<?php

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($_POST['proxystr'])) {

$proxy_arr = explode(';', $_POST['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'];

}

$user_id = intval($_SESSION['user_id']);

session_write_close();

include_once 'functions.php';

$error = array();

$message = array();

########## let user know when the file is bigger than the directives allow ##########

$directives = ' Your current settings in php.ini are:';

$directives .= '<br>upload_max_filesize: ' . ini_get('upload_max_filesize');

$directives .= '<br>post_max_size: ' . ini_get('post_max_size');

if (isset($_FILES['form_new_file']['error']) && $_FILES['form_new_file']['error'] > 0) {

if ($_FILES['form_new_file']['error'] == 1)

$error[] = "Error! The uploaded file size exceeds the <b>upload_max_filesize</b> directive in php.ini.$directives";

if ($_FILES['form_new_file']['error'] == 3)

$error[] = "Error! The uploaded file was only partially uploaded.";

if ($_FILES['form_new_file']['error'] == 6)

$error[] = "Error! Missing a temporary folder.";

if ($_FILES['form_new_file']['error'] == 7)

$error[] = "Error! Failed to write file to disk.";

if ($_FILES['form_new_file']['error'] == 8)

$error[] = "Error! File upload stopped by extension.";

}

if (isset($_FILES['form_supplementary_file']['error']) && $_FILES['form_supplementary_file']['error'] > 0) {

if ($_FILES['form_supplementary_file']['error'] == 1)

$error[] = "Error! The uploaded file size exceeds the <b>upload_max_filesize</b> directive in php.ini.$directives";

if ($_FILES['form_supplementary_file']['error'] == 3)

$error[] = "Error! The uploaded file was only partially uploaded.";

if ($_FILES['form_supplementary_file']['error'] == 6)

$error[] = "Error! Missing a temporary folder.";

if ($_FILES['form_supplementary_file']['error'] == 7)

$error[] = "Error! Failed to write file to disk.";

if ($_FILES['form_supplementary_file']['error'] == 8)

$error[] = "Error! File upload stopped by extension.";

}

########## clean temp directory ##########

$temp_files = glob(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_*.pdf', GLOB_NOSORT);

if (is_array($temp_files)) {

foreach ($temp_files as $temp_file) {

if (time() - filemtime($temp_file) > 3600)

@unlink($temp_file);

}

}

$temp_pngs = glob(IL_IMAGE_PATH . DIRECTORY_SEPARATOR . 'lib_*.jpg', GLOB_NOSORT);

if (is_array($temp_pngs)) {

foreach ($temp_pngs as $temp_png) {

if (time() - filemtime($temp_png) > 3600)

@unlink($temp_png);

}

}

if (isset($_POST['form_sent'])) {

if (isset($_POST['uid']))

$_POST['uid'] = array_filter($_POST['uid']);

if (isset($_POST['url']))

$_POST['url'] = array_filter($_POST['url']);

}

########## reference recording ##########

if (!empty($_POST['title']) && isset($_POST['form_sent'])) {

########## remove line breaks from certain POST values ##########

$order = array("\r\n", "\n", "\r");

$keys = array('affiliation', 'title', 'abstract', 'keywords');

while (list($key, $field) = each($keys)) {

if (!empty($_POST[$field])) {

$_POST[$field] = str_replace($order, ' ', $_POST[$field]);

}

}

########## record publication data, table library ##########

database_connect(IL_DATABASE_PATH, '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, custom1, custom2, custom3, custom4, bibtex, bibtex_type)

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, :custom1, :custom2, :custom3, :custom4, :bibtex, :bibtex_type)";

$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(':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', $added_by, PDO::PARAM_INT);

$stmt->bindParam(':custom1', $custom1, PDO::PARAM_STR);

$stmt->bindParam(':custom2', $custom2, PDO::PARAM_STR);

$stmt->bindParam(':custom3', $custom3, PDO::PARAM_STR);

$stmt->bindParam(':custom4', $custom4, PDO::PARAM_STR);

$stmt->bindParam(':bibtex', $bibtex, PDO::PARAM_STR);

$stmt->bindParam(':bibtex_type', $bibtex_type, PDO::PARAM_STR);

if (empty($_POST['authors']) && empty($_POST['last_name'])) {

$authors = '';

$authors_ascii = '';

} elseif (!empty($_POST['authors'])) {

$authors = htmlspecialchars_decode($_POST['authors']);

$authors_ascii = utf8_deaccent($authors);

} elseif (!empty($_POST['last_name'])) {

if (!empty($_POST['last_name']) && is_string($_POST['last_name'])) {

$_POST['last_name'] = json_decode($_POST['last_name'], true);

}

if (!empty($_POST['first_name']) && is_string($_POST['first_name'])) {

$_POST['first_name'] = json_decode($_POST['first_name'], true);

}

$names = array();

for ($i = 0; $i < count($_POST['last_name']); $i++) {

if (!empty($_POST['last_name'][$i])) {

// Get last and first name, deaccent.

$names[] = 'L:"' . $_POST['last_name'][$i] . '",F:"' . $_POST['first_name'][$i] . '"';

}

}

$authors = join(';', $names);

$authors_ascii = utf8_deaccent($authors);

}

empty($_POST['affiliation']) ? $affiliation = '' : $affiliation = $_POST['affiliation'];

$title = $_POST['title'];

$title_ascii = utf8_deaccent($title);

empty($_POST['journal_abbr']) ? $journal = '' : $journal = $_POST['journal_abbr'];

empty($_POST['secondary_title']) ? $secondary_title = '' : $secondary_title = $_POST['secondary_title'];

empty($_POST['tertiary_title']) ? $tertiary_title = '' : $tertiary_title = $_POST['tertiary_title'];

empty($_POST['year']) ? $year = '' : $year = $_POST['year'];

$addition_date = date('Y-m-d');

if (empty($_POST['abstract'])) {

$abstract = '';

$abstract_ascii = '';

} else {

$abstract = $_POST['abstract'];

$abstract_ascii = utf8_deaccent($abstract);

}

empty($_POST['rating']) ? $rating = '2' : $rating = $_POST['rating'];

empty($_POST['uid'][0]) ? $uid = '' : $uid = join('|', array_filter($_POST['uid']));

empty($_POST['volume']) ? $volume = '' : $volume = $_POST['volume'];

empty($_POST['issue']) ? $issue = '' : $issue = $_POST['issue'];

empty($_POST['pages']) ? $pages = '' : $pages = $_POST['pages'];

empty($_POST['editor']) ? $editor = '' : $editor = htmlspecialchars_decode($_POST['editor']);

empty($_POST['url'][0]) ? $url = '' : $url = join('|', array_filter($_POST['url']));

empty($_POST['reference_type']) ? $reference_type = 'article' : $reference_type = $_POST['reference_type'];

empty($_POST['publisher']) ? $publisher = '' : $publisher = $_POST['publisher'];

empty($_POST['place_published']) ? $place_published = '' : $place_published = $_POST['place_published'];

if (empty($_POST['keywords'])) {

$keywords = '';

} else {

$keywords = $_POST['keywords'];

empty($_POST['keyword_separator']) ? $keyword_separator = '/' : $keyword_separator = $_POST['keyword_separator'];

$keyword_array = explode($keyword_separator, $keywords);

function trim_value(&$value) {

$value = trim($value);

}

array_walk($keyword_array, 'trim_value');

$keywords = implode(' / ', $keyword_array);

}

empty($_POST['doi']) ? $doi = '' : $doi = $_POST['doi'];

empty($_POST['custom1']) ? $custom1 = '' : $custom1 = $_POST['custom1'];

empty($_POST['custom2']) ? $custom2 = '' : $custom2 = $_POST['custom2'];

empty($_POST['custom3']) ? $custom3 = '' : $custom3 = $_POST['custom3'];

empty($_POST['custom4']) ? $custom4 = '' : $custom4 = $_POST['custom4'];

empty($_POST['bibtex']) ? $bibtex = '' : $bibtex = $_POST['bibtex'];

empty($_POST['bibtex_type']) ? $bibtex_type = '' : $bibtex_type = trim($_POST['bibtex_type']);

$added_by = $user_id;

########## get the new filename and record item ##########

$dbHandle->exec("BEGIN IMMEDIATE TRANSACTION");

if (!empty($title))

$insert = $stmt->execute();

$stmt = null;

$id = $dbHandle->lastInsertId();

$new_file = str_pad($id, 5, "0", STR_PAD_LEFT) . '.pdf';

// Save default citation key.

if (empty($_POST['bibtex'])) {

$stmt = $dbHandle->prepare("UPDATE library SET bibtex=:bibtex WHERE id=:id");

$stmt->bindParam(':bibtex', $bibtex, PDO::PARAM_STR);

$stmt->bindParam(':id', $id, PDO::PARAM_INT);

empty($_POST['last_name'][0]) ? $bibtex_author = 'unknown' : $bibtex_author = utf8_deaccent($_POST['last_name'][0]);

empty($_POST['year']) ? $bibtex_year = '0000' : $bibtex_year = substr($_POST['year'], 0, 4);

$bibtex = $bibtex_author . '-' . $bibtex_year . '-ID' . $id;

$stmt->execute();

}

$dbHandle->exec("COMMIT");

if ($insert == false)

$error[] = htmlspecialchars('Error! The item has not been recorded.<br>' . $title);

if ($insert == true)

$message[] = htmlspecialchars('The item has been recorded.<br>' . $title);

####### record new category into categories, if not exists #########

$category_ids = array();

if (!empty($_POST['category2'])) {

$_POST['category2'] = preg_replace('/\s{2,}/', '', $_POST['category2']);

$_POST['category2'] = preg_replace('/^\s$/', '', $_POST['category2']);

$_POST['category2'] = array_filter($_POST['category2']);

$query = "INSERT INTO categories (category) VALUES (:category)";

$stmt = $dbHandle->prepare($query);

$stmt->bindParam(':category', $new_category, PDO::PARAM_STR);

$dbHandle->beginTransaction();

while (list($key, $new_category) = each($_POST['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;

}

}

$dbHandle->commit();

$stmt = null;

}

####### record new relations into filescategories #########

$categories = array();

if (!empty($_POST['category']) || !empty($category_ids)) {

$categories = array_merge((array) $_POST['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);

$dbHandle->beginTransaction();

while (list($key, $category_id) = each($categories)) {

if (!empty($id))

$stmt->execute();

}

$dbHandle->commit();

$stmt = null;

########## record publication data, table shelves ##########

if (isset($_POST['shelf'])) {

$user_query = $dbHandle->quote($user_id);

$rows = $dbHandle->exec("INSERT OR IGNORE INTO shelves (fileID,userID) VALUES ($id,$user_query)");

if ($rows == '0')

$error[] = htmlspecialchars("Warning! The item has not been added to shelf.<br>" . $title);

$rows = null;

}

########## record to projectsfiles ##########

if (isset($_POST['project']) && !empty($_POST['projectID'])) {

$rows = $dbHandle->exec("INSERT OR IGNORE INTO projectsfiles (projectID,fileID) VALUES (" . intval($_POST['projectID']) . ",$id)");

if ($rows == '0')

$error[] = htmlspecialchars("Warning! The item has not been added to the project." . $title);

$rows = null;

}

########## record to clipboard ##########

if (isset($_POST['clipboard'])) {

attach_clipboard($dbHandle);

$query = "INSERT OR IGNORE INTO files (id) VALUES(:fileid)";

$stmt = $dbHandle->prepare($query);

$stmt->bindParam(':fileid', $id);

$stmt->execute();

$stmt = null;

}

########## ANALYZE ##########

if (rand(1, 1000) == 500)

$dbHandle->exec("ANALYZE");

$dbHandle = null;

########## record pdf ##########

$hash = '';

if (isset($_FILES['form_new_file']))

$file_extension = pathinfo($_FILES['form_new_file']['name'], PATHINFO_EXTENSION);

if (isset($_FILES['form_new_file']) && is_uploaded_file($_FILES['form_new_file']['tmp_name'])) {

$pdf_contents = file_get_contents($_FILES['form_new_file']['tmp_name'], NULL, NULL, 0, 100);

if (stripos($pdf_contents, '%PDF') === 0) {

$move = move_uploaded_file($_FILES['form_new_file']['tmp_name'], IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

if ($move == false)

$error[] = "Error! The PDF file has not been recorded.<br>" . htmlspecialchars($title);

if ($move == true) {

$message[] = htmlspecialchars("The PDF file has been recorded.<br>" . $title);

$hash = md5_file(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

}

} elseif (in_array($file_extension, array('doc', 'docx', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {

$move = move_uploaded_file($_FILES['form_new_file']['tmp_name'], IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_FILES['form_new_file']['name']);

if (PHP_OS == 'Linux' || PHP_OS == 'Darwin')

putenv('HOME=' . IL_TEMP_PATH);

exec(select_soffice() . ' --headless --convert-to pdf --outdir "' . IL_TEMP_PATH . '" "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_FILES['form_new_file']['name'] . '"');

if (PHP_OS == 'Linux' || PHP_OS == 'Darwin')

putenv('HOME=""');

$converted_file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($_FILES['form_new_file']['name'], '.' . $file_extension) . '.pdf';

if (!is_file($converted_file)) {

$error[] = "Error! Conversion to PDF failed.<br>" . htmlspecialchars($title);

} else {

copy($converted_file, IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

$message[] = htmlspecialchars("The PDF file has been recorded.<br>" . $title);

unlink($converted_file);

}

$supplement_filename = sprintf("%05d", intval($new_file)) . $_FILES['form_new_file']['name'];

copy(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_FILES['form_new_file']['name'], IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $supplement_filename);

} else {

$error[] = "Error! No PDF was found.<br>" . $title;

}

}

if (!empty($_POST['form_new_file_link'])) {

$pdf_contents = proxy_file_get_contents($_POST['form_new_file_link'], $proxy_name, $proxy_port, $proxy_username, $proxy_password);

if (stripos($pdf_contents, '%PDF') === 0) {

$move = file_put_contents(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file, $pdf_contents);

if ($move == false)

$error[] = htmlspecialchars("Error! The PDF file has not been recorded.<br>" . $title);

if ($move == true) {

$message[] = htmlspecialchars("The PDF file has been recorded.<br>" . $title);

$hash = md5_file(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

}

} else {

$error[] = 'Error! I, Librarian could not find the PDF. Possible reasons:<br><br>You access the Web through a proxy server. Enter your proxy details in Tools->Settings.<br><br>The external service may be temporarily down. Try again later.<br><br>The link you provided is not for a PDF.';

}

}

if (isset($_POST['filename']) && is_readable(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_POST['filename'])) {

$_POST['filename'] = str_replace(array('\\', '/'), '', $_POST['filename']);

$copy = copy(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_POST['filename'], IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_POST['filename']);

if ($copy == false)

$error[] = htmlspecialchars('Error! The PDF file has not been recorded.<br>' . $title);

if ($copy == true) {

$message[] = htmlspecialchars("The PDF file has been recorded.<br>" . $title);

$hash = md5_file(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file);

}

}

//RECORD FILE HASH FOR DUPLICATE DETECTION

if (!empty($hash)) {

database_connect(IL_DATABASE_PATH, 'library');

$hash = $dbHandle->quote($hash);

$dbHandle->exec('UPDATE library SET filehash=' . $hash . ' WHERE id=' . $id);

$dbHandle = null;

}

########## record supplementary files ##########

if (!empty($_FILES['form_supplementary_file']['name'])) {

for ($i = 0; $i < count($_FILES['form_supplementary_file']['name']); $i++) {

if (is_uploaded_file($_FILES['form_supplementary_file']['tmp_name'][$i])) {

$supplement_filename = preg_replace('/[\/\\\]/', '_', $_FILES['form_supplementary_file']['name'][$i]);

$supplement_filename = preg_replace('/[^a-zA-Z0-9\-\_\.]/', '_', $supplement_filename);

$supplement_filename = sprintf("%05d", $new_file) . $supplement_filename;

$move = move_uploaded_file($_FILES['form_supplementary_file']['tmp_name'][$i], IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $supplement_filename);

if ($move == false)

$error[] = "Error! The supplementary file " . $_FILES['form_supplementary_file']['name'][$i] . " has not been recorded.";

if ($move == true)

$message[] = "The supplementary file file " . $_FILES['form_supplementary_file']['name'][$i] . " has been recorded.";

}

}

}

if (file_exists(IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file)) {

$unpack_dir = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file;

mkdir($unpack_dir);

exec(select_pdfdetach() . ' -saveall -o "' . $unpack_dir . '" "' . IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($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) . DIRECTORY_SEPARATOR . sprintf("%05d", intval($new_file)) . $unpacked_file);

}

rmdir($unpack_dir);

}

########## record graphical abstract ##########

if (isset($_FILES['form_graphical_abstract']) && is_uploaded_file($_FILES['form_graphical_abstract']['tmp_name'])) {

$extension = pathinfo($_FILES['form_graphical_abstract']['name'], PATHINFO_EXTENSION);

if (empty($extension))

$extension = 'jpg';

$new_name = sprintf("%05d", intval($new_file)) . 'graphical_abstract.' . $extension;

move_uploaded_file($_FILES['form_graphical_abstract']['tmp_name'], IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_name);

}

########## extract text from pdf ##########

if ((isset($copy) && $copy) || (isset($move) && $move)) {

system(select_pdftotext() . ' -enc UTF-8 "' . IL_PDF_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_file) . DIRECTORY_SEPARATOR . $new_file . '" "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file . '.txt"', $ret);

if (is_file(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file . ".txt")) {

$string = file_get_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file . ".txt");

unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $new_file . ".txt");

if (!empty($string)) {

$string = preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $string);

$order = array("\r\n", "\n", "\r");

$string = str_replace($order, ' ', $string);

$string = preg_replace('/\s{2,}/ui', ' ', $string);

database_connect(IL_DATABASE_PATH, 'fulltext');

$file_query = $dbHandle->quote($id);

$fulltext_query = $dbHandle->quote($string);

$dbHandle->beginTransaction();

$dbHandle->exec("DELETE FROM full_text WHERE fileID=$file_query");

$dbHandle->exec("INSERT INTO full_text (fileID,full_text) VALUES ($file_query,$fulltext_query)");

$dbHandle->commit();

$dbHandle = null;

} else {

$error[] = "Warning! The PDF file cannot be indexed for full text search.";

}

}

}

$_POST = array();

if (count($error) > 0 || count($message) > 0) {

$json = array();

if (count($error) > 0)

$json['error'] = $error;

if (count($message) > 0)

$json['message'] = $message;

$json_output = json_encode($json);

die($json_output);

}

########## no form data, only PDF, try to fetch DOI and PMID ##########

} elseif (isset($_POST['form_sent']) && ((isset($_FILES['form_new_file']) && is_uploaded_file($_FILES['form_new_file']['tmp_name'])) || !empty($_POST['form_new_file_link']))) {

$rand = uniqid('lib_' . mt_rand(10, 99));

if (isset($_FILES['form_new_file']) && is_uploaded_file($_FILES['form_new_file']['tmp_name'])) {

$pdf_contents = file_get_contents($_FILES['form_new_file']['tmp_name'], NULL, NULL, 0, 100);

if (stripos($pdf_contents, '%PDF') === 0) {

move_uploaded_file($_FILES['form_new_file']['tmp_name'], IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".pdf");

$_POST['title'] = $_FILES['form_new_file']['name'];

$_POST['tempfile'] = $rand . ".pdf";

} else {

$error[] = "Error! No PDF was found.";

}

}

if (!empty($_POST['form_new_file_link'])) {

$pdf_contents = proxy_file_get_contents($_POST['form_new_file_link'], $proxy_name, $proxy_port, $proxy_username, $proxy_password);

if (stripos($pdf_contents, '%PDF') === 0) {

if (!empty($pdf_contents))

file_put_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".pdf", $pdf_contents);

$_POST['title'] = $rand . ".pdf";

$_POST['tempfile'] = $rand . ".pdf";

} else {

die('Error! I, Librarian could not find the PDF. Possible reasons:<br><br>You access the Web through a proxy server. Enter your proxy details in Tools->Settings.<br><br>The external service may be temporarily down. Try again later.<br><br>The link you provided is not for a PDF.');

}

}

if (is_readable(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".pdf")) {

########## try to find DOI on the first page ##########

system(select_pdftotext() . ' -enc UTF-8 -l 1 "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . '.pdf" "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . '.txt"', $ret);

if (is_file(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt")) {

$string = file_get_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt");

unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt");

}

if (!empty($string)) {

$string = preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $string);

$order = array("\r\n", "\n", "\r");

$replace = ' ';

$string = str_replace($order, $replace, $string);

$order = array("\xe2\x80\x93", "\xe2\x80\x94");

$replace = '-';

$string = str_replace($order, $replace, $string);

preg_match('/10\.\d{4}\/\S+/ui', $string, $doi);

$doi = current($doi);

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);

}

$_POST['doi'] = $doi;

preg_match('/(?<=arXiv:)\S+/ui', $string, $arxiv_id);

$arxiv_id = current($arxiv_id);

}

if (empty($doi) && empty($arxiv_id)) {

########## try to find DOI in the whole PDF ##########

system(select_pdftotext() . ' -enc UTF-8 "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . '.pdf" "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . '.txt"', $ret);

if (is_file(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt")) {

$string = file_get_contents(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt");

unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $rand . ".txt");

}

if (!empty($string)) {

$string = preg_replace('/[^\x{0009}\x{000a}\x{000d}\x{0020}-\x{D7FF}\x{E000}-\x{FFFD}]+/u', ' ', $string);

$order = array("\r\n", "\n", "\r");

$replace = ' ';

$string = str_replace($order, $replace, $string);

$order = array("\xe2\x80\x93", "\xe2\x80\x94");

$replace = '-';

$string = str_replace($order, $replace, $string);

preg_match('/10\.\d{4}\/\S+/ui', $string, $doi);

$doi = current($doi);

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);

}

$_POST['doi'] = $doi;

preg_match('/(?<=arXiv:)\S+/ui', $string, $arxiv_id);

$arxiv_id = current($arxiv_id);

}

}

}

}

########## if user sent only DOI, or PMID, or PDF ##########

if (isset($_POST['form_sent']) && (!empty($doi) || !empty($_POST['doi']) || !empty($_POST['uid'][0]) || !empty($arxiv_id))) {

$pmid = '';

$nasa_id = '';

$isbn = '';

$ol_id = '';

$ieee_id = '';

if (!empty($_POST['doi'])) {

$doi = trim($_POST['doi']);

if (stripos($doi, 'doi:') === 0)

$doi = trim(substr($doi, 4));

if (stripos($doi, 'http') === 0)

$doi = trim(substr(parse_url($doi, PHP_URL_PATH), 1));

} else {

$doi = '';

}

foreach ($_POST['uid'] as $uid_element) {

$uid_array2 = explode(":", $uid_element);

$uid_array2[0] = trim(strtoupper($uid_array2[0]));

if ($uid_array2[0] == 'PMID')

$pmid = trim($uid_array2[1]);

if ($uid_array2[0] == 'ARXIV')

$arxiv_id = trim($uid_array2[1]);

if ($uid_array2[0] == 'NASAADS')

$nasa_id = trim($uid_array2[1]);

if ($uid_array2[0] == 'PAT') {

$patent_id = trim($uid_array2[1]);

$patent_id = str_replace(array(',', ' '), '', $patent_id);

$_POST['uid'] = $patent_id;

}

if ($uid_array2[0] == 'IEEE')

$ieee_id = trim($uid_array2[1]);

if ($uid_array2[0] == 'OL')

$ol_id = trim($uid_array2[1]);

if ($uid_array2[0] == 'ISBN')

$isbn = trim($uid_array2[1]);

}

$response = array();

//FETCH FROM ARXIV

if (empty($response) && !empty($arxiv_id)) {

fetch_from_arxiv($arxiv_id);

$_POST = array_replace_recursive($_POST, $response);

$_POST['form_new_file_link'] = 'http://arxiv.org/pdf/' . $arxiv_id;

}

//FETCH FROM PUBMED

if (empty($response) && (!empty($pmid) || (isset($_POST['fetch-pubmed']) && !empty($doi)))) {

fetch_from_pubmed($doi, $pmid);

$_POST = array_replace_recursive($_POST, $response);

}

// FETCH FROM NASA ADS

if (empty($response) && (!empty($nasa_id) || (isset($_POST['fetch-nasaads']) && !empty($doi) && empty($pmid)))) {

fetch_from_nasaads($doi, $nasa_id);

$_POST = array_replace_recursive($_POST, $response);

}

// FETCH FROM IEEE

if (empty($response) && (!empty($ieee_id) || (isset($_POST['fetch-ieee']) && !empty($doi) && empty($pmid) && empty($nasa_id)))) {

fetch_from_ieee($doi, $ieee_id);

$_POST = array_replace_recursive($_POST, $response);

}

// FETCH FROM CROSSREF

if (empty($response) && (isset($_POST['fetch-crossref']) && !empty($doi) && empty($pmid) && empty($nasa_id) && empty($ieee_id))) {

fetch_from_crossref($doi);

$_POST = array_replace_recursive($_POST, $response);

}

// FETCH FROM GOOGLE PATENTS

if (empty($response) && !empty($patent_id)) {

fetch_from_googlepatents($patent_id);

$_POST = array_replace_recursive($_POST, $response);

$_POST['reference_type'] = 'patent';

$_POST['url'][] = 'https://www.google.com/patents/' . $patent_id;

}

// FETCH FROM OPEN LIBRARY

if (empty($response) && (!empty($ol_id) || !empty($isbn))) {

fetch_from_ol($ol_id, $isbn);

if (isset($response['uid'])) {

$response['uid'] = array_merge_recursive($_POST['uid'], $response['uid']);

$response['uid'] = array_unique($response['uid']);

}

$_POST = array_replace_recursive($_POST, $response);

}

########## check for duplicate titles in table library ##########

database_connect(IL_DATABASE_PATH, 'library');

$result = null;

if (!empty($_POST['doi'])) {

$doi_query = $dbHandle->quote($_POST['doi']);

$result = $dbHandle->query("SELECT id,title FROM library WHERE doi=$doi_query LIMIT 1");

$result = $result->fetchAll(PDO::FETCH_ASSOC);

} elseif (!empty($_POST['title'])) {

$title_query = $dbHandle->quote($_POST['title']);

$result = $dbHandle->query("SELECT id,title FROM library WHERE title=$title_query LIMIT 1");

$result = $result->fetchAll(PDO::FETCH_ASSOC);

}

$dbHandle = null;

if (count($result) > 0) {

$error[] = "Warning! This article is a possible duplicate of:<br>

<a href=\"" . htmlspecialchars("stable.php?id=" . urlencode($result[0]['id'])) . "\" style=\"color:#fff;font-weight:bold\" target=\"_blank\">" . htmlspecialchars($result[0]['title']) . "</a>";

}

$result = null;

$paper_urls = array();

if (!empty($_POST['url']) && is_string($_POST['url'])) {

$paper_urls = explode('|', $_POST['url']);

}

if (!empty($_POST['form_new_file_link'])) {

$_POST['url'][] = $_POST['form_new_file_link'];

}

$paper_uids = array();

if (!empty($_POST['uid']) && is_string($_POST['uid']))

$paper_uids = explode('|', $_POST['uid']);

}

if (!empty($_POST['title']) && !isset($_POST['form_sent'])) {

########## check for duplicate titles in table library ##########

database_connect(IL_DATABASE_PATH, 'library');

$result = null;

if (!empty($_POST['doi'])) {

$doi_query = $dbHandle->quote($_POST['doi']);

$result = $dbHandle->query("SELECT id,title FROM library WHERE doi=$doi_query LIMIT 1");

$result = $result->fetchAll(PDO::FETCH_ASSOC);

} else {

$title_query = $dbHandle->quote($_POST['title']);

$result = $dbHandle->query("SELECT id,title FROM library WHERE title=" . $title_query . " LIMIT 1");

$result = $result->fetchAll(PDO::FETCH_ASSOC);

}

$dbHandle = null;

if (count($result) > 0) {

$error[] = "Warning! This article is a possible duplicate of:<br>

<a href=\"" . htmlspecialchars("stable.php?id=" . urlencode($result[0]['id'])) . "\" style=\"color:#fff;font-weight:bold\" target=\"_blank\">" . htmlspecialchars($result[0]['title']) . "</a>";

}

$result = null;

}

if (!empty($_POST['uid']) && is_array($_POST['uid'])) {

$paper_uids = array();

$paper_uids = $_POST['uid'];

foreach ($paper_uids as $paper_uid) {

$split_uid = array();

$split_uid = explode(':', $paper_uid);

if ($split_uid[0] == 'PMCID')

$web_pdf = 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC' . urlencode($split_uid[1]) . '/pdf';

}

}

if (!empty($_POST['url']) && is_array($_POST['url']) && empty($paper_urls)) {

$paper_urls = $_POST['url'];

}

if (!empty($_POST['form_new_file_link']))

$web_pdf = $_POST['form_new_file_link'];

if (!empty($error)) {

foreach ($error as $err) {

print '<div class="upload-errors" style="display:none">' . $err . '</div>';

}

}

if (!isset($_POST['form_sent']) && empty($_POST['title']) && empty($_GET['none'])) {

?>

<form enctype="multipart/form-data" action="upload.php" method="POST" class="uploadform">

<input type="hidden" name="form_sent">

<br><br>

<div style="width:80%;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>

Add single items using:

</div>

</div>

<div style="clear: both"></div>

<div class="item-sticker alternating_row ui-widget-content ui-corner-all" style="width:80%;margin:auto;padding:0">

<table class="alternating_row ui-corner-all" style="width:100%;border-spacing:1.5em;margin:auto">

<tr>

<td>

<b>Local PDF file</b><br>

<input type="file" name="form_new_file" accept="application/pdf">

</td>

</tr>

<tr>

<td>

<b>PDF from the Web</b><br>

<input type="text" name="form_new_file_link" value="" size="85" style="width:99%" placeholder="http://www.example.com/document.pdf">

</td>

</tr>

<tr>

<td>

<b>Database number</b>

<table>

<tr>

<td style="padding-right:0.5em">

<select>

<option value="">Database</option>

<option value="">--</option>

<option value="ARXIV">ArXiv</option>

<option value="PAT">Google Patents</option>

<option value="IEEE">IEEE Xplore</option>

<option value="ISBN">ISBN</option>

<option value="NASAADS">NASA ADS</option>

<option value="OL">Open Library</option>

<option value="PMID">PubMed</option>

</select>

</td>

<td style="width:99%">

<input type="text" size="80" name="uid[]" style="width:99%" value=""

placeholder="123467">

</td>

</tr>

</table>

</td>

</tr>

<tr>

<td>

<b>DOI number</b><br>

<input type="text" size="80" name="doi" style="width:99%" value="" placeholder="10.1000/182">

</td>

</tr>

<tr>

<td>

<b>Fetch DOI data from</b>

<table>

<tr>

<?php if (!isset($_SESSION['remove_pubmed'])) { ?>

<td class="select_span" style="line-height:22px;padding-right:1em">

<input type="checkbox" class="uploadcheckbox" style="display:none" name="fetch-pubmed" value="1" checked>

<i class="fa fa-check-square"></i>

PubMed

</td>

<?php

}

if (!isset($_SESSION['remove_nasaads'])) {

?>

<td class="select_span" style="line-height:22px;padding-right:1em">

<input type="checkbox" class="uploadcheckbox" style="display:none" name="fetch-nasaads" value="1" checked>

<i class="fa fa-check-square"></i>

NASA

</td>

<?php

}

if (!isset($_SESSION['remove_ieee'])) {

?>

<td class="select_span" style="line-height:22px;padding-right:1em">

<input type="checkbox" class="uploadcheckbox" style="display:none" name="fetch-ieee" value="1" checked>

<i class="fa fa-check-square"></i>

IEEE

</td>

<?php }

?>

<td class="select_span" style="line-height:22px;padding-right:1em">

<input type="checkbox" class="uploadcheckbox" style="display:none" name="fetch-crossref" value="1" checked>

<i class="fa fa-check-square"></i>

CrossRef

</td>

</tr>

</table>

<button class="uploadsave" style="margin-top:1.5em;width:10em"><i class="fa fa-save"></i> Proceed</button>

</td>

</tr>

</table>

</div>

<div class="item-sticker alternating_row ui-widget-content ui-corner-all" style="width:80%;margin:auto;padding:0;margin-top:2em">

<table cellspacing="0" class="alternating_row ui-corner-all" style="width:100%;border-spacing:1.5em;margin:auto">

<tr>

<td style="vertical-align: middle">

<b>Unpublished PDFs, office documents</b><br>

<button id="button-none" style="margin-top:1.5em;width:10em">Manual Upload</buttton>

</td>

</tr>

</table>

</div>

</form>

<?php

} else {

?>

<form>

<!-- This mock form is here due to IE and/or jQuery form plug-in bug. When form is inserted after ajaxSubmit dynamically, IE erases it. -->

<input type="submit" style="display:none">

</form>

<form enctype="multipart/form-data" action="upload.php" method="POST" class="uploadform">

<input type="hidden" name="form_sent">

<table cellspacing=0 style="width:100%;margin-top: 4px;margin-bottom: 1px;">

<tr>

<td>

<div class="ui-state-default ui-corner-all" style="float:left;margin-left:4px;padding:1px 4px;cursor:auto">