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functions.php
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<?php
function convert_type($input, $from, $to) {
$output = 'article';
$types = array(
array(
'ilib' => 'article',
'bibtex' => 'article',
'ris' => 'JOUR',
'endnote' => 'Journal Article'
),
array(
'ilib' => 'book',
'bibtex' => 'book',
'ris' => 'BOOK',
'endnote' => 'Book'
),
array(
'ilib' => 'chapter',
'bibtex' => 'inbook',
'ris' => 'CHAP',
'endnote' => 'Book Section'
),
array(
'ilib' => 'conference',
'bibtex' => 'inproceedings',
'ris' => 'CONF',
'endnote' => 'Conference Paper'
),
array(
'ilib' => 'manual',
'bibtex' => 'manual',
'ris' => 'STD',
'endnote' => 'Report'
),
array(
'ilib' => 'thesis',
'bibtex' => 'phdthesis',
'ris' => 'THES',
'endnote' => 'Thesis'
),
array(
'ilib' => 'patent',
'bibtex' => 'patent',
'ris' => 'PAT',
'endnote' => 'Patent'
),
array(
'ilib' => 'technical report',
'bibtex' => 'techreport',
'ris' => 'RPRT',
'endnote' => 'Report'
),
array(
'ilib' => 'electronic',
'bibtex' => 'electronic',
'ris' => 'ELEC',
'endnote' => 'Electronic Source'
)
);
foreach ($types as $type) {
if ($type[$from] == $input)
$output = $type[$to];
}
return $output;
}
function cache_name() {
global $temp_dir;
$isapc = ini_get('apc.enabled');
$clipboard = array();
if(isset($_SESSION['session_clipboard'])) $clipboard = $_SESSION['session_clipboard'];
if(isset($_SESSION['limit'])) $clipboard[] = $_SESSION['limit'];
if(isset($_SESSION['orderby'])) $clipboard[] = $_SESSION['orderby'];
if(isset($_SESSION['display'])) $clipboard[] = $_SESSION['display'];
$md5_cache_array = array_merge($_POST, $_GET, $clipboard);
unset($md5_cache_array['_']);
unset($md5_cache_array['proxystr']);
ksort($md5_cache_array);
$md5_cache_string = serialize($md5_cache_array);
$md5_cache = md5(__FILE__.$md5_cache_string);
$cache_name = $_SESSION['user_id'].'_file_'.$md5_cache;
if (empty($isapc)) $cache_name = $temp_dir . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR.$cache_name;
return $cache_name;
}
function database_change() {
global $database_path;
$ch_time = 0;
$ch_time2 = 0;
$tables = array();
$tables2 = array();
$tables_arr = func_get_args();
if (isset($tables_arr[0])) $tables = (array) $tables_arr[0];
if (isset($tables_arr[1])) $tables2 = (array) $tables_arr[1];
// READ DATABASE MTIME
if (count($tables) > 0) {
foreach ($tables as $table) {
$query_arr[] = "ch_table='".$table."'";
}
$query_str = join (' OR ', $query_arr);
$dbHandle = database_connect($database_path, 'library');
$result = $dbHandle->query("SELECT max(ch_time) FROM library_log
WHERE ".$query_str);
$ch_time = $result->fetchColumn();
$result = null;
$dbHandle = null;
}
if (count($tables2) > 0) {
foreach ($tables2 as $table) {
$query_arr[] = "ch_table='".$table."'";
}
$query_str = join (' OR ', $query_arr);
$dbHandle = database_connect($database_path, 'fulltext');
$result = $dbHandle->query("SELECT max(ch_time) FROM fulltext_log
WHERE ".$query_str);
$ch_time2 = $result->fetchColumn();
$result = null;
$dbHandle = null;
}
return max($ch_time, $ch_time2);
}
function cache_start($ch_time) {
global $cache_name;
$mtime = 0;
$isapc = ini_get('apc.enabled');
// READ CACHE MTIME
if (empty($isapc)) {
if (is_file($cache_name)) $mtime = filemtime($cache_name);
} else {
foreach (new APCIterator('user', '/^'.$cache_name.'$/', APC_ITER_MTIME) as $cache_item) {
$mtime = $cache_item['mtime'];
}
}
// EITHER SHOW CACHED PAGE OR CONTINUE
if ($ch_time < $mtime) {
if (empty($isapc)) {
if (file_exists($cache_name)) {
$cached_string = file_get_contents($cache_name);
echo gzuncompress($cached_string);
exit();
}
} else {
if ($cached_string = apc_fetch($cache_name)) {
$page = gzuncompress($cached_string);
echo $page;
exit();
}
}
}
ob_start();
}
function cache_store() {
global $cache_name;
$isapc = ini_get('apc.enabled');
// GET BUFFER CONTENTS
$bufferContent = ob_get_contents();
$bufferContent = gzcompress($bufferContent,1);
ob_end_flush();
// STORE BUFFER INTO CACHE
if (empty($isapc)) {
file_put_contents($cache_name, $bufferContent);
} else {
apc_store($cache_name, $bufferContent);
}
}
function cache_clear() {
//DELETE CACHED SHELF AND PROJECTS
global $temp_dir;
$isapc = ini_get('apc.enabled');
if (empty($isapc)) {
// DELETE USER'S FILE CACHE
// $clean_files = glob($temp_dir . DIRECTORY_SEPARATOR . 'lib_*' . DIRECTORY_SEPARATOR .'*', GLOB_NOSORT);
// foreach ($clean_files as $clean_file) {
// if (is_file($clean_file) && is_writable($clean_file))
// @unlink($clean_file);
// }
} else {
// DELETE USER'S APC CACHE
foreach (new APCIterator('user', '/.*_desktop_files$/', APC_ITER_KEY, 10000) as $item) {
apc_delete($item['key']);
}
foreach (new APCIterator('user', '/.*_shelf_files$/', APC_ITER_KEY, 10000) as $item) {
apc_delete($item['key']);
}
}
}
function save_export_files($files) {
global $temp_dir;
$filename = $temp_dir . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR . 'exportfiles';
$export_files = array();
$export_files['timestamp'] = time();
$export_files['files'] = $files;
$export_files_content = gzcompress(serialize($export_files), 1);
$isapc = ini_get('apc.enabled');
if (empty($isapc)) {
file_put_contents($filename, $export_files_content, LOCK_EX);
} else {
apc_store($_SESSION['user_id'].'_export_files', $export_files_content);
}
}
function read_export_files($ch_time) {
global $temp_dir;
$export_files_array['timestamp'] = 0;
$export_files_array['files'] = null;
$filename = $temp_dir . DIRECTORY_SEPARATOR . 'lib_' . session_id() . DIRECTORY_SEPARATOR . 'exportfiles';
$isapc = ini_get('apc.enabled');
if (!empty($isapc)) {
if ($export_files = apc_fetch($_SESSION['user_id'].'_export_files'))
$export_files_array = unserialize(gzuncompress($export_files));
} else {
if (is_readable($filename))
$export_files_array = unserialize(gzuncompress(file_get_contents($filename)));
}
if ($ch_time < $export_files_array['timestamp'])
return $export_files_array['files'];
}
function graphical_abstract($file) {
$filename = sprintf("%05d", intval($file));
$filename_array = glob('library/supplement/' . $filename . 'graphical_abstract.*');
if (!empty($filename_array[0]))
return $filename_array[0];
}
function get_username($dbHandle, $database_path, $userID) {
$dbHandle->exec("ATTACH DATABASE '" . $database_path . "users.sq3' AS usersdatabase");
$query = $dbHandle->quote($userID);
$result = $dbHandle->query("SELECT usersdatabase.users.username AS username FROM usersdatabase.users WHERE userID=$query LIMIT 1");
$username = $result->fetchColumn();
$dbHandle->exec("DETACH DATABASE '" . $database_path . "users.sq3'");
return $username;
}
function download_new_version($version, $proxy_name, $proxy_port, $proxy_username, $proxy_password) {
if ($_SESSION['auth'] && $_SESSION['permissions'] == 'A') {
session_write_close();
global $download_new_version;
$response_string = '';
$current_version = '';
$current_array = array();
if (isset($proxy_name) && !empty($proxy_name)) {
$proxy_fp = @fsockopen($proxy_name, $proxy_port, $e1, $e2, 5);
if ($proxy_fp) {
fputs($proxy_fp, "GET http://www.bioinformatics.org/librarian/newversion.php HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$response_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
} else {
return '';
}
} else {
$proxy_fp = @fsockopen('www.bioinformatics.org', 80, $e1, $e2, 5);
if ($proxy_fp) {
$pdf_string = '';
$cookies = array();
fputs($proxy_fp, "GET /librarian/newversion.php HTTP/1.0\r\n");
fputs($proxy_fp, "Host: www.bioinformatics.org\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n\r\n");
while (!feof($proxy_fp)) {
$response_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
} else {
return '';
}
}
$response_string = strstr($response_string, "current-version:");
$current_array = explode(":", $response_string);
if (count($current_array) == 2)
$current_version = $current_array[1];
if (version_compare($version, $current_version) == "-1")
$download_new_version = 'yes';
return $download_new_version;
}
}
/////////////create, upgrade, or connect to database//////////////////////
function database_connect($database_path, $database_name) {
global $dbHandle;
$database_exists = false;
if (is_file($database_path . 'library.sq3'))
$database_exists = true;
/////////////create databases//////////////////////
if (!$database_exists) {
try {
$dbHandle = new PDO('sqlite:' . $database_path . 'library.sq3');
} catch (PDOException $e) {
print "Error: " . $e->getMessage() . "<br/>";
print "PHP extensions PDO and PDO_SQLite must be installed. <a href=\"http://bioinformatics.org/librarian/installation.php\" target=\"_blank\">Help</a><br/>";
die();
}
$dbHandle->beginTransaction();
$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 ''
)");
$dbHandle->exec("CREATE TABLE shelves (
fileID integer NOT NULL DEFAULT '',
userID integer NOT NULL DEFAULT '',
UNIQUE (fileID,userID)
)");
$dbHandle->exec("CREATE TABLE categories (
categoryID integer PRIMARY KEY,
category text NOT NULL DEFAULT ''
)");
$dbHandle->exec("CREATE TABLE filescategories (
fileID integer NOT NULL,
categoryID integer NOT NULL,
UNIQUE(fileID,categoryID)
)");
$dbHandle->exec("CREATE TABLE projects (
projectID integer PRIMARY KEY,
userID integer NOT NULL,
project text NOT NULL
)");
$dbHandle->exec("CREATE TABLE projectsfiles (
projectID integer NOT NULL,
fileID integer NOT NULL,
UNIQUE (projectID,fileID)
)");
$dbHandle->exec("CREATE TABLE projectsusers (
projectID integer NOT NULL,
userID integer NOT NULL,
UNIQUE (projectID,userID)
)");
$dbHandle->exec("CREATE TABLE notes (
notesID integer PRIMARY KEY,
userID integer NOT NULL,
fileID integer NOT NULL,
notes text NOT NULL DEFAULT ''
)");
$dbHandle->exec("CREATE TABLE searches (
searchID integer PRIMARY KEY,
userID integer NOT NULL,
searchname text NOT NULL DEFAULT '',
searchfield text NOT NULL DEFAULT '',
searchvalue text NOT NULL DEFAULT ''
)");
$dbHandle->exec("CREATE TABLE yellowmarkers (
id INTEGER PRIMARY KEY,
userID INTEGER NOT NULL,
filename TEXT NOT NULL,
page INTEGER NOT NULL,
top TEXT NOT NULL,
left TEXT NOT NULL,
width TEXT NOT NULL,
UNIQUE (userID,filename,page,top,left)
)");
$dbHandle->exec("CREATE TABLE annotations (
id INTEGER PRIMARY KEY,
userID INTEGER NOT NULL,
filename TEXT NOT NULL,
page INTEGER NOT NULL,
top TEXT NOT NULL,
left TEXT NOT NULL,
annotation TEXT NOT NULL,
UNIQUE (userID,filename,page,top,left)
)");
$dbHandle->exec("CREATE INDEX journal_ind ON library (journal)");
$dbHandle->exec("CREATE INDEX secondary_title_ind ON library (secondary_title)");
$dbHandle->exec("CREATE INDEX addition_date_ind ON library (addition_date)");
$dbHandle->exec("CREATE TABLE library_log (
id integer PRIMARY KEY,
ch_table text NOT NULL DEFAULT '',
ch_time text NOT NULL DEFAULT ''
)");
$tables = array('annotations','categories','filescategories','flagged','library','notes',
'projects','projectsfiles','projectsusers','searches','shelves','yellowmarkers');
foreach ($tables as $table) {
$dbHandle->exec("INSERT INTO library_log (ch_table,ch_time)
VALUES('".$table."',strftime('%s','now'))");
$dbHandle->exec("CREATE TRIGGER trigger_".$table."_delete AFTER DELETE ON ".$table."
BEGIN
UPDATE library_log SET ch_time=strftime('%s','now') WHERE ch_table='".$table."';
END;");
$dbHandle->exec("CREATE TRIGGER trigger_".$table."_insert AFTER INSERT ON ".$table."
BEGIN
UPDATE library_log SET ch_time=strftime('%s','now') WHERE ch_table='".$table."';
END;");
$dbHandle->exec("CREATE TRIGGER trigger_".$table."_update AFTER UPDATE ON ".$table."
BEGIN
UPDATE library_log SET ch_time=strftime('%s','now') WHERE ch_table='".$table."';
END;");
}
$dbHandle->commit();
$dbHandle = null;
try {
$dbHandle = new PDO('sqlite:' . $database_path . 'fulltext.sq3');
} catch (PDOException $e) {
print "Error: " . $e->getMessage() . "<br/>";
print "PHP extensions PDO and PDO_SQLite must be installed. <a href=\"http://bioinformatics.org/librarian/installation.php\" target=\"_blank\">Help</a><br/>";
die();
}
$dbHandle->beginTransaction();
$dbHandle->exec("CREATE TABLE full_text (
id integer PRIMARY KEY,
fileID text NOT NULL DEFAULT '',
full_text text NOT NULL DEFAULT ''
)");
$dbHandle->exec("CREATE TABLE fulltext_log (
id integer PRIMARY KEY,
ch_table text NOT NULL DEFAULT '',
ch_time text NOT NULL DEFAULT ''
)");
$dbHandle->exec("INSERT INTO fulltext_log (ch_table,ch_time)
VALUES('full_text',strftime('%s','now'))");
$dbHandle->exec("CREATE TRIGGER trigger_fulltext_delete AFTER DELETE ON full_text
BEGIN
UPDATE fulltext_log SET ch_time=strftime('%s','now') WHERE ch_table='full_text';
END;");
$dbHandle->exec("CREATE TRIGGER trigger_fulltext_insert AFTER INSERT ON full_text
BEGIN
UPDATE fulltext_log SET ch_time=strftime('%s','now') WHERE ch_table='full_text';
END;");
$dbHandle->exec("CREATE TRIGGER trigger_fulltext_update AFTER UPDATE ON full_text
BEGIN
UPDATE fulltext_log SET ch_time=strftime('%s','now') WHERE ch_table='full_text';
END;");
$dbHandle->commit();
$dbHandle = null;
try {
$dbHandle = new PDO('sqlite:' . $database_path . 'users.sq3');
} catch (PDOException $e) {
print "Error: " . $e->getMessage() . "<br/>";
print "PHP extensions PDO and PDO_SQLite must be installed. <a href=\"http://bioinformatics.org/librarian/installation.php\" target=\"_blank\">Help</a><br/>";
die();
}
$dbHandle->beginTransaction();
$dbHandle->exec("CREATE TABLE users (
userID integer PRIMARY KEY,
username text UNIQUE NOT NULL DEFAULT '',
password text NOT NULL DEFAULT '',
permissions text NOT NULL DEFAULT 'U'
)");
$dbHandle->exec("CREATE TABLE settings (
userID integer NOT NULL DEFAULT '',
setting_name text NOT NULL DEFAULT '',
setting_value text NOT NULL DEFAULT ''
)");
$dbHandle->commit();
}
/////////////connect to database//////////////////////
try {
$dbHandle = new PDO('sqlite:' . $database_path . $database_name . '.sq3');
} catch (PDOException $e) {
print "Error: " . $e->getMessage() . "<br/>";
print "PHP extensions PDO and PDO_SQLite must be installed. <a href=\"http://bioinformatics.org/librarian/installation.php\" target=\"_blank\">Help</a><br/>";
die();
}
//SWITCH TO WAL MODE IF SQLITE >3.7.0
$result = $dbHandle->query('SELECT sqlite_version()');
$sqlite_version = $result->fetchColumn();
$result = null;
$journal_mode = 'DELETE';
if (version_compare($sqlite_version, "3.7.0", ">"))
$journal_mode = 'WAL';
$dbHandle->query('PRAGMA journal_mode=' . $journal_mode);
return $dbHandle;
}
/////////////sqlite_regexp//////////////////////
function sqlite_regexp($string1, $string2, $case) {
if ($case == 1) {
$pattern = '/([^a-zA-Z0-9]|^)' . $string2 . '([^a-zA-Z0-9]|$)/u';
} else {
$pattern = '/([^a-zA-Z0-9]|^)' . $string2 . '([^a-zA-Z0-9]|$)/ui';
}
if (preg_match($pattern, $string1) > 0) {
return true;
} else {
return false;
}
}
/////////////sqlite_strip_tags//////////////////////
function sqlite_strip_tags($string) {
return html_entity_decode(strip_tags($string), ENT_QUOTES, 'UTF-8');
}
/////////////sqlite_levenshtein//////////////////////
function sqlite_levenshtein($string1, $string2) {
$replacements = array('.', '&', 'and');
$string1 = str_ireplace($replacements, '', $string1);
$string2 = str_ireplace($replacements, '', $string2);
if (stripos($string1, 'the ') === 0)
$string1 = substr($string1, 4);
if (stripos($string2, 'the ') === 0)
$string2 = substr($string2, 4);
return levenshtein($string1, $string2);
}
/////////////select pdftotext//////////////////////
function select_pdftotext() {
global $pdftotext;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . 'pdftotext.exe')) {
$pdftotext = 'bin' . DIRECTORY_SEPARATOR . 'pdftotext.exe -enc UTF-8 ';
} elseif (PHP_OS == 'Linux') {
$pdftotext = "pdftotext -enc UTF-8 ";
} elseif (PHP_OS == 'Darwin' && is_executable(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdftotext.osx')) {
$pdftotext = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdftotext.osx -enc UTF-8 ';
}
return $pdftotext;
}
/////////////select pdfinfo//////////////////////
function select_pdfinfo() {
global $pdfinfo;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . 'pdfinfo.exe')) {
$pdfinfo = 'bin' . DIRECTORY_SEPARATOR . 'pdfinfo.exe ';
} elseif (PHP_OS == 'Linux') {
$pdfinfo = "pdfinfo ";
} elseif (PHP_OS == 'Darwin' && is_executable(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdfinfo.osx')) {
$pdfinfo = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdfinfo.osx ';
}
return $pdfinfo;
}
/////////////select pdftohtml//////////////////////
function select_pdftohtml() {
global $selected_pdftohtml;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . 'pdftohtml.exe')) {
$selected_pdftohtml = 'bin' . DIRECTORY_SEPARATOR . 'pdftohtml.exe';
} elseif (PHP_OS == 'Linux') {
$selected_pdftohtml = "pdftohtml";
} elseif (PHP_OS == 'Darwin' && is_executable(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdftohtml.osx')) {
$selected_pdftohtml = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'pdftohtml.osx';
}
return $selected_pdftohtml;
}
/////////////select bibutil//////////////////////
function select_bibutil($bibutil) {
global $selected_bibutil;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . $bibutil . '.exe')) {
$selected_bibutil = 'bin' . DIRECTORY_SEPARATOR . $bibutil . '.exe';
} elseif (PHP_OS == 'Linux') {
$selected_bibutil = $bibutil;
} elseif (PHP_OS == 'Darwin' && is_executable(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . $bibutil . '.osx')) {
$selected_bibutil = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . $bibutil . '.osx';
}
return $selected_bibutil;
}
/////////////select ghostscript//////////////////////
function select_ghostscript() {
global $selected_ghostscript;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . 'gs' . DIRECTORY_SEPARATOR . 'gswin32c.exe')) {
$selected_ghostscript = 'bin' . DIRECTORY_SEPARATOR . 'gs' . DIRECTORY_SEPARATOR . 'gswin32c.exe';
} elseif (PHP_OS == 'Linux') {
$selected_ghostscript = 'gs';
} elseif (PHP_OS == 'Darwin' && is_executable(dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'gs' . DIRECTORY_SEPARATOR . 'gs.osx')) {
$selected_ghostscript = dirname(__FILE__) . DIRECTORY_SEPARATOR . 'bin' . DIRECTORY_SEPARATOR . 'gs' . DIRECTORY_SEPARATOR . 'gs.osx';
}
return $selected_ghostscript;
}
/////////////select pdftk//////////////////////
function select_pdftk() {
global $pdftk;
if (strtoupper(substr(PHP_OS, 0, 3)) == 'WIN' && is_executable('bin' . DIRECTORY_SEPARATOR . 'pdftk' . DIRECTORY_SEPARATOR . 'pdftk.exe')) {
$pdftk = 'bin' . DIRECTORY_SEPARATOR . 'pdftk' . DIRECTORY_SEPARATOR . 'pdftk.exe ';
} elseif (PHP_OS == 'Linux') {
$pdftk = "pdftk ";
} elseif (PHP_OS == 'Darwin') {
$pdftk = '/usr/local/bin/pdftk ';
}
return $pdftk;
}
/////////////proxy_file_get_contents//////////////////////
function proxy_file_get_contents($url, $proxy_name, $proxy_port, $proxy_username, $proxy_password) {
global $pdf;
$pdf_string = '';
if (isset($proxy_name) && !empty($proxy_name)) {
$proxy_fp = @fsockopen($proxy_name, $proxy_port);
if ($proxy_fp) {
$pdf_string = '';
$cookies = array();
fputs($proxy_fp, "GET $url HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
if (empty($pdf)) {
$response = array();
$response = explode("\r\n", $pdf_string);
while (list($key, $value) = each($response)) {
if (stripos($value, "Location: ") === 0) {
if ($value != $url)
$new_url = trim(substr($value, 10));
}
if (stripos($value, "Set-Cookie: ") === 0) {
$cookies[] = trim($value);
}
}
if (!empty($new_url)) {
$pdf_string = '';
if (stripos($new_url, "http") !== 0)
$new_url = parse_url($url, PHP_URL_SCHEME) . '://' . parse_url($url, PHP_URL_HOST) . $new_url;
$proxy_fp = @fsockopen($proxy_name, $proxy_port);
fputs($proxy_fp, "GET $new_url HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
foreach ($cookies as $cookie) {
if (!empty($cookie))
fputs($proxy_fp, "Cookie: " . substr($cookie, 12) . "\r\n");
}
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
if (empty($pdf)) {
$response = array();
$response = explode("\r\n", $pdf_string);
while (list($key, $value) = each($response)) {
if (stripos($value, "Location: ") === 0) {
if ($value != $url)
$new_url = trim(substr($value, 10));
}
if (stripos($value, "Set-Cookie: ") === 0) {
$cookies[] = trim($value);
}
}
if (!empty($new_url)) {
$pdf_string = '';
if (stripos($new_url, "http") !== 0)
$new_url = parse_url($url, PHP_URL_SCHEME) . '://' . parse_url($url, PHP_URL_HOST) . $new_url;
$proxy_fp = @fsockopen($proxy_name, $proxy_port);
fputs($proxy_fp, "GET $new_url HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
foreach ($cookies as $cookie) {
if (!empty($cookie))
fputs($proxy_fp, "Cookie: " . substr($cookie, 12) . "\r\n");
}
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
}
}
}
}
}
} else {
$host = parse_url($url, PHP_URL_HOST);
$path = parse_url($url, PHP_URL_PATH);
$query = parse_url($url, PHP_URL_QUERY);
$proxy_fp = @fsockopen($host, 80);
if ($proxy_fp) {
$pdf_string = '';
$cookies = array();
fputs($proxy_fp, "GET $path?$query HTTP/1.0\r\n");
fputs($proxy_fp, "Host: $host\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
if (empty($pdf)) {
$response = array();
$response = explode("\r\n", $pdf_string);
while (list($key, $value) = each($response)) {
if (stripos($value, "Location: ") === 0) {
if ($value != $url)
$new_url = trim(substr($value, 10));
}
if (stripos($value, "Set-Cookie: ") === 0) {
$cookies[] = trim($value);
}
}
if (!empty($new_url)) {
$pdf_string = '';
if (stripos($new_url, "http") !== 0)
$new_url = parse_url($url, PHP_URL_SCHEME) . '://' . parse_url($url, PHP_URL_HOST) . $new_url;
$host = parse_url($new_url, PHP_URL_HOST);
$path = parse_url($new_url, PHP_URL_PATH);
$query = parse_url($new_url, PHP_URL_QUERY);
$proxy_fp = @fsockopen($host, 80);
fputs($proxy_fp, "GET $path?$query HTTP/1.0\r\n");
fputs($proxy_fp, "Host: $host\r\n");
foreach ($cookies as $cookie) {
if (!empty($cookie))
fputs($proxy_fp, "Cookie: " . substr($cookie, 12) . "\r\n");
}
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
if (empty($pdf)) {
$response = array();
$response = explode("\r\n", $pdf_string);
while (list($key, $value) = each($response)) {
if (stripos($value, "Location: ") === 0) {
if ($value != $url)
$new_url = trim(substr($value, 10));
}
if (stripos($value, "Set-Cookie: ") === 0) {
$cookies[] = trim($value);
}
}
if (!empty($new_url)) {
$pdf_string = '';
if (stripos($new_url, "http") !== 0)
$new_url = parse_url($url, PHP_URL_SCHEME) . '://' . parse_url($url, PHP_URL_HOST) . $new_url;
$host = parse_url($new_url, PHP_URL_HOST);
$path = parse_url($new_url, PHP_URL_PATH);
$query = parse_url($new_url, PHP_URL_QUERY);
$proxy_fp = @fsockopen($host, 80);
fputs($proxy_fp, "GET $path?$query HTTP/1.0\r\n");
fputs($proxy_fp, "Host: $host\r\n");
foreach ($cookies as $cookie) {
if (!empty($cookie))
fputs($proxy_fp, "Cookie: " . substr($cookie, 12) . "\r\n");
}
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n\r\n");
while (!feof($proxy_fp)) {
$pdf_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$pdf = strstr($pdf_string, "%PDF");
}
}
}
}
}
}
return $pdf;
}
/////////////proxy_simplexml_load_file//////////////////////
function proxy_simplexml_load_file($url, $proxy_name, $proxy_port, $proxy_username, $proxy_password) {
global $xml;
$xml = false;
$xml_string = '';
$xml_string2 = '';
if (isset($proxy_name) && !empty($proxy_name)) {
$proxy_fp = @fsockopen($proxy_name, $proxy_port, $errno, $errstr, 10);
if ($proxy_fp) {
fputs($proxy_fp, "GET $url HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$xml_string2 .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$xml_string = strstr($xml_string2, "<?xml");
$xml = simplexml_load_string($xml_string);
#JSTOR hack
if (empty($xml) && strpos($url, 'jstor') !== false) {
$xml = new XMLReader();
$xml->xml($xml_string);
}
#NASA PHYS hack
if (empty($xml) && strpos($url, 'adsabs') !== false) {
$response = array();
$response = explode("\r\n", $xml_string2);
while (list($key, $value) = each($response)) {
if (stripos($value, "Location: ") === 0) {
$new_url = trim(substr($value, 10));
if ($new_url != $url)
break;
}
}
if (!empty($new_url)) {
$xml_string = '';
if (stripos($new_url, "http") !== 0)
$new_url = parse_url($url, PHP_URL_SCHEME) . '://' . parse_url($url, PHP_URL_HOST) . $new_url;
$proxy_fp = @fsockopen($proxy_name, $proxy_port);
fputs($proxy_fp, "GET $new_url HTTP/1.0\r\nHost: $proxy_name\r\n");
fputs($proxy_fp, "User-Agent: \"$_SERVER[HTTP_USER_AGENT]\"\r\n");
fputs($proxy_fp, "Proxy-Authorization: Basic " . base64_encode("$proxy_username:$proxy_password") . "\r\n\r\n");
while (!feof($proxy_fp)) {
$xml_string .= fgets($proxy_fp, 128);
}
fclose($proxy_fp);
$xml_string = strstr($xml_string, "<?xml");
$xml = simplexml_load_string($xml_string);
}
}
}
} else {
ini_set('user_agent', $_SERVER['HTTP_USER_AGENT']);
$xml = @simplexml_load_file($url);
#JSTOR hack
if (strpos($url, 'jstor') !== false) {
$xml = new XMLReader();
$xml->open($url);
}
#NASA PHYS hack
if (empty($xml) && strpos($url, 'adsabs') !== false) {
$xml_string2 = '';
$host = parse_url($url, PHP_URL_HOST);
$path = parse_url($url, PHP_URL_PATH);
$query = parse_url($url, PHP_URL_QUERY);
$proxy_fp = @fsockopen($host, 80);
if ($proxy_fp) {