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@@ -33,22 +33,19 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
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$type_field = $entity->chado_column;
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$record = $entity->chado_record;
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$record_id = $entity->chado_record_id;
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+ $base_schema = chado_get_schema($base_table);
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+ $base_pkey = $base_schema['primary key'][0];
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// Convert the fields into a key/value list of fields and their values.
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$field_vals = tripal_chado_field_storage_merge_fields($fields, $entity_type, $entity);
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-dpm($field_vals);
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-return;
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- // Write the record for the base table.
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- $record_id = tripal_chado_field_storage_write_table(array(
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- 'entity' => $entity,
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- 'term' => $term,
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- 'op' => $op,
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- 'field_vals' => $field_vals,
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- 'base_table' => $base_table,
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- 'tablename' => $base_table,
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- 'type_field' => $type_field,
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- 'record_id' => $record_id,
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- ));
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+
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+ // Write the record for the base table. If this is an update then we'll have
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+ // the record_id and we need to add that to our values array.
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+ $values = $field_vals[$base_table][0];
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+ if ($record_id) {
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+ $values[$base_pkey] = $record_id;
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+ }
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+ $base_record_id = tripal_chado_field_storage_write_table($base_table, $values);
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// If this is an insert then add the chado_entity record.
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if ($op == FIELD_STORAGE_INSERT) {
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@@ -68,185 +65,108 @@ return;
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}
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// Now that we have handled the base table, we need to handle linking tables.
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- foreach ($fields as $field_id) {
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- // Get the field using the id.
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- $field = field_info_field_by_id($field_id);
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- $field_name = $field['field_name'];
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-
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- // If the field has a chado_table setting then we can try to write.
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- if (array_key_exists('settings', $field) and array_key_exists('chado_table', $field['settings'])) {
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-
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- // Skip fields that use the base table, as we've already handled those.
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- if ($field['settings']['chado_table'] != $base_table){
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- $field_table = $field['settings']['chado_table'];
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-
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- // Iterate through each record.
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- if (array_key_exists($field_name, $field_vals)) {
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- foreach ($field_vals[$field_name] as $delta => $fvals) {
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- tripal_chado_field_storage_write_table(array(
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- 'entity' => $entity,
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- 'term' => $term,
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- 'op' => $op,
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- 'field_vals' => $fvals,
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- 'base_table' => $base_table,
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- 'tablename' => $field_table
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- ));
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- }
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- }
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- }
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+ foreach ($field_vals as $table_name => $details) {
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+ // Skip the base table as we've already dealt with it.
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+ if ($table_name == $base_table) {
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+ continue;
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+ }
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+ foreach ($details as $delta => $values) {
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+ $record_id = tripal_chado_field_storage_write_table($table_name, $values);
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}
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}
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}
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/**
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+ * Write (inserts/oupdates) a nested array of values for a table.
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+ *
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+ * The $values array is of the same format used by chado_insert_record() and
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+ * chado_update_record(). However, both of those methods will use any nested
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+ * arrays (i.e. representing foreign keys) to select an appropriate record ID
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+ * that can be substituted as the value. Here, the nested arrays are
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+ * either inserted or updated as well, but the choice is determined if the
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+ * primary key value is present. If present an update occurs, if not present
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+ * then an insert occurs.
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*
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+ * This function is recursive and nested arrays from the lowest point of the
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+ * "tree" are dealt with first.
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+ *
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+ * @param $table_name
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+ * The name of the table on which the insertion/update is performed.
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+ * @param $values
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+ * The values array for the insertion.
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+ * @throws Exception
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+ * @return
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+ * The unique record ID.
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*/
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-function tripal_chado_field_storage_write_table($params) {
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- $entity = $params['entity'];
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- $term = $params['term'];
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- $op = $params['op'];
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- $field_vals = $params['field_vals'];
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- $base_table = $params['base_table'];
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- $tablename = $params['tablename'];
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- $type_field = array_key_exists('type_field', $params) ? $params['type_field'] : NULL;
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- $record_id = array_key_exists('record_id', $params) ? $params['record_id'] : NULL;
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- $depth = array_key_exists('depth', $params) ? $params['depth'] : 0;
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-
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- // Intialize the values array.
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- $values = array();
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-
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- // Get the schema for this table so that we can identify the primary key
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- // and foreign keys.
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- $schema = chado_get_schema($tablename);
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- $pkey_field = $schema['primary key'][0];
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- $fkey_fields = $schema['foreign keys'];
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- $fkey_fields_list = array();
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- $fkey_base_linker = NULL;
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-
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- // STEP 1: Recurse on the FK fields.
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- // Loop through the foreign keys so that we can recurse on those first.
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- foreach ($fkey_fields as $fk_table => $details) {
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- foreach ($details['columns'] as $local_id => $remote_id) {
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-
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- // If this is the base table then do not recurse on the type_id.
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- if ($tablename == $base_table && $local_id == $type_field) {
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- $values[$local_id] = $term->details['cvterm']->cvterm_id;
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- continue;
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- }
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-
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- // If this is a linking table, do not recurse on the fields that
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- // link back to the base table.
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- if ($tablename != $base_table && $details['table'] == $base_table) {
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- $fkey_base_linker = $local_id;
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- continue;
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- }
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-
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- // Get the value of the FK field as provided by the user.
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- $fk_val = NULL;
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- $fk_vals = array();
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- $fk_field_name = $tablename . '__' . $local_id;
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- if (array_key_exists($fk_field_name, $field_vals)) {
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- $fk_val = $field_vals[$fk_field_name][0][$tablename . '__' . $local_id];
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- $fk_vals = $field_vals[$fk_field_name][0];
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- }
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-
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- // Don't recurse if the value of the FK field is set to NULL. The
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- // Tripal Chado API value for NULL is '__NULL__'.
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- if ($fk_val == "__NULL__") {
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- $values[$local_id] = $fk_val;
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- continue;
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- }
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-
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- // Don't recuse if there are no fkvals.
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- if (count(array_keys($fk_vals)) == 0) {
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- continue;
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- }
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-
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- // Keep track of the FK fields so that in STEP 2 we don't have to
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- // loop through the $fk_fields again.
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- $fkey_fields_list[] = $local_id;
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-
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- // Recurse on the FK field.
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- $nparams = $params;
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- $nparams['field_vals'] = $fk_vals;
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- $nparams['tablename'] = $fk_table;
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- $nparams['type_field'] = NULL;
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- $nparams['record_id'] = $fk_val;
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- $nparams['depth'] = $depth + 1;
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- $fk_val = tripal_chado_field_storage_write_table($nparams);
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- if (isset($fk_val) and $fk_val != '' and $fk_val != 0) {
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- $values[$local_id] = $fk_val;
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- }
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- }
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- }
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-
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- // STEP 2: Loop through the non FK fields.
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- // Loop through the fields passed to the function and find any that
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- // are for this table. Then add their values to the $values array.
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- foreach ($field_vals as $field_name => $items) {
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- if (preg_match('/^' . $tablename . '__(.*)/', $field_name, $matches)) {
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- $chado_field = $matches[1];
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-
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- // Skip the PKey field. We won't ever insert a primary key and if
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- // one is provided in the fields then we use it for matching on an
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- // update. We don't add it to the $values array in either case.
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- if ($chado_field == $pkey_field) {
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- continue;
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- }
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-
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- // Skip FK fields as those should already have been dealt with the
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- // recursive code above.
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- if (in_array($chado_field, $fkey_fields_list)) {
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- continue;
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- }
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-
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- // If the value is empty then exclude this field
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- if (!$items[0][$tablename . '__' . $chado_field]) {
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- continue;
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- }
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-
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- // Add the value of the field to the $values arr for later insert/update.
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- $values[$chado_field] = $items[0][$tablename . '__' . $chado_field];
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- }
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- }
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-
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- // STEP 3: Insert/Update the record.
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- // If there are no values then return.
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- if (count($values) == 0) {
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- return $record_id;
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- }
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-
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- dpm($values);
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- // If we don't have an incoming record ID then this is an insert.
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- if ($record_id == NULL) {
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- // STEP 3a: Before inserting, we want to make sure the record does not
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- // already exist. Using the unique constraint check for a matching record.
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- $options = array('is_duplicate' => TRUE);
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- $is_duplicate = chado_select_record($tablename, array('*'), $values, $options);
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- if($is_duplicate) {
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- $record = chado_select_record($tablename, array('*'), $values);
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- return $record[0]->$pkey_field;
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- }
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+function tripal_chado_field_storage_write_table($table_name, $values) {
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+ $schema = chado_get_schema($table_name);
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+ $fkeys = $schema['foreign keys'];
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+ $pkey = $schema['primary key'][0];
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+
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+ // Before inserting or updating this table, recruse if there are any
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+ // nested FK array values.
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+ foreach ($values as $column => $value) {
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+ // If this value is an array then it must be a FK... let's recurse.
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+ if (is_array($value)) {
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+
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+ // Find the name of the FK table for this column.
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+ $fktable_name = '';
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+ foreach ($fkeys as $fktable => $details) {
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+ foreach ($details['columns'] as $fkey_lcolumn => $fkey_rcolumn) {
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+ if ($fkey_lcolumn == $column) {
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+ $fktable_name = $fktable;
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+ }
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+ }
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+ }
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+
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+ // Recurse on this recod.
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+ $record_id = tripal_chado_field_storage_write_table($fktable_name, $values[$column]);
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+ $values[$column] = $record_id;
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+ }
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+ }
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- // STEP 3b: Insert the reocrd
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- // Insert the values array as a new record in the table.
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- $record = chado_insert_record($tablename, $values);
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- if ($record === FALSE) {
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- throw new Exception('Could not insert Chado record into table: "' . $tablename . '".');
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- }
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- $record_id = $record[$pkey_field];
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- }
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- // We have an incoming record_id so this is an update.
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- else {
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- // TODO: what if the unique constraint matches another record? That is
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- // not being tested for here.
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- $match[$pkey_field] = $record_id;
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- if (!chado_update_record($tablename, $match, $values)) {
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- drupal_set_message("Could not update Chado record in table: $tablename.", 'error');
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- }
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- }
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+ // Fields with a cardinality greater than 1 will often submit an
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+ // empty form. We want to remove these empty submissions. We can detect
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+ // them if all of the fields are empty.
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+ $num_empty = 0;
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+ foreach ($values as $column => $value) {
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+ if (!$value) {
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+ $num_empty++;
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+ }
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+ }
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+ if ($num_empty == count(array_keys($values))) {
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+ return '';
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+ }
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- return $record_id;
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+ // If the primary key column has a value then this will be an udpate,
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+ // otherwise it's an insert.
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+ if (!$values[$pkey]) {
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+ // Before inserting, we want to make sure the record does not
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+ // already exist. Using the unique constraint check for a matching record.
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+ $options = array('is_duplicate' => TRUE);
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+ $is_duplicate = chado_select_record($table_name, array('*'), $values, $options);
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+ if($is_duplicate) {
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+ $record = chado_select_record($table_name, array('*'), $values);
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+ return $record[0]->$pkey_field;
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+ }
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+
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+ // Insert the values array as a new record in the table.
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+ $record = chado_insert_record($table_name, $values);
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+ if ($record === FALSE) {
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+ throw new Exception('Could not insert Chado record into table: "' . $tablename . '".');
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+ }
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+ return $record_id = $record[$pkey_field];
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+ }
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+ // We have an incoming record_id so this is an update.
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+ else {
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+ // TODO: what if the unique constraint matches another record? That is
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+ // not being tested for here.
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+ $match[$pkey] = $values[$pkey];
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+ if (!chado_update_record($table_name, $match, $values)) {
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+ drupal_set_message("Could not update Chado record in table: $tablename.", 'error');
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+ }
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+ return $values[$pkey];
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+ }
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}
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/**
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@@ -420,15 +340,19 @@ function tripal_chado_field_storage_merge_fields($fields, $entity_type, $entity)
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$parent_item_name = $matches[1];
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$sub_item_name = $matches[2];
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$sub_item = tripal_chado_field_storage_expand_field($sub_item_name, $value);
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- // If we've already encountered this table and column then we've
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- // already seen the numeric FK value or we've already added a
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- // subcolumn. If the former we want to convert this to an array
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- // so we can add the details.
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- if (array_key_exists($parent_item_name, $new_fields[$table_name][$delta]) and
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- !is_array($new_fields[$table_name][$delta][$parent_item_name])) {
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- $new_fields[$table_name][$delta][$parent_item_name] = array();
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+ if (count(array_keys($sub_item))) {
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+ // If we've already encountered this table and column then we've
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+ // already seen the numeric FK value or we've already added a
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+ // subcolumn. If the former we want to convert this to an array
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+ // so we can add the details.
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+ if (!array_key_exists($table_name, $new_fields) or
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+ !array_key_exists($delta, $new_fields[$table_name]) or
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+ !array_key_exists($parent_item_name, $new_fields[$table_name][$delta]) or
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+ !is_array($new_fields[$table_name][$delta][$parent_item_name])) {
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+ $new_fields[$table_name][$delta][$parent_item_name] = array();
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+ }
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+ $new_fields[$table_name][$delta][$parent_item_name] += $sub_item;
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}
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- $new_fields[$table_name][$delta][$parent_item_name] += $sub_item;
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}
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else {
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// If not seen this table and column then just add it. If we've
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Stephen Ficklin