function getGlobalDefaults($dbconn)
{
$defaults = array("ms_tol" => 6, "ms2_tol" => 20, "ms_tol_unit" => "ppm", "ms2_tol_unit" => "ppm", "missed_cleavages" => 4, "notes" => "", "customsettings" => "", "acquisitions" => array(), "sequences" => array());
$getMultiOptions = array("enzyme" => "SELECT id FROM enzyme WHERE is_default = TRUE", "ions" => "SELECT id FROM ion WHERE is_default = TRUE", "crosslinkers" => "SELECT id FROM crosslinker WHERE is_default = TRUE", "losses" => "SELECT id FROM loss WHERE is_default = TRUE", "fixedMods" => "SELECT id FROM modification WHERE is_default_fixed = TRUE", "varMods" => "SELECT id FROM modification WHERE is_default_var = TRUE");
foreach ($getMultiOptions as $key => $value) {
pg_prepare($dbconn, $key, $value);
$result = pg_execute($dbconn, $key, array());
$defaults[$key] = resultsAsArray($result);
}
//error_log (print_r($defaults, TRUE));
return $defaults;
}
$dbconn = pg_connect($connectionString) or die('Could not connect: ' . pg_last_error());
// Get user rights from database
$userRights = getUserRights($dbconn, $_SESSION["user_id"]);
$_SESSION["canAddNewSearch"] = $userRights["canAddNewSearch"];
$canSeeAll = $userRights["canSeeAll"];
if (!$userRights["canAddNewSearch"]) {
ajaxLoginRedirect();
} else {
$possibleValues = array();
$getFieldValues = array("enzymes" => array("q" => "SELECT id, name from enzyme ORDER by name"), "ions" => array("q" => "SELECT id, name from ion ORDER by name"), "xlinkers" => array("q" => "SELECT id, name from crosslinker ORDER by name"), "losses" => array("q" => "SELECT id, name from loss ORDER by name"), "modifications" => array("q" => "SELECT id, name from modification ORDER by name"), "previousAcqui" => $canSeeAll ? array("q" => "SELECT acquisition.id, name AS Name, to_char(upload_date, 'YYYY-MM-DD HH24:MI') AS Date, users.user_name AS User FROM acquisition JOIN users ON (acquisition.uploadedby = users.id) ORDER BY acquisition.id DESC") : array("q" => "SELECT acquisition.id, name AS Name, to_char(upload_date, 'YYYY-MM-DD HH24:MI') AS Date, users.user_name AS User FROM acquisition JOIN users ON (users.id = \$1 AND acquisition.uploadedby = users.id) ORDER BY acquisition.id DESC", "params" => [$_SESSION["user_id"]]), "previousSeq" => $canSeeAll ? array("q" => "SELECT sequence_file.id, name AS Name, to_char(upload_date, 'YYYY-MM-DD HH24:MI') AS Date, users.user_name AS User, file_name as file FROM sequence_file JOIN users ON (sequence_file.uploadedby = users.id) ORDER BY upload_date DESC") : array("q" => "SELECT sequence_file.id, name AS Name, to_char(upload_date, 'YYYY-MM-DD HH24:MI') AS Date, users.user_name AS User, file_name as file FROM sequence_file JOIN users ON (users.id = \$1 AND sequence_file.uploadedby = users.id) ORDER BY upload_date DESC", "params" => [$_SESSION["user_id"]]), "filenames" => array("q" => "SELECT acq_id, name FROM run ORDER by acq_id DESC"));
foreach ($getFieldValues as $key => $value) {
$query = $value["q"];
$params = isset($value["params"]) ? $value["params"] : array();
pg_prepare($dbconn, $key, $query);
$result = pg_execute($dbconn, $key, $params);
$possibleValues[$key] = resultsAsArray($result);
}
// Get basedir for file uploads
$query = "SELECT setting FROM base_setting WHERE name='base_directory_path';";
$baseDir = pg_fetch_row(pg_query($query))[0];
// Store this server side 'cos we don't need it client side
$_SESSION["baseDir"] = $baseDir;
echo json_encode($possibleValues);
}
//close connection
pg_close($dbconn);
} catch (Exception $e) {
$date = date("d-M-Y H:i:s");
echo json_encode(array("error" => "Error when querying database for default values<br>" . $date));
}
}
$previousSeq = resultsAsArray($res);
// Get crosslinkers from DB
$res = $conn->query("SELECT id, name, is_default from crosslinker WHERE name NOT LIKE '#%' ORDER by name;");
$xlinkers = resultsAsArray($res);
// Get enzymes from DB
$res = $conn->query("SELECT id, name, is_default from enzyme ORDER by name;");
$enzymes = resultsAsArray($res);
// Get modifications from DB
$res = $conn->query("SELECT id, name, is_default_fixed, is_default_var from modification WHERE name NOT LIKE '#%' ORDER by name;");
$mods = resultsAsArray($res);
// Get ions from DB
$res = $conn->query("SELECT id, name, is_default from ion WHERE name NOT LIKE '#%' ORDER by name;");
$ions = resultsAsArray($res);
// Get losses from DB
$res = $conn->query("SELECT id, name, is_default from loss WHERE name NOT LIKE '#%' ORDER by name;");
$losses = resultsAsArray($res);
// Get basedir for file uploads
$res = $conn->query("SELECT setting FROM base_setting WHERE name='base_directory_path';");
$baseDir = $res->fetch(PDO::FETCH_BOTH)[0];
// Store this server side 'cos we don't need it client side
$_SESSION["baseDir"] = $baseDir;
$conn = null;
echo json_encode(array("xlinkers" => $xlinkers, "enzymes" => $enzymes, "previousAcqui" => $previousAcqui, "previousSeq" => $previousSeq, "ions" => $ions, "modifications" => $mods, "losses" => $losses));
} catch (Exception $e) {
echo json_encode(array("error" => $e->getMessage()));
}
// Printing results in HTML, assuming id and name field in result set
function resultsAsArray($result)
{
//echo "<p>".$result."</p>";
$arr = array();