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@@ -349,9 +349,9 @@ function chado_set_active($dbname = 'default') {
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$search_path = chado_get_schema_name('drupal');
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// Change only if 'chado' has been specified.
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- // Notice that we leave the active_db set as chado but use the possibly
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- // user-altered schema name for the actual search path. This is to keep
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- // outward facing mentions of chado as "chado" while still allowing the user
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+ // Notice that we leave the active_db set as chado but use the possibly
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+ // user-altered schema name for the actual search path. This is to keep
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+ // outward facing mentions of chado as "chado" while still allowing the user
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// to alter the schema name used.
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if ($dbname == 'chado') {
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$active_db = 'chado';
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@@ -490,7 +490,7 @@ function chado_insert_record($table, $values, $options = []) {
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// that has all the values needed for insert with all foreign relationsihps
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// resolved.
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foreach ($values as $field => $value) {
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- // Make sure the field is in the table description. If not then return an
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+ // Make sure the field is in the table description. If not then return an
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// error message.
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if (!array_key_exists($field, $table_desc['fields'])) {
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tripal_report_error('tripal_chado', TRIPAL_ERROR,
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@@ -640,7 +640,7 @@ function chado_insert_record($table, $values, $options = []) {
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if ($options['return_record'] == TRUE and $result) {
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if (array_key_exists('primary key', $table_desc) and is_array($table_desc['primary key'])) {
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foreach ($table_desc['primary key'] as $field) {
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- $sql = "SELECT CURRVAL('{" . $table . "_" . $field . "_seq}')";
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+ $sql = "SELECT CURRVAL('{" . $table . "}_" . $field . "_seq')";
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$results = chado_query($sql);
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$value = $results->fetchField();
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if (!$value) {
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@@ -910,7 +910,7 @@ function chado_update_record($table, $match, $values, $options = NULL) {
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// If we have a result then add primary keys to return array.
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if ($options['return_record'] == TRUE and $result) {
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- // Only if we have a single result do we want to add the primary keys to the
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+ // Only if we have a single result do we want to add the primary keys to the
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// values array. If the update matched many records we can't add the pkeys.
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if (count($pkeys) == 1) {
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@@ -1430,7 +1430,7 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
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$where[] = $value;
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}
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// CASE 1c: If we have an integer indexed array and the first element is
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- // not an array then we have a simple array of values to be used for an
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+ // not an array then we have a simple array of values to be used for an
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// IN clause.
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elseif (is_int(key($value)) AND !is_array(current($value))) {
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@@ -1453,7 +1453,7 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
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$where[] = $subvalue;
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}
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}
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- // CASE 1e: We have a multi-dimensional array that doesn't fit any of
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+ // CASE 1e: We have a multi-dimensional array that doesn't fit any of
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// the above cases then we have a foreign key definition to follow.
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else {
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@@ -1701,7 +1701,7 @@ function chado_select_record_check_value_type(&$op, &$value, $type) {
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* $args = array( ':feature_uniquename' => $form_state['values']['uniquename']
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* );
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* $result = chado_query($sql, $args);
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- * while ($r = $results->fetchObject()) {
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+ * while ($r = $results->fetchObject()) {
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* // Do something with the record object $r
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* }
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* @endcode
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@@ -1728,30 +1728,51 @@ function chado_query($sql, $args = []) {
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// Remove carriage returns from the SQL.
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$sql = preg_replace('/\n/', ' ', $sql);
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+ // Get the current default Chado and Drupal schema prefixes.
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+ $chado_schema_name = chado_get_schema_name('chado');
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+ $drupal_schema_name = chado_get_schema_name('drupal');
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+
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// Prefix the tables with their correct schema.
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// Chado tables should be enclosed in curly brackets (ie: {feature} )
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// and Drupal tables should be enclosed in square brackets
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// (ie: [tripal_jobs] ).
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- $chado_schema_name = chado_get_schema_name('chado');
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- $drupal_schema_name = chado_get_schema_name('drupal');
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- $sql = preg_replace('/\{(.*?)\}/', $chado_schema_name . '.$1', $sql);
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- $sql = preg_replace('/\[(\w+)\]/', $drupal_schema_name . '.$1', $sql);
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+ $matches = [];
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+ if (preg_match_all('/\{(.*?)\}/', $sql, $matches)) {
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+ $matches = $matches[1];
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+ $chado_tables = array_unique(array_keys(chado_get_table_names(TRUE)));
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+ foreach ($matches as $match) {
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+ if (in_array($match, $chado_tables)) {
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+ $sql = preg_replace("/\{$match\}/", $chado_schema_name . '.' . $match, $sql);
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+ }
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+ }
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+ }
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+
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+ // Now set the Drupal prefix if the table is surrounded by square brackets.
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+ if (preg_match_all('/\[(.*?)\]/', $sql, $matches)) {
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+ $matches = $matches[1];
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+ $drupal_tables = array_unique(array_keys(drupal_get_schema()));
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+ foreach ($matches as $match) {
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+ if (in_array($match, $drupal_tables)) {
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+ $sql = preg_replace("/\[$match\]/", $drupal_schema_name . '.' . $match, $sql);
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+ }
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+ }
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+ }
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- // Add an alter hook to allow module developers to change the query right
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+ // Add an alter hook to allow module developers to change the query right
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// before it's executed. Since all queriying of chado by Tripal eventually
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// goes through this function, we only need to provide an alter hook at this
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- // point in order to ensure developers have complete control over the query
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- // being executed. For example, a module developer might want to remove
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- // schema prefixing from queries and rely on the search path. This alter
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+ // point in order to ensure developers have complete control over the query
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+ // being executed. For example, a module developer might want to remove
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+ // schema prefixing from queries and rely on the search path. This alter
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// hook would allow them to do that by implementing
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- // mymodule_chado_query_alter($sql, $args) and using a regular expression
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+ // mymodule_chado_query_alter($sql, $args) and using a regular expression
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// to remove table prefixing from the query.
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// @see hook_chado_query_alter().
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drupal_alter('chado_query', $sql, $args);
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// The featureloc table has some indexes that use function that call other
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- // functions and those calls do not reference a schema, therefore, any
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- // tables with featureloc must automaticaly have the chado schema set as
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+ // functions and those calls do not reference a schema, therefore, any
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+ // tables with featureloc must automaticaly have the chado schema set as
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// active to find.
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if (preg_match('/' . $chado_schema_name . '.featureloc/i', $sql) or preg_match('/' . $chado_schema_name . '.feature/i', $sql)) {
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$previous_db = chado_set_active('chado');
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@@ -1763,7 +1784,7 @@ function chado_query($sql, $args = []) {
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throw $e;
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}
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}
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- // For all other tables we should have everything in scope so just run the
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+ // For all other tables we should have everything in scope so just run the
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// query.
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else {
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$results = db_query($sql, $args);
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@@ -1817,11 +1838,11 @@ function hook_chado_query_alter(&$sql, &$args) {
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// The following code is an example of how this alter function might be used.
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// Say you would like only a portion of node => feature connections available
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- // for a period of time or under a specific condition. To "hide" the other
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- // connections you might create a temporary view of the chado_feature table
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+ // for a period of time or under a specific condition. To "hide" the other
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+ // connections you might create a temporary view of the chado_feature table
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// that only includes the connections you would like to be available. In order
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- // to ensure this view is used rather than the original chado_feature table
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- // you could alter all Tripal queries referring to chado_feature to instead
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+ // to ensure this view is used rather than the original chado_feature table
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+ // you could alter all Tripal queries referring to chado_feature to instead
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//refer to your view.
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if (preg_match('/(\w+)\.chado_feature/', $sql, $matches)) {
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Shawna Spoor