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batchimport.php
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batchimport.php
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<?php
#session is disabled for this script due to a bug in Win32, Apache or PHP which is not resolved as of 03/2009
#multiple system() or exec() commands will hang the script if session is activated
#session_start();
#if (isset($_SESSION['auth'])) {
##short ajax dir check###
if (isset($_GET['check_dir']) && !empty($_GET['directory'])) {
if (is_dir($_GET['directory']) && is_readable($_GET['directory'])) {
die('1');
} else {
die('0');
}
}
if (!empty($_GET['user']))
$user = $_GET['user'];
if (!empty($_GET['userID']))
$userID = $_GET['userID'];
if (!isset($_GET['commence'])) {
include_once 'data.php';
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;
}
}
}
} else {
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'])) {
database_connect($usersdatabase_path, 'users');
$batchimport_dir = get_setting($dbHandle, 'batchimport_dir');
$batchimport_recursive = get_setting($dbHandle, 'batchimport_recursive');
$dbHandle = null;
?>
<div style="margin:4px;font-weight:bold">PDF Batch Import</div><br><br>
<div class="item-sticker ui-widget-content ui-corner-all" style="width:600px;margin:auto">
<div class="alternating_row items ui-corner-top">
Import PDF files from directory*:<br>
<button class="open-dirs-button">Browse directories</button>
<form id="batchimportform" action="batchimport.php" method="GET">
<input type="text" name="directory" value="<?php print $batchimport_dir; ?>" size="45" style="width:540px"><br>
<table cellspacing=0 style="margin: 2px 0px 2px 0px">
<tr>
<td class="select_span">
<input type="checkbox" name="recursive" value="1" style="display:none" <?php print empty($batchimport_recursive) ? '' : 'checked' ?>>
<span class="ui-icon ui-icon-<?php print empty($batchimport_recursive) ? 'close' : 'check' ?>" style="float:left"></span>
Include files in subdirectories.
</td>
</tr>
</table>
</div>
<div class="separator" style="margin:0"></div>
<div class="alternating_row items ui-corner-bottom">
<button id="batchimportbutton">Import</button>
</form>
</div>
</div>
<?php
} else {
if (substr($_GET['directory'], -1) == DIRECTORY_SEPARATOR)
$_GET['directory'] = substr($_GET['directory'], 0, -1);
database_connect($usersdatabase_path, 'users');
save_setting($dbHandle, 'batchimport_dir', $_GET['directory']);
if (isset($_GET['recursive'])) {
save_setting($dbHandle, 'batchimport_recursive', $_GET['recursive']);
} else {
save_setting($dbHandle, 'batchimport_recursive', '');
}
$batchimport_database_pubmed = get_setting($dbHandle, 'batchimport_database_pubmed');
$batchimport_database_nasaads = get_setting($dbHandle, 'batchimport_database_nasaads');
$batchimport_database_crossref = get_setting($dbHandle, 'batchimport_database_crossref');
$batchimport_failed = get_setting($dbHandle, 'batchimport_failed');
$batchimport_log = get_setting($dbHandle, 'batchimport_log');
$dbHandle = null;
function list_dirs($directory) {
global $directories;
$dir_content = scandir($directory);
while (list($key, $value) = each($dir_content)) {
if (is_dir($directory . DIRECTORY_SEPARATOR . $value) && is_readable($directory . DIRECTORY_SEPARATOR . $value)
&& $value != '.' && $value != '..' && $value[0] != '.' && count($directories) < 2001) {
$directories[] = $directory . DIRECTORY_SEPARATOR . $value;
list_dirs($directory . DIRECTORY_SEPARATOR . $value);
}
}
return $directories;
}
$directories = array();
$pdf_files = array();
$directories[] = $_GET['directory'];
if (isset($_GET['recursive']))
$directories = list_dirs($_GET['directory']);
while (list($key, $directory) = each($directories)) {
$glob = glob($directory . DIRECTORY_SEPARATOR . '*.pdf');
$pdf_files = array_merge($pdf_files, $glob);
}
$pdf_count = count($pdf_files);
?>
<table cellspacing=0 style="width:100%;margin-top: 4px;margin-bottom: 1px;">
<tr>
<td>
<div class="ui-state-highlight ui-corner-top" style="float:right;margin-left:2px;margin-right:4px;padding-right:4px" id="open2">
<span class="ui-icon ui-icon-tag" style="float:left"></span>Categories
</div>
<div class="ui-state-highlight ui-corner-top clicked" style="float:right;padding-right:4px" id="open1">
<span class="ui-icon ui-icon-gear" style="float:left"></span>Options
</div>
<b> PDF Batch Import</b>
</td>
</tr>
</table>
<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 cellspacing="0" style="width: 100%;border-top: solid 1px #D5D6D9">
<tr>
<td valign="top" class="threedleft">
<button id="batchimportbutton2" <?php if ($pdf_count == 0)
print 'disabled'; ?>>Import</button>
</td>
<td valign="top" class="threedright">
<table cellspacing=0>
<tr>
<td class="select_span" style="line-height:22px;width:10em">
<input type="checkbox" checked class="uploadcheckbox" style="display:none" name="shelf">
<span class="ui-icon ui-icon-check" style="float:left;margin-top: 2px">
</span>Add to Shelf
</td>
<td class="select_span" style="line-height:22px;width: 10em;text-align:right">
<input type="checkbox" class="uploadcheckbox" style="display:none" name="project">
<div style="float:right">Add to Project </div>
<span class="ui-icon ui-icon-close" style="float:right;margin-top: 2px">
</span>
</td>
<td style="line-height:22px;width: 18em">
<select name="projectID" style="width:200px">
<?php
database_connect($database_path, 'library');
$id_query = $dbHandle->quote($_SESSION['user_id']);
$result = $dbHandle->query("SELECT DISTINCT projects.projectID,project FROM projects
LEFT OUTER JOIN projectsusers ON projects.projectID=projectsusers.projectID
WHERE projects.userID=$id_query OR projectsusers.userID=$id_query ORDER BY project COLLATE NOCASE ASC");
while ($project = $result->fetch(PDO::FETCH_ASSOC)) {
print '<option value="' . $project['projectID'] . '">' . htmlspecialchars($project['project']) . '</option>' . PHP_EOL;
}
$result = null;
$dbHandle = null;
?>
</select>
</td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing="0" style="width: 100%" id="table1">
<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="http://en.wikipedia.org/wiki/Digital_object_identifier" target="_blank">DOI</a> in order to track the corresponding metadata.)
<?php
if ($pdf_count > 100) {
?>
<div class="batch-errors" style="display:none">Warning! Uploading too many files<br> puts a load on the database servers and may
result in banning your access to the used database. If possible, limit the number of PDFs to 100 at a time.</div>
<?php
}
?>
</td></tr>
<tr><td class="threedleft">Select database:</td>
<td class="threedright">
<table cellspacing="0">
<tr>
<td class="select_span"><input type="checkbox" name="database_pubmed" value="1" style="display:none" <?php print (isset($batchimport_database_pubmed) && $batchimport_database_pubmed == '1') ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-<?php print (isset($batchimport_database_pubmed) && $batchimport_database_pubmed == '1') ? 'check' : 'close' ?>" style="float:left"></span>PubMed (biomedicine)</td>
</tr><tr>
<td class="select_span"><input type="checkbox" name="database_nasaads" value="1" style="display:none" <?php print (isset($batchimport_database_nasaads) && $batchimport_database_nasaads == '1') ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-<?php print (isset($batchimport_database_nasaads) && $batchimport_database_nasaads == '1') ? 'check' : 'close' ?>" style="float:left"></span>NASA ADS (physics, astronomy)</td>
</tr><tr>
<td class="select_span"><input type="checkbox" name="database_crossref" value="1" style="display:none" <?php print (isset($batchimport_database_crossref) && $batchimport_database_crossref == '1') ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-<?php print (isset($batchimport_database_crossref) && $batchimport_database_crossref == '1') ? 'check' : 'close' ?>" style="float:left"></span>CrossRef (other sciences)</td>
</tr>
</table>
</td></tr>
<tr><td class="threedleft">If metadata not found:</td>
<td class="threedright" style="line-height: 16px">
<table cellspacing="0">
<tr>
<td class="select_span" style="line-height: 16px">
<input type="checkbox" name="failed" value="1" style="display: none" <?php print (isset($batchimport_failed) && $batchimport_failed == '1') ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-<?php print (isset($batchimport_failed) && $batchimport_failed == '1') ? 'check' : 'close' ?>" style="float:left"></span>
Import the PDF into the category !unknown. All PDF files will be recorded and indexed!
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td class="threedleft">During import:</td>
<td class="threedright" style="line-height: 16px">
<table cellspacing="0">
<tr>
<td class="select_span" style="line-height: 16px">
<input type="radio" name="log" value="1" style="display: none" <?php print (empty($batchimport_log) || (isset($batchimport_log) && $batchimport_log == '1')) ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-radio-<?php print (empty($batchimport_log) || (isset($batchimport_log) && $batchimport_log == '1')) ? 'off' : 'on' ?>" style="float:left"></span>
Continue working, let the import run in background.
</td>
</tr>
<tr>
<td class="select_span" style="line-height: 16px">
<input type="radio" name="log" value="2" style="display: none" <?php print (isset($batchimport_log) && $batchimport_log == '2') ? 'checked' : '' ?>>
<span class="ui-icon ui-icon-radio-<?php print (isset($batchimport_log) && $batchimport_log == '2') ? 'off' : 'on' ?>" style="float:left"></span>
Watch the import log.
</td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing="0" style="width:100%;display:none" id="table2">
<tr>
<td class="threedleft">
Choose category:<br>
</td>
<td class="threedright">
<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
$category_string = null;
database_connect($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\"><span class=\"ui-icon ui-icon-close\" style=\"float:left\"></span>" . htmlspecialchars($category['category']) . "</td></tr>";
$i = $i + 1;
}
$result = null;
$dbHandle = null;
?>
</table>
</div>
<span class="ui-icon ui-icon-triangle-1-s enlargelist" style="cursor: pointer;float:left" id=""></span>
<span class="ui-icon ui-icon-triangle-1-n shrinklist" style="cursor: pointer;" id=""></span>
</td>
</tr>
<tr>
<td class="threedleft">
Add to new categories:
</td>
<td class="threedright">
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value=""><br>
<input type="text" size="30" name="category2[]" value="">
</td>
</tr>
</table>
</form>
<?php
}
} else {
print 'Super User or User permissions required.';
}
} else {
if (isset($_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 'data.php';
include_once 'functions.php';
########create log file###########
$log = $temp_dir . DIRECTORY_SEPARATOR . 'i-librarian' . DIRECTORY_SEPARATOR.$_GET['user'].'-librarian-import.log';
file_put_contents($log, '<b>Log:</b><br>');
$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 = $_GET['log'];
database_connect($usersdatabase_path, 'users');
save_setting($dbHandle, 'batchimport_database_pubmed', $database_pubmed);
save_setting($dbHandle, 'batchimport_database_nasaads', $database_nasaads);
save_setting($dbHandle, 'batchimport_database_crossref', $database_crossref);
save_setting($dbHandle, 'batchimport_failed', $failed);
save_setting($dbHandle, 'batchimport_log', $batchimport_log);
$dbHandle = null;
session_write_close();
include_once 'functions.php';
if (substr($_GET['directory'], -1) == DIRECTORY_SEPARATOR)
$_GET['directory'] = substr($_GET['directory'], 0, -1);
function list_dirs($directory) {
global $directories;
$dir_content = scandir($directory);
while (list($key, $value) = each($dir_content)) {
if (is_dir($directory . DIRECTORY_SEPARATOR . $value) && is_readable($directory . DIRECTORY_SEPARATOR . $value)
&& $value != '.' && $value != '..' && $value[0] != '.' && count($directories) < 2001) {
$directories[] = $directory . DIRECTORY_SEPARATOR . $value;
list_dirs($directory . DIRECTORY_SEPARATOR . $value);
}
}
return $directories;
}
$directories = array();
$files = array();
$directories[] = $_GET['directory'];
if ($_GET['recursive'] == 1)
$directories = list_dirs($_GET['directory']);
while (list($key, $directory) = each($directories)) {
$glob = glob($directory . DIRECTORY_SEPARATOR . '*.pdf');
$files = array_merge($files, $glob);
}
$stopwords = "a's, able, about, above, according, accordingly, across, actually, after, afterwards, again, against, ain't, all, allow, allows, almost, alone, along, already, also, although, always, am, among, amongst, an, and, another, any, anybody, anyhow, anyone, anything, anyway, anyways, anywhere, apart, appear, appreciate, appropriate, are, aren't, around, as, aside, ask, asking, associated, at, available, away, awfully, be, became, because, become, becomes, becoming, been, before, beforehand, behind, being, believe, below, beside, besides, best, better, between, beyond, both, brief, but, by, c'mon, c's, came, can, can't, cannot, cant, cause, causes, certain, certainly, changes, clearly, co, com, come, comes, concerning, consequently, consider, considering, contain, containing, contains, corresponding, could, couldn't, course, currently, definitely, described, despite, did, didn't, different, do, does, doesn't, doing, don't, done, down, downwards, during, each, edu, eg, eight, either, else, elsewhere, enough, entirely, especially, et, etc, even, ever, every, everybody, everyone, everything, everywhere, ex, exactly, example, except, far, few, fifth, figure, figures, first, five, followed, following, follows, for, former, formerly, forth, four, from, further, furthermore, get, gets, getting, given, gives, go, goes, going, gone, got, gotten, greetings, had, hadn't, happens, hardly, has, hasn't, have, haven't, having, he, he's, hello, help, hence, her, here, here's, hereafter, hereby, herein, hereupon, hers, herself, hi, him, himself, his, hither, hopefully, how, howbeit, however, i'd, i'll, i'm, i've, ie, if, ignored, immediate, in, inasmuch, inc, indeed, indicate, indicated, indicates, inner, insofar, instead, into, inward, is, isn't, it, it'd, it'll, it's, its, itself, just, keep, keeps, kept, know, knows, known, last, lately, later, latter, latterly, least, less, lest, let, let's, like, liked, likely, little, look, looking, looks, ltd, mainly, many, may, maybe, me, mean, meanwhile, merely, might, more, moreover, most, mostly, much, must, my, myself, name, namely, nd, near, nearly, necessary, need, needs, neither, never, nevertheless, new, next, nine, no, nobody, non, none, noone, nor, normally, not, nothing, novel, now, nowhere, obviously, of, off, often, oh, ok, okay, old, on, once, one, ones, only, onto, or, other, others, otherwise, ought, our, ours, ourselves, out, outside, over, overall, own, particular, particularly, per, perhaps, placed, please, plus, possible, presumably, probably, provides, que, quite, qv, rather, rd, re, really, reasonably, regarding, regardless, regards, relatively, respectively, right, said, same, saw, say, saying, says, second, secondly, see, seeing, seem, seemed, seeming, seems, seen, self, selves, sensible, sent, serious, seriously, seven, several, shall, she, should, shouldn't, since, six, so, some, somebody, somehow, someone, something, sometime, sometimes, somewhat, somewhere, soon, sorry, specified, specify, specifying, still, sub, such, sup, sure, t's, table, tables, take, taken, tell, tends, th, than, thank, thanks, thanx, that, that's, thats, the, their, theirs, them, themselves, then, thence, there, there's, thereafter, thereby, therefore, therein, theres, thereupon, these, they, they'd, they'll, they're, they've, think, third, this, thorough, thoroughly, those, though, three, through, throughout, thru, thus, to, together, too, took, toward, towards, tried, tries, truly, try, trying, twice, two, un, under, unfortunately, unless, unlikely, until, unto, up, upon, us, use, used, useful, uses, using, usually, value, various, very, via, viz, vs, want, wants, was, wasn't, way, we, we'd, we'll, we're, we've, welcome, well, went, were, weren't, what, what's, whatever, when, whence, whenever, where, where's, whereafter, whereas, whereby, wherein, whereupon, wherever, whether, which, while, whither, who, who's, whoever, whole, whom, whose, why, will, willing, wish, with, within, without, won't, wonder, would, would, wouldn't, yes, yet, you, you'd, you'll, you're, you've, your, yours, yourself, yourselves, zero";
$stopwords = explode(', ', $stopwords);
$patterns = join("\b/ui /\b", $stopwords);
$patterns = "/\b$patterns\b/ui";
$patterns = explode(" ", $patterns);
$order = array("\r\n", "\n", "\r");
$i = 0;
while (list($key, $file) = each($files)) {
$i = $i + 1;
if (is_readable($file)) {
$string = '';
$xml = '';
$record = '';
$count = '';
$url = '';
$authors = '';
$authors_array = array();
$affiliation = '';
$title = '';
$abstract = '';
$secondary_title = '';
$year = '';
$volume = '';
$issue = '';
$pages = '';
$last_page = '';
$journal = '';
$keywords = '';
$name_array = array();
$mesh_array = array();
$new_file = '';
$journal = '';
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$editor = '';
$reference_type = 'article';
$publisher = '';
$place_published = '';
$doi = '';
$authors_ascii = '';
$title_ascii = '';
$abstract_ascii = '';
$unpacked_files = array ();
if (file_exists($temp_dir . DIRECTORY_SEPARATOR . "librarian_temp" . $i . ".txt"))
unlink($temp_dir . DIRECTORY_SEPARATOR . "librarian_temp" . $i . ".txt");
########## extract text from pdf ##########
system(select_pdftotext() . '"' . $file . '" "' . $temp_dir . DIRECTORY_SEPARATOR . 'librarian_temp' . $i . '.txt"', $ret);
if (file_exists($temp_dir . DIRECTORY_SEPARATOR . "librarian_temp" . $i . ".txt"))
$string = file_get_contents($temp_dir . DIRECTORY_SEPARATOR . "librarian_temp" . $i . ".txt");
if (empty($string)) {
if (isset($_GET['failed']) && $_GET['failed'] == '1') {
database_connect($database_path, 'library');
record_unknown($dbHandle, $string, $database_path, $file, $userID);
$put = " ($i) " . basename($file) . ": Recorded into category !unknown. Full text not indexed (copying disallowed).<br>";
file_put_contents($log, $put, FILE_APPEND);
} else {
$put = " ($i) " . basename($file) . ": copying disallowed.<br>";
file_put_contents($log, $put, FILE_APPEND);
}
} else {
$string = preg_replace('/[^[\x09\x0A\x0D\x20-\x7E]|[\xC2-\xDF][\x80-\xBF]|\xE0[\xA0-\xBF][\x80-\xBF]|[\xE1-\xEC\xEE\xEF][\x80-\xBF]{2}|\xED[\x80-\x9F][\x80-\xBF]|\xF0[\x90-\xBF][\x80-\xBF]{2}|[\xF1-\xF3][\x80-\xBF]{3}|\xF4[\x80-\x8F][\x80-\xBF]{2}]/', ' ', $string);
$string = str_replace($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') {
$string = preg_replace($patterns, ' ', $string);
$string = preg_replace('/(^|\s)\S{1,2}(\s|$)/u', ' ', $string);
$string = preg_replace('/\s{2,}/u', " ", $string);
$fulltext_array = array();
$fulltext_unique = array();
$fulltext_array = explode(" ", $string);
$fulltext_unique = array_unique($fulltext_array);
$string = implode(" ", $fulltext_unique);
database_connect($database_path, 'library');
record_unknown($dbHandle, $string, $database_path, $file, $userID);
$put = " ($i) " . basename($file) . ": Recorded into category !unknown. DOI not found.<br>";
file_put_contents($log, $put, FILE_APPEND);
} else {
$put = " ($i) " . basename($file) . ": DOI not found.<br>";
file_put_contents($log, $put, FILE_APPEND);
}
} else {
$doi = $doi[0][0];
if (substr($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') {
$put = " ($i) " . basename($file) . ": Querying Pubmed with $doi <br>";
file_put_contents($log, $put, FILE_APPEND);
########## open esearch, fetch PMID ##########
$pmid = '';
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=Pubmed&term=" . $doi . "[AID]&usehistory=y&retstart=&retmax=1&sort=&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $_GET['proxy_name'], $_GET['proxy_port'], $_GET['proxy_username'], $_GET['proxy_password']);
if (empty($xml)) die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
$count = $xml->Count;
if ($count == 1)
$pmid = $xml->IdList->Id;
if (!empty($pmid)) {
########## open efetch, read xml ##########
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Pubmed&rettype=abstract&retmode=XML&id=" . $pmid . "&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $_GET['proxy_name'], $_GET['proxy_port'], $_GET['proxy_username'], $_GET['proxy_password']);
if (empty($xml)) die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
$uid = 'PMID:' . $pmid;
$url = "http://www.pubmed.org/$pmid";
$title = (string) $xml->PubmedArticle->MedlineCitation->Article->ArticleTitle;
$abstract_array = array();
$xml_abstract = $xml->PubmedArticle->MedlineCitation->Article->Abstract->AbstractText;
if (!empty($xml_abstract)) {
foreach ($xml_abstract as $mini_ab) {
foreach ($mini_ab->attributes() as $a => $b) {
if ($a == 'Label')
$mini_ab = $b . ": " . $mini_ab;
}
$abstract_array[] = "$mini_ab";
}
$abstract = implode(' ', $abstract_array);
}
$secondary_title = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->Title;
$day = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Day;
$month = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Month;
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year;
if (empty($year)) {
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->MedlineDate;
preg_match('/\d{4}/', $year, $year_match);
$year = $year_match[0];
}
if (!empty($year)) {
if (empty($day))
$day = '01';
if (empty($month))
$month = '01';
$year = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
}
$volume = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume;
$issue = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue;
$pages = (string) $xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn;
$journal = (string) $xml->PubmedArticle->MedlineCitation->MedlineJournalInfo->MedlineTA;
$affiliation = (string) $xml->PubmedArticle->MedlineCitation->Article->Affiliation;
$authors = $xml->PubmedArticle->MedlineCitation->Article->AuthorList->Author;
$name_array = array();
if (!empty($authors)) {
foreach ($authors as $author) {
$name_array[] = 'L:"' . $author->LastName . '",F:"' . $author->ForeName . '"';
}
}
if (isset($name_array))
$authors = join(";", $name_array);
$mesh = $xml->PubmedArticle->MedlineCitation->MeshHeadingList->MeshHeading;
if (!empty($mesh)) {
foreach ($mesh as $meshheading) {
$mesh_array[] = $meshheading->DescriptorName;
}
}
if (isset($mesh_array))
$keywords = join(" / ", $mesh_array);
}
}
if (isset($_GET['database_nasaads']) && $_GET['database_nasaads'] == '1' && empty($title)) {
$put = " ($i) " . basename($file) . ": Querying NASA ADS with $doi <br>";
file_put_contents($log, $put, FILE_APPEND);
############ NASA ADS ##############
$request_url = "http://adsabs.harvard.edu/cgi-bin/abs_connect?doi=" . $doi . "&data_type=XML&return_req=no_params&start_nr=1&nr_to_return=1";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
if (empty($xml)) die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
foreach ($xml->attributes() as $a => $b) {
if ($a == 'selected') {
$count = $b;
break;
}
}
if ($count == 1) {
$record = $xml->record;
$bibcode = (string) $record->bibcode;
$title = (string) $record->title;
$journal = (string) $record->journal;
if (strstr($journal, ","))
$secondary_title = substr($journal, 0, strpos($journal, ','));
$eprintid = (string) $record->eprintid;
if (!empty($eprintid))
$eprintid = substr($eprintid, strpos($eprintid, ":") + 1);
if (strstr($journal, "arXiv"))
$eprintid = substr($journal, strpos($journal, ":") + 1);
$volume = (string) $record->volume;
$pages = (string) $record->page;
$affiliation = $record->affiliation;
$year = (string) $record->pubdate;
$year = date('Y-m-d', strtotime($year));
$abstract = (string) $record->abstract;
$nasa_url = (string) $record->url;
foreach ($record->link as $links) {
foreach ($links->attributes() as $a => $b) {
if ($a == 'type' && $b == 'EJOURNAL') {
$ejournal_url = (string) $links->url;
} elseif ($a == 'type' && $b == 'PREPRINT') {
$preprint_url = (string) $links->url;
} elseif ($a == 'type' && $b == 'GIF') {
$gif_url = (string) $links->url;
}
}
}
$authors = $record->author;
$name_array = array();
if (!empty($authors)) {
foreach ($authors as $author) {
$author_array = explode (",", $author);
$name_array[] = 'L:"'.trim($author_array[0]).'",F:"'.trim($author_array[1]).'"';
}
}
if (isset($name_array))
$authors = join(";", $name_array);
$keywords = $record->keywords;
if (!empty($keywords)) {
foreach ($keywords as $keyword) {
$keywords_array[] = $keyword->keyword;
}
}
if (isset($keywords_array))
$keywords = join(" / ", $keywords_array);
$uid_array = array();
if (!empty($bibcode))
$uid_array[] = "NASAADS:$bibcode";
if (!empty($eprintid))
$uid_array[] = "ARXIV:$eprintid";
$uid = join("|", $uid_array);
$url_array = array();
$url_array[] = $nasa_url;
if (!empty($eprintid))
$url_array[] = "http://arxiv.org/abs/$eprintid";
$url = join("|", $url_array);
}
}
if (isset($_GET['database_crossref']) && $_GET['database_crossref'] == '1' && empty($title)) {
$put = " ($i) " . basename($file) . ": Querying CrossRef with $doi <br>";
file_put_contents($log, $put, FILE_APPEND);
############ CrossRef ##############
$request_url = "http://www.crossref.org/openurl/?id=doi:" . $doi . "&noredirect=true&pid=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
if (empty($xml)) die('Error! I, Librarian could not connect with an external web service. This usually indicates that you access the Web through a proxy server.
Enter your proxy details in Tools->Settings. Alternatively, the external service may be temporarily down. Try again later.');
$record = $xml->query_result->body->query;
$resolved = false;
foreach ($record->attributes() as $a => $b) {
if ($a == 'status' && $b == 'resolved') {
$resolved = true;
break;
}
}
if ($resolved) {
$secondary_title = (string) $record->journal_title;
$year = (string) $record->year;
$year = $year . '-01-01';
$volume = (string) $record->volume;
$pages = (string) $record->first_page;
$last_page = (string) $record->last_page;
if (!empty($last_page))
$pages = $pages . "-" . $last_page;
$title = (string) $record->article_title;
$authors = array ();
foreach ($record->contributors->contributor as $contributor) {
$authors1 = (string) $contributor->surname;
$authors2 = (string) $contributor->given_name;
$authors[] = 'L:"' . $authors1 . '",F:"' . $authors2 . '"';
}
$authors = join(";", $authors);
}
}
//TRY AGAIN WITH DOI ONE CHARACTER SHORTER
if (empty($title)) {
$doi = substr($doi, 0, -1);
if (isset($_GET['database_pubmed']) && $_GET['database_pubmed'] == '1') {
$put = " ($i) " . basename($file) . ": Querying PubMed again with $doi <br>";
file_put_contents($log, $put, FILE_APPEND);
########## open esearch, fetch PMID ##########
$pmid = '';
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=Pubmed&term=" . $doi . "[AID]&usehistory=y&retstart=&retmax=1&sort=&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $_GET['proxy_name'], $_GET['proxy_port'], $_GET['proxy_username'], $_GET['proxy_password']);
$count = $xml->Count;
if ($count == 1)
$pmid = $xml->IdList->Id;
if (!empty($pmid)) {
########## open efetch, read xml ##########
$request_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=Pubmed&rettype=abstract&retmode=XML&id=" . $pmid . "&tool=I,Librarian&email=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $_GET['proxy_name'], $_GET['proxy_port'], $_GET['proxy_username'], $_GET['proxy_password']);
$uid = 'PMID:' . $pmid;
$url = "http://www.pubmed.org/$pmid";
$title = (string) $xml->PubmedArticle->MedlineCitation->Article->ArticleTitle;
$abstract_array = array();
$xml_abstract = $xml->PubmedArticle->MedlineCitation->Article->Abstract->AbstractText;
if (!empty($xml_abstract)) {
foreach ($xml_abstract as $mini_ab) {
foreach ($mini_ab->attributes() as $a => $b) {
if ($a == 'Label')
$mini_ab = $b . ": " . $mini_ab;
}
$abstract_array[] = "$mini_ab";
}
$abstract = implode(' ', $abstract_array);
}
$secondary_title = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->Title;
$day = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Day;
$month = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Month;
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year;
if (empty($year)) {
$year = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->MedlineDate;
preg_match('/\d{4}/', $year, $year_match);
$year = $year_match[0];
}
if (!empty($year)) {
if (empty($day))
$day = '01';
if (empty($month))
$month = '01';
$year = date('Y-m-d', strtotime($day . '-' . $month . '-' . $year));
}
$volume = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume;
$issue = (string) $xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue;
$pages = (string) $xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn;
$journal = (string) $xml->PubmedArticle->MedlineCitation->MedlineJournalInfo->MedlineTA;
$affiliation = (string) $xml->PubmedArticle->MedlineCitation->Article->Affiliation;
$authors = $xml->PubmedArticle->MedlineCitation->Article->AuthorList->Author;
$name_array = array();
if (!empty($authors)) {
foreach ($authors as $author) {
$name_array[] = 'L:"' . $author->LastName . '",F:"' . $author->ForeName . '"';
}
}
if (isset($name_array))
$authors = join(";", $name_array);
$mesh = $xml->PubmedArticle->MedlineCitation->MeshHeadingList->MeshHeading;
if (!empty($mesh)) {
foreach ($mesh as $meshheading) {
$mesh_array[] = $meshheading->DescriptorName;
}
}
if (isset($mesh_array))
$keywords = join(" / ", $mesh_array);
}
}
if (isset($_GET['database_nasaads']) && $_GET['database_nasaads'] == '1' && empty($title)) {
$put = " ($i) " . basename($file) . ": Querying NASA ADS again with $doi <br>";
file_put_contents($log, $put, FILE_APPEND);
############ NASA ADS ##############
$request_url = "http://adsabs.harvard.edu/cgi-bin/abs_connect?doi=" . $doi . "&data_type=XML&return_req=no_params&start_nr=1&nr_to_return=1";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
foreach ($xml->attributes() as $a => $b) {
if ($a == 'selected') {
$count = $b;
break;
}
}
if ($count == 1) {
$record = $xml->record;
$bibcode = (string) $record->bibcode;
$title = (string) $record->title;
$journal = (string) $record->journal;
if (strstr($journal, ","))
$secondary_title = substr($journal, 0, strpos($journal, ','));
$eprintid = (string) $record->eprintid;
if (!empty($eprintid))
$eprintid = substr($eprintid, strpos($eprintid, ":") + 1);
if (strstr($journal, "arXiv"))
$eprintid = substr($journal, strpos($journal, ":") + 1);
$volume = (string) $record->volume;
$pages = (string) $record->page;
$affiliation = $record->affiliation;
$year = (string) $record->pubdate;
$year = date('Y-m-d', strtotime($year));
$abstract = (string) $record->abstract;
$nasa_url = (string) $record->url;
foreach ($record->link as $links) {
foreach ($links->attributes() as $a => $b) {
if ($a == 'type' && $b == 'EJOURNAL') {
$ejournal_url = (string) $links->url;
} elseif ($a == 'type' && $b == 'PREPRINT') {
$preprint_url = (string) $links->url;
} elseif ($a == 'type' && $b == 'GIF') {
$gif_url = (string) $links->url;
}
}
}
$authors = $record->author;
$name_array = array();
if (!empty($authors)) {
foreach ($authors as $author) {
$author_array = explode (",", $author);
$name_array[] = 'L:"'.trim($author_array[0]).'",F:"'.trim($author_array[1]).'"';
}
}
if (isset($name_array))
$authors = join(";", $name_array);
$keywords = $record->keywords;
if (!empty($keywords)) {
foreach ($keywords as $keyword) {
$keywords_array[] = $keyword->keyword;
}
}
if (isset($keywords_array))
$keywords = join(" / ", $keywords_array);
$uid_array = array();
if (!empty($bibcode))
$uid_array[] = "NASAADS:$bibcode";
if (!empty($eprintid))
$uid_array[] = "ARXIV:$eprintid";
$uid = join("|", $uid_array);
$url_array = array();
$url_array[] = $nasa_url;
if (!empty($eprintid))
$url_array[] = "http://arxiv.org/abs/$eprintid";
$url = join("|", $url_array);
}
}
if (isset($_GET['database_crossref']) && $_GET['database_crossref'] == '1' && empty($title)) {
$put = " ($i) " . basename($file) . ": Querying CrossRef again with $doi<br>";
file_put_contents($log, $put, FILE_APPEND);
############ CrossRef ##############
$request_url = "http://www.crossref.org/openurl/?id=doi:" . $doi . "&noredirect=true&pid=i.librarian.software@gmail.com";
$xml = proxy_simplexml_load_file($request_url, $proxy_name, $proxy_port, $proxy_username, $proxy_password);
$record = $xml->query_result->body->query;
$resolved = false;