/**
* @param Request $request
*
* @return string
* @throws NotFoundException
* @throws \Exception
*/
public function run(Request $request)
{
$repo = new TypeRepository($this->db);
$type = $repo->where('id', '=', $request->get('id'))->findSingle();
if (!$type) {
throw new NotFoundException('type not found');
}
$repo = new PublicationRepository($this->db);
$publications = $repo->where('type_id', '=', $request->get('id'))->order('date_published', 'DESC')->find();
$view = new TypeView($type, $publications);
return $view->display();
}
/**
* @param Request $request
*
* @return string
* @throws NotFoundException
* @throws \Exception
*/
public function run(Request $request)
{
$repo = new StudyFieldRepository($this->db);
$study_field = $repo->where('id', '=', $request->get('id'))->findSingle();
if (!$study_field) {
throw new NotFoundException('study field not found');
}
$repo = new PublicationRepository($this->db);
$publications = $repo->where('study_field_id', '=', $request->get('id'))->order('date_published', 'DESC')->find();
$view = new StudyFieldView($study_field, $publications);
return $view->display();
}
/**
* @param Publication $publication
*
* @return array
*/
private function createFields(Publication $publication)
{
$fields = array();
$fields[] = array('prism.title', $publication->getTitle());
// TODO: valid? Isn't it part of the dc subset of prism?
$fields[] = array('prism.publicationDate', $publication->getDatePublished('Y-m-d'));
$fields[] = array('prism.publicationYear', $publication->getDatePublished('Y'));
$fields[] = array('prism.publicationName', $publication->getJournal());
$fields[] = array('prism.publicationName', $publication->getBooktitle());
$fields[] = array('prism.volume', $publication->getVolume());
$fields[] = array('prism.number', $publication->getNumber());
$fields[] = array('prism.edition', $publication->getEdition());
$fields[] = array('prism.startingPage', $publication->getFirstPage());
$fields[] = array('prism.endingPage', $publication->getLastPage());
$file = $publication->getFullTextFile();
if ($file) {
$fields[] = array('prism.url', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
}
//$fields[] = array('prism.issn', false); // TODO
$fields[] = array('prism.isbn', $publication->getIsbn());
$fields[] = array('prism.copyright', $publication->getCopyright());
$fields[] = array('prism.organization', $publication->getInstitution());
// TODO: check if valid usage
$fields[] = array('prism.doi', $publication->getDoi());
return $fields;
}
/**
* @param Publication $publication
*
* @return array
*/
private function createFields(Publication $publication)
{
// NOTE: dc.citation.* are non standard tags recommended by Google Scholar
$fields = array();
foreach ($publication->getAuthors() as $author) {
if ($author->getLastName() && $author->getFirstName()) {
$fields[] = array('dc.creator', $author->getFirstName() . ' ' . $author->getLastName());
}
}
$fields[] = array('dc.title', $publication->getTitle());
// TODO: not dcterms.issued and YYYY-MM-DD according to https://wiki.whatwg.org/wiki/MetaExtensions?
$fields[] = array('dc.issued', $publication->getDatePublished('Y/m/d'));
$fields[] = array('dc.relation.ispartof', $publication->getJournal());
$fields[] = array('dc.relation.ispartof', $publication->getBooktitle());
$fields[] = array('dc.citation.volume', $publication->getVolume());
$fields[] = array('dc.citation.issue', $publication->getNumber());
$fields[] = array('dc.citation.spage', $publication->getFirstPage());
$fields[] = array('dc.citation.epage', $publication->getLastPage());
$file = $publication->getFullTextFile();
if ($file) {
$fields[] = array('dc.identifier', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
}
$fields[] = array('dc.publisher', $publication->getInstitution());
// used for institution, too
$fields[] = array('dc.publisher', $publication->getPublisher());
$fields[] = array('dc.identifier', $publication->getDoi());
return $fields;
}
/**
* @param Publication $publication
*
* @return array
* @throws Exception
*/
private function createFields(Publication $publication)
{
$fields = array();
$fields[] = array('TY', $this->encodeType($publication->getTypeName()));
foreach ($publication->getAuthors() as $keyword) {
if ($keyword->getLastName() && $keyword->getFirstName()) {
$fields[] = array('AU', $keyword->getLastName() . ', ' . $keyword->getFirstName());
}
}
$fields[] = array('T1', $publication->getTitle());
// TODO: check if valid
$fields[] = array('JA', $publication->getJournal());
// TODO: check if valid
$fields[] = array('TI', $publication->getBooktitle());
// TODO: check if valid
$fields[] = array('VL', $publication->getVolume());
$fields[] = array('IS', $publication->getNumber());
$fields[] = array('SP', $publication->getFirstPage());
$fields[] = array('EP', $publication->getLastPage());
$fields[] = array('PY', $publication->getDatePublished('Y/m/d'));
$fields[] = array('PB', $publication->getPublisher());
$fields[] = array('N1', $publication->getNote());
$file = $publication->getFullTextFile();
if ($file) {
$fields[] = array('L1', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
}
$fields[] = array('UR', $publication->getDoi());
$fields[] = array('SN', $publication->getIsbn());
$fields[] = array('AB', $publication->getAbstract());
foreach ($publication->getKeywords() as $keyword) {
$fields[] = array('KW', $keyword->getName());
}
return $fields;
}
/**
* @param Publication $publication
*
* @return array
*/
private function createFields(Publication $publication)
{
$fields = array();
$fields[] = array('citation_title', $publication->getTitle());
foreach ($publication->getAuthors() as $author) {
if ($author->getLastName() && $author->getFirstName()) {
$fields[] = array('citation_author', $author->getLastName() . ', ' . $author->getFirstName());
}
}
$fields[] = array('citation_publication_date', $publication->getDatePublished('Y/m/d'));
$fields[] = array('citation_journal_title', $publication->getJournal());
$fields[] = array('citation_conference_title', $publication->getBooktitle());
$fields[] = array('citation_volume', $publication->getVolume());
if ($publication->getTypeName() == 'techreport') {
$fields[] = array('citation_technical_report_number', $publication->getNumber());
} else {
$fields[] = array('citation_issue', $publication->getNumber());
}
$fields[] = array('citation_firstpage', $publication->getFirstPage());
$fields[] = array('citation_lastpage', $publication->getLastPage());
$file = $publication->getFullTextFile();
if ($file) {
$fields[] = array('citation_pdf_url', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
}
//$fields[] = array('citation_issn', false); // TODO
$fields[] = array('citation_isbn', $publication->getIsbn());
$fields[] = array('citation_publisher', $publication->getPublisher());
if ($publication->getTypeName() == 'techreport') {
$fields[] = array('citation_technical_report_institution', $publication->getInstitution());
} else {
if (in_array($publication->getTypeName(), array('phdthesis', 'mastersthesis'))) {
$fields[] = array('citation_dissertation_institution', $publication->getInstitution());
}
}
$fields[] = array('citation_doi', $publication->getDoi());
$keywords = '';
foreach ($publication->getKeywords() as $keyword) {
if ($keyword->getName()) {
$keywords .= $keyword->getName() . '; ';
}
}
$keywords = substr($keywords, 0, -2);
$fields[] = array('citation_keywords', $keywords);
return $fields;
}
/**
* @param Publication $publication
*
* @return array
* @throws Exception
*/
private function createFields(Publication $publication)
{
$fields = array();
$fields['type'] = $this->encodeTypes($publication->getTypeName());
$fields['id'] = 'TODO_' . $publication->getId();
// TODO
$fields['title'] = $publication->getTitle();
foreach ($publication->getAuthors() as $author) {
if ($author->getFirstName() && $author->getLastName()) {
$fields['author'][] = array('family' => $author->getLastName(), 'given' => $author->getFirstName());
}
}
$fields['issued'] = array('date-parts' => array($publication->getDatePublished('Y'), $publication->getDatePublished('m'), $publication->getDatePublished('d')));
$fields['container-title'] = $publication->getJournal();
// TODO
$fields['container-title'] = $publication->getBooktitle();
$fields['citation-number'] = $publication->getNumber();
$fields['volume'] = $publication->getVolume();
$fields['number'] = '';
// TODO
$fields['issue'] = '';
// TODO
$fields['page'] = '';
$fields['page-first'] = $publication->getFirstPage();
$fields['edition'] = $publication->getEdition();
$fields['abstract'] = $publication->getAbstract();
$fields['DOI'] = $publication->getDoi();
$fields['ISBN'] = $publication->getIsbn();
$fields['ISSN'] = '';
// TODO
$file = $publication->getFullTextFile();
if ($file) {
$fields['URL'] = Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true);
}
$fields['note'] = $publication->getNote();
$fields['publisher'] = $publication->getPublisher();
return $fields;
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return string
* @throws Exception
* @throws NotFoundException
*/
private function login(Request $request)
{
$errors = array();
if ($request->post('username') && $request->post('password')) {
$username = Validator::sanitizeText($request->post('username'));
$password = Validator::sanitizeText($request->post('password'));
if ($this->auth->login($username, $password)) {
$destination = !empty($_SESSION['referrer']) ? $_SESSION['referrer'] : Request::createUrl(array(), true);
$this->redirect($destination);
} else {
$errors[] = 'Invalid user name or password';
}
}
$view = new View('login', $errors);
return $view->display();
}
/**
* @param Publication $publication
* @param int $max_authors
*
* @return string
*/
public function showCitation(Publication $publication, $max_authors = 6)
{
$citation = '<div class="citation">';
/* shows the title and links to the publication page */
$url = Request::createUrl(array('p' => 'publication', 'id' => $publication->getId()));
$citation .= '<a href="' . $this->html($url) . '" class="title">' . $this->html($publication->getTitle()) . '</a><br/>';
/* creates list of authors */
$authors = $publication->getAuthors();
$num = count($authors);
$authors_string = '';
if ($num > 0) {
$i = 1;
foreach ($authors as $author) {
if ($i == 1) {
/* first author */
$authors_string .= $author->getFirstName(true) . ' ' . $author->getLastName();
} else {
if ($i > $max_authors) {
/* break with "et al." if too many authors */
$authors_string .= ' et al.';
break;
} else {
if ($i == $num) {
/* last author */
$authors_string .= ' and ' . $author->getFirstName(true) . ' ' . $author->getLastName();
} else {
/* all other authors */
$authors_string .= ', ' . $author->getFirstName(true) . ' ' . $author->getLastName();
}
}
}
$i++;
}
}
/* shows list of authors */
$citation .= '<span class="authors">' . $this->html($authors_string) . '</span>';
/* appends publish date behind the authors */
$citation .= ' <span class="year">(' . $this->html($publication->getDatePublished('Y')) . ')</span>';
/* shows journal or booktitle and additional data*/
if ($publication->getJournal()) {
$citation .= '<br/><span class="journal">' . $this->html($publication->getJournal()) . '</span>';
if ($publication->getVolume()) {
$citation .= ', <span class="volume">' . $this->html($publication->getVolume()) . '</span>';
if ($publication->getNumber()) {
$citation .= ' <span class="number">(' . $this->html($publication->getNumber()) . ')</span>';
}
}
if ($publication->getPages('-')) {
$citation .= ', <span class="pages">' . $this->html($publication->getPages('-')) . '</span>';
}
} else {
if ($publication->getBooktitle()) {
$citation .= '<br/>In: <span class="booktitle">' . $this->html($publication->getBooktitle()) . '</span>';
if ($publication->getPages('-')) {
$citation .= ', <span class="pages">' . $this->html($publication->getPages('-')) . '</span>';
}
}
}
$links = array();
/* shows full text link */
$file = $publication->getFullTextFile();
if ($file) {
$title = $file->getExtension() == '.pdf' ? 'PDF' : 'FULLTEXT';
$url = Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()));
$links[] = '<a href="' . $this->html($url) . '" target="_blank">' . $this->html($title) . '</a>';
}
/* shows DOI link */
if ($publication->getDoi()) {
$links[] = '<a href="http://dx.doi.org/' . $this->html($publication->getDoi()) . '" target="_blank">DOI</a>';
}
/* shows URLs */
if ($publication->getUrls()) {
foreach ($publication->getUrls() as $url) {
$links[] = '<a href="' . $this->html($url->getUrl()) . '" target="_blank">' . $this->html($url->getName()) . '</a>';
}
}
/* shows links if there are any */
if (!empty($links)) {
$citation .= '<br/><span class="links">' . implode(' - ', $links) . '</span>';
}
return $citation . '</div>';
}
/**
* @param Publication $publication
*
* @return string
* @throws Exception
*/
public function export(Publication $publication)
{
if (!$publication->getTypeName()) {
throw new Exception('publication type missing');
}
$authors = '';
foreach ($publication->getAuthors() as $author) {
if ($author->getFirstName() && $author->getLastName()) {
$authors .= $author->getFirstName() . ' ' . $author->getLastName() . ' and ';
}
}
$authors = substr($authors, 0, -5);
$keywords = '';
foreach ($publication->getKeywords() as $keyword) {
if ($keyword->getName()) {
$keywords .= $keyword->getName() . ', ';
}
}
$keywords = substr($keywords, 0, -2);
$fields = array();
$fields[] = array('author', $authors);
$fields[] = array('title', $publication->getTitle());
$fields[] = array('journal', $publication->getJournal());
$fields[] = array('volume', $publication->getVolume());
$fields[] = array('number', $publication->getNumber());
$fields[] = array('booktitle', $publication->getBooktitle());
$fields[] = array('series', $publication->getSeries());
$fields[] = array('edition', $publication->getEdition());
$fields[] = array('pages', $publication->getPages('--'));
$fields[] = array('note', $publication->getNote());
$fields[] = array('location', $publication->getLocation());
$fields[] = array('month', $publication->getDatePublished('F'));
$fields[] = array('year', $publication->getDatePublished('Y'));
$file = $publication->getFullTextFile();
$urls = $publication->getUrls();
if ($file) {
$fields[] = array('url', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
} else {
if ($urls && isset($urls[0])) {
$fields[] = array('url', $urls[0]);
}
}
//$fields[] = array('issn', false);
$fields[] = array('publisher', $publication->getPublisher());
$fields[] = array('institution', $publication->getInstitution());
$fields[] = array('school', $publication->getSchool());
$fields[] = array('address', $publication->getAddress());
$fields[] = array('howpublished', $publication->getHowpublished());
$fields[] = array('copyright', $publication->getCopyright());
$fields[] = array('doi', $publication->getDoi());
$fields[] = array('isbn', $publication->getIsbn());
$fields[] = array('abstract', $publication->getAbstract());
$fields[] = array('biburl', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId()), true));
$fields[] = array('keywords', $keywords);
$result = '@' . $publication->getTypeName() . '{' . $this->generateCiteKey($publication);
foreach ($fields as $field) {
if ($field[1]) {
$result .= ',' . "\n\t" . $field[0] . ' = {' . $this->encodeSpecialChars($field[1]) . '}';
}
}
$result .= "\n" . '}';
return $result;
}
/**
* @param Publication $publication
*
* @return array
*/
private function createFields(Publication $publication)
{
$fields = array();
foreach ($publication->getAuthors() as $author) {
if ($author->getFirstName() && $author->getLastName()) {
$fields[] = array('author', $author->getFirstName() . ' ' . $author->getLastName());
}
}
$fields[] = array('title', $publication->getTitle());
$fields[] = array('journal', $publication->getJournal());
$fields[] = array('booktitle', $publication->getBooktitle());
$fields[] = array('volume', $publication->getVolume());
$fields[] = array('number', $publication->getNumber());
$fields[] = array('series', $publication->getSeries());
$fields[] = array('edition', $publication->getEdition());
$fields[] = array('pages', $publication->getPages('--'));
$fields[] = array('month', $publication->getDatePublished('F'));
$fields[] = array('year', $publication->getDatePublished('Y'));
$file = $publication->getFullTextFile();
if ($file) {
$fields[] = array('url', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId(), 'file_id' => $file->getId()), true));
}
//$fields[] = array('issn', false); // TODO
$fields[] = array('isbn', $publication->getIsbn());
$fields[] = array('institution', $publication->getInstitution());
$fields[] = array('school', $publication->getSchool());
$fields[] = array('publisher', $publication->getPublisher());
$fields[] = array('ee', $publication->getDoi());
$fields[] = array('address', $publication->getAddress());
$fields[] = array('howpublished', $publication->getHowpublished());
$fields[] = array('note', $publication->getNote());
$fields[] = array('abstract', $publication->getAbstract());
$fields[] = array('biburl', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId()), true));
return $fields;
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return bool|int
* @throws PermissionRequiredException
* @throws exceptions\LoginRequiredException
*/
private function edit(Request $request)
{
if (!$this->auth->checkPermission(Auth::EDIT_KEYWORD)) {
throw new PermissionRequiredException(Auth::EDIT_KEYWORD);
}
$id = Validator::sanitizeNumber($request->get('id'));
if (!$id) {
throw new UnexpectedValueException();
}
$validator = $this->model->getValidator();
if ($validator->validate($request->post())) {
$input = $validator->getSanitizedResult();
$this->model->update($id, $input);
return true;
} else {
$this->errors = array_merge($this->errors, $validator->getErrors());
return false;
}
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return bool|int
*/
private function changePassword(Request $request)
{
$password = Validator::sanitizeText($request->post('password'));
if (!$password || !$this->auth->validateLogin($this->user->getName(), $password)) {
$this->errors[] = 'Invalid current password';
return false;
}
$password_new = Validator::sanitizeText($request->post('password_new'));
$password_confirm = Validator::sanitizeText($request->post('password_confirm'));
if (!$password_new || !$password_confirm) {
$this->errors[] = 'New password required but invalid';
return false;
}
if ($password_new !== $password_confirm) {
$this->errors[] = 'Entered passwords are not the same';
return false;
}
return $this->auth->setPassword($this->user->getName(), $password_new);
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return bool
* @throws \Exception
*/
private function submit(Request $request)
{
$input = $this->model->formatPost($request->post());
$_SESSION['input'] = $input;
try {
$result = $this->store_publication($input);
} catch (DBDuplicateEntryException $e) {
//$this->db->cancelTransaction();
// TODO make single error messages for each case
$this->errors[] = 'A publication with this name already exists or you tried to add the same author or keyword to this publication twice';
return false;
}
if (empty($this->errors) && $result) {
if ($this->next()) {
return true;
}
$this->clearForm();
$this->redirect(Request::createUrl(array('p' => 'browse', 'by' => 'recent')));
return true;
} else {
return false;
}
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return bool
*/
private function deleteUser(Request $request)
{
$user_id = Validator::sanitizeNumber($request->post('user_id'));
if (!$user_id) {
throw new UnexpectedValueException();
}
$model = new UserModel($this->db);
return $model->delete($user_id);
}
/**
* @return string|null
*/
public function getPublinUrl()
{
return Request::createUrl(array('p' => 'publication', 'id' => $this->id));
}
/**
* @return string
*/
public function showEditFiles()
{
$files = $this->publication->getFiles();
$string = '';
foreach ($files as $file) {
$url = Request::createUrl(array('p' => 'publication', 'id' => $this->publication->getId(), 'file_id' => $file->getId()));
$full_text = $file->isFullText() ? ' (full text)' : '';
$hidden = $file->isHidden() ? ' (hidden)' : '';
$restricted = $file->isRestricted() ? ' (restricted)' : '';
$string .= '<li>
<form action="#" method="post" accept-charset="utf-8">
<a href="' . $this->html($url) . '" target="_blank">' . $this->html($file->getTitle() . $file->getExtension()) . '</a>' . $this->html($full_text . $hidden . $restricted) . '
<input type="hidden" name="file_id" value="' . $this->html($file->getId()) . '"/>
<input type="hidden" name="action" value="removeFile"/>
<input type="submit" value="x" onclick="return confirm(\'Do you really want to delete the file ' . $this->html($file->getTitle() . $file->getExtension()) . '?\')"/>
</form>
</li>';
}
$string .= '<li><form action="#" method="post" enctype="multipart/form-data">
<label for="file">File:</label>
<input type="file" name="file" id="file"><br/>
<label for="title">Description:</label>
<input type="text" name="title" id="title"><br/>
<input type="checkbox" name="full_text" id="full_text" value="yes">
<label for="full_text">Full Text</label>
<input type="checkbox" name="restricted" id="restricted" value="yes"/>
<label for="restricted">Access Restricted</label>
<input type="checkbox" name="hidden" id="hidden" value="yes"/>
<label for="hidden">Hidden</label><br/>
<input type="hidden" name="action" value="addFile"/>
<input type="submit" value="Upload File"/>
</form></li>';
return $string;
}
/** @noinspection PhpUnusedPrivateMethodInspection
* @param Request $request
*
* @return bool|mixed
* @throws PermissionRequiredException
* @throws exceptions\LoginRequiredException
*/
private function addUrl(Request $request)
{
if (!$this->auth->checkPermission(Auth::EDIT_PUBLICATION)) {
throw new PermissionRequiredException(Auth::EDIT_PUBLICATION);
}
$id = Validator::sanitizeNumber($request->get('id'));
if (!$id) {
throw new UnexpectedValueException();
}
$url_model = new UrlModel($this->db);
$validator = $url_model->getValidator();
if ($validator->validate($request->post())) {
$data = $validator->getSanitizedResult();
$url = new Url($data);
try {
return $url_model->store($url, $id);
} catch (DBDuplicateEntryException $e) {
$this->errors[] = 'This url is already assigned to this publication';
return false;
}
} else {
$this->errors = array_merge($this->errors, $validator->getErrors());
return false;
}
}
/**
* @param Request $request
*
* @return bool
*/
public function searchAuthors(Request $request)
{
$field = Validator::sanitizeText($request->get('field'));
$search = Validator::sanitizeText($request->get('search'));
if (!$search) {
$this->errors[] = 'Your search input is invalid';
return false;
}
$search_words = explode(' ', $search);
$repo = new AuthorRepository($this->db);
switch (true) {
case $field === 'given':
foreach ($search_words as $word) {
$repo->where('given', 'LIKE', '%' . $word . '%');
}
break;
case $field === 'family':
foreach ($search_words as $word) {
$repo->where('family', 'LIKE', '%' . $word . '%');
}
break;
case $field === 'about':
foreach ($search_words as $word) {
$repo->where('about', 'LIKE', '%' . $word . '%');
}
break;
default:
throw new UnexpectedValueException();
}
$this->result = $repo->order('family', 'ASC')->find();
return true;
}
/**
* @param Publication $publication
* @param $metadataPrefix
*
* @return array
*/
private function createRecordMetadataFields(Publication $publication, $metadataPrefix)
{
if ($metadataPrefix == 'oai_dc') {
$fields = array();
$fields[] = array('dc:title', $publication->getTitle());
foreach ($publication->getAuthors() as $author) {
if ($author->getLastName() && $author->getFirstName()) {
$fields[] = array('dc:creator', $author->getLastName() . ', ' . $author->getFirstName());
}
}
$fields[] = array('dc:description', $publication->getAbstract());
$fields[] = array('dc:date', $publication->getDatePublished('Y'));
$fields[] = array('dc:publisher', $publication->getPublisher());
$fields[] = array('dc:type', 'Text');
$fields[] = array('dc:rights', $publication->getCopyright());
$fields[] = array('dc:identifier', $publication->getDoi());
$fields[] = array('dc:identifier', Request::createUrl(array('p' => 'publication', 'id' => $publication->getId())));
return $fields;
} else {
throw new UnexpectedValueException('Implementation for ' . $metadataPrefix . ' missing!');
}
}