Prepare breedbase for snpsnapp (gbsappui) integration

lib/SGN/Controller/AJAX/Login.pm

@@ -2,7 +2,8 @@
 package SGN::Controller::AJAX::Login;
 
 use Moose;
-use Data::Dumper;
+use CXGN::People::Login;
+use CXGN::People::Person;
 use CXGN::Login;
 
 BEGIN { extends 'Catalyst::Controller::REST' }
@@ -14,61 +15,83 @@ __PACKAGE__->config(
    );
 
 
-sub is_logged_in :Path('/user/logged_in') Args(0) { 
+sub is_logged_in :Path('/user/logged_in') Args(0) {
     my $self = shift;
     my $c = shift;
-
     $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
     $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
     $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
 
     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
     my $dbh = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id)->storage->dbh();
-    
+
     my $login = CXGN::Login->new($dbh);
-    
+
     if (my ($person_id, $user_type) = $login->has_session()) {
-	my $login_info = $login->get_login_info();
-	#print STDERR "LOGIN INFO: ".Dumper($login_info);
-    	$c->stash->{rest} = $login_info;
+        my $user_id = CXGN::People::Person->new($dbh,$person_id);
+        my $login_info = $login->get_login_info();
+        my $user = $c->user();
+        my $domain = $c->config->{main_production_site_url};
+        $c->stash->{rest} = $login -> get_login_info;
+        $c->stash->{rest} = {
+            first_name => $user->get_object->get_first_name(),
+            last_name => $user->get_object->get_last_name(),
+    	    username => $user->get_object->get_username(),
+            user_id => $person_id,
+            domain => $domain,
+    	};
     	return;
-    }
+    };
     $c->stash->{rest} = { user_id => 0 };
 }
 
-
 sub login_with_cookie :Path('/user/cookie_login') Args(1) {
     my $self = shift;
     my $c = shift;
-    my $cookie = shift
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+    $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+    $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
+    my $cookie = shift;
+    my $dbh = $c->dbc->dbh;
+    my @user_info = CXGN::Login->new($dbh)->query_from_cookie($cookie);
+    my $user_id = $user_info[0];
+    my $p = CXGN::People::Person->new($dbh, $user_id);
+    $c->stash->{rest} = {first_name => $p->get_first_name,
+	    last_name => $p->get_last_name,
+        username => $p->get_username,
+        user_id => $user_id,
+        email_address => $p->get_contact_email,
+    };
 }
 
 sub get_roles :Path('/user/get_roles') Args(0) {
     my $self = shift;
     my $c = shift;
-    
-    if (my $user = $c->user()) { 
+
+    if (my $user = $c->user()) {
 	my @roles = $user->get_object->get_roles();
 	$c->stash->{rest} = { roles => @roles };
 	return;
     }
     $c->stash->{rest} = { roles => 0 };
 }
 
-sub log_in :Path('/user/login') Args(0) { 
+sub log_in :Path('/user/login') Args(0) {
     my $self = shift;
     my $c = shift;
-
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+    $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+    $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
     my $login = CXGN::Login->new();
-    
+
     # implement
 
 }
-    
-sub log_out :Path('/user/logout') Args(0) { 
+
+sub log_out :Path('/user/logout') Args(0) {
     my $self = shift;
     my $c = shift;
-    
+
     # implement
 
 }

lib/SGN/Controller/AJAX/People.pm

@@ -72,6 +72,9 @@ sub people_and_roles : Path('/ajax/people/people_and_roles') : ActionClass('REST
 sub people_and_roles_GET : Args(0) {
     my $self = shift;
     my $c = shift;
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+    $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+    $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
     my $people_schema = $c->dbic_schema('CXGN::People::Schema');
     my $person_roles = CXGN::People::Roles->new({ people_schema=>$people_schema });

lib/SGN/Controller/AJAX/User.pm

@@ -2,6 +2,8 @@
 package SGN::Controller::AJAX::User;
 
 use Moose;
+use JSON;
+use URI::FromHash 'uri';
 use IO::File;
 use Data::Dumper;
 use HTML::Entities;
@@ -57,6 +59,20 @@ sub logout :Path('/ajax/user/logout') Args(0) {
     $c->stash->{rest} = { message => "User successfully logged out." };
 }
 
+sub logout_externally :Path('/ajax/user/logout_externally') QueryParam('redirect_uri') {
+    my $self = shift;
+    my $c = shift;
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+    $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+    $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
+#    my $redirect_uri = $c->request->param( 'redirect_uri' );
+    my $login = CXGN::Login->new($c->dbc->dbh());
+    $login->logout_user();
+#    $c->stash->{redirect_uri} = $redirect_uri;
+#    $c->stash->{template} = '/site/toolbar/logout_externally.mas';
+    $c->stash->{rest} = { message => "User successfully logged out." };
+}
+
 sub new_account :Path('/ajax/user/new') Args(0) {
     my $self = shift;
     my $c = shift;

lib/SGN/Controller/BrAPIClient.pm

@@ -4,40 +4,50 @@ package SGN::Controller::BrAPIClient;
 use Moose;
 use URI::FromHash 'uri';
 use JSON;
+use Data::Dumper;
 
 BEGIN { extends 'Catalyst::Controller' };
 
 sub authorize_client :Path('/brapi/authorize') QueryParam('redirect_uri') { #breedbase.org/brapi/authorize?success_url=fieldbook://&client_id=Field%20Book
     my $self = shift;
     my $c = shift;
-
-    my $authorized_clients = decode_json $c->get_conf('authorized_clients_JSON');;
-
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+	$c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+	$c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
+    my $authorized_clients = decode_json $c->get_conf('authorized_clients_JSON');
+
 	my %authorized_clients = %$authorized_clients;
-	
+
     my $redirect_uri = $c->request->param( 'redirect_uri' );
 	my @keys = keys %authorized_clients;
 	my $client_id = undef;
-
+    print STDERR "Authorized clients:\n ".Dumper( $authorized_clients);
 	while(my($k, $v) = each %authorized_clients) {
         if ($redirect_uri =~ m/^$k/) {
             $client_id = $v;
             last;
         }
     }
-
+    print STDERR "Redirect uri: $redirect_uri\n";
+    print STDERR "client_id: $client_id\n";
     if (defined $client_id) {
         if (!$c->user()) {  # redirect to login page
             $c->res->redirect( uri( path => '/user/login', query => { goto_url => "/brapi/authorize?redirect_uri=$redirect_uri" } ) );
             return;
         } else {
             my $user_name = $c->user()->get_object()->get_username();
+            my $user_id = $c->user()->get_object()->get_sp_person_id();
+            my $first_name = $c->user()->get_object()->get_first_name();
+            my $last_name = $c->user()->get_object()->get_last_name();
             my $access_token = CXGN::Login->new($c->dbc->dbh)->get_login_cookie();
             my $authorize_url = $redirect_uri . ( (index($redirect_uri, '?') != -1)?"&status=200&access_token=":"?status=200&access_token=") . $access_token;
             my $deny_url = $redirect_uri . "?status=401";
             $c->stash->{authorize_url} = $authorize_url;
             $c->stash->{deny_url} = $deny_url;
             $c->stash->{user_name} = $user_name;
+            $c->stash->{user_id} = $user_id;
+            $c->stash->{first_name} = $first_name;
+            $c->stash->{last_name} = $last_name;
             $c->stash->{client_id} = $client_id;
             $c->stash->{database_name} = $c->config->{project_name};
             $c->stash->{template} = '/brapi/authorize.mas';

lib/SGN/Controller/User.pm

@@ -8,7 +8,9 @@ BEGIN { extends 'Catalyst::Controller' };
 sub login :Path('/user/login') Args(0) {
     my $self = shift;
     my $c = shift;
-
+    $c->response->headers->header( "Access-Control-Allow-Origin" => '*' );
+    $c->response->headers->header( "Access-Control-Allow-Methods" => "POST, GET, PUT, DELETE" );
+    $c->response->headers->header( 'Access-Control-Allow-Headers' => 'DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization');
     $c->stash->{goto_url} = $c->req->param("goto_url");
 
     print STDERR "GOTOURL=".$c->stash->{goto_url}."\n";

mason/site/toolbar/logout_externally.mas

@@ -0,0 +1,12 @@
+<%args>
+$redirect_uri
+</%args>%>
+
+<b>Logging out...</b>
+
+<script>
+console.log(<% $redirect_uri %>);
+jQuery(document).ready(function () {
+   window.location.replace(<% $redirect_uri %>)
+});
+</script>

sgn.conf

@@ -499,7 +499,7 @@ na_extraction_method_options RNeasy Mini Kit, RNeasy Plus Mini Kit, RNeasy Plant
 
 
 #Authorized Clients for SSO
-authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://phenoapps.org/field-book":"fieldbook","https://fieldbook.phenoapps.org/": "fieldbook", "https://climmob.net":"ClimMob"}
+authorized_clients_JSON {"TEST://":"TEST","fieldbook://":"FieldBook App","https://apps.cipotato.org/hidap_sbase/":"HIDAP","https://phenoapps.org/field-book":"fieldbook","https://fieldbook.phenoapps.org/": "fieldbook","https://snpsnapp.breedbase.org":"snpsnapp","https://climmob.net":"ClimMob"}
 
 simsearch_datadir /home/production/simsearch_data
 

t/selenium2/tools/trial_compare.t

@@ -74,7 +74,7 @@ $d->while_logged_in_as('submitter', sub {
     # Change page to trial comparison
     $d->get_ok('/tools/trial/comparison/list');
 
-    sleep(6);
+    sleep(60);
 
     $d->find_element("trials_list_select", "id", "find trials select")->click();
     sleep(1);