Merge pull request #2515 from bgruening/realtime_communication

Add a simple Galaxy Communication Server for realtime communication between Galaxy users.

.gitignore

@@ -129,3 +129,4 @@ doc/build
 .DS_Store
 *.rej
 *~
+.idea/

client/galaxy/scripts/layout/generic-nav-view.js

@@ -0,0 +1,98 @@
+/** Real-time Communication feature **/
+define(['mvc/ui/ui-modal'], function( Modal ) {
+
+var GenericNavView = Backbone.View.extend({
+
+    initialize: function ( ) {
+        this.modal = null;
+    },
+
+    /** makes bootstrap modal and iframe inside it */
+    makeModalIframe: function( e ) {
+	// make modal
+	var host =  window.Galaxy.config.communication_server_host,
+	    port = window.Galaxy.config.communication_server_port,
+	    username = escape( window.Galaxy.user.attributes.username ),
+	    persistent_communication_rooms = escape( window.Galaxy.config.persistent_communication_rooms ),
+	    query_string = "?username=" + username + "&persistent_communication_rooms=" + persistent_communication_rooms,
+	    src = host + ":" + port + query_string,
+	    $el_chat_modal_header = null,
+	    $el_chat_modal_body = null,
+            iframe_template = '<iframe class="f-iframe fade in communication-iframe" src="' + src + '"> </iframe>',
+            header_template = '<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i>' +
+                              '<i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i>' + 
+	                      '<i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>',
+            frame_height = 350,
+            frame_width = 600,
+            class_names = 'ui-modal chat-modal';
+
+	// deletes the chat modal if already present and create one
+        if( $( '.chat-modal' ).length > 0 ) {
+            $( '.chat-modal' ).remove();
+	}
+        // creates a modal
+	GenericNavView.modal = new Modal.View({
+	    body            : iframe_template,
+	    height          : frame_height,
+	    width           : frame_width,
+	    closing_events  : true,
+	    title_separator : false,
+            cls             : class_names
+	});
+
+	// shows modal
+	GenericNavView.modal.show();
+        $el_chat_modal_header = $( '.chat-modal .modal-header' );
+        $el_chat_modal_body = $( '.chat-modal .modal-body' );
+	// adjusts the css of bootstrap modal for chat
+        $el_chat_modal_header.addClass('modal-header-body');
+        $el_chat_modal_body.addClass('modal-header-body');
+	$el_chat_modal_header.find( 'h4' ).remove();
+        $el_chat_modal_header.removeAttr( 'min-height padding border' );
+	$el_chat_modal_header.append( header_template );
+	// click event of the close button for chat
+	$( '.close-modal' ).click(function( e ) {
+	    $( '.chat-modal' ).css( 'display', 'none' );
+	});
+        // click event of expand and compress icon
+        $( '.expand-compress-modal' ).click(function( e ) {
+            if( $( '.expand-compress-modal' ).hasClass( 'fa-expand' ) ) {
+                $( '.chat-modal .modal-dialog' ).width( '1000px' );
+                $( '.chat-modal .modal-body' ).height( '575px' );
+                $( '.expand-compress-modal' ).removeClass( 'fa-expand' ).addClass( 'fa-compress' );
+                $( '.expand-compress-modal' ).attr('title', 'Minimize');
+                $( '.expand-compress-modal' ).css('margin-left', '96.2%');
+            }
+            else {
+                $( '.chat-modal .modal-dialog' ).width( frame_width + 'px' );
+                $( '.chat-modal .modal-body' ).height( frame_height + 'px' );
+                $( '.expand-compress-modal' ).removeClass( 'fa-compress' ).addClass( 'fa-expand' );
+                $( '.expand-compress-modal' ).attr('title', 'Maximize');
+                $( '.expand-compress-modal' ).css('margin-left', '93.2%');
+            }
+
+	});
+        return this;
+    },
+
+    /**renders the chat icon as a nav item*/
+    render: function() {
+        var self = this,
+            navItem = {};
+        navItem = {
+            id              : 'show-chat-online',
+            icon            : 'fa-comment-o',
+            tooltip         : 'Chat online',
+            visible         : false,
+            onclick         : self.makeModalIframe
+        }
+        return navItem;
+    }
+});
+
+return {
+    GenericNavView  : GenericNavView
+};
+
+});
+

client/galaxy/scripts/layout/menu.js

@@ -1,5 +1,5 @@
 /** Masthead Collection **/
-define(['mvc/tours'], function( Tours ) {
+define(['mvc/tours', 'layout/generic-nav-view'], function( Tours, GenericNav ) {
 var Collection = Backbone.Collection.extend({
     model: Backbone.Model.extend({
         defaults: {
@@ -11,6 +11,12 @@ var Collection = Backbone.Collection.extend({
         options = options || {};
         this.reset();
 
+        //
+        // Chat server tab
+        //
+        var extendedNavItem = new GenericNav.GenericNavView();
+        this.add(extendedNavItem.render()); 
+
         //
         // Analyze data tab.
         //

client/galaxy/scripts/layout/page.js

@@ -48,6 +48,7 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
         this.renderMessageBox();
         this.renderInactivityBox();
         this.renderPanels();
+        this._checkCommunicationServerOnline();
         return this;
     },
 
@@ -131,7 +132,35 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
         }
     },
 
-    toString : function() { return 'PageLayoutView'; }
+    toString : function() { return 'PageLayoutView'; },
+
+    /** Check if the communication server is online and show the icon otherwise hide the icon */
+    _checkCommunicationServerOnline: function(){
+        var host = window.Galaxy.config.communication_server_host,
+            port = window.Galaxy.config.communication_server_port,
+            $chat_icon_element = $( "#show-chat-online" );
+        /** Check if the user has deactivated the communication in it's personal settings */
+        if (window.Galaxy.user.attributes.preferences !== undefined && window.Galaxy.user.attributes.preferences.communication_server === '1') {
+            // See if the configured communication server is available
+            $.ajax({
+                url: host + ":" + port,
+            })
+            .success( function( data ) { 
+                    // enable communication only when a user is logged in
+                    if( window.Galaxy.user.id !== null ) {
+                        if( $chat_icon_element.css( "visibility")  === "hidden" ) {
+                            $chat_icon_element.css( "visibility", "visible" ); 
+                        }
+                    }
+            })
+            .error( function( data ) { 
+                // hide the communication icon if the communication server is not available
+                $chat_icon_element.css( "visibility", "hidden" ); 
+            });
+        } else {
+            $chat_icon_element.css( "visibility", "hidden" ); 
+        }
+    },
 });
 
 // ============================================================================

client/galaxy/style/less/base.less

@@ -1719,3 +1719,29 @@ div.toolTitleNoSection
 #for_bears {
     display: none;
 }
+
+// communication channel bootstrap modal 
+
+.chat-modal {
+    overflow: hidden;
+}
+
+.modal-header-body {
+    padding: 2px;
+}
+
+.communication-iframe {
+    width: 100%;
+    height: 100%;
+}
+
+.close-modal {
+    float: right; 
+    cursor: pointer;
+}
+
+.expand-compress-modal {
+    cursor: pointer;
+    font-size: 12px;
+    margin-left: 93.2%;
+}

config/galaxy.ini.sample

@@ -1206,6 +1206,12 @@ use_interactive = True
 
 #amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
 
+# Galaxy real time communication server settings
+#enable_communication_server = False
+#communication_server_host = http://localhost
+#communication_server_port = 7070
+# persistent_communication_rooms is a comma-separated list of rooms that should be always available.
+#persistent_communication_rooms = 
 
 
 # ---- Galaxy External Message Queue -------------------------------------------------

lib/galaxy/config.py

@@ -221,6 +221,10 @@ def __init__( self, **kwargs ):
         self.track_jobs_in_database = string_as_bool( kwargs.get( 'track_jobs_in_database', 'True') )
         self.start_job_runners = listify(kwargs.get( 'start_job_runners', '' ))
         self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) )
+        self.enable_communication_server = string_as_bool( kwargs.get( 'enable_communication_server', 'False' ) )
+        self.communication_server_host = kwargs.get( 'communication_server_host', 'http://localhost' )
+        self.communication_server_port = int( kwargs.get( 'communication_server_port', '7070' ) )
+        self.persistent_communication_rooms = listify( kwargs.get( "persistent_communication_rooms", [] ), do_strip=True )
         # External Service types used in sample tracking
         self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root )
         # Tasked job runner.

lib/galaxy/managers/configuration.py

@@ -53,6 +53,9 @@ def _defaults_to( default ):
             'biostar_url_redirect'      : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect',
                                                                         qualified=True ),
 
+            'communication_server_host' : _defaults_to( None ),
+            'communication_server_port' : _defaults_to( None ),
+            'persistent_communication_rooms' : _defaults_to( None ),
             'allow_user_creation'       : _defaults_to( False ),
             'use_remote_user'           : _defaults_to( None ),
             'remote_user_logout_href'   : _defaults_to( '' ),

lib/galaxy/managers/users.py

@@ -187,6 +187,10 @@ def get_or_create_valid_api_key( self, user ):
         return self.create_api_key( self, user )
 
     # ---- preferences
+    def preferences( self, user ):
+        log.warn(dict( (key, value) for key, value in user.preferences.items() ))
+        return dict( (key, value) for key, value in user.preferences.items() )
+
     # ---- roles and permissions
     def private_role( self, user ):
         return self.app.security_agent.get_private_user_role( user )
@@ -263,7 +267,7 @@ def __init__( self, app ):
             'purged',
             # 'active',
 
-            # 'preferences',
+            'preferences',
             #  all tags
             'tags_used',
             # all annotations
@@ -280,6 +284,8 @@ def add_serializers( self ):
             'update_time'   : self.serialize_date,
             'is_admin'      : lambda i, k, **c: self.user_manager.is_admin( i ),
 
+            'preferences'   : lambda i, k, **c: self.user_manager.preferences( i ),
+
             'total_disk_usage' : lambda i, k, **c: float( i.total_disk_usage ),
             'quota_percent' : lambda i, k, **c: self.user_manager.quota( i ),
 

lib/galaxy/util/__init__.py

@@ -808,7 +808,7 @@ def asbool(obj):
 
 
 def string_as_bool( string ):
-    if str( string ).lower() in ( 'true', 'yes', 'on' ):
+    if str( string ).lower() in ( 'true', 'yes', 'on', '1' ):
         return True
     else:
         return False

lib/galaxy/web/base/controller.py

@@ -238,7 +238,7 @@ class JSAppLauncher( BaseUIController ):
     DEFAULT_ENTRY_FN = "app"
     #: keys used when serializing current user for bootstrapped data
     USER_BOOTSTRAP_KEYS = ( 'id', 'email', 'username', 'is_admin', 'tags_used', 'requests',
-                            'total_disk_usage', 'nice_total_disk_usage', 'quota_percent' )
+                            'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'preferences' )
 
     def __init__( self, app ):
         super( JSAppLauncher, self ).__init__( app )

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -152,6 +152,7 @@ def __call__( self, environ, start_response ):
                 '/user/dbkeys',
                 '/user/toolbox_filters',
                 '/user/set_default_permissions',
+                '/user/change_communication',
             )
 
             admin_accessible_paths = (

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -17,6 +17,7 @@
 from galaxy import model
 from galaxy import util
 from galaxy import web
+from galaxy.util import string_as_bool
 from galaxy.exceptions import ObjectInvalid
 from galaxy.security.validate_user_input import (transform_publicname,
                                                  validate_email,
@@ -1189,6 +1190,46 @@ def change_password( self, trans, token=None, **kwd):
                                     display_top=kwd.get('redirect_home', False)
                                     )
 
+    @web.expose
+    def change_communication( self, trans, cntrller, **kwd):
+        """
+            Provides a form with which the user can activate/deactivate
+            the commnication server.
+        """
+        params = util.Params( kwd )
+        is_admin = cntrller == 'admin' and trans.user_is_admin()
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        user_id = params.get( 'user_id', None )
+        activated = ''
+
+        if user_id and is_admin:
+            user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( user_id ) )
+        else:
+            user = trans.user
+
+        if user and params.get( 'change_communication_button', False ):
+            communication_enabled = kwd.get( 'enable_communication_server', False )
+            if communication_enabled:
+                activated = 'checked'
+                user.preferences['communication_server'] = True
+                message = 'Your communication settings has been updated and activated.'
+            else:
+                activated = ''
+                user.preferences['communication_server'] = False
+                message = 'Your communication settings has been updated and deactivated.'
+            trans.sa_session.add( user )
+            trans.sa_session.flush()
+        else:
+            if string_as_bool( user.preferences.get('communication_server', '0') ):
+                activated = 'checked'
+
+        return trans.fill_template( '/user/communication_settings.mako',
+                                    cntrller=cntrller,
+                                    status=status,
+                                    activated=activated,
+                                    message=message )
+
     @web.expose
     def reset_password( self, trans, email=None, **kwd ):
         """Reset the user's password. Send an email with token that allows a password change."""