Replace Graphviz/DOT with a Java implementation (#7557)

Author: labkey-adam

api/build.gradle

@@ -381,6 +381,32 @@ dependencies {
         )
     )
 
+    BuildUtils.addExternalDependency(
+        project,
+        new ExternalDependency(
+            "org.graphper:graph-support-core:${graphSupportVersion}",
+            "graph-support-core",
+            "graph-support",
+            "https://github.com/jamisonjiang/graph-support",
+            ExternalDependency.APACHE_2_LICENSE_NAME,
+            ExternalDependency.APACHE_2_LICENSE_URL,
+            "Graphviz Java API",
+        )
+    )
+
+    BuildUtils.addExternalDependency(
+        project,
+        new ExternalDependency(
+            "org.graphper:graph-support-dot:${graphSupportVersion}",
+            "graph-support-dot",
+            "graph-support",
+            "https://github.com/jamisonjiang/graph-support",
+            ExternalDependency.APACHE_2_LICENSE_NAME,
+            ExternalDependency.APACHE_2_LICENSE_URL,
+            "DOT parsing support",
+        )
+    )
+
     BuildUtils.addExternalDependency(
         project,
         new ExternalDependency(

api/src/org/labkey/api/ApiModule.java

@@ -172,6 +172,7 @@
 import org.labkey.api.util.SessionHelper;
 import org.labkey.api.util.StringExpressionFactory;
 import org.labkey.api.util.StringUtilsLabKey;
+import org.labkey.api.util.SvgUtil;
 import org.labkey.api.util.SystemMaintenance;
 import org.labkey.api.util.SystemMaintenanceStartupListener;
 import org.labkey.api.util.URIUtil;
@@ -439,6 +440,7 @@ public void registerServlets(ServletContext servletCtx)
             StringExpressionFactory.TestCase.class,
             StringUtilsLabKey.TestCase.class,
             SubfolderWriter.TestCase.class,
+            SvgUtil.TestCase.class,
             SwapQueue.TestCase.class,
             TSVMapWriter.Tests.class,
             TSVWriter.TestCase.class,

api/src/org/labkey/api/action/SpringActionController.java

@@ -175,6 +175,16 @@ public static Collection<ActionDescriptor> getRegisteredActionDescriptors()
         return new ArrayList<>(_classToDescriptor.values());
     }
 
+    protected static String h(@Nullable CharSequence s)
+    {
+        return PageFlowUtil.filter(s);
+    }
+
+    protected static String h(@Nullable Object o)
+    {
+        return PageFlowUtil.filter(o);
+    }
+
     // I don't think there is an interface for this
     public interface ActionResolver
     {

api/src/org/labkey/api/attachments/SvgSource.java

@@ -5,6 +5,8 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Strings;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.SvgUtil;
+import org.labkey.api.util.SvgUtil.Size;
 import org.labkey.api.view.NotFoundException;
 
 import java.io.BufferedReader;
@@ -19,8 +21,7 @@
 public class SvgSource
 {
     private final String _filteredSvg;
-
-    private Float _height = null;
+    private final Float _height;
 
     public SvgSource(String svg)
     {
@@ -32,16 +33,11 @@ public SvgSource(String svg)
         if (!svg.contains("xmlns=\"" + SVGDOMImplementation.SVG_NAMESPACE_URI + "\"") && !svg.contains("xmlns='" + SVGDOMImplementation.SVG_NAMESPACE_URI + "'"))
             svg = svg.replace("<svg", "<svg xmlns='" + SVGDOMImplementation.SVG_NAMESPACE_URI + "'");
 
-        int idx = svg.indexOf("height=\"");
-        if (idx != -1)
-        {
-            int heightStart = idx + 8;
-            int end = svg.indexOf("\"",  heightStart);
-            _height = Float.parseFloat(svg.substring(heightStart, end));
-        }
+        Size size = SvgUtil.readHeight(svg);
+        _height = size != null ? size.value() : null;
 
         // remove xlink:title to prevent org.apache.batik.transcoder.TranscoderException (issue #16173)
-        svg = svg.replaceAll("xlink:title", "title");
+        svg = svg.replace("xlink:title", "title");
 
         // Reject hrefs. See #45819.
         if (Strings.CI.contains(svg, "xlink:href"))

api/src/org/labkey/api/module/ModuleDependencySorter.java

@@ -18,14 +18,16 @@
 
 import org.apache.commons.collections4.MultiValuedMap;
 import org.apache.commons.collections4.multimap.ArrayListValuedHashMap;
-import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.graphper.api.GraphResource;
+import org.graphper.api.Graphviz;
+import org.graphper.parser.DotParser;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
-import org.labkey.api.util.DotRunner;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.logging.LogHelper;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -34,12 +36,12 @@
 import java.util.stream.Collectors;
 
 /**
- * Orders modules so that each module will always be after all of the modules it depends on.
- * User: jeckels
- * Date: Jun 6, 2006
+ * Orders modules so that each module will always be after all the modules it depends on.
  */
 public class ModuleDependencySorter
 {
+    private static final Logger LOG = LogHelper.getLogger(ModuleDependencySorter.class, "Module dependency information");
+
     public List<Module> sortModulesByDependencies(List<Module> modules)
     {
         List<Pair<Module, Set<String>>> dependencies = new ArrayList<>();
@@ -101,7 +103,7 @@ public List<Module> sortModulesByDependencies(List<Module> modules)
             if (module.getName().equalsIgnoreCase("core"))
             {
                 result.remove(i);
-                result.add(0, module);
+                result.addFirst(module);
                 break;
             }
         }
@@ -128,41 +130,36 @@ private Module findModuleWithoutDependencies(List<Pair<Module, Set<String>>> dep
                 throw new IllegalArgumentException("Module '" + moduleName + "' (" + entry.getKey().getClass().getName() + ") is listed as being dependent on itself.");
         }
 
-        StringBuilder sb = new StringBuilder();
-        for (Pair<Module, Set<String>> dependencyInfo : dependencies)
-        {
-            if (!sb.isEmpty())
-            {
-                sb.append(", ");
-            }
-            sb.append(dependencyInfo.getKey().getName());
-        }
+        String involved = dependencies.stream()
+            .map(pair -> pair.getKey().getName())
+            .collect(Collectors.joining(", "));
 
         // Generate an SVG diagram that shows all remaining dependencies
         graphModuleDependencies(dependencies, "involved");
 
-        throw new IllegalArgumentException("Unable to resolve module dependencies. The following modules are somehow involved: " + sb);
+        throw new IllegalArgumentException("Unable to resolve module dependencies. The following modules are somehow involved: " + involved);
     }
 
 
     private void graphModuleDependencies(List<Pair<Module, Set<String>>> dependencies, @SuppressWarnings("SameParameterValue") String adjective)
     {
-        Logger log = LogManager.getLogger(ModuleDependencySorter.class);
-
         try
         {
             File dir = FileUtil.getTempDirectory();
             String dot = buildDigraph(dependencies);
+            Graphviz graph = DotParser.parse(dot);
             File svgFile = FileUtil.createTempFile("modules", ".svg", dir);
-            DotRunner runner = new DotRunner(dir, dot);
-            runner.addSvgOutput(svgFile);
-            runner.execute();
 
-            log.info("For a diagram of " + adjective + " module dependencies, see " + svgFile.getAbsolutePath());
+            try (GraphResource resource = graph.toSvg())
+            {
+                resource.save(svgFile.getParent(), svgFile.getName());
+            }
+
+            LOG.info("For a diagram of {} module dependencies, see {}", adjective, svgFile.getAbsolutePath());
         }
         catch (Exception e)
         {
-            log.error("Error running dot", e);
+            LOG.error("Error running dot", e);
         }
     }