOIN {1:dbxref} AS dx USING(dbxref_id)
           LEFT JOIN {1:db} USING(db_id)
         WHERE CONCAT(ct.name, ' (', db.name, ':', dx.accession, ')') = :term
-        LIMIT 1 
       ";
-    
+
       $connection = \Drupal::service('tripal_chado.database');
-      $result = $connection->query($sql, [':term' => $term]);
+      $result = $connection
+        ->query($sql, [':term' => $term])
+        ->fetchAll();
 
-      if($result) {
-        $id = $result->fetchField();
+      if(count($result) == 1) {
+        $id = $result[0]->cvterm_id;
       }
-    }
 
+      // If no match, and if a disambiguating CV was specified,
+      // try again using only that CV. This happens if the user
+      // types in the term and doesn't let the autocomplete
+      // append the (DB:accession).
+      else if ($cv_name) {
+        $sql = "
+          SELECT ct.cvterm_id FROM {1:cvterm} AS ct
+            LEFT JOIN {1:cv} AS cv USING(cv_id)
+          WHERE ct.name = :term AND cv.name = :cvname
+        ";
+
+        $result = $connection
+          ->query($sql, [':term' => $term, ':cvname' => $cv_name])
+          ->fetchAll();
+
+        if(count($result) == 1) {
+          $id = $result[0]->cvterm_id;
+        }
+      }
+    }
     return $id;
   }
 
   /**
    * Given a cvterm id number, return the matching cvterm record using
    * the format cvterm name (db.name:dbxref.accession).
-   * 
+   *
    * @param integer $id
    *   Cvterm id number to match.
-   * 
+   *
    * @return string
    *   Cvterm record in cvterm name (db.name:dbxref.accession) format.
    */
   public static function formatCVterm(int $id) {
     $term = null;
-    
+
     if ($id > 0) {
       $sql = "
-        SELECT CONCAT(ct.name, ' (', db.name, ':', dx.accession, ')') 
-        FROM {1:cvterm} AS ct 
-          LEFT JOIN {1:dbxref} AS dx USING(dbxref_id) 
+        SELECT CONCAT(ct.name, ' (', db.name, ':', dx.accession, ')')
+        FROM {1:cvterm} AS ct
+          LEFT JOIN {1:dbxref} AS dx USING(dbxref_id)
           LEFT JOIN {1:db} USING(db_id)
         WHERE ct.cvterm_id = :cvterm_id
-        LIMIT 1 
+        LIMIT 1
       ";
 
       $connection = \Drupal::service('tripal_chado.database');

tripal_chado/src/Controller/ChadoProjectAutocompleteController.php

@@ -12,22 +12,24 @@
 class ChadoProjectAutocompleteController extends ControllerBase {
   /**
    * Controller method, autocomplete project name.
-   * 
+   *
    * @param Request request
-   * @param int $type_id
-   *   Project type set in projectprop.type_id to restrict projects to specific type.
-   *   Default to 0, return projects regardless of type.
-   *   Must be declared in autocomplete route parameter ie. ['type_id' => 0]. 
+   *
    * @param int $count
    *   Desired number of matching names to suggest.
    *   Default to 5 items.
-   *   Must be declared in autocomplete route parameter ie. [count => 5].
-   * 
+   *   Must be declared in autocomplete route parameter i.e. ['count' => 5].
+   *
+   * @param int $type_id
+   *   Project type set in projectprop.type_id to restrict projects to specific type.
+   *   Default to 0, return projects regardless of type.
+   *   Must be declared in autocomplete route parameter i.e. ['type_id' => 0].
+   *
    * @return Json Object
    *   Matching project rows in an array where project name
    *   is both the value to the array keys label and value.
    */
-  public function handleAutocomplete(Request $request, int $type_id = 0, int $count = 5) {
+  public function handleAutocomplete(Request $request, int $count = 5, int $type_id = 0) {
     // Array to hold matching project records.
     $response = [];
 
@@ -40,7 +42,7 @@ public function handleAutocomplete(Request $request, int $type_id = 0, int $coun
         // long and result count is set to a value greater than 0.
 
         // Transform string as a search keyword pattern.
-        $keyword = '%' . strtolower($string) . '%';
+        $keyword = strtolower($string) . '%';
 
         if ($type_id > 0) {
           // Restrict to type provided by type_id in the route parameter.
@@ -54,7 +56,7 @@ public function handleAutocomplete(Request $request, int $type_id = 0, int $coun
           $args = [':keyword' => $keyword];
         }
 
-        // Prepare Chado database connection and execute sql query by providing value 
+        // Prepare Chado database connection and execute sql query by providing value
         // to :keyword and/or :type_id placeholder text.
         $connection = \Drupal::service('tripal_chado.database');
         $query = sprintf($sql, $count);
@@ -69,18 +71,18 @@ public function handleAutocomplete(Request $request, int $type_id = 0, int $coun
             ];
           }
         }
-      }  
+      }
     }
-    
+
     return new JsonResponse($response);
   }
 
   /**
    * Fetch the project id number, given a project name value.
-   * 
+   *
    * @param string $project
    *   Project name value.
-   * 
+   *
    * @return integer
    *   Project id number of the project name or 0 if no matching
    *   project record was found.
@@ -104,12 +106,12 @@ public static function getProjectId(string $project): int {
 
   /**
    * Fetch the project name, given a project id number.
-   * 
+   *
    * @param int $project
    *   Project id number value.
-   * 
+   *
    * @return string
-   *   Corresponding project name of the project id number or 
+   *   Corresponding project name of the project id number or
    *   empty string if no matching project record was found.
    */
   public static function getProjectName(int $project): string {
@@ -128,4 +130,4 @@ public static function getProjectName(int $project): string {
 
     return $name;
   }
-}
+}