From fc88801fcf049b7b8418a09ed3cec24cbeb82140 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 4 Feb 2025 20:40:29 -0500
Subject: [PATCH] Use `hidden` instead of `visible` as attribute name for
 consistency

---
 .../visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml  | 2 +-
 .../visualizations/jqplot/jqplot_box/config/jqplot_box.xml  | 2 +-
 .../jqplot/jqplot_histogram/config/jqplot_histogram.xml     | 2 +-
 .../jqplot/jqplot_line/config/jqplot_line.xml               | 2 +-
 .../jqplot/jqplot_scatter/config/jqplot_scatter.xml         | 2 +-
 .../visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml        | 2 +-
 .../nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml       | 2 +-
 .../nvd3/nvd3_histogram/config/nvd3_histogram.xml           | 2 +-
 .../config/nvd3_histogram_discrete.xml                      | 2 +-
 .../nvd3/nvd3_horizontal/config/nvd3_horizontal.xml         | 2 +-
 .../config/nvd3_horizontal_stacked.xml                      | 2 +-
 .../visualizations/nvd3/nvd3_line/config/nvd3_line.xml      | 2 +-
 .../nvd3/nvd3_line_focus/config/nvd3_line_focus.xml         | 2 +-
 .../visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml        | 2 +-
 .../nvd3/nvd3_scatter/config/nvd3_scatter.xml               | 2 +-
 .../nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml       | 2 +-
 .../nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml  | 2 +-
 .../config/nvd3_stackedarea_stream.xml                      | 2 +-
 config/plugins/visualizations/pv/config/pv.xml              | 2 +-
 .../visualizations/scatterplot/config/scatterplot.xml       | 2 +-
 lib/galaxy/visualization/plugins/config_parser.py           | 6 +++---
 lib/galaxy/visualization/plugins/registry.py                | 2 +-
 22 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml b/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
index 4dc9dfc63ef..ce49fcbac12 100644
--- a/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar diagram (jqPlot)" visible="false">
+<visualization name="Bar diagram (jqPlot)" hidden="true">
     <macros>
         <import>jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml b/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
index 0e440be10e8..95bda65f3c2 100644
--- a/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Box plot (jqPlot)" embeddable="false" visible="false">
+<visualization name="Box plot (jqPlot)" embeddable="false" hidden="true">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml b/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
index 7537a379893..86f70b18f18 100644
--- a/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Discrete Histogram (jqPlot)" embeddable="false" visible="false">
+<visualization name="Discrete Histogram (jqPlot)" embeddable="false" hidden="true">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml b/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
index 2791123bb26..aedc2447bb5 100644
--- a/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line chart (jqPlot)" visible="false">
+<visualization name="Line chart (jqPlot)" hidden="true">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml b/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
index 7347b2717d3..be15c600b85 100644
--- a/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
+++ b/config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatter plot (jqPlot)" visible="false">
+<visualization name="Scatter plot (jqPlot)" hidden="true">
     <macros>
         <import>../../jqplot_bar/config/jqplot_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
index 94e55dd22e6..7b12f235dc3 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar diagram (NVD3)" visible="false">
+<visualization name="Bar diagram (NVD3)" hidden="true">
     <macros>
         <import>nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml b/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
index 81e6c652f2d..5504726f652 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Stacked (NVD3)" visible="false">
+<visualization name="Bar Stacked (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml b/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
index 7db9332b905..6374b977639 100644
--- a/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Histogram (NVD3)" embeddable="false" visible="false">
+<visualization name="Histogram (NVD3)" embeddable="false" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml b/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
index 3dcfc0a0357..eb2f8f42cf6 100644
--- a/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Histogram Discrete (NVD3)" embeddable="false" visible="false">
+<visualization name="Histogram Discrete (NVD3)" embeddable="false" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml b/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
index 39b66e5f702..e56e5af6575 100644
--- a/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Horizontal (NVD3)" visible="false">
+<visualization name="Bar Horizontal (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml b/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
index 4875c8dcb91..5ca08fc9ded 100644
--- a/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Bar Horizontal Stacked (NVD3)" visible="false">
+<visualization name="Bar Horizontal Stacked (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml b/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
index 0a0145a2e74..8e116c315ff 100644
--- a/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line chart (NVD3)" visible="false">
+<visualization name="Line chart (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml b/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
index 8998dc8aeea..fa4bfdaa72f 100644
--- a/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Line with focus (NVD3)" visible="false">
+<visualization name="Line with focus (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml b/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
index 3e28b302506..2bb2b3f3949 100644
--- a/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Pie chart (NVD3)" visible="false">
+<visualization name="Pie chart (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml b/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
index 148e0756977..6ae2b000a19 100644
--- a/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatter plot (NVD3)" visible="false">
+<visualization name="Scatter plot (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
index ab21737e50c..694f4aa7c6e 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Stacked area (NVD3)" visible="false">
+<visualization name="Stacked area (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
index c25cf714e43..43d10fa8df8 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Expanded (NVD3)" visible="false">
+<visualization name="Expanded (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml b/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
index a34df97a071..f14a3bbe365 100644
--- a/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
+++ b/config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Stream (NVD3)" visible="false">
+<visualization name="Stream (NVD3)" hidden="true">
     <macros>
         <import>../../nvd3_bar/config/nvd3_shared.xml</import>
     </macros>
diff --git a/config/plugins/visualizations/pv/config/pv.xml b/config/plugins/visualizations/pv/config/pv.xml
index 0b62a5d45bb..43fa2d7a170 100644
--- a/config/plugins/visualizations/pv/config/pv.xml
+++ b/config/plugins/visualizations/pv/config/pv.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="PV Protein Viewer">
+<visualization name="PV Protein Viewer" hidden="true">
     <description>PV is a pdb/protein viewer hosted at https://biasmv.github.io/pv/.</description>
     <data_sources>
         <data_source>
diff --git a/config/plugins/visualizations/scatterplot/config/scatterplot.xml b/config/plugins/visualizations/scatterplot/config/scatterplot.xml
index 606aa04864e..bbb42cc8649 100644
--- a/config/plugins/visualizations/scatterplot/config/scatterplot.xml
+++ b/config/plugins/visualizations/scatterplot/config/scatterplot.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Scatterplot" visible="false">
+<visualization name="Scatterplot" hidden="true">
     <description>Creates a 2D-scatterplot from tabular datapoints</description>
     <data_sources>
         <data_source>
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index a26c6fd2084..09ec7acc6a9 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -81,9 +81,9 @@ class VisualizationsConfigParser:
             returned["embeddable"] = asbool(xml_tree.attrib.get("embeddable"))
 
         # record the visible flag - defaults to true
-        returned["visible"] = True
-        if "visible" in xml_tree.attrib:
-            returned["visible"] = asbool(xml_tree.attrib.get("visible"))
+        returned["hidden"] = False
+        if "hidden" in xml_tree.attrib:
+            returned["hidden"] = asbool(xml_tree.attrib.get("hidden"))
 
         # a (for now) text description of what the visualization does
         description = xml_tree.find("description")
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index 8d7141b3067..8f61141c5c8 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -233,7 +233,7 @@ class VisualizationsRegistry:
         """
         result = []
         for vis_name, vis_plugin in self.plugins.items():
-            if not vis_plugin.config.get("visible"):
+            if vis_plugin.config.get("hidden"):
                 continue
             if embeddable and not vis_plugin.config.get("embeddable"):
                 continue