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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/02/09 16:44:39 UTC
airavata-php-gateway git commit: adding partial download
Repository: airavata-php-gateway
Updated Branches:
refs/heads/dreg-gateway ba4e57427 -> 003801168
adding partial download
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/00380116
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/00380116
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/00380116
Branch: refs/heads/dreg-gateway
Commit: 003801168e2b404e02708566f9115ea96c563fb5
Parents: ba4e574
Author: root <ro...@osboxes>
Authored: Wed Feb 8 23:06:40 2017 +0000
Committer: root <ro...@osboxes>
Committed: Wed Feb 8 23:06:40 2017 +0000
----------------------------------------------------------------------
app/libraries/PartialDownload.php | 174 +++++++++++++++++++++++++++++++++
app/routes.php | 44 ++++++---
2 files changed, 205 insertions(+), 13 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/00380116/app/libraries/PartialDownload.php
----------------------------------------------------------------------
diff --git a/app/libraries/PartialDownload.php b/app/libraries/PartialDownload.php
new file mode 100644
index 0000000..eb10775
--- /dev/null
+++ b/app/libraries/PartialDownload.php
@@ -0,0 +1,174 @@
+<?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($filename);
+}
+
+//unset magic quotes; otherwise, file contents will be modified
+//set_magic_quotes_runtime(0);
+
+//do not send cache limiter header
+//ini_set('session.cache_limiter','none');
+
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/00380116/app/routes.php
----------------------------------------------------------------------
diff --git a/app/routes.php b/app/routes.php
index 955a77a..28f69d1 100755
--- a/app/routes.php
+++ b/app/routes.php
@@ -177,8 +177,9 @@ Route::get("gbrowser/{filelist}", function($filelist){
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($filelist[$i*2]). '",
name: "'. $filelist[$i*2-1] .'",
fixedscale:{min:0,max:20},
- colorpositive:"rgb(197,0,11)",
- height:50,
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
+ height:100,
mode: "show",
},'. "\n" ;
}
@@ -188,10 +189,11 @@ Route::get("gbrowser/{filelist}", function($filelist){
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($folder_path . '/out.dREG.pred.gz').'",
name: "dREG informative pos.:",
mode: "show",
- colorpositive:"#0000e5/#B30086",
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
backgroundcolor:"#ffffe5",
height:30,
- fixedscale:{min:0, max:1},
+ #fixedscale:{min:0, max:1},
},'. "\n";
$content = $content . '{
@@ -199,19 +201,20 @@ Route::get("gbrowser/{filelist}", function($filelist){
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.peak.gz').'",
name: "dREG Peak Calling:",
mode: "show",
- colorpositive:"#0000e5/#B30086",
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
backgroundcolor:"#ffffe5",
height:30,
- fixedscale:{min:0, max:1},
+ #fixedscale:{min:0, max:1},
},'. "\n";
$content = $content . '{
type:"bigwig",
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
name: "imputed DNase-I signal:",
- fixedscale:{min:0,max:20},
- colorpositive:"rgb(197,0,11)",
- height:50,
+ #fixedscale:{min:0,max:20},
+ colorpositive:"#00B306",
+ height:100,
mode: "show",
},'. "\n";
@@ -220,7 +223,8 @@ Route::get("gbrowser/{filelist}", function($filelist){
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
name: "dREG.HD relaxed peaks:",
mode: "show",
- colorpositive:"#0000e5/#B30086",
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
backgroundcolor:"#ffffe5",
height:30,
fixedscale:{min:0, max:1},
@@ -231,7 +235,8 @@ Route::get("gbrowser/{filelist}", function($filelist){
url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
name: "dREG.HD stringent peaks:",
mode: "show",
- colorpositive:"#0000e5/#B30086",
+ colorpositive:"#B30086",
+ colornegative:"#0000e5",
backgroundcolor:"#ffffe5",
height:30,
fixedscale:{min:0, max:1},
@@ -245,12 +250,25 @@ Route::get("gbrowser/{filelist}", function($filelist){
});
Route::get("gbfile/{file}", function($file){
- $file = base64_decode( $file );
+ $filename = pathinfo($file, PATHINFO_FILENAME);
+ $fileext = pathinfo($file, PATHINFO_EXTENSION);
+ if( $fileext != "")
+ $file = base64_decode( $filename ) .".".$fileext;
+ else
+ $file = base64_decode( $filename );
+
if(0 === strpos($file, '/')){
$file = substr($file, 1);
}
+
$downloadLink = Config::get('pga_config.airavata')['experiment-data-absolute-path'] . '/' . $file;
- return Response::download( $downloadLink);
+ if ( !file_exists($downloadLink) )
+ return Response::make('', 404);
+ else
+ {
+ include 'libraries/PartialDownload.php';
+ return byteserve( $downloadLink);
+ }
});
// dREG