// Now do the REST PUT
try {
$keepTrying = True;
$tempFailTries = 0;
while ($keepTrying) {
$irods_info[IRODS_USER_NAME] = $username;
// Note: in PHP 5.4, use JSON_UNESCAPED_SLASHES.
// we have PHP 5.3, so we have to remove those manually.
$irods_json = json_encode($irods_info);
$irods_json = str_replace('\\/', '/', $irods_json);
// error_log("Trying to create iRODS account with values: " . $irods_json);
///* Sign the data with the portal certificate (Is that correct?) */
//$irods_signed = smime_sign_message($irods_json, $portal_cert, $portal_key);
///* Encrypt the signed data for the iRODS SSL certificate */
//$irods_blob = smime_encrypt($irods_signed, $irods_cert);
$addstruct = doRESTCall($irods_url . IRODS_PUT_USER_URI . IRODS_SEND_JSON, $portal_irods_user, $portal_irods_pw, "PUT", $irods_json, "application/json", $irods_cert);
//error_log("PUT raw result: " . print_r($addstruct, true));
// look for (\r or \n or \r\n){2} and move past that
preg_match("/(\r|\n|\r\n){2}([^\r\n].+)\$/", $addstruct, $m);
if (!array_key_exists(2, $m)) {
error_log("Malformed PUT result to iRODS - error? Got: " . $addstruct);
throw new Exception("Failed to create iRODS account - server error: " . $addstruct);
}
// error_log("PUT result content: " . $m[2]);
$addjson = json_decode($m[2], true);
// Parse the result. If code 0, show username and password. Else show the error for now.
// Later if username taken, find another.
if (!is_null($addjson) && is_array($addjson) && array_key_exists(IRODS_ADD_RESPONSE_CODE, $addjson)) {
if ($addjson[IRODS_ADD_RESPONSE_CODE] == IRODS_ERROR::SUCCESS) {
$didCreate = True;
error_log("irods.php: Created account with username {$username} for " . $user->prettyName());
/**
* gets the transcript details for a gene
*
* @param string $geneName
*/
function doGetGeneTranscripts($geneName)
{
// parse the config file
$config = parse_ini_file("Config.ini", 1);
// generate the servie URL with the function name and params
$serviceURL = $config['HearSayREST']['CARNACTranscriptServiceHost'] . 'findByGeneName/' . $geneName;
// make the REST call
$data = doRESTCall($serviceURL);
//error_log($serviceURL . ", " . print_r(json_decode($data), true));
// send the data to the page
echo $data;
// terminate the data stream
die;
}
function removeGroup($project_id, $group_name, $user)
{
if (!isset($project_id) || $project_id == "-1" || !uuid_is_valid($project_id)) {
error_log("iRODS removeGroup: not a valid project ID. Nothing to do. {$project_id}");
return -1;
}
if (!isset($group_name) || is_null($group_name) || $group_name === '') {
error_log("iRODS removeGroup: not a valid group name. Nothing to do. {$project_id}, {$group_name}");
return -1;
}
error_log("iRODS removeGroup {$group_name}");
global $irods_url;
global $portal_irods_user;
global $portal_irods_pw;
global $irods_cert;
$removed = -1;
// -1=Error, 0=Success, 1=Already gone
try {
$rmstruct = doRESTCall($irods_url . IRODS_REMOVE_USER_URI1 . $group_name, $portal_irods_user, $portal_irods_pw, "DELETE", "", "", $irods_cert);
// look for (\r or \n or \r\n){2} and move past that
preg_match("/(\r|\n|\r\n){2}([^\r\n].+)\$/", $rmstruct, $m);
if (!array_key_exists(2, $m)) {
error_log("iRODS removeGroup: Malformed DELETE result from iRODS - error? Got: " . $rmstruct);
throw new Exception("Failed to remove iRODS group - server error: " . $rmstruct);
}
// FIXME: Comment this out when ready
error_log("DELETE result content: " . $m[2]);
$rmjson = json_decode($m[2], true);
// FIXME: Comment this out when ready
error_log("remove group result: " . print_r($rmjson, true));
if (is_array($rmjson)) {
$status = null;
$msg = null;
$groupCmdStatus = null;
if (array_key_exists("status", $rmjson)) {
$status = $rmjson["status"];
// Return true = 0 if removed the group, -1 on error
if ($status == IRODS_STATUS_ERROR) {
$removed = -1;
} elseif ($status == IRODS_STATUS_SUCCESS) {
$removed = 0;
}
}
if (array_key_exists("message", $rmjson)) {
$msg = $rmjson["message"];
// error_log("removeGroup result: '$msg'");
}
// Mike C says delete when the group doesn't exist returns SUCCESS
if (array_key_exists(IRODS_USER_GROUP_COMMAND_STATUS, $rmjson)) {
$groupCmdStatus = $rmjson[IRODS_USER_GROUP_COMMAND_STATUS];
if ($groupCmdStatus != IRODS_STATUS_SUCCESS) {
if ($groupCmdStatus === IRODS_STATUS_BAD_GROUP) {
error_log("iRODS: group {$group_name} not there to delete. ({$groupCmdStatus}: '{$msg}')");
$removed = 1;
} else {
error_log("iRODS failed to remove group {$group_name}: {$groupCmdStatus}: '{$msg}'");
}
}
} elseif ($removed === -1) {
error_log("iRODS failed to remove group {$group_name}: '{$msg}'");
}
} else {
$removed = -1;
error_log("iRODS malformed return from removeGroup: " . print_r($rmjson, true));
}
} catch (Exception $e) {
error_log("Error doing iRODS delete to remove group: " . $e->getMessage());
$removed = -1;
}
// Return 0 if removed the group, -1 on error, 1 if no such group
return $removed;
}