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@@ -27,7 +27,9 @@ function tripal_fields_field_storage_write($entity_type, $entity, $op, $fields)
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// Convert the fields into a key/value list of fields and their values.
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$field_vals = tripal_fields_field_storage_unnest_fields($fields, $entity_type, $entity);
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-
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+ $data_table = NULL;
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+ $type_field = NULL;
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+ $record_id = NULL;
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switch ($op) {
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case FIELD_STORAGE_INSERT:
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// Use the cvterm_id to look up tables where this term is used
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@@ -43,8 +45,21 @@ function tripal_fields_field_storage_write($entity_type, $entity, $op, $fields)
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$data_table = $usage->data_table;
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//$type_table = $usage->type_table;
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$type_field = $usage->field;
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+
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+ // Recursively write fields for the base table.
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tripal_fields_field_storage_write_recursive($entity_type, $entity,
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$op, $field_vals, $data_table, $type_field);
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+
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+ // Now get the new chado_entity that was just added.
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+ $details = db_select('chado_entity', 'ce')
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+ ->fields('ce')
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+ ->condition('entity_id', $entity->id)
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+ ->execute()
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+ ->fetchObject();
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+ $data_table = $details->data_table;
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+ $type_field = $details->field;
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+ $record_id = $details->record_id;
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+
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}
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break;
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@@ -56,17 +71,31 @@ function tripal_fields_field_storage_write($entity_type, $entity, $op, $fields)
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->condition('entity_id', $entity->id)
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->execute()
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->fetchObject();
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- $tablename = $details->data_table;
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+ $data_table = $details->data_table;
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$type_field = $details->field;
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$record_id = $details->record_id;
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tripal_fields_field_storage_write_recursive($entity_type, $entity,
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- $op, $field_vals, $tablename, $type_field, $record_id);
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+ $op, $field_vals, $data_table, $type_field, $record_id);
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if (!$details) {
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// TODO: what to do if record is missing!
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}
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break;
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}
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+
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+ // Recursively write fields for any referring tables that have
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+ // values in the $field_vals array. There should be a key for each
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+ // FK table in the $field_vals array.
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+ $schema = chado_get_schema($data_table);
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+ $rtables = $schema['referring_tables'];
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+ dpm($schema);
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+ foreach ($rtables as $rtable) {
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+ dpm($rtable);
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+ if (array_key_exists($rtable, $field_vals)) {
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+ tripal_fields_field_storage_write_recursive($entity_type, $entity,
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+ $op, $field_vals, $rtable, $type_field, $record_id, 1);
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+ }
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+ }
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}
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/**
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@@ -86,7 +115,7 @@ function tripal_fields_field_storage_write_recursive($entity_type, $entity,
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$fkey_fields_list = array();
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// STEP 1: Recurse on the FK fields.
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- // Loop through the foreign keys os that we can recurse on those first.
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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 => $remote_id) {
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// If this is the base table then do not recurse on the type_id. The
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@@ -96,6 +125,7 @@ function tripal_fields_field_storage_write_recursive($entity_type, $entity,
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$values[$local_id] = $entity->cvterm_id;
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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[] = $local_id;
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@@ -103,7 +133,22 @@ function tripal_fields_field_storage_write_recursive($entity_type, $entity,
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// Get the value of the FK field as provided by the user.
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$fk_val = NULL;
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$fk_field_name = $tablename . '__' . $local_id;
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- $fk_val = array_key_exists($fk_field_name, $field_vals) ? $field_vals[$fk_field_name] : NULL;
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+
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+ // If this is the base table then we'll find any values for the FK
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+ // fields as any other field. IF we are not at the base table,
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+ // then the FK values are in a sub element of the array where the
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+ // key of the field is the table name. Because we are looping
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+ // on FKs that are members of the current table we should always only
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+ // have one value.
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+ if ($depth == 0) {
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+ $fk_val = array_key_exists($fk_field_name, $field_vals) ? $field_vals[$fk_field_name] : NULL;
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+ }
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+ else {
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+ if (array_key_exists($fk_table, $field_vals) and
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+ array_key_exists($fk_field_name, $field_vals[$fk_table])) {
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+ $fk_val = $field_vals[$fk_table][$fk_field_name];
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+ }
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+ }
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// Don't recurse if the value of the FK field is set to NULL. The
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// Tripal Chado API value for NULL is '__NULL__'.
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@@ -214,12 +259,13 @@ function tripal_fields_field_storage_load($entity_type, $entities, $age, $fields
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foreach ($entities as $id => $entity) {
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- // Get the base table and record id for the fields of this entity.
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- $details = db_select('chado_entity', 'ce')
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+ // Get the base table and record id for the fields of this entity.
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+ $details = db_select('chado_entity', 'ce')
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->fields('ce')
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->condition('entity_id', $entity->id)
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->execute()
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->fetchObject();
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+
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if (!$details) {
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// TODO: what to do if record is missing!
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}
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@@ -275,32 +321,55 @@ function tripal_fields_field_storage_load($entity_type, $entities, $age, $fields
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*/
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function tripal_fields_field_storage_unnest_fields($fields, $entity_type, $entity) {
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$new_fields = array();
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+
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foreach ($fields as $field_id => $ids) {
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$field = field_info_field_by_id($field_id);
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$field_name = $field['field_name'];
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+
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// Currently, we only support one language, but for for the sake of
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// thoroughness we'll iterate through all possible languages.
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$all_languages = field_available_languages($entity_type, $field);
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$field_languages = array_intersect($all_languages, array_keys((array) $entity->$field_name));
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foreach ($field_languages as $langcode) {
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- $items = (array) $entity->{$field_name}[$langcode];
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+
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// The number of items is related to the cardinatily of the field.
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- // We should always only have one item because this is a field in a
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- // table. But we loop anyway.
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+ $items = (array) $entity->{$field_name}[$langcode];
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foreach ($items as $delta => $item) {
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- // If the $value is an array then this field has nested fields. We
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- // want to add those to our $new_fields list.
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- if (is_array($item['value'])) {
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- foreach ($item['value'] as $children) {
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- foreach ($children as $child_field_name => $child_value) {
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- if (preg_match('/^.*?__.*?$/', $child_field_name)) {
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+ // There must be a 'value' field.
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+ if (!array_key_exists('value', $item)) {
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+ continue;
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+ }
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+
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+ // Case 1: base table fields.
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+ // If the value is not an array then we can just use the value as is.
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+ // This occurs for fields of the base table.
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+ if (!is_array($item['value'])) {
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+ $new_fields[$field_name] = $item['value'];
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+ continue;
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+ }
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+
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+ // Case 2: foreign key fields.
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+ // If the value is an array then there are sub fields. This occurs
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+ // for fields that represent FKs with the base table.
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+ $i = 0;
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+ foreach ($item['value'] as $children) {
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+ foreach ($children as $child_field_name => $child_value) {
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+ $matches = array();
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+ if (preg_match('/^(.*?)__.*?$/', $child_field_name, $matches)) {
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+ $table_name = $matches[1];
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+ // Case 2a: the FK field is in the basee table.
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+ if ($table_name == $entity->chado_entity->data_table) {
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$new_fields[$child_field_name] = $child_value;
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}
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+ // Case 2b: the fields of the FK relationship are in the non
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+ // base table. We store these in an array with the key being
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+ // the table name.
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+ else {
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+ $new_fields[$table_name][$i][$child_field_name] = $child_value;
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+ }
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}
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}
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- }
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- else {
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- $new_fields[$field_name] = $item['value'];
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+ $i++;
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}
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}
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}
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Stephen Ficklin