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<?php
/**
* @file classes/article/SuppFileDAO.inc.php
*
* Copyright (c) 2013-2019 Simon Fraser University
* Copyright (c) 2003-2019 John Willinsky
* Distributed under the GNU GPL v2. For full terms see the file docs/COPYING.
*
* @class SuppFileDAO
* @ingroup article
* @see SuppFile
*
* @brief Operations for retrieving and modifying SuppFile objects.
*/
import('classes.article.SuppFile');
class SuppFileDAO extends DAO {
/**
* Get supp file objects cache.
* @return GenericCache
*/
function &_getSuppFileCache() {
if (!isset($this->suppFileCache)) {
$cacheManager =& CacheManager::getManager();
$this->suppFileCache =& $cacheManager->getObjectCache('suppfile', 0, array(&$this, '_suppFileCacheMiss'));
}
return $this->suppFileCache;
}
/**
* Callback when there is no object in cache.
* @param $cache GenericCache
* @param $id int The wanted object id.
* @return SuppFile
*/
function &_suppFileCacheMiss(&$cache, $id) {
$suppFile =& $this->getSuppFile($id, null, false);
$cache->setCache($id, $suppFile);
return $suppFile;
}
/**
* Flush the supp file galley cache.
*/
function flushCache() {
$cache =& $this->_getSuppFileCache();
$cache->flush();
unset($cache);
}
/**
* Retrieve a supplementary file by ID.
* @param $suppFileId int
* @param $articleId int optional
* @param $useCache boolean optional
* @return SuppFile
*/
function &getSuppFile($suppFileId, $articleId = null, $useCache = false) {
if ($useCache) {
$cache =& $this->_getSuppFileCache();
$returner = $cache->get($suppFileId);
if ($returner && $articleId != null && $articleId != $returner->getArticleId()) $returner = null;
return $returner;
}
$params = array($suppFileId);
if ($articleId) $params[] = $articleId;
$result =& $this->retrieve(
'SELECT s.*, a.file_name, a.original_file_name, a.file_type, a.file_size, a.date_uploaded, a.date_modified FROM article_supplementary_files s LEFT JOIN article_files a ON (s.file_id = a.file_id) WHERE s.supp_id = ?' . ($articleId?' AND s.article_id = ?':''),
$params
);
$returner = null;
if ($result->RecordCount() != 0) {
$returner =& $this->_returnSuppFileFromRow($result->GetRowAssoc(false));
}
$result->Close();
unset($result);
return $returner;
}
/**
* Retrieve a supplementary file by public supp file ID.
* @param $pubIdType string One of the NLM pub-id-type values or
* 'other::something' if not part of the official NLM list
* (see <http://dtd.nlm.nih.gov/publishing/tag-library/n-4zh0.html>).
* @param $pubId string
* @param $articleId int
* @return SuppFile
*/
function &getSuppFileByPubId($pubIdType, $pubId, $articleId = null) {
$suppFiles =& $this->getSuppFilesBySetting('pub-id::'.$pubIdType, $pubId, $articleId);
if (empty($suppFiles)) {
$suppFile = null;
} else {
assert(count($suppFiles) == 1);
$suppFile =& $suppFiles[0];
}
return $suppFile;
}
/**
* Find supp files by querying supp file settings.
* @param $settingName string
* @param $settingValue mixed
* @param $articleId int optional
* @param $journalId int optional
* @return array The supp files identified by setting.
*/
function &getSuppFilesBySetting($settingName, $settingValue, $articleId = null, $journalId = null) {
$params = array($settingName);
$sql = 'SELECT s.*, af.file_name, af.original_file_name, af.file_type, af.file_size, af.date_uploaded, af.date_modified
FROM article_supplementary_files s
LEFT JOIN article_files af ON s.file_id = af.file_id
INNER JOIN articles a ON a.article_id = s.article_id
LEFT JOIN published_articles pa ON s.article_id = pa.article_id ';
if (is_null($settingValue)) {
$sql .= 'LEFT JOIN article_supp_file_settings sfs ON s.supp_id = sfs.supp_id AND sfs.setting_name = ?
WHERE (sfs.setting_value IS NULL OR sfs.setting_value = \'\')';
} else {
$params[] = $settingValue;
$sql .= 'INNER JOIN article_supp_file_settings sfs ON s.supp_id = sfs.supp_id
WHERE sfs.setting_name = ? AND sfs.setting_value = ?';
}
if ($articleId) {
$params[] = (int) $articleId;
$sql .= ' AND s.article_id = ?';
}
if ($journalId) {
$params[] = (int) $journalId;
$sql .= ' AND a.journal_id = ?';
}
$sql .= ' ORDER BY a.journal_id, pa.issue_id, s.supp_id';
$result =& $this->retrieve($sql, $params);
$suppFiles = array();
while (!$result->EOF) {
$suppFiles[] =& $this->_returnSuppFileFromRow($result->GetRowAssoc(false));
$result->moveNext();
}
$result->Close();
return $suppFiles;
}
/**
* Retrieve all supplementary files for an article.
* @param $articleId int
* @return array SuppFiles
*/
function &getSuppFilesByArticle($articleId) {
$suppFiles = array();
$result =& $this->retrieve(
'SELECT s.*, a.file_name, a.original_file_name, a.file_type, a.file_size, a.date_uploaded, a.date_modified FROM article_supplementary_files s LEFT JOIN article_files a ON (s.file_id = a.file_id) WHERE s.article_id = ? ORDER BY s.seq',
(int) $articleId
);
while (!$result->EOF) {
$suppFiles[] =& $this->_returnSuppFileFromRow($result->GetRowAssoc(false));
$result->moveNext();
}
$result->Close();
unset($result);
return $suppFiles;
}
/**
* Retrieve all supplementary files of a journal.
* @param $journalId int
* @return DAOResultFactory
*/
function &getSuppFilesByJournalId($journalId) {
$result =& $this->retrieve(
'SELECT
s.*,
af.file_name, af.original_file_name, af.file_stage, af.file_type, af.file_size, af.date_uploaded, af.date_modified
FROM article_supplementary_files s
LEFT JOIN article_files af ON (s.file_id = af.file_id)
INNER JOIN articles a ON (s.article_id = a.article_id)
WHERE a.journal_id = ?',
(int) $journalId
);
$returner = new DAOResultFactory($result, $this, '_returnSuppFileFromRow');
return $returner;
}
/**
* Get the list of fields for which data is localized.
* @return array
*/
function getLocaleFieldNames() {
return array('title', 'creator', 'subject', 'typeOther', 'description', 'publisher', 'sponsor', 'source');
}
/**
* Get a list of additional fields that do not have
* dedicated accessors.
* @return array
*/
function getAdditionalFieldNames() {
$additionalFields = parent::getAdditionalFieldNames();
// FIXME: Move this to a PID plug-in.
$additionalFields[] = 'pub-id::publisher-id';
return $additionalFields;
}
/**
* Update the localized fields for this supp file.
* @param $suppFile
*/
function updateLocaleFields(&$suppFile) {
$this->updateDataObjectSettings('article_supp_file_settings', $suppFile, array(
'supp_id' => $suppFile->getId()
));
}
/**
* Internal function to return a SuppFile object from a row.
* @param $row array
* @return SuppFile
*/
function &_returnSuppFileFromRow(&$row) {
$suppFile = new SuppFile();
$suppFile->setId($row['supp_id']);
$suppFile->setRemoteURL($row['remote_url']);
$suppFile->setFileId($row['file_id']);
$suppFile->setArticleId($row['article_id']);
$suppFile->setType($row['type']);
$suppFile->setDateCreated($this->dateFromDB($row['date_created']));
$suppFile->setLanguage($row['language']);
$suppFile->setShowReviewers($row['show_reviewers']);
$suppFile->setDateSubmitted($this->datetimeFromDB($row['date_submitted']));
$suppFile->setSequence($row['seq']);
//ArticleFile set methods
$suppFile->setFileName($row['file_name']);
$suppFile->setOriginalFileName($row['original_file_name']);
$suppFile->setFileType($row['file_type']);
$suppFile->setFileSize($row['file_size']);
$suppFile->setDateModified($this->datetimeFromDB($row['date_modified']));
$suppFile->setDateUploaded($this->datetimeFromDB($row['date_uploaded']));
$this->getDataObjectSettings('article_supp_file_settings', 'supp_id', $row['supp_id'], $suppFile);
HookRegistry::call('SuppFileDAO::_returnSuppFileFromRow', array(&$suppFile, &$row));
return $suppFile;
}
/**
* Insert a new SuppFile.
* @param $suppFile SuppFile
*/
function insertSuppFile(&$suppFile) {
if ($suppFile->getDateSubmitted() == null) {
$suppFile->setDateSubmitted(Core::getCurrentDate());
}
if ($suppFile->getSequence() == null) {
$suppFile->setSequence($this->getNextSuppFileSequence($suppFile->getArticleId()));
}
$this->update(
sprintf('INSERT INTO article_supplementary_files
(remote_url, file_id, article_id, type, date_created, language, show_reviewers, date_submitted, seq)
VALUES
(?, ?, ?, ?, %s, ?, ?, %s, ?)',
$this->dateToDB($suppFile->getDateCreated()), $this->datetimeToDB($suppFile->getDateSubmitted())),
array(
$suppFile->getRemoteURL(),
$suppFile->getFileId(),
$suppFile->getArticleId(),
$suppFile->getType(),
$suppFile->getLanguage(),
$suppFile->getShowReviewers(),
$suppFile->getSequence()
)
);
$suppFile->setId($this->getInsertSuppFileId());
$this->updateLocaleFields($suppFile);
return $suppFile->getId();
}
/**
* Update an existing SuppFile.
* @param $suppFile SuppFile
*/
function updateSuppFile(&$suppFile) {
$returner = $this->update(
sprintf('UPDATE article_supplementary_files
SET
remote_url = ?,
file_id = ?,
type = ?,
date_created = %s,
language = ?,
show_reviewers = ?,
seq = ?
WHERE supp_id = ?',
$this->dateToDB($suppFile->getDateCreated())),
array(
$suppFile->getRemoteURL(),
$suppFile->getFileId(),
$suppFile->getType(),
$suppFile->getLanguage(),
$suppFile->getShowReviewers(),
$suppFile->getSequence(),
$suppFile->getId()
)
);
$this->updateLocaleFields($suppFile);
return $returner;
}
/**
* Delete a SuppFile.
* @param $suppFile SuppFile
*/
function deleteSuppFile(&$suppFile) {
return $this->deleteSuppFileById($suppFile->getId());
}
/**
* Delete a supplementary file by ID.
* @param $suppFileId int
* @param $articleId int optional
*/
function deleteSuppFileById($suppFileId, $articleId = null) {
if (isset($articleId)) {
$returner = $this->update('DELETE FROM article_supplementary_files WHERE supp_id = ? AND article_id = ?', array($suppFileId, $articleId));
if ($returner) $this->update('DELETE FROM article_supp_file_settings WHERE supp_id = ?', $suppFileId);
return $returner;
} else {
$this->update('DELETE FROM article_supp_file_settings WHERE supp_id = ?', $suppFileId);
return $this->update(
'DELETE FROM article_supplementary_files WHERE supp_id = ?', $suppFileId
);
}
}
/**
* Delete supplementary files by article.
* @param $articleId int
*/
function deleteSuppFilesByArticle($articleId) {
$suppFiles =& $this->getSuppFilesByArticle($articleId);
foreach ($suppFiles as $suppFile) {
$this->deleteSuppFile($suppFile);
}
}
/**
* Check if a supplementary file exists with the associated file ID.
* @param $articleId int
* @param $fileId int
* @return boolean
*/
function suppFileExistsByFileId($articleId, $fileId) {
$result =& $this->retrieve(
'SELECT COUNT(*) FROM article_supplementary_files
WHERE article_id = ? AND file_id = ?',
array($articleId, $fileId)
);
$returner = isset($result->fields[0]) && $result->fields[0] == 1 ? true : false;
$result->Close();
unset($result);
return $returner;
}
/**
* Sequentially renumber supplementary files for an article in their sequence order.
* @param $articleId int
*/
function resequenceSuppFiles($articleId) {
$result =& $this->retrieve(
'SELECT supp_id FROM article_supplementary_files WHERE article_id = ? ORDER BY seq',
$articleId
);
for ($i=1; !$result->EOF; $i++) {
list($suppId) = $result->fields;
$this->update(
'UPDATE article_supplementary_files SET seq = ? WHERE supp_id = ?',
array($i, $suppId)
);
$result->moveNext();
}
$result->close();
unset($result);
}
/**
* Get the the next sequence number for an article's supplementary files (i.e., current max + 1).
* @param $articleId int
* @return int
*/
function getNextSuppFileSequence($articleId) {
$result =& $this->retrieve(
'SELECT MAX(seq) + 1 FROM article_supplementary_files WHERE article_id = ?',
$articleId
);
$returner = floor($result->fields[0]);
$result->Close();
unset($result);
return $returner;
}
/**
* Get the ID of the last inserted supplementary file.
* @return int
*/
function getInsertSuppFileId() {
return $this->getInsertId('article_supplementary_files', 'supp_id');
}
/**
* Retrieve supp file by public supp file id or, failing that,
* internal supp file ID; public ID takes precedence.
* @param $suppId string
* @param $articleId int
* @return SuppFile object
*/
function &getSuppFileByBestSuppFileId($suppId, $articleId) {
$suppFile =& $this->getSuppFileByPubId('publisher-id', $suppId, $articleId);
if (!isset($suppFile) && ctype_digit("$suppId")) $suppFile =& $this->getSuppFile((int) $suppId, $articleId);
return $suppFile;
}
/**
* Checks if public identifier exists (other than for the specified
* supplementary file ID, which is treated as an exception).
* @param $pubIdType string One of the NLM pub-id-type values or
* 'other::something' if not part of the official NLM list
* (see <http://dtd.nlm.nih.gov/publishing/tag-library/n-4zh0.html>).
* @param $pubId string
* @param $suppId int An ID to be excluded from the search.
* @param $journalId int
* @return boolean
*/
function pubIdExists($pubIdType, $pubId, $suppId, $journalId) {
$result =& $this->retrieve(
'SELECT COUNT(*)
FROM article_supp_file_settings sfs
INNER JOIN article_supplementary_files f ON sfs.supp_id = f.supp_id
INNER JOIN articles a ON f.article_id = a.article_id
WHERE sfs.setting_name = ? AND sfs.setting_value = ? AND f.supp_id <> ? AND a.journal_id = ?',
array(
'pub-id::'.$pubIdType,
$pubId,
(int) $suppId,
(int) $journalId
)
);
$returner = $result->fields[0] ? true : false;
$result->Close();
return $returner;
}
/**
* Change the public ID of a supplementary file.
* @param $suppFileId int
* @param $pubIdType string One of the NLM pub-id-type values or
* 'other::something' if not part of the official NLM list
* (see <http://dtd.nlm.nih.gov/publishing/tag-library/n-4zh0.html>).
* @param $pubId string
*/
function changePubId($suppFileId, $pubIdType, $pubId) {
$idFields = array(
'supp_id', 'locale', 'setting_name'
);
$updateArray = array(
'supp_id' => $suppFileId,
'locale' => '',
'setting_name' => 'pub-id::'.$pubIdType,
'setting_type' => 'string',
'setting_value' => (string)$pubId
);
$this->replace('article_supp_file_settings', $updateArray, $idFields);
}
/**
* Delete the public IDs of all supplementary files in a journal.
* @param $journalId int
* @param $pubIdType string One of the NLM pub-id-type values or
* 'other::something' if not part of the official NLM list
* (see <http://dtd.nlm.nih.gov/publishing/tag-library/n-4zh0.html>).
*/
function deleteAllPubIds($journalId, $pubIdType) {
$journalId = (int) $journalId;
$settingName = 'pub-id::'.$pubIdType;
$suppFiles =& $this->getSuppFilesByJournalId($journalId);
while ($suppFile =& $suppFiles->next()) {
$this->update(
'DELETE FROM article_supp_file_settings WHERE setting_name = ? AND supp_id = ?',
array(
$settingName,
(int)$suppFile->getId()
)
);
unset($suppFile);
}
$this->flushCache();
}
/**
* Delete the public ID of a supp file.
* @param $suppFileId int
* @param $pubIdType string One of the NLM pub-id-type values or
* 'other::something' if not part of the official NLM list
* (see <http://dtd.nlm.nih.gov/publishing/tag-library/n-4zh0.html>).
*/
function deletePubId($suppFileId, $pubIdType) {
$settingName = 'pub-id::'.$pubIdType;
$this->update(
'DELETE FROM article_supp_file_settings WHERE setting_name = ? AND supp_id = ?',
array(
$settingName,
(int)$suppFileId
)
);
$this->flushCache();
}
}
?>