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@@ -16,9 +16,9 @@
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* drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
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* also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
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* contain the following tokens:
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- * - >field_name<
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+ * - <field_name>
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* Replaced by the name of the field to be excluded
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- * - >field_value<
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+ * - <field_value>
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* Replaced by the value of the field in the current record
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* Also keep in mind that if your criteria doesn't contain the >field_value< token then it will be
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* evaluated before the query is executed and if the field is excluded it won't be included in the
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@@ -30,7 +30,7 @@
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* @ingroup tripal_chado_query_api
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*/
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function tripal_core_exclude_type_by_default() {
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- return array('text' => 'strlen(">field_value< ") > 100');
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+ return array('text' => 'strlen("<field_value> ") > 250');
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}
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/**
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@@ -45,21 +45,21 @@ function tripal_core_exclude_type_by_default() {
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* drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
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* also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
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* contain the following tokens:
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- * - >field_name<
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+ * - <field_name>
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* Replaced by the name of the field to be excluded
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- * - >field_value<
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+ * - <field_value>
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* Replaced by the value of the field in the current record
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- * Also keep in mind that if your criteria doesn't contain the >field_value< token then it will be
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+ * Also keep in mind that if your criteria doesn't contain the <field_value> token then it will be
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* evaluated before the query is executed and if the field is excluded it won't be included in the
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* query.
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*
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* @return
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- * An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
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+ * An array of field => criteria where the type is excluded if the criteria evaluates to TRUE
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*
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* @ingroup tripal_chado_query_api
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*/
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function tripal_core_exclude_field_from_feature_by_default() {
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- return array();
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+ return array('residues' => 'TRUE');
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}
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/**
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@@ -161,7 +161,7 @@ function chado_generate_var($table, $values, $base_options = array()) {
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if (array_key_exists('return_array', $base_options)) {
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$return_array = 1;
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}
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- $include_fk = 0;
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+ $include_fk = FALSE;
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if (array_key_exists('include_fk', $base_options)) {
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$include_fk = $base_options['include_fk'];
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}
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@@ -185,7 +185,10 @@ function chado_generate_var($table, $values, $base_options = array()) {
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$table_columns = array_keys($table_desc['fields']);
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// Expandable fields without value needed for criteria--------------------------------------------
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+ // Add in the default expandable arrays
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+ // These are used for later expanding fields, tables, foreign keys and nodes
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$all->expandable_fields = array();
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+ $all->expandable_foreign_keys = array();
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if (array_key_exists('referring_tables', $table_desc) and $table_desc['referring_tables']) {
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$all->expandable_tables = $table_desc['referring_tables'];
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}
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@@ -194,19 +197,40 @@ function chado_generate_var($table, $values, $base_options = array()) {
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}
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$all->expandable_nodes = array();
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- /*
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+
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// Get fields to be removed by name.................................
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+ // This gets all implementations of hook_exclude_field_from_<table>_by_default()
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+ // where <table> is the current table a variable is being created for.
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+
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+ // This allows modules to specify that some fields should be excluded by default
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+ // For example, tripal core provides a tripal_core_exclude_field_from_feature_by_default()
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+ // which says that we usually don't want to include the residues field by default since
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+ // it can be very large and cause performance issues.
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+
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+ // If a field is excluded by default it can always be expanded at a later point by calling
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+ // chado_expand_var($chado_var, 'field', <field name as shown in expandable_fields array>);
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+
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+ // First get an array of all the fields to be removed for the current table
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+ // module_invoke_all() is drupal's way of invoking all implementations of the specified
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+ // hook and merging all of the results.
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+
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+ // $fields_to_remove should be an array with the keys matching field names
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+ // and the values being strings to be executed using php_eval() to determine whether
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+ // to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
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$fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');
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+
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+ // Now, for each field to be removed
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foreach ($fields_to_remove as $field_name => $criteria) {
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- //replace >field_name< with the current field name &
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- $criteria = preg_replace('/>field_name< /', addslashes($field_name), $criteria);
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+
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+ //replace <field_name> with the current field name
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+ $criteria = preg_replace('/<field_name> /', addslashes($field_name), $criteria);
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// if field_value needed we can't deal with this field yet
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- if (preg_match('/>field_value< /', $criteria)) {
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+ if (preg_match('/<field_value> /', $criteria)) {
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break;
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}
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//if criteria then remove from query
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- // @coder-ignore: only module designers can populate $criteria -not security risk
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+ // @coder-ignore: only module designers can populate $criteria -not a security risk
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$success = php_eval('<?php return ' . $criteria . '; ?>');
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if ($success) {
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unset($table_columns[array_search($field_name, $table_columns)]);
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@@ -215,29 +239,54 @@ function chado_generate_var($table, $values, $base_options = array()) {
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}
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}
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- //Get fields to be removed by type................................
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+ // Get fields to be removed by type................................
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+ // This gets all implementations of hook_exclude_type_by_default().
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+
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+ // This allows modules to specify that some types of fields should be excluded by default
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+ // For example, tripal core provides a tripal_core_exclude_type_by_default() which says
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+ // that text fields are often very large and if they are longer than 250 characters then
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+ // we want to exclude them by default
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+
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+ // If a field is excluded by default it can always be expanded at a later point by calling
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+ // chado_expand_var($chado_var, 'field', <field name as shown in expandable_fields array>);
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+
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+ // First get an array of all the types of fields to be removed for the current table
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+ // module_invoke_all() is drupal's way of invoking all implementations of the specified
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+ // hook and merging all of the results.
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+
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+ // $types_to_remove should be an array with the keys matching field names
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+ // and the values being strings to be executed using php_eval() to determine whether
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+ // to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
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+ // (ie: array('text' => 'strlen("<field_value> ") > 100');
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$types_to_remove = module_invoke_all('exclude_type_by_default');
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+
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+ // Get a list of all the types of fields
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+ // the key is the type of field and the value is an array of fields of this type
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$field_types = array();
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foreach ($table_desc['fields'] as $field_name => $field_array) {
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$field_types[$field_array['type']][] = $field_name;
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}
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+
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+ // We want to use the types to remove in conjunction with our table field descriptions
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+ // to determine which fields might need to be removed
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foreach ($types_to_remove as $field_type => $criteria) {
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+
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// if there are fields of that type to remove
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- if (is_array($field_types[$field_type])) {
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- //replace >field_name< with the current field name &
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- $criteria = preg_replace('/>field_name< /', addslashes($field_name), $criteria);
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+ if (isset($field_types[$field_type])) {
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+
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+ // Do any processing needed on the php criteria
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+ //replace <field_name> with the current field name
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+ $criteria = preg_replace('/<field_name> /', addslashes($field_name), $criteria);
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foreach ($field_types[$field_type] as $field_name) {
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// if field_value needed we can't deal with this field yet
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- if (preg_match('/>field_value< /', $criteria)) {
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+ if (preg_match('/<field_value>/', $criteria)) {
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$fields_to_remove[$field_name] = $criteria;
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continue;
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}
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- // if field_value needed we can't deal with this field yet
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- if (preg_match('/>field_value< /', $criteria)) {
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- break;
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- }
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- //if criteria then remove from query
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- // @coder-ignore: only module designers can populate $criteria -not security risk
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+
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+ // if criteria then remove from query
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+ // (as long as <field_value> is not needed for the criteria to be evaluated)
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+ // @coder-ignore: only module designers can populate $criteria -not a security risk
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$success = php_eval('<?php return ' . $criteria . '; ?>');
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if ($success) {
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unset($table_columns[array_search($field_name, $table_columns)]);
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@@ -246,7 +295,7 @@ function chado_generate_var($table, $values, $base_options = array()) {
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} //end of foreach field of that type
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}
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} //end of foreach type to be removed
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-*/
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+
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// get the values for the record in the current table---------------------------------------------
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$results = chado_select_record($table, $table_columns, $values, $base_options);
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@@ -254,6 +303,7 @@ function chado_generate_var($table, $values, $base_options = array()) {
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foreach ($results as $key => $object) {
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// Add empty expandable_x arrays
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$object->expandable_fields = $all->expandable_fields;
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+ $object->expandable_foreign_keys = $all->expandable_foreign_keys;
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$object->expandable_tables = $all->expandable_tables;
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$object->expandable_nodes = $all->expandable_nodes;
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// add curent table
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@@ -277,23 +327,39 @@ function chado_generate_var($table, $values, $base_options = array()) {
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}
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// remove any fields where criteria needs to be evalulated---------------------------------------
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-/* foreach ($fields_to_remove as $field_name => $criteria) {
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+ // The fields to be removed can be populated by implementing either
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+ // hook_exclude_field_from_<table>_by_default() where <table> is the current table
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+ // OR hook_exclude_type_by_default() where there are fields of the specified type in the current table
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+ // It only reaches this point if the criteria specified for whether or not to
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+ // exclude the field includes <field_value> which means it has to be evaluated after
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+ // the query has been executed
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+ foreach ($fields_to_remove as $field_name => $criteria) {
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+
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+ // If the field is an object then we don't support exclusion of it
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+ // For example, if the field is a foreign key
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if (!isset($object->{$field_name})) {
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break;
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}
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- $criteria = preg_replace('/>field_value< /', addslashes($object->{$field_name}), $criteria);
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+
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+ // replace <field_value> with the actual value of the field from the query
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+ $criteria = preg_replace('/<field_value>/', addslashes($object->{$field_name}), $criteria);
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+
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+ // evaluate the criteria, if TRUE is returned then exclude the field
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+ // excluded fields can be expanded later by calling
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+ // chado_expand_var($var, 'field', <field name as shown in expandable_fields array>);
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$success = php_eval('<?php return ' . $criteria . '; ?>');
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if ($success) {
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unset($object->{$field_name});
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$object->expandable_fields[] = $table . '.' . $field_name;
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}
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}
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-*/
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+
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// recursively follow foreign key relationships nesting objects as we go------------------------
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if ($table_desc['foreign keys']) {
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foreach ($table_desc['foreign keys'] as $foreign_key_array) {
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$foreign_table = $foreign_key_array['table'];
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foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {
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+
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// Note: Foreign key is the field in the current table whereas primary_key is the field in
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// the table referenced by the foreign key
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//Dont do anything if the foreign key is empty
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@@ -301,17 +367,20 @@ function chado_generate_var($table, $values, $base_options = array()) {
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continue;
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}
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- if ($include_fk) {
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+ if (is_array($include_fk)) {
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// don't recurse if the callee has supplied an $fk_include list and this
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// FK table is not in the list.
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if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
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- continue;
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- }
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- // if we have the option but it is not an array then we don't recurse any furutehr
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- if (!is_array($include_fk)) {
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+ $object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
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continue;
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}
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}
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+ // if we have the option but it is not an array then we don't recurse any furutehr
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+ if ($include_fk === TRUE) {
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+ $object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
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+ continue;
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+ }
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+
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// get the record from the foreign table
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$foreign_values = array($primary_key => $object->{$foreign_key});
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$options = array();
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@@ -332,6 +401,14 @@ function chado_generate_var($table, $values, $base_options = array()) {
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);
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unset($object->{$foreign_key}->expandable_fields);
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}
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+ if (property_exists($object->{$foreign_key}, 'expandable_foreign_keys') and
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+ is_array($object->{$foreign_key}->expandable_foreign_keys)) {
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+ $object->expandable_foreign_keys = array_merge(
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+ $object->expandable_foreign_keys,
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+ $object->{$foreign_key}->expandable_foreign_keys
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+ );
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+ unset($object->{$foreign_key}->expandable_foreign_keys);
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+ }
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if (property_exists($object->{$foreign_key}, 'expandable_tables') and
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is_array($object->{$foreign_key}->expandable_tables)) {
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$object->expandable_tables = array_merge(
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@@ -484,20 +561,33 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
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$tablename = $matches[1];
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$fieldname = $matches[2];
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$table_desc = chado_get_schema($tablename);
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- $values = array();
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- foreach ($table_desc['primary key'] as $key) {
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- if(property_exists($object, $key)) {
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- $values[$key] = $object->{$key};
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- }
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- }
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+
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+ // BASE CASE: the field is from the current table
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if ($base_table == $tablename) {
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- //get the field
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+ // Use the table description to fully describe the current object
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+ // in a $values array to be used to select the field from chado
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+ $values = array();
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+ foreach ($table_desc['primary key'] as $key) {
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+ if(property_exists($object, $key)) {
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+ $values[$key] = $object->{$key};
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+ }
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+ }
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+
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+ // Retrieve the field from Chado
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$results = chado_select_record($tablename, array($fieldname), $values);
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- $object->{$fieldname} = $results[0]->{$fieldname};
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- $object->expanded = $to_expand;
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+
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+ // Check that the field was retrieved correctly
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+ if (isset($results[0])) {
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+ $object->{$fieldname} = $results[0]->{$fieldname};
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+ $object->expanded = $to_expand;
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+ }
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+ // If it wasn't retrieved correctly, we need to warn the administrator
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+
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}
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+ // RECURSIVE CASE: the field is in a nested object
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else {
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- //We need to recurse -the field is in a nested object
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+ // We want to look at each field and if it's an object then we want to
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+ // attempt to expand the field in it via recursion
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foreach ((array) $object as $field_name => $field_value) {
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if (is_object($field_value)) {
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$object->{$field_name} = chado_expand_var(
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@@ -509,22 +599,110 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
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} //end of for each field in the current object
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}
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}
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+ // Otherwise we weren't able to extract the parts of the field to expand
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+ // Thus we will warn the administrator
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else {
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tripal_report_error('tripal_core', TRIPAL_ERROR,
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'chado_expand_var: Field (%field) not in the right format. " .
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- "It should be <tablename>.<fieldname>');
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+ "It should be <tablename>.<fieldname>', array('%field' => $to_expand));
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}
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break;
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+
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+ case "foreign_key": //--------------------------------------------------------------------------
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+ if (preg_match('/(\w+)\.(\w+) => (\w+)/', $to_expand, $matches)) {
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+ $table_name = $matches[1];
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+ $field_name = $matches[2];
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+ $foreign_table = $matches[3];
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+ $table_desc = chado_get_schema($table_name);
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+
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+ // BASE CASE: The foreign key is from the current table
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+ if ($base_table == $table_name) {
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+
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+ // Get the value of the foreign key from the object
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+ $field_value = $object->{$field_name};
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+
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+ // Get the name of the field in the foreign table using the table description
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|
|
+ // For example, with the feature.type_id => cvterm.cvterm_id we need cvterm_id
|
|
|
+ $foreign_field_name = FALSE;
|
|
|
+ foreach ($table_desc['foreign keys'][$foreign_table]['columns'] as $left => $right) {
|
|
|
+ if ($right == $field_name) {
|
|
|
+ $foreign_field_name = $left;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Check that we were able to determine the field name in the foreign table
|
|
|
+ if ($foreign_field_name) {
|
|
|
+
|
|
|
+ // Generate a chado variable of the foreign key
|
|
|
+ // For example, if the foreign key to expand is feature.type_id
|
|
|
+ // then we want to generate a chado cvterm variable that matches the feature.type_id
|
|
|
+ $foreign_var = chado_generate_var(
|
|
|
+ $foreign_table, // thus in the example above, generate a cvterm var
|
|
|
+ array($foreign_field_name => $field_value), // where the cvterm.cvterm_id = feature.type_id value
|
|
|
+ $table_options //pass in the same options given to this function
|
|
|
+ );
|
|
|
+
|
|
|
+ // Check that the foreign object was returned
|
|
|
+ if ($foreign_var) {
|
|
|
+
|
|
|
+ // It was so now we can add this chado variable to our current object
|
|
|
+ // in place of the key value
|
|
|
+ $object->{$field_name} = $foreign_var;
|
|
|
+ $object->expanded = $to_expand;
|
|
|
+
|
|
|
+ }
|
|
|
+ // Otherwise we weren't able to expand the foreign key
|
|
|
+ else {
|
|
|
+ tripal_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
+ 'chado_expand_var: unable to retrieve the object desribed by the foreign key
|
|
|
+ while trying to expand %fk.',
|
|
|
+ array('%fk' => $to_expand));
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // Else we were unable to determine the field name in the foreign table
|
|
|
+ else {
|
|
|
+ tripal_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
+ 'chado_expand_var: unable to determine the field name in the table the foreign
|
|
|
+ key points to while trying to expand %fk.',
|
|
|
+ array('%fk' => $to_expand));
|
|
|
+ }
|
|
|
+
|
|
|
+ }
|
|
|
+ // RECURSIVE CASE: Check any nested objects
|
|
|
+ else {
|
|
|
+
|
|
|
+ foreach ((array) $object as $field_name => $field_value) {
|
|
|
+ if (is_object($field_value)) {
|
|
|
+ $object->{$field_name} = chado_expand_var(
|
|
|
+ $field_value,
|
|
|
+ 'foreign_key',
|
|
|
+ $to_expand
|
|
|
+ );
|
|
|
+ }
|
|
|
+ } //end of for each field in the current object
|
|
|
+
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // Otherwise we weren't able to extract the parts of the foreign key to expand
|
|
|
+ // Thus we will warn the administrator
|
|
|
+ else {
|
|
|
+ tripal_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
+ 'chado_expand_var: foreign_key (%fk) not in the right format. " .
|
|
|
+ "It should be <tablename>.<fieldname>', array('%fk' => $to_expand));
|
|
|
+ }
|
|
|
+ break;
|
|
|
+
|
|
|
case "table": //--------------------------------------------------------------------------------
|
|
|
$foreign_table = $to_expand;
|
|
|
|
|
|
- // don't expand the table it already is expanded
|
|
|
+ // RECURSIVE BASE CASE: don't expand the table it already is expanded
|
|
|
if (array_key_exists($foreign_table, $object)) {
|
|
|
return $object;
|
|
|
}
|
|
|
$foreign_table_desc = chado_get_schema($foreign_table);
|
|
|
|
|
|
- // If it's connected to the base table via a FK constraint
|
|
|
+ // BASE CASE: If it's connected to the base table via a FK constraint
|
|
|
+ // then we have all the information needed to expand it now
|
|
|
if (array_key_exists($base_table, $foreign_table_desc['foreign keys'])) {
|
|
|
foreach ($foreign_table_desc['foreign keys'][$base_table]['columns'] as $left => $right) {
|
|
|
// if the FK value in the base table is not there then we can't expand it, so just skip it.
|
|
|
@@ -574,11 +752,16 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
- // if the foreign table is not connected to the base table through a FK constraint
|
|
|
+ // RECURSIVE CASE: if the table is not connected directly to the current base table
|
|
|
+ // through a foreign key relationship, then maybe it has a relationship to
|
|
|
+ // one of the nested objects.
|
|
|
else {
|
|
|
+
|
|
|
// We need to recurse -the table has a relationship to one of the nested objects
|
|
|
+ // We assume it's a nested object if the value of the field is an object
|
|
|
$did_expansion = 0;
|
|
|
foreach ((array) $object as $field_name => $field_value) {
|
|
|
+
|
|
|
// if we have a nested object ->expand the table in it
|
|
|
// check to see if the $field_name is a valid chado table, we don't need
|
|
|
// to call chado_expand_var on fields that aren't tables
|
|
|
@@ -588,6 +771,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
|
|
|
$object->{$field_name} = chado_expand_var($field_value, 'table', $foreign_table);
|
|
|
}
|
|
|
}
|
|
|
+
|
|
|
// if we did not expand this table we should return a message that the foreign table
|
|
|
// could not be expanded
|
|
|
if (!$did_expansion) {
|
|
|
@@ -598,11 +782,19 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
|
|
|
}
|
|
|
}
|
|
|
break;
|
|
|
+
|
|
|
case "node": //---------------------------------------------------------------------------------
|
|
|
- //if the node to be expanded is for our base table, then just expand it
|
|
|
+
|
|
|
+ // BASE CASE: if the node to be expanded is for our base table, then just expand it
|
|
|
if ($object->tablename == $to_expand) {
|
|
|
+
|
|
|
+ // Load the node based on the current objects nid (node primary key)
|
|
|
$node = node_load($object->nid);
|
|
|
+
|
|
|
+ // If we have successfully loaded the node...
|
|
|
if ($node) {
|
|
|
+
|
|
|
+ // Move expandable arrays from the object into the node
|
|
|
$object->expanded = $to_expand;
|
|
|
$node->expandable_fields = $object->expandable_fields;
|
|
|
unset($object->expandable_fields);
|
|
|
@@ -610,16 +802,29 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
|
|
|
unset($object->expandable_tables);
|
|
|
$node->expandable_nodes = $object->expandable_nodes;
|
|
|
unset($object->expandable_nodes);
|
|
|
+
|
|
|
+ // The node becomes the base object with the obejct added to it.
|
|
|
+ // For example, we may start with a feature object with a name, uniquename , type, etc.
|
|
|
+ // After expanding we will return the node and at $node->feature you will find the original object
|
|
|
$node->{$base_table} = $object;
|
|
|
$object = $node;
|
|
|
+
|
|
|
}
|
|
|
+ // Else we were unable to load the node
|
|
|
else {
|
|
|
+
|
|
|
+ // Warn the administrator
|
|
|
tripal_report_error('tripal_core', TRIPAL_ERROR, 'chado_expand_var: No node matches the nid (%nid) supplied.',
|
|
|
array('%nid' => $object->nid));
|
|
|
} //end of if node
|
|
|
+
|
|
|
}
|
|
|
+ // RECURSIVE CASE: check to see if the node to be expanded associates with a
|
|
|
+ // chado table within one of the nested objects.
|
|
|
else {
|
|
|
- //We need to recurse -the node to expand is one of the nested objects
|
|
|
+
|
|
|
+ // We need to recurse -the node to expand is one of the nested objects
|
|
|
+ // We assume it's a nested object if the field value is an object
|
|
|
foreach ((array) $object as $field_name => $field_value) {
|
|
|
if (is_object($field_value)) {
|
|
|
$object->{$field_name} = chado_expand_var(
|
|
|
@@ -631,41 +836,144 @@ function chado_expand_var($object, $type, $to_expand, $table_options = array())
|
|
|
} //end of for each field in the current object
|
|
|
}
|
|
|
break;
|
|
|
+
|
|
|
+ // The $type to be expanded is not yet supported
|
|
|
default:
|
|
|
tripal_report_error('tripal_core', TRIPAL_ERROR, 'chado_expand_var: Unrecognized type (%type). Should be one of "field", "table", "node".',
|
|
|
array('%type' => $type));
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
- // move extended array downwards
|
|
|
+ // Move expandable arrays downwards -------------------------------
|
|
|
+ // If the type was either table or foreign key then a new chado variable was generated
|
|
|
+ // this variable will have it's own expandable array's which need to be moved down
|
|
|
+ // and merged with the base objects expandable arrays
|
|
|
+
|
|
|
+ // Thus, check all nested objects for expandable arrays
|
|
|
+ // and if they have them, move them downwards
|
|
|
+ foreach ( (array)$object as $field_name => $field_value) {
|
|
|
+ if (is_object($field_value)) {
|
|
|
+
|
|
|
+ // The current nested object has expandable arrays
|
|
|
+ if (isset($field_value->expandable_fields)) {
|
|
|
+
|
|
|
+ // Move expandable fields downwards
|
|
|
+ if (isset($field_value->expandable_fields) and is_array($field_value->expandable_fields)) {
|
|
|
+
|
|
|
+ // If the current object has it's own expandable fields then merge them
|
|
|
+ if (isset($object->expandable_fields)) {
|
|
|
+ $object->expandable_fields = array_merge(
|
|
|
+ $object->expandable_fields,
|
|
|
+ $object->{$field_name}->expandable_fields
|
|
|
+ );
|
|
|
+ unset($object->{$field_name}->expandable_fields);
|
|
|
+
|
|
|
+ }
|
|
|
+ // Otherwise, just move the expandable fields downwards
|
|
|
+ else {
|
|
|
+ $object->expandable_fields = $object->{$field_name}->expandable_fields;
|
|
|
+ unset($object->{$field_name}->expandable_fields);
|
|
|
+ }
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ // Move expandable foreign keys downwards
|
|
|
+ if (isset($field_value->expandable_foreign_keys) and is_array($field_value->expandable_foreign_keys)) {
|
|
|
+
|
|
|
+ // If the current object has it's own expandable foreign keys then merge them
|
|
|
+ if (isset($object->expandable_foreign_keys)) {
|
|
|
+ $object->expandable_foreign_keys = array_merge(
|
|
|
+ $object->expandable_foreign_keys,
|
|
|
+ $object->{$field_name}->expandable_foreign_keys
|
|
|
+ );
|
|
|
+ unset($object->{$field_name}->expandable_foreign_keys);
|
|
|
+
|
|
|
+ }
|
|
|
+ // Otherwise, just move the expandable foreign keys downwards
|
|
|
+ else {
|
|
|
+ $object->expandable_foreign_keys = $object->{$field_name}->expandable_foreign_keys;
|
|
|
+ unset($object->{$field_name}->expandable_foreign_keys);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Move expandable tables downwards
|
|
|
+ if (isset($field_value->expandable_tables) and is_array($field_value->expandable_tables)) {
|
|
|
+
|
|
|
+ // If the current object has it's own expandable tables then merge them
|
|
|
+ if (isset($object->expandable_tables)) {
|
|
|
+ $object->expandable_tables = array_merge(
|
|
|
+ $object->expandable_tables,
|
|
|
+ $object->{$field_name}->expandable_tables
|
|
|
+ );
|
|
|
+ unset($object->{$field_name}->expandable_tables);
|
|
|
+
|
|
|
+ }
|
|
|
+ // Otherwise, just move the expandable tables downwards
|
|
|
+ else {
|
|
|
+ $object->expandable_tables = $object->{$field_name}->expandable_tables;
|
|
|
+ unset($object->{$field_name}->expandable_tables);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Move expandable nodes downwards
|
|
|
+ if (isset($field_value->expandable_nodes) and is_array($field_value->expandable_nodes)) {
|
|
|
+
|
|
|
+ // If the current object has it's own expandable tables then merge them
|
|
|
+ if (isset($object->expandable_nodes)) {
|
|
|
+ $object->expandable_nodes = array_merge(
|
|
|
+ $object->expandable_nodes,
|
|
|
+ $object->{$field_name}->expandable_nodes
|
|
|
+ );
|
|
|
+ unset($object->{$field_name}->expandable_nodes);
|
|
|
+
|
|
|
+ }
|
|
|
+ // Otherwise, just move the expandable tables downwards
|
|
|
+ else {
|
|
|
+ $object->expandable_nodes = $object->{$field_name}->expandable_nodes;
|
|
|
+ unset($object->{$field_name}->expandable_nodes);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Move extended array downwards ----------------------------------
|
|
|
+ // This tells us what we have expanded (ie: that we succeeded)
|
|
|
+ // and is needed to remove the entry from the expandable array
|
|
|
+
|
|
|
+ // If there is no expanded field in the current object then check any of the nested objects
|
|
|
+ // and move it down
|
|
|
if (!property_exists($object, 'expanded')) {
|
|
|
- //if there's no extended field then go hunting for it
|
|
|
+
|
|
|
+ // It's a nested object if the value is an object
|
|
|
foreach ( (array)$object as $field_name => $field_value) {
|
|
|
if (is_object($field_value)) {
|
|
|
+
|
|
|
+ // Check if the current nested object has an expanded array
|
|
|
if (isset($field_value->expanded)) {
|
|
|
+
|
|
|
+ // If so, then move it downwards
|
|
|
$object->expanded = $field_value->expanded;
|
|
|
unset($field_value->expanded);
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
- //try again becasue now we might have moved it down
|
|
|
+
|
|
|
+ // Check again if there is an expanded field in the current object
|
|
|
+ // We check again because it might have been moved downwards above
|
|
|
if (property_exists($object, 'expanded')) {
|
|
|
+
|
|
|
+ // If so, then remove the expanded identifier from the correct expandable array
|
|
|
$expandable_name = 'expandable_' . $type . 's';
|
|
|
if (property_exists($object, $expandable_name) and $object->{$expandable_name}) {
|
|
|
$key_to_remove = array_search($object->expanded, $object->{$expandable_name});
|
|
|
unset($object->{$expandable_name}[$key_to_remove]);
|
|
|
unset($object->expanded);
|
|
|
+
|
|
|
}
|
|
|
- else {
|
|
|
- // if there is an expandable array then we've reached the base object
|
|
|
- // if we get here and don't have anything expanded then something went wrong
|
|
|
- // tripal_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- // 'chado_expand_var: Unable to expand the %type %to_expand',
|
|
|
- // array('%type'=>$type, '%to_expand'=>$to_expand),
|
|
|
- // );
|
|
|
- } //end of it we've reached the base object
|
|
|
}
|
|
|
|
|
|
+ // Finally, Return the object!
|
|
|
return $object;
|
|
|
}
|
Stephen Ficklin