/**
* export pdf avec mpdf et liste d'index : Technique HTML to PDF
*/
public function actionExportPdf()
{
$criteria = new EMongoCriteria();
$criteria->sort('name', EMongoCriteria::SORT_ASC);
$models = Biobank::model()->findAll($criteria);
BiobanksPDFExporter::exporter($models);
}
public function run()
{
$users = User::model()->findAll();
foreach ($users as $user) {
$criteria = new EMongoCriteria();
$criteria->id = $user->biobank_id;
$biobank = Biobank::model()->find($criteria);
if ($user->biobank_id === "") {
$user->unsetAttributes(array('biobank_id'));
$user->biobank_id = null;
$user->update();
}
if (!isset($user->biobank_id)) {
$user->biobank_id = null;
$user->update();
} else {
if (is_a($user->biobank_id, 'MongoId')) {
$user->biobank_id = (string) $user->biobank_id;
$user->update();
} else {
$biobank = Biobank::model()->findByAttributes(array('id' => $user->biobank_id));
if ($biobank != null) {
$user->biobank_id = (string) $biobank->_id;
$user->update();
}
}
}
}
}
public function run($args)
{
include_once dirname(dirname(dirname(__FILE__))) . DIRECTORY_SEPARATOR . 'CommonTools.php';
$biobankList = Biobank::model()->findAll();
foreach ($biobankList as $biobank) {
if (isset($biobank->ville)) {
$biobank->address->city = $biobank->ville;
unset($biobank->ville);
}
if (isset($biobank->adresse)) {
$biobank->address->street = $biobank->adresse;
$biobank->address->zip = str_ireplace(' ', '', extract_zipcode($biobank->address->street));
$biobank->address->street = str_ireplace($biobank->address->zip, '', $biobank->address->street);
$biobank->address->street = str_ireplace($biobank->address->city, '', $biobank->address->street);
unset($biobank->adresse);
}
if (isset($biobank->region)) {
$biobank->address->initSoftAttribute('region');
$biobank->address->region = $biobank->region;
unset($biobank->region);
}
$biobank->address->country = 'fr';
$biobank->save(false);
}
}
/**
* Returns the data model based on the primary key given in the GET variable.
* If the data model is not found, an HTTP exception will be raised.
* @param integer $id the ID of the model to be loaded
* @return Biobank the loaded model
* @throws CHttpException
*/
public function loadModel($id)
{
$model = Biobank::model()->findByPk(new MongoID($id));
if ($model === null) {
throw new CHttpException(404, 'The requested page does not exist.');
}
return $model;
}
public function getBiobankName()
{
$biobank = Biobank::model()->findByAttributes(array('id' => $this->biobank_id));
if ($biobank != null) {
return $biobank->identifier;
} else {
return null;
}
}
public function run($args)
{
include_once dirname(dirname(dirname(__FILE__))) . DIRECTORY_SEPARATOR . 'StatTools.php';
$biobanks = Biobank::model()->findAll(array('select' => array('id')));
foreach ($biobanks as $biobank) {
$result = StatTools::saveBiobankStats($biobank->id);
$message = $result === true ? "Statistiques de la biobanque n°{$biobank->id} bien calculées" : "Une erreur est apparue lors de la sauvegarde des statistiques de la biobanque n°{$biobank->id} : {$result}";
echo $message . "\n";
}
StatTools::saveAverageRate();
echo "Statistiques globales enregistrées. \n";
}
/**
* retourne la reparttion des echantillons par ville
* Fournit un tableau aossicatif de nom entier
*
* @return array[array(string,int)]
*/
public static function getRepartitionSamplesByTown()
{
$result = array();
$biobanks = Biobank::model()->findAll();
foreach ($biobanks as $biobank) {
$criteria = new EMongoCriteria();
$criteria->biobank_id = (string) $biobank->_id;
$compte = Sample::model()->count($criteria);
if ($compte != 0) {
$result[] = array($biobank->address->city, $compte);
}
}
return $result;
}
public function run($args)
{
include_once dirname(dirname(dirname(__FILE__))) . DIRECTORY_SEPARATOR . 'CommonMailer.php';
$biobanks = Biobank::model()->findAll();
foreach ($biobanks as $biobank) {
$lastImportDate = FileImported::model()->getDateLastImportByBiobank($biobank->id);
$today = date('Y-m-d H:i:s');
$diffSec = strtotime($today) - strtotime($lastImportDate);
$diffJours = round($diffSec / 60 / 60 / 24, 0);
if ($diffJours >= 30 && ($diffJours - 30) % 5 == 0) {
CommonMailer::sendMailRelanceExport($biobank->getContact(), $lastImportDate, $diffJours);
}
}
echo "Check des imports effectués et relances envoyées\n";
}
public function run()
{
echo 'Massive Run for samples';
$biobanks = Biobank::model()->findAll();
foreach ($biobanks as $biobank) {
$modifier = new EMongoModifier();
$modifier->addModifier('biobank_id', 'set', (string) $biobank->_id);
$criteria = new EMongoCriteria();
$criteria->biobank_id = $biobank->id;
$status = Sample::model()->updateAll($modifier, $criteria);
$criteriaAfter = new EMongoCriteria();
$criteriaAfter->biobank_id = (string) $biobank->_id;
$count = Sample::model()->count($criteriaAfter);
echo "Done for biobank {$biobank->_id} - {$biobank->name} : {$count}\n";
}
}
public function run($args)
{
//uppar case for each last name of contact
$criteria = new EMongoCriteria();
$criteria->sort('last_name', EMongoCriteria::SORT_ASC);
$contacts = Contact::model()->findAll($criteria);
foreach ($contacts as $model) {
//last name to upper case automatically /prevent pb to sort and display
// echo $model->_id."\n";
$model->last_name = mb_strtoupper($model->last_name, "UTF-8");
//convertie first name en lower case et mettant les caracteres en utf-8 ( cas possible de bug sur chaines mixtes)
$model->first_name = mb_strtolower($model->first_name, "UTF-8");
//phone without withespace, point a 0> +33
$model->phone = mb_ereg_replace('/\\s+/', '', $model->phone);
$model->phone = mb_ereg_replace('/\\./', '', $model->phone);
//replace first zero and add +33
$model->phone = mb_ereg_replace('/^0/', '+33', $model->phone);
//pays = FR
$model->pays = "FR";
$model->inactive = 0;
//catch exception on update if problem ( utf8 encoding for example?)
try {
$model->update();
} catch (Exception $e) {
echo 'Exception reçue pour le model: ' . $model->_id . " " . $model->last_name . " " . $model->first_name, $e->getMessage(), "\n";
//detection de le ncodage si pb d estring
echo "first name encoding :" . mb_detect_encoding($model->first_name) . "\n";
}
}
//update relation biobank->contact_id if old id contact, si ancien attribut id utilisé alors on mets le nouvel attribut _id
$criteriaB = new EMongoCriteria();
$criteriaB->sort('name', EMongoCriteria::SORT_ASC);
$biobanks = Biobank::model()->findAll($criteriaB);
foreach ($biobanks as $biobank) {
$contact = Contact::model()->findByAttributes(array('id' => $biobank->contact_id));
if ($contact != null) {
// echo "current value from migration:" . $contact->last_name . " " . $contact->first_name."\n";
$biobank->contact_id = $contact->_id;
$biobank->update();
}
}
}
<?php
/* @var $this SearchBiobankController */
/* @var $data Biobank */
?>
<div class='view'>
<?php
foreach (Biobank::Model()->attributeExportedLabels() as $attribute => $value) {
if (isset($data->{$attribute})) {
?>
<b><?php
echo CHtml::encode($data->getAttributeLabel($attribute));
?>
:</b>
<?php
switch ($attribute) {
case 'contact_id':
echo $data->contact_id != null && !empty($data->contact_id) ? CHtml::encode($data->getShortContact()) . '<br>' . CHtml::encode($data->getEmailContact()) . '<br>' . CHtml::encode($data->getPhoneContact()) : "";
break;
case 'address':
echo nl2br($data->getAddress());
break;
case 'website':
echo CHtml::link($data->website, 'http://' . $data->website, array('target' => 'blank'));
break;
default:
echo CHtml::encode($data->{$attribute});
break;
}
?>
<br />
<div class="wide form">
<?php
$form = $this->beginWidget('CActiveForm', array('action' => Yii::app()->createUrl($this->route), 'method' => 'get'));
?>
<table>
<tr>
<td>
<?php
echo $form->label($model, 'biobank_id');
?>
<?php
$biobank = new Biobank();
echo $form->dropDownList($model, 'biobank_id', $biobank->getArrayBiobank($biobank_id));
?>
</td>
<td>
<?php
echo $form->label($model, 'field_age_min');
?>
<?php
echo $form->textField($model, 'field_age_min', array('size' => 10, 'maxlength' => 3));
?>
</td>
<td>
<?php
echo $form->label($model, 'storage_conditions');
echo $form->dropDownList($model, 'storage_conditions', $model->getArrayStorage(), array('prompt' => '----'));
?>
</td>
<?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;
?>
<div class="form">
<?php
<?php
$form = $this->beginWidget('CActiveForm', array('action' => Yii::app()->createUrl($this->route)));
?>
<table>
<tr>
<td>
<?php
echo $form->label($model, 'biobank_id');
?>
<?php
if ($this->layout == '//layouts/vitrine_layout') {
$biobank = $_SESSION['vitrine']['biobank'];
echo $form->dropDownList($model, 'biobank_id', array($biobank->id => $biobank->identifier));
} else {
$biobank = new Biobank();
echo $form->dropDownList($model, 'biobank_id', $biobank->getArrayBiobanks(), array('prompt' => '----', 'style' => 'width:145px'));
}
?>
</td>
<td>
<?php
echo $form->label($model, 'field_age_min');
?>
<?php
echo $form->textField($model, 'field_age_min', array('size' => 10, 'maxlength' => 3));
?>
</td>
<td>
<?php
echo $form->label($model, 'storage_conditions');
/**
* get biobank name of this contact
* usefull in view contacts for site
* @return type
*/
public function getBiobankName()
{
$result = 'Not defined';
if ($this->biobank_id != null && isset($this->biobank_id)) {
$biobank = Biobank::model()->findByPK(new MongoID($this->biobank_id));
if (isset($biobank)) {
$result = $biobank->name;
}
}
return $result;
}
/**
* display catalog of biobanks with contacts and agregated infos
*/
public function actionCatalog()
{
$model = new Biobank('search');
$model->unsetAttributes();
// clear any default values
if (isset($_GET['Biobank'])) {
$model->attributes = $_GET['Biobank'];
}
//make the search
//render the biobanks
$this->render('catalog', array('model' => $model));
}
<div class="form">
<?php
$form = $this->beginWidget('CActiveForm', array('id' => 'biobank_manUploaded-form', 'enableAjaxValidation' => false, 'htmlOptions' => array('enctype' => 'text/html', 'accept-charset' => "UTF-8")));
?>
<?php
echo $form->errorSummary($biobankIdentifier);
?>
<div class="row" >
<?php
$criteria = new EMongoCriteria();
$criteria->sort('identifier', EMongoCriteria::SORT_ASC);
echo $form->DropDownList($biobankIdentifier, 'identifier', CHtml::listData(Biobank::model()->findAll($criteria), 'identifier', 'identifierAndName'), array('empty' => 'select brif code'));
?>
<?php
echo $form->error($biobankIdentifier, 'identifier');
?>
</div>
<?php
$this->endWidget();
?>
</div>
<!-- form -->
/**
* retourne le modele de la biobanque fournit par l id mongo
* null sinon
*/
public function getBiobank($mongoId)
{
if ($mongoId != null) {
return Biobank::model()->findByPk(new MongoId($mongoId));
} else {
return null;
}
}
<h1><?php
echo Yii::t('common', 'sample') . ' #' . $model->biobank_id . '_' . $model->id_sample;
?>
</h1>
<div style="float:left;">
<h3 >Caracteristics</h3>
<?php
$this->widget('zii.widgets.CDetailView', array('data' => $model, 'attributes' => array('id_depositor', 'id_sample', 'consent_ethical', 'gender', 'age', 'collect_date', array('name' => 'storage_conditions', 'value' => $model->getLiteralStorageCondition()), 'consent', 'supply', 'max_delay_delivery', 'detail_treatment', 'disease_outcome', 'authentication_method', 'patient_birth_date', 'tumor_diagnosis')));
?>
</div>
<div style="float:left;padding-left:10px;">
<div>
<h3 style="margin-bottom:-5px;" >Notes</h3>
<?php
$notesDataProvider = new CArrayDataProvider($model->notes, array('keyField' => 'key'));
$this->widget('zii.widgets.grid.CGridView', array('dataProvider' => $notesDataProvider, 'template' => '{items}{pager}', 'columns' => array(array('header' => 'Key', 'value' => '$data->key'), array('header' => 'Value', 'value' => '$data->value'))));
?>
</div>
<div>
<h3 >Biobank informations</h3>
<?php
$data = Biobank::model()->findByPk(new MongoId($model->biobank_id));
$this->widget('zii.widgets.CDetailView', array('data' => $data, 'attributes' => array(array('name' => 'biobank', 'value' => $data->identifier), array('name' => 'contact', 'value' => $data->getShortContact()), array('name' => 'email', 'value' => $data->getEmailContact()), array('name' => 'phone', 'value' => $data->getPhoneContact()))));
?>
</div>
</div>
<div style="clear:both;"></div>
/**
* export xls des biobanques
*/
public function actionExportXls()
{
$model = new Biobank('search');
$model->unsetAttributes();
if (isset($_GET['Biobank'])) {
$model->attributes = $_GET['Biobank'];
}
if (isset($_SESSION['criteria']) && $_SESSION['criteria'] != null && $_SESSION['criteria'] instanceof EMongoCriteria) {
$criteria = $_SESSION['criteria'];
} else {
$criteria = new EMongoCriteria();
}
$biobanks = Biobank::model()->findAll($criteria);
$data = array(1 => array_keys(Biobank::model()->attributeExportedLabels()));
setlocale(LC_ALL, 'fr_FR.UTF-8');
foreach ($biobanks as $biobank) {
$line = array();
foreach (array_keys($biobank->attributeExportedLabels()) as $attribute) {
if (isset($biobank->{$attribute}) && $biobank->{$attribute} != null && !empty($biobank->{$attribute})) {
$line[] = iconv("UTF-8", "ASCII//TRANSLIT", $biobank->{$attribute});
//solution la moins pire qui ne fait pas bugge les accents mais les convertit en caractere generique
} else {
$line[] = "-";
}
}
$line[] = iconv("UTF-8", "ASCII//TRANSLIT", $biobank->getShortContact());
$line[] = iconv("UTF-8", "ASCII//TRANSLIT", $biobank->getEmailContact());
$contact = $biobank->getContact();
if ($contact != null) {
$line[] = iconv("UTF-8", "ASCII//TRANSLIT", $contact->getFullAddress());
} else {
$line[] = "No address";
}
$data[] = $line;
}
Yii::import('application.extensions.phpexcel.JPhpExcel');
$xls = new JPhpExcel('UTF-8', true, 'Biobank list');
$xls->addArray($data);
$xls->generateXML('Biobank list');
}
/**
* 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;
}
?>
</div>
<div class="row">
<?php
echo $form->labelEx($model, 'inactif');
echo $form->dropDownList($model, 'inactif', User::model()->getArrayInactif(), array('prompt' => '----'));
?>
<?php
echo $form->error($model, 'inactif');
?>
</div>
<div class="row">
<?php
echo $form->labelEx($model, 'biobank_id');
echo $form->dropDownList($model, 'biobank_id', Biobank::model()->getArrayBiobanks(), array('prompt' => '----'));
echo $form->error($model, 'biobank_id');
?>
</div>
<div class="row buttons">
<?php
echo CHtml::submitButton($model->isNewRecord ? 'Create' : 'Save');
?>
</div>
<?php
$this->endWidget();
?>
</div><!-- form -->
$countDisplayedColumns = 0;
foreach ($prefs as $property => $propertyValue) {
if ($property != 'id_user' && $property != '_id') {
if ($propertyValue) {
$visibility = "table_cell";
$countDisplayedColumns++;
} else {
$visibility = 'display:none';
}
if ($property == 'notes') {
$columns[] = addColumn($property, $model->getAttributeLabel($property), '$data->getShortNotes()', $visibility);
} elseif ($property == 'biobank_id') {
$columns[] = addColumn('biobank_id', $model->getAttributeLabel('biobank_id'), '$data->getBiobankName()', $visibility);
} elseif ($property == 'collection_name') {
$columns[] = addColumn('collection_name', Biobank::model()->getAttributeLabel('collection_name'), '$data->biobank->collection_name', $visibility);
} elseif ($property == 'collection_id') {
$columns[] = addColumn('collection_id', Biobank::model()->getAttributeLabel('collection_id'), '$data->biobank->collection_id', $visibility);
} elseif ($property == 'collect_date') {
$columns[] = addColumn('collect_date', $model->getAttributeLabel('collect_date'), '$data->collect_date', $visibility);
//TODO normaliser les dates de collecte avant d activer cette feature
// $columns [] = getArrayColumn('collect_date', $model->getAttributeLabel('collect_date'), 'CommonTools::toShortDateFR($data->collect_date)', $visibility);
} elseif ($property == 'storage_conditions') {
$columns[] = addColumn('storage_conditions', $model->getAttributeLabel('storage_conditions'), '$data->getLiteralStorageCondition()', $visibility);
} else {
$columns[] = addColumn($property, $model->getAttributeLabel($property), '$data->' . $property, $visibility);
}
}
}
//popup de choix des colonnes à afficher
$columns[] = array('class' => 'CButtonColumn', 'header' => CHtml::link($imageSelect, '#', array('onclick' => '$("#selectPopup").dialog("open");return false;')), 'template' => '{view}', 'buttons' => array('view' => array('url' => 'Yii::app()->createUrl("site/view",array("id"=>"$data->_id", "asDialog"=>1))', 'click' => 'function(){window.open(this.href,"_blank","left=100,top=100,width=760,height=650,toolbar=0,resizable=1, location=no");return false;}')));
$this->widget('zii.widgets.grid.CGridView', array('id' => 'sample-grid', 'dataProvider' => $model->searchWithNotes(), 'columns' => $columns));
/**
* Envoie une demande aux contacts des biobanques concernées par une demande
*/
public function actionEnvoyer()
{
if (isset($_GET['demande_id'])) {
$demande = $this->loadModel($_GET['demande_id']);
if (!empty($demande->titre) && !empty($demande->detail) && !empty($demande->sampleList)) {
$samples = $demande->getArraySamples();
$biobankIdList = $demande->getBiobanksFromSamples($samples);
$demandeSent = false;
foreach ($biobankIdList as $biobankId) {
$biobank = Biobank::model()->findByPk(new MongoId($biobankId));
if ($biobank->contact_id != null) {
$contact = Contact::model()->findByPk(new MongoId($biobank->contact_id));
if ($contact != null) {
$concernSamplesList = array();
foreach ($samples as $sample) {
if ($sample->biobank_id == $biobankId) {
$concernSamplesList[] = $sample;
}
}
// PB si pas envoyer a une biuobank alors pas sauvegarder
if (CommonMailer::sendDemande($contact, $demande->titre . ' : ' . $biobank->identifier, $demande->detail, $concernSamplesList) == 1) {
$demandeSent = true;
}
} else {
}
}
}
if ($demandeSent) {
$demande->envoi = 1;
$demande->save();
$this->actionCreateNewDemand();
Yii::app()->user->setFlash('success', 'Votre demande a bien été envoyée aux différents sites');
$this->render('view', array_merge(array('model' => $this->loadModel($demande->_id), isset($_GET['layout']) || isset($layout) && $layout != null ? array('layout' => $_GET['layout']) : array())));
} else {
Yii::app()->user->setFlash('error', 'Un problème est apparu, les demandes n\'ont pas été transmises');
$this->redirect(array_merge(array('updateAndSend', 'id' => Yii::app()->session['activeDemand'][0]->_id), isset($_GET['layout']) ? array('layout' => $_GET['layout']) : array()));
//
}
} else {
Yii::app()->user->setFlash('notice', 'Merci de completer votre demande avant de l\'envoyer');
$this->redirect(array_merge(array('updateAndSend', 'id' => $demande->_id), isset($_GET['layout']) ? array('layout' => $_GET['layout']) : array()));
//
}
}
}
$this->widget('application.widgets.charting.CBarsChartWidget', array('id' => 'columnchart-count-files-month', 'theme' => 'Distinctive', 'title' => '', 'data' => StatTools::getCountFilesReceptionByMonth(), 'width' => 380, 'heigth' => 250, 'xAxisRotation' => 0));
$this->endWidget();
?>
</div>
<div style="float:left;width:430px;padding-left:10px;">
<?php
$this->beginWidget('zii.widgets.CPortlet', array('title' => "<i class='icon-adjust'></i>" . Yii::t('common', 'LoSaCh')));
//affichage du graphe de repartition par ville des echantillons
$this->widget('application.widgets.charting.CPieChartWidget', array('id' => 'piechart-collab', 'theme' => 'WatersEdge', 'width' => 380, 'height' => 250, 'data' => StatTools::getRepartitionSamplesByTown(), 'title' => 'Location by biobank'));
$this->endWidget();
?>
</div>
</div>
<div style="clear:both;">
<div style="float:left;width:430px;">
<?php
$this->beginWidget('zii.widgets.CPortlet', array('title' => "<i class='icon-adjust'></i>" . Yii::t('common', 'BioBkReg')));
$this->widget('zii.widgets.grid.CGridView', array('id' => 'echantillon-grid', 'dataProvider' => Biobank::model()->search(), 'columns' => array('identifier', 'name', array('header' => 'collection name', 'value' => 'CommonTools::getShortValue($data->collection_name)'), array('header' => 'Main contact', 'value' => '$data->getShortContact()'))));
$this->endWidget();
?>
</div>
<div style="float:left;width:430px;padding-left:10px;">
<?php
$this->beginWidget('zii.widgets.CPortlet', array('title' => "<i class='icon-share'></i>" . Yii::t('common', 'SaReAct')));
$this->widget('application.widgets.charting.CBarsChartWidget', array('id' => 'columnchart-count-month', 'theme' => 'Distinctive', 'title' => '', 'data' => StatTools::getCountReceptionByMonth(), 'width' => 380, 'heigth' => 250, 'xAxisRotation' => 0));
$this->endWidget();
?>
</div>
</div>
<div style="clear:both;"/>
public function getBiobankName()
{
$result = null;
if (isset($this->biobank_id) && $this->biobank_id != null && $this->biobank_id != '') {
$biobank = Biobank::model()->findByPk(new MongoId($this->biobank_id));
if ($biobank != null) {
$result = $biobank->name;
}
}
return $result;
}
/**
*
* @return array customized attribute labels (name=>label)
*/
public function attributeLabels()
{
return array('id_user' => Yii::t('common', 'idUser'), 'id' => Yii::t('sample', 'id'), 'biobank_id' => Yii::t('sample', 'biobank_id'), 'consent_ethical' => Yii::t('sample', 'consent_ethical'), 'id_depositor' => Yii::t('sample', 'id_depositor'), 'id_sample' => Yii::t('sample', 'id_sample'), 'gender' => Yii::t('sample', 'gender'), 'age' => Yii::t('sample', 'age'), 'collect_date' => Yii::t('sample', 'collect_date'), 'storage_conditions' => Yii::t('sample', 'storage_conditions'), 'consent' => Yii::t('sample', 'consent'), 'supply' => Yii::t('sample', 'supply'), 'max_delay_delivery' => Yii::t('sample', 'max_delay_delivery'), 'detail_treatment' => Yii::t('sample', 'detail_treatment'), 'disease_outcome' => Yii::t('sample', 'disease_outcome'), 'authentication_method' => Yii::t('sample', 'authentication_method'), 'patient_birth_date' => Yii::t('sample', 'patient_birth_date'), 'tumor_diagnosis' => Yii::t('sample', 'tumor_diagnosis'), 'file_imported_id' => Yii::t('sample', 'file_imported_id'), 'notes' => Yii::t('sample', 'notes'), 'collection_name' => Biobank::model()->getAttributeLabel('collection_name'), 'collection_id' => Biobank::model()->getAttributeLabel('collection_id'));
}
public function actionUploadAll()
{
$model = new Biobank();
$listFile = array();
// $fichier = null;
$biobankIdentifier = new BiobankIdentifierForm();
if (!isset($model->presentation)) {
$model->initSoftAttribute('presentation');
}
if (!isset($model->thematiques)) {
$model->initSoftAttribute('thematiques');
}
if (!isset($model->publications)) {
$model->initSoftAttribute('publications');
}
if (!isset($model->reseaux)) {
$model->initSoftAttribute('reseaux');
}
if (!isset($model->qualite)) {
$model->initSoftAttribute('qualite');
}
if (!isset($model->projetRecherche)) {
$model->initSoftAttribute('projetRecherche');
}
if (!isset($model->activeLogo)) {
$model->initSoftAttribute('activeLogo');
}
if (is_dir(Yii::app()->basePath . '/../images/extractedLogos/')) {
$listFile = scandir(Yii::app()->basePath . '/../images/extractedLogos/');
}
// if (isset($listFile[2]) && !is_dir($listFile[2]))
// $fichier = $listFile[2];
// if (isset($_POST['Biobank'])) {
// $model->attributes = $_POST['Biobank'];
// if (isset($_POST['importLogo']) && $_POST['importLogo'] == 1) {
// $file = $folder . $fichier;
// $model->initSoftAttribute('activeLogo');
//
// $model->activeLogo = (string) $this->logoUpload($file, $model);
// if (rename($file, $folder . 'done/' . $fichier)) {
// $listFile = scandir(Yii::app()->basePath . '/../images/extractedLogos/');
// $fichier = $listFile[2];
// Yii::app()->user->setFlash('success', 'renamed');
// } else {
// Yii::app()->user->setFlash('error', 'error on rename');
// }
// Yii::app()->user->setFlash('success', 'imported');
// } else {
// Yii::app()->user->setFlash('success', 'logo not imported');
// }
//
// if (isset($_FILES['Logo'])) {
//
//
// $model->activeLogo = (string) $this->storeLogo($_FILES['Logo'], $model);
// }
// if ($model->save()) {
//
// Yii::app()->user->setFlash('success', Yii::app()->user->getFlash('success') . 'Biobank infos saved');
// }
// if (isset($_FILES['Logo'])) {
//
// $model->initSoftAttribute('activeLogo');
// $model->activeLogo = (string) $this->storeLogo($_FILES['Logo'], $model);
// }
/* if ($model->update()) {
Yii::app()->user->setFlash('success', Yii::app()->user->getFlash('success') . 'Biobank infos saved');
unset($_POST['Biobank']);
} else {
// $list = '';
// foreach ($model->errors as $errorName => $errorName)
// $list .= "<li>$errorName</li>";
// Yii::app()->user->setFlash('error', 'error on save : <ul>' . $list . '</ul>');
} */
// }*/
// } else {
// Yii::app()->user->setFlash('error', 'biobank not found');
// }
if (isset($_POST['BiobankIdentifierForm']) && isset($_POST['BiobankIdentifierForm']['identifier']) && $_POST['BiobankIdentifierForm']['identifier'] != "") {
$model = Biobank::model()->findByAttributes(array('identifier' => $_POST['BiobankIdentifierForm']['identifier']));
}
if (isset($_POST['Biobank'])) {
$model = Biobank::model()->findByAttributes(array('identifier' => $_POST['Biobank']['identifier']));
if (!isset($model->presentation)) {
$model->initSoftAttribute('presentation');
}
$model->presentation = $_POST['Biobank']['presentation'];
// print_r($model->getErrors());
if (!isset($model->thematiques)) {
$model->initSoftAttribute('thematiques');
}
$model->thematiques = $_POST['Biobank']['thematiques'];
if (!isset($model->publications)) {
$model->initSoftAttribute('publications');
}
$model->publications = $_POST['Biobank']['publications'];
if (!isset($model->reseaux)) {
$model->initSoftAttribute('reseaux');
}
$model->reseaux = $_POST['Biobank']['reseaux'];
if (!isset($model->qualite)) {
$model->initSoftAttribute('qualite');
}
$model->qualite = $_POST['Biobank']['qualite'];
if (!isset($model->projetRecherche)) {
$model->initSoftAttribute('projetRecherche');
}
$model->projetRecherche = $_POST['Biobank']['projetRecherche'];
if ($model->save(false)) {
Yii::app()->user->setFlash('success', 'La biobanque a bien été mise à jour.');
} else {
Yii::app()->user->setFlash('error', 'La biobanque n\'a pas pu être mise à jour');
}
}
// if ($fichier != '.' && $fichier != '..') {
$this->render('upload', array('model' => $model, 'listLogos' => $listFile, 'biobankIdentifier' => $biobankIdentifier));
// }
}
/**
* FIXME fonction etrange retour bizarre, action de controller melangée
* @return type
*/
public static function getBiobankInfo()
{
$id = $_SESSION['biobank_id'];
$biobank = Biobank::getBiobank($id);
if ($biobank != null) {
if (isset($biobank->logo) && $biobank->logo != null) {
$logo = $biobank->logo;
$_SESSION['vitrine'] = array('biobank' => $biobank, 'biobankLogo' => $logo);
}
return $id;
} else {
Yii::app()->user->setFlash('error', yii::t('common', 'noBiobankFound'));
//Yii::app()->controller->redirect(Yii::app()->createUrl('site/biobanks'));
}
}
public function getBiobank()
{
$biobank = Biobank::model()->findByPk(new MongoId($this->biobank_id));
if ($biobank != null) {
return $biobank;
} else {
return null;
}
}
