switch all select objects to chado select objects

includes/repositories/EUtilsAssemblyRepository.inc

@@ -202,20 +202,21 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
       throw new Exception('The organism_analysis linker table doesnt exist.  No way to link this organism.');
     }
 
-    $result = db_select('chado.organism_analysis', 't')
-      ->fields('t', ['organism_analysis_id'])
+    $query = chado_db_select('organism_analysis', 't');
+    $result = $query->fields('t', ['organism_analysis_id'])
       ->condition('t.organism_id', $organism->organism_id)
       ->condition('t.analysis_id', $this->base_record_id)
       ->execute()
       ->fetchField();
 
     if (!$result) {
-      $result = db_insert('chado.organism_analysis')
-        ->fields([
-          'organism_id' => $organism->organism_id,
-          'analysis_id' => $this->base_record_id,
-        ])
-        ->execute();
+      $values = [
+        'organism_id' => $organism->organism_id,
+        'analysis_id' => $this->base_record_id,
+      ];
+
+      $result = chado_insert_record('organism_analysis', $values);
+
     }
 
     if (!$result) {
@@ -238,7 +239,7 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
 
     $base = $this->base_fields;
 
-    $id = db_insert('chado.analysis')->fields([
+    $values = [
       'name' => $base['name'],
       'description' => $base['description'] ?? '',
       'program' => $base['program'],
@@ -248,14 +249,17 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
       'sourceversion' => $base['sourceversion'] ?? '',
       'sourceuri' => $base['sourceuri'] ?? '',
       'timeexecuted' => $base['timeexecuted'] ?? date_now(),
-    ])->execute();
+    ];
+    $record = chado_insert_record('analysis', $values);
+
+    $id = $record['analysis_id'];
 
     if (!$id) {
       throw new Exception('Unable to create chado.analysis record');
     }
 
-    $analysis = db_select('chado.analysis', 't')
-      ->fields('t')
+    $query = chado_db_select('analysis', 't');
+    $analysis = $query->fields('t')
       ->condition('analysis_id', $id)
       ->execute()
       ->fetchObject();
@@ -278,8 +282,8 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
       return static::$cache['analysis'];
     }
 
-    $exists = db_select('chado.analysis', 't')
-      ->fields('t')
+    $query = chado_db_select('analysis', 't');
+    $exists = $query->fields('t')
       ->condition('name', $base['name'])
       ->condition('program', $base['program'])
       ->condition('programversion', $base['programversion'])
@@ -298,11 +302,13 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
   /**
    * Associates FTPs as properties.
    *
-   * @param $ftps
+   * @param array $ftps
    *   Array of key value pars, where the key is the XML FTP type, the value is
    *   the FTP address.
+   *
+   * @throws \Exception
    */
-  public function addFTPLinks($ftps) {
+  public function addFTPLinks(array $ftps) {
 
     $cvterm_id = chado_get_cvterm(['id' => 'local:ncbi_FTP_links'])->cvterm_id;
     foreach ($ftps as $type => $ftp) {
@@ -318,6 +324,11 @@ class EUtilsAssemblyRepository extends EUtilsRepository {
    *   The type/category passed from the parser.
    *
    * @return bool
+   *   Output of chado_insert_property.
+   *
+   * @see createProperty
+   *
+   * @throws \Exception
    */
   private function setAnalysisType(string $type) {
 

includes/repositories/EUtilsBioProjectRepository.inc

@@ -77,7 +77,6 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
       $this->createPubs($pubs);
     }
 
-
     return $project;
   }
 
@@ -108,8 +107,8 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
       throw new Exception('Unable to create chado.project record');
     }
 
-    $project = db_select('chado.project', 't')
-      ->fields('t')
+    $query = chado_db_select('project', 't');
+    $project = $query->fields('t')
       ->condition('project_id', $id)
       ->execute()
       ->fetchObject();
@@ -121,8 +120,10 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
    * Get project from db or cache.
    *
    * @param string $name
+   *   Chado project name field.
    *
    * @return null
+   *   Returns a project object or NULL.
    */
   public function getProject($name) {
     // If the project is available in our static cache, return it.
@@ -131,8 +132,8 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
     }
 
     // Find the project and add it to the cache.
-    $project = db_select('chado.project', 'p')
-      ->fields('p')
+    $query = chado_db_select('project', 't');
+    $project = $query->fields('t')
       ->condition('name', $name)
       ->execute()
       ->fetchObject();
@@ -184,7 +185,8 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
     foreach ($accessions as $db => $accession) {
       try {
         $data[] = $this->createAccession(['db' => $db, 'value' => $accession]);
-      } catch (Exception $exception) {
+      }
+      catch (Exception $exception) {
         // For the time being, ignore all exceptions.
       }
     }
@@ -227,7 +229,7 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
   public function linkBiomaterial($record) {
     $biomaterial_id = $record->biomaterial_id;
 
-    db_insert('chado.biomaterial_project')->fields([
+    chado_insert_record('biomaterial_project', [
       'biomaterial_id' => $biomaterial_id,
       'project_id' => $this->base_record_id,
     ]);
@@ -238,13 +240,13 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
    * Links an analysis to the base project record.
    *
    * @param $record
-   *   Assembly record object.
+   *   Assembly/analysis record object.
    */
   private function linkAssembly($record) {
     $analysis_id = $record->analysis_id;
 
-    $exists = db_select('chado.project_analysis', 't')
-      ->fields('t')
+    $query = chado_db_select('project_analysis', 't');
+    $exists = $query->fields('t')
       ->condition('project_id', $this->base_record_id)
       ->condition('analysis_id', $analysis_id)
       ->execute()
@@ -278,8 +280,10 @@ class EUtilsBioProjectRepository extends EUtilsRepository {
           'project_id' => $this->base_record_id,
           'pub_id' => $pub->pub_id,
         ];
-        $exists = db_select('chado.project_pub', 't')
-          ->fields('t')
+
+        $query = chado_db_select('project_pub', 't');
+
+        $exists = $query->fields('t')
           ->condition('project_id', $this->base_record_id)
           ->condition('pub_id', $pub->pub_id)
           ->execute()

includes/repositories/EUtilsBioSampleRepository.inc

@@ -134,7 +134,9 @@ class EUtilsBioSampleRepository extends EUtilsRepository {
       throw new Exception('Unable to create chado.biomaterial record');
     }
 
-    $biosample = db_select('chado.biomaterial', 'B')->fields('B')->condition(
+    $query = chado_db_select('biomaterial', 'B');
+
+    $biosample = $query->fields('B')->condition(
       'biomaterial_id', $id
     )->execute()->fetchObject();
 
@@ -145,8 +147,10 @@ class EUtilsBioSampleRepository extends EUtilsRepository {
    * Get biosample from db or cache.
    *
    * @param string $name
+   *   Name for the name field of biomaterial table.
    *
-   * @return null
+   * @return mixed
+   *   The Chado biosample record.
    */
   public function getBioSample($name) {
     // If the biosample is available in our static cache, return it.
@@ -155,17 +159,17 @@ class EUtilsBioSampleRepository extends EUtilsRepository {
     }
 
     // Find the biosample and add it to the cache.
-    $biosample = db_select('chado.biomaterial', 'b')
-      ->fields('b')
+    $query = chado_db_select('biomaterial', 'b');
+
+    // Name is in fact a unique key.
+    $biosample = $query->fields('b')
       ->condition('name', $name)
       ->execute()
       ->fetchObject();
 
     if ($biosample) {
       return static::$cache['biosamples'][$name] = $biosample;
     }
-
-    return NULL;
   }
 
   /**

includes/repositories/EUtilsPubmedRepository.inc

@@ -17,6 +17,11 @@ class EUtilsPubmedRepository extends EUtilsRepository {
     'description',
   ];
 
+  /**
+   * Required base table attribute.
+   *
+   * @var string
+   */
   protected $base_table = 'pub';
 
   /**
@@ -27,14 +32,14 @@ class EUtilsPubmedRepository extends EUtilsRepository {
    *
    * @return pub
    *   A Chado publication record object.
-   **/
+   */
   public function create(array $data) {
     module_load_include('inc', 'tripal_chado', '/includes/loaders/tripal_chado.pub_importers');
 
     tripal_pub_add_publications([$data], FALSE);
     $uname = $data['Citation'];
-    $pub = db_select('chado.pub', 'p')->fields('p')->condition('p.uniquename', $uname)->execute()->fetchObject();
-
+    $connection = chado_db_select('pub', 'p');
+    $pub = $connection->fields('p')->condition('p.uniquename', $uname)->execute()->fetchObject();
     return $pub;
   }