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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Public Member Functions | |
| construct ($table=NULL, $left_table=NULL, $left_field=NULL, $field=NULL, $extra=array(), $type= 'LEFT', $added=NULL) | |
| join ($table, &$query) | |
| aggregate_join (&$query, $opt) | |
| get_aggregate_sql_for_table_field ($opt) | |
| create_single_join (&$query, $right_spec, $left_spec, $join_type) | |
Definition at line 23 of file views_handler_join_chado_aggregator.inc.
| views_handler_join_chado_aggregator::aggregate_join | ( | &$ | query, |
| $ | opt | ||
| ) |
Definition at line 64 of file views_handler_join_chado_aggregator.inc.
{
// 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']) {
$sql = $this->get_aggregate_sql_for_table_field($opt);
// Create the join (full SQL) ----------------
$output[] = $this->create_single_join(
$query,
array(
'table' => $opt['table'],
'field' => $opt['field'],
'table_sql' => $sql,
'is_drupal' => FALSE,
),
array(
'table' => $opt['left_table'],
'field' => $opt['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' => $opt['table'],
'field' => $opt['field'],
'is_drupal' => FALSE,
);
$left_table_spec = array(
'table' => $opt['left_table'],
'field' => $opt['left_field'],
);
switch ($opt['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 $output;
}
| views_handler_join_chado_aggregator::construct | ( | $ | table = NULL, |
| $ | left_table = NULL, |
||
| $ | left_field = NULL, |
||
| $ | field = NULL, |
||
| $ | extra = array(), |
||
| $ | type = 'LEFT', |
||
| $ | added = NULL |
||
| ) |
Definition at line 28 of file views_handler_join_chado_aggregator.inc.
{
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) {
$this->postgresql_9up = TRUE;
}
}
| views_handler_join_chado_aggregator::create_single_join | ( | &$ | query, |
| $ | right_spec, | ||
| $ | left_spec, | ||
| $ | join_type | ||
| ) |
Creates SQL for a single join based on parameters Join will be: <type> JOIN (<query creating one-to-one table using array_agg>)
<qualified left="" field>="">=<qualified right="" field>="">
Definition at line 259 of file views_handler_join_chado_aggregator.inc.
{
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;
}
| views_handler_join_chado_aggregator::get_aggregate_sql_for_table_field | ( | $ | opt | ) |
Create the SQL needed to aggregate a table
Definition at line 131 of file views_handler_join_chado_aggregator.inc.
{
// Determine Order BY's for aggregates
$order_by = array();
if (!is_array($opt['sort'])) {
$opt['sort'] = array();
}
foreach ($opt['sort'] as $s) {
$order_by[] = $s['table'] . '.' . $s['field'] . ' ' . $s['order'];
}
// get table description (if defined via schema api)
$table_desc = tripal_core_get_chado_table_schema($opt['table']);
$select_fields[ $opt['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'] != $opt['left_table']) {
foreach ( $defn['columns'] as $left => $right) {
$left = $opt['table'] . '.' . $left;
$right = $defn['table'] . '.' . $right;
$joins[] = "LEFT JOIN $defn[table] $defn[table] ON $left=$right";
}
// Fields to be selected from joined table
$join_table = tripal_core_get_chado_table_schema($defn['table']);
$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 != $opt['table']) {
$alias = $table . '_';
}
if ($fname != $opt['field']) {
// Add sort to aggregate field if postgreSQL 9.0+
if ($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 . "::' ||" . $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')";
$resource = chado_query($sql);
while ($r = db_fetch_object($resource)) {
$table = $opt['table'];
$alias = ''; //no alias needed if table is current table (only option if no schema api definition)
$fname = $r->column;
if ($fname != $opt['field']) {
// Add sort to aggregate field if postgreSQL 9.0+
if ($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 . "::' ||" . $table . '.' . $fname;
}
else {
$fields[] = $fname;
$composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
}
}
}
// composite field
// (combines all other fields before aggregating)
// Add sort to aggregate field if postgreSQL 9.0+
if ($opt['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 ' . $opt['table']
.' ' . implode(' ', $joins);
if (!empty($opt['filter'])) {
$sql .= ' WHERE ' . implode(' AND ', $opt['filter']);
}
$sql .= ' GROUP BY ' . $opt['field'];
return $sql;
}
| views_handler_join_chado_aggregator::join | ( | $ | table, |
| &$ | query | ||
| ) |
Creates SQL including aggregation query used in join
Definition at line 46 of file views_handler_join_chado_aggregator.inc.
{
$opt = array(
'table' => $this->definition['table'],
'field' => $this->definition['field'],
'left_table' => $this->definition['left_table'],
'left_field' => $this->definition['left_field'],
'table_aggregated' => $this->definition['table_aggregated'],
'sort' => $this->sort,
'filter' => $this->filter,
'postgresql_9up' => $this->postgresql_9up,
);
$output = $this->aggregate_join($query, $opt);
return implode("\n", $output);
}
1.7.4