/** 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); }