Remove MD Parse Library

The library which supported MD parsing to HTML has been removed due to it's dependency causing "class not found" error when packaged into a Jar file. Now using plain HTML.
virtualcell · Feb 6, 2024 · dc31510 · dc31510
1 parent 6b5a2af
commit dc31510
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Showing 4 changed files with 46 additions and 50 deletions.
diff --git a/view-simulation-results/pom.xml b/view-simulation-results/pom.xml
@@ -157,12 +157,6 @@
             <artifactId>jsoup</artifactId>
             <version>1.16.1</version>
         </dependency>
-
-        <dependency>
-            <groupId>org.commonmark</groupId>
-            <artifactId>commonmark</artifactId>
-            <version>0.20.0</version>
-        </dependency>
     </dependencies>
 
 </project>
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/HelpExplanation.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/HelpExplanation.java
@@ -1,16 +1,12 @@
 package org.vcell.N5.UI;
 
-import org.commonmark.node.Node;
-import org.commonmark.parser.Parser;
-import org.commonmark.renderer.html.HtmlRenderer;
+
+import com.google.common.io.CharStreams;
 
 import javax.swing.*;
 import java.awt.*;
-import java.io.FileReader;
-import java.io.IOException;
+import java.io.*;
 import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 
 public class HelpExplanation {
     private JDialog jDialog;
@@ -22,17 +18,14 @@ public HelpExplanation(){
         JPanel helperPanel = new JPanel();
         JTextPane textPane = new JTextPane();
 
-        Parser parser = Parser.builder().build();
-        String md;
-        URL mdPath = ClassLoader.getSystemClassLoader().getResource("Help.md");
+        String text;
         try {
-            md = new String(Files.readAllBytes(Paths.get(mdPath.getPath())));
+            InputStream inputStream = ClassLoader.getSystemResourceAsStream("Help.html");
+            text = CharStreams.toString(new InputStreamReader(inputStream));
+//            text = new String(Files.readAllBytes(Paths.get(mdPath.getPath())));
         } catch (IOException e) {
             throw new RuntimeException(e);
         }
-        Node node = parser.parse(md);
-        HtmlRenderer renderer = HtmlRenderer.builder().build();
-        String text = renderer.render(node);
         textPane.setContentType("text/html");
         textPane.setSize(width, height);
         textPane.setPreferredSize(new Dimension(width, height));

diff --git a/view-simulation-results/src/main/resources/Help.html b/view-simulation-results/src/main/resources/Help.html
@@ -0,0 +1,39 @@
+<!DOCTYPE html>
+<html lang="en">
+    <h3>Intro</h3>
+        <p>
+            The VCell (https://vcell.org/) application can export spatial simulation results into multiple formats, with
+            .N5 (https://imagej.net/libs/n5) being one of them. N5 exports are
+            stored remotely on VCell servers, allowing applications such as ImageJ
+            to directly access the results of these simulations and perform analyses.
+        </p>
+    <h3>VCell Spatial Simulation</h3>
+        <p>
+            Simulation solvers generating 2- or 3-dimensional spatial
+            domains can be visualized in ImageJ using this plugin.
+            Spatial dimensions and time directly correspond to fields within an ImageJ
+            image. The image's channels depict different variables within a simulation.
+        </p>
+    <h3>N5 and Datasets</h3>
+        <p>
+            Each N5 store is a direct mapping to a VCell simulation, and contains one or more
+            datasets. Each dataset holds numerical data and metadata corresponding to an Image in ImageJ.
+            Each N5 store is fully identified through its N5 URL which can be shared and opened by other applications
+            which support the N5 format.
+        </p>
+    <h3>Accessing Simulation Results</h3>
+        <p>For VCell exports generated from your local VCell installation:</p>
+        <ul>
+            <li>
+                <p>Either, Click the recent export button.</p>
+            </li>
+            <li>
+                <p>Or, Open the export table and view all past exports with their affiliated metadata.</p>
+            </li>
+        </ul>
+        <p>From N5 URL (VCell Install Not Required):</p>
+        <ul>
+            <li>Click the 'Remote Files' button, paste the N5 URL,
+                then select dataset from list.</li>
+        </ul>
+</html>
diff --git a/view-simulation-results/src/main/resources/Help.md b/view-simulation-results/src/main/resources/Help.md