function UserAnswers($answers, $userId = -1, $position = -1)
{
CommonTools::initializeCommonObjects($this);
$this->userId = $userId;
$this->setAnswers($answers);
$this->setPosition($position);
}
function formatConfirmedAnswerRow($answersByUser, $questions, $position, $adminMode)
{
$configurations = CommonTools::getConfigurations();
$webRoot = $configurations->webRoot;
$rowClass = SignupGadgetAnswerFormater::getRowClass();
$return = "<tr class=\"{$rowClass}\">";
$debugger = CommonTools::getDebugger();
$debugger->debugVar($answersByUser, "answerByUser", "formatConfirmedAnswerRow");
$return .= "<td class=\"answer-position\">" . $answersByUser->getPosition() . "</td>";
$lastAnswer = null;
// Could be any answer, not only last answer
foreach ($questions as $question) {
// Gets answer to questin
$answerObject = $answersByUser->getAnswerToQuestion($question->getId());
if (is_a($answerObject, "Answer")) {
$return .= "<td class=\"answer\">" . $answerObject->getReadableAnswer() . "</td>";
$lastAnswer = $answerObject;
} else {
// Joku virheilmotus tähänkö?
}
}
if ($adminMode && $lastAnswer != null) {
$return .= "<td class=\"edit-answer\"><a href=\"" . $webRoot . "admin/editanswer/" . $lastAnswer->getSignupId() . "/?userid=" . $lastAnswer->getUserId() . "\">[muokkaa]</a></td>";
$return .= "<td class=\"delete-answer\"><a href=\"" . $webRoot . "admin/deleteanswer/" . $lastAnswer->getSignupId() . "/?userid=" . $lastAnswer->getUserId() . "\">[poista]</a></td>";
}
$return .= "</tr>\n";
return $return;
}
function selectSearchSignupGadget($keyword)
{
// Split search line into keywords
$keywords = split(" ", $keyword);
// clear previous entry forms
$this->removeAll();
$whereclause = "WHERE";
$isFirst = true;
foreach ($keywords as $word) {
if ($isFirst) {
$whereclause = $whereclause . " title LIKE '%{$word}%'";
$isFirst = false;
} else {
// I'm not sure if AND is better than OR...
$whereclause = $whereclause . " AND title LIKE '%{$word}%'";
}
}
$sql = "SELECT id, opens, closes, title, description, eventdate, send_confirmation, confirmation_message " . "FROM ilmo_masiinat {$whereclause} ORDER BY id DESC";
/* print_r(get_class_methods($whereclause));
print($whereclause->getDebugInfo());
die(); */
$result = $this->database->doSelectQuery($sql, array(), array());
// Adds gadgets to signupGadgets variable
while ($row = $result->fetchRow(MDB2_FETCHMODE_ASSOC)) {
$singleGadget = new SignupGadget($row['id'], $row['title'], $row['description'], strtotime($row['eventdate']), strtotime($row['opens']), strtotime($row['closes']), CommonTools::sqlToBoolean($row['send_confirmation']), $row['confirmation_message']);
array_push($this->signupGadgets, $singleGadget);
}
}
/**
* display the current logo into simple image format.
* @return simple img
*/
public function toSimpleImage()
{
$splitStringArray = split(".", $this->filename);
$extension = end($splitStringArray);
$result = CommonTools::data_uri($this->getBytes(), "image/" . $extension);
return $result;
}
function formatConfirmedAnswerRow($answersByUser, $questions, $position, $adminMode)
{
$configurations = CommonTools::getConfigurations();
$webRoot = $configurations->webRoot;
$rowClass = SignupGadgetAnswerFormater::getRowClass();
$return = "<tr class=\"{$rowClass}\">";
$debugger = CommonTools::getDebugger();
$debugger->debugVar($answersByUser, "answerByUser", "formatConfirmedAnswerRow");
$return .= "<td class=\"answer-position\">" . $answersByUser->getPosition() . "</td>";
$lastAnswer = null;
// Could be any answer, not only last answer
foreach ($questions as $question) {
// Gets answer to questin
$answerObject = $answersByUser->getAnswerToQuestion($question->getId());
if ($answerObject == null) {
// We get null-values when the signup machine gets more options added after users
// have already submitted their answers. So in order not to truly mess up the
// nice table we are creating, add an empty table cell.
$return .= '<td class="answer"></td>';
} else {
if (is_a($answerObject, "Answer")) {
$return .= "<td class=\"answer\">" . $answerObject->getReadableAnswer() . "</td>";
$lastAnswer = $answerObject;
} else {
// Joku virheilmotus tähänkö?
}
}
}
if ($adminMode && $lastAnswer != null) {
$return .= "<td class=\"edit-answer\"><a href=\"" . $webRoot . "admin/editanswer/" . $lastAnswer->getSignupId() . "/?userid=" . $lastAnswer->getUserId() . "\">[muokkaa]</a></td>";
$return .= "<td class=\"delete-answer\"><a href=\"" . $webRoot . "admin/deleteanswer/" . $lastAnswer->getSignupId() . "/?userid=" . $lastAnswer->getUserId() . "\">[poista]</a></td>";
}
$return .= "</tr>\n";
return $return;
}
function Email($address)
{
// Initializes the debugger
CommonTools::initializeCommonObjects($this);
if (!Email::isValidEmail($address)) {
$this->debugger->error("The email address is invalid");
} else {
$this->address = $address;
}
}
function getAnswersInCsvFormat($signupGadget)
{
$answersByUsersArray = $signupGadget->getAllAnswersByUsers();
$questions = $signupGadget->getAllQuestions();
// Print questions
print "Sija;";
foreach ($questions as $question) {
print $question->getQuestion() . ";";
}
print "\n";
foreach ($answersByUsersArray as $userId => $answersByUser) {
// Unconfirmed?
if ($answersByUser == null) {
print "-\r\n";
// Adds windows style line delimeter
continue;
}
$answerRow = "";
$answerRow .= $answersByUser->getPosition() . ";";
// Print answers
foreach ($questions as $questionId => $question) {
$answerObject = $answersByUser->getAnswerToQuestion($questionId);
$answerString = "";
if ($answerObject != null) {
if ($question->getType() == "checkbox") {
$answerString = CommonTools::arrayToReadableFormat($answerObject->getAnswer());
} else {
$answerString = $answerObject->getAnswer();
}
}
$answerString = html_entity_decode($answerString, ENT_QUOTES);
// Remove new line characters
$answerString = stripslashes(str_replace("\r\n", "", $answerString));
// Windows
$answerString = stripslashes(str_replace("\n", "", $answerString));
// Unix
// Because semicolon is the line delimeter, rudely replace all the semicolons to commas
$answerString = stripslashes(str_replace(";", ",", $answerString));
$answerRow .= $answerString . ";";
}
// Remove the last semicolon
$answerRow = substr($answerRow, 0, -1);
print "{$answerRow}\r\n";
// Adds windows style line delimeter
}
}
/**
* Luo uuden käyttäjälle lähetettävän vahvistusviestin
* @param string message Viesti käyttäjälle
* @param string email Käyttäjän email
* @param SignupGadget signupgadget Tiedot ilmosta
* @param array answers vastaukset masiinaan
*/
public function ConfirmationMail($message, Email $email, $signupGadget, $answers = null)
{
CommonTools::initializeCommonObjects($this);
$this->message = $message;
$this->email = $email;
$this->signupGadget = $signupGadget;
$this->answers = $answers;
if (!is_a($email, 'Email')) {
$this->debugger->error("email parameter must be an instance of Email class");
}
// Tulostetaan ilmoittautumisen vahvistus vain jos käyttäjän id on annettu
if ($answers != null) {
$questions = $this->signupGadget->getAllQuestions();
$this->message .= "\n\n*** Ilmoittautumisesi tiedot ***\n\n";
foreach ($answers as $answer) {
// Gets answer to question
if (is_a($answer, "Answer")) {
$this->message .= $answer->getQuestion()->getQuestion() . ": " . $answer->getReadableAnswer() . "\n";
} else {
// Tähän joku virhe?
}
}
}
}
/**
* Displays the contact page
*/
public function actionContactus()
{
CommonTools::getBiobankInfo();
$model = new ContactForm();
if (isset($_POST['ContactForm'])) {
$model->attributes = $_POST['ContactForm'];
if ($model->validate()) {
$name = '=?UTF-8?B?' . base64_encode($model->name) . '?=';
$subject = '=?UTF-8?B?' . base64_encode($model->subject) . '?=';
$headers = "From: {$name} <{$model->email}>\r\n" . "Reply-To: {$model->email}\r\n" . "MIME-Version: 1.0\r\n" . "Content-type: text/plain; charset=UTF-8";
mail(Yii::app()->params['adminEmail'], $subject, $model->body, $headers);
Yii::app()->user->setFlash('contact', 'Thank you for contacting us. We will respond to you as soon as possible.');
$this->refresh();
}
}
$this->render('../site/contact', array('model' => $model));
}
<link rel="stylesheet" type="text/css" href="<?php
echo Yii::app()->request->baseUrl;
?>
/css/form.css" />
<script src="//ajax.googleapis.com/ajax/libs/dojo/1.9.3/dojo/dojo.js"></script>
</head>
<?php
CommonTools::getBiobankInfo();
$splitStringArray = split(".", $_SESSION['vitrine']['biobankLogo']->filename);
$extention = end($splitStringArray);
?>
<body class="container" id="page" >
<div style="float:left;">
<a href="http://www.biobanques.eu" target="_blank"><img src="<?php
echo CommonTools::data_uri($_SESSION['vitrine']['biobankLogo']->getBytes(), "image/{$extention}");
?>
" alt="1 photo" style="height:120px;"/></a>
</div>
<div style="float:left;">
<h1><?php
echo $_SESSION['vitrine']['biobank']->identifier;
?>
</h1>
</div>
<div style="float:right;padding-right:20px;padding-top:20px;">
<div >
<?php
?>
<?php
/**
* Création des listes d'attributs à affciher dans les différentes parties
* La liste $attributes_oblig représente la liste des attributs obligatoire, et doit être présente.
* Elle ne doit pas être ajoutée à la liste d'onglets
*
* La liste $attributes_other regroupe tous les attributs non présents dans les autres listes. Elle doit être ajoutée en dernière à la liste d'onglets
*/
$attributes_oblig = array('identifier', 'name', 'collection_name', 'collection_id', 'biobank_class', 'diagnosis_available', array('attributeName' => 'contact_id', 'value' => Contact::model()->getArrayContacts()), 'address');
$attributes_facult = array('website', 'folder_reception', 'folder_done', 'date_entry', 'passphrase', 'longitude', 'latitude');
$listOnglets['facultatif'] = $attributes_facult;
$attributes_qualite = array('cert_ISO9001', 'cert_NFS96900', 'cert_autres', 'observations');
$listOnglets['qualite'] = $attributes_qualite;
$attributes_info = array(array('attributeName' => 'gest_software', 'value' => CommonTools::getSoftwareList()), 'other_software', array('attributeName' => 'connector_installed', 'value' => array('Oui' => 'Oui', 'Non' => 'Non')), 'connector_version');
$listOnglets['info'] = $attributes_info;
$attributes_sampling = array(array('attributeName' => 'sampling_practice', 'value' => Biobank::model()->getArraySamplingPractice()), 'sampling_disease_group', 'sampling_disease_group_code', 'nbs_dna_samples_affected', 'nbs_dna_samples_relatives', 'nbs_cdna_samples_affected', 'nbs_cdna_samples_relatives', 'nbs_wholeblood_samples_affected', 'nbs_wholeblood_samples_relatives', 'nbs_bloodcellisolates_samples_affected', 'nbs_bloodcellisolates_samples_relatives', 'nbs_serum_samples_affected', 'nbs_serum_samples_relatives', 'nbs_plasma_samples_affected', 'nbs_plasma_samples_relatives', 'nbs_fluids_samples_affected', 'nbs_fluids_samples_relatives', 'nbs_tissuescryopreserved_samples_affected', 'nbs_tissuescryopreserved_samples_relatives', 'nbs_tissuesparaffinembedded_samples_affected', 'nbs_tissuesparaffinembedded_samples_relatives', 'nbs_celllines_samples_affected', 'nbs_celllines_samples_relatives', 'nbs_other_samples_affected', 'nbs_other_samples_relatives', 'nbs_other_specification');
$listOnglets['sampling'] = $attributes_sampling;
//make array of attributes stored but not defined in the common model
$attributes_other = array();
$definedAttributes = array_merge($attributes_oblig, $attributes_facult, $attributes_qualite, $attributes_info, $attributes_sampling, array('_id', 'contact_id', 'gest_software', 'connector_installed', 'vitrine', 'sampling_practice'));
$att = $model->getAttributes();
foreach ($att as $attributeName => $attributeValue) {
if (!in_array($attributeName, $definedAttributes)) {
$attributes_other[] = $attributeName;
}
}
$listOnglets['other'] = $attributes_other;
?>
public function indexForBiobank($id)
{
$lastImportDate = FileImported::model()->getDateLastImportByBiobank($id);
$today = date('Y-m-d H:i:s');
$diffSec = strtotime($today) - strtotime($lastImportDate);
$diffJours = round($diffSec / 60 / 60 / 24, 0);
$args = array();
$args['diffJours'] = $diffJours;
if (Yii::app()->getLocale()->id == "fr") {
$args['lastImportDate'] = CommonTools::toShortDateFR($lastImportDate);
} else {
if (Yii::app()->getLocale()->id == "en") {
$args['lastImportDate'] = CommonTools::toShortDateEN($lastImportDate);
}
}
$args['status'] = 'success';
if ($diffJours < 10) {
$args['status'] = 'success';
} elseif ($diffJours < 30) {
$args['status'] = 'notice';
} else {
$args['status'] = 'error';
}
Yii::app()->user->setFlash($args['status'], Yii::t('myBiobank', 'lastImportMessage' . '_' . $args['status'], $args));
$model = $this->loadModel($id);
Yii::app()->params['biobank'] = $model;
$this->render('index', array('model' => $model));
}
public function getShortValue($attribute)
{
return CommonTools::getShortValue($this->{$attribute});
}
function updateToDatabase()
{
$answer = null;
if ($this->question->getType() == "checkbox") {
$answer = CommonTools::arrayToSql($this->answer);
} else {
$answer = htmlentities($this->answer, ENT_QUOTES);
}
$question_id = $this->question->getId();
$user_id = $this->getUserId();
$sql = "UPDATE ilmo_answers SET answer='{$answer}' WHERE " . "question_id='{$question_id}' AND user_id='{$user_id}'";
$this->database->doQuery($sql);
}
<?php
//recuperation des preferences d dattributs affiches du user
$prefs = CommonTools::getPreferences();
//recuperation des noms des attributs affichables des colonnes du grid
$scriptCB = '';
foreach ($prefs as $property => $propertyValue) {
if ($property != 'id_user') {
$scriptCB = $scriptCB . '$(\'#Preferences_' . $property . '\').change(function(){
$(\'.col_' . $property . '\').toggle();
$(\'.prefs-form form\').submit();
return false;
});
';
}
}
// recharge le tableau d'affichage des échantillons après envoi du formulaire de recherche avancée
Yii::app()->clientScript->registerScript('search', "\n \$('.search-button').click(function(){\n \t\$('.search-form').toggle();\n \treturn false;\n });\n\n\$('.prefs-button').click(function(){\n\t\$('.prefs-form').toggle();\n\treturn false;\n});\n\n\$('.search-form form').submit(function(){\n\t\$('#sample-grid').yiiGridView('update', {\n\t\tdata: \$(this).serialize()\n\t});\n\treturn false;\n});\n\$('.prefs-form form').submit(function(){\n\t\$('#sample-grid').yiiGridView('update', {\n\t\tdata: \$(this).serialize()\n\t});\n\n\treturn false;\n});\n{$scriptCB};\n");
//
?>
<h1><?php
echo Yii::t('common', 'searchsamples');
?>
</h1>
<div style="margin: 5px;"><?php
echo Yii::t('common', 'totalnumbersamples');
?>
: <b><?php
echo $model->count();
?>
</b>.<br>
function arrayToReadableFormat($array)
{
$arrayString = "";
$atLeastOneValueSet = false;
foreach ($array as $id) {
if ($id >= 0) {
$arrayString .= "{$id}, ";
$atLeastOneValueSet = true;
} else {
$debugger = CommonTools::getDebugger();
$debugger->error("The array must include only positive integer values", "idArrayToSql");
}
}
if ($atLeastOneValueSet) {
// Remove last comma
$arrayString = substr($arrayString, 0, -2);
}
return $arrayString;
}
require_once "classes/Configurations.php";
require_once "classes/Page.php";
require_once "classes/SignupGadgets.php";
require_once "classes/Debugger.php";
require_once "classes/SignupGadget.php";
require_once "classes/CommonTools.php";
/* Implementations of the most critical classes */
$configurations = new Configurations();
$page = new Page(1);
$debugger = new Debugger();
$database = new Database();
/* The code */
$signupGadgets = new SignupGadgets();
// Check if the search was performed
$searchString = CommonTools::GET('search');
$year = CommonTools::GET('year');
// Is the search performed?
if ($searchString != null && $searchString != "") {
$debugger->debug("Searching signup gadgets using search string {$searchString}", "index.php");
$signupGadgets->selectSearchSignupGadget($searchString);
} else {
if ($year != null && $year != "") {
$signupGadgets->selectSignupGadgetsByYear($year);
} else {
$signupGadgets->selectOpenGadgetsOrClosedDuringLastDays(7);
}
}
// Get all selected gadgets to array
$signupGadgets_array = $signupGadgets->getSignupGadgets();
// Print table headers
$page->addContent("<table id=\"signup-gadgets\">");
function formatQuestionCheckbox($question, $value)
{
$return = "";
$return .= "<div class=\"question-container\">";
$return .= "<p class=\"question-label\"><span>" . $question->getQuestion() . "</span>";
if ($question->getRequired()) {
$return .= " <span class=\"required\">*</span>";
}
$return .= "</p>";
$i = 0;
foreach ($question->getOptions() as $option) {
$selected = "";
$debugger = CommonTools::getDebugger();
// $debugger->debug("Option: $option, inArray: " . in_array($option, $value), "questionCheckbox");
$debugger->debugVar($value, "value", "checkBox");
if (is_array($value) && in_array($option, $value)) {
$selected = "checked=\"checked\"";
}
$option = htmlentities($option);
$return .= "<p class=\"question-checkbox-label\"><input class=\"question-checkbox\" type=\"checkbox\" name=\"" . $question->getId() . "-{$i}\" size=\"30\" value=\"{$option}\" {$selected} />{$option}</p>";
$i++;
}
$return .= "</div>";
return $return;
}
/**
* get biobank infos and convert into an LDIF format
* @return string
*/
private function getBiobanksLDIF()
{
$result = "\ndn: c=fr,ou=biobanks,dc=directory,dc=bbmri-eric,dc=eu\nobjectClass: country\nobjectClass: top\nc: fr\n\n";
//FIXME Mandatory empty line here ( TODO use ldif exporter to check syntax)
$biobanks = Biobank::model()->findAll();
foreach ($biobanks as $biobank) {
$attributes = array();
$attributes['biobankCountry'] = "FR";
$attributes['biobankID'] = "bbmri-eric:ID:FR_" . $biobank->identifier;
$attributes['biobankName'] = $biobank->name;
$attributes['biobankJuridicalPerson'] = $biobank->name;
//TODO flase in cappital
$attributes['biobankMaterialStoredDNA'] = "FALSE";
$attributes['biobankMaterialStoredRNA'] = "FALSE";
// $attributes['biobankMaterialStoredcDNAmRNA'] = "FALSE";
// $attributes['biobankMaterialStoredmicroRNA'] = "FALSE";
// $attributes['biobankMaterialStoredWholeBlood'] = "FALSE";
// $attributes['biobankMaterialStoredPBC'] = "FALSE";
$attributes['biobankMaterialStoredBlood'] = "FALSE";
$attributes['biobankMaterialStoredPlasma'] = "FALSE";
$attributes['biobankMaterialStoredSerum'] = "FALSE";
// $attributes['biobankMaterialStoredTissueCryo'] = "FALSE";
$attributes['biobankMaterialStoredTissueFrozen'] = "FALSE";
// $attributes['biobankMaterialStoredTissueParaffin'] = "FALSE";
$attributes['biobankMaterialStoredTissueFFPE'] = "FALSE";
// $attributes['biobankMaterialStoredCellLines'] = "FALSE";
$attributes['biobankMaterialStoredImmortalizedCellLines'] = "FALSE";
$attributes['biobankMaterialStoredUrine'] = "FALSE";
$attributes['biobankMaterialStoredSaliva'] = "FALSE";
$attributes['biobankMaterialStoredFaeces'] = "FALSE";
// $attributes['biobankMaterialStoredPathogen'] = "FALSE";
$attributes['biobankMaterialStoredIsolatedPathogen'] = "FALSE";
$attributes['biobankMaterialStoredOther'] = "FALSE";
//TODO each biobank need to sign a chart between bbmri and the biobank (TODO to discuss)
$attributes['biobankPartnerCharterSigned'] = "FALSE";
//nmber of samples 10^n n=number
$attributes['biobankSize'] = "1";
$attributes['objectClass'] = "biobankClinical";
//TODO implementer la valeur de ce champ Si biobankClinical Diagnosis obligatoire
$attributes['diagnosisAvailable'] = "urn:miriam:icd:D*";
$contact = $biobank->getContact();
$attributes['biobankContactCountry'] = "FR";
//TODO get pays avec FR pas integer $contact->pays;
//TODO info de contact obligatoire lever un warning si pas affectée pour l export
if ($contact != null) {
$attributes['biobankContactFirstName'] = $contact->first_name;
$attributes['biobankContactLastName'] = $contact->last_name;
$attributes['biobankContactPhone'] = CommonTools::getIntPhone($contact->phone);
$attributes['biobankContactAddress'] = $contact->adresse;
$attributes['biobankContactZIP'] = $contact->code_postal;
$attributes['biobankContactCity'] = $contact->ville;
//TODO contact email need to be filled
if (isset($contact->email)) {
$attributes['biobankContactEmail'] = $contact->email;
} else {
$attributes['biobankContactEmail'] = $contact->email;
}
} else {
$attributes['biobankContactEmail'] = "N/A";
Yii::log("contact must be filled for export LDIF. Biobank without contact:" . $biobank->name, CLogger::LEVEL_WARNING, "application");
}
$this->checkAttributesComplianceWithBBMRI($attributes);
$result .= "dn: biobankID=" . trim($attributes['biobankID']) . ",c=fr,ou=biobanks,dc=directory,dc=bbmri-eric,dc=eu\n";
//TODO recuperer le diagnistique agréger
foreach ($attributes as $key => $value) {
if (isset($value)) {
//$result.=$key . ":: " . base64_encode(trim($value)) . "\n";
$result .= $key . ":: " . trim($value) . "\n";
}
}
//FIXME mandatory empty line
$result .= "objectClass: biobank\n\n";
}
return $result;
}
function insertToDatabase()
{
// Change options array to sql format
$id = $this->getSignupId();
$questionString = $this->getQuestion();
$type = $this->getType();
$options = CommonTools::arrayToSql($this->getOptions());
$public = CommonTools::booleanToSql($this->getPublic());
$required = CommonTools::booleanToSql($this->getRequired());
$sql = "INSERT INTO ilmo_questions " . "(ilmo_id, question, type, options, public, required) " . "VALUES " . "({$id}, '{$questionString}', '{$type}', '{$options}', " . "{$public}, {$required})";
// do query
$this->database->doQuery($sql);
}
<footer>
<div style="text-align:center;background-color: white;">
Copyright Inserm - Version 1.6 alpha rev. <?php
include 'revision_number.php';
?>
- Project Biobanques <a href="http://www.biobanques.eu">www.biobanques.eu</a>
</div>
</footer>
<?php
if (!CommonTools::isInDevMode()) {
?>
<!-- code google analytics pour tracking du suivi -->
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-44379278-1']);
_gaq.push(['_trackPageview']);
(function () {
var ga = document.createElement('script');
ga.type = 'text/javascript';
ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
})();
</script>
<?php
}
public function createFicheNeuropath()
{
$index = 0;
$criteria = new EMongoCriteria();
$criteria->login = "******";
$user = User::model()->find($criteria);
$neuropath = Neuropath::model()->findAll();
if ($neuropath != null) {
foreach ($neuropath as $neuro) {
$answer = new Answer();
$answer->creator = "Bernard TE";
$answer->id = "neuropath_filemaker_form";
$answer->type = "neuropathologique";
$answer->login = new MongoId($user->_id);
$answer->questionnaireMongoId = new MongoId();
$answer->name = "Import Neuropath";
$answer->last_modified = DateTime::createFromFormat('d/m/Y', date('d/m/Y'));
$answer->description = "Données neuropathologiques de la base FileMaker";
$answer->last_updated = DateTime::createFromFormat('d/m/Y', date('d/m/Y'));
$answerGroup = new AnswerGroup();
$answerGroup->id = "onglet";
$answerGroup->title = "Données neuropathologiques FileMaker";
$answerGroup->title_fr = $answerGroup->title;
foreach ($neuro as $k => $v) {
if ($k != "_id") {
if ($k == "id_cbsd") {
$answer->id_patient = (string) $v;
} else {
$answerQuestion = new AnswerQuestion();
$answerQuestion->id = $k;
$answerQuestion->label = $k;
$answerQuestion->label_fr = $k;
if (is_numeric($v)) {
$answerQuestion->type = "number";
} elseif (CommonTools::isDate($v)) {
$answerQuestion->type = "date";
} else {
$answerQuestion->type = "input";
}
$answerQuestion->style = "";
if ($answerQuestion->type == "date") {
$answerQuestion->answer = DateTime::createFromFormat('d/m/Y', date('d/m/Y', strtotime($v)));
} else {
$answerQuestion->answer = $v;
}
$answerGroup->answers[] = $answerQuestion;
}
}
}
$answer->answers_group[] = $answerGroup;
$answer->save();
}
}
}
/**
* testing method to check if function return an object
*/
public function testWsAddPatient()
{
$patient = $this->patient();
$this->assertInternalType('string', CommonTools::wsAddPatient($patient));
// TODO : test exception
}
function parseNormalAnswer($question)
{
global $userId;
$answerFromPost = CommonTools::POST($question->getId());
return new Answer($answerFromPost, $userId, $question);
}
/**
* affichage de la page de recherche des echantillons
*/
public function actionSearch()
{
$model = new Sample('search');
$model->unsetAttributes();
$biobankId = null;
if (isset($_GET['id']) && isset($_GET['layout']) && $_GET['layout'] == 'vitrine_layout') {
$biobankId = $_GET['id'];
}
$model->biobank_id = $biobankId;
$user = CommonTools::getConnectedUser();
if (isset($_GET['Preferences'])) {
$user->preferences->attributes = $_GET['Preferences'];
$user->disableBehavior('LoggableBehavior');
if ($user->validate(array('preferences'))) {
$user->save(false);
} else {
var_dump($user->preferences->errors);
}
}
if (isset($_GET['Sample'])) {
$model->attributes = $_GET['Sample'];
//Used to search terms in model->biobank->collection_id and model->biobank->collection_name
$arrayOfBiobanks = array();
if (!empty($_GET['collection_id'])) {
$criteria = new EMongoCriteria();
$listWords = explode(",", $_GET['collection_id']);
$regexId = "";
foreach ($listWords as $word) {
$regexId .= "{$word}|";
}
$regexId = substr($regexId, 0, -1);
$criteria->addCond('collection_id', '==', new MongoRegex("/({$regexId})/i"));
$criteria->select(array('_id'));
$biobanks = Biobank::model()->findAll($criteria);
foreach ($biobanks as $biobank) {
$arrayOfBiobanks[(string) $biobank->_id] = (string) $biobank->_id;
}
}
if (!empty($_GET['collection_name'])) {
$criteria = new EMongoCriteria();
$listWords = explode(",", $_GET['collection_name']);
$regexId = "";
foreach ($listWords as $word) {
$regexId .= "{$word}|";
}
$regexId = substr($regexId, 0, -1);
$criteria->addCond('collection_name', '==', new MongoRegex("/({$regexId})/i"));
$criteria->select(array('_id'));
$biobanks = Biobank::model()->findAll($criteria);
foreach ($biobanks as $biobank) {
$arrayOfBiobanks[$biobank->_id] = (string) $biobank->_id;
}
}
if (!empty($arrayOfBiobanks)) {
// $model->arrayOfBiobanks;
$model->setArrayOfBiobanks(array_values($arrayOfBiobanks));
}
$content = '';
foreach ($_GET['Sample'] as $key => $value) {
if (is_array($value)) {
foreach ($value as $vkey => $vval) {
$content = $content . (string) $vkey . '=' . str_replace(';', ',', (string) $vval) . ';';
}
} else {
if ($value != null && !empty($value) && (string) $value != '0') {
$content = $content . (string) $key . '=' . str_replace(';', ',', (string) $value) . ';';
}
}
}
if (Yii::app()->session['SampleForm'] != $_GET['Sample']) {
$_GET['Echantillon_page'] = null;
$this->logAdvancedSearch($content);
}
Yii::app()->session['SampleForm'] = $_GET['Sample'];
}
//form de la recherche intelligente
$smartForm = new SampleSmartForm();
if (isset($_POST['SampleSmartForm'])) {
$model->unsetAttributes();
$smartForm->attributes = $_POST['SampleSmartForm'];
if (Yii::app()->session['keywords'] != $smartForm->keywords) {
$_GET['Echantillon_page'] = null;
$this->logSmartSearch($smartForm->keywords);
}
Yii::app()->session['keywords'] = $smartForm->keywords;
$model = SmartResearcherTool::search($smartForm->keywords, $biobankId);
}
$this->render('search_samples', array('model' => $model, 'smartForm' => $smartForm));
}
/**
* send an email to indicate to the admin that there is a new user to confirm
* @param type $user
* @return type
*/
public static function sendSubscribeAdminMail($user)
{
$base = CommonTools::isInDevMode() ? CommonMailer::DEV_URL : CommonMailer::PROD_URL;
$to = Yii::app()->params['adminEmail'];
$subject = "Inscription d'un nouvel utilisateur sur ebiobanques.fr";
$userDetails = '';
foreach ($user->getAttributes() as $label => $value) {
$userDetails .= "<li>{$label} : {$value}</li>";
}
$body = "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/1999/REC-html401-19991224/strict.dtd\">\n\t\t\t\t<?xml version=\"1.0\" encoding=\"utf-8\"?>\n\t\t\t\t<html><head>\n\t\t\t\t<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\">\t<title>Inscription d'un nouvel utilisateur sur ebiobanques.fr</title>\n\t\t\t\t</head><body>\n\t\t\t\t{$user->prenom} {$user->nom} s'est inscrit sur le site ebiobanques.fr.<br>\n\t\t\t\t\t\tDétails :<br>\n\t<ul>{$userDetails}</ul><br>\n\tVous pouvez valider cet utilisateur en cliquant sur ce lien : <a href={$base}/index.php/user/validate/id/{$user->_id}\">Valider l'utilisateur</a>, le <a href={$base}/index.php/user/refuseRegistration/id/{$user->_id}\">désactiver</a>\n\t ou le retrouver dans <a href={$base}/index.php/user/admin\">la liste des utilisateurs</a>.\n\t</body>\n\t\t";
return CommonMailer::sendMail($to, $subject, $body);
}
/**
* Gets user's position from database
*/
function selectPositionFromDatabase()
{
$sql = "SELECT ilmo_id, id_string, confirmed FROM ilmo_users WHERE " . "ilmo_id = {$this->newSignupid} ORDER BY time";
$result = $this->database->doQuery($sql);
$position = 1;
$unconfirmedSignups = 0;
$foundIdFromQueue = false;
// Tries to find current users
while ($row = $result->fetchRow(MDB2_FETCHMODE_ASSOC)) {
$this->debugger->debug("id_string: " . $row['id_string'] . ", sessionId: " . $this->sessionId, "selectPositionFromDatabase");
if ($row['id_string'] == $this->sessionId) {
// User's id found!
$foundIdFromQueue = true;
break;
} else {
$position++;
if (CommonTools::sqlToBoolean($row['confirmed']) == false) {
$unconfirmedSignups++;
}
}
}
// Sets position
if ($foundIdFromQueue) {
$this->position = $position;
$this->unconfirmedSignups = $unconfirmedSignups;
} else {
$this->position = -1;
$this->unconfirmedSignups = -1;
}
}
public function actionAdmin()
{
$model = new UploadedFile();
if (isset($_FILES['uploadFileField']) && $_FILES['uploadFileField']['error'] == 0) {
$add = false;
if (isset($_POST['UploadedFile']['addOrReplace']) && $_POST['UploadedFile']['addOrReplace'] == 'add') {
$add = true;
}
$fileId = $this->uploadEchFile($_FILES['uploadFileField']);
if ($fileId != null) {
$file = CommonTools::importFile($this->loadModel($fileId), $add);
} else {
}
}
$datas[] = new SampleProperty("id_sample", "Identification number of the biological material", "Text");
$datas[] = new SampleProperty("id_depositor", "Identification of depositor", "Text");
$datas[] = new SampleProperty("id_familiy", "Identification number of the family", "Text");
$datas[] = new SampleProperty("id_donor", "Identification number of the donor", "Text");
$datas[] = new SampleProperty("consent_ethical", "Consent/Approval by ethical commitee", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("gender", "Gender of donor", "Fixed values(Male, Female, Hermaphrodite, Unknown) : M, F, H, U ");
$datas[] = new SampleProperty("age", "Age of donor", "Integer");
$datas[] = new SampleProperty("pathology", "Pathology of family with OMIM number", "Integer (unique six-digit number)");
$datas[] = new SampleProperty("status_sample", "Status of the biological materiel", "Fixed Values( A=Affected, NA= Non-affected, IS=indication of suspected diagnosis, IT=indication of grade of tumor+value) : ");
$datas[] = new SampleProperty("collect_date", "date of collect of the material", "ISO-standard (8601) time format : 2014-04-18");
$datas[] = new SampleProperty("nature_sample_dna", "nature of the human biological material where dna was extracted from", "fixed values ( affected, non affected)");
$datas[] = new SampleProperty("storage_conditions", "preservation or storage conditions", "fixed values (LN=liquid nitrogen, 80=-80C, RT=room temperature, 4=4°C, 20=-20°C)");
$datas[] = new SampleProperty("quantity", "quantity of biological material", "for dna concentration µg/µl and number of µl");
$datas[] = new SampleProperty("disease_diagnosis", "Disease diagnosis", "Text");
$datas[] = new SampleProperty("origin", "Origin of the biological material", "Organ and tissue");
$datas[] = new SampleProperty("hazard_status", "hazard status", "Text");
$datas[] = new SampleProperty("nature_sample_tissue", "nature of the human biological material", "fixed values ( T=tissue, S=slide,C=cells, P=pellet)");
$datas[] = new SampleProperty("processing_method", "documentation on processing method", "Text");
$datas[] = new SampleProperty("nature_sample_cells", "nature of the cells", "fixed values(epithelia, fibroblast,myphocyt)");
$datas[] = new SampleProperty("culture_condition", "culture condition", "medium and subculture routine");
$datas[] = new SampleProperty("consent", "consent", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("family_tree", "family tree", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("available_relatives_samples", "samples from relatives available", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("supply", "form of supply", "Text");
$datas[] = new SampleProperty("max_delay_delivery", "maximum delay for delivery", "Integer ( hours)");
$datas[] = new SampleProperty("karyotype", "karyotype", "Text");
$datas[] = new SampleProperty("quantity_families", "quantity of families and subjects available for the specific disease", "Integer");
$datas[] = new SampleProperty("detail_treatment", "detail information of treatment/medications", "Text");
$datas[] = new SampleProperty("disease_outcome", "information on disease outcome", "Text");
$datas[] = new SampleProperty("associated_clinical_data", "associated clinical data", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("associated_molecular_data", "associated molecular data ( ref associated clinical data OCDE)", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("associated_imagin_data", "associated imagin data ( ref associated clinical data OCDE)", "Fixed values(Yes, No, Unknown) : Y,N,U");
$datas[] = new SampleProperty("life_style", "information on life style", "Text");
$datas[] = new SampleProperty("family_history", "information on family history", "Text");
$datas[] = new SampleProperty("authentication_method", "dna fingerprinting or another method of authentication", "Text");
$datas[] = new SampleProperty("hazard_status", "hazard status", "Text");
$datas[] = new SampleProperty("details_diagnosis", "details of diagnosis", "Text");
$datas[] = new SampleProperty("related_biological_material", "related biological material", "Fixed Values : DNA Biopsy, tissue,serum, dna");
$datas[] = new SampleProperty("quantity_available", "Quantiy available", "Text");
$datas[] = new SampleProperty("concentration_available", "Concentration available", "Text");
$datas[] = new SampleProperty("samples_characteristics", "characteristics of the sample", "Text (sample composition, content tumour cells)");
$datas[] = new SampleProperty("delay_freezing", "delay of freezing", "Integer(minutes)");
$datas[] = new SampleProperty("cells_characterization", "characterization of cells", "Text (doubling time, tumorigenicity, karyotype etc)");
$datas[] = new SampleProperty("number_of_passage", "number of passage", "Text");
$datas[] = new SampleProperty("morphology_and_growth_characteristics", "morphology and growth characteristics", "Text");
$datas[] = new SampleProperty("reference_paper", "reference paper", "Text");
$datas[] = new SampleProperty("biobank_id", "biobank id", "Text : Use BRIF Code to store this variable");
$datas[] = new SampleProperty("biobank_name", "biobank name", "Text");
$datas[] = new SampleProperty("biobank_date_entry", "Date of Entry", " ISO-standard (8601) time format when data about the biobank was reported into a database. : 2014-04-18T06:28:42Z");
$datas[] = new SampleProperty("biobank_collection_id", "Sample Collection/Study ID*", "Text : Textual string depicting the unique ID or acronym for the sample collection or study");
$datas[] = new SampleProperty("biobank_collection_name", "Collection/Study name*", "Text : Textual string of letters denoting the name of the study in English");
$datas[] = new SampleProperty("patient_birth_date", "birth date patient", "Date format ISO 8601 : YYYY-MM-DD exemple 2014-04-18");
$datas[] = new SampleProperty("tumor_diagnosis", "tumor_diagnosis", "Text : CIM 10 format");
$dataProviderProperties = new CArrayDataProvider($datas, array('keyField' => false, 'pagination' => false));
$model->addOrReplace = 'add';
$this->render('admin', array('model' => $model, 'dataProviderProperties' => $dataProviderProperties));
}
protected static function analyzeCsv($bytes, $biobank_id, $fileImportedId, $add)
{
$import = fopen(CommonTools::data_uri($bytes, 'text/csv'), 'r');
$row = 1;
$keysArray = array();
$listBadSamples = array();
$newSamples = array();
// $tempSaveList = new MongoInsertBatch(Sample::model()->getCollection());
$tempSaveList = array();
/**
* Version 1 : Les champs non repertorés sont ajoutés en notes
*/
while (($data = fgetcsv($import, 1000, ",")) !== FALSE) {
/*
* Traitement de la ligne d'entete
*/
if ($row == 1) {
foreach ($data as $key => $value) {
if ($value != null && $value != "") {
$keysArray[$key] = $value;
}
}
} else {
$model = new Sample();
$model->disableBehavior('LoggableBehavior');
$model->_id = new MongoId();
while (!$model->validate(array('_id'))) {
$model->_id = new MongoId();
}
$model->biobank_id = $biobank_id;
$model->file_imported_id = $fileImportedId;
foreach ($keysArray as $key2 => $value2) {
if ($value2 != "biobank_id" && $value2 != "file_imported_id") {
if (in_array($value2, Sample::model()->attributeNames())) {
$model->{$value2} = $data[$key2];
if (!$model->validate(array($value2))) {
// Yii::log("Problem with item" . $model->getAttributeLabel($value2) . ",set to null.\n " . implode(", ", $model->errors[$value2]), CLogger::LEVEL_ERROR);
$model->{$value2} = null;
}
} else {
$note = new Note();
$note->key = $value2;
$note->value = $data[$key2];
$model->notes[] = $note->attributes;
}
}
}
if (!$model->validate()) {
Yii::log("Problem with sample validation " . print_R($model->errors, true), CLogger::LEVEL_ERROR);
$listBadSamples[] = $row;
} else {
$tempSaveList[] = $model->attributes;
// $tempSaveList->add($model->attributes);
$newSamples[] = $model->_id;
}
}
$row++;
if ($row != 2 && $row % 400 == 2) {
Yii::log("Nb treated : " . $row, 'error');
Sample::model()->getCollection()->batchInsert($tempSaveList, array());
$tempSaveList = array();
//$tempSaveList->execute(array());
//$tempSaveList = new MongoInsertBatch(Sample::model()->getCollection());
}
}
Sample::model()->getCollection()->batchInsert($tempSaveList, array("w" => 1));
/*
* Version 2 : seuls nes champs dont la colonne est annotée avec le préfixe 'notes' sont pris en note
*/
// while (($data = fgetcsv($import, 1000, ",")) !== FALSE) {
//
// /*
// * Traitement de la ligne d'entete
// */
//
//
//
// if ($row == 1) {
// foreach ($data as $key => $value) {
// if (in_array($value, Sample::model()->attributeNames())) {
// $keysArray[$key] = $value;
// } elseif (substr($value, 0, 5) == 'notes') {
// $keysArray[$key] = $value;
// }
// }
// /*
// * Traitement des lignes de données
// */
// } else {
// $model = new Sample();
// $model->disableBehavior('LoggableBehavior');
// $model->biobank_id = $biobank_id;
// $model->file_imported_id = $fileImportedId;
// foreach ($keysArray as $key2 => $value2) {
// if (substr($value2, 0, 5) != 'notes') {
//
// $model->$value2 = $data[$key2];
// if (!$model->validate($value2)) {
//
// Yii::log("Problem with item" . $model->getAttributeLabel($value2) . ",set to null.", CLogger::LEVEL_ERROR);
// $model->$value2 = null;
// }
// } else {
//
// $noteKey = end(explode(':', $value2));
// $note = new Note();
// $note->key = $noteKey;
// $note->value = $data[$key2];
// $model->notes[] = $note;
// }
// }
//
// if (!$model->save()) {
// $listBadSamples[] = $row;
// } else {
// $newSamples[] = $model->_id;
// }
// }
// $row++;
// }
fclose($import);
if (!$add && count($newSamples) > 0) {
$deleteCriteria = new EMongoCriteria();
$deleteCriteria->biobank_id('==', $biobank_id);
$deleteCriteria->_id('notIn', $newSamples);
Sample::model()->deleteAll($deleteCriteria);
}
if (count($listBadSamples) != 0) {
$log = '';
foreach ($listBadSamples as $badSample) {
$log = 'Error with manual import. File id : ' . $fileImportedId . ' - line : ' . $badSample;
Yii::log($log, CLogger::LEVEL_ERROR);
}
}
return count($listBadSamples);
}
/**
* test the method to translate a mysql date to another date format
*/
public function testToDate()
{
$madate = "2000-12-27 23:45:00";
$this->assertEquals("27/12/2000", CommonTools::toDate("d/m/Y", $madate));
}
