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";
}
}
/**
* Deletes a particular model.
* If deletion is successful, the browser will be redirected to the 'admin' page.
* @param integer $id the ID of the model to be deleted
*/
public function actionDelete($id)
{
$model = $this->loadModel($id);
$name = $model->name;
$sampleCount = Sample::model()->countByAttributes(array('biobank_id' => (string) $model->id));
$adminCount = User::model()->countByAttributes(array('biobank_id' => (string) $model->_id));
if ($adminCount == 0 && $sampleCount == 0) {
try {
$model->delete();
Yii::app()->user->setFlash('success', 'La biobanque a bien été supprimée.');
} catch (Exception $ex) {
Yii::app()->user->setFlash('error', 'La biobanque n\'a pas pu être supprimée : ' . $ex->getMessage());
}
} else {
$message = "Suppression de la biobanque \"{$name}\" impossible : ";
if ($adminCount > 0) {
$message .= "<br> - Il reste {$adminCount} administrateur(s) lié(s) à la biobanque.";
}
if ($sampleCount > 0) {
$message .= "<br> reste {$sampleCount} échantillon(s) lié(s) à la biobanque.";
}
Yii::app()->user->setFlash('error', $message);
}
// if AJAX request (triggered by deletion via admin grid view), we should not redirect the browser
if (!isset($_GET['ajax'])) {
$this->redirect(isset($_POST['returnUrl']) ? $_POST['returnUrl'] : array('admin'));
} else {
$flashMessages = Yii::app()->user->getFlashes();
$flashMessagesHtml = '';
if ($flashMessages) {
foreach ($flashMessages as $key => $message) {
$flashMessagesHtml .= '<br><div class="flash-' . $key . '">' . $message . "</div>";
}
}
echo $flashMessagesHtml;
}
}
public function loadEchModel($id)
{
$model = Sample::model()->findByPk(new MongoID($id));
if ($model === null) {
throw new CHttpException(404, 'The requested page does not exist.');
}
return $model;
}
<?php
echo CHtml::activeDropDownList($model, 'dataset_id', CHtml::listData(Util::getDois(), 'id', 'identifier'));
?>
<?php
echo $form->error($model, 'dataset_id');
?>
</div>
</div>
<div class="control-group">
<?php
echo $form->labelEx($model, 'sample_id', array('class' => 'control-label'));
?>
<div class="controls">
<?php
echo CHtml::activeDropDownList($model, 'sample_id', CHtml::listData(Sample::model()->findAll(), 'id', 'id'));
?>
<?php
echo $form->error($model, 'sample_id');
?>
</div>
</div>
<div class="row buttons">
<a href="/adminDatasetSample/admin" class="btn">Cancel</a>
<?php
echo CHtml::submitButton($model->isNewRecord ? 'Create' : 'Save', array('class' => 'btn'));
?>
</div>
<?php
/**
* effectue le calcul de statistiques de la biobanque fournie en parametre si elle possede des echantillons,
* @param type $biobank_id
* @return null
*/
public static function getCompletionRateByBiobank($biobank_id)
{
//nombre total d'échantillons de la biobanque
$criteria = new EMongoCriteria();
$criteria->biobank_id = $biobank_id;
$compte = Sample::model()->count($criteria);
if ($compte != 0 && $compte != null) {
$details = array();
$rateCount = 0;
$listAttributes = StatTools::getAttributesForRating();
foreach ($listAttributes as $attributeName => $attributeConstraint) {
$echCriteria = new EMongoCriteria();
$echCriteria->biobank_id = $biobank_id;
$echCriteria->addCond($attributeName, "exists", true);
if (is_array($attributeConstraint)) {
foreach ($attributeConstraint as $operator => $values) {
$echCriteria->addCond($attributeName, $operator, $values);
}
}
$nbEch = Sample::model()->count($echCriteria);
$details[$attributeName] = round($nbEch / $compte * 100, 2);
$rateCount += $nbEch;
}
$rate = $rateCount / ($compte * count($listAttributes));
return array($rate * 100, $details);
} else {
return null;
}
}
<h1>View File #<?php
echo $model->id;
?>
</h1>
<? if (Yii::app()->user->checkAccess('admin')) { ?>
<div class="actionBar">
[<?php
echo MyHtml::link('Manage Files', array('admin'));
?>
]
</div>
<? } ?>
<?php
$sample_id = FileSample::model()->find('file_id=:file_id', array(':file_id' => $model->id));
if (isset($sample_id)) {
$sample_name = Sample::model()->find('id=:id', array(':id' => $sample_id->sample_id));
}
$name = "Not Set";
if (isset($sample_id) && isset($sample_name)) {
$name = $sample_name->name;
}
$this->widget('zii.widgets.CDetailView', array('data' => $model, 'attributes' => array('id', 'dataset_id', 'name', 'location', 'extension', 'size', 'description', 'date_stamp', 'format_id', 'type_id', array('name' => 'Sample', 'value' => $name))));
$tabCount = 0;
foreach ($globalStats[0]->values as $attributeName => $attribute) {
$datas = array();
for ($i = 0; $i <= $max; $i++) {
if (isset($biobankStats[$max - $i])) {
$datas['biobanque'][] = $biobankStats[$max - $i]->values[$attributeName];
} else {
$datas['biobanque'][] = null;
}
if (isset($globalStats[$max - $i])) {
$datas['global'][] = $globalStats[$max - $i]->values[$attributeName];
} else {
$datas['global'][] = null;
}
}
$listWidgets[$attributeName] = array('label' => Sample::model()->getAttributeLabel($attributeName), 'url' => Yii::app()->createUrl('mybiobank/detailGraph'), 'ajax' => array('type' => 'POST', 'update' => '#detailData', 'data' => array('datas' => $datas, 'attributeName' => $attributeName, 'theme' => $theme)));
}
?>
<div style="overflow: hidden;display: inline-block">
<div id="detailsMenu" style="float:left;width:200px;padding-left:5px;padding-right:5px;padding-top:5px;">
<div class="span-5 last">
<?php
$this->beginWidget('zii.widgets.CPortlet', array('title' => 'Détails'));
$this->widget('ext.AjaxMenu', array('items' => $listWidgets));
$this->endWidget();
?>
</div></div>
public function getAllSamples()
{
$criteria = new CdbCriteria();
$criteria->join = "join dataset_sample ds on ds.sample_id = t.id";
$criteria->addCondition("ds.dataset_id = " . $this->id);
return Sample::model()->findAll($criteria);
}
public function getSamples()
{
$samples = array();
if ($this->sampleList != null) {
foreach ($this->sampleList as $sampleDemand) {
$samples[] = new MongoID($sampleDemand->id_sample);
}
}
$dataProvider = Sample::model()->getSamplesFromArray($samples);
return $dataProvider;
}
/**
* print de la liste dechantillons
*/
public function actionPrint()
{
// $model = new Sample('search');
if (isset($_SESSION['criteria']) && $_SESSION['criteria'] != null && $_SESSION['criteria'] instanceof EMongoCriteria) {
$criteria = $_SESSION['criteria'];
} else {
$criteria = new EMongoCriteria();
}
$criteria->limit(200);
$dataProvider = new EMongoDocumentDataProvider('Sample', array('criteria' => $criteria, 'pagination' => false));
$columns = array();
foreach (Sample::model()->attributeExportedLabels() as $key => $value) {
if ($key == 'notes') {
$columns[] = $this->addColumn($key, $value, '$data->getShortNotes()');
} elseif ($key == 'biobank_id') {
$columns[] = $this->addColumn('biobank_id', $value, '$data->getBiobankName()');
} elseif ($key == 'collect_date') {
$columns[] = $this->addColumn('collect_date', $value, '$data->collect_date');
//TODO normaliser les dates de collecte avant d activer cette feature
// $columns [] = getArrayColumn('collect_date', $value, 'CommonTools::toShortDateFR($data->collect_date)');
} elseif ($key == 'storage_conditions') {
$columns[] = $this->addColumn('storage_conditions', $value, '$data->getLiteralStorageCondition()');
} else {
$columns[] = $this->addColumn($key, $value, '$data->' . $key);
}
}
$this->render('print', array('dataProvider' => $dataProvider, 'columns' => $columns));
}
$visibility = 'display:none';
}
if ($property == 'notes') {
$columns[] = array('class' => 'DataColumn', 'name' => $property, 'id' => 'col_' . $property, 'header' => Sample::model()->getAttributeLabel($property), 'value' => '$data->getShortNotes()', 'htmlOptions' => array('class' => "col_{$property}", 'style' => $visibility), 'headerHtmlOptions' => array('class' => "col_{$property}", 'style' => $visibility));
} elseif ($property == 'biobank_id') {
$columns[] = array('class' => 'DataColumn', 'name' => Yii::t('sample', 'biobank_id'), 'id' => 'col_' . $property, 'header' => Sample::model()->getAttributeLabel($property), 'value' => 'Biobank::model()->findByPk(new MongoId($data->biobank_id))->name', 'htmlOptions' => array('class' => "col_{$property}", 'style' => $visibility), 'headerHtmlOptions' => array('class' => "col_{$property}", 'style' => $visibility));
} elseif ($property == 'collect_date') {
$columns[] = array('class' => 'DataColumn', 'name' => $property, 'id' => 'col_' . $property, 'header' => Sample::model()->getAttributeLabel($property), 'value' => 'CommonTools::toShortDateFR($data->collect_date)', 'htmlOptions' => array('class' => "col_{$property}", 'style' => $visibility), 'headerHtmlOptions' => array('class' => "col_{$property}", 'style' => $visibility));
} elseif ($property == 'storage_conditions') {
$columns[] = array('class' => 'DataColumn', 'name' => $property, 'id' => 'col_' . $property, 'header' => Sample::model()->getAttributeLabel($property), 'value' => '$data->getLiteralStorageCondition()', 'htmlOptions' => array('class' => "col_{$property}", 'style' => $visibility), 'headerHtmlOptions' => array('class' => "col_{$property}", 'style' => $visibility));
} elseif ($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);
} else {
$columns[] = array('class' => 'DataColumn', 'name' => $property, 'id' => 'col_' . $property, 'value' => '$data->' . $property, 'header' => Sample::model()->getAttributeLabel($property), 'htmlOptions' => array('class' => "col_{$property}", 'style' => $visibility), 'headerHtmlOptions' => array('class' => "col_{$property}", 'style' => $visibility));
}
}
}
//
$columns[] = array('header' => Yii::t('demande', 'sampleDetail'), 'class' => 'CLinkColumn', 'labelExpression' => '$data->_id', 'urlExpression' => 'Yii::app()->createUrl("site/view",array("id"=>"$data->_id"))', 'linkHtmlOptions' => array('onclick' => 'window.open(this.href,"SampleDetail","left=100,top=100,width=760,height=650,toolbar=0,resizable=0, location=no");return false;'), 'htmlOptions' => array('style' => 'text-align:center'), 'imageUrl' => $imageSampleDetail);
?>
<h1><?php
echo Yii::t('common', 'demande') . ' ' . $model->titre;
?>
</h1>
<?php
echo $this->renderPartial('_form', array('model' => $model));
?>
public function actionDelete1($id)
{
if (isset($_SESSION['samples'])) {
$info = $_SESSION['samples'];
foreach ($info as $key => $value) {
if ($value['id'] == $id) {
unset($info[$key]);
$_SESSION['samples'] = $info;
$vars = array('samples');
//Dataset::storeSession($vars);
$condition = 'id=' . $id;
$sample_id = DatasetSample::model()->findByAttributes(array('id' => $id))->sample_id;
DatasetSample::model()->deleteAll($condition);
Sample::model()->deleteAll('id=' . $sample_id);
$this->redirect("/adminDatasetSample/create1");
}
}
}
}
public function testgetShortNotes()
{
$sample = Sample::model();
$this->assertNotNull($sample);
//$sample=Sample::model()->search());
}
<?php
echo CHtml::activeDropDownList($model, 'type_id', CHtml::listData(FileType::model()->findAll(), 'id', 'name'));
?>
<?php
echo $form->error($model, 'type_id');
?>
</div>
</div>
<div class="control-group">
<?php
echo $form->labelEx($model, 'sample_name', array('class' => 'control-label'));
?>
<div class="controls">
<?php
echo CHtml::activeDropDownList($model, 'sample_name', CHtml::listData(Sample::model()->findAll(), 'id', 'name'), array('empty' => 'None'));
?>
<?php
echo $form->error($model, 'sample_name');
?>
</div>
</div>
<?php
if (!$model->isNewRecord) {
?>
<div class="control-group">
<a href="#" role="button" class="btn btn-attr">New Attribute </a>
<br/>
<div class="js-new-attr" style="display:none;">
<?php
if ($stats != null) {
$complete = $stats->globalRate;
} else {
$complete = 0;
}
$roundcomplete = round($complete);
$uncomplete = 100 - $roundcomplete;
$data = array(array('Complet : ' . $roundcomplete . '%', $roundcomplete), array('Incomplet : ' . $uncomplete . "%", $uncomplete));
$this->beginWidget('zii.widgets.CPortlet', array('title' => "<i class = 'icon-adjust'></i> " . Yii::t('myBiobank', 'samplesCompletionRate') . " - {$model->identifier}"));
// affichage du graphe de completude des echantillons
$this->widget('application.widgets.charting.CPieChartWidget', array('id' => 'piechart-collab', 'theme' => 'WatersEdge', 'width' => 380, 'height' => 250, 'data' => $data, 'title' => '<a class="detail-button" href="#">détails</a>'));
$this->endWidget();
?>
</div>
<!-- affichage du tableau de stats detaillées -->
<div style="float: left; width: 330px; padding-left: 10px; padding-top: 10px; display: none" class="detail_tab">
<h4><b>Détails des taux de complétude.</b></h4>
<?php
if ($stats != null) {
foreach ($stats->values as $valueName => $value) {
$attributes[] = array('label' => Sample::model()->getAttributeLabel($valueName), 'value' => $value . '%');
}
$this->widget('zii.widgets.CDetailView', array('data' => $stats->values, 'attributes' => $attributes));
?>
</div>
</div>
<div style="clear: both;" />
<?php
}
protected static function analyzeCsv($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);
}
public function getSample()
{
$criteria = new CDbCriteria();
$criteria->join = "LEFT JOIN file_sample fs ON fs.sample_id = t.id";
$criteria->compare('fs.file_id', $this->id);
return Sample::model()->find($criteria);
}
