public function __construct()
{
parent::__construct('view_authors', 'Author Information', 'view_author.php');
if ($this->loginError) {
return;
}
$this->loadHttpVars(true, false);
$this->use_mootools = true;
// check if this author id is valid
if (!isset($this->author_id) || !is_numeric($this->author_id)) {
$this->pageError = true;
return;
}
$auth = new pdAuthor();
$auth->dbLoad($this->db, $this->author_id, pdAuthor::DB_LOAD_PUBS_MIN | pdAuthor::DB_LOAD_INTERESTS);
if (isset($_SERVER['HTTP_REFERER']) && strpos($_SERVER['HTTP_REFERER'], 'Admin/add_author.php?author_id=') !== false) {
// the user added or changed an author
echo "Your change has been sumitted.<br/><hr/>\n";
}
echo '<h3>', $auth->name;
if ($this->access_level > 0) {
echo $this->getAuthorIcons($auth, 0x6);
}
echo '</h3>', $this->authorShow($auth);
echo "<hr><a href='list_author.php?tab=" . $auth->name[0] . "'>Author List</a>";
}
public static function &newFromDb(&$db, $author_id, $flags = self::DB_LOAD_ALL)
{
assert('is_numeric($author_id)');
$author = new pdAuthor();
$author->dbLoad($db, $author_id, $flags);
return $author;
}
public function __construct()
{
parent::__construct('delete_author', 'Delete Author', 'Admin/delete_author.php');
if ($this->loginError) {
return;
}
$this->loadHttpVars();
if (!isset($this->author_id) || !is_numeric($this->author_id)) {
$this->pageError = true;
return;
}
$author = new pdAuthor();
$result = $author->dbLoad($this->db, $this->author_id);
if (!$result) {
$this->pageError = true;
return;
}
$pub_list = pdPubList::create($this->db, array('author_id' => $this->author_id));
if (isset($pub_list) && count($pub_list) > 0) {
echo 'Cannot delete Author <b>', $author->name, '</b>.<p/>', 'The author has the following publications in the database:', displayPubList($this->db, $pub_list, true, -1, null, null, '../');
return;
}
$form =& $this->confirmForm('deleter');
$form->addElement('hidden', 'author_id', $this->author_id);
if ($form->validate()) {
$values = $form->exportValues();
// This is where the actual deletion happens.
$name = $author->name;
$author->dbDelete($this->db);
echo 'You have successfully removed the following author from the database:', '<p/><b>', $name, '</b>';
} else {
if (!isset($this->author_id) || !is_numeric($this->author_id)) {
$this->pageError = true;
return;
}
$renderer = new HTML_QuickForm_Renderer_QuickHtml();
$form->accept($renderer);
$table = new HTML_Table(array('width' => '100%', 'border' => '0', 'cellpadding' => '6', 'cellspacing' => '0'));
$table->addRow(array('Name:', $author->name));
if (isset($author->title) && trim($author->title != '')) {
$table->addRow(array('Title:', $author->title));
}
$table->addRow(array('Email:', $author->email));
$table->addRow(array('Organization:', $author->organization));
$cell = '';
if (isset($author->webpage) && trim($author->webpage != '')) {
$cell = '<a href="' . $author->webpage . '">' . $author->webpage . '</a>';
} else {
$cell = "none";
}
$table->addRow(array('Web page:', $cell));
$table->updateColAttributes(0, array('class' => 'emph', 'width' => '25%'));
echo '<h3>Delete Author</h3><p/>Delete the following author?';
$this->form =& $form;
$this->renderer =& $renderer;
$this->table =& $table;
}
}
public function __construct()
{
parent::__construct('aicml_staff');
if ($this->loginError) {
return;
}
echo '<h1>AICML Staff</h1>';
$table = new HTML_Table(array('class' => 'stats'));
$table->addRow(array('Name', 'Start', 'End', 'Num Pubs', 'Pub Ids'));
$table->setRowType(0, 'th');
//pdDb::debugOn();
$staff_list = pdAicmlStaffList::create($this->db);
foreach ($staff_list as $staff_id => $author_id) {
$staff = pdAicmlStaff::newFromDb($this->db, $staff_id, pdAicmlStaff::DB_LOAD_PUBS_MIN);
$author = pdAuthor::newFromDb($this->db, $author_id, pdAuthor::DB_LOAD_MIN);
//debugVar('staff', array($staff, $author));
$pub_links = array();
if (isset($staff->pub_ids)) {
foreach ($staff->pub_ids as $pub_id) {
$pub_links[] = '<a href="../view_publication.php?pub_id=' . $pub_id . '">' . $pub_id . '</a>';
}
}
$table->addRow(array($author->name, $staff->start_date, $staff->end_date, count($staff->pub_ids), implode(', ', $pub_links)), array('class' => 'stats_odd'));
}
echo $table->toHtml();
}
public function __construct()
{
parent::__construct('all_authors');
if ($this->loginError) {
return;
}
$this->loadHttpVars(true, false);
if (!isset($this->tab)) {
$this->tab = 'A';
} else {
$tab = strtoupper($this->tab);
if (strlen($tab) != 1 || ord($tab) < ord('A') || ord($tab) > ord('Z')) {
$this->pageError = true;
return;
}
}
$auth_list = pdAuthorList::create($this->db, null, $this->tab);
echo $this->alphaSelMenu($this->tab, get_class($this) . '.php');
echo "<h2>Authors</h2>";
if (empty($auth_list) || count($auth_list) == 0) {
echo 'No authors with last name starting with ', $this->tab, '<br/>';
return;
}
foreach ($auth_list as $author_id => $name) {
$author = new pdAuthor();
$author->dbLoad($this->db, $author_id, pdAuthor::DB_LOAD_BASIC | pdAuthor::DB_LOAD_PUBS_MIN);
$name = '<span class="emph"><a href="view_author.php?author_id=' . $author_id . '">' . $name . '</a> ';
$icons = $this->getAuthorIcons($author) . '</span>';
$info = array();
if ($author->title != '') {
$info[] = '<span class="small">' . $author->title . '</span>';
}
if ($author->organization != '') {
$info[] = '<span class="small">' . $author->organization . '</span>';
}
$info[] .= '<a href="list_publication.php?author_id=' . $author_id . '&menu=0"><span class="small" style="color:#000;font-weight:normal;">' . 'Publication entries in database: ' . $author->totalPublications . '</span>';
$table = new HTML_Table(array('class' => 'publist'));
$table->addRow(array($name . '<br/>' . implode('<br/>', $info), $icons));
$table->updateColAttributes(1, array('class' => 'icons'), NULL);
echo $table->toHtml();
unset($table);
}
}
public function __construct()
{
parent::__construct('view_publications');
if ($this->loginError) {
return;
}
$this->loadHttpVars();
if (!isset($this->menu)) {
$this->menu = 1;
}
if (isset($this->year)) {
$pub_list = pdPubList::create($this->db, array('year_cat' => $this->year));
$title = '<h1>Publications in ' . $this->year . '</h1>';
} else {
if (isset($this->venue_id)) {
$vl = pdVenueList::create($this->db);
if (!array_key_exists($this->venue_id, $vl)) {
$this->pageError = true;
return;
}
$pub_list = pdPubList::create($this->db, array('venue_id' => $this->venue_id));
$title = '<h1>Publications in Venue "' . $vl[$this->venue_id] . '"</h1>';
} else {
if (isset($this->cat_id)) {
$cl = pdCatList::create($this->db);
if (!array_key_exists($this->cat_id, $cl)) {
$this->pageError = true;
return;
}
$pub_list = pdPubList::create($this->db, array('cat_id' => $this->cat_id));
$title = '<h1>Publications in Category "' . $cl[$this->cat_id] . '"</h1>';
} else {
if (isset($this->keyword)) {
$pub_list = pdPubList::create($this->db, array('keyword' => $this->keyword));
$title = '<h1>Publications with keyword "' . $this->keyword . '"</h1>';
} else {
if (isset($this->author_id)) {
// If there exists an author_id, only extract the publications for
// that author
//
// This is used when viewing an author.
$pub_list = pdPubList::create($this->db, array('author_id_cat' => $this->author_id));
$auth = new pdAuthor();
$auth->dbLoad($this->db, $this->author_id, pdAuthor::DB_LOAD_BASIC);
$title = '<h1>Publications by ' . $auth->name . '</h1>';
} else {
if (isset($this->by) || !isset($_GET) == 0) {
if (count($_GET) == 0) {
$viewCat = 'year';
} else {
$viewCat = $this->by;
}
$this->pubSelect($viewCat);
return;
} else {
$this->pageError = true;
}
}
}
}
}
}
if ($this->menu) {
echo $this->pubSelMenu(), "<br/>\n";
}
echo $title;
echo displayPubList($this->db, $pub_list);
}
public function processForm()
{
$form =& $this->form;
$values =& $form->exportValues();
// check if user pressed "Next Step >>" button and did not enter
// a name
if (isset($values['next_step']) && isset($_SESSION['state']) && $_SESSION['state'] == 'pub_add') {
if ((!isset($values['firstname']) || $values['firstname'] == '') && (!isset($values['lastname']) || $values['lastname'] == '')) {
header('Location: add_pub3.php');
return;
}
}
// if user has not entered a name then bring
if (isset($values['add_another']) && isset($_SESSION['state']) && $_SESSION['state'] == 'pub_add') {
if ((!isset($values['firstname']) || $values['firstname'] == '') && (!isset($values['lastname']) || $values['lastname'] == '')) {
header('Location: add_author.php');
return;
}
}
$author = new pdAuthor();
if ($this->author_id != null) {
$author->author_id = $this->author_id;
}
$author->name = $values['lastname'] . ', ' . $values['firstname'];
$author->firstname = $values['firstname'];
$author->lastname = $values['lastname'];
$author->title = $values['title'];
$author->email = $values['email'];
$author->organization = $values['organization'];
$author->webpage = $values['webpage'];
$author->interests = array();
if (isset($values['interests']) && count($values['interests']) > 0) {
foreach ($values['interests'] as $int_id) {
$author->interests[$int_id] = $this->all_interests[$int_id];
}
}
if (isset($values['newInterests']) && count($values['newInterests']) > 0) {
$author->interests = array_merge($author->interests, $values['newInterests']);
}
// check if an author with a similar name already exists
if ($this->author_id == null) {
$like_authors = pdAuthorList::create($this->db, $values['firstname'], $values['lastname']);
if (count($like_authors) > 0) {
$_SESSION['new_author'] = $author;
header('Location: author_confirm.php');
return;
}
}
$author->dbSave($this->db);
if (isset($_SESSION['state']) && $_SESSION['state'] == 'pub_add') {
assert('isset($_SESSION["pub"])');
$pub =& $_SESSION['pub'];
$pub->addAuthor($this->db, $author->author_id);
if ($this->debug) {
return;
}
if (isset($values['finish'])) {
header('Location: add_pub_submit.php');
} else {
if (isset($values['add_another'])) {
header('Location: add_author.php');
} else {
header('Location: add_pub2.php');
}
}
return;
}
header('Location: ../view_author.php?author_id=' . $author->author_id);
}
#!/usr/bin/env php
<?php
require_once '../includes/defines.php';
require_once 'includes/functions.php';
require_once 'includes/pdDb.php';
require_once 'includes/pdAuthorList.php';
require_once 'includes/pdPubList.php';
$db = new pdDb(array('name' => 'pubDB'));
$authors = pdAuthorList::create($db);
if (count($authors) == 0) {
echo 'No authors in database';
$db->close();
exit;
}
foreach ($authors as $auth_id => $name) {
$author = new pdAuthor();
$author->dbLoad($db, $auth_id);
foreach ($author->pub_list as $pub) {
$pub->dbLoad($db, $pub->pub_id);
$auth_names = array();
foreach ($pub->authors as $other_auths) {
$auth_names[] = $other_auths->name;
}
echo $author->name, "\t", $pub->title, "\t";
echo implode("\t", array_diff($auth_names, array($author->name)));
echo "\n";
}
}
$db->close();
foreach ($all_interests as $k => $i) {
if (is_numeric($i)) {
$numeric_interests[$k] = $i;
}
}
if (count($numeric_interests) == 0) {
exit(0);
}
//pdDb::debugOn();
//debugVar('n', $numeric_interests);
$q = $db->select(array('author', 'author_interest', 'interest'), array('author.author_id', 'interest.interest_id', 'interest.interest'), array('interest.interest_id' => array_keys($numeric_interests), 'interest.interest_id=author_interest.interest_id', 'author.author_id=author_interest.author_id'));
$authors = array();
$author_info_list = array();
foreach ($q as $r) {
if (!isset($authors[$r->author_id])) {
$authors[$r->author_id] = pdAuthor::newFromDb($db, $r->author_id, pdAuthor::DB_LOAD_BASIC | pdAuthor::DB_LOAD_INTERESTS);
}
$author_info_list[] = array('interest_id' => $r->interest_id, 'new_interest' => array($all_interests[$r->interest_id] => $all_interests[$all_interests[$r->interest_id]]), 'author' => &$authors[$r->author_id]);
}
//debugVar('$author_info_list', $author_info_list);
foreach ($author_info_list as $info) {
$info['author']->interests = $info['author']->interests + $info['new_interest'];
unset($info['author']->interests[$info['interest_id']]);
}
//debugVar('$authors', $authors);
foreach ($authors as $author) {
$author->dbSave($db);
}
debugVar('$numeric_interests', $numeric_interests);
foreach ($numeric_interests as $k => $i) {
$q = $db->select('author_interest', '*', array('interest_id' => $k));
public function __construct()
{
parent::__construct('batch_add_authors');
if ($this->loginError) {
return;
}
$this->use_mootools = true;
$form = new HTML_QuickForm('batch_add', 'post', null, '_self', 'multipart/form-data');
$tooltip = <<<TOOLTIP_END
New Authors::A semi-colon separated list of author names. Names can be in the following
formats:
<ul>
<li>fist last</li>
<li>fist initials last</li>
<li>last, first</li>
<li>last, first initials</li>
</ul>
TOOLTIP_END;
$form->addGroup(array(HTML_QuickForm::createElement('textarea', 'new_authors', null, array('cols' => 60, 'rows' => 10)), HTML_QuickForm::createElement('static', 'kwgroup_help', null, '<span class="small">Name format is: GIVEN_NAME1 [GIVEN_NAME2 .. etc.] LAST_NAME. Separate using semi-colons (;)</span>')), 'new_auth_group', "<span class=\"Tips1\" title=\"{$tooltip}\">New Authors:</span>", '<br/>', false);
$form->addGroup(array(HTML_QuickForm::createElement('submit', 'submit', 'Add New Authors'), HTML_QuickForm::createElement('button', 'cancel', 'Cancel', array('onclick' => 'history.back()'))), null, null, ' ', false);
if ($form->validate()) {
$values = $form->exportValues();
$values['new_authors'] = preg_replace("/;\\s*;/", ';', $values['new_authors']);
$new_authors = preg_split('/;\\s*/', $values['new_authors']);
$fl_auth_list = pdAuthorList::create($this->db, null, null, true);
$in_db_auths = array_intersect($fl_auth_list, $new_authors);
$new_auths = array_diff($new_authors, $fl_auth_list);
foreach ($new_auths as $auth_name) {
$auth = new pdAuthor();
$auth->nameSet($auth_name);
$auth->dbSave($this->db);
unset($auth);
}
if (count($in_db_auths) > 0) {
echo 'These authors were already in the database:<ul>';
foreach ($in_db_auths as $auth_name) {
echo '<li>', $auth_name, '</li>';
}
}
if (count($new_auths) > 0) {
if (count($in_db_auths) > 0) {
echo '</ul>', 'Only these authors were added to the database:', '<ul>';
} else {
echo 'These authors were added to the database:<ul>';
}
foreach ($new_auths as $auth_name) {
echo '<li>', $auth_name, '</li>';
}
echo '</ul>';
} else {
echo '</ul>No authors were added to the database.';
}
} else {
echo '<h2>Batch Add Authors</h2>';
$renderer =& $form->defaultRenderer();
$form->setRequiredNote('<font color="#FF0000">*</font> shows the required fields.');
$form->accept($renderer);
$this->form =& $form;
$this->renderer =& $renderer;
$this->js = <<<JS_END
window.addEvent('domready', function() {
var Tips1 = new Tips(\$\$('.Tips1'));
});
JS_END;
}
}
public function addAuthor($db, $mixed)
{
if (is_object($mixed)) {
// check if publication already has this author
if (isset($this->authors)) {
foreach ($this->authors as $author) {
if ($author->author_id == $mixed->author_id) {
return;
}
}
}
$this->authors[] = $mixed;
return;
} else {
if (is_array($mixed)) {
// replaces all authors
unset($this->authors);
// assigns each author
foreach ($mixed as $index => $author_id) {
$author = new pdAuthor();
$result = $author->dbLoad($db, $author_id, pdAuthor::DB_LOAD_BASIC);
assert('$result');
$this->authors[$index] = $author;
}
return;
}
}
// check if publication already has this author
if (isset($this->authors) && count($this->authors) > 0) {
foreach ($this->authors as $author) {
assert('$author->author_id != $mixed');
}
}
assert('is_numeric($mixed)');
$author = new pdAuthor();
$result = $author->dbLoad($db, $mixed, pdAuthor::DB_LOAD_BASIC);
assert('$result');
$this->authors[] = $author;
}
David Horn,
Kimmen Sjölander,
Steven L. Salzberg,
Dennis Vitkup,
Stanley Letovsky,
Daniel Segrè,
Charles DeLisi,
Richard J. Roberts,
Martin Steffen,
Simon Kasif
AUTHORS_NEW_END;
$db = new pdDb(array('server' => "localhost", 'user' => "dummy", 'passwd' => "ozzy498", 'name' => "pubdbdev"));
// this array contains the names in the format: FIRST OTHER LAST
$authors_in_db = pdAuthorList::create($db, null, null, true);
var_dump($authors_in_db);
$authors = array();
foreach (explode(',', $authors_new_raw) as $author_name) {
if (in_array($author_name, $authors_in_db)) {
exit("author {$author_name} already exists in the database");
}
$author = new pdAuthor();
$author->nameSet($author_name);
$authors[] = $author;
}
print "adding " . count($authors) . " new authors...\n";
// none of the authors already exist in the database, they can be saved
foreach ($authors as $author) {
$author->dbSave($db);
}
print "new authors added.\n";
//var_dump($authors);
<?php
/**
* This script is meant to be called in response to an AJAX request.
*
* It returns a listing of all the publication by a specified author. The
* author is specified in the URL query string.
*/
require_once '../includes/defines.php';
require_once 'includes/functions.php';
require_once 'includes/htmlUtils.php';
require_once 'includes/pdDb.php';
require_once 'includes/pdAuthor.php';
if (!isset($_GET['author_id'])) {
exit('script called with invalid arguments');
}
$db = pdDb::defaultNew();
$auth = new pdAuthor();
$auth->dbLoad($db, $_GET['author_id'], pdAuthor::DB_LOAD_PUBS_ALL | pdAuthor::DB_LOAD_INTERESTS);
if (!is_array($auth->pub_list)) {
exit('Author with id ' . $_GET['author_id'] . ' does not have any publication entries in the database');
}
echo displayPubList($db, $auth->pub_list);