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Merge pull request #1105 from tripal/1100-tv3-references_field
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Fix for long running sio__references field
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@laceysanderson
laceysanderson committed Oct 15, 2020
2 parents 137b499 + ca28735 commit 8eab8f8
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Showing 3 changed files with 174 additions and 92 deletions.
116 changes: 58 additions & 58 deletions tripal_chado/api/tripal_chado.variables.api.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -119,13 +119,13 @@
* property table (e.g. featureprop) and you want the CV and accession
* but do not want the DB the following array would work:
*
* $table_options = array(
* 'include_fk' => array(
* 'type_id' => array(
* $table_options = [
* 'include_fk' => [
* 'type_id' => [
* 'cv_id' => 1,
* 'dbxref_id' => 1,
* )
* )
* ]
* ]
* );
*
* The above array will expand the 'type_id' of the property table but only
Expand Down Expand Up @@ -198,19 +198,19 @@ function chado_generate_var($table, $values, $base_options = []) {

// This allows modules to specify that some fields should be excluded by default
// For example, tripal core provides a tripal_chado_exclude_field_from_feature_by_default()
// which says that we usually don't want to include the residues field by
// which says that we usually don't want to include the residues field by
// default since it can be very large and cause performance issues.

// If a field is excluded by default it can always be expanded at a later
// point by calling chado_expand_var($chado_var, 'field',
// If a field is excluded by default it can always be expanded at a later
// point by calling chado_expand_var($chado_var, 'field',
// <field name as shown in expandable_fields array>);

// First get an array of all the fields to be removed for the current table
// module_invoke_all() is drupal's way of invoking all implementations of the
// module_invoke_all() is drupal's way of invoking all implementations of the
// specified hook and merging all of the results.

// $fields_to_remove should be an array with the keys matching field names
// and the values being strings to be executed using php_eval() to determine
// and the values being strings to be executed using php_eval() to determine
// whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
$fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');

Expand All @@ -226,7 +226,7 @@ function chado_generate_var($table, $values, $base_options = []) {
}

// If criteria then remove from query
// @coder-ignore: only module designers can populate $criteria -not a
// @coder-ignore: only module designers can populate $criteria -not a
// security risk.
$success = php_eval('<?php return ' . $criteria . '; ?>');
if ($success) {
Expand All @@ -239,35 +239,35 @@ function chado_generate_var($table, $values, $base_options = []) {
// Get fields to be removed by type................................
// This gets all implementations of hook_exclude_type_by_default().

// This allows modules to specify that some types of fields should be excluded
// by default For example, tripal core provides a
// tripal_chado_exclude_type_by_default() which says that text fields are
// This allows modules to specify that some types of fields should be excluded
// by default For example, tripal core provides a
// tripal_chado_exclude_type_by_default() which says that text fields are
// often very large and if they are longer than 250 characters then
// we want to exclude them by default

// If a field is excluded by default it can always be expanded at a later
// point by calling chado_expand_var($chado_var, 'field',
// If a field is excluded by default it can always be expanded at a later
// point by calling chado_expand_var($chado_var, 'field',
//<field name as shown in expandable_fields array>);

// First get an array of all the types of fields to be removed for the current
// table module_invoke_all() is drupal's way of invoking all implementations
// table module_invoke_all() is drupal's way of invoking all implementations
// of the specified hook and merging all of the results.

// $types_to_remove should be an array with the keys matching field names
// and the values being strings to be executed using php_eval() to determine
// and the values being strings to be executed using php_eval() to determine
// whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
// (ie: array('text' => 'strlen("<field_value> ") > 100');
$types_to_remove = module_invoke_all('exclude_type_by_default');

// Get a list of all the types of fields
// the key is the type of field and the value is an array of fields of this
// the key is the type of field and the value is an array of fields of this
// type.
$field_types = [];
foreach ($table_desc['fields'] as $field_name => $field_array) {
$field_types[$field_array['type']][] = $field_name;
}

// We want to use the types to remove in conjunction with our table field
// We want to use the types to remove in conjunction with our table field
// descriptions to determine which fields might need to be removed.
foreach ($types_to_remove as $field_type => $criteria) {

Expand All @@ -286,8 +286,8 @@ function chado_generate_var($table, $values, $base_options = []) {
}

// If criteria then remove from query
// (as long as <field_value> is not needed for the criteria to be
// evaluated) @coder-ignore: only module designers can populate
// (as long as <field_value> is not needed for the criteria to be
// evaluated) @coder-ignore: only module designers can populate
//$criteria -not a security risk.
$success = php_eval('<?php return ' . $criteria . '; ?>');
if ($success) {
Expand Down Expand Up @@ -316,7 +316,7 @@ function chado_generate_var($table, $values, $base_options = []) {

// For Tripal v2 compatibility
// check if the current table maps to a node type-------------------------
// If this table is connected to a node there will be a chado_tablename
// If this table is connected to a node there will be a chado_tablename
// table in drupal.
$base_tables = chado_get_base_tables();
if (module_exists('tripal_core') and db_table_exists('chado_' . $table)) {
Expand Down Expand Up @@ -344,10 +344,10 @@ function chado_generate_var($table, $values, $base_options = []) {

// Remove any fields where criteria needs to be evalulated----------------
// The fields to be removed can be populated by implementing either
// hook_exclude_field_from_<table>_by_default() where <table> is the
// current table OR hook_exclude_type_by_default() where there are fields
// of the specified type in the current table It only reaches this point
// if the criteria specified for whether or not to exclude the field
// hook_exclude_field_from_<table>_by_default() where <table> is the
// current table OR hook_exclude_type_by_default() where there are fields
// of the specified type in the current table It only reaches this point
// if the criteria specified for whether or not to exclude the field
// includes <field_value> which means it has to be evaluated after
// the query has been executed.
foreach ($fields_to_remove as $field_name => $criteria) {
Expand All @@ -358,7 +358,7 @@ function chado_generate_var($table, $values, $base_options = []) {
break;
}

// Replace <field_value> with the actual value of the field from the
// Replace <field_value> with the actual value of the field from the
// query.
$field_name_safe = preg_replace('/\'|"|\\\/', '\\1', $object->{$field_name});
$criteria = preg_replace('/<field_value>/', $field_name_safe, $criteria);
Expand All @@ -379,22 +379,22 @@ function chado_generate_var($table, $values, $base_options = []) {
$foreign_table = $foreign_key_array['table'];
foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {

// Note: Foreign key is the field in the current table whereas
// primary_key is the field in the table referenced by the foreign
// Note: Foreign key is the field in the current table whereas
// primary_key is the field in the table referenced by the foreign
// key, don't do anything if the foreign key is empty
if (empty($object->{$foreign_key})) {
continue;
}

if (is_array($include_fk)) {
// Don't recurse if the callee has supplied an $fk_include list
// Don't recurse if the callee has supplied an $fk_include list
// and this FK table is not in the list.
if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
$object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
continue;
}
}
// If we have the option but it is not an array then we don't
// If we have the option but it is not an array then we don't
// recurse any further.
if ($include_fk === TRUE) {
$object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
Expand Down Expand Up @@ -713,8 +713,8 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// Get the value of the foreign key from the object
$field_value = $object->{$field_name};

// Get the name of the field in the foreign table using the table
// description For example, with the
// Get the name of the field in the foreign table using the table
// description 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 => $right) {
Expand All @@ -729,7 +729,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {

// 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
// then we want to generate a chado cvterm variable that matches the
// feature.type_id.
$foreign_var = chado_generate_var(
$foreign_table, // thus in the example above, generate a cvterm var
Expand All @@ -740,7 +740,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// Check that the foreign object was returned.
if ($foreign_var) {

// It was so now we can add this chado variable to our current
// 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 = $to_expand;
Expand Down Expand Up @@ -778,7 +778,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {

}
}
// Otherwise we weren't able to extract the parts of the foreign key to
// 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_chado', TRIPAL_ERROR,
Expand All @@ -796,8 +796,8 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}
$foreign_table_desc = chado_get_schema($foreign_table);

// If we don't get a foreign_table (which could happen of a custom
// table is not correctly defined or the table name is mispelled then we
// If we don't get a foreign_table (which could happen of a custom
// table is not correctly defined or the table name is mispelled then we
// should return gracefully.
if (!is_array($foreign_table_desc)) {
return $object;
Expand Down Expand Up @@ -837,16 +837,16 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
$filter_criteria = [$left => $object->{$right}];
}

// Generate a new object for this table using the FK values in the
// Generate a new object for this table using the FK values in the
// base table.
$new_options = $table_options;
$foreign_object = chado_generate_var($foreign_table, $filter_criteria, $new_options);

// If the generation of the object was successful, update the base
// If the generation of the object was successful, update the base
// object to include it.
if ($foreign_object) {
// In the case where the foreign key relationship exists more
// than once with the same table we want to alter the array
// than once with the same table we want to alter the array
// structure to include the field name.
if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
if (!property_exists($object, $foreign_table)) {
Expand All @@ -867,7 +867,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// If the object returned is NULL then handle that.
else {
// In the case where the foreign key relationship exists more
// than once with the same table we want to alter the array
// than once with the same table we want to alter the array
// structure to include the field name.
if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
if (!property_exists($object, $foreign_table)) {
Expand All @@ -881,18 +881,18 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}
}
}
// RECURSIVE CASE: if the table is not connected directly to the current
// base table through a foreign key relationship, then maybe it has a
// 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
// 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) {

// CASE #1: This field is an already expanded foreign key and the
// CASE #1: This field is an already expanded foreign key and the
// table to be expanded is in the table referenced by the foreign key.

// First of all it can only be expanded if it's an object
Expand All @@ -902,10 +902,10 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}

// CASE #2: This field is an already expanded object (ie: the field is
// actually the expanded table name) and the table to be expanded is
// actually the expanded table name) and the table to be expanded is
// related to it.

// Check to see if the $field_name is a valid chado table, we don't
// 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.
$check = chado_get_schema($field_name);
if ($check) {
Expand All @@ -914,7 +914,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}
}

// If we did not expand this table we should return a message that the
// If we did not expand this table we should return a message that the
// foreign tabl could not be expanded.
if (!$did_expansion) {
tripal_report_error('tripal_chado', TRIPAL_ERROR, 'chado_expand_var: Could not expand %table. ' .
Expand All @@ -929,7 +929,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {

case "node": //-------------------------------------------------------------

// BASE CASE: if the node to be expanded is for our base table, then just
// BASE CASE: if the node to be expanded is for our base table, then just
// expand it.
if ($object->tablename == $to_expand) {

Expand All @@ -940,7 +940,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}
// Try to get the nid based on the tablename.
else {
// Invoke all hook_node_info to avoid hard-coding the chado_$table
// Invoke all hook_node_info to avoid hard-coding the chado_$table
// assumption..
foreach (module_invoke_all('node_info') as $node_info) {
if (array_key_exists('chado_node_api', $node_info)) {
Expand Down Expand Up @@ -973,7 +973,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
unset($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,
// 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} = $object;
Expand All @@ -993,7 +993,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}
} //End of if node.
}
// RECURSIVE CASE: check to see if the node to be expanded associates with
// RECURSIVE CASE: check to see if the node to be expanded associates with
// a chado table within one of the nested objects.
else {

Expand All @@ -1019,7 +1019,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
}

// Move expandable arrays downwards -------------------------------
// If the type was either table or foreign key then a new chado variable was
// 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.

Expand Down Expand Up @@ -1054,7 +1054,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// Move expandable foreign keys downwards.
if (isset($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
// If the current object has it's own expandable foreign keys then
// merge them.
if (isset($object->expandable_foreign_keys)) {
$object->expandable_foreign_keys = array_merge(
Expand Down Expand Up @@ -1116,7 +1116,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// 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
// 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')) {

Expand All @@ -1139,7 +1139,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
// We check again because it might have been moved downwards above.
if (property_exists($object, 'expanded')) {

// If so, then remove the expanded identifier from the correct expandable
// 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}) {
Expand Down

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