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Merge pull request #7917 from dannon/release_static_fixes

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[19.05] Interactive Environment Fixes
This commit is contained in:
Marius van den Beek
2019-05-10 21:52:55 +02:00
committed by GitHub
parent ccab5f9ac3 349ac80412
commit 99a86eaf10
29 changed files with 298 additions and 328 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/galaxy/scripts/bundleEntries.js
+3
View File
@@ -32,6 +32,9 @@ export { default as HDAModel } from "mvc/history/hda-model";
export { default as LegacyGridView } from "legacy/grid/grid-view";
export { create_chart, create_histogram } from "reports/run_stats";
export { default as ToolshedGroups } from "toolshed/toolshed.groups";
export { default as IES } from "galaxy.interactive_environments";
export { Toast } from "ui/toast"; // TODO: remove when external consumers are updated/gone (IES right now)
export function adminToolshed(options) {
new AdminToolshed.GalaxyApp(options);
client/galaxy/scripts/galaxy.interactive_environments.js
+27 -16
View File
@@ -1,6 +1,6 @@
/* global $ */
/* global toastr */
// TODO: this file is transpiled and used directly without bundling; fix imports when that is no longer the case.
import $ from "jquery";
import { Toast } from "ui/toast";
/**
* Internal function to remove content from the main area and add the notebook.
* Not idempotent
@@ -35,7 +35,7 @@ export function make_spin_state(
sleep_step,
log_attempts
) {
var s = {
return {
type: typeof type !== "undefined" ? type : "GIE spin",
ajax_timeout: typeof ajax_timeout_init !== "undefined" ? ajax_timeout_init : 2000,
ajax_timeout_max: typeof ajax_timeout_max !== "undefined" ? ajax_timeout_max : 16000,
@@ -46,7 +46,6 @@ export function make_spin_state(
log_attempts: typeof log_attempts !== "undefined" ? log_attempts : true,
count: 0
};
return s;
}
/* Log/display an error when spinning fails. */
@@ -54,8 +53,8 @@ export function spin_error(console_msg, user_msg, clear) {
console.log(console_msg);
if (clear) clear_main_area();
if (typeof user_msg == "string") {
toastr.clear();
toastr.error(user_msg, "Error", {
Toast.clear();
Toast.error(user_msg, "Error", {
closeButton: true,
timeOut: 0,
extendedTimeOut: 0,
@@ -112,7 +111,7 @@ export function spin(url, bool_response, success_callback, timeout_callback, err
}
}
};
if (bool_response) ajax_params["dataType"] = "json";
if (bool_response) ajax_params.dataType = "json";
$.ajax(ajax_params);
};
console.log(`Setting up new spinner for ${spin_state.type} on ${url}`);
@@ -131,7 +130,7 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
var message_once = (message, spin_state) => {
if (spin_state.count == 1) {
display_spinner();
toastr.info(message, null, {
Toast.info(message, null, {
closeButton: true,
timeOut: 0,
extendedTimeOut: 0,
@@ -141,22 +140,22 @@ function spin_until(url, bool_response, messages, success_callback, spin_state)
};
var wrapped_success = data => {
if (!bool_response || (bool_response && data == true)) {
console.log(messages["success"]);
console.log(messages.success);
clear_main_area();
toastr.clear();
Toast.clear();
success_callback();
} else if (bool_response && data == false) {
message_once(messages["not_ready"], spin_state);
message_once(messages.not_ready, spin_state);
return false; // keep spinning
} else {
spin_error(`Invalid response to ${spin_state.type} request`, messages["invalid_response"], true);
spin_error(`Invalid response to ${spin_state.type} request`, messages.invalid_response, true);
}
return true; // stop spinning
};
var timeout_error = (jqxhr, status, error) => {
message_once(messages["waiting"], spin_state);
message_once(messages.waiting, spin_state);
if (spin_state.count == warn_at) {
toastr.warning(messages["wait_warn"], "Warning", {
Toast.warning(messages.wait_warn, "Warning", {
closeButton: true,
timeOut: 0,
extendedTimeOut: 0,
@@ -235,7 +234,7 @@ export function keepAlive(notebookAccessURL) {
if (request_count > 30) {
window.clearInterval(interval);
clear_main_area();
toastr.error("Could not connect to IE, contact your administrator", "Error", {
Toast.error("Could not connect to IE, contact your administrator", "Error", {
closeButton: true,
timeOut: 20000,
tapToDismiss: false
@@ -245,3 +244,15 @@ export function keepAlive(notebookAccessURL) {
});
}, 10000);
}
export default {
append_notebook,
clear_main_area,
display_spinner,
make_spin_state,
spin_error,
spin,
test_ie_availability,
load_when_ready,
keepAlive
};
config/galaxy.yml.sample
+9 -10
View File
@@ -144,7 +144,7 @@ galaxy:
# than 5 milliseconds.
#slow_query_log_threshold: 0
# Enable's a per request sql debugging option. If this is set to true,
# Enables a per request sql debugging option. If this is set to true,
# append ?sql_debug=1 to web request URLs to enable detailed logging
# on the backend of SQL queries generated during that request. This is
# useful for debugging slow endpoints during development.
@@ -333,7 +333,7 @@ galaxy:
# be used for job destinations with Docker enabled.
#enable_beta_mulled_containers: false
# Container resolvers configuration (beta). Setup a file describing
# Container resolvers configuration (beta). Set up a file describing
# container resolvers to use when discovering containers for Galaxy.
# If this is set to None, the default containers loaded is determined
# by enable_beta_mulled_containers.
@@ -632,7 +632,7 @@ galaxy:
# Galaxy can display data at various external browsers. These options
# specify which browsers should be available. URLs and builds
# available at these browsers are defined in the specifield files. If
# available at these browsers are defined in the specified files. If
# use_remote_user = True, display application servers will be denied
# access to Galaxy and so displaying datasets in these sites will
# fail. display_servers contains a list of hostnames which should be
@@ -693,11 +693,10 @@ galaxy:
# URL (with schema http/https) of the Galaxy instance as accessible
# within your local network - if specified used as a default by pulsar
# file staging and Jupyter Docker container for communicating back
# with Galaxy via the API. If you are attempting to setup GIEs on Mac
# OS X with Docker for Mac - this should likely be the IP address of
# your machine on the virtualbox network (vboxnet0) setup for the
# Docker host VM. This can found by running ifconfig and using the IP
# address of the network vboxnet0.
# with Galaxy via the API. If you are attempting to set up GIEs on
# Mac OS X with Docker Desktop for Mac and your Galaxy instance runs
# on port 8080 this should be 'http://host.docker.internal:8080'. For
# more details see https://docs.docker.com/docker-for-mac/networking/
#galaxy_infrastructure_url: http://localhost:8080
# If the above URL cannot be determined ahead of time in dynamic
@@ -877,11 +876,11 @@ galaxy:
# for IPC, set that here.
#dynamic_proxy_session_map: database/session_map.sqlite
# Set the port and IP for the the dynamic proxy to bind to, this must
# Set the port and IP for the dynamic proxy to bind to, this must
# match the external configuration if dynamic_proxy_manage is False.
#dynamic_proxy_bind_port: 8800
# Set the port and IP for the the dynamic proxy to bind to, this must
# Set the port and IP for the dynamic proxy to bind to, this must
# match the external configuration if dynamic_proxy_manage is False.
#dynamic_proxy_bind_ip: 0.0.0.0
config/plugins/interactive_environments/askomics/static/js/askomics.js
-9
View File
@@ -1,9 +0,0 @@
var IES = window.IES;
function load_askomics(url){
$( document ).ready(function() {
IES.test_ie_availability(url, function(){
IES.append_notebook(url);
});
});
}
config/plugins/interactive_environments/askomics/static/js/main.js
+9
View File
@@ -0,0 +1,9 @@
var IES = window.IES;
function load_askomics(url) {
$(document).ready(function() {
IES.test_ie_availability(url, function() {
IES.append_notebook(url);
});
});
}
config/plugins/interactive_environments/askomics/templates/askomics.mako
+2 -5
View File
@@ -34,16 +34,13 @@ url = ie_request.url_template('${PROXY_URL}/login_api_gie?key=' + askomics_api_k
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
<script type="text/javascript">
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments', 'plugin/askomics'], function(IES){
window.IES = IES;
load_askomics(url);
});
load_askomics(url);
</script>
<div id="main" width="100%" height="100%">
</div>
config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js → config/plugins/interactive_environments/bam_iobio/static/js/main.js
+15 -15
View File
@@ -2,20 +2,20 @@
var IES = window.IES;
var toastr = window.toastr;
function message_failed_auth(password){
toastr.info(
"Automatic authorization failed.",
"Please login manually",
{'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false}
);
function message_failed_auth(password) {
toastr.info("Automatic authorization failed.", "Please login manually", {
closeButton: true,
timeOut: 100000,
tapToDismiss: false
});
}
function message_failed_connection(){
toastr.error(
"Could not connect to BAM iobio. Please contact your administrator.",
"Security warning",
{'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
);
function message_failed_connection() {
toastr.error("Could not connect to BAM iobio. Please contact your administrator.", "Security warning", {
closeButton: true,
timeOut: 20000,
tapToDismiss: true
});
}
/**
@@ -25,10 +25,10 @@ function message_failed_connection(){
* @param {String} notebook_access_url: the URL embeded in the page and loaded
*
*/
function load_notebook(notebook_access_url){
function load_notebook(notebook_access_url) {
// Test notebook_login_url for accessibility, executing the login+load function whenever
// we've successfully connected to the IE.
IES.test_ie_availability(notebook_access_url, function(){
IES.test_ie_availability(notebook_access_url, function() {
_handle_notebook_loading(notebook_access_url);
});
}
@@ -36,6 +36,6 @@ function load_notebook(notebook_access_url){
/**
* Must be implemented by IEs
*/
function _handle_notebook_loading(notebook_access_url){
function _handle_notebook_loading(notebook_access_url) {
IES.append_notebook(notebook_access_url);
}
config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
+4 -10
View File
@@ -24,6 +24,7 @@ root = h.url_for( '/' )
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
@@ -31,12 +32,8 @@ root = h.url_for( '/' )
${ ie.default_javascript_variables() }
var notebook_access_url = '${ notebook_access_url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments', 'plugin/bam_iobio'], function(IES){
window.IES = IES;
IES.display_spinner();
});
IES.display_spinner();
toastr.info(
"BAM io.bio is starting up!",
@@ -46,11 +43,8 @@ root = h.url_for( '/' )
var startup = function(){
// Load notebook
requirejs(['galaxy.interactive_environments', 'plugin/bam_iobio'], function(IES){
window.IES = IES;
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
};
config/plugins/interactive_environments/cellxgene/templates/cellxgene.mako
+4 -7
View File
@@ -21,14 +21,11 @@
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments'], function (IES) {
$( document ).ready(function() {
IES.keepAlive(url);
IES.test_ie_availability(url, function() {
IES.append_notebook(url);
});
$( document ).ready(function() {
IES.keepAlive(url);
IES.test_ie_availability(url, function() {
IES.append_notebook(url);
});
});
config/plugins/interactive_environments/common/templates/ie.mako
+12 -18
View File
@@ -1,3 +1,10 @@
<%def name="load_default_js()">
${h.css( 'base' ) }
${h.js('bundled/libs.chunk',
'bundled/base.chunk',
'bundled/generic.bundled')}
</%def>
<%def name="default_javascript_variables()">
// Globals
@@ -10,28 +17,15 @@ ie_password = '${ ie_request.notebook_pw }';
var galaxy_root = '${ ie_request.attr.root }';
var app_root = '${ ie_request.attr.app_root }';
var ie_readiness_url = '${ h.url_for("/interactive_environments/ready") }';
</%def>
<%def name="load_default_js()">
${h.css( 'base' ) }
${h.js( 'libs/jquery/jquery',
'libs/toastr',
'libs/require')}
</%def>
<%def name="plugin_require_config()">
require.config({
baseUrl: app_root,
paths: {
"plugin" : app_root + "js",
"galaxy.interactive_environments": "${h.url_for('/static/scripts/galaxy.interactive_environments')}",
},
urlArgs: "v=${app.server_starttime}",
});
window.IES = bundleEntries.IES;
window.toastr = bundleEntries.Toast;
window.onbeforeunload = function() {
return 'You are leaving your Interactive Environment.';
};
</%def>
<%def name="load_default_app()">
<script src="${'%sjs/main.js?v=%s' % (ie_request.attr.app_root, app.server_starttime)}" type="text/javascript"></script>
</%def>
config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js → config/plugins/interactive_environments/ethercalc/static/js/main.js
+2 -2
View File
@@ -2,8 +2,8 @@
var IES = window.IES;
var toastr = window.toastr;
function load_notebook(url){
IES.test_ie_availability(url, function(){
function load_notebook(url) {
IES.test_ie_availability(url, function() {
IES.append_notebook(url);
});
}
config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
+4 -7
View File
@@ -18,20 +18,17 @@ url = ie_request.url_template('${PROXY_URL}/ethercalc/')
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
<script type="text/javascript">
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
// Keep container running and load IE
requirejs(['galaxy.interactive_environments', 'plugin/ethercalc'], function(IES){
window.IES = IES;
IES.keepAlive(url);
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
IES.keepAlive(url);
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
</script>
<div id="main" width="100%" height="100%">
config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js → config/plugins/interactive_environments/hicbrowser/static/js/main.js
+3 -3
View File
@@ -3,12 +3,12 @@ var IES = window.IES;
// Load an interactive environment (IE) from a remote URL
// @param {String} hicexplorer_access_url: the URL embeded in the page and loaded
function load_hicexplorer(hicexplorer_access_url){
function load_hicexplorer(hicexplorer_access_url) {
// When the page has completely loaded...
$( document ).ready(function() {
$(document).ready(function() {
// Test if we can access the GIE, and if so, execute the function
// to load the GIE for the user.
IES.test_ie_availability(hicexplorer_access_url, function(){
IES.test_ie_availability(hicexplorer_access_url, function() {
IES.append_notebook(hicexplorer_access_url);
});
});
config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
+2 -7
View File
@@ -29,19 +29,14 @@
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
<script type="text/javascript">
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments', 'plugin/hicbrowser'], function (IES) {
window.IES = IES;
load_hicexplorer(url);
});
load_hicexplorer(url);
</script>
<div id="main" width="100%" height="100%">
config/plugins/interactive_environments/jupyter/static/js/jupyter.js → config/plugins/interactive_environments/jupyter/static/js/main.js
+58 -44
View File
@@ -2,23 +2,25 @@
var IES = window.IES;
var toastr = window.toastr;
function message_failed_auth(password){
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>",
"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}
{ closeButton: true, timeOut: 100000, tapToDismiss: false }
);
}
function message_failed_connection(){
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}
"Security warning",
{ closeButton: true, timeOut: 20000, tapToDismiss: true }
);
}
function message_no_auth(){
function message_no_auth() {
// No longer a security issue, proxy validates Galaxy session token.
/*
toastr.warning(
@@ -29,7 +31,6 @@ function message_no_auth(){
*/
}
/**
* Load an interactive environment (IE) from a remote URL
* @param {String} password: password used to authenticate to the remote resource
@@ -37,68 +38,82 @@ function message_no_auth(){
* @param {String} notebook_access_url: the URL embeded in the page and loaded
*
*/
function load_notebook(password, notebook_login_url, notebook_access_url){
function load_notebook(password, notebook_login_url, notebook_access_url) {
// Test notebook_login_url for accessibility, executing the login+load function whenever
// we've successfully connected to the IE.
IES.test_ie_availability(notebook_login_url, function(){
IES.test_ie_availability(notebook_login_url, function() {
_handle_notebook_loading(password, notebook_login_url, notebook_access_url);
keep_alive();
});
}
function keep_alive(){
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.
*/
* 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 warn_at = 4;
var count_max = 60;
// we sleep 15 seconds between requests and the default timeout for the Jupyter container is 120 seconds, so start
// with a pretty high ajax timeout. sleep starts low because we want to get the warning up pretty quickly
var spin_state = IES.make_spin_state("IE keepalive", 8000, 16000, 2000, 5000, 15000, 5000, false);
var success = function(){
var success = function() {
console.log("IE keepalive request succeeded");
toastr.clear();
if(spin_state.count >= warn_at){
if (spin_state.count >= warn_at) {
toastr.clear();
toastr.success(
"Interactive environment connection restored",
{'closeButton': true, 'timeOut': 5000, 'extendedTimeOut': 2000, 'tapToDismiss': true}
);
toastr.success("Interactive environment connection restored", {
closeButton: true,
timeOut: 5000,
extendedTimeOut: 2000,
tapToDismiss: true
});
}
spin_state.count = 0;
spin_state.timeout_count = 0;
spin_state.error_count = 0;
return false; // keep spinning
return false; // keep spinning
};
var timeout_error = function(jqxhr, status, error){
console.log("IE keepalive request failed " + spin_state.count + " time(s) of " + count_max + " max: " + status + ": " + error);
if(spin_state.count == warn_at){
var timeout_error = function(jqxhr, status, error) {
console.log(
"IE keepalive request failed " +
spin_state.count +
" time(s) of " +
count_max +
" max: " +
status +
": " +
error
);
if (spin_state.count == warn_at) {
toastr.warning(
"Your browser has been unable to contact the interactive environment for "
+ spin_state.count + " consecutive attempts, if you do not reestablish "
+ "a connection, your IE container may be terminated.",
"Your browser has been unable to contact the interactive environment for " +
spin_state.count +
" consecutive attempts, if you do not reestablish " +
"a connection, your IE container may be terminated.",
"Warning",
{'closeButton': true, 'timeOut': 0, 'extendedTimeOut': 0, 'tapToDismiss': false}
{ closeButton: true, timeOut: 0, extendedTimeOut: 0, tapToDismiss: false }
);
return false; // keep spinning
}else if(spin_state.count >= count_max){
IES.spin_error("IE keepalive failure limit reached", "Lost connection to interactive environment, contact your administrator", false);
return true; // stop spinning
return false; // keep spinning
} else if (spin_state.count >= count_max) {
IES.spin_error(
"IE keepalive failure limit reached",
"Lost connection to interactive environment, contact your administrator",
false
);
return true; // stop spinning
}
};
console.log("IE keepalive worker starting");
IES.spin(notebook_keepalive_url, false, success, timeout_error, timeout_error, spin_state);
}
/**
* Must be implemented by IEs
*/
function _handle_notebook_loading(password, notebook_login_url, notebook_access_url){
if ( ie_password_auth ) {
function _handle_notebook_loading(password, notebook_login_url, notebook_access_url) {
if (ie_password_auth) {
// Make an AJAX POST
$.ajax({
type: "POST",
@@ -106,29 +121,28 @@ function _handle_notebook_loading(password, notebook_login_url, notebook_access_
url: notebook_login_url,
// With our password
data: {
'password': password
password: password
},
xhrFields: {
withCredentials: true
},
// If that is successful, load the notebook
success: function(){
success: function() {
IES.append_notebook(notebook_access_url);
},
error: function(jqxhr, status, error){
if(ie_password_auth){
error: function(jqxhr, status, error) {
if (ie_password_auth) {
// Failure happens due to CORS
message_failed_auth(password);
IES.append_notebook(notebook_access_url);
}else{
} else {
message_failed_connection();
// Do we want to try and load the notebook anyway? Just in case?
IES.append_notebook(notebook_access_url);
}
}
});
}
else {
} else {
// Not using password auth, just embed it to avoid content-origin issues.
message_no_auth();
IES.append_notebook(notebook_access_url);
config/plugins/interactive_environments/jupyter/templates/jupyter.mako
+3 -8
View File
@@ -50,6 +50,7 @@ notebook_keepalive_url = ie_request.url_template('${PROXY_URL}/ipython/tree')
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
@@ -58,16 +59,10 @@ ${ ie.default_javascript_variables() }
var notebook_login_url = '${ notebook_login_url }';
var notebook_access_url = '${ notebook_access_url }';
var notebook_keepalive_url = '${ notebook_keepalive_url }';
${ ie.plugin_require_config() }
// Load notebook
requirejs(['galaxy.interactive_environments', 'plugin/jupyter'], function(IES){
// This global is not awesome, get rid of it when possible (when IES are a part of the build process)
window.IES = IES;
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(ie_password, notebook_login_url, notebook_access_url);
});
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(ie_password, notebook_login_url, notebook_access_url);
});
config/plugins/interactive_environments/neo/static/js/neo.js → config/plugins/interactive_environments/neo/static/js/main.js
+2 -2
View File
@@ -3,10 +3,10 @@ var IES = window.IES;
// Load an interactive environment (IE) from a remote URL
// @param {String} notebook_access_url: the URL embeded in the page and loaded
function load_notebook(notebook_access_url){
function load_notebook(notebook_access_url) {
// Test if we can access the GIE, and if so, execute the function
// to load the GIE for the user.
IES.test_ie_availability(notebook_access_url, function(){
IES.test_ie_availability(notebook_access_url, function() {
IES.append_notebook(notebook_access_url);
});
}
config/plugins/interactive_environments/neo/templates/neo.mako
+4 -10
View File
@@ -23,20 +23,14 @@
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
<script type="text/javascript">
${ ie.default_javascript_variables() }
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments', 'plugin/neo'], function (IES) {
window.IES = IES;
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
</script>
config/plugins/interactive_environments/phinch/static/js/main.js
+54
View File
@@ -0,0 +1,54 @@
// Globals to be rid of
var IES = window.IES;
var toastr = window.toastr;
function load_notebook(url) {
IES.test_ie_availability(url, function() {
append_notebook(url);
});
}
function append_notebook(url) {
IES.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;
var interval = window.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) {
window.clearInterval(interval);
IES.clear_main_area();
toastr.error("Could not connect to IE, contact your administrator", "Error", {
closeButton: true,
timeOut: 20000,
tapToDismiss: false
});
}
}
});
}, 10000);
}
config/plugins/interactive_environments/phinch/static/js/phinch.js
-54
View File
@@ -1,54 +0,0 @@
// Globals to be rid of
var IES = window.IES;
var toastr = window.toastr;
function load_notebook(url){
IES.test_ie_availability(url, function(){
append_notebook(url);
});
}
function append_notebook(url){
IES.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;
var interval = window.setInterval(function(){
$.ajax({
url: notebook_access_url,
xhrFields: {
withCredentials: true
},
type: "GET",
timeout: 500,
success: function(){
console.log("Connected to IE, returning");
},
error: function(jqxhr, status, error){
request_count++;
console.log("Request " + request_count);
if(request_count > 30){
window.clearInterval(interval);
IES.clear_main_area();
toastr.error(
"Could not connect to IE, contact your administrator",
"Error",
{'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false}
);
}
}
});
}, 10000);
}
config/plugins/interactive_environments/phinch/templates/phinch.mako
+5 -8
View File
@@ -21,21 +21,18 @@ url = ie_request.url_template('${PROXY_URL}/phinch/')
%>
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body>
<script type="text/javascript">
${ ie.default_javascript_variables() }
var url = '${ url }';
${ ie.plugin_require_config() }
// Keep container running and load notebook
requirejs(['galaxy.interactive_environments', 'plugin/phinch'], function(IES){
window.IES = IES;
keep_alive(url);
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
keep_alive(url);
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(url);
});
</script>
config/plugins/interactive_environments/rstudio/static/js/main.js
Executable
+24
View File
@@ -0,0 +1,24 @@
// Assumed globals we need to get rid of
var IES = window.IES;
var toastr = window.toastr;
function message_failed_connection() {
toastr.error("Could not connect to RStudio. Please contact your administrator.", "Security warning", {
closeButton: true,
timeOut: 20000,
tapToDismiss: true
});
}
/**
* Load an interactive environment (IE) from a remote URL
* @param {String} notebook_access_url: the URL embeded in the page and loaded
*
*/
function load_notebook(notebook_access_url) {
// Test notebook_login_url for accessibility, executing the login+load function whenever
// we've successfully connected to the IE.
IES.test_ie_availability(notebook_access_url, function() {
IES.append_notebook(notebook_access_url);
});
}
config/plugins/interactive_environments/rstudio/static/js/rstudio.js
-32
View File
@@ -1,32 +0,0 @@
// Assumed globals we need to get rid of
var IES = window.IES;
var toastr = window.toastr;
function message_failed_connection(){
toastr.error(
"Could not connect to RStudio. Please contact your administrator.",
"Security warning",
{'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true}
);
}
/**
* Load an interactive environment (IE) from a remote URL
* @param {String} notebook_access_url: the URL embeded in the page and loaded
*
*/
function load_notebook(notebook_access_url){
// Test notebook_login_url for accessibility, executing the login+load function whenever
// we've successfully connected to the IE.
IES.test_ie_availability(notebook_access_url, function(){
$.ajax({
type: 'GET',
url: notebook_access_url,
success: function(response_text){
IES.append_notebook(notebook_access_url);
}
});
});
}
config/plugins/interactive_environments/rstudio/templates/rstudio.mako
+3 -6
View File
@@ -27,18 +27,15 @@ notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/')
<html>
<head>
${ ie.load_default_js() }
${ ie.load_default_app() }
</head>
<body style="margin: 0px">
<script type="text/javascript">
${ ie.default_javascript_variables() }
var notebook_access_url = '${ notebook_access_url }';
${ ie.plugin_require_config() }
requirejs(['galaxy.interactive_environments', 'plugin/rstudio'], function(IES){
window.IES = IES;
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
</script>
<div id="main" width="100%" height="100%">
doc/source/admin/galaxy_options.rst
+12 -14
View File
@@ -105,7 +105,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable's a per request sql debugging option. If this is set to
Enables a per request sql debugging option. If this is set to
true, append ?sql_debug=1 to web request URLs to enable detailed
logging on the backend of SQL queries generated during that
request. This is useful for debugging slow endpoints during
@@ -517,7 +517,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Container resolvers configuration (beta). Setup a file describing
Container resolvers configuration (beta). Set up a file describing
container resolvers to use when discovering containers for Galaxy.
If this is set to None, the default containers loaded is
determined by enable_beta_mulled_containers.
@@ -1175,7 +1175,7 @@
:Description:
Galaxy can display data at various external browsers. These
options specify which browsers should be available. URLs and
builds available at these browsers are defined in the specifield
builds available at these browsers are defined in the specified
files. If use_remote_user = True, display application servers
will be denied access to Galaxy and so displaying datasets in
these sites will fail. display_servers contains a list of
@@ -1301,11 +1301,11 @@
URL (with schema http/https) of the Galaxy instance as accessible
within your local network - if specified used as a default by
pulsar file staging and Jupyter Docker container for communicating
back with Galaxy via the API. If you are attempting to setup GIEs
on Mac OS X with Docker for Mac - this should likely be the IP
address of your machine on the virtualbox network (vboxnet0) setup
for the Docker host VM. This can found by running ifconfig and
using the IP address of the network vboxnet0.
back with Galaxy via the API. If you are attempting to set up
GIEs on Mac OS X with Docker Desktop for Mac and your Galaxy
instance runs on port 8080 this should be
'http://host.docker.internal:8080'. For more details see
https://docs.docker.com/docker-for-mac/networking/
:Default: ``http://localhost:8080``
:Type: str
@@ -1732,9 +1732,8 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the port and IP for the the dynamic proxy to bind to, this
must match the external configuration if dynamic_proxy_manage is
False.
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is False.
:Default: ``8800``
:Type: int
@@ -1744,9 +1743,8 @@
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the port and IP for the the dynamic proxy to bind to, this
must match the external configuration if dynamic_proxy_manage is
False.
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is False.
:Default: ``0.0.0.0``
:Type: str
doc/source/admin/special_topics/interactive_environments.rst
+6 -10
View File
@@ -36,17 +36,13 @@ and `Ansible Galaxy <https://galaxy.ansible.com/detail#/role/6056>`__.
Setting up the Proxy
^^^^^^^^^^^^^^^^^^^^
Currently the Galaxy proxy is a NodeJS+Sqlite3 proxy.
The Galaxy IE Proxy is a NodeJS+Sqlite3 application. The NodeJS that is
installed by default into the Galaxy Virtualenv is suitable for an execution
environment for the Galaxy IE Proxy.
- Node has recently upgraded, and our proxy is pinned to an old version of
sqlite3. As such you'll currently need to have an older version of Node
available (0.10.X - 0.11.X vintage).
- One can use `NVM <https://github.com/creationix/nvm>`__ to install and manage multiple versions of Node.
- We're working on solutions in this space to provide a better deployment
mechanism here and fewer dependencies.
- Please note that if you have NodeJS installed under Ubuntu, it often
installs to ``/usr/bin/nodejs``, whereas ``npm`` expects it to be
``/usr/bin/node``. You will need to create that symlink yourself.
- Note that if you have NodeJS installed under Ubuntu, it often installs to
``/usr/bin/nodejs``, whereas ``npm`` expects it to be ``/usr/bin/node``. You
may need to create that symlink yourself.
Once Node and npm are ready to go, you'll need to install the dependencies
doc/source/dev/interactive_environments.rst
+7 -13
View File
@@ -205,9 +205,10 @@ We'll continue appending to our ``helloworld.mako`` the HTML code that's actuall
<html>
<head>
<!-- Loads some necessary javascript libraries. Specifically jquery,
toastr, and requirejs -->
<!-- Loads core Galaxy javascript libraries for a 'generic' entrypoint. -->
${ ie.load_default_js() }
<!-- This will load code from static/main.js, often used to handle things like login -->
${ ie.load_default_app() }
</head>
<body>
@@ -217,18 +218,11 @@ We'll continue appending to our ``helloworld.mako`` the HTML code that's actuall
var notebook_login_url = 'unused';
var notebook_access_url = '${ notebook_access_url }';
// Load code with require.js
${ ie.plugin_require_config() }
// Load notebook
// This will load code from static/helloworld.js, often used to handle
// things like Login. The load_notebook function will eventually append
// an IFrame to the <div id="main" /> below.
requirejs(['galaxy.interactive_environments', 'plugin/helloworld'], function(IES){
window.IES = IES
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
// The load_notebook function will eventually append an IFrame to the <div id="main" /> below.
IES.load_when_ready(ie_readiness_url, function(){
load_notebook(notebook_access_url);
});
</script>
<div id="main" width="100%" height="100%">
@@ -262,7 +256,7 @@ authentication of users, so you don't have to worry about it, and can just
assume that only the correct user will have access to a given notebook.
In the ``static/`` directory, we generally create a ``js/`` directory below that,
and create a ``{gie}.js`` (so, ``static/js/helloworld.js``) file in there.
and create a ``main.js`` file in there.
That file will have a function, ``load_notebook`` which will check if the GIE is available,
and when it is, display it to the user.
lib/galaxy/visualization/plugins/interactive_environments.py
+6 -1
View File
@@ -19,7 +19,10 @@ from galaxy import model, web
from galaxy.containers import ContainerPort
from galaxy.containers.docker_model import DockerVolume
from galaxy.managers import api_keys
from galaxy.util import string_as_bool_or_none
from galaxy.util import (
string_as_bool_or_none,
unicodify
)
from galaxy.util.bunch import Bunch
@@ -432,6 +435,8 @@ class InteractiveEnvironmentRequest(object):
))
p = Popen(raw_cmd, stdout=PIPE, stderr=PIPE, close_fds=True)
stdout, stderr = p.communicate()
stdout = unicodify(stdout)
stderr = unicodify(stderr)
if p.returncode != 0:
log.error("Container Launch error\n\n%s\n%s" % (stdout, stderr))
return None
lib/galaxy/webapps/galaxy/config_schema.yml
+18 -17
View File
@@ -102,10 +102,10 @@ mapping:
default: false
required: false
desc: |
Enable's a per request sql debugging option. If this is set to true, append
?sql_debug=1 to web request URLs to enable detailed logging on the backend of SQL
queries generated during that request. This is useful for debugging slow endpoints
during development.
Enables a per request sql debugging option. If this is set to true,
append ?sql_debug=1 to web request URLs to enable detailed logging on
the backend of SQL queries generated during that request. This is
useful for debugging slow endpoints during development.
install_database_connection:
type: str
@@ -397,9 +397,9 @@ mapping:
default: ''
required: false
desc: |
Container resolvers configuration (beta). Setup a file describing container
resolvers to use when discovering containers for Galaxy. If this is set to
None, the default containers loaded is determined by
Container resolvers configuration (beta). Set up a file describing
container resolvers to use when discovering containers for Galaxy. If
this is set to None, the default containers loaded is determined by
enable_beta_mulled_containers.
involucro_path:
@@ -874,7 +874,7 @@ mapping:
desc: |
Galaxy can display data at various external browsers. These options specify
which browsers should be available. URLs and builds available at these
browsers are defined in the specifield files.
browsers are defined in the specified files.
If use_remote_user = True, display application servers will be denied access
to Galaxy and so displaying datasets in these sites will fail.
@@ -970,14 +970,15 @@ mapping:
default: http://localhost:8080
required: false
desc: |
URL (with schema http/https) of the Galaxy instance as accessible within your
local network - if specified used as a default by pulsar file staging and
Jupyter Docker container for communicating back with Galaxy via the API.
URL (with schema http/https) of the Galaxy instance as accessible
within your local network - if specified used as a default by pulsar
file staging and Jupyter Docker container for communicating back with
Galaxy via the API.
If you are attempting to setup GIEs on Mac OS X with Docker for Mac - this
should likely be the IP address of your machine on the virtualbox network (vboxnet0)
setup for the Docker host VM. This can found by running ifconfig and using the
IP address of the network vboxnet0.
If you are attempting to set up GIEs on Mac OS X with Docker Desktop
for Mac and your Galaxy instance runs on port 8080 this should be
'http://host.docker.internal:8080'. For more details see
https://docs.docker.com/docker-for-mac/networking/
galaxy_infrastructure_web_port:
type: int
@@ -1292,7 +1293,7 @@ mapping:
default: 8800
required: false
desc: |
Set the port and IP for the the dynamic proxy to bind to, this must match
Set the port and IP for the dynamic proxy to bind to, this must match
the external configuration if dynamic_proxy_manage is False.
dynamic_proxy_bind_ip:
@@ -1300,7 +1301,7 @@ mapping:
default: 0.0.0.0
required: false
desc: |
Set the port and IP for the the dynamic proxy to bind to, this must match
Set the port and IP for the dynamic proxy to bind to, this must match
the external configuration if dynamic_proxy_manage is False.
dynamic_proxy_debug: