$extension = pathinfo($_FILES['form_graphical_abstract']['name'], PATHINFO_EXTENSION);
if (empty($extension)) {
$extension = 'jpg';
}
$new_name = sprintf("%05d", intval($_POST['file'])) . 'graphical_abstract.' . $extension;
move_uploaded_file($_FILES['form_graphical_abstract']['tmp_name'], IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($new_name) . DIRECTORY_SEPARATOR . $new_name);
}
########## replace PDF ##########
if (isset($_FILES['form_new_file']) && is_uploaded_file($_FILES['form_new_file']['tmp_name'])) {
$file_extension = pathinfo($_FILES['form_new_file']['name'], PATHINFO_EXTENSION);
if (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)) {
die("Error! Conversion to PDF failed.<br>" . htmlspecialchars($title));
} else {
copy($converted_file, IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR . $_POST['filename']);
$supplement_filename = sprintf("%05d", intval($_POST['filename'])) . $_FILES['form_new_file']['name'];
copy(IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_FILES['form_new_file']['name'], IL_SUPPLEMENT_PATH . DIRECTORY_SEPARATOR . get_subfolder($supplement_filename) . DIRECTORY_SEPARATOR . $supplement_filename);
unlink($converted_file);
}
} else {
move_uploaded_file($_FILES['form_new_file']['tmp_name'], IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR . $_POST['filename']);
}
$user_dir = IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id();
session_write_close();
$order = array("\r\n", "\n", "\r");
$i = 0;
if (isset($_FILES['Filedata']) && is_uploaded_file($_FILES['Filedata']['tmp_name'])) {
$file = $_FILES['Filedata']['tmp_name'];
$orig_filename = $_FILES['Filedata']['name'];
if (isset($_FILES['Filedata'])) {
$file_extension = pathinfo($orig_filename, PATHINFO_EXTENSION);
}
if (in_array($file_extension, array('doc', 'docx', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {
$move = move_uploaded_file($file, IL_TEMP_PATH . DIRECTORY_SEPARATOR . $orig_filename);
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 . $orig_filename . '"');
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=""');
}
$file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($orig_filename, '.' . $file_extension) . '.pdf';
}
$i = $i + 1;
if (is_readable($file)) {
$string = '';
$xml = '';
$record = '';
$count = '';
$url = array();
$authors = '';
$authors_array = array();
$affiliation = '';
$doi = '';
$authors_ascii = '';
$title_ascii = '';
$abstract_ascii = '';
$unpacked_files = array();
$temp_file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . $_GET['user'] . "_librarian_temp" . $i . ".txt";
if (file_exists($temp_file)) {
unlink($temp_file);
}
//convert office to pdf
$file_extension = pathinfo($file, PATHINFO_EXTENSION);
if (in_array($file_extension, array('doc', 'docx', 'xls', 'xlsx', 'ppt', 'pptx', 'odt', 'ods', 'odp'))) {
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=' . IL_TEMP_PATH);
}
exec(select_soffice() . ' --headless --convert-to pdf --outdir "' . IL_TEMP_PATH . '" "' . $file . '"');
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=""');
}
//copy file to temp to add it to supplement later
copy($file, IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($file));
$title = basename($file);
//pdf file
$file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . basename($file, '.' . $file_extension) . '.pdf';
}
########## extract text from pdf ##########
system(select_pdftotext() . ' -enc UTF-8 "' . $file . '" "' . $temp_file . '"', $ret);
if (file_exists($temp_file)) {
$string = file_get_contents($temp_file);
}
if (empty($string)) {
exec(select_ghostscript() . ' -sDEVICE=png16m -r15 -dTextAlphaBits=1 -dGraphicsAlphaBits=1 -dFirstPage=1 -dLastPage=1 -o "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test.png" test.pdf');
if (file_exists(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test.png')) {
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test.png');
die('OK');
} else {
die;
}
} elseif ($_GET['binary'] == 'tesseract') {
exec(select_tesseract() . ' "' . __DIR__ . DIRECTORY_SEPARATOR . 'test.bmp" "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test-tesseract"');
if (is_readable(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test-tesseract.txt') && filesize(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test-tesseract.txt') > 0) {
unlink(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test-tesseract.txt');
die('OK');
} else {
die;
}
} elseif ($_GET['binary'] == 'soffice') {
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=' . IL_TEMP_PATH);
}
exec(select_soffice() . ' --headless --convert-to pdf --outdir "' . IL_TEMP_PATH . '" "' . __DIR__ . DIRECTORY_SEPARATOR . 'test.odt"');
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=""');
}
$converted_file = IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'test.pdf';
if (!is_file($converted_file)) {
die;
} else {
unlink($converted_file);
die('OK');
}
}
//INSERT CITATIONS
$i = 0;
preg_match_all('/\\\\{\\S+\\-\\S+\\-ID\\d+\\\\}/', $rtf_string, $ids);
foreach ($ids[0] as $target) {
$rtf_string = str_replace($target, $_POST['cites'][$i], $rtf_string);
$i++;
}
//INSERT BIBLIOGRAPHY
$position = strrpos($rtf_string, '}');
$rtf_string = substr($rtf_string, 0, $position - 1) . PHP_EOL . $_POST['bibliography'] . PHP_EOL . '}';
//CONVERT RTF TO DOC, DOCX, ODT TO RTF
if (in_array($file_extension, array('doc', 'docx', 'odt'))) {
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=' . IL_TEMP_PATH);
}
exec(select_soffice() . ' --headless --convert-to ' . $file_extension . ' --outdir "' . IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id() . '" "' . $temp_file . '"');
if (PHP_OS == 'Linux' || PHP_OS == 'Darwin') {
putenv('HOME=""');
}
rename(IL_TEMP_PATH . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR . basename(str_replace('\\', '/', urldecode($_POST['rtfname']))), $output_file);
if (!is_file($output_file)) {
$errors[] = "Error! RTF conversion failed.";
$response['errors'] = $errors;
$content = json_encode($response, JSON_HEX_APOS);
die($content);
}
}
//WRITE MODIFIED FILE
$put = file_put_contents($output_file, $rtf_string);
if (!$put) {
$errors[] = 'Error! Could not write to manuscript file.';
