Add InteractiveTools.

client/galaxy/scripts/components/ToolEntryPoints/ToolEntryPoints.vue

@@ -0,0 +1,65 @@
+<template>
+    <div class="infomessagelarge">
+        <p v-if="entryPoints.length==0" >
+            Waiting for InteractiveTool result view(s) to become available.
+        </p>
+        <p v-else-if="entryPoints.length==1" >
+            <span v-if="entryPoints[0].active" >
+                There is an InteractiveTool result view available, <a :href="entryPoints[0].target">click here to display</a>.
+            </span>
+            <span v-else>
+                There is an InteractiveTool result view available, waiting for view to become active...
+            </span>
+        </p>
+        <p v-else>
+            There are multiple InteractiveTool result views available:
+            <ul>
+                <li v-for="entryPoint of entryPoints" v-bind:key="entryPoint.id" >
+                    {{ entryPoint.name }}
+                    <span v-if="entryPoint.active">
+                        (<a :href="entryPoints[0].target">click here to display</a>)
+                    </span>
+                    <span v-else>
+                        (waiting to become active...)
+                    </span>
+                </li>
+            </ul>
+        </p>
+
+        You may also access all active InteractiveTools from the User menu.
+    </div>
+</template>
+
+<script>
+import { clearPolling, pollUntilActive } from "mvc/entrypoints/poll";
+export default {
+    props: {
+        jobId: {
+            type: String,
+            required: true
+        }
+    },
+    data() {
+        return {
+            entryPoints: [],
+        };
+    },
+    created: function() {
+        this.pollEntryPoints();
+    },
+    beforeDestroy: function(){
+        clearPolling();
+    },
+    methods: {
+        pollEntryPoints: function() {
+            const onUpdate = (entryPoints) => {
+                this.entryPoints = entryPoints;
+            }
+            const onError = (e) => {
+                console.error(e);
+            }
+            pollUntilActive(onUpdate, onError, {"job_id": this.jobId})
+        }
+    }
+};
+</script>

client/galaxy/scripts/entry/analysis/AnalysisRouter.js

@@ -22,6 +22,7 @@ import UserPreferences from "mvc/user/user-preferences";
 import CustomBuilds from "mvc/user/user-custom-builds";
 import Tours from "mvc/tours";
 import GridView from "mvc/grid/grid-view";
+import EntryPointGridView from "mvc/entrypoints/view";
 import GridShared from "mvc/grid/grid-shared";
 import Workflows from "mvc/workflow/workflow";
 import WorkflowImport from "components/WorkflowImport.vue";
@@ -74,7 +75,8 @@ export const getAnalysisRouter = Galaxy =>
             "(/)datasets(/)list(/)": "show_datasets",
             "(/)custom_builds": "show_custom_builds",
             "(/)datasets/edit": "show_dataset_edit_attributes",
-            "(/)datasets/error": "show_dataset_error"
+            "(/)datasets/error": "show_dataset_error",
+            "(/)realtime_entry_points(/)list": "show_realtime_list"
         },
 
         require_login: ["show_user", "show_user_form", "show_workflows", "show_cloud_auth"],
@@ -111,6 +113,15 @@ export const getAnalysisRouter = Galaxy =>
             this.page.display(new FormWrapper.View(_.extend(model.get(form_id), { active_tab: "user" })));
         },
 
+        show_realtime_list: function() {
+            this.page.display(
+                new EntryPointGridView({
+                    url_base: `${getAppRoot()}realtime/list`,
+                    active_tab: "analysis"
+                })
+            );
+        },
+
         show_cloud_auth: function() {
             this._display_vue_helper(CloudAuth);
         },

client/galaxy/scripts/layout/menu.js

@@ -301,6 +301,12 @@ const Collection = Backbone.Collection.extend({
                     {
                         title: _l("Visualizations"),
                         url: "visualizations/list",
+                        target: "__use_router__",
+                        divider: true,
+                    },
+                    {
+                        title: _l("Active InteractiveTools"),
+                        url: "realtime_entry_points/list",
                         target: "__use_router__"
                     }
                 ]

client/galaxy/scripts/mvc/entrypoints/poll.js

@@ -0,0 +1,33 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+
+let interval;
+
+export const clearPolling = () => {
+    clearInterval(interval);
+}
+
+export const pollUntilActive = (onUpdate, onError, params) => {
+    clearPolling();
+    const url = getAppRoot() + `api/entry_points`;
+    console.log(params);
+    axios
+        .get(url, {params: params})
+        .then(response => {
+            const entryPoints = [];
+            let allReady = true;
+            response.data.forEach((entryPoint, i) => {
+                entryPoints.push(entryPoint);
+                if(! entryPoint.active) {
+                    allReady = false;
+                }
+            });
+            onUpdate(entryPoints)
+            if(! allReady || entryPoints.length == 0) {
+                interval = setInterval(() => {
+                    pollUntilActive(onUpdate, onError, params);
+                }, 3000);
+            }
+        })
+        .catch(onError);
+}

client/galaxy/scripts/mvc/entrypoints/view.js

@@ -0,0 +1,34 @@
+import $ from "jquery";
+import GridView from "mvc/grid/grid-view";
+import { clearPolling, pollUntilActive } from "mvc/entrypoints/poll";
+
+
+export default GridView.extend({
+    init_grid_elements: function() {
+        GridView.prototype.init_grid_elements.call(this);
+
+        const activated = {};
+
+        const onUpdate = (entryPoints) => {
+            entryPoints.forEach((entryPoint) => {
+                const entryPointId = entryPoint.id;
+                if (entryPoint.active && ! activated[entryPointId]) {
+                    const $link = $(`.entry-point-link[entry_point_id='${entryPointId}']`)
+                    if ($link.length > 0) {
+                        $link.attr("href", entryPoint["target"]);
+                        activated[entryPointId] = true;
+                    }
+                }
+            });
+        }
+        const onError = (e) => {
+            console.error(e);
+        }
+        pollUntilActive(onUpdate, onError, {"running": true});
+    },
+    remove: function() {
+        // Your processing code here
+        clearPolling();
+        GridView.prototype.remove.apply(this, arguments);
+    }
+});

client/galaxy/scripts/mvc/tool/tool-form.js

@@ -11,6 +11,8 @@ import Ui from "mvc/ui/ui-misc";
 import Modal from "mvc/ui/ui-modal";
 import ToolFormBase from "mvc/tool/tool-form-base";
 import Webhooks from "mvc/webhooks";
+import Vue from "vue";
+import ToolEntryPoints from "components/ToolEntryPoints/ToolEntryPoints";
 
 const View = Backbone.View.extend({
     initialize: function(options) {
@@ -230,6 +232,19 @@ const View = Backbone.View.extend({
             success: response => {
                 callback && callback();
                 this.$el.children().hide();
+                if (response.produces_entry_points) {
+                    for (const job of response.jobs) {
+                        const toolEntryPointsInstance = Vue.extend(ToolEntryPoints);
+                        const vm = document.createElement("div");
+                        this.$el.append(vm);
+                        const instance = new toolEntryPointsInstance({
+                            propsData: {
+                                jobId: job.id
+                            }
+                        });
+                        instance.$mount(vm);
+                    }
+                }
                 this.$el.append(this._templateSuccess(response, job_def));
                 this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running

config/galaxy.yml.realtime

@@ -0,0 +1,28 @@
+uwsgi:
+
+  http: localhost:8080
+
+  threads: 8
+
+  http-raw-body: True
+
+  offload-threads: 8
+
+  master: true
+
+  module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
+
+  realtime_map: database/realtime_map.sqlite
+  python-raw: scripts/realtime/key_type_token_mapping.py
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.localhost:8080)$ goto:realtime
+  route-run: goto:endendend
+  route-label: realtime
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.localhost:8080)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $2 $1 $3 $4 $0 5
+  route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
+  route: .* break:404 Not Found
+  route-label: endendend
+
+
+galaxy:
+
+  realtime_prefix: realtime

config/job_conf.xml.realtime

@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<!-- A sample job config for RealTimeTools using local runner. -->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <destinations default="docker_dispatch">
+        <destination id="local" runner="local"/>
+
+        <destination id="docker_local" runner="local">
+          <param id="docker_enabled">true</param>
+          <param id="docker_volumes">$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro</param>
+          <param id="docker_sudo">false</param>
+          <param id="docker_net">bridge</param>
+          <param id="docker_auto_rm">true</param>
+          <param id="require_container">true</param>
+          <param id="docker_set_user"></param>
+        </destination>
+
+        <destination id="docker_dispatch" runner="dynamic">
+            <param id="type">docker_dispatch</param>
+            <param id="docker_destination_id">docker_local</param>
+            <param id="default_destination_id">local</param>
+        </destination>
+
+    </destinations>
+
+</job_conf> 

doc/source/admin/special_topics/realtimetools.rst

@@ -0,0 +1,125 @@
+Galaxy RealTimeTools
+=====================================
+
+A Galaxy RealTimeTool allows launching a container-backed Galaxy Tool 
+and enabling a Galaxy User to gain access to content inside in real-time.
+
+
+How Galaxy RealTimeTools work
+-----------------------------
+
+A RealTimeTool is defined in the same familiar way as standard Galaxy Tools,
+but are specified with **tool_type="realtime"**, and providing additional entry point
+information:
+
+.. code-block:: xml
+
+        <realtime>
+            <entry_point name="Display name">
+                <port>80</port>
+                <url><![CDATA[optional/path/can/be/${templated}]]></url>
+            </entry_point>
+        </realtime>
+
+**Note** that name, port, and url are each able to be templated from the RealTimeTool's parameter dictionary.
+
+
+
+Some important benefits of using Galaxy RealTimeTools
+-----------------------------------------------------
+
+- You can have and access **any number of RealTimeTools at a time** (admin configurable)
+- If you accidentally close the **RealTimeTool browser window**, you can **regain access** by selecting from a **list of active RealTimeTools**
+- A single **RealTimeTool** can **grant access** to **multiple running applications, servers, and interfaces**
+- **RealTimeTools** can be **added to** Galaxy **Workflows**
+- **Native, out-of-the box support for RealTimeTools** in Galaxy via uWSGI proxying
+- **RealTimeTools** are **bonafide Galaxy Tools**; just specify **tool_type as "realtime"** and list the ports you want to expose
+- **RealTimeTools** can be **added** to and **installed from the ToolShed**.
+- **R Shiny apps**, **Javascript-based VNC** access to desktop environments, **genome-browsers-in-a-box**, **interactive notebook environments**, etc, are all possible with **RealTimeTools**
+
+
+
+Server-side configuration of Galaxy RealTimeTools
+-------------------------------------------------
+
+The **galaxy.yml** file will need to be populated as seen in **config/galaxy.yml.realtime**.
+
+In the **uwsgi:** section:
+
+.. code-block:: yaml
+
+  http-raw-body: true
+  # master: true
+
+  realtime_map: database/realtime_map.sqlite
+  python-raw: scripts/realtime/key_type_token_mapping.py
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.localhost:8080)$ goto:realtime
+  route-run: goto:endendend
+  route-label: realtime
+  route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(realtime\.localhost:8080)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $2 $1 $3 $4 $0 5
+  route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
+  route-label: endendend
+
+In the **galaxy:** section:
+
+.. code-block:: yaml
+
+  realtime_prefix: realtime
+
+
+The admin should modify the **route-host**s and **realtime_prefix** to match their preferred configuration.
+
+
+An example **job_conf.xml** file as seen in **config/galaxy.yml.realtime**:
+
+.. code-block:: xml
+
+        <job_conf>
+            <plugins>
+                <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+            </plugins>
+            <destinations default="docker_dispatch">
+                <destination id="local" runner="local"/>
+                <destination id="docker_local" runner="local">
+                  <param id="docker_enabled">true</param>
+                  <param id="docker_volumes">$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro</param>
+                  <param id="docker_sudo">false</param>
+                  <param id="docker_net">bridge</param>
+                  <param id="docker_auto_rm">true</param>
+                  <param id="require_container">true</param>
+                </destination>
+                <destination id="docker_dispatch" runner="dynamic">
+                    <param id="type">docker_dispatch</param>
+                    <param id="docker_destination_id">docker_local</param>
+                    <param id="default_destination_id">local</param>
+                </destination>
+            </destinations>
+        </job_conf> 
+
+
+Alternatively to the local job runner, RealTimeTools have been enabled for the condor job runner, e.g.:
+
+.. code-block:: xml
+
+        <destination id="condor" runner="condor">
+            <param id="docker_enabled">true</param>
+            <param id="docker_sudo">false</param>
+        </destination>
+
+
+**Note on resource consumption:** Keep in mind that Distributed Resource Management (DRM) / cluster systems may have a maximum runtime configured for jobs. From the Galaxy point of view, such a container could run as long as the user desires, this may not be advisable and an admin may want to restrict the runtime of RealTimeTools *(and jobs in general)*. However, if the job is killed by the DRM, the user is not informed beforehand and data in the container could be discarded.
+
+Two **example test RealTimeTools** have been defined, and can be added to the **config/tool_conf.xml**:
+
+.. code-block:: xml
+
+        <tool file="../test/functional/tools/realtimetool_juypter_notebook.xml" />
+        <tool file="../test/functional/tools/realtimetool_cellxgene.xml" />
+
+
+A few words on the condor integration
+-------------------------------------
+
+Galaxy needs to be able to stop a container gracefully. This is not a problem with the local job runner, where we assume that Docker is either running on the same host. However, if you are using production scale DRM, like condor, then your job is running
+somewhere on your cluster and you can not easily **docker stop** your container. For the condor integration we are using a great
+condor feature and commandline utility called **condor_ssh_to_job**. This tool (assuming your condor setup is configured correctly) will bring us directly to the host in question and we can execute the **docker stop** command. Galaxy will simply run **condor_ssh_to_job <condor_job_id> docker stop <container_name>** to stop the container gracefully.