Merge pull request #1400 from bgruening/jupyter

Add Jupyter Interactive Environment
2026-09-24 16:30:27 +08:00 · 2015-12-27 11:46:44 -06:00
parent 4e55f7e519 6ac01675f3
commit 798c7e20c3
4 changed files with 252 additions and 0 deletions
@@ -0,0 +1,43 @@
+[main]
+# Following options are ignored if using the Galaxy dynamic proxy but
+# are useful if mapping a range of ports for environment consumption.
+#password_auth = False
+#ssl = False
+
+[docker]
+# Command to launch docker container. For example `sudo docker` or `docker-lxc`.
+# If you need to use a command like `sg` you can do that here, just be sure to
+# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'`
+#
+# It is recommended that you use command_inject if you need to inject
+# additional parameters. This command string is re-used for a `docker inspect`
+# command and will likely cause errors if it is extensively modified, past the
+# usual group/sudo changes.
+#command = docker {docker_args}
+
+# The docker image name that should be started.
+image = bgruening/docker-jupyter-notebook:16.01
+
+# Additional arguments that are passed to the `docker run` command.
+command_inject = --sig-proxy=true -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120
+
+# URL to access the Galaxy API with from the spawn Docker containter, 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
+
+# Try to set the tempdirectory to world execute - this can fix the issue 
+# where 'sudo docker' is not able to mount the folder otherwise.
+# "finalize namespace chdir to /import permission denied"
+#wx_tempdir = False
+
+# Overwride the IE tempdirectory. This can be useful if you regular tempdir is
+# located on an NFS share, which does not work well as Docker volume. In this case
+# you can have a shared sshfs share which you can use as temporary directory to
+# share data between the IE and Galaxy.
+#docker_galaxy_temp_dir = None
+
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
+<interactive_environment name="Jupyter (Programming Environment)">
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</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">jupyter.mako</entry_point>
+</interactive_environment>
@@ -0,0 +1,123 @@
+function message_failed_auth(password){
+    toastr.info(
+        "Automatic authorization failed. You can manually login with:<br>" + password + "<br> <a href='https://github.com/bgruening/galaxy-ipython/wiki/Automatic-Authorization-Failed' target='_blank'>More details ...</a>",
+        "Please login manually",
+        {'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false}
+    );
+}
+
+function message_failed_connection(){
+    toastr.error(
+        "Could not connect to Jupyter Notebook. Please contact your administrator. <a href='https://github.com/bgruening/galaxy-ipython/wiki/Could-not-connect-to-IPython-Notebook' target='_blank'>More details ...</a>",
+    "Security warning",
+        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
+    );
+}
+
+function message_no_auth(){
+    // No longer a security issue, proxy validates Galaxy session token.
+    /*
+    toastr.warning(
+        "IPython Notebook was lunched without authentication. This is a security issue. <a href='https://github.com/bgruening/galaxy-ipython/wiki/IPython-Notebook-was-lunched-without-authentication' target='_blank'>More details ...</a>",
+        "Security warning",
+        {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false}
+    );
+    */
+}
+
+
+/**
+ * Load an interactive environment (IE) from a remote URL
+ * @param {String} password: password used to authenticate to the remote resource
+ * @param {String} notebook_login_url: URL that should be POSTed to for login
+ * @param {String} notebook_access_url: the URL embeded in the page and loaded
+ *
+ */
+function load_notebook(password, notebook_login_url, notebook_access_url){
+    $( document ).ready(function() {
+        // Test notebook_login_url for accessibility, executing the login+load function whenever
+        // we've successfully connected to the IE.
+        test_ie_availability(notebook_login_url, function(){
+            _handle_notebook_loading(password, notebook_login_url, notebook_access_url);
+        });
+    });
+}
+
+
+function keep_alive(){
+    /**
+    * 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}
+                    );
+                }
+            }
+        });
+    }, 30000);
+}
+
+
+/**
+ * Must be implemented by IEs
+ */
+function _handle_notebook_loading(password, notebook_login_url, notebook_access_url){
+    if ( ie_password_auth ) {
+        // Make an AJAX POST
+        $.ajax({
+            type: "POST",
+            // to the Login URL
+            url: notebook_login_url,
+            // With our password
+            data: {
+                'password': password
+            },
+            xhrFields: {
+                withCredentials: true
+            },
+            // If that is successful, load the notebook
+            success: function(){
+                append_notebook(notebook_access_url);
+            },
+            error: function(jqxhr, status, error){
+                if(ie_password_auth){
+                    // Failure happens due to CORS
+                    message_failed_auth(password);
+                    append_notebook(notebook_access_url);
+                }else{
+                    message_failed_connection();
+                    // Do we want to try and load the notebook anyway? Just in case?
+                    append_notebook(notebook_access_url);
+                }
+            }
+        });
+    }
+    else {
+        // Not using password auth, just embed it to avoid content-origin issues.
+        message_no_auth();
+        append_notebook(notebook_access_url);
+    }
+}
@@ -0,0 +1,70 @@
+<%namespace name="ie" file="ie.mako" />
+
+<%
+import os
+import shutil
+import hashlib
+
+# Sets ID and sets up a lot of other variables
+ie_request.load_deploy_config()
+ie_request.attr.docker_port = 8888
+ie_request.attr.import_volume = False
+
+if ie_request.attr.PASSWORD_AUTH:
+    m = hashlib.sha1()
+    m.update( ie_request.notebook_pw + ie_request.notebook_pw_salt )
+    PASSWORD = 'sha1:%s:%s' % (ie_request.notebook_pw_salt, m.hexdigest())
+else:
+    PASSWORD = "none"
+
+## Jupyter Notbook Specific
+if hda.datatype.__class__.__name__ == "Ipynb":
+    DATASET_HID = hda.hid
+else:
+    DATASET_HID = None
+
+# Add all environment variables collected from Galaxy's IE infrastructure
+ie_request.launch(env_override={
+    'notebook_password': PASSWORD,
+    'dataset_hid': DATASET_HID,
+})
+
+## General IE specific
+# Access URLs for the notebook from within galaxy.
+notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/notebooks/ipython_galaxy_notebook.ipynb')
+notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/login?next=${PROXY_PREFIX}%2Fipython%2Ftree')
+
+%>
+<html>
+<head>
+${ ie.load_default_js() }
+</head>
+<body>
+
+<script type="text/javascript">
+${ ie.default_javascript_variables() }
+var notebook_login_url = '${ notebook_login_url }';
+var notebook_access_url = '${ notebook_access_url }';
+${ ie.plugin_require_config() }
+
+// Keep container running
+requirejs(['interactive_environments', 'plugin/jupyter'], function(){
+    keep_alive();
+});
+
+
+// Load notebook
+
+requirejs(['interactive_environments', 'plugin/jupyter'], function(){
+    load_notebook(ie_password, notebook_login_url, notebook_access_url);
+});
+
+
+
+
+
+</script>
+<div id="main" width="100%" height="100%">
+</div>
+</body>
+</html>