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@@ -119,13 +119,13 @@
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* property table (e.g. featureprop) and you want the CV and accession
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* but do not want the DB the following array would work:
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*
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- * $table_options = array(
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- * 'include_fk' => array(
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- * 'type_id' => array(
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+ * $table_options = [
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+ * 'include_fk' => [
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+ * 'type_id' => [
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* 'cv_id' => 1,
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* 'dbxref_id' => 1,
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- * )
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- * )
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+ * ]
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+ * ]
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* );
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*
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* The above array will expand the 'type_id' of the property table but only
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@@ -198,19 +198,19 @@ function chado_generate_var($table, $values, $base_options = []) {
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// This allows modules to specify that some fields should be excluded by default
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// For example, tripal core provides a tripal_chado_exclude_field_from_feature_by_default()
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- // which says that we usually don't want to include the residues field by
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+ // which says that we usually don't want to include the residues field by
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// default since it can be very large and cause performance issues.
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- // If a field is excluded by default it can always be expanded at a later
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- // point by calling chado_expand_var($chado_var, 'field',
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+ // If a field is excluded by default it can always be expanded at a later
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+ // point by calling chado_expand_var($chado_var, 'field',
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// <field name as shown in expandable_fields array>);
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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
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+ // module_invoke_all() is drupal's way of invoking all implementations of the
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// specified hook and merging all of the results.
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// $fields_to_remove should be an array with the keys matching field names
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- // and the values being strings to be executed using php_eval() to determine
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+ // and the values being strings to be executed using php_eval() to determine
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// whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
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$fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');
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@@ -226,7 +226,7 @@ function chado_generate_var($table, $values, $base_options = []) {
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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 a
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+ // @coder-ignore: only module designers can populate $criteria -not a
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// security risk.
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$success = php_eval('<?php return ' . $criteria . '; ?>');
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if ($success) {
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@@ -239,35 +239,35 @@ function chado_generate_var($table, $values, $base_options = []) {
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// Get fields to be removed by type................................
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// This gets all implementations of hook_exclude_type_by_default().
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- // This allows modules to specify that some types of fields should be excluded
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- // by default For example, tripal core provides a
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- // tripal_chado_exclude_type_by_default() which says that text fields are
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+ // This allows modules to specify that some types of fields should be excluded
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+ // by default For example, tripal core provides a
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+ // tripal_chado_exclude_type_by_default() which says that text fields are
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// often very large and if they are longer than 250 characters then
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// we want to exclude them by default
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- // If a field is excluded by default it can always be expanded at a later
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- // point by calling chado_expand_var($chado_var, 'field',
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+ // If a field is excluded by default it can always be expanded at a later
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+ // point by calling chado_expand_var($chado_var, 'field',
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//<field name as shown in expandable_fields array>);
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// First get an array of all the types of fields to be removed for the current
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- // table module_invoke_all() is drupal's way of invoking all implementations
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+ // table module_invoke_all() is drupal's way of invoking all implementations
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// of the specified hook and merging all of the results.
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// $types_to_remove should be an array with the keys matching field names
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- // and the values being strings to be executed using php_eval() to determine
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+ // and the values being strings to be executed using php_eval() to determine
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// whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
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// (ie: array('text' => 'strlen("<field_value> ") > 100');
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$types_to_remove = module_invoke_all('exclude_type_by_default');
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// 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
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+ // the key is the type of field and the value is an array of fields of this
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// type.
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$field_types = [];
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foreach ($table_desc['fields'] as $field_name => $field_array) {
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$field_types[$field_array['type']][] = $field_name;
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}
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- // We want to use the types to remove in conjunction with our table field
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+ // We want to use the types to remove in conjunction with our table field
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// descriptions to determine which fields might need to be removed.
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foreach ($types_to_remove as $field_type => $criteria) {
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@@ -286,8 +286,8 @@ function chado_generate_var($table, $values, $base_options = []) {
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}
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// If criteria then remove from query
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- // (as long as <field_value> is not needed for the criteria to be
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- // evaluated) @coder-ignore: only module designers can populate
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+ // (as long as <field_value> is not needed for the criteria to be
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+ // evaluated) @coder-ignore: only module designers can populate
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//$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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@@ -316,7 +316,7 @@ function chado_generate_var($table, $values, $base_options = []) {
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// For Tripal v2 compatibility
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// check if the current table maps to a node type-------------------------
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- // If this table is connected to a node there will be a chado_tablename
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+ // If this table is connected to a node there will be a chado_tablename
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// table in drupal.
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$base_tables = chado_get_base_tables();
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if (module_exists('tripal_core') and db_table_exists('chado_' . $table)) {
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@@ -344,10 +344,10 @@ function chado_generate_var($table, $values, $base_options = []) {
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// Remove any fields where criteria needs to be evalulated----------------
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// The fields to be removed can be populated by implementing either
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- // hook_exclude_field_from_<table>_by_default() where <table> is the
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- // current table OR hook_exclude_type_by_default() where there are fields
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- // of the specified type in the current table It only reaches this point
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- // if the criteria specified for whether or not to exclude the field
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+ // hook_exclude_field_from_<table>_by_default() where <table> is the
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+ // current table OR hook_exclude_type_by_default() where there are fields
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+ // of the specified type in the current table It only reaches this point
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+ // if the criteria specified for whether or not to exclude the field
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// includes <field_value> which means it has to be evaluated after
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// the query has been executed.
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foreach ($fields_to_remove as $field_name => $criteria) {
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@@ -358,7 +358,7 @@ function chado_generate_var($table, $values, $base_options = []) {
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break;
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}
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- // Replace <field_value> with the actual value of the field from the
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+ // Replace <field_value> with the actual value of the field from the
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// query.
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$field_name_safe = preg_replace('/\'|"|\\\/', '\\1', $object->{$field_name});
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$criteria = preg_replace('/<field_value>/', $field_name_safe, $criteria);
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@@ -379,22 +379,22 @@ function chado_generate_var($table, $values, $base_options = []) {
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$foreign_table = $foreign_key_array['table'];
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foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {
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- // Note: Foreign key is the field in the current table whereas
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- // primary_key is the field in the table referenced by the foreign
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+ // Note: Foreign key is the field in the current table whereas
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+ // primary_key is the field in the table referenced by the foreign
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// key, don't do anything if the foreign key is empty
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if (empty($object->{$foreign_key})) {
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continue;
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}
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if (is_array($include_fk)) {
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- // Don't recurse if the callee has supplied an $fk_include list
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+ // Don't recurse if the callee has supplied an $fk_include list
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// and this FK table is not in the list.
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if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
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$object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
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continue;
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}
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}
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- // If we have the option but it is not an array then we don't
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+ // If we have the option but it is not an array then we don't
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// recurse any further.
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if ($include_fk === TRUE) {
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$object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
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@@ -713,8 +713,8 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// Get the value of the foreign key from the object
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$field_value = $object->{$field_name};
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- // Get the name of the field in the foreign table using the table
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- // description For example, with the
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+ // Get the name of the field in the foreign table using the table
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+ // description For example, with the
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// feature.type_id => cvterm.cvterm_id we need cvterm_id
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$foreign_field_name = FALSE;
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foreach ($table_desc['foreign keys'][$foreign_table]['columns'] as $left => $right) {
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@@ -729,7 +729,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// Generate a chado variable of the foreign key
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// For example, if the foreign key to expand is feature.type_id
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- // then we want to generate a chado cvterm variable that matches the
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+ // then we want to generate a chado cvterm variable that matches the
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// feature.type_id.
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$foreign_var = chado_generate_var(
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$foreign_table, // thus in the example above, generate a cvterm var
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@@ -740,7 +740,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// Check that the foreign object was returned.
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if ($foreign_var) {
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- // It was so now we can add this chado variable to our current
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+ // It was so now we can add this chado variable to our current
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// object in place of the key value.
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$object->{$field_name} = $foreign_var;
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$object->expanded = $to_expand;
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@@ -778,7 +778,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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}
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- // Otherwise we weren't able to extract the parts of the foreign key to
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+ // Otherwise we weren't able to extract the parts of the foreign key to
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// expand thus we will warn the administrator.
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else {
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tripal_report_error('tripal_chado', TRIPAL_ERROR,
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@@ -796,8 +796,8 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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$foreign_table_desc = chado_get_schema($foreign_table);
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- // If we don't get a foreign_table (which could happen of a custom
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- // table is not correctly defined or the table name is mispelled then we
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+ // If we don't get a foreign_table (which could happen of a custom
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+ // table is not correctly defined or the table name is mispelled then we
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// should return gracefully.
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if (!is_array($foreign_table_desc)) {
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return $object;
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@@ -837,16 +837,16 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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$filter_criteria = [$left => $object->{$right}];
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}
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- // Generate a new object for this table using the FK values in the
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+ // Generate a new object for this table using the FK values in the
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// base table.
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$new_options = $table_options;
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$foreign_object = chado_generate_var($foreign_table, $filter_criteria, $new_options);
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- // If the generation of the object was successful, update the base
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+ // If the generation of the object was successful, update the base
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// object to include it.
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if ($foreign_object) {
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// In the case where the foreign key relationship exists more
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- // than once with the same table we want to alter the array
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+ // than once with the same table we want to alter the array
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// structure to include the field name.
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if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
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if (!property_exists($object, $foreign_table)) {
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@@ -867,7 +867,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// If the object returned is NULL then handle that.
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else {
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// In the case where the foreign key relationship exists more
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- // than once with the same table we want to alter the array
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+ // than once with the same table we want to alter the array
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// structure to include the field name.
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if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
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if (!property_exists($object, $foreign_table)) {
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@@ -881,18 +881,18 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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}
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}
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- // RECURSIVE CASE: if the table is not connected directly to the current
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- // base table through a foreign key relationship, then maybe it has a
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+ // RECURSIVE CASE: if the table is not connected directly to the current
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+ // base table through a foreign key relationship, then maybe it has a
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// relationship to one of the nested objects.
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else {
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// We need to recurse -the table has a relationship to one of the nested
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- // objects. We assume it's a nested object if the value of the field is
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+ // objects. We assume it's a nested object if the value of the field is
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// an object.
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$did_expansion = 0;
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foreach ((array) $object as $field_name => $field_value) {
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- // CASE #1: This field is an already expanded foreign key and the
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+ // CASE #1: This field is an already expanded foreign key and the
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// table to be expanded is in the table referenced by the foreign key.
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// First of all it can only be expanded if it's an object
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@@ -902,10 +902,10 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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// CASE #2: This field is an already expanded object (ie: the field is
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- // actually the expanded table name) and the table to be expanded is
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+ // actually the expanded table name) and the table to be expanded is
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// related to it.
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- // Check to see if the $field_name is a valid chado table, we don't
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+ // Check to see if the $field_name is a valid chado table, we don't
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// need to call chado_expand_var on fields that aren't tables.
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$check = chado_get_schema($field_name);
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if ($check) {
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@@ -914,7 +914,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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}
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- // If we did not expand this table we should return a message that the
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+ // If we did not expand this table we should return a message that the
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// foreign tabl could not be expanded.
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if (!$did_expansion) {
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tripal_report_error('tripal_chado', TRIPAL_ERROR, 'chado_expand_var: Could not expand %table. ' .
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@@ -929,7 +929,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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case "node": //-------------------------------------------------------------
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- // BASE CASE: if the node to be expanded is for our base table, then just
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+ // BASE CASE: if the node to be expanded is for our base table, then just
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// expand it.
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if ($object->tablename == $to_expand) {
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@@ -940,7 +940,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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// Try to get the nid based on the tablename.
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else {
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- // Invoke all hook_node_info to avoid hard-coding the chado_$table
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+ // Invoke all hook_node_info to avoid hard-coding the chado_$table
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// assumption..
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foreach (module_invoke_all('node_info') as $node_info) {
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if (array_key_exists('chado_node_api', $node_info)) {
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@@ -973,7 +973,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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unset($object->expandable_nodes);
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// The node becomes the base object with the obejct added to it.
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- // For example, we may start with a feature object with a name,
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+ // For example, we may start with a feature object with a name,
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// uniquename , type, etc. After expanding we will return the node and
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// at $node->feature you will find the original object.
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$node->{$base_table} = $object;
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@@ -993,7 +993,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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} //End of if node.
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}
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- // RECURSIVE CASE: check to see if the node to be expanded associates with
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+ // RECURSIVE CASE: check to see if the node to be expanded associates with
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// a chado table within one of the nested objects.
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else {
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@@ -1019,7 +1019,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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}
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// Move expandable arrays downwards -------------------------------
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- // If the type was either table or foreign key then a new chado variable was
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+ // If the type was either table or foreign key then a new chado variable was
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// generated this variable will have it's own expandable array's which need to
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// be moved down and merged with the base objects expandable arrays.
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@@ -1054,7 +1054,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// Move expandable foreign keys downwards.
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if (isset($field_value->expandable_foreign_keys) and is_array($field_value->expandable_foreign_keys)) {
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- // If the current object has it's own expandable foreign keys then
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+ // If the current object has it's own expandable foreign keys then
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// merge them.
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if (isset($object->expandable_foreign_keys)) {
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$object->expandable_foreign_keys = array_merge(
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@@ -1116,7 +1116,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// This tells us what we have expanded (ie: that we succeeded)
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// and is needed to remove the entry from the expandable array.
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- // If there is no expanded field in the current object then check any of the
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+ // If there is no expanded field in the current object then check any of the
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// nested objects and move it down.
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if (!property_exists($object, 'expanded')) {
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@@ -1139,7 +1139,7 @@ function chado_expand_var($object, $type, $to_expand, $table_options = []) {
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// We check again because it might have been moved downwards above.
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if (property_exists($object, 'expanded')) {
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- // If so, then remove the expanded identifier from the correct expandable
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+ // If so, then remove the expanded identifier from the correct expandable
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// array..
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$expandable_name = 'expandable_' . $type . 's';
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if (property_exists($object, $expandable_name) and $object->{$expandable_name}) {
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Stephen Ficklin