Graphviz and module override fixes.

synthetichealth · Mar 20, 2024 · 2c97526 · 2c97526
1 parent de32971
commit 2c97526
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Showing 2 changed files with 20 additions and 4 deletions.
diff --git a/src/main/java/Graphviz.java b/src/main/java/Graphviz.java
@@ -1,5 +1,6 @@
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
+import com.google.gson.JsonNull;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
 import com.google.gson.stream.JsonReader;
@@ -8,6 +9,7 @@
 import guru.nidi.graphviz.attribute.Label;
 import guru.nidi.graphviz.attribute.Records;
 import guru.nidi.graphviz.attribute.Style;
+import guru.nidi.graphviz.engine.Engine;
 import guru.nidi.graphviz.engine.Format;
 import guru.nidi.graphviz.engine.GraphvizException;
 import guru.nidi.graphviz.model.Factory;
@@ -24,12 +26,10 @@
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
-import java.util.Calendar;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
-import java.util.TimeZone;
 
 import org.mitre.synthea.engine.Module;
 import org.mitre.synthea.export.Exporter;
@@ -278,8 +278,16 @@ private static void generateJsonModuleGraph(JsonObject module, File outputFolder
 
     File outputFile = outputFolder.toPath().resolve(relativePath + ".png").toFile();
     outputFile.mkdirs();
-    guru.nidi.graphviz.engine.Graphviz.fromGraph(g)
+
+    try {
+      guru.nidi.graphviz.engine.Graphviz.fromGraph(g).engine(Engine.DOT)
+      .render(Format.PNG).toFile(outputFile);
+    } catch (guru.nidi.graphviz.engine.GraphvizException gve) {
+      if (gve.getMessage().contains("Command took too long to execute")) {
+        guru.nidi.graphviz.engine.Graphviz.fromGraph(g).engine(Engine.FDP)
         .render(Format.PNG).toFile(outputFile);
+      }
+    }
   }
 
   private static String getStateDescription(JsonObject state) {
@@ -321,7 +329,13 @@ private static String getStateDescription(JsonObject state) {
         }
         break;
       case "SetAttribute":
-        String v = state.has("value") ? state.get("value").getAsString() : null;
+        String v = "null";
+        if (state.has("value")) {
+          JsonElement e = state.get("value");
+          if (e != null && e != JsonNull.INSTANCE) {
+            v = e.getAsString();
+          }
+        }
         details.append("Set ").append(state.get("attribute").getAsString()).append(" = ").append(v);
         break;
       case "Symptom":

diff --git a/src/main/java/org/mitre/synthea/helpers/ModuleOverrides.java b/src/main/java/org/mitre/synthea/helpers/ModuleOverrides.java
@@ -148,6 +148,8 @@ private void processModule(Path modulesPath, Path modulePath, List<String> lines
     }
 
     try {
+      moduleFilename = moduleFilename.replace(" ", "\\ ").replace(":", "\\:");
+
       String moduleRelativePath = modulesPath.getParent().relativize(modulePath).toString();
       JsonReader reader = new JsonReader(new StringReader(
                Utilities.readResource(moduleRelativePath)));