From 528898b3b3c56047c9bbeeace8196d9cdc7add2a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 30 Jul 2024 14:13:55 +0300
Subject: [PATCH 01/14] Add vis parameters to script based visualizations

---
 .../common/templates/script_entry_point.mako          | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index dfdf4137666b..82d33bc868c0 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -3,8 +3,17 @@
 
 ## No stylesheets
 <%def name="stylesheets()"></%def>
-## No javascript libraries
+
+## Create a container, attach data and import script file
 <%def name="late_javascripts()">
+    <% container = script_attributes.get("container") or "app" %>
+    <% data_incoming = {
+        "visualization_id": visualization_id,
+        "visualization_name": visualization_name,
+        "visualization_plugin": visualization_plugin,
+        "visualization_config": config }
+    %>
+    <div id="${container}" data-incoming='${h.dumps(data_incoming)}'></div>
     <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_attributes.items() ]) %>
     <script type="text/javascript" ${tag_attrs}></script>
 </%def>

From 59b189d3cb6201665bd96d1c3c7cd50648633323 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 1 Aug 2024 13:53:51 +0300
Subject: [PATCH 02/14] Limit allowed script tags, allow adding stylesheet for
 now

---
 .../common/templates/script_entry_point.mako  | 22 ++++++++++++++-----
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index 82d33bc868c0..8895ff868a10 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -1,19 +1,29 @@
 # -*- coding: utf-8 -*-
 <%inherit file="visualization_base.mako"/>
 
-## No stylesheets
-<%def name="stylesheets()"></%def>
+## Add stylesheet
+<%def name="stylesheets()">
+    <% css = script_attributes.get("css") %>
+    %if css is not None:
+        <link rel="stylesheet" href="${css}">
+    %endif
+</%def>
 
 ## Create a container, attach data and import script file
-<%def name="late_javascripts()">
-    <% container = script_attributes.get("container") or "app" %>
+<%def name="get_body()">
+    ## Collect incoming data
     <% data_incoming = {
         "visualization_id": visualization_id,
         "visualization_name": visualization_name,
         "visualization_plugin": visualization_plugin,
         "visualization_config": config }
     %>
+
+    ## Create a container with default identifier `app`
+    <% container = script_attributes.get("container") or "app" %>
     <div id="${container}" data-incoming='${h.dumps(data_incoming)}'></div>
-    <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_attributes.items() ]) %>
-    <script type="text/javascript" ${tag_attrs}></script>
+
+    ## Add script tag
+    <% src = script_attributes.get("src") %>
+    <script type="text/javascript" src=${src}></script>
 </%def>

From f0d148cdc783a6717d04060304d6d8cccd2d8ef7 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 3 Aug 2024 13:07:01 +0300
Subject: [PATCH 03/14] Allow changing the script type, add root to
 visualization config

---
 .../visualizations/common/templates/script_entry_point.mako | 6 ++++--
 lib/galaxy/visualization/plugins/config_parser.py           | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index 8895ff868a10..2837c717ad2f 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -13,6 +13,7 @@
 <%def name="get_body()">
     ## Collect incoming data
     <% data_incoming = {
+        "root": h.url_for("/"),
         "visualization_id": visualization_id,
         "visualization_name": visualization_name,
         "visualization_plugin": visualization_plugin,
@@ -24,6 +25,7 @@
     <div id="${container}" data-incoming='${h.dumps(data_incoming)}'></div>
 
     ## Add script tag
-    <% src = script_attributes.get("src") %>
-    <script type="text/javascript" src=${src}></script>
+    <% script_src = script_attributes.get("src") %>
+    <% script_type = script_attributes.get("type") or "module" %>
+    <script type="${script_type}" src=${script_src}></script>
 </%def>
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index 85b1ccc79be9..160f52acef2c 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -221,7 +221,7 @@ def parse(self, xml_tree):
         # when no tests are given, default to isinstance( object, model_class )
         returned["tests"] = self.parse_tests(xml_tree.findall("test"))
 
-        # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_clas, tests
+        # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_class, tests
         returned["to_params"] = {}
         if to_params := self.parse_to_params(xml_tree.findall("to_param")):
             returned["to_params"] = to_params

From 151ff346871c848e1ff9e29b70cbd123e9e3405d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 6 Aug 2024 14:45:56 +0300
Subject: [PATCH 04/14] Escape title

---
 .../common/templates/script_entry_point.mako      | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index 2837c717ad2f..677be72b02b5 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -12,12 +12,15 @@
 ## Create a container, attach data and import script file
 <%def name="get_body()">
     ## Collect incoming data
-    <% data_incoming = {
-        "root": h.url_for("/"),
-        "visualization_id": visualization_id,
-        "visualization_name": visualization_name,
-        "visualization_plugin": visualization_plugin,
-        "visualization_config": config }
+    <%
+        from markupsafe import escape
+        data_incoming = {
+            "root": h.url_for("/"),
+            "visualization_id": visualization_id,
+            "visualization_name": visualization_name,
+            "visualization_plugin": visualization_plugin,
+            "visualization_title": escape(title),
+            "visualization_config": config }
     %>
 
     ## Create a container with default identifier `app`

From 550ee0406ff27085c9718f2fd3632511e34b431f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 6 Aug 2024 17:29:51 +0300
Subject: [PATCH 05/14] Use Unnamed Visualization as default name for new
 visualizations

---
 lib/galaxy/visualization/plugins/plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index dfe625e53dcb..c53f7977834a 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -161,7 +161,7 @@ def _build_render_vars(self, config: Dict[str, Any], trans=None, **kwargs) -> Di
         render_vars.update(
             visualization_name=self.name,
             visualization_display_name=self.config["name"],
-            title=kwargs.get("title", None),
+            title=kwargs.get("title", "Unnamed Visualization"),
             saved_visualization=None,
             visualization_id=None,
             visualization_plugin=self.to_dict(),

From 0fbb153ed5b967fc7876f78891157cd059eab710 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 07:29:56 +0300
Subject: [PATCH 06/14] Fix default visualization name test

---
 .../unit/app/visualizations/plugins/test_VisualizationPlugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
index baf72fe065c8..ecab69c4554c 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
@@ -74,7 +74,7 @@ def test_build_render_vars_default(self):
         render_vars = plugin._build_render_vars(config)
         assert render_vars["visualization_name"] == plugin.name
         assert render_vars["visualization_display_name"] == plugin.config["name"]
-        assert render_vars["title"] is None
+        assert render_vars["title"] is "Unnamed Visualization"
         assert render_vars["saved_visualization"] is None
         assert render_vars["visualization_id"] is None
         assert render_vars["query"] == {}

From 1a1e8a9e92a5f3250e4b8a6d0f9c7ec391f7d7bc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 09:55:23 +0300
Subject: [PATCH 07/14] Adjust script viz unit tests, fix typo

---
 .../common/templates/script_entry_point.mako           |  2 +-
 lib/galaxy/app_unittest_utils/galaxy_mock.py           | 10 ++++++++--
 .../visualizations/plugins/test_VisualizationPlugin.py |  2 +-
 .../plugins/test_VisualizationsRegistry.py             | 10 +++++-----
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index 677be72b02b5..d5a9946f9cf4 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -30,5 +30,5 @@
     ## Add script tag
     <% script_src = script_attributes.get("src") %>
     <% script_type = script_attributes.get("type") or "module" %>
-    <script type="${script_type}" src=${script_src}></script>
+    <script type="${script_type}" src="${script_src}"></script>
 </%def>
diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index 95715c042543..47c44bd19384 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -430,8 +430,14 @@ def remove(self):
 
 
 class MockTemplateHelpers:
-    def js(*js_files):
+    def css(*css_files):
         pass
 
-    def css(*css_files):
+    def dumps(*kwargs):
+        return {}
+
+    def js(*js_files):
         pass
+
+    def url_for(*kwargs):
+        return "/"
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
index ecab69c4554c..772c54bb925e 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
@@ -74,7 +74,7 @@ def test_build_render_vars_default(self):
         render_vars = plugin._build_render_vars(config)
         assert render_vars["visualization_name"] == plugin.name
         assert render_vars["visualization_display_name"] == plugin.config["name"]
-        assert render_vars["title"] is "Unnamed Visualization"
+        assert render_vars["title"] == "Unnamed Visualization"
         assert render_vars["saved_visualization"] is None
         assert render_vars["visualization_id"] is None
         assert render_vars["query"] == {}
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index 1c7f9707f047..7a95bf980589 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -15,7 +15,7 @@
 
 glx_dir = galaxy_directory()
 template_cache_dir = os.path.join(glx_dir, "database", "compiled_templates")
-addtional_templates_dir = os.path.join(glx_dir, "config", "plugins", "visualizations", "common", "templates")
+additional_templates_dir = os.path.join(glx_dir, "config", "plugins", "visualizations", "common", "templates")
 vis_reg_path = "config/plugins/visualizations"
 
 config1 = """\
@@ -144,7 +144,7 @@ def test_script_entry(self):
                     <model_class>HistoryDatasetAssociation</model_class>
                 </data_source>
             </data_sources>
-            <entry_point entry_point_type="script" data-main="one" src="bler"></entry_point>
+            <entry_point entry_point_type="script" container="mycontainer" src="bler"></entry_point>
         </visualization>
         """
         )
@@ -167,11 +167,11 @@ def test_script_entry(self):
         assert script_entry.serves_templates
 
         trans = galaxy_mock.MockTrans()
-        script_entry._set_up_template_plugin(mock_app_dir.root_path, [addtional_templates_dir])
-        response = script_entry._render({}, trans=trans, embedded=True)
+        script_entry._set_up_template_plugin(mock_app_dir.root_path, [additional_templates_dir])
+        response = script_entry.render(trans=trans, embedded=True)
         assert 'src="bler"' in response
         assert 'type="text/javascript"' in response
-        assert 'data-main="one"' in response
+        assert 'id="mycontainer"' in response
         mock_app_dir.remove()
 
 

From ff08779efb913a3b3e94e8174d3affba495af857 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 14:02:49 +0300
Subject: [PATCH 08/14] Remove legacy example, add option to link remote script
 sources

---
 .../common/templates/script_entry_point.mako  |   8 ++-
 .../visualizations/example/config/example.xml |  45 ---------------
 .../visualizations/example/package.json       |  24 --------
 .../visualizations/example/src/script.js      |  54 ------------------
 .../visualizations/example/static/logo.png    | Bin 7438 -> 0 bytes
 lib/galaxy/app_unittest_utils/galaxy_mock.py  |   3 +
 lib/galaxy/web/framework/helpers/__init__.py  |  12 ++++
 7 files changed, 20 insertions(+), 126 deletions(-)
 delete mode 100644 config/plugins/visualizations/example/config/example.xml
 delete mode 100644 config/plugins/visualizations/example/package.json
 delete mode 100644 config/plugins/visualizations/example/src/script.js
 delete mode 100644 config/plugins/visualizations/example/static/logo.png

diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index d5a9946f9cf4..80ad34908930 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -3,9 +3,10 @@
 
 ## Add stylesheet
 <%def name="stylesheets()">
-    <% css = script_attributes.get("css") %>
-    %if css is not None:
-        <link rel="stylesheet" href="${css}">
+    <% script_css = script_attributes.get("css") %>
+    %if script_css is not None:
+        <% script_css = script_css if h.is_url(script_css) else f"{static_url}{script_css}" %>
+        <link rel="stylesheet" href="${script_css}">
     %endif
 </%def>
 
@@ -29,6 +30,7 @@
 
     ## Add script tag
     <% script_src = script_attributes.get("src") %>
+    <% script_src = script_src if h.is_url(script_src) else f"{static_url}{script_src}" %>
     <% script_type = script_attributes.get("type") or "module" %>
     <script type="${script_type}" src="${script_src}"></script>
 </%def>
diff --git a/config/plugins/visualizations/example/config/example.xml b/config/plugins/visualizations/example/config/example.xml
deleted file mode 100644
index cc2dd898fb79..000000000000
--- a/config/plugins/visualizations/example/config/example.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Example" embeddable="false">
-    <description>This is a developer example which demonstrates how to implement and configure a basic d3-based plugin for charts.</description>
-    <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">tabular.CSV</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="chart" src="script.js"/>
-    <settings>
-        <input>
-            <name>data_dialog</name>
-            <label>Some data selector</label>
-            <type>data_dialog</type>
-            <multiple>false</multiple>
-        </input>
-    </settings>
-    <groups>
-        <input>
-            <name>x</name>
-            <label>Bubble x-position</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
-        </input>
-        <input>
-            <name>y</name>
-            <label>Bubbles y-position</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
-        </input>
-        <input>
-            <name>z</name>
-            <label>Bubble size</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
-        </input>
-    </groups>
-</visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/example/package.json b/config/plugins/visualizations/example/package.json
deleted file mode 100644
index 199cab67b083..000000000000
--- a/config/plugins/visualizations/example/package.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.2.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "@galaxyproject/charts": "^0.1.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "d3": "^4.12.2",
-        "jquery": "^3.1.1",
-        "underscore": "^1.8.3"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "2.11.0"
-    }
-}
diff --git a/config/plugins/visualizations/example/src/script.js b/config/plugins/visualizations/example/src/script.js
deleted file mode 100644
index 4fda38c2380d..000000000000
--- a/config/plugins/visualizations/example/src/script.js
+++ /dev/null
@@ -1,54 +0,0 @@
-import * as d3 from "d3";
-import * as _ from "underscore";
-import { request as requestDatasets } from "@galaxyproject/charts/lib/utilities/datasets";
-
-_.extend(window.bundleEntries || {}, {
-    load: function(options) {
-        var chart = options.chart;
-        var root = options.root;
-        requestDatasets({
-            root: root,
-            dataset_id: chart.get("dataset_id"),
-            dataset_groups: chart.groups,
-            success: function(groups) {
-                var colors = d3.scaleOrdinal(d3.schemeCategory20);
-                var error = null;
-                _.each(groups, function(group, group_index) {
-                    try {
-                        $("#" + options.target).append("<svg id='myexample'/>");
-                        var svg = d3.select("#myexample");
-                        var height = parseInt(svg.style("height"));
-                        var width = parseInt(svg.style("width"));
-                        var maxValue = d3.max(group.values, function(d) {
-                            return Math.max(d.x, d.y);
-                        });
-                        svg
-                            .selectAll("bubbles")
-                            .data(group.values)
-                            .enter()
-                            .append("circle")
-                            .attr("r", function(d) {
-                                return Math.abs(d.z) * 20 / maxValue;
-                            })
-                            .attr("cy", function(d, i) {
-                                return height * d.y / maxValue;
-                            })
-                            .attr("cx", function(d) {
-                                return width * d.x / maxValue;
-                            })
-                            .style("stroke", colors(group_index))
-                            .style("fill", "white");
-                    } catch (err) {
-                        error = err;
-                    }
-                });
-                if (error) {
-                    chart.state("failed", error);
-                } else {
-                    chart.state("ok", "Workshop chart has been drawn.");
-                }
-                options.process.resolve();
-            }
-        });
-    }
-});
diff --git a/config/plugins/visualizations/example/static/logo.png b/config/plugins/visualizations/example/static/logo.png
deleted file mode 100644
index 0c13459935bbbc23dec5b7c05450b19b106b22f4..0000000000000000000000000000000000000000
GIT binary patch
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HcmV?d00001

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z?v}Zbw`Oo5y7{-eeKX*#;-J||!+Uh&<!2P4SaOOZ$oe9A-?yMAs_^B+MNtk=RKtmo
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YLo*twr)q-!b8DgeR!zQI)->?{071nJnE(I)

diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index 47c44bd19384..0fcec287878f 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -439,5 +439,8 @@ def dumps(*kwargs):
     def js(*js_files):
         pass
 
+    def is_url(*kwargs):
+        return True
+
     def url_for(*kwargs):
         return "/"
diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index 7fde6906cf19..49fff0ee72c7 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -6,6 +6,7 @@
 GalaxyWebTransaction in galaxy/webapps/base/webapp.py
 """
 
+import re
 from datetime import (
     datetime,
     timedelta,
@@ -105,6 +106,17 @@ def is_true(val):
     return val is True or val in ["True", "true", "T", "t"]
 
 
+def is_url(val):
+    """
+    Regular expression to match common URL protocols
+    """
+    if val is not None:
+        url_pattern = re.compile(r"^(https?:\/\/|ftp:\/\/)")
+        return bool(url_pattern.match(val))
+    else:
+        return False
+
+
 def to_js_bool(val):
     """
     Prints javascript boolean for passed value.

From 7827a2de8a2b689eba1d1cce27f011dd9573ee8b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 14:24:26 +0300
Subject: [PATCH 09/14] Remove legacy example from staging script

---
 client/gulpfile.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/gulpfile.js b/client/gulpfile.js
index 873bae0c0bd8..2915734bad78 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -17,7 +17,6 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "cytoscape",
     "drawrna",
     "editor",
-    "example",
     "fits_image_viewer",
     "h5web",
     "heatmap/heatmap_default",

From db22b485c6bcb09181e50c8382358586d6da7bc6 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 15:05:41 +0300
Subject: [PATCH 10/14] Add additional test conditions for script based plugins

---
 lib/galaxy/web/framework/helpers/__init__.py              | 5 +++++
 .../visualizations/plugins/test_VisualizationsRegistry.py | 8 ++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index 49fff0ee72c7..f6f90bc54820 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -109,6 +109,11 @@ def is_true(val):
 def is_url(val):
     """
     Regular expression to match common URL protocols
+
+    >>> assert is_url(None) == False
+    >>> assert is_url("is_url") == False
+    >>> assert is_url("http://is_url") == True
+    >>> assert is_url("https://is_url") == True
     """
     if val is not None:
         url_pattern = re.compile(r"^(https?:\/\/|ftp:\/\/)")
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index 7a95bf980589..ee87feb61f39 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -144,7 +144,7 @@ def test_script_entry(self):
                     <model_class>HistoryDatasetAssociation</model_class>
                 </data_source>
             </data_sources>
-            <entry_point entry_point_type="script" container="mycontainer" src="bler"></entry_point>
+            <entry_point entry_point_type="script" container="mycontainer" src="mysrc" css="mycss"></entry_point>
         </visualization>
         """
         )
@@ -169,9 +169,9 @@ def test_script_entry(self):
         trans = galaxy_mock.MockTrans()
         script_entry._set_up_template_plugin(mock_app_dir.root_path, [additional_templates_dir])
         response = script_entry.render(trans=trans, embedded=True)
-        assert 'src="bler"' in response
-        assert 'type="text/javascript"' in response
-        assert 'id="mycontainer"' in response
+        assert '<script type="module" src="mysrc">' in response
+        assert '<link rel="stylesheet" href="mycss">' in response
+        assert '<div id="mycontainer" data-incoming=\'{}\'></div>' in response
         mock_app_dir.remove()
 
 

From 54413998603450de472e790382ef4b5cfc3dfc93 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 15:59:50 +0300
Subject: [PATCH 11/14] Add new minimal example plugin

---
 client/gulpfile.js                              |   1 +
 .../visualizations/example/config/example.xml   |  16 ++++++++++++++++
 .../visualizations/example/static/logo.png      | Bin 0 -> 7438 bytes
 .../visualizations/example/static/script.js     |   4 ++++
 .../plugins/test_VisualizationsRegistry.py      |   2 +-
 5 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 config/plugins/visualizations/example/config/example.xml
 create mode 100644 config/plugins/visualizations/example/static/logo.png
 create mode 100644 config/plugins/visualizations/example/static/script.js

diff --git a/client/gulpfile.js b/client/gulpfile.js
index 2915734bad78..873bae0c0bd8 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -17,6 +17,7 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "cytoscape",
     "drawrna",
     "editor",
+    "example",
     "fits_image_viewer",
     "h5web",
     "heatmap/heatmap_default",
diff --git a/config/plugins/visualizations/example/config/example.xml b/config/plugins/visualizations/example/config/example.xml
new file mode 100644
index 000000000000..7dbd35772190
--- /dev/null
+++ b/config/plugins/visualizations/example/config/example.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Minimal Example" embeddable="false">
+    <description>Welcome to the Minimal JS-Based Example Plugin.</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</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="script" src="script.js" />
+</visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/example/static/logo.png b/config/plugins/visualizations/example/static/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..0c13459935bbbc23dec5b7c05450b19b106b22f4
GIT binary patch
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diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
new file mode 100644
index 000000000000..a8a5b9f01147
--- /dev/null
+++ b/config/plugins/visualizations/example/static/script.js
@@ -0,0 +1,4 @@
+var element = document.getElementById("app");
+var div = document.createElement('div');
+div.innerHTML = JSON.stringify(JSON.parse(element.getAttribute("data-incoming")));
+document.body.appendChild(div);
\ No newline at end of file
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index ee87feb61f39..6f5ce4274e70 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -171,7 +171,7 @@ def test_script_entry(self):
         response = script_entry.render(trans=trans, embedded=True)
         assert '<script type="module" src="mysrc">' in response
         assert '<link rel="stylesheet" href="mycss">' in response
-        assert '<div id="mycontainer" data-incoming=\'{}\'></div>' in response
+        assert "<div id=\"mycontainer\" data-incoming='{}'></div>" in response
         mock_app_dir.remove()
 
 

From 3365eaddd39da4b8502d24e1da6b5df6c18cb3ed Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 4 Sep 2024 17:01:42 +0300
Subject: [PATCH 12/14] Use innerText in example plugin

---
 config/plugins/visualizations/example/static/script.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
index a8a5b9f01147..c44077784036 100644
--- a/config/plugins/visualizations/example/static/script.js
+++ b/config/plugins/visualizations/example/static/script.js
@@ -1,4 +1,4 @@
 var element = document.getElementById("app");
 var div = document.createElement('div');
-div.innerHTML = JSON.stringify(JSON.parse(element.getAttribute("data-incoming")));
+div.innerText = JSON.stringify(JSON.parse(element.getAttribute("data-incoming")));
 document.body.appendChild(div);
\ No newline at end of file

From a24ac91671bb71c4d84b178af70d29764ac8de71 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Sep 2024 05:36:27 +0300
Subject: [PATCH 13/14] Update minimal plugin example

---
 .../visualizations/example/static/script.js   | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
index c44077784036..2a299587cf65 100644
--- a/config/plugins/visualizations/example/static/script.js
+++ b/config/plugins/visualizations/example/static/script.js
@@ -1,4 +1,28 @@
-var element = document.getElementById("app");
-var div = document.createElement('div');
-div.innerText = JSON.stringify(JSON.parse(element.getAttribute("data-incoming")));
-document.body.appendChild(div);
\ No newline at end of file
+const { visualization_plugin: plugin, root } = JSON.parse(document.getElementById("app").dataset.incoming);
+
+const div = Object.assign(document.createElement("div"), {
+    style: "border: 2px solid #25537b; border-radius: 1rem; padding: 1rem"
+});
+
+const img = Object.assign(document.createElement("img"), {
+    src: root + plugin.logo,
+    style: "height: 3rem"
+});
+
+div.appendChild(img);
+
+Object.entries(plugin).forEach(([key, value]) => {
+    const row = document.createElement("div");
+    const spanKey = Object.assign(document.createElement("span"), {
+        innerText: `${key}: `,
+        style: "font-weight: bold"
+    });
+    const spanValue = Object.assign(document.createElement("span"), {
+        innerText: value
+    });
+    row.appendChild(spanKey);
+    row.appendChild(spanValue);
+    div.appendChild(row);
+});
+
+document.body.appendChild(div);

From 4e3eebd98353fac2d4389b30a0f92d824bfca5a0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 5 Sep 2024 10:06:23 +0300
Subject: [PATCH 14/14] Add sections and dataset id to example

---
 .../visualizations/example/config/example.xml | 19 ++++++++++++++++++-
 .../visualizations/example/static/script.js   | 15 ++++++++++-----
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/config/plugins/visualizations/example/config/example.xml b/config/plugins/visualizations/example/config/example.xml
index 7dbd35772190..4fe2e0f38ff5 100644
--- a/config/plugins/visualizations/example/config/example.xml
+++ b/config/plugins/visualizations/example/config/example.xml
@@ -13,4 +13,21 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <entry_point entry_point_type="script" src="script.js" />
-</visualization>
\ No newline at end of file
+    <settings>
+        <input>
+            <name>setting_input</name>
+            <help>setting help</help>
+            <type>setting_type</type>
+        </input>
+    </settings>
+    <groups>
+        <input>
+            <name>group_input</name>
+            <help>group help</help>
+            <type>group_type</type>
+        </input>
+    </groups>
+    <specs>
+        <spec_name>spec_value</spec_name>
+    </specs>
+</visualization>
diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
index 2a299587cf65..e17270b74957 100644
--- a/config/plugins/visualizations/example/static/script.js
+++ b/config/plugins/visualizations/example/static/script.js
@@ -1,28 +1,33 @@
-const { visualization_plugin: plugin, root } = JSON.parse(document.getElementById("app").dataset.incoming);
+const { visualization_config, visualization_plugin, root } = JSON.parse(document.getElementById("app").dataset.incoming);
 
 const div = Object.assign(document.createElement("div"), {
     style: "border: 2px solid #25537b; border-radius: 1rem; padding: 1rem"
 });
 
 const img = Object.assign(document.createElement("img"), {
-    src: root + plugin.logo,
+    src: root + visualization_plugin.logo,
     style: "height: 3rem"
 });
-
 div.appendChild(img);
 
-Object.entries(plugin).forEach(([key, value]) => {
+Object.entries(visualization_plugin).forEach(([key, value]) => {
     const row = document.createElement("div");
     const spanKey = Object.assign(document.createElement("span"), {
         innerText: `${key}: `,
         style: "font-weight: bold"
     });
     const spanValue = Object.assign(document.createElement("span"), {
-        innerText: value
+        innerText: JSON.stringify(value)
     });
     row.appendChild(spanKey);
     row.appendChild(spanValue);
     div.appendChild(row);
 });
 
+const dataset = Object.assign(document.createElement("div"), {
+    innerText: `You have selected dataset: ${visualization_config.dataset_id}.`,
+    style: "font-weight: bold; padding-top: 1rem;"
+});
+div.appendChild(dataset);
+
 document.body.appendChild(div);