tripal/tripal_views/views/handlers/views_handler_join_chado_aggregator.inc

<?php

/**
 * @file
 * Handler to allow joins between records via a linking table
 *
 * Example Usage:
 *   To join the analysisprop table to the analysis table,
 *   Use the following code in the analysisprop hook_views_data:
 *   @code
        $data['analysisprop']['table']['join']['analysis'] = array(
          'left_field' => 'analysis_id',
          'field' => 'analysis_id',
          'handler' => 'views_handler_join_chado_aggregator',
          'pre-aggregated' => TRUE | FALSE //whether the table is already aggregated (contains arrays)
          'table_aggregated' => CURRENT | LEFT //the table which has many records for each record in the other
        );
 *   @endcode
 */
class views_handler_join_chado_aggregator extends views_join {

  // PHP 4 doesn't call constructors of the base class automatically from a
  // constructor of a derived class. It is your responsibility to propagate
  // the call to constructors upstream where appropriate.
  function construct($table = NULL, $left_table = NULL, $left_field = NULL, $field = NULL, $extra = array(), $type = 'LEFT', $added = NULL) {
    parent::construct($table, $left_table, $left_field, $field, $extra, $type);

    // Determine the postgresql version
    $postgresql_version = pg_version();
    $this->postgresql_version = $postgresql_version['client'];

    // If version is 9.0+ then indicate
    // Needed to apply sorting for aggregated fields
    if (intval($postgresql_version['client']) >= 9) {
      $this->postgresql_9up = TRUE;
    }

  }

  /**
   * Creates SQL including aggregation query used in join
   */
  function join($table, &$query) {
    $output = array();
    
    // Create the table SQL (used in join) -------
    // query creating one-to-one table using array_agg
    
    // Only aggregate each field if it the join table hadn't been pre-aggregated
    // Example where it might be pre-aggregated: Materialized view
    if (!$this->definition['pre-aggregated']) {
      // Determine Order BY's for aggregates
      $order_by = array();
      if (!is_array($this->sort)) { $this->sort = array(); }
      foreach ($this->sort as $s) {
        $order_by[] = $s['table'].'.'.$s['field'].' '.$s['order'];
      }
        
      // get table description (if defined via schema api)
      $table_desc = module_invoke_all('chado_'.$this->definition['table'].'_schema');
      $select_fields[ $this->definition['table'] ] = $table_desc['fields'];
      
      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'] != $this->left_table) {
            foreach( $defn['columns'] as $left => $right) {
              $left = $this->definition['table'] .'.'. $left;
              $right = $defn[table] .'.'. $right;
              $joins[] = "LEFT JOIN $defn[table] $defn[table] ON $left=$right";
            }
            
            // Fields to be selected from joined table
            $join_table = module_invoke_all('chado_'.$defn['table'].'_schema');
            $select_fields[ $defn['table'] ] = $join_table['fields'];
          } 
        }
        
        // Fields to be selected
        foreach ($select_fields as $table => $table_fields) {
          foreach ($table_fields as $fname => $f) {
            $alias = '';
            if ($table != $this->definition['table']) {
              $alias = $table .'_';
            }
            
            if ($fname != $this->definition['field']) {
              // Add sort to aggregate field if postgreSQL 9.0+
              if ($this->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.$fname."::' ||".$table.'.'.$fname;
            } else {
              $fields[] = $fname;
              $composite_field_parts[] = "'".$alias.$fname."::' ||".$table.'.'.$fname;
            }
          }
        }
      
      // There is no definition in schema api
      // then use postgresql select
      } else {
        
        // No known foreign key reelationships
        $joins = array();
        
        // Fields to be selected
        $sql = "SELECT 
                  attname as column, 
                  format_type(atttypid, atttypmod) as datatype 
                FROM pg_attribute, pg_type 
                WHERE typname='nd_genotype_experiment' 
                  AND attrelid=typrelid 
                  AND attname NOT IN ('cmin','cmax','ctid','oid','tableoid','xmin','xmax')";
        $previous_db = tripal_db_set_active('chado');
        $resource = db_query($sql);
        tripal_db_set_active($previous_db);
        while ($r = db_fetch_object($resource)) {
          $table = $this->definition['table'];
          $alias = ''; //no alias needed if table is current table (only option if no schema api definition)
          $fname = $r->column;
          
          if ($fname != $this->definition['field']) {
            // Add sort to aggregate field if postgreSQL 9.0+
            if ($this->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.$fname."::' ||".$table.'.'.$fname;
          } else {
            $fields[] = $fname;
            $composite_field_parts[] = "'".$alias.$fname."::' ||".$table.'.'.$fname;
          }
        }
        
      }
      
      // composite field 
      // (combines all other fields before aggregating)
      // Add sort to aggregate field if postgreSQL 9.0+
      if ($this->postgresql_9up && !empty($order_by)) {
        $composite_field = "array_agg('{'||".implode(" || ',' || ",$composite_field_parts)."||'}' ORDER BY ".implode(',',$order_by).") as all";
      } else {
        $composite_field = "array_agg('{'||".implode(" || ',' || ",$composite_field_parts)."||'}') as all";
      }
      $fields[] = $composite_field;
        
      // SQL to use in the join
      $sql = 'SELECT '.implode(', ',$fields)
        .' FROM '.$this->definition['table']
        .' '.implode(' ',$joins);
   
      if (!empty($this->filter)) {
        $sql .= ' WHERE '.implode(', ', $this->filter);
      }
      
      $sql .= ' GROUP BY '.$this->definition['field'];
      
      // Create the join (full SQL) ----------------
      $output[] = $this->create_single_join(
        $query,
        array(
          'table' => $this->definition['table'],
          'field' => $this->definition['field'],
          'table_sql' => $sql,
          'is_drupal' => FALSE,
        ),
        array(
          'table' => $this->definition['left_table'],
          'field' => $this->definition['left_field'],
        ),
        'LEFT'
      );
    
    // Otherwise the table has been pre-aggregated
    // Then only need to do a regular join with any in where
    } else {

      // Create the join

      $current_table_spec = array(
        'table' => $this->definition['table'],
        'field' => $this->definition['field'],
        'is_drupal' => FALSE,
      );
      $left_table_spec = array(
        'table' => $this->definition['left_table'],
        'field' => $this->definition['left_field'],
      );
      
      switch ($this->definition['table_aggregated']) {
        default:
        case 'CURRENT':
          $current_table_spec['pre-aggregated'] = TRUE;
        break;
        case 'LEFT':
          $left_table_spec['pre-aggregated'] = TRUE;
        break;
      }
      
      $output[] = $this->create_single_join(
        $query,
        $current_table_spec,
        $left_table_spec,
        'LEFT'
      );
    }
    
    return implode("\n",$output);
  }

  /**
   * Creates SQL for a single join based on parameters
   * Join will be: <type> JOIN (<query creating one-to-one table using array_agg>) <table alias>
   *                  ON <qualified left field>=<qualified right field>
   */
  function create_single_join(&$query, $right_spec, $left_spec, $join_type) {

    if ($right_spec['table']) {
      $right = $query->get_table_info($right_spec['table']);
      if (!$right['alias']) {
        $right['alias'] = $right_spec['table'];
      }
      $right_field = "$right[alias].$right_spec[field]";

      // Add any() around field if already aggregated
      if ($right_spec['pre-aggregated']) {
        $right_field = "any(".$right_field.")";
      }
      
      // Add drupal { } around table 
      if ($right_spec['is_drupal']) {
        $right_table = '{' . $right_spec['table'] . '}';
      }
      else {
        $right_table = $right_spec['table'];
      }
    }

    if ($left_spec['table']) {
      $left = $query->get_table_info($left_spec['table']);
      if (!$left['alias']) {
        $left['alias'] = $left_spec['table'];
      }
      $left_field = "$left[alias].$left_spec[field]";
    }
    else {
      // This can be used if left_field is a formula or something. It should be used only *very* rarely.
      $left_field = $this->left_spec['field'];
    }

    // Add any() around field if already aggregated
    if ($left_spec['pre-aggregated']) {
      $left_field = "any(".$left_field.")";
    }
    
    // Concatenate parts together to form join sql
    if (!empty($right_spec[table_sql])) {
      $output = " $join_type JOIN ($right_spec[table_sql]) $right[alias] ON $left_field = $right_field";
    } else {
      $output = " $join_type JOIN $right_spec[table] $right[alias] ON $left_field = $right_field";
    }
    
    return $output;
  }

}