Merge branch '6.x-1.x' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-1.x

tripal_views/views/handlers/chado_wrapper_functions.inc

@@ -18,12 +18,15 @@ function chado_wrapper_split_array_agg_results($handler, &$values) {
 
   if ($handler->aggregated) {
     foreach ($values as $k => $v) {
-
-      if (preg_match('/^{(.*)}$/', $v->{$handler->field_alias}, $matches)) {
-        $values[$k]->{$handler->field_alias} = str_getcsv($matches[1]);
-      }
-      else {
-        $values[$k]->{$handler->field_alias} = array();
+      // Some custom handlers re-use the same field
+      // This ensures that an already split value doesn't get re-split
+      if (!is_array($v->{$handler->field_alias})) {
+        if (preg_match('/^{(.*)}$/', $v->{$handler->field_alias}, $matches)) {
+          $values[$k]->{$handler->field_alias} = str_getcsv($matches[1]);
+        }
+        else {
+          $values[$k]->{$handler->field_alias} = array();
+        }
       }
     }
   }
@@ -71,7 +74,10 @@ function chado_wrapper_is_aggregated_by_result($handler, $values) {
     $i++;
   }
 
-  if (preg_match('/^{.*}$/', $values[$i]->{$handler->field_alias})) {
+  if (is_array($values[$i]->{$handler->field_alias})) {
+    $aggregated = TRUE;
+  }
+  elseif (preg_match('/^{.*}$/', $values[$i]->{$handler->field_alias})) {
     $aggregated = TRUE;
   }
 

tripal_views/views/handlers/tripal_views_handler_field_aggregate.inc

@@ -97,34 +97,35 @@ class tripal_views_handler_field_aggregate extends chado_views_handler_field {
   function split_aggregated_result_with_keys(&$value) {
 
     foreach ($value as $k => $v) {
-
-      if (preg_match('/.*::.*/',$v)) {
-        $subparts = explode(',', $v);
-        $token_values = array();
-        foreach ($subparts as $ssk => $ssv) {
-          if (preg_match('/(.*)::(.*)/', $ssv, $matches)) {
-            $values[ $matches[1] ] = $matches[2];
-            $tokens[ '[' . $this->options['id'] . '-' . $matches[1] . ']' ] = $matches[2];
+      if (!is_array($v)) {
+        if (preg_match('/.*::.*/',$v)) {
+          $subparts = explode(',', $v);
+          $token_values = array();
+          foreach ($subparts as $ssk => $ssv) {
+            if (preg_match('/(.*)::(.*)/', $ssv, $matches)) {
+              $values[ $matches[1] ] = $matches[2];
+              $tokens[ '[' . $this->options['id'] . '-' . $matches[1] . ']' ] = $matches[2];
+            }
           }
-        }
 
-        if ($this->options['format']['format_string']) {
-          $value[$k] = str_replace(array_keys($tokens), $tokens, $this->options['format']['format_string']);
-        }
-        else {
-          $value[$k] = $values;
-        }
-      }
-      else {
-        if ($this->options['format']['format_string']) {
-          $value[$k] = '';
+          if ($this->options['format']['format_string']) {
+            $value[$k] = str_replace(array_keys($tokens), $tokens, $this->options['format']['format_string']);
+          }
+          else {
+            $value[$k] = $values;
+          }
         }
         else {
-          $value[$k] = array();
+          if ($this->options['format']['format_string']) {
+            $value[$k] = '';
+          }
+          else {
+            $value[$k] = array();
+          }
         }
+        $value = array_filter($value);
       }
     }
-    $value = array_filter($value);
   }
 
 }

tripal_views/views/handlers/views_handler_join_chado_aggregator.inc

@@ -53,6 +53,7 @@ class views_handler_join_chado_aggregator extends views_join {
       'table_aggregated' => $this->definition['table_aggregated'],
       'sort' => $this->sort,
       'filter' => $this->filter,
+      'additional_joins' => $this->additional_joins,
       'postgresql_9up' => $this->postgresql_9up,
     );
 
@@ -143,21 +144,23 @@ class views_handler_join_chado_aggregator extends views_join {
     $table_desc = tripal_core_get_chado_table_schema($opt['table']);
     $select_fields[ $opt['table'] ] = $table_desc['fields'];
 
+
+    $joins = array();
     if (!empty($table_desc)) {
       // Add joins to tables with a foreign key in this table
       // (ie: add join to cvterm if this table has a type_id
-      $joins = array();
       foreach ($table_desc['foreign keys'] as $defn) {
         if ($defn['table'] != $opt['left_table']) {
           foreach ( $defn['columns'] as $left => $right) {
+            $table_alias = 'fk_' . $defn['table']  . '_' . $left;
             $left = $opt['table'] . '.' . $left;
-            $right = $defn['table'] . '.' . $right;
-            $joins[] = "LEFT JOIN $defn[table] $defn[table] ON $left=$right";
-          }
+            $right = $table_alias . '.' . $right;
+            $joins[] = "LEFT JOIN $defn[table] $table_alias ON $left=$right";
 
-          // Fields to be selected from joined table
-          $join_table = tripal_core_get_chado_table_schema($defn['table']);
-          $select_fields[ $defn['table'] ] = $join_table['fields'];
+            // Fields to be selected from joined table
+            $join_table = tripal_core_get_chado_table_schema($defn['table']);
+            $select_fields[ $table_alias ] = $join_table['fields'];
+          }
         }
       }
 
@@ -177,11 +180,11 @@ class views_handler_join_chado_aggregator extends views_join {
             else {
               $fields[] = 'array_agg(' . $table . '.' . $fname . ') as '. $alias . $fname;
             }
-            $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
+            $composite_field_parts[] = "'" . $alias . $fname . "::' || COALESCE(CAST(" . $table . '.' . $fname . " as text), '')";
           }
           else {
             $fields[] = $fname;
-            $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
+            $composite_field_parts[] = "'" . $alias . $fname . "::' || COALESCE(CAST(" . $table . '.' . $fname . " as text), '')";
           }
         }
       }
@@ -191,8 +194,8 @@ class views_handler_join_chado_aggregator extends views_join {
     }
     else {
 
-      // No known foreign key reelationships
-      $joins = array();
+      // No known foreign key relationships
+      // so don't add to $joins
 
       // Fields to be selected
       $sql = "SELECT
@@ -216,16 +219,42 @@ class views_handler_join_chado_aggregator extends views_join {
           else {
             $fields[] = 'array_agg(' . $table . '.' . $fname . ') as ' . $alias . $fname;
           }
-          $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
+          $composite_field_parts[] = "'" . $alias . $fname . "::' || COALESCE(CAST(" . $table . '.' . $fname . " as text), '')";
         }
         else {
           $fields[] = $fname;
-          $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
+          $composite_field_parts[] = "'" . $alias . $fname . "::' || COALESCE(CAST(" . $table . '.' . $fname . " as text), '')";
         }
       }
 
     }
 
+    // Add in any additional joins specified by handlers
+    if (!empty($opt['additional_joins'])) {
+      foreach ($opt['additional_joins'] as $join_defn) {
+
+        // Add the join SQL in
+        $table = ($join_defn['table_alias']) ? $join_defn['table_alias'] : 'adt_' . $join_defn['table'] . '_' . $join_defn['left_field'];
+        $left = $join_defn['left_table'] . '.' . $join_defn['left_field'];
+        $right = $table . '.' . $join_defn['field'];
+        $joins[] = "LEFT JOIN $join_defn[table] $table ON $left=$right";
+
+        // Add to the fields and composite field
+        $join_table_desc = tripal_core_get_chado_table_schema($join_defn['table']);
+        $alias = $table . '_';
+        foreach ($join_table_desc['fields'] as $fname => $fdesc) {
+          // Add sort to aggregate field if postgreSQL 9.0+
+          if ($opt['postgresql_9up'] && !empty($order_by)) {
+            $fields[] = 'array_agg(' . $table . '.' . $fname . ' ORDER BY ' . implode(',', $order_by) . ') as ' . $alias . $fname;
+          }
+          else {
+            $fields[] = 'array_agg(' . $table . '.' . $fname . ') as ' . $alias . $fname;
+          }
+          $composite_field_parts[] = "'" . $alias . $fname . "::' || COALESCE(CAST(" . $table . '.' . $fname . " as text), '')";
+        }
+      }
+    }
+
     // composite field
     // (combines all other fields before aggregating)
     // Add sort to aggregate field if postgreSQL 9.0+