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import.php
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<?php
include_once 'data.php';
ini_set('max_execution_time', 1800);
if (isset($_SESSION['auth']) && ($_SESSION['permissions'] == 'A' || $_SESSION['permissions'] == 'U')) {
include_once 'functions.php';
if (isset($_POST['form_sent']) && !isset($_FILES['form_import_file']) && empty($_POST['form_import_textarea']))
die();
if (isset($_POST['form_sent']) && isset($_POST['file_type']) && (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name']) || !empty($_POST['form_import_textarea']))) {
function trim_value(&$value) {
$value = trim($value);
}
$user_id = $_SESSION['user_id'];
session_write_close();
$record_count = 0;
$duplicate_count = 0;
$pdf_count = 0;
$ids = array();
$dbname = uniqid() . '-temp.sq3';
$fdbname = uniqid() . '-ftemp.sq3';
$dbHandle = new PDO('sqlite:' . $database_path . $dbname);
$fdbHandle = new PDO('sqlite:' . $database_path . $fdbname);
$dbHandle->beginTransaction();
$create = $dbHandle->exec("CREATE TABLE library (
id integer PRIMARY KEY,
file text NOT NULL DEFAULT '',
authors text NOT NULL DEFAULT '',
affiliation text NOT NULL DEFAULT '',
title text NOT NULL DEFAULT '',
journal text NOT NULL DEFAULT '',
secondary_title text NOT NULL DEFAULT '',
year text NOT NULL DEFAULT '',
volume text NOT NULL DEFAULT '',
issue text NOT NULL DEFAULT '',
pages text NOT NULL DEFAULT '',
abstract text NOT NULL DEFAULT '',
keywords text NOT NULL DEFAULT '',
editor text NOT NULL DEFAULT '',
publisher text NOT NULL DEFAULT '',
place_published text NOT NULL DEFAULT '',
reference_type text NOT NULL DEFAULT '',
uid text NOT NULL DEFAULT '',
doi text NOT NULL DEFAULT '',
url text NOT NULL DEFAULT '',
addition_date text NOT NULL DEFAULT '',
rating integer NOT NULL DEFAULT '',
authors_ascii text NOT NULL DEFAULT '',
title_ascii text NOT NULL DEFAULT '',
abstract_ascii text NOT NULL DEFAULT '',
added_by integer NOT NULL DEFAULT '',
modified_by integer NOT NULL DEFAULT '',
modified_date text NOT NULL DEFAULT '',
custom1 text NOT NULL DEFAULT '',
custom2 text NOT NULL DEFAULT '',
custom3 text NOT NULL DEFAULT '',
custom4 text NOT NULL DEFAULT '',
bibtex text NOT NULL DEFAULT ''
)");
$create = null;
$create = $dbHandle->exec("CREATE TABLE notes (
notesID integer PRIMARY KEY,
userID integer NOT NULL,
fileID integer NOT NULL,
notes text NOT NULL DEFAULT ''
)");
$create = null;
$dbHandle->commit();
$create = $fdbHandle->exec("CREATE TABLE full_text (
id integer PRIMARY KEY,
fileID text NOT NULL DEFAULT '',
full_text text NOT NULL DEFAULT ''
)");
$create = null;
$query = "INSERT INTO library (file, authors, affiliation, title, journal, year, addition_date, abstract, rating, uid, volume, issue, pages, secondary_title, editor,
url, reference_type, publisher, place_published, keywords, doi, authors_ascii, title_ascii, abstract_ascii, added_by, bibtex)
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, :editor,
:url, :reference_type, :publisher, :place_published, :keywords, :doi, :authors_ascii, :title_ascii, :abstract_ascii, :added_by, :bibtex)";
$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, 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(':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', $added_by, PDO::PARAM_INT);
$stmt->bindParam(':bibtex', $bibtex, PDO::PARAM_STR);
$query = "INSERT INTO notes (userID, fileID, notes) VALUES (:userID, :fileID, :notes)";
$stmt2 = $dbHandle->prepare($query);
$stmt2->bindParam(':userID', $user_id, PDO::PARAM_INT);
$stmt2->bindParam(':fileID', $last_id, PDO::PARAM_INT);
$stmt2->bindParam(':notes', $notes, PDO::PARAM_STR);
if ($_POST['file_type'] == "endnote") {
if (is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
try {
if (!$xml = @simplexml_load_file($_FILES['form_import_file']['tmp_name'])) {
throw new Exception('Not a valid XML file.');
}
} catch (Exception $e) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
print "Error! " . $e->getMessage();
die();
}
} elseif (!empty($_POST['form_import_textarea'])) {
try {
if (!$xml = @simplexml_load_string($_POST['form_import_textarea'])) {
throw new Exception('Not a valid XML.');
}
} catch (Exception $e) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
print "Error! " . $e->getMessage();
die();
}
}
$records = $xml->records->record;
$record_count = count($records);
$dbHandle->beginTransaction();
foreach ($records as $record) {
$authors = '';
$authors_ascii = '';
$authors_obj = $record->contributors->authors->author;
if (!empty($authors_obj)) {
$authors2 = array();
foreach ($authors_obj as $author) {
$author = strip_tags($author->asXML());
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$authors2[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $authors2);
$authors_ascii = utf8_deaccent($authors);
}
$affiliation = '';
$affiliation_obj = $record->{'auth-address'};
if (!empty($affiliation_obj))
$affiliation = strip_tags($affiliation_obj->asXML());
$title = '';
$title_obj = $record->titles->title;
if (!empty($title_obj))
$title = strip_tags($title_obj->asXML());
if (empty($title))
$title = 'No title.';
$title_ascii = utf8_deaccent($title);
$journal = '';
$journal_obj = $record->titles->{'secondary-title'};
if (!empty($journal_obj))
$journal = strip_tags($journal_obj->asXML());
$journal = str_replace(".", "", strip_tags($journal));
$year = '';
$year_obj = $record->dates->year;
if (!empty($year_obj))
$year = strip_tags($year_obj->asXML());
$addition_date = date('Y-m-d');
$abstract = '';
$abstract_obj = $record->abstract;
if (!empty($abstract_obj))
$abstract = strip_tags($abstract_obj->asXML());
$abstract_ascii = utf8_deaccent($abstract);
$rating = 2;
$uid = '';
$doi = '';
$uid_obj = $record->{'accession-num'};
if (!empty($uid_obj)) {
$uid = strip_tags($uid_obj->asXML());
if (preg_match('/10\.\d{4}\/\S+/ui', $uid) == 1) {
$doi = $uid;
$uid = '';
}
}
$volume = '';
$volume_obj = $record->volume;
if (!empty($volume_obj)) $volume = strip_tags($volume_obj->asXML());
$issue = '';
$issue_obj = $record->number;
if (!empty($issue_obj)) $issue = strip_tags($issue_obj->asXML());
$pages = '';
$pages_obj = $record->pages;
if (!empty($pages_obj)) $pages = strip_tags($pages_obj->asXML());
$secondary_title = '';
$editor = '';
$reference_type = 'article';
foreach ($record->{'ref-type'}->attributes() as $a => $b) {
if ($a == 'name') {
$reference_type = convert_type($b, 'endnote', 'ilib');
break;
}
}
$publisher = '';
$place_published = '';
$keywords = '';
$keywords2 = array();
$keywords_obj = $record->keywords;
if (!empty($keywords_obj)) {
foreach ($keywords_obj->keyword as $keyword) {
if (!empty($keyword)) {
$keyword = strip_tags($keyword->asXML());
$keywords2[] = preg_replace('/\[|\]|\||\"|\/|\*/', ' ', $keyword);
}
}
$keywords = join(" / ", $keywords2);
}
$bibtex = '';
$url = '';
$urls = '';
$urls2 = array();
$urls_obj = $record->urls->{'related-urls'}->url;
if (!empty($urls_obj)) {
foreach ($urls_obj as $url) {
if (!empty($url)) {
$url = strip_tags($url->asXML());
$urls2[] = $url;
} else {
$urls2[] = '';
}
}
$url = join("|", $urls2);
}
$added_by = $user_id;
foreach ($record->database->attributes() as $a => $b) {
if ($a == 'path') {
$pdf_path1 = dirname($b) . DIRECTORY_SEPARATOR . basename($record->database, ".enl") . ".Data" . DIRECTORY_SEPARATOR;
break;
}
}
$pdf_path2 = $record->urls->{'pdf-urls'}->url;
$file_to_copy = '';
if (!empty($pdf_path2)) {
if (strstr($pdf_path2, "internal-pdf"))
$pdf_path = $pdf_path1 . 'PDF' . DIRECTORY_SEPARATOR . substr($pdf_path2, 15);
if (strstr($pdf_path2, "file:"))
$pdf_path = substr($pdf_path2, 7);
$file_to_copy = strtr($pdf_path, "/", DIRECTORY_SEPARATOR);
}
if (!empty($title))
$insert = $stmt->execute();
$result = $dbHandle->query("SELECT last_insert_rowid() FROM library");
$last_id = $result->fetchColumn();
$ids[] = $last_id;
$result = null;
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('No records found.');
}
if (is_file($file_to_copy) && is_readable($file_to_copy)) {
$result = $dbHandle->query("SELECT file FROM library WHERE id=" . $last_id);
$pdf_filename = $result->fetchColumn();
$pdf_filename = 'temp-' . $pdf_filename;
$result = null;
copy($file_to_copy, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'library' . DIRECTORY_SEPARATOR . $pdf_filename);
system(select_pdftotext() . '"' . $file_to_copy . '" "' . $temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . '.txt"');
if (is_file($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt")) {
$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, 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, 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);
$string = file_get_contents($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
unlink($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
if (!empty($string)) {
$patterns = join("\b/ui /\b", $stopwords);
$patterns = "/\b$patterns\b/ui";
$patterns = explode(" ", $patterns);
$order = array("\r\n", "\n", "\r");
$string = str_replace($order, ' ', $string);
$string = preg_replace($patterns, '', $string);
$string = preg_replace('/\s{2,}/ui', ' ', $string);
$fulltext_array = array();
$fulltext_unique = array();
$fulltext_array = explode(" ", $string);
$fulltext_unique = array_unique($fulltext_array);
$string = implode(" ", $fulltext_unique);
$fulltext_query = $fdbHandle->quote($string);
$fdbHandle->exec("INSERT INTO full_text (fileID,full_text) VALUES (" . $last_id . ",$fulltext_query)");
}
}
}
}
$dbHandle->commit();
$insert = null;
$stmt = null;
}
if ($_POST['file_type'] == "RIS") {
if (is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode('ER -', $file_contents);
array_walk($file_records, 'trim');
$file_records = array_filter($file_records);
$record_count = count($file_records) - 1;
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$bibtex = '';
$affiliation = '';
$added_by = $user_id;
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
$title = preg_match("/(?<=T1 - |TI - ).+/u", $record, $title_match);
if ($title == 1) {
$record_array = explode("\n", $record);
$type_match = array();
$journal_match = array();
$secondary_title_match = array();
$volume_match = array();
$issue_match = array();
$year_match = array();
$start_page_match = array();
$end_page_match = array();
$publisher_match = array();
$place_published_match = array();
$url_match = array();
$keywords_match = array();
$editors_match = array();
$authors_match = array();
$file_to_copy_match = array();
$doi_match = array();
$notes_match = array();
foreach ($record_array as $line) {
if (strpos($line, "TY") === 0)
$type_match[0] = trim(substr($line, 6));
if (strpos($line, "JA") === 0 || strpos($line, "J2") === 0)
$journal_match[0] = trim(substr($line, 6));
if (strpos($line, "JF") === 0 || strpos($line, "JO") === 0 || strpos($line, "T2") === 0)
$secondary_title_match[0] = trim(substr($line, 6));
if (strpos($line, "VL") === 0)
$volume_match[0] = trim(substr($line, 6));
if (strpos($line, "IS") === 0)
$issue_match[0] = trim(substr($line, 6));
if (strpos($line, "PY") === 0 || strpos($line, "Y1") === 0)
$year_match[0] = trim(substr($line, 6));
if (strpos($line, "SP") === 0)
$start_page_match[0] = trim(substr($line, 6));
if (strpos($line, "EP") === 0)
$end_page_match[0] = trim(substr($line, 6));
if (strpos($line, "PB") === 0)
$publisher_match[0] = trim(substr($line, 6));
if (strpos($line, "CY") === 0)
$place_published_match[0] = trim(substr($line, 6));
if (strpos($line, "UR") === 0)
$url_match[0][] = trim(substr($line, 6));
if (strpos($line, "KW") === 0)
$keywords_match[0][] = trim(substr($line, 6));
if (strpos($line, "ED") === 0 || strpos($line, "A2") === 0)
$editors_match[0][] = trim(substr($line, 6));
if (strpos($line, "AU") === 0 || strpos($line, "A1") === 0)
$authors_match[0][] = trim(substr($line, 6));
if (strpos($line, "L1") === 0)
$file_to_copy_match[0] = trim(substr($line, 6));
if (strpos($line, "DO") === 0)
$doi_match[0] = trim(substr($line, 6));
if (strpos($line, "N1") === 0)
$notes_match[0][] = trim(substr($line, 6));
}
preg_match("/(?<=AB - \n|AB - |AB - \r\n|N2 - \n|N2 - |N2 - \r\n).+/u", $record, $abstract_match);
preg_match("/(?<=N1 - doi:|M3 - doi: DOI:).+|(10\.\d{4}\/\S+)/u", $record, $doi_match);
$authors = '';
$authors_ascii = '';
if (!empty($authors_match[0])) {
$name_array = array();
foreach ($authors_match[0] as $author) {
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$name_array[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $name_array);
$authors_ascii = utf8_deaccent($authors);
}
$title = '';
$title_ascii = '';
if (!empty($title_match[0])) {
$title = trim($title_match[0]);
$title_ascii = utf8_deaccent($title);
}
$journal = '';
if (!empty($journal_match[0]))
$journal = trim(str_replace(".", "", $journal_match[0]));
$year = '';
if (!empty($year_match[0])) {
$year = intval(substr($year_match[0], 0, 4));
if ($year == 0) {
preg_match('/\d{4}/u', $year_match[0], $year_match2);
if (!empty($year_match2[0]))
$year = $year_match2[0];
}
}
$abstract = '';
$abstract_ascii = '';
if (!empty($abstract_match[0])) {
$abstract = trim($abstract_match[0]);
$abstract_ascii = utf8_deaccent($abstract);
}
$volume = '';
if (!empty($volume_match[0]))
$volume = trim($volume_match[0]);
$issue = '';
if (!empty($issue_match[0]))
$issue = trim($issue_match[0]);
$pages = '';
if (!empty($start_page_match[0]))
$pages = trim($start_page_match[0]);
if (!empty($end_page_match[0]))
$pages .= '-' . trim($end_page_match[0]);
$secondary_title = '';
if (!empty($secondary_title_match[0]))
$secondary_title = trim($secondary_title_match[0]);
$url = '';
if (!empty($url_match[0])) {
array_walk($url_match[0], 'trim_value');
$url = join('|', $url_match[0]);
}
$publisher = '';
if (!empty($publisher_match[0]))
$publisher = trim($publisher_match[0]);
$place_published = '';
if (!empty($place_published_match[0]))
$publisher = trim($place_published_match[0]);
$editor = '';
if (!empty($editors_match[0])) {
$order = array("\r\n", "\n", "\r");
$editors_match[0] = str_replace($order, ' ', $editors_match[0]);
$editors_match[0] = join("#", $editors_match[0]);
$patterns = array(',', '.', '#', ' ');
$replacements = array(' ', '', ', ', ' ');
$editor = str_replace($patterns, $replacements, $editors_match[0]);
}
$reference_type = 'article';
if (!empty($type_match[0]))
$reference_type = convert_type(trim($type_match[0]), 'ris', 'ilib');
$keywords = '';
if (!empty($keywords_match[0])) {
$order = array("\r\n", "\n", "\r");
$keywords_match[0] = str_replace($order, ' ', $keywords_match[0]);
$patterns = array('[', ']', '|', '"', '/', '*');
$keywords_match[0] = str_replace($patterns, ' ', $keywords_match[0]);
array_walk($keywords_match[0], 'trim_value');
$keywords_match[0] = join("#", $keywords_match[0]);
$keywords = str_replace("#", " / ", $keywords_match[0]);
}
$doi = '';
if (!empty($doi_match[0]))
$doi = trim($doi_match[0]);
$notes = '';
if (!empty($notes_match[0])) {
$notes = join(' ', $notes_match[0]);
}
$file_to_copy = '';
if (isset($file_to_copy_match[0]))
$file_to_copy = $file_to_copy_match[0];
if (strpos($file_to_copy, "file://") === 0)
$file_to_copy = preg_replace('/(file:\/\/.*\/)(.*)/Ui', "$2", $file_to_copy);
if (substr(strtoupper(PHP_OS), 0, 3) != 'WIN')
$file_to_copy = '/' . $file_to_copy;
if (!empty($title))
$insert = $stmt->execute();
$result = $dbHandle->query("SELECT last_insert_rowid() FROM library");
$last_id = $result->fetchColumn();
$ids[] = $last_id;
$result = null;
$insert = null;
if (!empty($notes)) {
$user_id = $_SESSION['user_id'];
$insert = $stmt2->execute();
$insert = null;
}
if (is_file($file_to_copy) && is_readable($file_to_copy)) {
$result = $dbHandle->query("SELECT file FROM library WHERE id=" . $last_id);
$pdf_filename = $result->fetchColumn();
$pdf_filename = 'temp-' . $pdf_filename;
$result = null;
copy($file_to_copy, dirname(__FILE__) . DIRECTORY_SEPARATOR . 'library' . DIRECTORY_SEPARATOR . $pdf_filename);
system(select_pdftotext() . '"' . $file_to_copy . '" "' . $temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . '.txt"');
if (is_file($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt")) {
$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, 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, 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);
$string = file_get_contents($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
unlink($temp_dir . DIRECTORY_SEPARATOR . $pdf_filename . ".txt");
if (!empty($string)) {
$patterns = join("\b/ui /\b", $stopwords);
$patterns = "/\b$patterns\b/ui";
$patterns = explode(" ", $patterns);
$order = array("\r\n", "\n", "\r");
$string = str_replace($order, ' ', $string);
$string = preg_replace($patterns, '', $string);
$string = preg_replace('/\s{2,}/ui', ' ', $string);
$fulltext_array = array();
$fulltext_unique = array();
$fulltext_array = explode(" ", $string);
$fulltext_unique = array_unique($fulltext_array);
$string = implode(" ", $fulltext_unique);
$fulltext_query = $fdbHandle->quote($string);
$fdbHandle->exec("INSERT INTO full_text (fileID,full_text) VALUES (" . $last_id . ",$fulltext_query)");
}
}
}
}
}
$dbHandle->commit();
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('No records found.');
}
$insert = null;
$stmt = null;
$stmt2 = null;
}
}
if ($_POST['file_type'] == "isi") {
if (is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode("\nER\n", $file_contents);
$record_count = count($file_records) - 1;
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
$record = str_replace("\n ", "{#}", $record);
if (!empty($record) && !ctype_cntrl($record) && strstr($record, "TI ")) {
preg_match("/(?<=TI ).+/u", $record, $title_match);
preg_match("/(?<=SO ).+/u", $record, $secondary_title_match);
preg_match("/(?<=VL ).+/u", $record, $volume_match);
preg_match("/(?<=IS ).+/u", $record, $issue_match);
preg_match("/(?<=PY ).+/u", $record, $year_match);
preg_match("/(?<=BP ).+/u", $record, $start_page_match);
preg_match("/(?<=EP ).+/u", $record, $end_page_match);
preg_match("/(?<=AB ).+/u", $record, $abstract_match);
preg_match("/(?<=AU ).+/u", $record, $authors_match);
preg_match("/(?<=DI ).+/u", $record, $doi_match);
preg_match("/(?<=ID ).+/u", $record, $keywords_match);
preg_match("/(?<=JI ).+/u", $record, $journal_match);
$authors = '';
$authors_ascii = '';
$name_array = array();
if (!empty($authors_match[0])) {
$name_array = array();
$authors_match[0] = explode("{#}", $authors_match[0]);
foreach ($authors_match[0] as $author) {
$author_array = explode(",", $author);
$first_name = '';
if (isset($author_array[1]))
$first_name = $author_array[1];
$name_array[] = 'L:"' . trim($author_array[0]) . '",F:"' . trim($first_name) . '"';
}
$authors = join(";", $name_array);
$authors_ascii = utf8_deaccent($authors);
}
$affiliation = '';
$title = '';
$title_ascii = '';
if (!empty($title_match[0])) {
$title = trim($title_match[0]);
$title = str_replace("{#}", " ", $title);
$title_ascii = utf8_deaccent($title);
}
$journal = '';
if (!empty($journal_match[0]))
$journal = trim(str_replace(".", "", $journal_match[0]));
$year = '';
if (!empty($year_match[0]))
$year = intval(substr($year_match[0], 0, 4));
$addition_date = date('Y-m-d');
$abstract = '';
$abstract_ascii = '';
if (!empty($abstract_match[0])) {
$abstract = trim($abstract_match[0]);
$abstract = str_replace("{#}", " ", $abstract);
$abstract_ascii = utf8_deaccent($abstract);
}
$rating = 2;
$uid = '';
$bibtex = '';
$volume = '';
if (!empty($volume_match[0]))
$volume = trim($volume_match[0]);
$issue = '';
if (!empty($issue_match[0]))
$issue = trim($issue_match[0]);
$pages = '';
if (!empty($start_page_match[0]))
$pages = trim($start_page_match[0]);
if (!empty($end_page_match[0]))
$pages .= '-' . trim($end_page_match[0]);
$secondary_title = '';
if (!empty($secondary_title_match[0])) {
$secondary_title = str_replace("{#}", " ", $secondary_title_match[0]);
$secondary_title = ucfirst(strtolower(trim($secondary_title)));
}
$editor = '';
$reference_type = 'article';
$publisher = '';
$place_published = '';
$url = '';
$keywords = '';
if (!empty($keywords_match[0])) {
$keywords = str_replace("{#}", " ", $keywords_match[0]);
$keywords = preg_replace('/\[|\]|\||\"|\/|\*/u', ' ', $keywords);
$keywords = str_replace("; ", " / ", $keywords);
$keywords = ucwords(strtolower($keywords));
}
$doi = '';
if (!empty($doi_match[0]))
$doi = trim($doi_match[0]);
$added_by = $user_id;
if (!empty($title))
$insert = $stmt->execute();
$last_id = $dbHandle->query("SELECT last_insert_rowid() FROM library");
$ids[] = $last_id->fetchColumn();
$last_id = null;
}
}
$dbHandle->commit();
$item_count = count($ids);
if (!isset($ids) || count($ids) == 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('No records found.');
}
$insert = null;
$stmt = null;
}
}
if ($_POST['file_type'] == "bibtex") {
if (isset($_FILES['form_import_file']) && is_uploaded_file($_FILES['form_import_file']['tmp_name'])) {
$file_contents = file_get_contents($_FILES['form_import_file']['tmp_name']);
if (strpos($file_contents, "%PDF") === 0) {
$stmt = null;
$dbHandle = null;
$fdbHandle = null;
unlink($database_path . $dbname);
unlink($database_path . $fdbname);
die('Error! PDF files cannot be parsed. Please upload one of the indicated file types.');
}
} elseif (!empty($_POST['form_import_textarea'])) {
$file_contents = $_POST['form_import_textarea'];
}
if (!empty($file_contents)) {
$tempfilename = tempnam($temp_dir, "lib");
file_put_contents($tempfilename, $file_contents);
exec(select_bibutil("bib2xml") . " -i unicode $tempfilename > $tempfilename.xml");
exec(select_bibutil("xml2ris") . " -o unicode -nb $tempfilename.xml > $tempfilename.xml.ris");
$file_contents = file_get_contents($tempfilename . ".xml.ris");
unlink($tempfilename);
unlink($tempfilename . '.xml');
unlink($tempfilename . '.xml.ris');
####### sniff UTF-8 encoding ###########
$isutf = '';
$isutf = preg_match('/^.{1}/us', $file_contents);
if ($isutf != 1)
$file_contents = utf8_encode($file_contents);
$file_records = explode('ER -', $file_contents);
array_walk($file_records, 'trim');
$file_records = array_filter($file_records);
$record_count = count($file_records) - 1;
$dbHandle->beginTransaction();
foreach ($file_records as $record) {
$title = preg_match("/(?<=T1 - |TI - ).+/u", $record, $title_match);
if ($title == 1) {
$addition_date = date('Y-m-d');
$rating = 2;
$uid = '';
$affiliation = '';
$added_by = $user_id;
$record_array = explode("\n", $record);
$type_match = array();
$journal_match = array();
$secondary_title_match = array();
$volume_match = array();
$issue_match = array();
$year_match = array();
$start_page_match = array();
$end_page_match = array();
$publisher_match = array();
$place_published_match = array();
$url_match = array();
$keywords_match = array();
$editors_match = array();
$authors_match = array();
$bibtex_match = array();
$abstract_match = array();
$doi_match = array();
$file_to_copy_match = array();
foreach ($record_array as $line) {
if (strpos($line, "TY") === 0)
$type_match[0] = trim(substr($line, 6));
if (strpos($line, "JA") === 0)
$journal_match[0] = substr($line, 6);
if (strpos($line, "JF") === 0 || strpos($line, "JO") === 0)
$secondary_title_match[0] = substr($line, 6);
if (strpos($line, "VL") === 0)
$volume_match[0] = substr($line, 6);
if (strpos($line, "IS") === 0)
$issue_match[0] = substr($line, 6);
if (strpos($line, "PY") === 0 || strpos($line, "Y1") === 0)
$year_match[0] = substr($line, 6);
if (strpos($line, "SP") === 0)
$start_page_match[0] = substr($line, 6);
if (strpos($line, "EP") === 0)