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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/02/06 19:32:27 UTC
airavata-php-gateway git commit: bug in json file for genome browser
Repository: airavata-php-gateway
Updated Branches:
refs/heads/dreg-gateway e11970022 -> cbd43e133
bug in json file for 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/cbd43e13
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/cbd43e13
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/cbd43e13
Branch: refs/heads/dreg-gateway
Commit: cbd43e133203d0403d2486715fc18ab6ebe585f7
Parents: e119700
Author: root <ro...@osboxes>
Authored: Mon Feb 6 16:02:23 2017 +0000
Committer: root <ro...@osboxes>
Committed: Mon Feb 6 16:02:23 2017 +0000
----------------------------------------------------------------------
app/libraries/ExperimentUtilities.php | 4 +-
app/routes.php | 73 +++++--------------
app/views/partials/experiment-info.blade.php | 40 +++++++++-
public/themes/dreg/assets/img/cornell-logo.png | Bin 23327 -> 23321 bytes
public/themes/dreg/assets/img/dankolab-logo.png | Bin 228884 -> 56271 bytes
5 files changed, 56 insertions(+), 61 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/cbd43e13/app/libraries/ExperimentUtilities.php
----------------------------------------------------------------------
diff --git a/app/libraries/ExperimentUtilities.php b/app/libraries/ExperimentUtilities.php
index 12718f1..d3a900b 100755
--- a/app/libraries/ExperimentUtilities.php
+++ b/app/libraries/ExperimentUtilities.php
@@ -100,7 +100,7 @@ class ExperimentUtilities
}
echo '<p>' . $input->name . ': <a target="_blank" href="' . URL::to("/") . '/download/?id='
- . $input->value . '">' . $fileName . ' <span class="glyphicon glyphicon-new-window"></span></a></p>';
+ . $input->value . '">' . $fileName . ' <span class="glyphicon glyphicon-save"></span></a></p>';
}else if($input->type == DataType::URI_COLLECTION) {
$uriList = $input->value;
@@ -122,7 +122,7 @@ class ExperimentUtilities
}
$optFilesHtml = $optFilesHtml . '<a target="_blank" href="' . URL::to("/") . '/download/?id='
- . $uri . '">' . $fileName . ' <span class="glyphicon glyphicon-new-window"></span></a> ';
+ . $uri . '">' . $fileName . ' <span class="glyphicon glyphicon-save"></span></a> ';
}
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/cbd43e13/app/routes.php
----------------------------------------------------------------------
diff --git a/app/routes.php b/app/routes.php
index 05bec1e..b1a18d6 100755
--- a/app/routes.php
+++ b/app/routes.php
@@ -162,59 +162,20 @@ Route::get("files/get","FilemanagerController@get");
// Added by dREG
Route::get("gbrowser", function(){
-
- $experiment = ExperimentUtilities::get_experiment(Input::get('expId'));
-
- if(0 === strpos($experiment->userConfigurationData->experimentDataDir, Config::get("pga_config.airavata")['experiment-data-absolute-path'])){
- $expDataDir = str_replace(Config::get("pga_config.airavata")['experiment-data-absolute-path'], "", $experiment->userConfigurationData->experimentDataDir);
- }else{
- $expDataDir = $experiment->userConfigurationData->experimentDataDir;
- }
-
- $folder_path = $expDataDir . 'ARCHIVE';
- if(strpos($folder_path, "/")==0)
- $folder_path = substr($folder_path, 1);
-
- ob_start();
- ExperimentUtilities::list_input_files($experiment->experimentInputs);
- $html = ob_get_contents();
- ob_end_clean();
-
- $DOM = new DOMDocument;
- $DOM->loadHTML( $html . "<H1>A</H1>");
-
- $content = "[\n";
- $items = $DOM->getElementsByTagName('a');
- for ($i = 0; $i < $items->length; $i++)
- {
- $fname = $items->item($i)->nodeValue ;
- $fhref = $items->item($i)->getAttribute("href") ;
- if(strpos($fhref, 'airavata-dp:')===false)
- {
- }
- else
- {
- $id= substr($fhref, strpos($fhref, 'airavata-dp:') );
- }
-
- $dataProductModel = Airavata::getDataProduct(Session::get('authz-token'), $id);
- $currentOutputPath = "";
- foreach ($dataProductModel->replicaLocations as $rp) {
- if($rp->replicaLocationCategory == Airavata\Model\Data\Replica\ReplicaLocationCategory::GATEWAY_DATA_STORE){
- $currentOutputPath = $rp->filePath;
- break;
- }
- }
-
- $dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
- $fpath = str_replace($dataRoot, "", parse_url($currentOutputPath, PHP_URL_PATH));
- if(strpos($fpath, "/")==0)
- $fpath = substr($fpath, 1);
-
+ $protocol = 'http';
+ if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https')
+ $protocol = 'https';
+
+ $dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
+ $filelist = explode("\n", urldecode( Input::get('filelist') ) );
+ $folder_path=$filelist[0]. "ARCHIVE" ;
+ $content = "";
+
+ for($i=1; $i<3; $i++){
$content = $content . ' {
type:"bigwig",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/download?path='. $fpath . '",
- name: "'. $fname.'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $filelist[$i*2] . '",
+ name: "'. $filelist[$i*2-1] .'",
fixedscale:{min:0,max:20},
colorpositive:"rgb(197,0,11)",
height:50,
@@ -224,7 +185,7 @@ Route::get("gbrowser", function(){
$content = $content . '{
type:"bedgraph",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/gbfile?path='. $folder_path . '/out.dREG.pred.gz",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $folder_path . '/out.dREG.pred.gz",
name: "dREG informative pos.:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -235,7 +196,7 @@ Route::get("gbrowser", function(){
$content = $content . '{
type:"bedgraph",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/gbfile?path='. $folder_path . '/out.dREG.peak.gz",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $folder_path . '/out.dREG.peak.gz",
name: "dREG Peak Calling:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -246,7 +207,7 @@ Route::get("gbrowser", function(){
$content = $content . '{
type:"bigwig",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/gbfile?path='. $folder_path . '/out.dREG.HD.imputedDnase.bw",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $folder_path . '/out.dREG.HD.imputedDnase.bw",
name: "imputed DNase-I signal:",
fixedscale:{min:0,max:20},
colorpositive:"rgb(197,0,11)",
@@ -256,7 +217,7 @@ Route::get("gbrowser", function(){
$content = $content . '{
type:"bedgraph",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/gbfile?path='. $folder_path . '/out.dREG.HD.relaxed.bed",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $folder_path . '/out.dREG.HD.relaxed.bed",
name: "dREG.HD relaxed peaks:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -267,7 +228,7 @@ Route::get("gbrowser", function(){
$content = $content . '{
type:"bedgraph",
- url:"http://'. $_SERVER['HTTP_HOST'] .'/gbfile?path='. $folder_path . '/out.dREG.HD.stringent.bed",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/download?path='. $folder_path . '/out.dREG.HD.stringent.bed",
name: "dREG.HD stringent peaks:",
mode: "show",
colorpositive:"#0000e5/#B30086",
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/cbd43e13/app/views/partials/experiment-info.blade.php
----------------------------------------------------------------------
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
old mode 100644
new mode 100755
index 2144873..5a4e4a5
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -204,7 +204,7 @@
<script type="text/javascript">
function download(d) {
if (d == 'Download one result') return;
- window.open('https://{{$_SERVER['HTTP_HOST']}}/download?path={{$expDataDir}}/ARCHIVE/' + d);
+ window.open('/download?path={{$expDataDir}}/ARCHIVE/' + d);
}
</script>
@@ -218,10 +218,44 @@ function download(d) {
</select>
-<a href="/download?path={{$expDataDir}}/ARCHIVE/out.dREG.tar.gz" target="_blank"><span class="glyphicon glyphicon-save" style="width:20px"></span>Download All Results</a>
+<a href="/download?path={{$expDataDir}}/ARCHIVE/out.dREG.tar.gz" target="_blank">Download All Results <span class="glyphicon glyphicon-save" style="width:20px"></span></a>
-<a href="http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub=https://{{$_SERVER['HTTP_HOST']}}/gbrowser?expId={{$_GET['expId']}}" target="_blank"><span class="glyphicon glyphicon-new-window" style="width:20px"></span>Genome Browser</a>
+<?php
+ $filelist="";
+ $dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
+
+ if( count( $experiment->experimentInputs) > 0 )
+ foreach( $experiment->experimentInputs as $input)
+ if ($input->type == Airavata\Model\Application\Io\DataType::URI) {
+
+ $dataProductModel = Airavata::getDataProduct(Session::get('authz-token'), $input->value);
+ $currentOutputPath = "";
+ foreach ($dataProductModel->replicaLocations as $rp)
+ if($rp->replicaLocationCategory == Airavata\Model\Data\Replica\ReplicaLocationCategory::GATEWAY_DATA_STORE){
+ $currentOutputPath = $rp->filePath;
+ break;
+ }
+
+ $path = str_replace($dataRoot, "", parse_url($currentOutputPath, PHP_URL_PATH));
+ $filelist = $filelist . $input->name . "\n". $path. "\n";
+ }
+
+ $protocol = 'http';
+ if ( isset($_SERVER['HTTPS']) && ($_SERVER['HTTPS'] == 'on' || $_SERVER['HTTPS'] == 1) || isset($_SERVER['HTTP_X_FORWARDED_PROTO']) && $_SERVER['HTTP_X_FORWARDED_PROTO'] == 'https')
+ $protocol = 'https';
+
+ if(0 === strpos($experiment->userConfigurationData->experimentDataDir, Config::get("pga_config.airavata")['experiment-data-absolute-path'])){
+ $expDataDir = str_replace(Config::get("pga_config.airavata")['experiment-data-absolute-path'], "", $experiment->userConfigurationData->experimentDataDir);
+ }else{
+ $expDataDir = $experiment->userConfigurationData->experimentDataDir;
+ }
+
+ $filelist=$expDataDir ."\n". $filelist;
+?>
+
+<a href="http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub={{$protocol}}://{{$_SERVER['HTTP_HOST']}}/gbrowser?filelist={{urlencode($filelist)}}" target="_blank">
+Genome Browser <span class="glyphicon glyphicon-new-window" style="width:20px"></span></a>
</td>
</tr>
{{-- dREG --}}
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/cbd43e13/public/themes/dreg/assets/img/cornell-logo.png
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diff --git a/public/themes/dreg/assets/img/cornell-logo.png b/public/themes/dreg/assets/img/cornell-logo.png
index b47e640..b567aa1 100755
Binary files a/public/themes/dreg/assets/img/cornell-logo.png and b/public/themes/dreg/assets/img/cornell-logo.png differ
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/cbd43e13/public/themes/dreg/assets/img/dankolab-logo.png
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diff --git a/public/themes/dreg/assets/img/dankolab-logo.png b/public/themes/dreg/assets/img/dankolab-logo.png
index 9210291..b12ce4e 100755
Binary files a/public/themes/dreg/assets/img/dankolab-logo.png and b/public/themes/dreg/assets/img/dankolab-logo.png differ