Templates and Keep modules

src/main/java/App.java

@@ -1,6 +1,10 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 import java.util.Arrays;
 import java.util.LinkedList;
@@ -195,12 +199,21 @@
             }
           } else if (currArg.equals("-k")) {
             String value = argsQ.poll();
+            // first check if it's an absolute path, or path relative to .
             File keepPatientsModule = new File(value);
             if (keepPatientsModule.exists()) {
-              options.keepPatientsModulePath = keepPatientsModule;
+              options.keepPatientsModulePath = keepPatientsModule.toPath();
             } else {
-              throw new FileNotFoundException(String.format(
-                  "Specified keep-patients file (%s) does not exist", value));
+              // look inside the src/main/resources/keep_modules folder
+              URI keepModulesURI = App.class.getClassLoader().getResource("keep_modules").toURI();
+              Utilities.enableReadingURIFromJar(keepModulesURI);
+              Path possibleLocation = Paths.get(keepModulesURI).resolve(value);
+              if (Files.exists(possibleLocation)) {
+                options.keepPatientsModulePath = possibleLocation;
+              } else {
+                throw new FileNotFoundException(String.format(
+                    "Specified keep-patients file (%s) does not exist", value));
+              }
             }
           } else if (currArg.equals("-fm")) {
             String value = argsQ.poll();

src/main/java/org/mitre/synthea/engine/Generator.java

@@ -141,7 +141,7 @@ public static class GeneratorOptions {
      *  value of -1 will evolve the population to the current system time. */
     public int daysToTravelForward = -1;
     /** Path to a module defining which patients should be kept and exported. */
-    public File keepPatientsModulePath;
+    public Path keepPatientsModulePath;
   }
 
   /**
@@ -278,8 +278,8 @@ private void init() {
 
     if (options.keepPatientsModulePath != null) {
       try {
-        Path path = options.keepPatientsModulePath.toPath().toAbsolutePath();
-        this.keepPatientsModule = Module.loadFile(path, false, null, true);
+        this.keepPatientsModule =
+            Module.loadFile(options.keepPatientsModulePath, false, null, true);
       } catch (Exception e) {
         throw new ExceptionInInitializerError(e);
       }

src/main/java/org/mitre/synthea/engine/Module.java

@@ -16,11 +16,9 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
-import java.nio.file.FileSystemNotFoundException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.nio.file.spi.FileSystemProvider;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -102,7 +100,7 @@ private static Map<String, ModuleSupplier> loadModules() {
    */
   public static Path getModulesPath() throws URISyntaxException, IOException {
     URI modulesURI = Module.class.getClassLoader().getResource("modules").toURI();
-    fixPathFromJar(modulesURI);
+    Utilities.enableReadingURIFromJar(modulesURI);
     return Paths.get(modulesURI);
   }
 
@@ -166,23 +164,6 @@ public static void addModules(File dir) {
                       submoduleCount);
   }
 
-  private static void fixPathFromJar(URI uri) throws IOException {
-    // this function is a hack to enable reading modules from within a JAR file
-    // see https://stackoverflow.com/a/48298758
-    if ("jar".equals(uri.getScheme())) {
-      for (FileSystemProvider provider: FileSystemProvider.installedProviders()) {
-        if (provider.getScheme().equalsIgnoreCase("jar")) {
-          try {
-            provider.getFileSystem(uri);
-          } catch (FileSystemNotFoundException e) {
-            // in this case we need to initialize it first:
-            provider.newFileSystem(uri, Collections.emptyMap());
-          }
-        }
-      }
-    }
-  }
-
   /**
    * Create a relative path from a folder to a file, removing the file extension and normalizing
    * path segment separators.

src/main/java/org/mitre/synthea/helpers/Utilities.java

@@ -10,16 +10,20 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.net.URI;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.FileSystemNotFoundException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.spi.FileSystemProvider;
 import java.time.Instant;
 import java.time.LocalDate;
 import java.time.ZoneOffset;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Calendar;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Random;
@@ -638,4 +642,29 @@
     });
     return input;
   }
+
+  /**
+   * Enable reading the given URI from within a JAR file.
+   * For example, for command-line args which may refer to internal or external paths.
+   * Note that it's not always possible to know when a user-provided path
+   * is within a JAR file, so this method should be called if it is possible the
+   * path refers to an internal location.
+   * @param uri URI to be accessed
+   */
+  public static void enableReadingURIFromJar(URI uri) throws IOException {
+    // this function is a hack to enable reading modules from within a JAR file
+    // see https://stackoverflow.com/a/48298758
+    if ("jar".equals(uri.getScheme())) {
+      for (FileSystemProvider provider: FileSystemProvider.installedProviders()) {
+        if (provider.getScheme().equalsIgnoreCase("jar")) {
+          try {
+            provider.getFileSystem(uri);
+          } catch (FileSystemNotFoundException e) {
+            // in this case we need to initialize it first:
+            provider.newFileSystem(uri, Collections.emptyMap());
+          }
+        }
+      }
+    }
+  }
 }

src/main/resources/keep_modules/keep_diabetes.json

@@ -0,0 +1,42 @@
+{
+  "name": "Generated Keep Module", 
+  "states": { 
+    "Initial": { 
+      "type": "Initial", 
+      "name": "Initial", 
+      "conditional_transition": [ 
+        { 
+          "transition": "Keep", 
+          "condition": { 
+            "condition_type": "And", 
+            "conditions": [ 
+              { 
+                "condition_type": "Active Condition", 
+                "codes": [ 
+                  { 
+                    "system": "SNOMED-CT", 
+                    "code": "44054006", 
+                    "display": "Diabetes" 
+                  } 
+                ] 
+              } 
+            ] 
+          } 
+        }, 
+        { 
+          "transition": "Terminal" 
+        } 
+      ] 
+    }, 
+    "Terminal": { 
+      "type": "Terminal", 
+      "name": "Terminal" 
+    }, 
+    "Keep": { 
+      "type": "Terminal", 
+      "name": "Keep" 
+    } 
+  }, 
+  "gmf_version": 2 
+} 
+

src/main/resources/keep_modules/keep_hospice.json

@@ -0,0 +1,28 @@
+{
+  "name": "keep_hospice",
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "Attribute",
+            "attribute": "hospice",
+            "operator": "is not nil"
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal"
+    }
+  },
+  "gmf_version": 2
+}