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 <root@osboxes> Authored: Mon Feb 6 16:02:23 2017 +0000 Committer: root <root@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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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
