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batchimport.php
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<?php
##short ajax dir check###
if (isset($_GET['check_dir']) && !empty($_GET['directory'])) {
if (is_dir($_GET['directory']) && is_readable($_GET['directory'])) {
die('1');
} else {
die('0');
}
}
include_once 'data.php';
if ($hosted == true)
die();
if (!empty($_GET['user']))
$user = md5($_GET['user']);
if (!empty($_GET['userID']))
$userID = $_GET['userID'];
if (!isset($_GET['commence'])) {
if (isset($_SESSION['auth']) && ($_SESSION['permissions'] == 'A' || $_SESSION['permissions'] == 'U')) {
$proxy_name = '';
$proxy_port = '';
$proxy_username = '';
$proxy_password = '';
if (isset($_SESSION['connection']) && ($_SESSION['connection'] == "autodetect" || $_SESSION['connection'] == "url")) {
if (!empty($_GET['proxystr'])) {
$proxy_arr = explode(';', $_GET['proxystr']);
foreach ($proxy_arr as $proxy_str) {
if (stripos(trim($proxy_str), 'PROXY') === 0) {
$proxy_str = trim(substr($proxy_str, 6));
$proxy_name = parse_url($proxy_str, PHP_URL_HOST);
$proxy_port = parse_url($proxy_str, PHP_URL_PORT);
$proxy_username = parse_url($proxy_str, PHP_URL_USER);
$proxy_password = parse_url($proxy_str, PHP_URL_PASS);
break;
}
}
}
} elseif (isset($_SESSION['connection']) && $_SESSION['connection'] == "proxy") {
if (isset($_SESSION['proxy_name']))
$proxy_name = $_SESSION['proxy_name'];
if (isset($_SESSION['proxy_port']))
$proxy_port = $_SESSION['proxy_port'];
if (isset($_SESSION['proxy_username']))
$proxy_username = $_SESSION['proxy_username'];
if (isset($_SESSION['proxy_password']))
$proxy_password = $_SESSION['proxy_password'];
}
include_once 'functions.php';
if (empty($_GET['directory'])) {
$batchimport_dir = get_setting('batchimport_dir');
$batchimport_recursive = get_setting('batchimport_recursive');
?>
<br>
<br>
<div style="width:600px;margin:auto">
<div class="ui-state-default ui-corner-all" style="float:left;margin-bottom:4px;padding:1px 4px;cursor:auto">
<i class="fa fa-signin"></i>
PDF Batch Import
</div>
</div>
<div style="clear:both"></div>
<div class="item-sticker ui-widget-content ui-corner-all" style="width:600px;margin:auto">
<form id="batchimportform" action="batchimport.php" method="GET">
<div class="alternating_row items ui-corner-top">
Import PDF files from directory:<br>
<button class="open-dirs-button" title="Browse directories"><i class="fa fa-folder-open"></i></button>
<input type="text" name="directory" value="<?php print $batchimport_dir; ?>" size="45" style="width:510px"><br>
<table cellspacing=0 style="margin: 2px 0px 2px 0px">
<tr>
<td class="select_span">
<input type="checkbox" name="recursive" value="1" style="display:none" <?php print empty($batchimport_recursive) ? '' : 'checked' ?>>
<i class="fa fa-<?php print empty($batchimport_recursive) ? 'square-o' : 'check-square' ?>"></i>
Include files in subdirectories.
</td>
</tr>
</table>
</div>
<div class="separator" style="margin:0"></div>
<div class="alternating_row items ui-corner-bottom">
<button id="batchimportbutton"><i class="fa fa-save"></i> Import</button>
</div>
</form>
</div>
<?php
} else {
if (substr($_GET['directory'], -1) == DIRECTORY_SEPARATOR)
$_GET['directory'] = substr($_GET['directory'], 0, -1);
database_connect(IL_USER_DATABASE_PATH, 'users');
save_setting($dbHandle, 'batchimport_dir', $_GET['directory']);
if (isset($_GET['recursive'])) {
save_setting($dbHandle, 'batchimport_recursive', $_GET['recursive']);
} else {
save_setting($dbHandle, 'batchimport_recursive', '');
}
$dbHandle = null;
$batchimport_database_pubmed = get_setting('batchimport_database_pubmed');
$batchimport_database_nasaads = get_setting('batchimport_database_nasaads');
$batchimport_database_crossref = get_setting('batchimport_database_crossref');
$batchimport_failed = get_setting('batchimport_failed');
$batchimport_log = get_setting('batchimport_log');
$pdf_files = array();
if (isset($_GET['recursive'])) {
$lit = new RecursiveIteratorIterator(new RecursiveDirectoryIterator($_GET['directory']), RecursiveIteratorIterator::LEAVES_ONLY, RecursiveIteratorIterator::CATCH_GET_CHILD);
$lit->rewind();
while ($lit->valid()) {
$file = $lit->key();
if (is_readable($file) && in_array(pathinfo($file, PATHINFO_EXTENSION), array('pdf', 'doc', 'docx', 'vsd', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {
$pdf_files[] = $file;
}
$lit->next();
}
} else {
$pdf_files = glob($_GET['directory'] . DIRECTORY_SEPARATOR . '*.{pdf,doc,docx,xls,xlsx,ppt,pptx,odt,ods,odp}', GLOB_NOSORT | GLOB_BRACE);
}
$pdf_count = count($pdf_files);
?>
<div class="ui-state-default ui-corner-all" style="float:left;margin:4px;padding:1px 4px;cursor:auto">
<i class="fa fa-signin"></i>
PDF Batch Import
</div>
<div style="clear:both"></div>
<form id="batchimportform2" action="batchimport.php" method="GET">
<input type="hidden" name="commence" value="">
<input type="hidden" name="directory" value="<?php print htmlspecialchars($_GET['directory']); ?>">
<input type="hidden" name="recursive" value="<?php print isset($_GET['recursive']) ? '1' : '0'; ?>">
<input type="hidden" name="user" value="<?php print htmlspecialchars($_SESSION['user']); ?>">
<input type="hidden" name="userID" value="<?php print htmlspecialchars($_SESSION['user_id']); ?>">
<input type="hidden" name="proxy_name" value="<?php print htmlspecialchars($proxy_name); ?>">
<input type="hidden" name="proxy_port" value="<?php print htmlspecialchars($proxy_port); ?>">
<input type="hidden" name="proxy_username" value="<?php print htmlspecialchars($proxy_username); ?>">
<input type="hidden" name="proxy_password" value="<?php print htmlspecialchars($proxy_password); ?>">
<table style="width: 100%;" class="threed">
<tr>
<td valign="top" class="threedleft">
<button id="batchimportbutton2" <?php
if ($pdf_count == 0)
print 'disabled';
?>><i class="fa fa-save"></i> Import</button>
</td>
<td valign="top" class="threedright">
<table cellspacing=0>
<tr>
<td class="select_span" style="line-height:22px;width:10em">
<input type="checkbox" checked class="uploadcheckbox" style="display:none" name="shelf">
<i class="fa fa-check-square"></i>
Add to Shelf
</td>
<td class="select_span" style="line-height:22px;width: 10em;text-align:right">
<input type="checkbox" class="uploadcheckbox" style="display:none" name="project">
<i class="fa fa-square-o"></i>
Add to Project
</td>
<td style="line-height:22px;width: 18em">
<select name="projectID" style="width:200px">
<?php
database_connect(IL_DATABASE_PATH, 'library');
$desktop_projects = array();
$desktop_projects = read_desktop($dbHandle);
foreach ($desktop_projects as $project) {
print '<option value="' . $project['projectID'] . '">' . htmlspecialchars($project['project']) . '</option>' . PHP_EOL;
}
$dbHandle = null;
?>
</select>
</td>
</tr>
</table>
</td>
</tr>
</table>
<table style="width: 100%" id="table1" class="threed">
<tr><td class="threedleft">Info:</td>
<td class="threedright" style="padding-left: 18px">
Found <?php print $pdf_count; ?> file<?php print ($pdf_count == 1) ? '' : 's'; ?>.
(Note that PDFs must contain a <a href="https://en.wikipedia.org/wiki/Digital_object_identifier" target="_blank">DOI</a> in order to track the corresponding metadata.)
<?php
if ($pdf_count > 100) {
?>
<div class="batch-errors" style="display:none">Warning! Uploading too many files<br> puts a load on the database servers and may
result in banning your access to the used database. If possible, limit the number of PDFs to 100 at a time.</div>
<?php
}
?>
</td>
</tr>
<tr><td class="threedleft">Select database:</td>
<td class="threedright">
<table>
<?php if (!isset($_SESSION['remove_pubmed'])) { ?>
<tr>
<td class="select_span"><input type="checkbox" name="database_pubmed" value="1" style="display:none" <?php print (isset($batchimport_database_pubmed) && $batchimport_database_pubmed == '1') ? 'checked' : '' ?>>
<i class="fa fa-<?php print (isset($batchimport_database_pubmed) && $batchimport_database_pubmed == '1') ? 'check-square' : 'square-o' ?>"></i> PubMed (biomedicine)
</td>
</tr>
<?php
}
if (!isset($_SESSION['remove_nasaads'])) {
?>
<tr>
<td class="select_span"><input type="checkbox" name="database_nasaads" value="1" style="display:none" <?php print (isset($batchimport_database_nasaads) && $batchimport_database_nasaads == '1') ? 'checked' : '' ?>>
<i class="fa fa-<?php print (isset($batchimport_database_nasaads) && $batchimport_database_nasaads == '1') ? 'check-square' : 'square-o' ?>"></i> NASA ADS (physics, astronomy)
</td>
</tr>
<?php } ?>
<tr>
<td class="select_span"><input type="checkbox" name="database_crossref" value="1" style="display:none" <?php print (isset($batchimport_database_crossref) && $batchimport_database_crossref == '1') ? 'checked' : '' ?>>
<i class="fa fa-<?php print (isset($batchimport_database_crossref) && $batchimport_database_crossref == '1') ? 'check-square' : 'square-o' ?>"></i> CrossRef (other sciences)
</td>
</tr>
</table>
</td></tr>
<tr><td class="threedleft">If metadata not found:</td>
<td class="threedright" style="line-height: 16px">
<table cellspacing="0">
<tr>
<td class="select_span" style="line-height: 16px">
<input type="checkbox" name="failed" value="1" style="display: none" <?php print (isset($batchimport_failed) && $batchimport_failed == '1') ? 'checked' : '' ?>>
<i class="fa fa-<?php print (isset($batchimport_failed) && $batchimport_failed == '1') ? 'check-square' : 'square-o' ?>"></i>
Import the PDF into the category !unknown. All PDF files will be recorded and indexed!
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td class="threedleft">During import:</td>
<td class="threedright" style="line-height: 16px">
<table cellspacing="0">
<tr>
<td class="select_span" style="line-height: 16px">
<input type="radio" name="log" value="1" style="display: none" <?php print (empty($batchimport_log) || (isset($batchimport_log) && $batchimport_log == '1')) ? 'checked' : '' ?>>
<i class="fa fa-circle<?php print (empty($batchimport_log) || (isset($batchimport_log) && $batchimport_log == '1')) ? '' : '-o' ?>"></i>
Continue working, let the import run in background.
</td>
</tr>
<tr>
<td class="select_span" style="line-height: 16px">
<input type="radio" name="log" value="2" style="display: none" <?php print (isset($batchimport_log) && $batchimport_log == '2') ? 'checked' : '' ?>>
<i class="fa fa-circle<?php print (isset($batchimport_log) && $batchimport_log == '2') ? '' : '-o' ?>"></i>
Watch the import log.
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td class="threedleft">
Choose category:<br>
</td>
<td class="threedright">
<input type="text" id="filtercategories" value="" placeholder="Filter categories" style="width:300px;margin:0.75em 0">
<div class="categorydiv" style="width: 99%;overflow:scroll; height: 400px;background-color: white;color: black;border: 1px solid #C5C6C9">
<table cellspacing=0 style="float:left;width: 49%">
<?php
$category_string = null;
database_connect(IL_DATABASE_PATH, 'library');
$result = $dbHandle->query("SELECT count(*) FROM categories");
$totalcount = $result->fetchColumn();
$result = null;
$i = 1;
$isdiv = null;
$result = $dbHandle->query("SELECT categoryID,category FROM categories ORDER BY category COLLATE NOCASE ASC");
while ($category = $result->fetch(PDO::FETCH_ASSOC)) {
if ($i > (1 + $totalcount / 2) && !$isdiv) {
print '</table><table cellspacing=0 style="width: 49%;float: right;padding:2px">';
$isdiv = true;
}
print PHP_EOL . '<tr><td class="select_span">';
print "<input type=\"checkbox\" name=\"category[]\" value=\"" . htmlspecialchars($category['categoryID']) . "\"";
print " style=\"display:none\"> <i class=\"fa fa-square-o\"></i> " . htmlspecialchars($category['category']) . "</td></tr>";
$i = $i + 1;
}
$result = null;
$dbHandle = null;
?>
</table>
</div>
</td>
</tr>
<tr>
<td class="threedleft">
Add to new categories:
</td>
<td class="threedright">
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value="">
</td>
</tr>
</table>
</form>
<?php
}
} else {
print 'Super User or User permissions required.';
}
} else {
if (isset($_GET['proxy_name']))
$proxy_name = $_GET['proxy_name'];
if (isset($_GET['proxy_port']))
$proxy_port = $_GET['proxy_port'];
if (isset($_GET['proxy_username']))
$proxy_username = $_GET['proxy_username'];
if (isset($_GET['proxy_password']))
$proxy_password = $_GET['proxy_password'];
include_once 'functions.php';
########create log file###########
$log = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $user . '-librarian-import.log';
file_put_contents($log, '');
$database_pubmed = '';
$database_nasaads = '';
$database_crossref = '';
$failed = '';
$batchimport_log = '';
if (isset($_GET['database_pubmed']))
$database_pubmed = $_GET['database_pubmed'];
if (isset($_GET['database_nasaads']))
$database_nasaads = $_GET['database_nasaads'];
if (isset($_GET['database_crossref']))
$database_crossref = $_GET['database_crossref'];
if (isset($_GET['failed']))
$failed = $_GET['failed'];
if (isset($_GET['log']))
$batchimport_log = $_GET['log'];
database_connect(IL_USER_DATABASE_PATH, 'users');
save_settings($dbHandle, array(
'batchimport_database_pubmed' => $database_pubmed,
'batchimport_database_nasaads' => $database_nasaads,
'batchimport_database_crossref' => $database_crossref,
'batchimport_failed' => $failed,
'batchimport_log' => $batchimport_log
));
$dbHandle = null;
$user_dir = IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id();
session_write_close();
include_once 'functions.php';
if (substr($_GET['directory'], -1) == DIRECTORY_SEPARATOR)
$_GET['directory'] = substr($_GET['directory'], 0, -1);
$files = array();
if (!empty($_GET['recursive'])) {
$lit = new RecursiveIteratorIterator(new RecursiveDirectoryIterator($_GET['directory']), RecursiveIteratorIterator::LEAVES_ONLY, RecursiveIteratorIterator::CATCH_GET_CHILD);
$lit->rewind();
while ($lit->valid()) {
$file = $lit->key();
if (is_readable($file) && in_array(pathinfo($file, PATHINFO_EXTENSION), array('pdf', 'doc', 'docx', 'vsd', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {
$files[] = $file;
}
$lit->next();
}
} else {
$files = glob($_GET['directory'] . DIRECTORY_SEPARATOR . '*.{pdf,doc,docx,xls,xlsx,ppt,pptx,odt,ods,odp}', GLOB_NOSORT | GLOB_BRACE);
}
$order = array("\r\n", "\n", "\r");
$i = 0;
while (list($key, $file) = each($files)) {
set_time_limit(600);
$i = $i + 1;
if (is_readable($file)) {
$string = '';
$xml = '';
$record = '';
$count = '';
$url = '';
$authors = '';
$authors_array = array();
$affiliation = '';
$title = '';
$abstract = '';
$secondary_title = '';
$tertiary_title = '';
$year = '';
$volume = '';
$issue = '';
$pages = '';
$last_page = '';
$journal_abbr = '';
$keywords = '';
$name_array = array();
$mesh_array = array();
$new_file = '';
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$editor = '';
$reference_type = 'article';
$publisher = '';
$place_published = '';
$doi = '';
$authors_ascii = '';
$title_ascii = '';
$abstract_ascii = '';
$unpacked_files = array();
$temp_file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $user . "_librarian_temp" . $i . ".txt";
if (file_exists($temp_file))
unlink($temp_file);
//convert office to pdf
$file_extension = pathinfo($file, PATHINFO_EXTENSION);
if (in_array($file_extension, array('doc', 'docx', 'vsd', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin')
putenv('HOME=' . IL_TEMP_PATH);
exec(select_soffice() . ' --headless --convert-to pdf --outdir ' . escapeshellarg(IL_TEMP_PATH) . ' ' . escapeshellarg($file));
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin')
putenv('HOME=""');
//copy file to temp to add it to supplement later
copy($file, IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($file));
$title = basename($file);
//pdf file
$file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($file, '.' . $file_extension) . '.pdf';
}
########## extract text from pdf ##########
system(select_pdftotext() . ' -enc UTF-8 -f 1 -l 3 ' . escapeshellarg($file) . ' ' . escapeshellarg($temp_file));
if (file_exists($temp_file))
$string = file_get_contents($temp_file);
if (empty($string)) {
if (isset($_GET['failed']) && $_GET['failed'] == '1') {
database_connect(IL_DATABASE_PATH, 'library');
record_unknown($dbHandle, $title, $file, $userID);
$put = "<hr> " . basename($file) . ": Recorded into category !unknown. Full text not indexed (copying disallowed).<br>";
file_put_contents($log, $put . file_get_contents($log));
} else {
$put = "<hr> " . basename($file) . ": copying disallowed.<br>";
file_put_contents($log, $put . file_get_contents($log));
}
} else {
$string = str_replace($order, ' ', $string);
$order = array("\xe2\x80\x93", "\xe2\x80\x94");
$replace = '-';
$string = str_replace($order, $replace, $string);
preg_match_all('/10\.\d{4}\/\S+/ui', $string, $doi, PREG_PATTERN_ORDER);
if (count($doi[0]) < 1) {
if (isset($_GET['failed']) && $_GET['failed'] == '1') {
database_connect(IL_DATABASE_PATH, 'library');
record_unknown($dbHandle, $title, $file, $userID);
$put = "<hr> " . basename($file) . ": Recorded into category !unknown. DOI not found.<br>";
file_put_contents($log, $put . file_get_contents($log));
} else {
$put = "<hr> " . basename($file) . ": DOI not found.<br>";
file_put_contents($log, $put . file_get_contents($log));
}
} else {
$doi = $doi[0][0];
if (substr($doi, -1) == '.')
$doi = substr($doi, 0, -1);
if (substr($doi, -1) == ',')
$doi = substr($doi, 0, -1);
if (substr($doi, -1) == ';')
$doi = substr($doi, 0, -1);
if (substr($doi, -1) == ')' || substr($doi, -1) == ']') {
preg_match_all('/(.)(doi:\s?)?(10\.\d{4}\/\S+)/ui', $string, $doi2, PREG_PATTERN_ORDER);
if (substr($doi, -1) == ')' && $doi2[1][0] == '(')
$doi = substr($doi, 0, -1);
if (substr($doi, -1) == ']' && $doi2[1][0] == '[')
$doi = substr($doi, 0, -1);
}
$title = '';
if (isset($_GET['database_pubmed']) && $_GET['database_pubmed'] == '1') {
$put = " " . basename($file) . ": Querying Pubmed with $doi <br>";
file_put_contents($log, $put . file_get_contents($log));
$response = array();
fetch_from_pubmed($doi, '');
extract($response);
$uid = join("|", (array) $uid);
$url = join("|", (array) $url);
}
if (isset($_GET['database_nasaads']) && $_GET['database_nasaads'] == '1' && empty($title)) {
$put = " " . basename($file) . ": Querying NASA ADS with $doi <br>";
file_put_contents($log, $put . file_get_contents($log));
$response = array();
fetch_from_nasaads($doi, '');
extract($response);
$uid = join("|", (array) $uid);
$url = join("|", (array) $url);
}
if (isset($_GET['database_crossref']) && $_GET['database_crossref'] == '1' && empty($title)) {
$put = " " . basename($file) . ": Querying CrossRef with $doi <br>";
file_put_contents($log, $put . file_get_contents($log));
############ CrossRef ##############
$response = array();
fetch_from_crossref($doi);
extract($response);
}
//TRY AGAIN WITH DOI ONE CHARACTER SHORTER
if (empty($title)) {
$doi = substr($doi, 0, -1);
if (isset($_GET['database_pubmed']) && $_GET['database_pubmed'] == '1') {
$put = " " . basename($file) . ": Querying PubMed again with $doi <br>";
file_put_contents($log, $put . file_get_contents($log));
########## open esearch, fetch PMID ##########
$response = array();
fetch_from_pubmed($doi, '');
extract($response);
$uid = join("|", (array) $uid);
$url = join("|", (array) $url);
}
if (isset($_GET['database_nasaads']) && $_GET['database_nasaads'] == '1' && empty($title)) {
$put = " " . basename($file) . ": Querying NASA ADS again with $doi <br>";
file_put_contents($log, $put . file_get_contents($log));
$response = array();
fetch_from_nasaads($doi, '');
extract($response);
$uid = join("|", (array) $uid);
$url = join("|", (array) $url);
}
if (isset($_GET['database_crossref']) && $_GET['database_crossref'] == '1' && empty($title)) {
$put = " " . basename($file) . ": Querying CrossRef again with $doi<br>";
file_put_contents($log, $put . file_get_contents($log));
############ CrossRef ##############
$response = array();
fetch_from_crossref($doi);
extract($response);
}
}
if (empty($title)) {
if (isset($_GET['failed']) && $_GET['failed'] == '1') {
$string = preg_replace('/(^|\s)\S{1,2}(\s|$)/', ' ', $string);
$string = preg_replace('/\s{2,}/', " ", $string);
database_connect(IL_DATABASE_PATH, 'library');
record_unknown($dbHandle, $title, $string, $file, $userID);
$put = "<hr> " . basename($file) . ": Recorded into category !unknown. No database record found.<br>";
file_put_contents($log, $put . file_get_contents($log));
} else {
$put = "<hr> " . basename($file) . ": No database record found.<br>";
file_put_contents($log, $put . file_get_contents($log));
}
}
if (!empty($title)) {
database_connect(IL_DATABASE_PATH, 'library');
if (!empty($authors))
$authors_ascii = utf8_deaccent($authors);
$title_ascii = utf8_deaccent($title);
if (!empty($abstract))
$abstract_ascii = utf8_deaccent($abstract);
########## record publication data, table library ##########
$query = "INSERT INTO library (file, authors, affiliation, title, journal, year, addition_date, abstract, rating, uid, volume, issue, pages,
secondary_title, tertiary_title, editor,
url, reference_type, publisher, place_published, keywords, doi, authors_ascii, title_ascii, abstract_ascii, added_by)
VALUES ((SELECT IFNULL((SELECT SUBSTR('0000' || CAST(MAX(file)+1 AS TEXT) || '.pdf',-9,9) FROM library),'00001.pdf')), :authors, :affiliation,
:title, :journal, :year, :addition_date, :abstract, :rating, :uid, :volume, :issue, :pages, :secondary_title, :tertiary_title, :editor,
:url, :reference_type, :publisher, :place_published, :keywords, :doi, :authors_ascii, :title_ascii, :abstract_ascii, :added_by)";
$stmt = $dbHandle->prepare($query);
$stmt->bindParam(':authors', $authors, PDO::PARAM_STR);
$stmt->bindParam(':affiliation', $affiliation, PDO::PARAM_STR);
$stmt->bindParam(':title', $title, PDO::PARAM_STR);
$stmt->bindParam(':journal', $journal_abbr, PDO::PARAM_STR);
$stmt->bindParam(':year', $year, PDO::PARAM_STR);
$stmt->bindParam(':addition_date', $addition_date, PDO::PARAM_STR);
$stmt->bindParam(':abstract', $abstract, PDO::PARAM_STR);
$stmt->bindParam(':rating', $rating, PDO::PARAM_INT);
$stmt->bindParam(':uid', $uid, PDO::PARAM_STR);
$stmt->bindParam(':volume', $volume, PDO::PARAM_STR);
$stmt->bindParam(':issue', $issue, PDO::PARAM_STR);
$stmt->bindParam(':pages', $pages, PDO::PARAM_STR);
$stmt->bindParam(':secondary_title', $secondary_title, PDO::PARAM_STR);
$stmt->bindParam(':tertiary_title', $tertiary_title, PDO::PARAM_STR);
$stmt->bindParam(':editor', $editor, PDO::PARAM_STR);
$stmt->bindParam(':url', $url, PDO::PARAM_STR);
$stmt->bindParam(':reference_type', $reference_type, PDO::PARAM_STR);
$stmt->bindParam(':publisher', $publisher, PDO::PARAM_STR);
$stmt->bindParam(':place_published', $place_published, PDO::PARAM_STR);
$stmt->bindParam(':keywords', $keywords, PDO::PARAM_STR);
$stmt->bindParam(':doi', $doi, PDO::PARAM_STR);
$stmt->bindParam(':authors_ascii', $authors_ascii, PDO::PARAM_STR);
$stmt->bindParam(':title_ascii', $title_ascii, PDO::PARAM_STR);
$stmt->bindParam(':abstract_ascii', $abstract_ascii, PDO::PARAM_STR);
$stmt->bindParam(':added_by', $userID, PDO::PARAM_INT);
$dbHandle->beginTransaction();
$stmt->execute();
$stmt = null;
$id = $dbHandle->lastInsertId();
$new_file = str_pad($id, 5, "0", STR_PAD_LEFT) . '.pdf';
// Save citation key.
$stmt6 = $dbHandle->prepare("UPDATE library SET bibtex=:bibtex WHERE id=:id");
$stmt6->bindParam(':bibtex', $bibtex, PDO::PARAM_STR);
$stmt6->bindParam(':id', $id, PDO::PARAM_INT);
$bibtex_author = 'unknown';
if (!empty($last_name[0])) {
$bibtex_author = utf8_deaccent($last_name[0]);
$bibtex_author = str_replace(' ', '', $bibtex_author);
}
empty($year) ? $bibtex_year = '0000' : $bibtex_year = substr($year, 0, 4);
$bibtex = $bibtex_author . '-' . $bibtex_year . '-ID' . $id;
$insert = $stmt6->execute();
$insert = null;
if (isset($_GET['shelf']) && !empty($userID)) {
$user_query = $dbHandle->quote($userID);
$file_query = $dbHandle->quote($id);
$dbHandle->exec("INSERT OR IGNORE INTO shelves (userID,fileID) VALUES ($user_query,$file_query)");
}
if (isset($_GET['project']) && !empty($_GET['projectID'])) {
$dbHandle->exec("INSERT OR IGNORE INTO projectsfiles (projectID,fileID) VALUES (" . intval($_GET['projectID']) . "," . intval($id) . ")");
}
####### record new category into categories, if not exists #########
if (!empty($_GET['category2'])) {
$_GET['category2'] = preg_replace('/\s{2,}/', '', $_GET['category2']);
$_GET['category2'] = preg_replace('/^\s$/', '', $_GET['category2']);
$_GET['category2'] = array_filter($_GET['category2']);
$query = "INSERT INTO categories (category) VALUES (:category)";
$stmt = $dbHandle->prepare($query);
$stmt->bindParam(':category', $new_category, PDO::PARAM_STR);
while (list($key, $new_category) = each($_GET['category2'])) {
$new_category_quoted = $dbHandle->quote($new_category);
$result = $dbHandle->query("SELECT categoryID FROM categories WHERE category=$new_category_quoted");
$exists = $result->fetchColumn();
$category_ids[] = $exists;
$result = null;
if (empty($exists)) {
$stmt->execute();
$last_id = $dbHandle->query("SELECT last_insert_rowid() FROM categories");
$category_ids[] = $last_id->fetchColumn();
$last_id = null;
}
}
$stmt = null;
}
####### record new relations into filescategories #########
$categories = array();
if (!empty($_GET['category']) || !empty($category_ids)) {
$categories = array_merge((array) $_GET['category'], (array) $category_ids);
$categories = array_filter(array_unique($categories));
}
$query = "INSERT OR IGNORE INTO filescategories (fileID,categoryID) VALUES (:fileid,:categoryid)";
$stmt = $dbHandle->prepare($query);
$stmt->bindParam(':fileid', $id);
$stmt->bindParam(':categoryid', $category_id);
while (list($key, $category_id) = each($categories)) {
if (!empty($id))
$stmt->execute();
}
$stmt = null;
$dbHandle->commit();
copy($file, IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file, IL_PDF_PATH) . DIRECTORY_SEPARATOR . $new_file);
$hash = md5_file(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);
//RECORD FILE HASH FOR DUPLICATE DETECTION
if (!empty($hash)) {
$hash = $dbHandle->quote($hash);
$dbHandle->exec('UPDATE library SET filehash=' . $hash . ' WHERE id=' . $id);
}
$dbHandle = null;
recordFulltext($id, $new_file);
$unpack_dir = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file;
mkdir($unpack_dir);
exec(select_pdfdetach() . ' -saveall -o ' . escapeshellarg($unpack_dir) . ' ' . escapeshellarg(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file));
$unpacked_files = scandir($unpack_dir);
foreach ($unpacked_files as $unpacked_file) {
if (is_file($unpack_dir . DIRECTORY_SEPARATOR . $unpacked_file))
rename($unpack_dir . DIRECTORY_SEPARATOR . $unpacked_file,
IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file, IL_SUPPLEMENT_PATH) . DIRECTORY_SEPARATOR . sprintf("%05d", intval($new_file)) . $unpacked_file);
}
rmdir($unpack_dir);
$put = "<hr> " . basename($file) . ": Recorded.<br>";
file_put_contents($log, $put . file_get_contents($log));
}
}
}
} else {
$put = "<hr> " . basename($file) . ": Not readable.<br>";
file_put_contents($log, $put . file_get_contents($log));
}
} ####while loop
########## ANALYZE ##########
database_connect(IL_DATABASE_PATH, 'library');
if (rand(1, 1000) == 500)
$dbHandle->exec("ANALYZE");
$dbHandle = null;
###### clean the temp directory ########
for ($j = $i; $j >= 1; $j--) {
$temp_file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $user . "_librarian_temp" . $j . ".txt";
if (file_exists($temp_file))
unlink($temp_file);
}
print "OK";
sleep(1);
@unlink($log);
}