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Posted to commits@airavata.apache.org by ma...@apache.org on 2019/06/02 17:22:48 UTC
[airavata-php-gateway] 01/14: adding a prefix for output file
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 1fe068716937b1695479f890e0a3e7e1c5b7e345
Author: root <ro...@osboxes>
AuthorDate: Wed Mar 14 16:09:31 2018 +0000
adding a prefix for output file
---
app/libraries/FileTransfer.php | 46 ++++++++++++++++++++++------
app/views/partials/experiment-info.blade.php | 38 ++++++++++++++++++-----
2 files changed, 66 insertions(+), 18 deletions(-)
diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php
index c59b280..73882a6 100644
--- a/app/libraries/FileTransfer.php
+++ b/app/libraries/FileTransfer.php
@@ -24,15 +24,16 @@ class FileTransfer {
$filelist = explode("\n", RBase64::decode( $filelist ) );
$folder_path=$filelist[0]. "ARCHIVE" ;
$content = "[ \n";
+ $out_prefix = $filelist[3];
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[2]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[1]). '",
name: "'. $filelist[1] .'",
#fixedscale:{min:0,max:20},
summarymethod:"max",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
height:100,
mode: "show",
},'. "\n" ;
@@ -40,19 +41,19 @@ class FileTransfer {
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[4]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($filelist[0].'/'.$filelist[2]). '",
name: "'. $filelist[3] .'",
#fixedscale:{min:0,max:20},
summarymethod:"min",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
+ colorpositive:"#C5000B",
+ colornegative:"#0084D1",
height:100,
mode: "show",
},'. "\n" ;
$content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'",
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dREG.infp.bw').'",
name: "dREG Info. Sites:",
mode: "show",
colorpositive:"#B30086",
@@ -63,8 +64,8 @@ class FileTransfer {
},'. "\n";
$content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'",
+ type:"bigwig",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/'. $out_prefix .'.dREG.peak.score.bw').'",
name: "dREG Peak Calling:",
mode: "show",
colorpositive:"#B30086",
@@ -76,6 +77,31 @@ class FileTransfer {
#$content = $content . '{
+ # type:"bedgraph",
+ # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.infp.bed.gz').'",
+ # name: "dREG Info. Sites:",
+ # mode: "show",
+ # colorpositive:"#B30086",
+ # colornegative:"#0000e5",
+ # backgroundcolor:"#ffffe5",
+ # height:40,
+ # fixedscale:{min:0, max:1},
+ #},'. "\n";
+
+ #$content = $content . '{
+ # type:"bedgraph",
+ # url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.peak.score.bed.gz').'",
+ # name: "dREG Peak Calling:",
+ # mode: "show",
+ # colorpositive:"#B30086",
+ # colornegative:"#0000e5",
+ # backgroundcolor:"#ffffe5",
+ # height:40,
+ # fixedscale:{min:0.2, max:1.0},
+ #},'. "\n";
+
+
+ #$content = $content . '{
# type:"bigwig",
# url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
# name: "imputed DNase-I signal:",
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index 4f43aee..268058b 100755
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -200,16 +200,32 @@
}
$dataRoot = Config::get("pga_config.airavata")["experiment-data-absolute-path"];
+
+
+ $param_prefix = "out";
+ if( count( $experiment->experimentInputs) > 0 )
+ foreach( $experiment->experimentInputs as $input)
+ {
+ if ($input->applicationArgument == "prefix") {
+ $param_prefix = $input->value;
+ }
+ }
?>
<td>
<select id="download">
<option value=''>Select results</option>
-@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/out.dREG.tar.gz') )
- <option value="out.dREG.tar.gz">Full results</option>
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.tar.gz') )
+ <option value=<?php echo $param_prefix.".tar.gz" ?>>Full results</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.infp.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.infp.bed.gz"?>>dREG informative sites</option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.peak.full.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.peak.full.bed.gz"?>>dREG peaks </option>
+@endif
+@if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/'.$param_prefix.'.dREG.peak.score.bed.gz') )
+ <option value=<?php echo $param_prefix.".dREG.peak.score.bed.gz"?>>dREG peak(only with scores)</option>
@endif
- <option value="out.dREG.infp.bed.gz">dREG informative sites</option>
- <option value="out.dREG.peak.full.bed.gz">dREG peaks </option>
- <option value="out.dREG.peak.score.bed.gz">dREG peak(only with scores)</option>
</select>
<a href="" target="_blank" id="retLinks">Download <span class="glyphicon glyphicon-save" style="width:20px"></span></a>
@@ -497,12 +513,18 @@
$currentOutputPath = $rp->filePath;
break;
}
-
- $path = str_replace($dataRoot, "", parse_url($currentOutputPath, PHP_URL_PATH));
- $filelist = $filelist . $input->name . "\n". $path. "\n";
+ $path = str_replace($dataRoot.$expDataDir, "", parse_url($currentOutputPath, PHP_URL_PATH));
+ $filelist = $filelist . $path. "\n";
+ }
+ else
+ {
+ $filelist = $filelist . $input->value. "\n";
}
$filelist = $expDataDir ."\n". $filelist;
+ // in case no prefix label for output file in the interface, put "out" at the end
+ $filelist = $filelist . "out\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';