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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/02/15 14:38:35 UTC
[01/12] airavata-php-gateway git commit: fixing AIRAVATA-2265 : in
SciGaP latest record should be on top of the list in Gateway requests.
Repository: airavata-php-gateway
Updated Branches:
refs/heads/dreg-gateway 003801168 -> 75929d779
fixing AIRAVATA-2265 : in SciGaP latest record should be on top of the list in Gateway requests.
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/f436e6a5
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/f436e6a5
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/f436e6a5
Branch: refs/heads/dreg-gateway
Commit: f436e6a5227a703562f17b9f460f8350b10937da
Parents: dae6cd7
Author: scnakandala <su...@gmail.com>
Authored: Mon Jan 30 10:50:40 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Jan 30 10:50:40 2017 -0500
----------------------------------------------------------------------
app/controllers/AdminController.php | 6 ++++++
1 file changed, 6 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/f436e6a5/app/controllers/AdminController.php
----------------------------------------------------------------------
diff --git a/app/controllers/AdminController.php b/app/controllers/AdminController.php
index 9735b9a..d0aa3e5 100644
--- a/app/controllers/AdminController.php
+++ b/app/controllers/AdminController.php
@@ -99,12 +99,18 @@ class AdminController extends BaseController {
}
+ private function cmp($a, $b)
+ {
+ return strcmp($b->requestCreationTime, $a->requestCreationTime);
+ }
+
public function gatewayView(){
//only for super admin
//Session::put("super-admin", true);
$gatewaysInfo = CRUtilities::getAllGatewayProfilesData();
$gateways = $gatewaysInfo["gateways"];
+ usort($gateways, array($this, "cmp"));
$tokens = AdminUtilities::get_all_ssh_tokens();
$pwdTokens = AdminUtilities::get_all_pwd_tokens();
$srData = SRUtilities::getEditSRData();
[04/12] airavata-php-gateway git commit: fixing wrong parameter names
in compute resource pref
Posted by ma...@apache.org.
fixing wrong parameter names in compute resource pref
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/6f55b5b1
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/6f55b5b1
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/6f55b5b1
Branch: refs/heads/dreg-gateway
Commit: 6f55b5b18dd38d39e5276b5b573c05790abf75b4
Parents: c4c63b7
Author: scnakandala <su...@gmail.com>
Authored: Tue Feb 7 14:02:22 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Tue Feb 7 14:02:22 2017 -0500
----------------------------------------------------------------------
app/views/partials/compute-resource-preferences.blade.php | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/6f55b5b1/app/views/partials/compute-resource-preferences.blade.php
----------------------------------------------------------------------
diff --git a/app/views/partials/compute-resource-preferences.blade.php b/app/views/partials/compute-resource-preferences.blade.php
index 86f0b3d..62a3a39 100644
--- a/app/views/partials/compute-resource-preferences.blade.php
+++ b/app/views/partials/compute-resource-preferences.blade.php
@@ -106,7 +106,7 @@
<label class="control-label col-md-3">Gateway Id for Usage Reporting</label>
<div class="col-md-9">
- <input type="text" name="allocationProjectNumber" class="form-control"
+ <input type="text" name="usageReportingGatewayId" class="form-control"
value="@if( isset( $preferences) ) {{$preferences->usageReportingGatewayId }}@endif"/>
<small>Enter Id of the Gateway using this resource if it requires reporting its usage back to the resource.</small>
</div>
[10/12] airavata-php-gateway git commit: Making sidebar sticky.
Posted by ma...@apache.org.
Making sidebar sticky.
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/db5eba49
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/db5eba49
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/db5eba49
Branch: refs/heads/dreg-gateway
Commit: db5eba49bec763e2aa49d19748f9169b98a72ada
Parents: dc971cb
Author: Nipurn Doshi <ni...@gmail.com>
Authored: Sun Feb 12 16:27:52 2017 -0800
Committer: Nipurn Doshi <ni...@gmail.com>
Committed: Sun Feb 12 16:27:52 2017 -0800
----------------------------------------------------------------------
app/views/layout/basic.blade.php | 10 +++++++---
app/views/partials/dashboard-block.blade.php | 6 ++----
public/css/admin.css | 10 ++++++++--
3 files changed, 17 insertions(+), 9 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/db5eba49/app/views/layout/basic.blade.php
----------------------------------------------------------------------
diff --git a/app/views/layout/basic.blade.php b/app/views/layout/basic.blade.php
index b621ecd..3e5e396 100755
--- a/app/views/layout/basic.blade.php
+++ b/app/views/layout/basic.blade.php
@@ -14,6 +14,9 @@ $title = Session::get("portal-title");
position: relative;
z-index:101;
}
+.content-area{
+ margin: 20px 0;
+}
</style>
<div class="theme-header">
<!-- Header from theme -->
@@ -92,12 +95,13 @@ var fullName = "{{Session::get("user-profile")["firstname"] . " " . Session::get
//put sidebar below all headers in admin dashboards
if( $(".side-nav").length > 0){
var headerHeight = $(".pga-header").height() + $(".theme-header").height();
- $(".side-nav").css("padding-top", headerHeight);
-
+ $(".side-nav").css("top", headerHeight);
+ $(".side-nav").affix();
var selectedDashboardHeight = $(window).height() - headerHeight;
+
if( selectedDashboardHeight < $(".side-nav").height())
{
- $(".side-nav").height( selectedDashboardHeight).css("overflow-y", "scroll").css("overflow-x", "none");
+ $(".side-nav").height( selectedDashboardHeight);
}
}
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/db5eba49/app/views/partials/dashboard-block.blade.php
----------------------------------------------------------------------
diff --git a/app/views/partials/dashboard-block.blade.php b/app/views/partials/dashboard-block.blade.php
index d2b5220..8a07d78 100644
--- a/app/views/partials/dashboard-block.blade.php
+++ b/app/views/partials/dashboard-block.blade.php
@@ -1,7 +1,5 @@
-<div class="collapse navbar-collapse navbar-ex1-collapse">
- <ul class="nav navbar-nav side-nav">
-
-
+<div class="collapse navbar-collapse navbar-ex1-collapse" >
+ <ul class="nav navbar-nav side-nav" data-spy="affix" >
<li
@if( Session::has("admin-nav") && Session::get("admin-nav") == "exp-statistics") class="active" @endif>
<a class="dashboard-link" href="{{ URL::to('/')}}/admin/dashboard/experiments">
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/db5eba49/public/css/admin.css
----------------------------------------------------------------------
diff --git a/public/css/admin.css b/public/css/admin.css
index 9d49c68..a1b18b4 100644
--- a/public/css/admin.css
+++ b/public/css/admin.css
@@ -116,12 +116,15 @@ ul.alert-dropdown {
width: 200px;
}
+.affix{
+ top:0;
+}
+
/* Side Navigation */
@media(min-width:768px) {
.side-nav {
- position: fixed;
- top:0;
+ position:fixed;
z-index: 100;
left: 225px;
width: 225px;
@@ -129,6 +132,9 @@ ul.alert-dropdown {
border: none;
border-radius: 0;
background-color: #222;
+
+ overflow-y: auto;
+ overflow-x: none;
}
.side-nav>li>a {
[11/12] airavata-php-gateway git commit: Merge branch 'develop' of
https://git-wip-us.apache.org/repos/asf/airavata-php-gateway into develop
Posted by ma...@apache.org.
Merge branch 'develop' of https://git-wip-us.apache.org/repos/asf/airavata-php-gateway into develop
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/f199d9b8
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/f199d9b8
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/f199d9b8
Branch: refs/heads/dreg-gateway
Commit: f199d9b8b8c87117e6c8f457836167e20ab6b046
Parents: db5eba4 9765c1e
Author: Nipurn Doshi <ni...@gmail.com>
Authored: Sun Feb 12 16:28:14 2017 -0800
Committer: Nipurn Doshi <ni...@gmail.com>
Committed: Sun Feb 12 16:28:14 2017 -0800
----------------------------------------------------------------------
app/config/pga_config.php.template | 8 +++
app/controllers/AccountController.php | 24 +++++--
app/controllers/AdminController.php | 65 ++++++++++--------
app/controllers/ExperimentController.php | 6 +-
app/libraries/CommonUtilities.php | 4 ++
app/views/account/dashboard.blade.php | 5 ++
app/views/admin/manage-gateway.blade.php | 70 +++++++++-----------
.../compute-resource-preferences.blade.php | 2 +-
app/views/storage-resource/edit.blade.php | 1 +
9 files changed, 113 insertions(+), 72 deletions(-)
----------------------------------------------------------------------
[05/12] airavata-php-gateway git commit: AIRAVATA-2312 Removing
unused method
Posted by ma...@apache.org.
AIRAVATA-2312 Removing unused method
AdminController::updateUserRoles isn't routed to or referenced internally
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/773e542c
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/773e542c
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/773e542c
Branch: refs/heads/dreg-gateway
Commit: 773e542c47fbaa1db59739852c2d67717aea3bdd
Parents: 6f55b5b
Author: Marcus Christie <ma...@iu.edu>
Authored: Thu Feb 9 10:22:55 2017 -0500
Committer: Marcus Christie <ma...@iu.edu>
Committed: Thu Feb 9 10:22:55 2017 -0500
----------------------------------------------------------------------
app/controllers/AdminController.php | 15 ---------------
1 file changed, 15 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/773e542c/app/controllers/AdminController.php
----------------------------------------------------------------------
diff --git a/app/controllers/AdminController.php b/app/controllers/AdminController.php
index d0aa3e5..1ecce03 100644
--- a/app/controllers/AdminController.php
+++ b/app/controllers/AdminController.php
@@ -278,21 +278,6 @@ class AdminController extends BaseController {
return View::make("admin/manage-credentials", array("tokens" => $tokens , "pwdTokens" => $pwdTokens) );
}
- public function updateUserRoles(){
- if( Input::has("add")){
- WSIS::updateUserRoles(Input::get("username"), array("new"=> Input::get("roles"), "deleted" => array() ) );
- $roles = WSIS::getUserRoles(Input::get("username"));
- if(in_array(Config::get("pga_config.wsis")["admin-role-name"], $roles) || in_array(Config::get("pga_config.wsis")["read-only-admin-role-name"], $roles)
- || in_array(Config::get("pga_config.wsis")["user-role-name"], $roles)){
- $userProfile = WSIS::getUserProfile(Input::get("username"));
- $recipients = array($userProfile["email"]);
- $this->sendAccessGrantedEmailToTheUser(Input::get("username"), $recipients);
- }
- }
- else
- return WSIS::updateUserRoles(Input::get("username"), array("new"=> array(), "deleted" => Input::get("roles") ) );
- }
-
private function sendAccessGrantedEmailToTheUser($username, $recipients){
$mail = new PHPMailer;
[07/12] airavata-php-gateway git commit: http HEAD
Posted by ma...@apache.org.
http HEAD
Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/206e8d1f
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/206e8d1f
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/206e8d1f
Branch: refs/heads/dreg-gateway
Commit: 206e8d1f07762ccfa3158ebf74e1a727d4bc9826
Parents: ba4e574
Author: root <ro...@osboxes>
Authored: Fri Feb 10 04:51:46 2017 +0000
Committer: root <ro...@osboxes>
Committed: Fri Feb 10 04:51:46 2017 +0000
----------------------------------------------------------------------
app/routes.php | 83 ++++++++++++++++++++++++++++++++++-------------------
1 file changed, 54 insertions(+), 29 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/206e8d1f/app/routes.php
----------------------------------------------------------------------
diff --git a/app/routes.php b/app/routes.php
index 955a77a..4189d13 100755
--- a/app/routes.php
+++ b/app/routes.php
@@ -171,10 +171,12 @@ Route::get("gbrowser/{filelist}", function($filelist){
$folder_path=$filelist[0]. "ARCHIVE" ;
$content = "[ \n";
+include("base32.php");
+
for($i=1; $i<3; $i++){
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($filelist[$i*2]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($filelist[$i*2]). '",
name: "'. $filelist[$i*2-1] .'",
fixedscale:{min:0,max:20},
colorpositive:"rgb(197,0,11)",
@@ -183,9 +185,9 @@ Route::get("gbrowser/{filelist}", function($filelist){
},'. "\n" ;
}
- $content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($folder_path . '/out.dREG.pred.gz').'",
+ $content = $content . '{
+ type:"bedgraph",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($folder_path . '/out.dREG.pred.gz').'",
name: "dREG informative pos.:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -196,7 +198,7 @@ Route::get("gbrowser/{filelist}", function($filelist){
$content = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.peak.gz').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.peak.gz').'",
name: "dREG Peak Calling:",
mode: "show",
colorpositive:"#0000e5/#B30086",
@@ -207,7 +209,7 @@ Route::get("gbrowser/{filelist}", function($filelist){
$content = $content . '{
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
name: "imputed DNase-I signal:",
fixedscale:{min:0,max:20},
colorpositive:"rgb(197,0,11)",
@@ -215,27 +217,27 @@ Route::get("gbrowser/{filelist}", function($filelist){
mode: "show",
},'. "\n";
- $content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
- name: "dREG.HD relaxed peaks:",
- mode: "show",
- colorpositive:"#0000e5/#B30086",
- backgroundcolor:"#ffffe5",
- height:30,
- fixedscale:{min:0, max:1},
- },'. "\n";
-
- $content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
- name: "dREG.HD stringent peaks:",
- mode: "show",
- colorpositive:"#0000e5/#B30086",
- backgroundcolor:"#ffffe5",
- height:30,
- fixedscale:{min:0, max:1},
- },'. "\n";
+// $content = $content . '{
+// type:"bedgraph",
+// url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
+// name: "dREG.HD relaxed peaks:",
+// mode: "show",
+// colorpositive:"#0000e5/#B30086",
+// backgroundcolor:"#ffffe5",
+// height:30,
+// fixedscale:{min:0, max:1},
+// },'. "\n";
+
+// $content = $content . '{
+// type:"bedgraph",
+// url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
+// name: "dREG.HD stringent peaks:",
+// mode: "show",
+// colorpositive:"#0000e5/#B30086",
+// backgroundcolor:"#ffffe5",
+// height:30,
+// fixedscale:{min:0, max:1},
+// },'. "\n";
$content = $content . ']';
@@ -244,15 +246,38 @@ Route::get("gbrowser/{filelist}", function($filelist){
->header('Content-Type', 'text/plain');
});
+
Route::get("gbfile/{file}", function($file){
- $file = base64_decode( $file );
+ $filename = pathinfo($file, PATHINFO_FILENAME);
+ $fileext = pathinfo($file, PATHINFO_EXTENSION);
+include("base32.php");
+ if( $fileext != "")
+ $file = base32::decode( $filename ) .".".$fileext;
+ else
+ $file = base32::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('', 204);
+ else
+ {
+ if ($_SERVER["REQUEST_METHOD"]=="GET")
+ {
+ include 'libraries/PartialDownload.php';
+ return byteserve( $downloadLink);
+ }
+ else
+ return Response::make("", 200)
+ ->header('Content-Length', filesize($downloadLink));
+ }
+
});
+
// dREG
/*
[06/12] airavata-php-gateway git commit: AIRAVATA-2312 Adds
'initial-role-name' to pga_config.php
Posted by ma...@apache.org.
AIRAVATA-2312 Adds 'initial-role-name' to pga_config.php
'initial-role-name' defaults to 'user-pending' but can be customized to
automatically assign new users to the given role. The main use case for
this is to set 'initial-role-name' to 'gateway-user' to provide new
users access to the gateway without needing admin intervention.
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/9765c1e2
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/9765c1e2
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/9765c1e2
Branch: refs/heads/dreg-gateway
Commit: 9765c1e250992c9ee870243081795e6aa2312948
Parents: 773e542
Author: Marcus Christie <ma...@iu.edu>
Authored: Thu Feb 9 11:17:49 2017 -0500
Committer: Marcus Christie <ma...@iu.edu>
Committed: Thu Feb 9 11:17:49 2017 -0500
----------------------------------------------------------------------
app/config/pga_config.php.template | 8 ++++++
app/controllers/AccountController.php | 9 +++---
app/controllers/AdminController.php | 44 ++++++++++++++++++++++--------
app/libraries/CommonUtilities.php | 4 +++
4 files changed, 50 insertions(+), 15 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9765c1e2/app/config/pga_config.php.template
----------------------------------------------------------------------
diff --git a/app/config/pga_config.php.template b/app/config/pga_config.php.template
index ac378f6..8370364 100644
--- a/app/config/pga_config.php.template
+++ b/app/config/pga_config.php.template
@@ -24,6 +24,14 @@ return array(
'user-role-name' => 'Internal/everyone',
/**
+ * Initial user role. This is the initial user role assigned to a new
+ * user. Set this to one of the three roles above to automatically
+ * grant new users that role, or set to some other role ('user-pending')
+ * to require admin approval before users have access.
+ */
+ 'initial-role-name' => 'user-pending',
+
+ /**
* Tenant Domain
*/
'tenant-domain' => 'master.airavata',
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9765c1e2/app/controllers/AccountController.php
----------------------------------------------------------------------
diff --git a/app/controllers/AccountController.php b/app/controllers/AccountController.php
index 1490ee1..a9ac6b4 100644
--- a/app/controllers/AccountController.php
+++ b/app/controllers/AccountController.php
@@ -56,14 +56,15 @@ class AccountController extends BaseController
WSIS::registerUserAccount($username, $password, $email, $first_name, $last_name, $organization, $address, $country, $telephone, $mobile, $im, $url,
Config::get('pga_config.wsis')['tenant-domain']);
- /*add user to role - user-pending */
+ /*add user to the initial role */
+ $initialRoleName = CommonUtilities::getInitialRoleName();
$allRoles = WSIS::getAllRoles();
- if(! in_array( "user-pending", $allRoles)){
- WSIS::addRole( "user-pending");
+ if(! in_array( $initialRoleName, $allRoles)){
+ WSIS::addRole( $initialRoleName);
}
- $userRoles["new"] = "user-pending";
+ $userRoles["new"] = $initialRoleName;
if( Config::get('pga_config.portal')['super-admin-portal'] == true ){
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9765c1e2/app/controllers/AdminController.php
----------------------------------------------------------------------
diff --git a/app/controllers/AdminController.php b/app/controllers/AdminController.php
index 1ecce03..6dd27bd 100644
--- a/app/controllers/AdminController.php
+++ b/app/controllers/AdminController.php
@@ -236,22 +236,44 @@ class AdminController extends BaseController {
$recipients = array($userProfile["email"]);
$this->sendAccessGrantedEmailToTheUser(Input::get("username"), $recipients);
- // remove the pending role when access is granted, unless
- // the admin is trying to add the user to the pending role
- if(in_array("user-pending", $newCurrentRoles) && !in_array("user-pending", $roles["new"])) {
- $userRoles["new"] = array();
- $userRoles["deleted"] = "user-pending";
- WSIS::updateUserRoles( $username, $userRoles);
- } else if(in_array("user-pending", $newCurrentRoles) && in_array("user-pending", $roles["new"])) {
- // When user-pending role added remove all roles except for user-pending and Internal/everyone
- $userRoles["new"] = array();
- $userRoles["deleted"] = array_diff($newCurrentRoles, array("user-pending", "Internal/everyone"));
- WSIS::updateUserRoles( $username, $userRoles);
+ // remove the initial role when the initial role isn't a privileged
+ // role and the admin has now assigned the user to a privileged
+ // role, unless the admin is trying to add the user back to the
+ // initial role
+ if (!$this->isInitialRoleOneOfPrivilegedRoles()) {
+
+ $initialRoleName = CommonUtilities::getInitialRoleName();
+ if(in_array($initialRoleName, $newCurrentRoles) && !in_array($initialRoleName, $roles["new"])) {
+ $userRoles["new"] = array();
+ $userRoles["deleted"] = $initialRoleName;
+ WSIS::updateUserRoles( $username, $userRoles);
+ } else if(in_array($initialRoleName, $newCurrentRoles) && in_array($initialRoleName, $roles["new"])) {
+ // When initial role added remove all roles except for initial role and Internal/everyone
+ $userRoles["new"] = array();
+ $userRoles["deleted"] = array_diff($newCurrentRoles, array($initialRoleName, "Internal/everyone"));
+ WSIS::updateUserRoles( $username, $userRoles);
+ }
}
}
return Redirect::to("admin/dashboard/roles")->with( "message", "Roles has been added.");
}
+ /*
+ * Return true if the initial-role-name is one of the three privileged
+ * roles. This is used to figure out whether the initial-role-name is a
+ * 'user-pending' kind of role (returns false), or whether the initial role
+ * is a privileged role (returns true) and no admin intervention is
+ * necessary.
+ */
+ private function isInitialRoleOneOfPrivilegedRoles() {
+
+ $initialRoleName = CommonUtilities::getInitialRoleName();
+ $adminRoleName = Config::get("pga_config.wsis")["admin-role-name"];
+ $adminReadOnlyRoleName = Config::get("pga_config.wsis")["read-only-admin-role-name"];
+ $userRoleName = Config::get("pga_config.wsis")["user-role-name"];
+ return in_array($initialRoleName, array($adminRoleName, $adminReadOnlyRoleName, $userRoleName));
+ }
+
public function removeRoleFromUser(){
$roles["deleted"] = array(Input::all()["roleName"]);
$roles["new"] = array();
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9765c1e2/app/libraries/CommonUtilities.php
----------------------------------------------------------------------
diff --git a/app/libraries/CommonUtilities.php b/app/libraries/CommonUtilities.php
index 585016f..53f790e 100644
--- a/app/libraries/CommonUtilities.php
+++ b/app/libraries/CommonUtilities.php
@@ -438,5 +438,9 @@ class CommonUtilities
return false;
}
}
+
+ public static function getInitialRoleName() {
+ return Config::get('pga_config.wsis.initial-role-name', 'user-pending');
+ }
}
[03/12] airavata-php-gateway git commit: AIRAVATA-2266 : When tried
to create tenant it asked to enter the auth key and the secret
Posted by ma...@apache.org.
AIRAVATA-2266 : When tried to create tenant it asked to enter the auth key and the secret
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/c4c63b78
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/c4c63b78
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/c4c63b78
Branch: refs/heads/dreg-gateway
Commit: c4c63b78e4c57b7b80e4082083b25cd8e2395282
Parents: 4c47e54
Author: scnakandala <su...@gmail.com>
Authored: Mon Jan 30 13:51:02 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Jan 30 13:51:02 2017 -0500
----------------------------------------------------------------------
app/views/admin/manage-gateway.blade.php | 70 ++++++++++++---------------
1 file changed, 30 insertions(+), 40 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/c4c63b78/app/views/admin/manage-gateway.blade.php
----------------------------------------------------------------------
diff --git a/app/views/admin/manage-gateway.blade.php b/app/views/admin/manage-gateway.blade.php
index 099bec8..795af43 100644
--- a/app/views/admin/manage-gateway.blade.php
+++ b/app/views/admin/manage-gateway.blade.php
@@ -638,52 +638,42 @@
dataObj[updateGatewayData[i].name] = updateGatewayData[i].value;
}
- if( updateVal == "createTenant" &&
- ( $.trim( dataObj['oauthClientId'] ) == "" || $.trim( dataObj['oauthClientSecret'] ) == "") ){
- $(".submit-actions").before("<div class='alert alert-danger fail-alert'>Tenant creation requires Oauth Client Id and Oauth Client Secret fields to be filled.</div>");
- $(".loading-gif").remove();
- }
- else
- {
- $.ajax({
- url: "{{URL::to('/')}}/admin/update-gateway-request",
- method: "GET",
- data: updateGatewayData
- }).done( function( data){
- $(".loading-gif").remove();
- if( data == -1 ){
- //errors only with -1
- if( updateVal == "createTenant"){
- $(".submit-actions").before("<div class='alert alert-danger fail-alert'>Tenant creation has failed as Tenant with the same Domain name- airavata." + $(".gatewayAcronym").val() + " already exists in Identity Server. Please change Gateway Acronym and try again.");
- }
- else{
- $(".submit-actions").before("<div class='alert alert-danger fail-alert'>Error updating Gateway. Please try again.");
- }
+ $.ajax({
+ url: "{{URL::to('/')}}/admin/update-gateway-request",
+ method: "GET",
+ data: updateGatewayData
+ }).done( function( data){
+ $(".loading-gif").remove();
+ if( data == -1 ){
+ //errors only with -1
+ if( updateVal == "createTenant"){
+ $(".submit-actions").before("<div class='alert alert-danger fail-alert'>Tenant creation has failed as Tenant with the same Domain name- airavata." + $(".gatewayAcronym").val() + " already exists in Identity Server. Please change Gateway Acronym and try again.");
}
else{
- if( updateVal == "createTenant"){
- $(".submit-actions").before("<div class='alert alert-success success-alert'>Tenant has been created with domain name- airavata." + $(".gatewayAcronym").val());
- $(".notCreatedGateway").addClass("hide");
-
- $(".createdGateway").removeClass("hide");
+ $(".submit-actions").before("<div class='alert alert-danger fail-alert'>Error updating Gateway. Please try again.");
+ }
+ }
+ else{
+ if( updateVal == "createTenant"){
+ $(".submit-actions").before("<div class='alert alert-success success-alert'>Tenant has been created with domain name- airavata." + $(".gatewayAcronym").val());
+ $(".notCreatedGateway").addClass("hide");
- }
- else{
- $(".submit-actions").before("<div class='alert alert-success success-alert'>Gateway has been updated successfully.");
- }
+ $(".createdGateway").removeClass("hide");
- //refresh data next time if same popup is opened.
- var gatewayIdWithoutSpaces = dataObj['gateway_id'].replace(/\s+/g, '-');
- $("#view-" + gatewayIdWithoutSpaces).data("gatewayobject", data);
- $("#view-" + gatewayIdWithoutSpaces ).parent().parent().find(".form-gatewayName").html( dataObj['gatewayName']);
- $("#view-" + gatewayIdWithoutSpaces ).parent().parent().find(".form-gatewayURL").html( dataObj['gatewayURL']);
}
- //$(".onTenantComplete").removeClass("hide");
- //$(".onTenantLoad").addClass("hide");
- //$(".onTenantComplete").removeClass("hide");
- });
- }
+ else{
+ $(".submit-actions").before("<div class='alert alert-success success-alert'>Gateway has been updated successfully.");
+ }
+
+ //refresh data next time if same popup is opened.
+ var gatewayIdWithoutSpaces = dataObj['gateway_id'].replace(/\s+/g, '-');
+ $("#view-" + gatewayIdWithoutSpaces).data("gatewayobject", data);
+ $("#view-" + gatewayIdWithoutSpaces ).parent().parent().find(".form-gatewayName").html( dataObj['gatewayName']);
+ $("#view-" + gatewayIdWithoutSpaces ).parent().parent().find(".form-gatewayURL").html( dataObj['gatewayURL']);
+ }
+ });
+
});
$(".gaStatuses option[value=REQUESTED]").prop("selected", true);
[02/12] airavata-php-gateway git commit: fixing AIRAVATA-2267 : In
view credential please show the domain.
Posted by ma...@apache.org.
fixing AIRAVATA-2267 : In view credential please show the domain.
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/4c47e540
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/4c47e540
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/4c47e540
Branch: refs/heads/dreg-gateway
Commit: 4c47e5408c6f83fbc9b6704750c860ae0af37bd6
Parents: f436e6a
Author: scnakandala <su...@gmail.com>
Authored: Mon Jan 30 11:15:01 2017 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Mon Jan 30 11:15:01 2017 -0500
----------------------------------------------------------------------
app/views/account/dashboard.blade.php | 5 +++++
1 file changed, 5 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/4c47e540/app/views/account/dashboard.blade.php
----------------------------------------------------------------------
diff --git a/app/views/account/dashboard.blade.php b/app/views/account/dashboard.blade.php
index f23b40e..d59f78f 100644
--- a/app/views/account/dashboard.blade.php
+++ b/app/views/account/dashboard.blade.php
@@ -187,6 +187,10 @@
<td class="gateway-url"></td>
</tr>
<tr>
+ <td>Gateway Domain</td>
+ <td class="gateway-domain"></td>
+ </tr>
+ <tr>
<td>Admin Username</td>
<td class="admin-username"></td>
</tr>
@@ -491,6 +495,7 @@
$(".admin-password").html( gatewayObject["identityServerPasswordToken"]);
$(".gateway-id").html( gatewayObject["gatewayId"]);
$(".gateway-url").html( gatewayObject["gatewayURL"]);
+ $(".gateway-domain").html( gatewayObject["domain"]);
$(".oauth-client-key").html( gatewayObject["oauthClientId"]);
$(".oauth-client-secret").html( gatewayObject["oauthClientSecret"]);
$("#viewCredentials").modal("show");
[08/12] airavata-php-gateway git commit: Merge HEAD route
Posted by ma...@apache.org.
Merge HEAD route
Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/2c64ac00
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/2c64ac00
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/2c64ac00
Branch: refs/heads/dreg-gateway
Commit: 2c64ac007a96233abaa3b6ef1a30fba968a966e2
Parents: 206e8d1 0038011
Author: root <ro...@osboxes>
Authored: Fri Feb 10 04:54:19 2017 +0000
Committer: root <ro...@osboxes>
Committed: Fri Feb 10 04:54:19 2017 +0000
----------------------------------------------------------------------
app/libraries/PartialDownload.php | 174 +++++++++++++++++++++++++++++++++
app/routes.php | 63 ++++++------
2 files changed, 206 insertions(+), 31 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/2c64ac00/app/routes.php
----------------------------------------------------------------------
diff --cc app/routes.php
index 4189d13,28f69d1..a9f40be
--- a/app/routes.php
+++ b/app/routes.php
@@@ -176,70 -174,75 +176,72 @@@ include("base32.php")
for($i=1; $i<3; $i++){
$content = $content . ' {
type:"bigwig",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($filelist[$i*2]). '",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($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" ;
}
- $content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode($folder_path . '/out.dREG.pred.gz').'",
+ $content = $content . '{
+ type:"bedgraph",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode($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 = $content . '{
type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.peak.gz').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::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( $folder_path . '/out.dREG.HD.imputedDnase.bw').'",
+ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::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";
- // $content = $content . '{
- // type:"bedgraph",
- // url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
- // name: "dREG.HD relaxed peaks:",
- // mode: "show",
- // colorpositive:"#0000e5/#B30086",
- // backgroundcolor:"#ffffe5",
- // height:30,
- // fixedscale:{min:0, max:1},
- // },'. "\n";
-
- // $content = $content . '{
- // type:"bedgraph",
- // url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
- // name: "dREG.HD stringent peaks:",
- // mode: "show",
- // colorpositive:"#0000e5/#B30086",
- // backgroundcolor:"#ffffe5",
- // height:30,
- // fixedscale:{min:0, max:1},
- // },'. "\n";
+ $content = $content . '{
+ type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
++ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.relaxed.bed').'",
+ name: "dREG.HD relaxed peaks:",
+ mode: "show",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
++ colorpositive:"#0000e5/#B30086",
+ backgroundcolor:"#ffffe5",
+ height:30,
+ fixedscale:{min:0, max:1},
+ },'. "\n";
+ $content = $content . '{
- type:"bedgraph",
- url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base64_encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
++ type:"bedgraph",
++ url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.base32::encode( $folder_path . '/out.dREG.HD.stringent.bed').'",
+ name: "dREG.HD stringent peaks:",
+ mode: "show",
- colorpositive:"#B30086",
- colornegative:"#0000e5",
++ colorpositive:"#0000e5/#B30086",
+ backgroundcolor:"#ffffe5",
+ height:30,
+ fixedscale:{min:0, max:1},
+ },'. "\n";
-
$content = $content . ']';
return Response::make($content, 200)
@@@ -262,22 -263,14 +264,21 @@@ include("base32.php")
$downloadLink = Config::get('pga_config.airavata')['experiment-data-absolute-path'] . '/' . $file;
if ( !file_exists($downloadLink) )
- return Response::make('', 404);
+ return Response::make('', 204);
else
{
- include 'libraries/PartialDownload.php';
- return byteserve( $downloadLink);
+ if ($_SERVER["REQUEST_METHOD"]=="GET")
+ {
+ include 'libraries/PartialDownload.php';
+ return byteserve( $downloadLink);
+ }
+ else
+ return Response::make("", 200)
+ ->header('Content-Length', filesize($downloadLink));
}
-
});
+
// dREG
/*
[09/12] airavata-php-gateway git commit: modification for file
download from genome browser
Posted by ma...@apache.org.
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));
[12/12] airavata-php-gateway git commit: Merge remote-tracking branch
'origin/develop' into dreg-gateway
Posted by ma...@apache.org.
Merge remote-tracking branch 'origin/develop' into dreg-gateway
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/75929d77
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/75929d77
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/75929d77
Branch: refs/heads/dreg-gateway
Commit: 75929d7798e5a1bc2ff820d03b1ce85175408f8c
Parents: d5533b0 f199d9b
Author: Marcus Christie <ma...@iu.edu>
Authored: Wed Feb 15 09:36:06 2017 -0500
Committer: Marcus Christie <ma...@iu.edu>
Committed: Wed Feb 15 09:36:06 2017 -0500
----------------------------------------------------------------------
app/config/pga_config.php.template | 8 +++
app/controllers/AccountController.php | 9 +--
app/controllers/AdminController.php | 65 ++++++++++--------
app/libraries/CommonUtilities.php | 4 ++
app/views/account/dashboard.blade.php | 5 ++
app/views/admin/manage-gateway.blade.php | 70 +++++++++-----------
app/views/layout/basic.blade.php | 10 ++-
.../compute-resource-preferences.blade.php | 2 +-
app/views/partials/dashboard-block.blade.php | 6 +-
public/css/admin.css | 10 ++-
10 files changed, 109 insertions(+), 80 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/75929d77/app/libraries/CommonUtilities.php
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/75929d77/app/views/account/dashboard.blade.php
----------------------------------------------------------------------