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Replace Graphviz/DOT with a Java implementation #7557

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28a09b5
Replace Graphviz/DOT with a Java implementation
labkey-adam Apr 7, 2026
7564bc2
Eliminate DotSvgAction
labkey-adam Apr 7, 2026
84f3a4a
Refactor experiment graphs to use graph-support
labkey-adam Apr 8, 2026
61ba07f
SvgUtil to read and set SVG sizes. Use it to scale experiment diagrams.
labkey-adam Apr 11, 2026
3bb1cdf
Fix NPE
labkey-jeckels Apr 11, 2026
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26 changes: 26 additions & 0 deletions api/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
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2 changes: 2 additions & 0 deletions api/src/org/labkey/api/ApiModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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,
Expand Down
16 changes: 6 additions & 10 deletions api/src/org/labkey/api/attachments/SvgSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -19,8 +21,7 @@
public class SvgSource
{
private final String _filteredSvg;

private Float _height = null;
private final Float _height;

public SvgSource(String svg)
{
Expand All @@ -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"))
Expand Down
43 changes: 20 additions & 23 deletions api/src/org/labkey/api/module/ModuleDependencySorter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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<>();
Expand Down Expand Up @@ -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;
}
}
Expand All @@ -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);
}
}

Expand Down
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