Merge pull request #18651 from guerler/parse_missing_viz_config

Parse stored config details to script-based visualizations

config/plugins/visualizations/common/templates/script_entry_point.mako

@@ -1,10 +1,36 @@
 # -*- coding: utf-8 -*-
 <%inherit file="visualization_base.mako"/>
 
-## No stylesheets
-<%def name="stylesheets()"></%def>
-## No javascript libraries
-<%def name="late_javascripts()">
-    <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_attributes.items() ]) %>
-    <script type="text/javascript" ${tag_attrs}></script>
+## Add stylesheet
+<%def name="stylesheets()">
+    <% script_css = script_attributes.get("css") %>
+    %if script_css is not None:
+        <% script_css = script_css if h.is_url(script_css) else f"{static_url}{script_css}" %>
+        <link rel="stylesheet" href="${script_css}">
+    %endif
+</%def>
+
+## Create a container, attach data and import script file
+<%def name="get_body()">
+    ## Collect incoming data
+    <%
+        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`
+    <% container = script_attributes.get("container") or "app" %>
+    <div id="${container}" data-incoming='${h.dumps(data_incoming)}'></div>
+
+    ## 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>

config/plugins/visualizations/example/config/example.xml

@@ -1,45 +1,33 @@
 <?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>
+<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>
-            <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"/>
+    <entry_point entry_point_type="script" src="script.js" />
     <settings>
         <input>
-            <name>data_dialog</name>
-            <label>Some data selector</label>
-            <type>data_dialog</type>
-            <multiple>false</multiple>
+            <name>setting_input</name>
+            <help>setting help</help>
+            <type>setting_type</type>
         </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>
+            <name>group_input</name>
+            <help>group help</help>
+            <type>group_type</type>
         </input>
     </groups>
-</visualization>
+    <specs>
+        <spec_name>spec_value</spec_name>
+    </specs>
+</visualization>

config/plugins/visualizations/example/static/script.js

@@ -0,0 +1,33 @@
+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 + visualization_plugin.logo,
+    style: "height: 3rem"
+});
+div.appendChild(img);
+
+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: 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);

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -430,8 +430,17 @@ 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 is_url(*kwargs):
+        return True
+
+    def url_for(*kwargs):
+        return "/"

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

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(),

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 +106,22 @@ 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
+
+    >>> 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:\/\/)")
+        return bool(url_pattern.match(val))
+    else:
+        return False
+
+
 def to_js_bool(val):
     """
     Prints javascript boolean for passed value.

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"] == "Unnamed Visualization"
         assert render_vars["saved_visualization"] is None
         assert render_vars["visualization_id"] is None
         assert render_vars["query"] == {}

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="mysrc" css="mycss"></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)
-        assert 'src="bler"' in response
-        assert 'type="text/javascript"' in response
-        assert 'data-main="one"' in response
+        script_entry._set_up_template_plugin(mock_app_dir.root_path, [additional_templates_dir])
+        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
         mock_app_dir.remove()