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Hide outdated visualizations from visualizations activity panel #19353

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Hide outdated visualizations from visualizations activity panel #19353

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e3f8432
Add optional visible attribute to visualization xml
guerler Dec 19, 2024
24faf70
Do not list outdated visualizations in plugin list
guerler Dec 19, 2024
c4380e6
Consolidate overlapping get_plugins/get_visualization helper
guerler Dec 19, 2024
1066eb3
Hide custom scatter plot, users should use plotly instead
guerler Dec 19, 2024
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Bar diagram (jqPlot)">
<visualization name="Bar diagram (jqPlot)" visible="false">
<macros>
<import>jqplot_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Box plot (jqPlot)" embeddable="false">
<visualization name="Box plot (jqPlot)" embeddable="false" visible="false">
<macros>
<import>../../jqplot_bar/config/jqplot_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Discrete Histogram (jqPlot)" embeddable="false">
<visualization name="Discrete Histogram (jqPlot)" embeddable="false" visible="false">
<macros>
<import>../../jqplot_bar/config/jqplot_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Line chart (jqPlot)">
<visualization name="Line chart (jqPlot)" visible="false">
<macros>
<import>../../jqplot_bar/config/jqplot_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Scatter plot (jqPlot)">
<visualization name="Scatter plot (jqPlot)" visible="false">
<macros>
<import>../../jqplot_bar/config/jqplot_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Bar diagram (NVD3)">
<visualization name="Bar diagram (NVD3)" visible="false">
<macros>
<import>nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Bar Stacked (NVD3)">
<visualization name="Bar Stacked (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Histogram (NVD3)" embeddable="false">
<visualization name="Histogram (NVD3)" embeddable="false" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion ...ig/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Histogram Discrete (NVD3)" embeddable="false">
<visualization name="Histogram Discrete (NVD3)" embeddable="false" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Bar Horizontal (NVD3)">
<visualization name="Bar Horizontal (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion ...ig/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Bar Horizontal Stacked (NVD3)">
<visualization name="Bar Horizontal Stacked (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Line chart (NVD3)">
<visualization name="Line chart (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Line with focus (NVD3)">
<visualization name="Line with focus (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Pie chart (NVD3)">
<visualization name="Pie chart (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Scatter plot (NVD3)">
<visualization name="Scatter plot (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Stacked area (NVD3)">
<visualization name="Stacked area (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Expanded (NVD3)">
<visualization name="Expanded (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion ...ig/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Stream (NVD3)">
<visualization name="Stream (NVD3)" visible="false">
<macros>
<import>../../nvd3_bar/config/nvd3_shared.xml</import>
</macros>
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2 changes: 1 addition & 1 deletion config/plugins/visualizations/scatterplot/config/scatterplot.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="Scatterplot">
<visualization name="Scatterplot" visible="false">
<description>Creates a 2D-scatterplot from tabular datapoints</description>
<data_sources>
<data_source>
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5 changes: 5 additions & 0 deletions lib/galaxy/visualization/plugins/config_parser.py
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Expand Up @@ -80,6 +80,11 @@ def parse_visualization(self, xml_tree):
if "embeddable" in xml_tree.attrib:
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"))

# a (for now) text description of what the visualization does
description = xml_tree.find("description")
returned["description"] = description.text.strip() if description is not None else None
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26 changes: 11 additions & 15 deletions lib/galaxy/visualization/plugins/registry.py
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Expand Up @@ -225,26 +225,22 @@ def get_plugin(self, key):
raise ObjectNotFound(f"Unknown or invalid visualization: {key}")
return self.plugins[key]

def get_plugins(self, embeddable=None):
result = []
for plugin in self.plugins.values():
if embeddable and not plugin.config.get("embeddable"):
continue
result.append(plugin.to_dict())
return sorted(result, key=lambda k: k.get("html"))

# -- building links to visualizations from objects --
def get_visualizations(self, trans, target_object):
def get_visualizations(self, trans, target_object=None, embeddable=None):
"""
Get the names of visualizations usable on the `target_object` and
the urls to call in order to render the visualizations.
"""
applicable_visualizations = []
for vis_name in self.plugins:
url_data = self.get_visualization(trans, vis_name, target_object)
if url_data:
applicable_visualizations.append(url_data)
return sorted(applicable_visualizations, key=lambda k: k.get("html"))
result = []
for vis_name, vis_plugin in self.plugins.items():
if not vis_plugin.config.get("visible"):
continue
if embeddable and not vis_plugin.config.get("embeddable"):
continue
if target_object is not None and self.get_visualization(trans, vis_name, target_object) is None:
continue
result.append(vis_plugin.to_dict())
return sorted(result, key=lambda k: k.get("html"))

def get_visualization(self, trans, visualization_name, target_object):
"""
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9 changes: 4 additions & 5 deletions lib/galaxy/webapps/galaxy/api/plugins.py
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Expand Up @@ -36,12 +36,11 @@ def index(self, trans, **kwargs):
GET /api/plugins:
"""
registry = self._get_registry()
embeddable = asbool(kwargs.get("embeddable"))
target_object = None
if (dataset_id := kwargs.get("dataset_id")) is not None:
hda = self.hda_manager.get_accessible(self.decode_id(dataset_id), trans.user)
return registry.get_visualizations(trans, hda)
else:
embeddable = asbool(kwargs.get("embeddable"))
return registry.get_plugins(embeddable=embeddable)
target_object = self.hda_manager.get_accessible(self.decode_id(dataset_id), trans.user)
return registry.get_visualizations(trans, target_object=target_object, embeddable=embeddable)

@expose_api
def show(self, trans, id, **kwargs):
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