Merge pull request #61 from molgenis/feat/utils3.0.0

Fix inheritance matcher broken when running as jar

pom.xml

@@ -12,7 +12,7 @@
 
   <groupId>org.molgenis</groupId>
   <artifactId>vip-inheritance-matcher</artifactId>
-  <version>3.3.0</version>
+  <version>3.3.1</version>
 
   <name>vip-inheritance-matcher</name>
   <description>Annotates VCF samples with mendelian violation and possible compound flags and

src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java

@@ -3,22 +3,41 @@
 import org.molgenis.vcf.utils.metadata.FieldMetadataService;
 import org.molgenis.vcf.utils.metadata.FieldMetadataServiceImpl;
 import org.springframework.stereotype.Component;
-import org.springframework.util.ResourceUtils;
 
 import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
 
 /**
  * Quirky class to enable reuse of {@link FieldMetadataService} from vip-utils
  */
 @Component
 public class VepMetadataServiceFactoryImpl implements VepMetadataServiceFactory {
+    private static final String EMPTY_METADATA_JSON = """
+                {
+                  "format": {
+                  },
+                  "info": {
+                    "CSQ": {
+                      "nestedFields": {
+                      }
+                    }
+                  }
+                }
+                """;
 
     @Override
+    @SuppressWarnings("java:S5443")
     public FieldMetadataService create() {
         File json;
         try {
-            json = ResourceUtils.getFile("classpath:metadata.json");
-        } catch (FileNotFoundException e) {
+            Path path = Files.createTempFile("metadata", ".json");
+            byte[] buf = EMPTY_METADATA_JSON.getBytes(StandardCharsets.UTF_8);
+            Files.write(path, buf);
+            json = path.toFile();
+            json.deleteOnExit();
+        } catch (IOException e) {
             throw new UncheckedIOException(e);
         }
         return new FieldMetadataServiceImpl(json);