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@@ -3,6 +3,83 @@
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require_once "tripal_core.schema_v1.2.api.inc";
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require_once "tripal_core.schema_v1.11.api.inc";
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+// Globals used by Tripals Error catching functions
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+// Should match those defined by watchdog
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+define('TRIPAL_CRITICAL',2);
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+define('TRIPAL_ERROR',3);
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+define('TRIPAL_WARNING',4);
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+define('TRIPAL_NOTICE',5);
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+define('TRIPAL_INFO',6);
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+define('TRIPAL_DEBUG',7);
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+
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+/**
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+ * Provide better error notice for Tripal
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+ * @param $type
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+ * The catagory to which this message belongs. Can be any string, but the general
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+ * practice is to use the name of the module.
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+ * @param $message
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+ * The message to store in the log. Keep $message translatable by not concatenating
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+ * dynamic values into it! Variables in the message should be added by using placeholder
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+ * strings alongside the variables argument to declare the value of the placeholders.
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+ * See t() for documentation on how $message and $variables interact.
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+ * @param $variables
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+ * Array of variables to replace in the message on display or NULL if message is
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+ * already translated or not possible to translate.
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+ * @param $severity
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+ * The severity of the message; one of the following values:
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+ * - TRIPAL_CRITICAL: Critical conditions.
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+ * - TRIPAL_ERROR: Error conditions.
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+ * - TRIPAL_WARNING: Warning conditions.
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+ * - TRIPAL_NOTICE: (default) Normal but significant conditions.
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+ * - TRIPAL_INFO: Informational messages.
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+ * - TRIPAL_DEBUG: Debug-level messages.
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+ * @param $options
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+ * An array of options. Some available options include:
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+ * - print: prints the error message to the screen. Useful when display is the command-line
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+ */
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+function tripal_core_report_error($type, $severity, $message, $variables = array(), $options = array()) {
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+
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+ // Get human-readable severity string
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+ $severity_string = '';
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+ switch ($severity) {
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+ case TRIPAL_CRITICAL:
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+ $severity_string = 'CRITICAL';
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+ break;
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+ case TRIPAL_ERROR:
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+ $severity_string = 'ERROR';
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+ break;
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+ case TRIPAL_WARNING:
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+ $severity_string = 'WARNING';
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+ break;
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+ case TRIPAL_NOTICE:
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+ $severity_string = 'NOTICE';
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+ break;
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+ case TRIPAL_INFO:
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+ $severity_string = 'INFO';
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+ break;
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+ case TRIPAL_DEBUG:
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+ $severity_string = 'DEBUG';
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+ break;
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+ }
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+
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+ // Send to watchdog
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+ try {
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+ watchdog($type, $message, $variables, $severity);
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+ }
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+ catch (Exception $e) {
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+ print "CRITICAL (TRIPAL_CORE): Unable to register error message with watchdog";
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+ $options['print'] = TRUE;
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+ }
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+
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+ // If print option supplied then print directly to the screen
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+ if (isset($options['print'])) {
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+ if (sizeof($variables) > 0) {
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+ $message = str_replace(array_keys($variables), $variables, $message);
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+ }
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+ print $severity_string . ' (' . strtoupper($type) . '):' . $message . "\n";
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+ }
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+}
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+
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/**
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* @file
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* The Tripal Core API
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@@ -96,12 +173,26 @@ require_once "tripal_core.schema_v1.11.api.inc";
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*/
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function tripal_core_chado_insert($table, $values, $options = array()) {
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+ $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
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+
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if (!is_array($values)) {
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- watchdog('tripal_core', 'Cannot pass non array as values for inserting.', array(), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass non array as values for inserting.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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if (count($values)==0) {
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- watchdog('tripal_core', 'Cannot pass an empty array as values for inserting.', array(), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass an empty array as values for inserting.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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@@ -130,7 +221,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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// get the table description
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$table_desc = tripal_core_get_chado_table_schema($table);
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if (empty($table_desc)) {
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- watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_WARNING,
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+ 'tripal_core_chado_insert; There is no table description for !table_name',
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+ array('!table_name' => $table),
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+ array('print' => $print_errors)
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+ );
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}
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// iterate through the values array and create a new 'insert_values' array
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@@ -140,9 +237,14 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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// make sure the field is in the table description. If not then return an error
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// message
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if (!array_key_exists($field, $table_desc['fields'])) {
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- watchdog('tripal_core', "tripal_core_chado_insert: The field '%field' does not exist " .
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- "for the table '%table'. Cannot perform insert. Values: %array",
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- array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ "tripal_core_chado_insert; The field '%field' does not exist " .
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+ "for the table '%table'. Cannot perform insert. Values: %array",
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+ array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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@@ -151,10 +253,22 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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$results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
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if (sizeof($results) > 1) {
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- watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
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+ array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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+ array('print' => $print_errors)
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+ );
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}
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elseif (sizeof($results) < 1) {
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- //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_DEBUG,
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+ 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
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+ array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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+ array('print' => $print_errors)
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+ );
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}
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else {
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$insert_values[$field] = $results[0];
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@@ -190,8 +304,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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}
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// now check the constraint
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if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals)) {
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- watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate record into $table table: " .
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- print_r($values, 1), array(), 'WATCHDOG_ERROR');
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ "tripal_core_chado_insert; Cannot insert duplicate record into $table table: !values",
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+ array('!values' => print_r($values, TRUE)),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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}
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@@ -203,7 +322,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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if (array_key_exists($pkey, $insert_values)) {
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$coptions = array('statement_name' => 'pqsel_' . $table . '_' . $pkey);
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if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]), $coptions)) {
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- watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'tripal_core_chado_insert; Cannot insert duplicate primary key into !table table: !values',
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+ array('!table' => $table, '!values' => print_r($values, TRUE)),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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}
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@@ -212,9 +337,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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// make sure required fields have a value
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if (!is_array($table_desc['fields'])) {
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$table_desc['fields'] = array();
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- watchdog('tripal_core', "tripal_core_chado_insert: %table missing fields: \n %schema",
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- array('%table' => $table, '%schema' => print_r($table_desc, 1)), WATCHDOG_WARNING);
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-
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_WARNING,
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+ "tripal_core_chado_insert; %table missing fields: \n %schema",
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+ array('%table' => $table, '%schema' => print_r($table_desc, 1)),
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+ array('print' => $print_errors)
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+ );
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}
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foreach ($table_desc['fields'] as $field => $def) {
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// a field is considered missing if it cannot be NULL and there is no default
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@@ -223,8 +352,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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!array_key_exists($field, $insert_values) and
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!array_key_exists('default', $def) and
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strcmp($def['type'], serial) != 0) {
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- watchdog('tripal_core', "tripal_core_chado_insert: Field $table.$field cannot be NULL: " .
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- print_r($values, 1), array(), 'WATCHDOG_ERROR');
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ "tripal_core_chado_insert; Field %table.%field cannot be NULL: %values",
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+ array('%table' => $table, '%field' => $field, '%values' => print_r($values, 1)),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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}
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@@ -259,8 +393,13 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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$results = chado_query($sql);
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$value = $results->fetchObject();
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if (!$value) {
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- watchdog('tripal_core', "tripal_core_chado_insert: not able to retrieve primary key after insert: %sql",
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- array('%sql' => $sql), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ "tripal_core_chado_insert; not able to retrieve primary key after insert: %sql",
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+ array('%sql' => $sql),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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$values[$field] = $value;
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@@ -272,14 +411,20 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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return TRUE;
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}
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else {
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- watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert record into '%table': " . print_r($values, 1),
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- array('%table' => $table), 'WATCHDOG_ERROR');
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'tripal_core_chado_insert; Cannot insert record into "%table": %values',
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+ array('%table' => $table, '%values' => print_r($values, 1)),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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return FALSE;
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}
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+
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/**
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* Provides a generic routine for updating into any Chado table
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*
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@@ -344,25 +489,47 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
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*/
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function tripal_core_chado_update($table, $match, $values, $options = NULL) {
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+ $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
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+
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if (!is_array($values)) {
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- watchdog('tripal_core', 'Cannot pass non array as values for updating.', array(),
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- WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass non array as values for updating.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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if (count($values)==0) {
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- watchdog('tripal_core', 'Cannot pass an empty array as values for updating.', array(),
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- WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass an empty array as values for updating.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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if (!is_array($match)) {
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- watchdog('tripal_core', 'Cannot pass non array as values for matching.', array(),
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- WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass non array as values for matching.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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if (count($match)==0) {
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- watchdog('tripal_core', 'Cannot pass an empty array as values for matching.', array(),
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- WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'Cannot pass an empty array as values for matching.',
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+ array(),
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+ array('print' => $print_errors)
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+ );
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return FALSE;
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}
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@@ -410,10 +577,22 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
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if (is_array($value)) {
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$results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
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if (sizeof($results) > 1) {
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- watchdog('tripal_core', 'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_ERROR,
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+ 'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
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+ array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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+ array('print' => $print_errors)
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+ );
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}
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elseif (sizeof($results) < 1) {
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- //watchdog('tripal_core', 'tripal_core_chado_update: When trying to find record to update, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
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+ tripal_core_report_error(
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+ 'tripal_core',
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+ TRIPAL_DEBUG,
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+ 'tripal_core_chado_update: When trying to find record to update, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
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+ array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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+ array('print' => $print_errors)
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+ );
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}
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else {
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$update_matches[$field] = $results[0];
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@@ -431,10 +610,22 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
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// select the value from the foreign key relationship for this value
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$results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
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|
if (sizeof($results) > 1) {
|
|
|
- watchdog('tripal_core', 'tripal_core_chado_update: When trying to find update values, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'tripal_core_chado_update: When trying to find update values, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
+ array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
}
|
|
|
elseif (sizeof($results) < 1) {
|
|
|
- //watchdog('tripal_core', 'tripal_core_chado_update: When trying to find update values, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_DEBUG,
|
|
|
+ 'tripal_core_chado_update: When trying to find update values, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
+ array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
}
|
|
|
else {
|
|
|
$update_values[$field] = $results[0];
|
|
|
@@ -491,7 +682,13 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
|
|
|
return TRUE;
|
|
|
}
|
|
|
else {
|
|
|
- watchdog('tripal_core', "Cannot update record in $table table. \nMatch:" . print_r($match, 1) . "\nValues: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ "tripal_core_chado_update: Cannot update record in %table table. \nMatch: %match \nValues: %values",
|
|
|
+ array('%table' => table, '%match' => print_r($match,TRUE), '%values' => print_r($values, 1)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
@@ -747,19 +944,36 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
|
|
|
*/
|
|
|
function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
|
|
|
|
|
|
+ $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
|
|
|
+
|
|
|
if (!is_array($values)) {
|
|
|
- watchdog('tripal_core', 'Cannot pass non array as values for selecting.', array(),
|
|
|
- WATCHDOG_ERROR);
|
|
|
- return FALSE;
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'Cannot pass non array as values for selecting.',
|
|
|
+ array(),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
+ return FALSE;
|
|
|
}
|
|
|
if (!is_array($columns)) {
|
|
|
- watchdog('tripal_core', 'Cannot pass non array as columns for selecting.', array(),
|
|
|
- WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'Cannot pass non array as columns for selecting.',
|
|
|
+ array(),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
if (count($columns)==0) {
|
|
|
- watchdog('tripal_core', 'Cannot pass an empty array as columns for selecting.', array(),
|
|
|
- WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'Cannot pass an empty array as columns for selecting.',
|
|
|
+ array(),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
@@ -793,11 +1007,23 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
|
|
|
|
|
|
// check that our columns and values arguments are proper arrays
|
|
|
if (!is_array($columns)) {
|
|
|
- watchdog('tripal_core', 'the $columns argument for tripal_core_chado_select must be an array.');
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'tripal_core_chado_select; the $columns argument must be an array. Columns:%columns',
|
|
|
+ array('%columns' => print_r($columns, TRUE)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
if (!is_array($values)) {
|
|
|
- watchdog('tripal_core', 'the $values argument for tripal_core_chado_select must be an array.');
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'tripal_core_chado_select; the $values argument must be an array. Values:%values',
|
|
|
+ array('%values' => print_r($values, TRUE)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
@@ -868,9 +1094,13 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
|
|
|
// and there is no default value then we cannot check if the record
|
|
|
// is a duplicate so return FALSE
|
|
|
else {
|
|
|
- watchdog('tripal_core', "tripal_core_chado_select: There is no value for %field"
|
|
|
- . " thus we cannot check if this record is unique",
|
|
|
- array('%field' => $field), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'tripal_core_chado_select: There is no value for %field thus we cannot check if this record is unique',
|
|
|
+ array('%field' => $field),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return FALSE;
|
|
|
}
|
|
|
}
|
|
|
@@ -897,9 +1127,13 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
|
|
|
// make sure the field is in the table description. If not then return an error
|
|
|
// message
|
|
|
if (!array_key_exists($field, $table_desc['fields'])) {
|
|
|
- watchdog('tripal_core', "tripal_core_chado_select: The field '%field' does not exist " .
|
|
|
- "for the table '%table'. Cannot perform query. Values: %array",
|
|
|
- array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'tripal_core_chado_select: The field "%field" does not exist for the table "%table". Cannot perform query. Values: %array',
|
|
|
+ array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)),
|
|
|
+ array('print' => $print_errors)
|
|
|
+ );
|
|
|
return array();
|
|
|
}
|
|
|
|
|
|
@@ -1907,8 +2141,14 @@ function chado_query($sql, $args = array()) {
|
|
|
|
|
|
$is_local = tripal_core_is_chado_local();
|
|
|
|
|
|
+ // Args should be an array
|
|
|
if (!is_array($args)) {
|
|
|
- watchdog('tripal_core', 'Need to pass an array to chado_query, "%value" passed instead. Query: %query', array('%value' => $args, '%query' => $sql), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error(
|
|
|
+ 'tripal_core',
|
|
|
+ TRIPAL_ERROR,
|
|
|
+ 'chado_query; Need to pass an array to chado_query, "%value" passed instead. Query: %query',
|
|
|
+ array('%value' => $args, '%query' => $sql)
|
|
|
+ );
|
|
|
$args = array($args);
|
|
|
}
|
|
|
|
|
|
@@ -2466,7 +2706,7 @@ function tripal_core_schema_exists($schema) {
|
|
|
$name = $results->fetchObject();
|
|
|
if (strcmp($name->nspname, $schema) != 0) {
|
|
|
return FALSE;
|
|
|
- }
|
|
|
+ }
|
|
|
return TRUE;
|
|
|
}
|
|
|
|
|
|
@@ -2796,7 +3036,7 @@ function tripal_core_is_chado_installed() {
|
|
|
return TRUE;
|
|
|
}
|
|
|
|
|
|
- // check to make sure the chado schema exists
|
|
|
+ // check to make sure the chado schema exists
|
|
|
return tripal_core_chado_schema_exists();
|
|
|
}
|
|
|
|
Stephen Ficklin