/**
* Populates the DDE ignore fields for each instrument and runs
* the ignoreColumn function on the instrument for the given fields
* @param $instruments
* @throws Exception
*/
function detectIgnoreColumns($instruments)
{
$instrumentFields = array();
foreach ($instruments as $instrument) {
echo "Checking DDE ignore fields for " . $instrument . "\n";
$file = "../project/instruments/NDB_BVL_Instrument_{$instrument}.class.inc";
if (file_exists($file)) {
include $file;
$instance =& NDB_BVL_Instrument::factory($instrument, null, null);
$DDEIgnoreFields = $instance->_doubleDataEntryDiffIgnoreColumns;
if ($DDEIgnoreFields != null) {
foreach ($DDEIgnoreFields as $key => $DDEField) {
if (!in_array($DDEField, $this->defaultFields)) {
$instrumentFields = array_merge($instrumentFields, array($DDEField => $instrument));
}
}
} else {
echo "No DDE ignore fields found for " . $instrument . "\n";
}
if (!$this->instrumentSpecified) {
defaultIgnoreColumns();
}
ignoreColumn($instrument, $instrumentFields);
}
}
}
/**
* Construct a request handler for candidate instrument data
* @param string $method The HTTP method to be handled
* @param string $CandID The CandID this API call is for
* @param string $Visit The Visit this API call is for
* @param string $Instrument The instrument this API call is for
* @param boolean $bDDE If true, handle DDE instrument instead of
* normal instrument data
* @param boolean $bFlags If true, include instrument flag data in
* serialization
*/
public function __construct($method, $CandID, $Visit, $Instrument, $bDDE, $bFlags)
{
if (empty($this->AllowedMethods)) {
$this->AllowedMethods = ['GET', 'PUT', 'PATCH', 'OPTIONS'];
}
$this->AutoHandleRequestDelegation = false;
$this->bDDE = $bDDE;
$this->bFlags = $bFlags;
parent::__construct($method, $CandID, $Visit);
// instruments may need access to project libraries
set_include_path(get_include_path() . ":" . __DIR__ . "/../../../../project/libraries");
include_once "NDB_BVL_Instrument.class.inc";
$CommentID = $this->DB->pselectOne("SELECT CommentID FROM flag f\n LEFT JOIN session s ON (s.ID=f.SessionID AND s.Visit_label=:VL)\n LEFT JOIN candidate c USING (CandID)\n WHERE Test_name=:TN AND s.CandID=:CID AND\n s.Active='Y' AND c.Active='Y' AND f.CommentID NOT LIKE 'DDE%'", array('VL' => $this->VisitLabel, 'TN' => $Instrument, 'CID' => $this->CandID));
if (empty($CommentID)) {
$this->header("HTTP/1.1 404 Not Found");
$this->error("Invalid instrument for candidate");
$this->safeExit(0);
}
if ($this->bDDE) {
$CommentID = 'DDE_' . $CommentID;
}
try {
$this->Instrument = \NDB_BVL_Instrument::factory($Instrument, $CommentID, null, true);
} catch (Exception $e) {
$this->header("HTTP/1.1 404 Not Found");
$this->error("Invalid instrument");
$this->safeExit(0);
}
$this->handleRequest();
}
/**
* Construct the object to handle requests. This will instantiate
* the NDB_BVL_Instrument object and call toJSON to return the
* JSON to the client.
*
* @param string $method The HTTP method used for the request
* @param string $Instrument The instrument to be serialized
*/
function __construct($method, $Instrument)
{
$this->AutoHandleRequestDelegation = false;
parent::__construct($method);
try {
$this->Instrument = \NDB_BVL_Instrument::factory($Instrument, null, null, true);
} catch (\Exception $e) {
$this->header("HTTP/1.1 404 Not Found");
$this->error("Invalid Instrument");
$this->safeExit(0);
}
// JSON is used by both calculateETag and handleGET, so do it
// before either is called.
$this->JSONString = $this->Instrument->toJSON();
$this->handleRequest();
}
AND s.Active='Y' and s.Cancelled='N'
AND c.Active='Y' and c.Cancelled='N'", $Missings);
print $t . ":" . count($Missings) . "\n";
foreach($Missings as $row) {
$date = explode('-', $row['Date_taken']);
$dateArray = array ('Y' => $date[0], 'M' => $date[1], 'd' => $date[2]);
$instrument =& NDB_BVL_Instrument::factory('mullen', $row['CommentID'], null);
$instrument->_saveValues(array('Date_taken' => $dateArray));
}
*/
//}
$instruments = Utility::getAllInstruments();
foreach ($instruments as $inst) {
// Now works with vineland
//if($inst == 'vineland' || $inst=="vineland_proband" || $inst=="vineland_subject") continue;
$DB->select("SELECT i.CommentID, i.Date_taken FROM {$inst} i JOIN flag f USING(CommentID) JOIN session s ON (s.ID=f.SessionID) JOIN candidate c USING(CandID) WHERE c.Active='Y' and s.Active='Y' AND i.Candidate_Age IS NULL AND i.Date_taken IS NOT NULL", $CommentIDs);
print "{$inst} (" . count($CommentIDs) . ")\n";
$db->select("SELECT TABLE_NAME FROM information_schema.columns WHERE TABLE_SCHEMA='{$database['database']}' AND COLUMN_NAME='Date_taken' AND TABLE_NAME='{$inst}'", $tables);
if (count($tables) > 0) {
foreach ($CommentIDs as $row) {
$date = explode('-', $row['Date_taken']);
$dateArray = array('Y' => $date[0], 'M' => $date[1], 'd' => $date[2]);
$instrument =& NDB_BVL_Instrument::factory($inst, $row['CommentID'], null, false);
if ($instrument && !empty($row['Date_taken'])) {
//print_r($dateArray);
$instrument->_saveValues(array('Date_taken' => $dateArray));
}
}
}
}
print_r($instruments);
/**
* *Detect those conflicts which are currently in the conflicts_unresolved table
* But should be excluded based on the _doubleDataEntryDiffIgnoreColumns array
*
* @param String $instrument The instrument used for conflict detection
* @param Array $commentids Used for creation of instrument-instantiation
* @param Array $current_conflicts An array of current conflicts detected
*
* @return Array $conflicts_to_excluded Array of confllicts to be execluded
*/
function detectConflictsTobeExcluded($instrument, $commentids, $current_conflicts)
{
$conflicts_to_excluded = array();
$instance1 =& NDB_BVL_Instrument::factory($instrument, $commentids[0]['CommentID'], null);
$ignore_columns = $instance1->_doubleDataEntryDiffIgnoreColumns;
foreach ($current_conflicts as $conflict) {
/**
* if the field is part of the ignore_columns,
* and it doesn exist in the conflict array
* then track it
*/
if (in_array($conflict['FieldName'], $ignore_columns)) {
$conflicts_to_excluded[] = $conflict;
}
}
return $conflicts_to_excluded;
}
<?php
/**
* This returns the instrument passed in by the Instrument GET parameter
* and serializes it as JSON for the REST API.
*
* PHP Version 5
*
* @category Loris
* @package API
* @author Dave MacFarlane <*****@*****.**>
* @license Loris license
* @link https://github.com/aces/Loris
*/
//Load config file and ensure paths are correct
set_include_path(get_include_path() . ":" . __DIR__ . "../../../php/libraries");
// Ensures the user is logged in, and parses the config file.
require_once "NDB_Client.class.inc";
$client = new NDB_Client();
$client->initialize("../../../project/config.xml");
require_once 'NDB_BVL_Instrument.class.inc';
$Instrument = $_REQUEST['Instrument'];
$a = NDB_BVL_Instrument::factory($Instrument, null, null);
print $a->toJSON();
log_msg("------------------------------");
$query = "SELECT s.CandID, s.Visit_label, s.ID as SessionID, t.CommentID, c.PSCID\n FROM candidate as c, session as s, flag as f, {$test_name} as t\n WHERE c.CandID=s.CandID AND s.ID=f.SessionID AND f.CommentID=t.CommentID\n AND s.Active = 'Y' AND c.Active='Y' \n AND f.Test_name = '{$test_name}' AND f.Administration <> 'None' AND f.Administration IS NOT NULL";
if ($action == 'one') {
$query .= " AND s.ID = '{$sessionID}' AND s.CandID='{$candID}'";
}
$db->select($query, $result);
// return error if no candidates/timepoint matched the args
if (!is_array($result) || count($result) == 0) {
fwrite(STDERR, "No records match the criteria returned for candidate ({$candID}), timepoint ({$sessionID})!\n");
return false;
}
fwrite(STDERR, "Start \n");
// loop the list and derive scores for each record
foreach ($result as $record) {
// make an instance of the instrument's object
$instrument =& NDB_BVL_Instrument::factory($test_name, $record['CommentID'], null);
// check if the instrument has a scoring method
if (!method_exists($instrument, "score")) {
fwrite(STDERR, "Error, the instrument ({$test_name}) does not have a scoring feature \n");
return false;
}
// print out candidate/session info
fwrite(STDERR, "Candidate: " . $record['CandID'] . "/" . $record['Visit_label'] . "/" . $record['SessionID'] . ":: ({$record['PSCID']})\n");
//fwrite(STDERR, "Candidate: ".$instrument->_dob."/"."Test_name:".$test_name."/". $instrument->_pls3Age."/".$instrument->getDateOfAdministration().":: \n");
// call the score function
$db->selectRow("SELECT * FROM {$test_name} WHERE CommentID='{$record['CommentID']}'", $oldRecord);
$success = $instrument->score();
$db->selectRow("SELECT * FROM {$test_name} WHERE CommentID='{$record['CommentID']}'", $newRecord);
unset($oldRecord['Testdate']);
unset($newRecord['Testdate']);
$diff = array_diff_assoc($oldRecord, $newRecord);
if (PEAR::isError($timePoint)) {
$tpl_data['error_message'][] = $timePoint->getMessage();
} else {
$tpl_data['visitLabel'] = $timePoint->getVisitLabel();
}
$tpl_data['sessionID'] = $_REQUEST['sessionID'];
}
if (!empty($_REQUEST['commentID'])) {
$tpl_data['commentID'] = $_REQUEST["commentID"];
$subtest = isset($_REQUEST['subtest']) ? $subtest : null;
if (!empty($_REQUEST['test_name'])) {
$InstrumentPath = $paths['base'] . "project/instruments/NDB_BVL_Instrument_" . $_REQUEST['test_name'] . ".class.inc";
if (file_exists($InstrumentPath)) {
// otherwise create an instrument_<test_name> object
include_once $InstrumentPath;
$instrument =& NDB_BVL_Instrument::factory($_REQUEST['test_name'], $_REQUEST['commentID'], $subtest);
if (PEAR::isError($instrument)) {
$tpl_data['error_message'][] = $instrument->getMessage();
}
$tpl_data['instrument_name'] = $instrument->getFullName();
} else {
$tpl_data['instrument_name'] = $_REQUEST['test_name'];
}
///get the fields names....
// "Add Feedback" Form" - option array for select boxes - 2 arrays;
// one is for labels
$field_names = Utility::getSourcefields($_REQUEST['test_name']);
$Fields['Across All Fields'] = 'Across All Fields';
foreach ($field_names as $field_name) {
$Fields[$field_name['SourceField']] = $field_name['SourceField'];
}
//$query = "select * from test_names where Test_name like 'a%' order by Test_name"; //for rapid testing
$DB->select($query, $instruments);
if (PEAR::isError($instruments)) {
PEAR::raiseError("Couldn't get instruments. " . $instruments->getMessage());
}
foreach ($instruments as $instrument) {
//Query to pull the data from the DB
$Test_name = $instrument['Test_name'];
if ($Test_name == 'prefrontal_task') {
$query = "select c.PSCID, c.CandID, s.SubprojectID, s.Visit_label, s.Submitted, s.Current_stage, s.Screening, s.Visit, f.Administration, e.full_name as Examiner_name, f.Data_entry, 'See validity_of_data field' as Validity, i.* from candidate c, session s, flag f, {$Test_name} i left outer join examiners e on i.Examiner = e.examinerID where c.PSCID not like 'dcc%' and c.PSCID not like '0%' and c.PSCID not like '1%' and c.PSCID not like '2%' and c.PSCID != 'scanner' and i.CommentID not like 'DDE%' and c.CandID = s.CandID and s.ID = f.sessionID and f.CommentID = i.CommentID AND c.Active='Y' AND s.Active='Y' order by s.Visit_label, c.PSCID";
} else {
if ($Test_name == 'radiology_review') {
$query = "select c.PSCID, c.CandID, s.SubprojectID, s.Visit_label, s.Submitted, s.Current_stage, s.Screening, s.Visit, f.Administration, e.full_name as Examiner_name, f.Data_entry, f.Validity, 'Site review:', i.*, 'Final Review:', COALESCE(fr.Review_Done, 0) as Review_Done, fr.Final_Review_Results, fr.Final_Exclusionary, fr.Final_Incidental_Findings, fre.full_name as Final_Examiner_Name, fr.Final_Review_Results2, fre2.full_name as Final_Examiner2_Name, fr.Final_Exclusionary2, COALESCE(fr.Review_Done2, 0) as Review_Done2, fr.Final_Incidental_Findings2, fr.Finalized from candidate c, session s, flag f, {$Test_name} i left join final_radiological_review fr ON (fr.CommentID=i.CommentID) left outer join examiners e on (i.Examiner = e.examinerID) left join examiners fre ON (fr.Final_Examiner=fre.examinerID) left join examiners fre2 ON (fre2.examinerID=fr.Final_Examiner2) where c.PSCID not like 'dcc%' and c.PSCID not like '0%' and c.PSCID not like '1%' and c.PSCID not like '2%' and c.PSCID != 'scanner' and i.CommentID not like 'DDE%' and c.CandID = s.CandID and s.ID = f.sessionID and f.CommentID = i.CommentID AND c.Active='Y' AND s.Active='Y' order by s.Visit_label, c.PSCID";
} else {
if (is_file("../project/instruments/NDB_BVL_Instrument_{$Test_name}.class.inc")) {
$instrument =& NDB_BVL_Instrument::factory($Test_name, '', false);
if ($instrument->ValidityEnabled == true) {
$query = "select c.PSCID, c.CandID, s.SubprojectID, s.Visit_label, s.Submitted, s.Current_stage, s.Screening, s.Visit, f.Administration, e.full_name as Examiner_name, f.Data_entry, f.Validity, i.* from candidate c, session s, flag f, {$Test_name} i left outer join examiners e on i.Examiner = e.examinerID where c.PSCID not like 'dcc%' and c.PSCID not like '0%' and c.PSCID not like '1%' and c.PSCID not like '2%' and c.PSCID != 'scanner' and i.CommentID not like 'DDE%' and c.CandID = s.CandID and s.ID = f.sessionID and f.CommentID = i.CommentID AND c.Active='Y' AND s.Active='Y' order by s.Visit_label, c.PSCID";
} else {
$query = "select c.PSCID, c.CandID, s.SubprojectID, s.Visit_label, s.Submitted, s.Current_stage, s.Screening, s.Visit, f.Administration, e.full_name as Examiner_name, f.Data_entry, i.* from candidate c, session s, flag f, {$Test_name} i left outer join examiners e on i.Examiner = e.examinerID where c.PSCID not like 'dcc%' and c.PSCID not like '0%' and c.PSCID not like '1%' and c.PSCID not like '2%' and c.PSCID != 'scanner' and i.CommentID not like 'DDE%' and c.CandID = s.CandID and s.ID = f.sessionID and f.CommentID = i.CommentID AND c.Active='Y' AND s.Active='Y' order by s.Visit_label, c.PSCID";
}
} else {
$query = "select c.PSCID, c.CandID, s.SubprojectID, s.Visit_label, s.Submitted, s.Current_stage, s.Screening, s.Visit, f.Administration, e.full_name as Examiner_name, f.Data_entry, f.Validity, i.* from candidate c, session s, flag f, {$Test_name} i left outer join examiners e on i.Examiner = e.examinerID where c.PSCID not like 'dcc%' and c.PSCID not like '0%' and c.PSCID not like '1%' and c.PSCID not like '2%' and c.PSCID != 'scanner' and i.CommentID not like 'DDE%' and c.CandID = s.CandID and s.ID = f.sessionID and f.CommentID = i.CommentID AND c.Active='Y' AND s.Active='Y' order by s.Visit_label, c.PSCID";
}
}
}
$DB->select($query, $instrument_table);
if (PEAR::isError($instrument_table)) {
print "Cannot pull instrument table data " . $instrument_table->getMessage() . "<br>\n";
die;
}