You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by ma...@apache.org on 2017/02/15 14:38:43 UTC
[09/12] airavata-php-gateway git commit: modification for file
download from genome browser
modification for file download from genome browser
Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/d5533b06
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/d5533b06
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/d5533b06
Branch: refs/heads/dreg-gateway
Commit: d5533b068720e5ea1770ab16811539cfd8106ad9
Parents: 2c64ac0
Author: root <ro...@osboxes>
Authored: Sat Feb 11 04:53:36 2017 +0000
Committer: root <ro...@osboxes>
Committed: Sat Feb 11 04:53:36 2017 +0000
----------------------------------------------------------------------
app/libraries/PartialDownload.php | 174 ---------------------------------
app/libraries/basecode.php | 98 +++++++++++++++++++
app/routes.php | 40 ++++----
3 files changed, 118 insertions(+), 194 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/d5533b06/app/libraries/PartialDownload.php
----------------------------------------------------------------------
diff --git a/app/libraries/PartialDownload.php b/app/libraries/PartialDownload.php
deleted file mode 100644
index eb10775..0000000
--- a/app/libraries/PartialDownload.php
+++ /dev/null
@@ -1,174 +0,0 @@
-<?php
-/*
-
-The following byte serving code is (C) 2004 Razvan Florian. You may find the latest version at
-http://www.coneural.org/florian/papers/04_byteserving.php
-
-*/
-function set_range($range, $filesize, &$first, &$last){
- /*
- Sets the first and last bytes of a range, given a range expressed as a string
- and the size of the file.
-
- If the end of the range is not specified, or the end of the range is greater
- than the length of the file, $last is set as the end of the file.
-
- If the begining of the range is not specified, the meaning of the value after
- the dash is "get the last n bytes of the file".
-
- If $first is greater than $last, the range is not satisfiable, and we should
- return a response with a status of 416 (Requested range not satisfiable).
-
- Examples:
- $range='0-499', $filesize=1000 => $first=0, $last=499 .
- $range='500-', $filesize=1000 => $first=500, $last=999 .
- $range='500-1200', $filesize=1000 => $first=500, $last=999 .
- $range='-200', $filesize=1000 => $first=800, $last=999 .
-
- */
- $dash=strpos($range,'-');
- $first=trim(substr($range,0,$dash));
- $last=trim(substr($range,$dash+1));
- if ($first=='') {
- //suffix byte range: gets last n bytes
- $suffix=$last;
- $last=$filesize-1;
- $first=$filesize-$suffix;
- if($first<0) $first=0;
- } else {
- if ($last=='' || $last>$filesize-1) $last=$filesize-1;
- }
- if($first>$last){
- //unsatisfiable range
- header("Status: 416 Requested range not satisfiable");
- header("Content-Range: */$filesize");
- exit;
- }
-}
-
-function buffered_read($file, $bytes, $buffer_size=1024){
- /*
- Outputs up to $bytes from the file $file to standard output, $buffer_size bytes at a time.
- */
- $bytes_left=$bytes;
- while($bytes_left>0 && !feof($file)){
- if($bytes_left>$buffer_size)
- $bytes_to_read=$buffer_size;
- else
- $bytes_to_read=$bytes_left;
- $bytes_left-=$bytes_to_read;
- $contents=fread($file, $bytes_to_read);
- echo $contents;
- flush();
- }
-}
-
-function byteserve($filename){
- /*
- Byteserves the file $filename.
-
- When there is a request for a single range, the content is transmitted
- with a Content-Range header, and a Content-Length header showing the number
- of bytes actually transferred.
-
- When there is a request for multiple ranges, these are transmitted as a
- multipart message. The multipart media type used for this purpose is
- "multipart/byteranges".
- */
-
- $fileext = strtoupper( pathinfo($filename, PATHINFO_EXTENSION) );
- $filesize=filesize($filename);
- $file=fopen($filename,"rb");
-
- $ranges=NULL;
- if ($_SERVER['REQUEST_METHOD']=='GET' && isset($_SERVER['HTTP_RANGE']) && $range=stristr(trim($_SERVER['HTTP_RANGE']),'bytes=')){
- $range=substr($range,6);
- $boundary='g45d64df96bmdf4sdgh45hf5';//set a random boundary
- $ranges=explode(',',$range);
- }
-
- if($ranges && count($ranges)){
- header("HTTP/1.1 206 Partial content");
- header("Accept-Ranges: bytes");
- if(count($ranges)>1){
- /*
- More than one range is requested.
- */
-
- //compute content length
- $content_length=0;
- foreach ($ranges as $range){
- set_range($range, $filesize, $first, $last);
- $content_length+=strlen("\r\n--$boundary\r\n");
-if ($fileext=="PDF")
- $content_length+=strlen("Content-type: application/pdf\r\n");
-else
- $content_length+=strlen("Content-type: application/octet-stream\r\n");
- $content_length+=strlen("Content-range: bytes $first-$last/$filesize\r\n\r\n");
- $content_length+=$last-$first+1;
- }
- $content_length+=strlen("\r\n--$boundary--\r\n");
-
- //output headers
- header("Content-Length: $content_length");
- //see http://httpd.apache.org/docs/misc/known_client_problems.html for an discussion of x-byteranges vs. byteranges
- header("Content-Type: multipart/x-byteranges; boundary=$boundary");
-
- //output the content
- foreach ($ranges as $range){
- set_range($range, $filesize, $first, $last);
- echo "\r\n--$boundary\r\n";
-if ($fileext=="PDF")
- echo "Content-type: application/pdf\r\n";
-else
- echo "Content-type: application/octet-stream\r\n";
- echo "Content-range: bytes $first-$last/$filesize\r\n\r\n";
- fseek($file,$first);
- buffered_read ($file, $last-$first+1);
- }
- echo "\r\n--$boundary--\r\n";
- } else {
- /*
- A single range is requested.
- */
- $range=$ranges[0];
- set_range($range, $filesize, $first, $last);
- header("Content-Length: ".($last-$first+1) );
- header("Content-Range: bytes $first-$last/$filesize");
-if ($fileext=="PDF")
- header("Content-Type: application/pdf");
-else
- header("Content-Type: application/octet-stream");
- fseek($file,$first);
- buffered_read($file, $last-$first+1);
- }
- } else{
- //no byteserving
- header("Accept-Ranges: bytes");
- header("Content-Length: $filesize");
-if ($fileext=="PDF")
- header("Content-Type: application/pdf");
-else
- header("Content-Type: application/octet-stream");
- readfile($filename);
- }
- fclose($file);
-}
-
-function serve($filename, $download=0){
- //Just serves the file without byteserving
- //if $download=true, then the save file dialog appears
- $filesize=filesize($filename);
- header("Content-Length: $filesize");
- header("Content-Type: application/octet-stream");
- $filename_parts=pathinfo($filename);
- if($download) header('Content-disposition: attachment; filename='.$filename_parts['basename']);
- readfile($filename);
-}
-
-//unset magic quotes; otherwise, file contents will be modified
-//set_magic_quotes_runtime(0);
-
-//do not send cache limiter header
-//ini_set('session.cache_limiter','none');
-
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/d5533b06/app/libraries/basecode.php
----------------------------------------------------------------------
diff --git a/app/libraries/basecode.php b/app/libraries/basecode.php
new file mode 100644
index 0000000..bab9fd2
--- /dev/null
+++ b/app/libraries/basecode.php
@@ -0,0 +1,98 @@
+<?php
+class Base32
+{
+ const BITS_5_RIGHT = 31;
+ protected static $CHARS = '0123456789abcdefghijklmnopqrstuv';
+
+ public static function encode($data)
+ {
+ $dataSize = strlen($data);
+ $res = '';
+ $remainder = 0;
+ $remainderSize = 0;
+
+ for ($i = 0; $i < $dataSize; $i++)
+ {
+ $b = ord($data[$i]);
+ $remainder = ($remainder << 8) | $b;
+ $remainderSize += 8;
+ while ($remainderSize > 4)
+ {
+ $remainderSize -= 5;
+ $c = $remainder & (self::BITS_5_RIGHT << $remainderSize);
+ $c >>= $remainderSize;
+ $res .= self::$CHARS[$c];
+ }
+ }
+ if ($remainderSize > 0)
+ {
+ // remainderSize < 5:
+ $remainder <<= (5 - $remainderSize);
+ $c = $remainder & self::BITS_5_RIGHT;
+ $res .= self::$CHARS[$c];
+ }
+
+ return $res;
+ }
+
+ public static function decode($data)
+ {
+ $data = strtolower($data);
+ $dataSize = strlen($data);
+ $buf = 0;
+ $bufSize = 0;
+ $res = '';
+
+ for ($i = 0; $i < $dataSize; $i++)
+ {
+ $c = $data[$i];
+ $b = strpos(self::$CHARS, $c);
+ if ($b === false)
+ throw new Exception('Encoded string is invalid, it contains unknown char #'.ord($c));
+ $buf = ($buf << 5) | $b;
+ $bufSize += 5;
+ if ($bufSize > 7)
+ {
+ $bufSize -= 8;
+ $b = ($buf & (0xff << $bufSize)) >> $bufSize;
+ $res .= chr($b);
+ }
+ }
+
+ return $res;
+ }
+}
+
+function rbase64_encode($string){
+ $string = base64_encode($string);
+ $reversed_string="";
+ $string_length = strlen($string);
+
+ for($i=$string_length-1;$i>-1;$i--)
+ {
+ if ($string[$i]==='=')
+ $reversed_string .= '_';
+ else
+ $reversed_string .= $string[$i];
+ }
+ return $reversed_string;
+}
+
+
+function rbase64_decode($rstring){
+ $string="";
+ $string_length = strlen($rstring);
+
+ for($i=$string_length-1;$i>-1;$i--)
+ {
+ if ($rstring[$i]==='_')
+ $string .= '=';
+ else
+ $string .= $rstring[$i];
+ }
+
+ return base64_decode($string);
+}
+
+
+?>
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/d5533b06/app/routes.php
----------------------------------------------------------------------
diff --git a/app/routes.php b/app/routes.php
index a9f40be..81e1ca5 100755
--- a/app/routes.php
+++ b/app/routes.php
@@ -171,14 +171,14 @@ Route::get("gbrowser/{filelist}", function($filelist){
$folder_path=$filelist[0]. "ARCHIVE" ;
$content = "[ \n";
-include("base32.php");
-
+ include("libraries/basecode.php");
+
for($i=1; $i<3; $i++){
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($filelist[$i*2]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode($filelist[$i*2]). '",
name: "'. $filelist[$i*2-1] .'",
- fixedscale:{min:0,max:20},
+ #fixedscale:{min:0,max:20},
colorpositive:"#B30086",
colornegative:"#0000e5",
height:100,
@@ -186,9 +186,10 @@ include("base32.php");
},'. "\n" ;
}
- $content = $content . '{
+
+ $content = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($folder_path . '/out.dREG.pred.gz').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode($folder_path . '/out.dREG.pred.gz').'",
name: "dREG informative pos.:",
mode: "show",
colorpositive:"#B30086",
@@ -198,9 +199,9 @@ include("base32.php");
#fixedscale:{min:0, max:1},
},'. "\n";
- $content = $content . '{
+ $content = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.peak.gz').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode( $folder_path . '/out.dREG.peak.gz').'",
name: "dREG Peak Calling:",
mode: "show",
colorpositive:"#B30086",
@@ -210,9 +211,9 @@ include("base32.php");
#fixedscale:{min:0, max:1},
},'. "\n";
- $content = $content . '{
+ $content = $content . '{
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
name: "imputed DNase-I signal:",
#fixedscale:{min:0,max:20},
colorpositive:"#00B306",
@@ -222,7 +223,7 @@ include("base32.php");
$content = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode( $folder_path . '/out.dREG.HD.relaxed.bed.gz').'",
name: "dREG.HD relaxed peaks:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -233,7 +234,7 @@ include("base32.php");
$content = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.rbase64_encode( $folder_path . '/out.dREG.HD.stringent.bed.gz').'",
name: "dREG.HD stringent peaks:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -252,26 +253,25 @@ include("base32.php");
Route::get("gbfile/{file}", function($file){
$filename = pathinfo($file, PATHINFO_FILENAME);
$fileext = pathinfo($file, PATHINFO_EXTENSION);
-include("base32.php");
+
+ include("libraries/basecode.php");
if( $fileext != "")
- $file = base32::decode( $filename ) .".".$fileext;
+ $file = rbase64_decode( $filename ) .".".$fileext;
else
- $file = base32::decode( $filename );
+ $file = rbase64_decode( $filename );
if(0 === strpos($file, '/')){
$file = substr($file, 1);
}
$downloadLink = Config::get('pga_config.airavata')['experiment-data-absolute-path'] . '/' . $file;
+
if ( !file_exists($downloadLink) )
- return Response::make('', 204);
+ return Response::make("", 204);
else
{
if ($_SERVER["REQUEST_METHOD"]=="GET")
- {
- include 'libraries/PartialDownload.php';
- return byteserve( $downloadLink);
- }
+ return Response::download($downloadLink);
else
return Response::make("", 200)
->header('Content-Length', filesize($downloadLink));