diff --git a/config/plugins/visualizations/chiraviz/src/js/rna-viz.js b/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
index eefaa3a1a0f..93bc6d57ae9 100644
--- a/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
+++ b/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
@@ -1,6 +1,6 @@
/***
-Chimera interactions viewer. It reads sqlite file
+Chimera interactions viewer. It reads sqlite file
and shows up the list of interactions and a summary
in multiple plots, comic alignments
diff --git a/config/plugins/visualizations/chiraviz/templates/chiraviz.mako b/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
index 5dd60ad2e75..2bbba694758 100644
--- a/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
+++ b/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
@@ -18,7 +18,7 @@
-
${h.stylesheet_link( root + 'static/plugins/visualizations/graphviz/static/css/style.css' )}
+ ${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/jquery.min.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/cytoscape.min.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/collapse.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js' )}
diff --git a/config/plugins/visualizations/h5web/src/script.js b/config/plugins/visualizations/h5web/src/script.js
index db416ab2e35..a596cf214d6 100644
--- a/config/plugins/visualizations/h5web/src/script.js
+++ b/config/plugins/visualizations/h5web/src/script.js
@@ -1,8 +1,8 @@
/**
* Visualizer interface for h5web (https://github.com/silx-kit/h5web)
- *
+ *
* This relies on Galaxy being able to serve files using the
- * h5grove protocol (https://silx-kit.github.io/h5grove/).
+ * h5grove protocol (https://silx-kit.github.io/h5grove/).
* This provides efficient access to the contents of the
* HDF5 file and avoids having to read the whole file at any
* point.
@@ -13,6 +13,12 @@ import React, { StrictMode } from 'react'
import {render as reactRender} from 'react-dom'
import {App, H5GroveProvider} from '@h5web/app'
+/* This will be part of the charts/viz standard lib in 23.1 */
+const slashCleanup = /(\/)+/g;
+function prefixedDownloadUrl(root, path) {
+ return `${root}/${path}`.replace(slashCleanup, "/");
+}
+
function MyApp(props) {
return (
,
document.getElementById(options.target)
diff --git a/config/plugins/visualizations/heatmap/heatmap_default/src/script.js b/config/plugins/visualizations/heatmap/heatmap_default/src/script.js
index 5ea473ec19a..d9bf0966f02 100644
--- a/config/plugins/visualizations/heatmap/heatmap_default/src/script.js
+++ b/config/plugins/visualizations/heatmap/heatmap_default/src/script.js
@@ -468,7 +468,7 @@ window.bundleEntries.heatmap_default = function (options) {
}
window.bundleEntries.heatmap_cluster = function (options) {
- options.targets = createContainers(options.chart, options.target);
+ options.targets = createContainers("svg", options.chart, options.target);
requestJobs(
options.chart,
requestCharts(options.chart, "heatmap"),
diff --git a/config/plugins/visualizations/hyphyvision/templates/hyphyvision.mako b/config/plugins/visualizations/hyphyvision/templates/hyphyvision.mako
index 0b0950c88f8..995a4afa937 100644
--- a/config/plugins/visualizations/hyphyvision/templates/hyphyvision.mako
+++ b/config/plugins/visualizations/hyphyvision/templates/hyphyvision.mako
@@ -1,5 +1,5 @@
<%
- app_root = "/static/plugins/visualizations/hyphyvision/static/"
+ app_root = h.url_for("/static/plugins/visualizations/hyphyvision/static/")
%>
diff --git a/config/plugins/visualizations/mvpapp/templates/mvpapp.mako b/config/plugins/visualizations/mvpapp/templates/mvpapp.mako
index 2158a236a7c..b7419db9ab8 100644
--- a/config/plugins/visualizations/mvpapp/templates/mvpapp.mako
+++ b/config/plugins/visualizations/mvpapp/templates/mvpapp.mako
@@ -29,7 +29,7 @@
-
+
@@ -73,7 +73,7 @@ ${h.javascript_link(app_root + "dist/script.js")}
$(document).ready(function (){
var config = {
dbkey: '${hda.get_metadata().dbkey}',
- href: document.location.origin,
+ href: document.location.origin + '${h.url_for( "/" )}'.replace(/\/$/, ''),
dataName: '${hda.name}',
historyID: '${trans.security.encode_id( hda.history_id )}',
datasetID: '${trans.security.encode_id( hda.id )}',
diff --git a/config/plugins/visualizations/openlayers/src/script.js b/config/plugins/visualizations/openlayers/src/script.js
index 48b1dcf9faa..90922403fa7 100644
--- a/config/plugins/visualizations/openlayers/src/script.js
+++ b/config/plugins/visualizations/openlayers/src/script.js
@@ -215,8 +215,7 @@ var MapViewer = (function(mv) {
const sourceVec = new Vector({ format: formatType, url: filePath, wrapX: false });
mv.createMap(filePath, sourceVec, options, chart, styleFunction, target);
} else if (fileType === "shp") {
- const fileUrl = prefixedDownloadUrl(options.root, filePath);
- axios.get(fileUrl, { responseType: "arraybuffer" }).then(shpfile => {
+ axios.get(filePath, { responseType: "arraybuffer" }).then(shpfile => {
console.debug(shpfile);
shp(shpfile.data).then(
geojson => {
diff --git a/config/plugins/visualizations/scatterplot/src/scatterplot.js b/config/plugins/visualizations/scatterplot/src/scatterplot.js
index 8124b8e6b58..c167d136999 100644
--- a/config/plugins/visualizations/scatterplot/src/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot.js
@@ -821,7 +821,7 @@ var ScatterplotDisplay = Backbone.View.extend({
var view = this,
config = this.model.get("config"),
//TODO: very tied to datasets - should be generalized eventually
- baseUrl = window.parent && window.parent.galaxy_config ? window.parent.galaxy_config.root : "/",
+ baseUrl = window.parent && window.parent.options ? window.parent.options.root : "/",
xhr = $.getJSON(baseUrl + "api/datasets/" + this.dataset.id, {
data_type: "raw_data",
provider: "dataset-column",
@@ -986,7 +986,7 @@ var ScatterplotDisplay = Backbone.View.extend({
}
var view = this;
var config = this.model.get("config");
- var meanWorker = new window.Worker("worker-stats.js");
+ var meanWorker = new window.Worker("./static/worker-stats.js");
meanWorker.postMessage({
data: this.data,
keys: [config.xColumn, config.yColumn]
diff --git a/config/plugins/visualizations/scatterplot/src/numeric-column-stats.js b/config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
similarity index 100%
rename from config/plugins/visualizations/scatterplot/src/numeric-column-stats.js
rename to config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
diff --git a/config/plugins/visualizations/scatterplot/static/scatterplot.js b/config/plugins/visualizations/scatterplot/static/scatterplot.js
index 523503e467d..5d5f56081db 100644
--- a/config/plugins/visualizations/scatterplot/static/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot.js
@@ -1,58 +1,376 @@
-parcelRequire=function(e,r,n,t){var i="function"==typeof parcelRequire&&parcelRequire,o="function"==typeof require&&require;function u(n,t){if(!r[n]){if(!e[n]){var f="function"==typeof parcelRequire&&parcelRequire;if(!t&&f)return f(n,!0);if(i)return i(n,!0);if(o&&"string"==typeof n)return o(n);var c=new Error("Cannot find module '"+n+"'");throw c.code="MODULE_NOT_FOUND",c}p.resolve=function(r){return e[n][1][r]||r},p.cache={};var l=r[n]=new u.Module(n);e[n][0].call(l.exports,p,l,l.exports,this)}return r[n].exports;function p(e){return u(p.resolve(e))}}u.isParcelRequire=!0,u.Module=function(e){this.id=e,this.bundle=u,this.exports={}},u.modules=e,u.cache=r,u.parent=i,u.register=function(r,n){e[r]=[function(e,r){r.exports=n},{}]};for(var f=0;f1)for(var n=1;n1)for(var n=1;n0&&t-1 in e)}w.fn=w.prototype={jquery:"3.3.1",constructor:w,length:0,toArray:function(){return a.call(this)},get:function(e){return null==e?a.call(this):e<0?this[e+this.length]:this[e]},pushStack:function(e){var 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