/** testGetSetValue */
public function testGetSetValue()
{
Zend_Registry::set('modulesEnable', $this->enabledModules);
Zend_Registry::set('notifier', new MIDAS_Notifier(false, null));
/** @var Validation_ScalarResultModel $scalarResultModel */
$scalarResultModel = MidasLoader::loadModel('ScalarResult', 'validation');
$daos = $scalarResultModel->getAll();
$sr = $daos[0];
$folder = new FolderDao();
$folder->setName('result');
$folder->setDescription('result');
$folder->setParentId(-1);
$this->Folder->save($folder);
$trainingItem = new ItemDao();
$trainingItem->setName('img00.mha');
$trainingItem->setDescription('training img 00');
$trainingItem->setType(0);
$this->Item->save($trainingItem);
$scalarResultModel->setFolder($sr, $folder);
$scalarResultModel->setItem($sr, $trainingItem);
$sr->setValue(90.009);
$scalarResultModel->save($sr);
$daos = $scalarResultModel->getAll();
$sr = $daos[0];
$this->assertEquals(90.009, $sr->getValue());
}
/** Import a directory recursively */
private function _recursiveParseDirectory($path, $currentdir)
{
$it = new DirectoryIterator($path);
foreach ($it as $fileInfo) {
if ($fileInfo->isDot()) {
continue;
}
// If the file/dir is not readable (permission issue)
if (!$fileInfo->isReadable()) {
$this->getLogger()->crit($fileInfo->getPathName() . ' cannot be imported. Not readable.');
continue;
}
// If this is too slow we'll figure something out
if ($this->_checkStopImport()) {
return false;
}
if ($fileInfo->isDir()) {
// we have a directory
// If the the directory actually doesn't exist at this point,
// skip it.
if (!file_exists($fileInfo->getPathName())) {
continue;
}
// Get the files in the directory and skip the folder if it does not
// contain any files and we aren't set to import empty directories. The
// count($files) <= 2 is there to account for our our friends . and ..
$files = scandir($fileInfo->getPathName());
if (!$this->importemptydirectories && $files && count($files) <= 2) {
continue;
}
// Find if the child exists
$child = $this->Folder->getFolderByName($currentdir, $fileInfo->getFilename());
// If the folder does not exist, create one.
if (!$child) {
$child = new FolderDao();
$child->setName($fileInfo->getFilename());
$child->setParentId($currentdir->getFolderId());
$child->setDateCreation(date('Y-m-d H:i:s'));
$child->setDescription('');
$this->Folder->save($child);
$this->Folderpolicyuser->createPolicy($this->userSession->Dao, $child, MIDAS_POLICY_ADMIN);
}
// Keep descending
$this->_recursiveParseDirectory($fileInfo->getPathName(), $child);
} else {
// We have a file
$this->_incrementFileProcessed();
$newrevision = true;
$item = $this->Folder->getItemByName($currentdir, $fileInfo->getFilename());
if (!$item) {
// Create an item
$item = new ItemDao();
$item->setName($fileInfo->getFilename());
$item->setDescription('');
$item->setPrivacyStatus(MIDAS_PRIVACY_PRIVATE);
// Must set this flag private initially
$this->Item->save($item, true);
// Set the policy of the item
$this->Itempolicyuser->createPolicy($this->userSession->Dao, $item, MIDAS_POLICY_ADMIN);
// Add the item to the current directory
$this->Folder->addItem($currentdir, $item);
}
// Check if the bistream has been updated based on the local date
$revision = $this->ItemRevision->getLatestRevision($item);
if ($revision) {
$newrevision = false;
$bitstream = $this->ItemRevision->getBitstreamByName($revision, $fileInfo->getFilename());
$curMD5 = UtilityComponent::md5file($fileInfo->getPathName());
$diskFileIsNewer = strtotime($bitstream->getDate()) < filemtime($fileInfo->getPathName());
$md5IsDifferent = $bitstream->getChecksum() != $curMD5;
if (!$bitstream || $diskFileIsNewer && $md5IsDifferent) {
$newrevision = true;
}
}
if ($newrevision) {
// Create a revision for the item
$itemRevisionDao = new ItemRevisionDao();
$itemRevisionDao->setChanges('Initial revision');
$itemRevisionDao->setUser_id($this->userSession->Dao->getUserId());
$this->Item->addRevision($item, $itemRevisionDao);
// Add bitstreams to the revision
$this->getLogger()->debug('create New Bitstream');
$bitstreamDao = new BitstreamDao();
$bitstreamDao->setName($fileInfo->getFilename());
$bitstreamDao->setPath($fileInfo->getPathName());
$bitstreamDao->fillPropertiesFromPath();
// Set the Assetstore
$bitstreamDao->setAssetstoreId($this->assetstoreid);
// Upload the bitstream
$assetstoreDao = $this->Assetstore->load($this->assetstoreid);
$this->Component->Upload->uploadBitstream($bitstreamDao, $assetstoreDao, true);
$this->ItemRevision->addBitstream($itemRevisionDao, $bitstreamDao);
}
}
}
unset($it);
return true;
}
/**
* Test getting all scalar results for a given dashboard.
* @SuppressWarnings controlCloseCurly
*/
public function testGetAllScores()
{
// Acquire the dashboard from the database
/** @var Validation_DashboardModel $dashboardModel */
$dashboardModel = MidasLoader::loadModel('Dashboard', 'validation');
/** @var ItemModel $itemModel */
$itemModel = MidasLoader::loadModel('Item');
/** @var FolderModel $folderModel */
$folderModel = MidasLoader::loadModel('Folder');
$dashboardDao = $dashboardModel->load(1);
$folderDao = $folderModel->load(1000);
// Create additional result item
$resultItem = null;
$createdItems = array();
$expected = array();
for ($i = 0; $i < 2; ++$i) {
$resultItem = new ItemDao();
$resultItem->setName('img0' . $i . '.mha');
$resultItem->setDescription('result img ' . $i);
$resultItem->setType(0);
$itemModel->save($resultItem);
$createdItems[$resultItem->getKey()] = $i * 5 + 10;
$folderModel->addItem($folderDao, $resultItem);
}
$expected[$folderDao->getKey()] = $createdItems;
$dashboardModel->addResult($dashboardDao, $folderDao);
$dashboardModel->setScores($dashboardDao, $folderDao, $createdItems);
// Add a result folder
$this->params['token'] = $this->_loginUsingApiKey();
$this->params['method'] = 'midas.validation.addresultfolder';
$this->params['dashboard_id'] = 1;
$this->params['folder_id'] = 1001;
$this->request->setMethod('POST');
$resp = $this->_callJsonApi();
$this->_assertStatusOk($resp);
$this->assertEquals(1, $resp->data->dashboard_id);
$this->resetAll();
// Add a scalar result
$this->params['token'] = $this->_loginUsingApiKeyAsAdmin();
$this->params['method'] = 'midas.validation.setscalarresult';
$this->params['dashboard_id'] = 1;
$this->params['folder_id'] = 1001;
$this->params['item_id'] = 1000;
$this->params['value'] = 3;
$this->request->setMethod('POST');
$resp = $this->_callJsonApi();
$this->_assertStatusOk($resp);
$this->resetAll();
// Add a scalar result
$this->params['token'] = $this->_loginUsingApiKeyAsAdmin();
$this->params['method'] = 'midas.validation.setscalarresult';
$this->params['dashboard_id'] = 1;
$this->params['folder_id'] = 1001;
$this->params['item_id'] = 1001;
$this->params['value'] = 7;
$this->request->setMethod('POST');
$resp = $this->_callJsonApi();
$this->_assertStatusOk($resp);
$this->resetAll();
$this->params['method'] = 'midas.validation.getallscores';
$this->params['dashboard_id'] = 1;
$this->params['folder_id'] = 1001;
$this->request->setMethod('POST');
$resp = $this->_callJsonApi();
$this->_assertStatusOk($resp);
$expected[1001] = array();
$expected[1001][1000] = 3;
$expected[1001][1001] = 7;
$this->assertEquals(1, $resp->data->dashboard_id);
// Crazy looping because the json is parsed in as an object rather than
// an array (not really a bad thing, just something to work around)
$scores = $resp->data->scores;
foreach ($expected as $folderId => $items) {
foreach ($items as $itemId => $val) {
$this->assertEquals($val, $scores->{$folderId}->{$itemId});
}
}
}
/**
* Save upload item in the database.
*
* @param UserDao $userDao
* @param string $name
* @param string $url
* @param null|int $parent
* @param int $sizebytes
* @param string $checksum
* @return ItemDao
* @throws Zend_Exception
*/
public function createLinkItem($userDao, $name, $url, $parent = null, $sizebytes = 0, $checksum = ' ')
{
/** @var ItemModel $itemModel */
$itemModel = MidasLoader::loadModel('Item');
/** @var FolderModel $folderModel */
$folderModel = MidasLoader::loadModel('Folder');
/** @var AssetstoreModel $assetstoreModel */
$assetstoreModel = MidasLoader::loadModel('Assetstore');
/** @var ItemRevisionModel $itemRevisionModel */
$itemRevisionModel = MidasLoader::loadModel('ItemRevision');
if ($userDao == null) {
throw new Zend_Exception('Please log in');
}
if (is_numeric($parent)) {
$parent = $folderModel->load($parent);
}
if ($parent == false || !$folderModel->policyCheck($parent, $userDao, MIDAS_POLICY_WRITE)) {
throw new Zend_Exception('Parent permissions errors');
}
Zend_Loader::loadClass('ItemDao', BASE_PATH . '/core/models/dao');
$item = new ItemDao();
$item->setName($name);
$item->setDescription('');
$item->setSizebytes($sizebytes);
$item->setType(0);
$item->setPrivacyStatus(MIDAS_PRIVACY_PRIVATE);
// Must set this flag private initially
$itemModel->save($item, false);
$folderModel->addItem($parent, $item);
$itemModel->copyParentPolicies($item, $parent);
Zend_Loader::loadClass('ItemRevisionDao', BASE_PATH . '/core/models/dao');
$itemRevisionDao = new ItemRevisionDao();
$itemRevisionDao->setChanges('Initial revision');
$itemRevisionDao->setUser_id($userDao->getKey());
$itemRevisionDao->setDate(date('Y-m-d H:i:s'));
$itemRevisionDao->setLicenseId(null);
$itemModel->addRevision($item, $itemRevisionDao);
// Add bitstreams to the revision
Zend_Loader::loadClass('BitstreamDao', BASE_PATH . '/core/models/dao');
$bitstreamDao = new BitstreamDao();
$bitstreamDao->setName($url);
$bitstreamDao->setPath($url);
$bitstreamDao->setMimetype('url');
$bitstreamDao->setSizebytes($sizebytes);
$bitstreamDao->setChecksum($checksum);
$assetstoreDao = $assetstoreModel->getDefault();
$bitstreamDao->setAssetstoreId($assetstoreDao->getKey());
$itemRevisionModel->addBitstream($itemRevisionDao, $bitstreamDao);
$this->getLogger()->debug('Link item created (' . $item->getName() . ', id=' . $item->getKey() . ')');
return $item;
}
/**
* Test that calling removeItem from a folder deletes a non-shared item.
*/
public function testRemoveItemDeletesNonSharedItem()
{
$folder = $this->Folder->createFolder('TestFolder1', 'Description', 0);
$this->assertTrue($folder->saved);
$item = new ItemDao();
$item->setName('subItem');
$item->setDescription('test item to be deleted');
$item->setType(0);
$this->Item->save($item);
$this->assertTrue($item->saved);
$this->Folder->addItem($folder, $item);
$items = $folder->getItems();
$this->assertEquals(1, count($items));
$this->assertEquals($items[0]->getName(), 'subItem');
$itemid = $items[0]->getKey();
// Make sure item is deleted when it is removed from its only parent
$this->Folder->removeItem($folder, $item);
$item = $this->Item->load($itemid);
$this->assertEquals(false, $item, 'Item should have been deleted');
}
/**
* Function to create the items.
*
* @param int $collectionId
* @param int $parentFolderid
*/
private function _createFolderForItem($collectionId, $parentFolderid)
{
/** @var FolderModel $Folder */
$Folder = MidasLoader::loadModel('Folder');
/** @var ItemModel $Item */
$Item = MidasLoader::loadModel('Item');
/** @var ItemRevisionModel $ItemRevision */
$ItemRevision = MidasLoader::loadModel('ItemRevision');
/** @var GroupModel $Group */
$Group = MidasLoader::loadModel('Group');
/** @var AssetstoreModel $Assetstore */
$Assetstore = MidasLoader::loadModel('Assetstore');
/** @var FolderpolicygroupModel $Folderpolicygroup */
$Folderpolicygroup = MidasLoader::loadModel('Folderpolicygroup');
/** @var FolderpolicyuserModel $Folderpolicyuser */
$Folderpolicyuser = MidasLoader::loadModel('Folderpolicyuser');
/** @var ItempolicygroupModel $Itempolicygroup */
$Itempolicygroup = MidasLoader::loadModel('Itempolicygroup');
/** @var ItempolicyuserModel $Itempolicyuser */
$Itempolicyuser = MidasLoader::loadModel('Itempolicyuser');
/** @var UserModel $User */
$User = MidasLoader::loadModel('User');
$colquery = pg_query('SELECT i.item_id, mtitle.text_value AS title, mabstract.text_value AS abstract ' . 'FROM item AS i ' . 'LEFT JOIN metadatavalue AS mtitle ON (i.item_id = mtitle.item_id AND mtitle.metadata_field_id = 64) ' . 'LEFT JOIN metadatavalue AS mabstract ON (i.item_id = mabstract.item_id AND mabstract.metadata_field_id = 27) ' . 'WHERE i.owning_collection=' . $collectionId);
while ($colquery_array = pg_fetch_array($colquery)) {
$item_id = $colquery_array['item_id'];
$title = $colquery_array['title'];
// If title is empty we skip this item
if (empty($title)) {
continue;
}
$abstract = $colquery_array['abstract'];
$folderDao = false;
try {
// Create the folder for the item
$folderDao = $Folder->createFolder($title, $abstract, $parentFolderid);
// Assign the policies to the folder as the same as the parent folder
$folder = $Folder->load($parentFolderid);
$policyGroup = $folder->getFolderpolicygroup();
$policyUser = $folder->getFolderpolicyuser();
foreach ($policyGroup as $policy) {
$group = $policy->getGroup();
$policyValue = $policy->getPolicy();
$Folderpolicygroup->createPolicy($group, $folderDao, $policyValue);
}
foreach ($policyUser as $policy) {
$user = $policy->getUser();
$policyValue = $policy->getPolicy();
$Folderpolicyuser->createPolicy($user, $folderDao, $policyValue);
}
// Add specific policies for users (not dealing with groups)
$policyquery = pg_query('SELECT max(action_id) AS actionid, eperson.eperson_id, eperson.email
FROM resourcepolicy
LEFT JOIN eperson ON (eperson.eperson_id=resourcepolicy.eperson_id)
WHERE epersongroup_id IS NULL AND resource_type_id=' . MIDAS2_RESOURCE_ITEM . ' AND resource_id=' . $item_id . ' GROUP BY eperson.eperson_id, email');
while ($policyquery_array = pg_fetch_array($policyquery)) {
$actionid = $policyquery_array['actionid'];
$email = $policyquery_array['email'];
if ($actionid > 1) {
$policyValue = MIDAS_POLICY_ADMIN;
} elseif ($actionid == 1) {
$policyValue = MIDAS_POLICY_WRITE;
} else {
$policyValue = MIDAS_POLICY_READ;
}
$userDao = $User->getByEmail($email);
$Folderpolicyuser->createPolicy($userDao, $folderDao, $policyValue);
}
} catch (Zend_Exception $e) {
$this->getLogger()->info($e->getMessage());
Zend_Debug::dump($e);
// we continue
}
if ($folderDao) {
// Create the item from the bitstreams
$bitquery = pg_query('SELECT b.bitstream_id, b.name, b.description, b.internal_id FROM bitstream AS b, item2bitstream AS i2b ' . 'WHERE i2b.bitstream_id = b.bitstream_id AND i2b.item_id=' . $item_id);
while ($bitquery_array = pg_fetch_array($bitquery)) {
$filename = $bitquery_array['name'];
$itemdao = new ItemDao();
$itemdao->setName($filename);
// Get the number of downloads and set it
$itemstatsquery = pg_query('SELECT downloads from midas_resourcelog WHERE
resource_id_type=' . MIDAS2_RESOURCE_ITEM . ' AND resource_id=' . $item_id);
$itemstats_array = pg_fetch_array($itemstatsquery);
if ($itemstats_array) {
$itemdao->setView($itemstats_array['downloads']);
$itemdao->setDownload($itemstats_array['downloads']);
}
$Item->save($itemdao);
// Just check if the group anonymous can access the item
$policyquery = pg_query('SELECT policy_id FROM resourcepolicy WHERE resource_type_id=' . MIDAS2_RESOURCE_ITEM . ' AND resource_id=' . $item_id . ' AND epersongroup_id=0');
if (pg_num_rows($policyquery) > 0) {
$anonymousGroup = $Group->load(MIDAS_GROUP_ANONYMOUS_KEY);
$Itempolicygroup->createPolicy($anonymousGroup, $itemdao, MIDAS_POLICY_READ);
}
// Add specific policies for users
$policyquery = pg_query('SELECT max(action_id) AS actionid, eperson.eperson_id, eperson.email
FROM resourcepolicy
LEFT JOIN eperson ON (eperson.eperson_id=resourcepolicy.eperson_id)
WHERE epersongroup_id IS NULL AND resource_type_id=' . MIDAS2_RESOURCE_ITEM . ' AND resource_id=' . $item_id . ' GROUP BY eperson.eperson_id, email');
while ($policyquery_array = pg_fetch_array($policyquery)) {
$actionid = $policyquery_array['actionid'];
$email = $policyquery_array['email'];
if ($actionid > 1) {
$policyValue = MIDAS_POLICY_ADMIN;
} elseif ($actionid == 1) {
$policyValue = MIDAS_POLICY_WRITE;
} else {
$policyValue = MIDAS_POLICY_READ;
}
$userDao = $User->getByEmail($email);
// Set the policy of the item
$Itempolicyuser->createPolicy($userDao, $itemdao, $policyValue);
}
// Add the item to the current directory
$Folder->addItem($folderDao, $itemdao);
// Create a revision for the item
$itemRevisionDao = new ItemRevisionDao();
$itemRevisionDao->setChanges('Initial revision');
$itemRevisionDao->setUser_id($this->userId);
$Item->addRevision($itemdao, $itemRevisionDao);
// Add the metadata
/** @var MetadataModel $MetadataModel */
$MetadataModel = MidasLoader::loadModel('Metadata');
//
$metadataquery = pg_query('SELECT metadata_field_id, text_value FROM metadatavalue WHERE item_id=' . $item_id);
while ($metadata_array = pg_fetch_array($metadataquery)) {
$text_value = $metadata_array['text_value'];
$metadata_field_id = $metadata_array['metadata_field_id'];
// Do not check 64 and 27 because they are stored as field and not metadata
// in MIDAS3
switch ($metadata_field_id) {
case 3:
$element = 'contributor';
$qualifier = 'author';
break;
case 11:
$element = 'date';
$qualifier = 'uploaded';
break;
case 14:
$element = 'date';
$qualifier = 'created';
break;
case 15:
$element = 'date';
$qualifier = 'issued';
break;
case 18:
$element = 'identifier';
$qualifier = 'citation';
break;
case 25:
$element = 'identifier';
$qualifier = 'uri';
break;
case 26:
$element = 'description';
$qualifier = 'general';
break;
case 28:
$element = 'description';
$qualifier = 'provenance';
break;
case 29:
$element = 'description';
$qualifier = 'sponsorship';
break;
case 39:
$element = 'description';
$qualifier = 'publisher';
break;
case 57:
$element = 'subject';
$qualifier = 'keyword';
break;
case 68:
$element = 'subject';
$qualifier = 'ocis';
break;
case 75:
$element = 'identifier';
$qualifier = 'pubmed';
break;
case 74:
$element = 'identifier';
$qualifier = 'doi';
break;
default:
$element = '';
$qualifier = '';
}
if ($element != '') {
$MetadataModel->addMetadataValue($itemRevisionDao, MIDAS_METADATA_TEXT, $element, $qualifier, $text_value);
}
}
// Add bitstreams to the revision
$bitstreamDao = new BitstreamDao();
$bitstreamDao->setName($filename);
// Compute the path from the internalid
// We are assuming only one assetstore
$internal_id = $bitquery_array['internal_id'];
$filepath = $this->midas2Assetstore . '/';
$filepath .= substr($internal_id, 0, 2) . '/';
$filepath .= substr($internal_id, 2, 2) . '/';
$filepath .= substr($internal_id, 4, 2) . '/';
$filepath .= $internal_id;
// Check that the file exists
if (file_exists($filepath)) {
// Upload the bitstream
$assetstoreDao = $Assetstore->load($this->assetstoreId);
$bitstreamDao->setPath($filepath);
$bitstreamDao->fillPropertiesFromPath();
$bitstreamDao->setAssetstoreId($this->assetstoreId);
$UploadComponent = new UploadComponent();
$UploadComponent->uploadBitstream($bitstreamDao, $assetstoreDao);
// Upload the bitstream if necessary (based on the assetstore type)
$ItemRevision->addBitstream($itemRevisionDao, $bitstreamDao);
unset($UploadComponent);
}
}
} else {
echo 'Cannot create Folder for item: ' . $title . '<br>';
}
}
}
/**
* test addResult function.
*/
public function testSetScore()
{
// Create training, testing, and truth folders
$testingFolder = new FolderDao();
$testingFolder->setName('testing');
$testingFolder->setDescription('testing');
$testingFolder->setParentId(-1);
$this->Folder->save($testingFolder);
$trainingFolder = new FolderDao();
$trainingFolder->setName('training');
$trainingFolder->setDescription('training');
$trainingFolder->setParentId(-1);
$this->Folder->save($trainingFolder);
$truthFolder = new FolderDao();
$truthFolder->setName('truth');
$truthFolder->setDescription('truth');
$truthFolder->setParentId(-1);
$this->Folder->save($truthFolder);
// Create result folder
$resultFolder = new FolderDao();
$resultFolder->setName('result');
$resultFolder->setDescription('result');
$resultFolder->setParentId(-1);
$this->Folder->save($resultFolder);
// Add items to the folders
$trainingItem = null;
$testingItem = null;
$truthItem = null;
$resultItem = null;
for ($i = 0; $i < 3; ++$i) {
$trainingItem = new ItemDao();
$testingItem = new ItemDao();
$truthItem = new ItemDao();
$resultItem = new ItemDao();
$trainingItem->setName('img0' . $i . '.mha');
$testingItem->setName('img0' . $i . '.mha');
$truthItem->setName('img0' . $i . '.mha');
$resultItem->setName('img0' . $i . '.mha');
$trainingItem->setDescription('training img ' . $i);
$testingItem->setDescription('testing img ' . $i);
$truthItem->setDescription('truth img ' . $i);
$resultItem->setDescription('result img ' . $i);
$trainingItem->setType(0);
$testingItem->setType(0);
$truthItem->setType(0);
$resultItem->setType(0);
$this->Item->save($trainingItem);
$this->Item->save($testingItem);
$this->Item->save($truthItem);
$this->Item->save($resultItem);
$this->Folder->addItem($trainingFolder, $trainingItem);
$this->Folder->addItem($testingFolder, $testingItem);
$this->Folder->addItem($truthFolder, $truthItem);
$this->Folder->addItem($resultFolder, $resultItem);
}
// Acquire the dashboard from the database
/** @var Validation_DashboardModel $dashboardModel */
$dashboardModel = MidasLoader::loadModel('Dashboard', 'validation');
$daos = $dashboardModel->getAll();
$dao = $daos[0];
// Add testing, training, and truth to the dashboard
$dashboardModel->setTraining($dao, $trainingFolder);
$dashboardModel->setTesting($dao, $testingFolder);
$dashboardModel->setTruth($dao, $truthFolder);
// Reload the dashboard and check it for consistency
$daos = $dashboardModel->getAll();
$dao = $daos[0];
$dashboardModel->addResult($dao, $resultFolder);
// Get the results
$results = $dao->getResults();
$firstResult = $results[2];
$items = $firstResult->getItems();
$values = array();
$count = 0;
foreach ($items as $item) {
$values[$item->getKey()] = $count * 15;
$dashboardModel->setScore($dao, $firstResult, $item, $count * 15);
++$count;
}
$daos = $dashboardModel->getAll();
$dao = $daos[0];
$this->assertEquals(3, count($dao->getScores()));
$scores = $dashboardModel->getScores($dao, $resultFolder);
$this->assertEquals($values, $scores);
}
