tripal · laceysanderson · Apr 14, 2024 · Apr 28, 2024 · Apr 28, 2024 · Apr 29, 2024
diff --git a/tripal/src/Services/TripalPublish.php b/tripal/src/Services/TripalPublish.php
@@ -620,9 +620,12 @@ protected function insertEntities($matches, $titles) {
    *   An associative array of entities
    *
    * @return array
-   *   An associative array of matched entities keyed by the
-   *   entity_id with a value of the entity id. This is an
-   *   associative array to take advantage of quick lookups.
+   *   An associative array of the following format:
+   *   [entity_id] =>
+   *     [field delta] =>
+   *       [property key] => [value]
+   *   indicating which datastore records we already have values published for.
+   *   Only required property types will be listed.
    */
   protected function findFieldItems($field_name, $entities) {
     $database = \Drupal::database();
@@ -635,10 +638,19 @@ protected function findFieldItems($field_name, $entities) {
     $this->setItemsHandled(0);
     $this->setTotalItems($num_batches);
 
+    // We also want to put the required field values in the return lookup array.
+    $required_property_column_names = [];
+    $mapping = [];
+    foreach (array_keys($this->required_types[$field_name]) as $key) {
+      $required_property_column_names[] = $field_name . '_' . $key;
+      $mapping[ $field_name . '_' . $key ] = $key;
+    }
+
     $items = [];
 
     $sql = "
-      SELECT entity_id FROM {" . $field_table . "}\n
+      SELECT entity_id, delta, " . implode(', ', $required_property_column_names) . "\n
+      FROM {" . $field_table . "}\n
       WHERE bundle = :bundle\n
         AND entity_id IN (:entity_ids[])\n";
 
@@ -652,15 +664,20 @@ protected function findFieldItems($field_name, $entities) {
       $total++;
       $i++;
 
-      // If we've reached the size of the batch then let's do the insert.
+      // If we've reached the size of the batch then let's do the query.
       if ($i == $batch_size or $total == $num_matches) {
         $args = [
           ':bundle' => $this->bundle,
           ':entity_ids[]' => $batch_ids
         ];
         $results = $database->query($sql, $args);
         while ($result = $results->fetchAssoc()) {
-          $items[$result['entity_id']] = $result['entity_id'];
+          // Compile required property values.
+          $required_property_values = [];
+          foreach ($mapping as $column_name => $key) {
+            $required_property_values[$key] = $result[$column_name];
+          }
+          $items[$result['entity_id']][$result['delta']] = $required_property_values;
         }
         $this->setItemsHandled($batch_num);
         $batch_num++;
@@ -671,6 +688,7 @@ protected function findFieldItems($field_name, $entities) {
         $batch_ids = [];
       }
     }
+
     return $items;
   }
 
@@ -709,7 +727,12 @@ protected function countFieldMatches(string $field_name, array $matches) : int {
    * @param array $entities
    *   An associative array that maps entity titles to their keys.
    * @param array $existing
-   *   An associative array of entities that already have an existing item for this field.
+   *   An associative array of the following format:
+   *   [entity_id] =>
+   *     [field delta] =>
+   *       [property key] => [value]
+   *   indicating which datastore records we already have values published for.
+   *   Only required property types will be listed.
    */
   protected function insertFieldItems($field_name, $matches, $titles, $entities, $existing) {
 
@@ -739,6 +762,11 @@ protected function insertFieldItems($field_name, $matches, $titles, $entities, $
     $sql = '';
     $args = [];
 
+    // In order to check if there is a published field entry for this datastore record,
+    // we will want to check the required property type values. Here we are getting
+    // that list since it is contant for this field.
+    $required_property_keys = array_keys($this->required_types[$field_name]);
+
     // Iterate through the matches.
     foreach ($matches as $match) {
       $title = $titles[$total];
@@ -749,11 +777,19 @@ protected function insertFieldItems($field_name, $matches, $titles, $entities, $
         $j++;
         $total++;
 
-        // No need to add items to those that are already published.
-        if (array_key_exists($entity_id, $existing)) {
+        // Check if we have an existing entry for this particular datastore record.
+        if (isset($delta, $existing[$entity_id])) {
+          /** @debug
+          $required_property_values = [];
+            foreach ($required_property_keys as $key) {
+            $required_property_values[$key] = $match[$field_name][$delta][$key]['value']->getValue();
+          }
+          print "SKIPPING: Not publishing $entity_id|$delta because the required property values are already published:" . print_r($required_property_values, TRUE);
+          */
           continue;
         }
 
+        // @debug print "-- PUBLISHING: $entity_id|$delta " . print_r($required_property_values, TRUE);
         // Add items to those that are not already published.
         $sql .= "(:bundle_$j, :deleted_$j, :entity_id_$j, :revision_id_$j, :langcode_$j, :delta_$j, ";
         $args[":bundle_$j"] = $this->bundle;
@@ -762,10 +798,11 @@ protected function insertFieldItems($field_name, $matches, $titles, $entities, $
         $args[":revision_id_$j"] = 1;
         $args[":langcode_$j"] = 'und';
         $args[":delta_$j"] = $delta;
-        foreach (array_keys($this->required_types[$field_name]) as $key) {
+        foreach ($required_property_keys as $key) {
+          $value = $match[$field_name][$delta][$key]['value']->getValue();
           $placeholder = ':' . $field_name . '_'. $key . '_' . $j;
           $sql .=  $placeholder . ', ';
-          $args[$placeholder] = $match[$field_name][$delta][$key]['value']->getValue();
+          $args[$placeholder] = $value;
         }
         $sql = rtrim($sql, ", ");
         $sql .= "),\n";
@@ -847,6 +884,24 @@ public function publish($filters = []) {
     $this->logger->notice("Step  1 of 6: Find matching records... ");
     $matches = $this->storage->findValues($search_values);
 
+    /* @debug matches array *
+    print "\nDebuggin Matches after findValues():\n";
+    foreach ($matches as $entity_id => $lvl1) {
+      foreach ($lvl1 as $field_name => $lvl2) {
+        if ($field_name == 'contact_project') {
+          foreach ($lvl2 as $delta => $lvl3) {
+            $debug_values = [];
+            foreach ($lvl3 as $key => $valueobj) {
+              $debug_values[$key] = $valueobj['value']->getValue();
+            }
+            print "Match $entity_id|$field_name|$delta: " . print_r($debug_values, TRUE);
+          }
+        }
+      }
+    }
+    * */
+
+
     $this->logger->notice("Step  2 of 6: Generate page titles...");
     $titles = $this->getEntityTitles($matches);
 
@@ -857,6 +912,23 @@ public function publish($filters = []) {
     // need to publish these matches.
     list($new_matches, $new_titles) = $this->excludeExisting($matches, $titles, $existing);
 
+    /* @debug matches array
+    print "\nDebuggin Matches after exclude existing:\n";
+    foreach ($matches as $entity_id => $lvl1) {
+      foreach ($lvl1 as $field_name => $lvl2) {
+        if ($field_name == 'contact_project') {
+          foreach ($lvl2 as $delta => $lvl3) {
+            $debug_values = [];
+            foreach ($lvl3 as $key => $valueobj) {
+              $debug_values[$key] = $valueobj['value']->getValue();
+            }
+            print "Match $entity_id|$field_name|$delta: " . print_r($debug_values, TRUE);
+          }
+        }
+      }
+    }
+    */
+
     // Note: entities are not tied to any storage backend. An entity
     // references an "object".  The information about that object
     // is in the form of fields and can come from any number of data storage

diff --git a/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php b/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php
@@ -298,6 +298,13 @@ public function findValues($values) {
     // Build the ChadoRecords object.
     $this->records = new ChadoRecords($this->field_debugger, $this->logger, $this->connection);
     $this->buildChadoRecords($values, TRUE);
+    /** @debug
+    print "Checking records after buildChadoRecords():\n";
+    $records_array_debug = $this->records->getRecordsArray();
+    foreach ($records_array_debug as $table_name => $lvl1) {
+      print "Chado storage $table_name: " . print_r($lvl1, true);
+    }
+    */
 
     // Start an array to keep track of the results we find.
     // Each element in this array will be a clone of the full $values array
@@ -319,6 +326,11 @@ public function findValues($values) {
         // Now for each matching base record we need to select
         // the ancillary tables.
         foreach ($matches as $match) {
+          /* @debug
+          $records_array_debug = $match->getRecordsArray();
+          foreach ($records_array_debug as $table_name => $lvl1) {
+            print "Chado storage $table_name: " . print_r($lvl1, true);
+          }*/
 
           // Clone the value array for this match.
           $new_values = $this->cloneValues($values);
@@ -574,6 +586,8 @@ protected function buildChadoRecords($values, bool $is_find = FALSE) {
           $prop_type = $this->getPropertyType($field_name, $key);
           $prop_storage_settings = $prop_type->getStorageSettings();
 
+          // @debug if ($field_name == 'contact_project') { print "$field_name|$delta|$key: " . print_r($prop_storage_settings, TRUE); }
+
           // Make sure we have an action for this property.
           if (!array_key_exists('action', $prop_storage_settings)) {
             $this->logger->error($this->t('Cannot store the property, @field.@prop ("@label"), in Chado. The property is missing an action in the property settings: @settings',
@@ -605,7 +619,6 @@ protected function buildChadoRecords($values, bool $is_find = FALSE) {
           $context['delta'] = $delta;
           $context['action'] = $action;
 
-
           // Get the path array for this field and add any joins if any are needed.
           if (array_key_exists('path', $prop_storage_settings)) {
 
@@ -830,6 +843,11 @@ protected function handleStoreLink(array $context, StoragePropertyValue $prop_va
     $this->records->addColumn($elements, TRUE);
 
     $this->records->addCondition($elements);
+
+    // If this is a find then we want to add the join as well.
+    if ($context['is_find']) {
+      $this->handleJoins($context['path_array'], $context);
+    }
   }
 
   /**

diff --git a/tripal_chado/src/TripalStorage/ChadoRecords.php b/tripal_chado/src/TripalStorage/ChadoRecords.php
@@ -1655,7 +1655,7 @@ public function findRecords(string $base_table, string $table_alias) {
     // Get informatino about this Chado table.
     $chado_table = $this->getTableFromAlias($base_table, $table_alias);
 
-    // Iterate through each item of the table and perform an insert.
+    // Iterate through each item of the table...
     $items = $this->getTableItems($base_table, $table_alias);
     foreach ($items as $delta => $record) {