Containers interface and GIE bugfixes

client/galaxy/scripts/galaxy.interactive_environments.js

@@ -17,12 +17,30 @@ function display_spinner(){
         $('#main').append('<img id="spinner" src="' + galaxy_root + 'static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">');
 }
 
+function not_ready(timeout, timeout_values, timeout_time_max, timeout_time_step) {
+    if(timeout_values.count == 0){
+        display_spinner();
+        toastr.info(
+            "Galaxy is launching a container in which to run this interactive environment. Please wait...",
+            {'closeButton': true, 'tapToDismiss': false}
+        );
+    }
+    timeout_values.count++;
+    if(timeout_values.time < timeout_time_max){
+        timeout_values.time += timeout_time_step;
+    }
+    console.log("Readiness request " + timeout_values.count + " sleeping " + timeout_values.time / 1000 + "s");
+    window.setTimeout(timeout, timeout_values.time)
+}
+
 /**
  * Check a URL for a boolean true/false and call a callback when done.
  */
 function load_when_ready(url, success_callback){
-    var request_count = 0;
-    var timeout_time = 1000;
+    var ajax_timeout = 500;
+    var ajax_timeout_max = 10000;
+    var ajax_timeout_step = 250;
+    var timeout_values = { time: 1000, count: 0 };
     var timeout_time_max = 15000;
     var timeout_time_step = 1000;
     var timeout = function(){
@@ -32,7 +50,7 @@ function load_when_ready(url, success_callback){
                 withCredentials: true
             },
             type: "GET",
-            timeout: 500,
+            timeout: ajax_timeout,
             dataType: "json",
             success: function(data){
                 if(data == true){
@@ -41,19 +59,7 @@ function load_when_ready(url, success_callback){
                     toastr.clear();
                     success_callback();
                 }else if(data == false){
-                    if(request_count == 0){
-                        display_spinner();
-                        toastr.info(
-                            "Galaxy is launching a container in which to run this interactive environment. Please wait...",
-                            {'closeButton': true, 'tapToDismiss': false}
-                        );
-                    }
-                    request_count++;
-                    if(timeout_time < timeout_time_max){
-                        timeout_time += timeout_time_step;
-                    }
-                    console.log("Readiness request " + request_count + " sleeping " + timeout_time / 1000 + "s");
-                    window.setTimeout(timeout, timeout_time)
+                    not_ready(timeout, timeout_values, timeout_time_max, timeout_time_step);
                 }else{
                     clear_main_area();
                     toastr.clear();
@@ -63,10 +69,26 @@ function load_when_ready(url, success_callback){
                         {'closeButton': true, 'tapToDismiss': false}
                     );
                 }
+            },
+            error: function(jqXHR, textStatus, errorThrown){
+                if(textStatus == "timeout"){
+                    if(ajax_timeout < ajax_timeout_max){
+                        ajax_timeout += ajax_timeout_step;
+                    }
+                    not_ready(timeout, timeout_values, timeout_time_max, timeout_time_step);
+                }else{
+                    clear_main_area();
+                    toastr.clear();
+                    toastr.error(
+                        "Galaxy encountered an error while attempting to determine the readiness of this interactive environment, contact your administrator.",
+                        "Error",
+                        {'closeButton': true, 'tapToDismiss': false}
+                    );
+                }
             }
         });
     }
-    window.setTimeout(timeout, timeout_time);
+    window.setTimeout(timeout, timeout_values.time);
 }
 
 

config/containers_conf.yml.sample

@@ -109,6 +109,10 @@
 #  https://github.com/docker/docker/issues/31427
 #    resolve_image_digest: no
 
+# If a container run request is received that defines volumes to attach, should those volumes be ignored? Swarm mode
+# does not support mounting volumes.
+#    ignore_volumes: no
+
 ## For the following `service_create_*_constraint` options, if set, the swarm manager automatically sets a corresponding
 ## label on nodes it spawns for services with the given constraints.
 

config/plugins/interactive_environments/common/templates/ie.mako

@@ -9,7 +9,7 @@ ie_password = '${ ie_request.notebook_pw }';
 
 var galaxy_root = '${ ie_request.attr.root }';
 var app_root = '${ ie_request.attr.app_root }';
-var ie_readiness_url = '${ ie_request.url_template("${PROXY_PREFIX}/interactive_environments/ready") }';
+var ie_readiness_url = '${ h.url_for("/interactive_environments/ready") }';
 </%def>
 
 

config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js

@@ -1,8 +1,6 @@
 function load_notebook(url){
-    $( document ).ready(function() {
-        test_ie_availability(url, function(){
-            append_notebook(url)
-        });
+    test_ie_availability(url, function(){
+        append_notebook(url)
     });
 }
 

config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako

@@ -31,7 +31,9 @@ requirejs(['interactive_environments', 'plugin/ethercalc'], function(){
 });
 
 requirejs(['interactive_environments', 'plugin/ethercalc'], function(){
-    load_notebook(url);
+    load_when_ready(ie_readiness_url, function(){
+        load_notebook(url);
+    });
 });
 </script>
 <div id="main" width="100%" height="100%">

lib/galaxy/containers/docker_swarm.py

@@ -25,6 +25,7 @@ class DockerSwarmInterface(DockerInterface):
 
     container_class = DockerService
     conf_defaults = {
+        'ignore_volumes': False,
         'node_prefix': None,
         'service_create_image_constraint': False,
         'service_create_cpus_constraint': False,
@@ -64,6 +65,22 @@ def run_in_container(self, command, image=None, **kwopts):
             )
         elif kwopts.get('detach', None):
             del kwopts['detach']
+        if kwopts.get('volumes', None):
+            if self._conf.ignore_volumes:
+                log.warning(
+                    "'volumes' kwopt is set and not supported in Docker swarm "
+                    "mode, volumes will not be passed (set 'ignore_volumes: "
+                    "False' in containers config to fail instead): %s" % kwopts['volumes']
+                )
+                del kwopts['volumes']
+            else:
+                raise ContainerRunError(
+                    "'volumes' kwopt is set and not supported in Docker swarm "
+                    "mode (set 'ignore_volumes: True' in containers config to "
+                    "warn instead): %s" % kwopts['volumes'],
+                    image=image,
+                    command=command
+                )
         service = self.service_create(command, image=image, **kwopts)
         self._run_swarm_manager()
         return service