Merge pull request #1647 from shiltemann/dev

Phinch interactive environment
2026-09-24 16:30:27 +08:00 · 2016-02-08 18:23:01 +01:00
parent faeedd6f82 674bf530c6
commit 6a3452afff
4 changed files with 133 additions and 0 deletions
@@ -0,0 +1,21 @@
+[main]
+# Unused
+
+[docker]
+# Command to execute docker. For example `sudo docker` or `docker-lxc`.
+command = docker {docker_args}
+
+# The docker image name that should be started.
+image = shiltemann/docker-phinch-galaxy:16.04
+
+# Additional arguments that are passed to the `docker run` command.
+#command_inject = --sig-proxy=true -e DEBUG=false
+
+# URL to access the Galaxy API with from the spawn Docker container, if empty
+# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
+# Docker host of the spawned container if that is also not set.
+#galaxy_url =
+
+# The Docker hostname. It can be useful to run the Docker daemon on a different
+# host than Galaxy.
+#docker_hostname = localhost
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
+<interactive_environment name="Phinch">
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">Biom1</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">phinch.mako</entry_point>
+</interactive_environment>
@@ -0,0 +1,51 @@
+function load_notebook(url){
+    $( document ).ready(function() {
+        test_ie_availability(url, function(){
+            append_notebook(url)
+        });
+    });
+}
+
+function append_notebook(url){
+    clear_main_area();
+    $('#main').append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:auto;" scrolling="yes" src="'+ url +'"></iframe>'
+    );
+}
+
+
+function keep_alive(notebook_access_url){
+    /**
+    * This is needed to keep the container alive. If the user leaves this site
+    * this function is not constantly pinging the container, the container will
+    * terminate itself.
+    */
+
+    var request_count = 0;
+    interval = setInterval(function(){
+        $.ajax({
+            url: notebook_access_url,
+            xhrFields: {
+                withCredentials: true
+            },
+            type: "GET",
+            timeout: 500,
+            success: function(){
+                console.log("Connected to IE, returning");
+            },
+            error: function(jqxhr, status, error){
+                request_count++;
+                console.log("Request " + request_count);
+                if(request_count > 30){
+                    clearInterval(interval);
+                    clear_main_area();
+                    toastr.error(
+                        "Could not connect to IE, contact your administrator",
+                        "Error",
+                        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false}
+                    );
+                }
+            }
+        });
+    }, 10000);
+}
+
@@ -0,0 +1,46 @@
+<%namespace name="ie" file="ie.mako" />
+<%
+
+import os
+
+# Sets ID and sets up a lot of other variables
+ie_request.load_deploy_config()
+
+
+# Launch the IE. This builds and runs the docker command in the background.
+ie_request.launch(env_override={
+    'dataset_hid': hda.hid,
+    'dataset_filename': hda.file_name
+})
+
+# Only once the container is launched can we template our URLs. The ie_request
+# doesn't have all of the information needed until the container is running.
+url = ie_request.url_template('${PROXY_URL}/phinch/')
+
+
+%>
+<html>
+<head>
+${ ie.load_default_js() }
+</head>
+<body>
+<script type="text/javascript">
+${ ie.default_javascript_variables() }
+var url = '${ url }';
+${ ie.plugin_require_config() }
+
+// Keep container running
+requirejs(['interactive_environments', 'plugin/phinch'], function(){
+    keep_alive(url);
+});
+
+// Load notebook
+requirejs(['interactive_environments', 'plugin/phinch'], function(){
+    load_notebook(url);
+});
+
+</script>
+<div id="main" style="width: 100%; height: 100%; overflow:hidden;">
+</div>
+</body>
+</html>