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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/02/22 16:29:50 UTC
[1/3] airavata-php-gateway git commit: sync codes to remove
user-pending status
Repository: airavata-php-gateway
Updated Branches:
refs/heads/dreg-gateway 8f3d7621e -> dc0c79c41
sync codes to remove user-pending status
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/9549e183
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/9549e183
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/9549e183
Branch: refs/heads/dreg-gateway
Commit: 9549e1838086b63aefbb212e49ac529f7341def5
Parents: d426398
Author: root <ro...@osboxes>
Authored: Tue Feb 21 20:25:55 2017 +0000
Committer: root <ro...@osboxes>
Committed: Tue Feb 21 20:25:55 2017 +0000
----------------------------------------------------------------------
app/config/pga_config.php.template | 8 +++
app/controllers/AccountController.php | 9 +--
app/controllers/AdminController.php | 65 ++++++++++--------
app/libraries/CommonUtilities.php | 4 ++
app/storage/.gitignore | 1 -
app/storage/cache/.gitignore | 2 -
app/storage/logs/.gitignore | 2 -
app/storage/meta/.gitignore | 2 -
app/storage/sessions/.gitignore | 2 -
app/storage/views/.gitignore | 2 -
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 +-
.../partials/experiment-queue-block.blade.php | 0
public/css/admin.css | 10 ++-
17 files changed, 109 insertions(+), 91 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/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/9549e183/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"] = $initialRoleName;
if( Config::get('pga_config.portal')['super-admin-portal'] == true ){
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/controllers/AdminController.php
----------------------------------------------------------------------
diff --git a/app/controllers/AdminController.php b/app/controllers/AdminController.php
index 9735b9a..6dd27bd 100644
--- a/app/controllers/AdminController.php
+++ b/app/controllers/AdminController.php
@@ -99,12 +99,18 @@ class AdminController extends BaseController {
}
+ private function cmp($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();
@@ -230,22 +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();
@@ -272,21 +300,6 @@ 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;
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/libraries/CommonUtilities.php
----------------------------------------------------------------------
diff --git a/app/libraries/CommonUtilities.php b/app/libraries/CommonUtilities.php
index 6792dcc..957f922 100644
--- a/app/libraries/CommonUtilities.php
+++ b/app/libraries/CommonUtilities.php
@@ -461,5 +461,9 @@ class CommonUtilities
return false;
}
}
+
+ public static function getInitialRoleName() {
+ return Config::get('pga_config.wsis.initial-role-name', 'user-pending');
+ }
}
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/.gitignore b/app/storage/.gitignore
deleted file mode 100644
index 35b719c..0000000
--- a/app/storage/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-services.manifest
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/cache/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/cache/.gitignore b/app/storage/cache/.gitignore
deleted file mode 100644
index c96a04f..0000000
--- a/app/storage/cache/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/logs/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/logs/.gitignore b/app/storage/logs/.gitignore
deleted file mode 100644
index c96a04f..0000000
--- a/app/storage/logs/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/meta/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/meta/.gitignore b/app/storage/meta/.gitignore
deleted file mode 100644
index c96a04f..0000000
--- a/app/storage/meta/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/sessions/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/sessions/.gitignore b/app/storage/sessions/.gitignore
deleted file mode 100644
index c96a04f..0000000
--- a/app/storage/sessions/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/storage/views/.gitignore
----------------------------------------------------------------------
diff --git a/app/storage/views/.gitignore b/app/storage/views/.gitignore
deleted file mode 100644
index c96a04f..0000000
--- a/app/storage/views/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*
-!.gitignore
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/app/views/account/dashboard.blade.php
----------------------------------------------------------------------
diff --git a/app/views/account/dashboard.blade.php b/app/views/account/dashboard.blade.php
index c67747b..340059c 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>
@@ -510,6 +514,7 @@
$(".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");
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/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);
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/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/9549e183/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>
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/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/9549e183/app/views/partials/experiment-queue-block.blade.php
----------------------------------------------------------------------
diff --git a/app/views/partials/experiment-queue-block.blade.php b/app/views/partials/experiment-queue-block.blade.php
old mode 100644
new mode 100755
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/9549e183/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 {
[3/3] airavata-php-gateway git commit: Merge branch 'dreg-gateway' of
https://github.com/Danko-Lab/airavata-php-gateway into dreg-gateway
Posted by ma...@apache.org.
Merge branch 'dreg-gateway' of https://github.com/Danko-Lab/airavata-php-gateway 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/dc0c79c4
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/dc0c79c4
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/dc0c79c4
Branch: refs/heads/dreg-gateway
Commit: dc0c79c4117c7e3ca0f54ea48e8bb06b7e8df714
Parents: 8f3d762 135022f
Author: Marcus Christie <ma...@iu.edu>
Authored: Wed Feb 22 11:27:36 2017 -0500
Committer: Marcus Christie <ma...@iu.edu>
Committed: Wed Feb 22 11:27:36 2017 -0500
----------------------------------------------------------------------
app/storage/.gitignore | 1 -
app/storage/cache/.gitignore | 2 --
app/storage/logs/.gitignore | 2 --
app/storage/meta/.gitignore | 2 --
app/storage/sessions/.gitignore | 2 --
app/storage/views/.gitignore | 2 --
.../partials/experiment-queue-block.blade.php | 0
.../themes/dreg/assets/img/dreg.exp.summary.png | Bin 48376 -> 52211 bytes
public/themes/dreg/assets/img/dreg.gbview.png | Bin 0 -> 110820 bytes
public/themes/dreg/partials/doc.blade.php | 14 ++++++++++----
10 files changed, 10 insertions(+), 15 deletions(-)
----------------------------------------------------------------------
[2/3] airavata-php-gateway git commit: Update on the document page
Posted by ma...@apache.org.
Update on the document page
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/135022fb
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/135022fb
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/135022fb
Branch: refs/heads/dreg-gateway
Commit: 135022fb4b14b221ddde4f804b6aceb094f5d90c
Parents: 9549e18
Author: root <ro...@osboxes>
Authored: Tue Feb 21 20:58:17 2017 +0000
Committer: root <ro...@osboxes>
Committed: Tue Feb 21 20:58:17 2017 +0000
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.../themes/dreg/assets/img/dreg.exp.summary.png | Bin 48376 -> 52211 bytes
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@@ -36,14 +36,14 @@ Select the menu 'Start dREG' below the dREG logo to create an data analysis for
<p class="description" style="padding:16px">
4) <b>Select bigWig files</b><br>
-Select bigWig files representing PRO-seq, GRO-seq, or ChRO-seq signal on the plus and minus strand.
+Select bigWig files representing PRO-seq, GRO-seq, or ChRO-seq signal on the plus and minus strand. Please notice that two GPU resources are available now, currently it is easier to get the computation resources on <A href="http://comet.sdsc.xsede.org/">Comet.sdsc.xsede.org</A> than <A href="https://www.psc.edu/index.php/bridges">Bridges.psc.edu</A>.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment create" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.create.exp2.png" ></img></div>
<p class="description" style="padding:16px">
5) <b>Submit the job</b><br>
-Click the 'save and launch' button. BigWig file are transferred to the XSEDE server and a GPU queue is scheduled to run dREG. After submitting, the user can check the status in the next web page, as shown below. Depend on the queue status, the job maybe wait for a long time to start prediction. Once started, it will only take 1-4 hours to complete.</p>
+Click the 'save and launch' button. BigWig file are transferred to the XSEDE server and a GPU queue is scheduled to run dREG. After submitting, the user can check the status in the next web page, as shown below. Depend on the queue status, the job maybe wait for a long time to start prediction. Once started, it will only take 1-4 hours to complete.</p>
<p class="description" style="padding:16px">
@@ -54,13 +54,19 @@ The user can check the status of their 'experiment' by clicking the menu 'Saved
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can click <B>'Download Results'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page. Or the user can check the results in the Genome Browser by clicking <b>'Switch to Genome Browser'</B> link.
+Once a job is completed, the user can click <B>'Download All Results'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list.
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
<p class="description" style="padding:16px">
- 8) <b>Check the storage</b><br>
+ 8) <b>Switch to Genome Browser</b><br>
+The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Genome Browser'</B> link. </p>
+
+<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.gbview.png"></img></div>
+
+ <p class="description" style="padding:16px">
+ 9) <b>Check the storage</b><br>
the user can click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments). The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div>