From fb3b276a44b75326ec517838357a4b2ee78ea89a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 20 Nov 2024 20:52:52 +0300
Subject: [PATCH] Remove legacy

---
 .../config/heatmap_cluster.xml                |   0
 .../config/heatmap_shared.xml                 |   0
 .../heatmap_cluster/static/logo.svg           |  18 +
 .../config/heatmap_default.xml                |  19 +
 .../heatmap_default/config/heatmap_shared.xml | 481 ++++++++++++++++++
 .../heatmap_default/static/logo.svg           |  18 +
 6 files changed, 536 insertions(+)
 rename config/plugins/visualizations/{heatmap => }/heatmap_cluster/config/heatmap_cluster.xml (100%)
 rename config/plugins/visualizations/{heatmap/heatmap_default => heatmap_cluster}/config/heatmap_shared.xml (100%)
 create mode 100644 config/plugins/visualizations/heatmap_cluster/static/logo.svg
 create mode 100644 config/plugins/visualizations/heatmap_default/config/heatmap_default.xml
 create mode 100644 config/plugins/visualizations/heatmap_default/config/heatmap_shared.xml
 create mode 100644 config/plugins/visualizations/heatmap_default/static/logo.svg

diff --git a/config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml b/config/plugins/visualizations/heatmap_cluster/config/heatmap_cluster.xml
similarity index 100%
rename from config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
rename to config/plugins/visualizations/heatmap_cluster/config/heatmap_cluster.xml
diff --git a/config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml b/config/plugins/visualizations/heatmap_cluster/config/heatmap_shared.xml
similarity index 100%
rename from config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
rename to config/plugins/visualizations/heatmap_cluster/config/heatmap_shared.xml
diff --git a/config/plugins/visualizations/heatmap_cluster/static/logo.svg b/config/plugins/visualizations/heatmap_cluster/static/logo.svg
new file mode 100644
index 000000000000..27fd576b39f2
--- /dev/null
+++ b/config/plugins/visualizations/heatmap_cluster/static/logo.svg
@@ -0,0 +1,18 @@
+<svg width="200" height="200" viewBox="0 0 5 5" xmlns="http://www.w3.org/2000/svg">
+  <rect x="0.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#2E3192" stroke="transparent" stroke-width="0.05" />
+</svg>
diff --git a/config/plugins/visualizations/heatmap_default/config/heatmap_default.xml b/config/plugins/visualizations/heatmap_default/config/heatmap_default.xml
new file mode 100644
index 000000000000..0dc94cf9e4e1
--- /dev/null
+++ b/config/plugins/visualizations/heatmap_default/config/heatmap_default.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Heatmap" embeddable="false" logo="logo.svg">
+    <macros>
+        <import>heatmap_shared.xml</import>
+    </macros>
+    <description>Renders a heatmap from matrix data provided in 3-column format (x, y, observation).</description>
+    <requirements>
+        <requirement type="npm" version="0.0.0" package="@galaxyproject/heatmap"/>
+    </requirements>
+    <expand macro="shared"/>
+    <specs>
+        <exports>
+            <exports>pdf</exports>
+            <exports>png</exports>
+            <exports>svg</exports>
+        </exports>
+    </specs>
+</visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/heatmap_default/config/heatmap_shared.xml b/config/plugins/visualizations/heatmap_default/config/heatmap_shared.xml
new file mode 100644
index 000000000000..7a7df175e5ea
--- /dev/null
+++ b/config/plugins/visualizations/heatmap_default/config/heatmap_shared.xml
@@ -0,0 +1,481 @@
+<macros>
+<xml name="shared">
+    <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="script" src="dist/index.js" css="dist/index.css" />
+    <tracks>
+        <input>
+            <label>Provide a label</label>
+            <name>key</name>
+            <type>text</type>
+            <placeholder>Data label</placeholder>
+            <value>Data label</value>
+        </input>
+        <input>
+            <label>Column labels</label>
+            <name>x</name>
+            <type>data_column</type>
+        </input>
+        <input>
+            <label>Row labels</label>
+            <name>y</name>
+            <type>data_column</type>
+        </input>
+        <input>
+            <label>Observation</label>
+            <name>z</name>
+            <type>data_column</type>
+            <is_number>true</is_number>
+        </input>
+    </tracks>
+    <settings>
+        <input>
+            <name>color_set</name>
+            <label>Color scheme</label>
+            <help>Select a color scheme for your heatmap.</help>
+            <type>select</type>
+            <value>jet</value>
+            <data>
+                <data>
+                    <label>Cold-to-Hot</label>
+                    <value>hot</value>
+                </data>
+                <data>
+                    <label>Cool</label>
+                    <value>cool</value>
+                </data>
+                <data>
+                    <label>Copper</label>
+                    <value>copper</value>
+                </data>
+                <data>
+                    <label>Gray scale</label>
+                    <value>gray</value>
+                </data>
+                <data>
+                    <label>Jet</label>
+                    <value>jet</value>
+                </data>
+                <data>
+                    <label>No-Green</label>
+                    <value>no_green</value>
+                </data>
+                <data>
+                    <label>Ocean</label>
+                    <value>ocean</value>
+                </data>
+                <data>
+                    <label>Polar</label>
+                    <value>polar</value>
+                </data>
+                <data>
+                    <label>Red-to-Green</label>
+                    <value>redgreen</value>
+                </data>
+                <data>
+                    <label>Red-to-Green (saturated)</label>
+                    <value>red2green</value>
+                </data>
+                <data>
+                    <label>Relief</label>
+                    <value>relief</value>
+                </data>
+                <data>
+                    <label>Seismograph</label>
+                    <value>seis</value>
+                </data>
+                <data>
+                    <label>Sealand</label>
+                    <value>sealand</value>
+                </data>
+                <data>
+                    <label>Split</label>
+                    <value>split</value>
+                </data>
+                <data>
+                    <label>Wysiwyg</label>
+                    <value>wysiwyg</value>
+                </data>
+            </data>
+        </input>
+        <input>
+            <name>url_template</name>
+            <label>Url template</label>
+            <help>Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.</help>
+            <type>text</type>
+            <value></value>
+            <placeholder>http://someurl.com?id=__LABEL__</placeholder>
+        </input>
+        <input>
+            <name>x_axis_label</name>
+            <label>X-Axis label</label>
+            <help>Provide a label for the axis.</help>
+            <type>text</type>
+            <value>X-axis</value>
+            <placeholder>Axis label</placeholder>
+        </input>
+        <input>
+            <name>x_axis_type</name>
+            <type>conditional</type>
+            <test_param>
+                <name>type</name>
+                <label>X-Axis value type</label>
+                <type>select</type>
+                <value>auto</value>
+                <help>Select the value type of the axis.</help>
+                <data>
+                    <data>
+                        <value>hide</value>
+                        <label>-- Do not show values --</label>
+                    </data>
+                    <data>
+                        <value>auto</value>
+                        <label>Auto</label>
+                    </data>
+                    <data>
+                        <value>d</value>
+                        <label>Integer</label>
+                    </data>
+                    <data>
+                        <value>e</value>
+                        <label>Exponent</label>
+                    </data>
+                    <data>
+                        <value>f</value>
+                        <label>Float</label>
+                    </data>
+                    <data>
+                        <value>p</value>
+                        <label>Percent</label>
+                    </data>
+                    <data>
+                        <value>s</value>
+                        <label>SI-prefix</label>
+                    </data>
+                </data>
+            </test_param>
+            <cases>
+                <cases>
+                    <value>hide</value>
+                </cases>
+                <cases>
+                    <value>auto</value>
+                </cases>
+                <cases>
+                    <value>d</value>
+                </cases>
+                <cases>
+                    <value>e</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>f</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>p</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>s</value>
+                </cases>
+            </cases>
+        </input>
+        <input>
+            <name>y_axis_label</name>
+            <label>Y-Axis label</label>
+            <help>Provide a label for the axis.</help>
+            <type>text</type>
+            <value>Y-axis</value>
+            <placeholder>Axis label</placeholder>
+        </input>
+        <input>
+            <name>y_axis_type</name>
+            <type>conditional</type>
+            <test_param>
+                <name>type</name>
+                <label>Y-Axis value type</label>
+                <type>select</type>
+                <value>auto</value>
+                <help>Select the value type of the axis.</help>
+                <data>
+                    <data>
+                        <value>hide</value>
+                        <label>-- Do not show values --</label>
+                    </data>
+                    <data>
+                        <value>auto</value>
+                        <label>Auto</label>
+                    </data>
+                    <data>
+                        <value>d</value>
+                        <label>Integer</label>
+                    </data>
+                    <data>
+                        <value>e</value>
+                        <label>Exponent</label>
+                    </data>
+                    <data>
+                        <value>f</value>
+                        <label>Float</label>
+                    </data>
+                    <data>
+                        <value>p</value>
+                        <label>Percent</label>
+                    </data>
+                    <data>
+                        <value>s</value>
+                        <label>SI-prefix</label>
+                    </data>
+                </data>
+            </test_param>
+            <cases>
+                <cases>
+                    <value>hide</value>
+                </cases>
+                <cases>
+                    <value>auto</value>
+                </cases>
+                <cases>
+                    <value>d</value>
+                </cases>
+                <cases>
+                    <value>e</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>f</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>p</value>
+                    <inputs>
+                        <inputs>
+                            <name>precision</name>
+                            <label>Axis tick format</label>
+                            <help>Select the tick format for the axis.</help>
+                            <type>select</type>
+                            <value>1</value>
+                            <data>
+                                <data>
+                                    <label>0.00001</label>
+                                    <value>5</value>
+                                </data>
+                                <data>
+                                    <label>0.0001</label>
+                                    <value>4</value>
+                                </data>
+                                <data>
+                                    <label>0.001</label>
+                                    <value>3</value>
+                                </data>
+                                <data>
+                                    <label>0.01</label>
+                                    <value>2</value>
+                                </data>
+                                <data>
+                                    <label>0.1</label>
+                                    <value>1</value>
+                                </data>
+                                <data>
+                                    <label>1</label>
+                                    <value>0</value>
+                                </data>
+                            </data>
+                        </inputs>
+                    </inputs>
+                </cases>
+                <cases>
+                    <value>s</value>
+                </cases>
+            </cases>
+        </input>
+        <input>
+            <name>show_legend</name>
+            <label>Show legend</label>
+            <help>Would you like to add a legend?</help>
+            <type>boolean</type>
+            <value>true</value>
+        </input>
+    </settings>
+</xml>
+</macros>
\ No newline at end of file
diff --git a/config/plugins/visualizations/heatmap_default/static/logo.svg b/config/plugins/visualizations/heatmap_default/static/logo.svg
new file mode 100644
index 000000000000..41c80b8f2c16
--- /dev/null
+++ b/config/plugins/visualizations/heatmap_default/static/logo.svg
@@ -0,0 +1,18 @@
+<svg width="200" height="200" viewBox="0 0 5 5" xmlns="http://www.w3.org/2000/svg">
+  <rect x="0.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="0.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="1.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="2.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="3.0" y="2.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="0.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
+  <rect x="1.0" y="3.0" width="0.8" height="0.8" rx="0.2" ry="0.2" fill="#E30A17" stroke="transparent" stroke-width="0.05" />
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