Move to utils version 3.0.0

.travis.yml

@@ -19,7 +19,9 @@ before_install:
 script:
   - mvn clean install sonar:sonar -Pcoverage -Dsonar.projectKey=molgenis_vip-inheritance-matcher
 before_deploy:
+  # workaround for: https://travis-ci.community/t/deployments-are-failing-due-to-uri-dependency/14375
   - yes | gem update --system --force
+  - gem install faraday-net_http -v '3.3.0' # workaround for the workaround - https://travis-ci.community/t/cannot-load-such-file-faraday-net-http-loaderror/14455/3
   - gem install bundler
   - gem install uri
   - gem install logger

pom.xml

@@ -47,7 +47,7 @@
     <!-- [WARNING] Plugin validation issues were detected, see https://github.com/jacoco/jacoco/issues/1435 -->
     <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
     <samtools.htsjdk.version>4.1.1</samtools.htsjdk.version>
-    <vip.utils.version>2.0.2</vip.utils.version>
+    <vip.utils.version>3.0.0</vip.utils.version>
   </properties>
 
   <profiles>

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

@@ -1,47 +1,26 @@
 package org.molgenis.vcf.inheritance.matcher.util;
 
-import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import org.molgenis.vcf.utils.metadata.FieldMetadataService;
-import org.molgenis.vcf.utils.metadata.AbstractFieldMetadataService;
-import org.molgenis.vcf.utils.model.FieldMetadata;
-import org.molgenis.vcf.utils.vep.VepMetadataService;
+import org.molgenis.vcf.utils.metadata.FieldMetadataServiceImpl;
 import org.springframework.stereotype.Component;
+import org.springframework.util.ResourceUtils;
 
-import java.io.ByteArrayInputStream;
-
-import static java.nio.charset.StandardCharsets.UTF_8;
+import java.io.*;
 
 /**
- * Quirky class to enable reuse of {@link VepMetadataService} from vip-utils
+ * Quirky class to enable reuse of {@link FieldMetadataService} from vip-utils
  */
 @Component
 public class VepMetadataServiceFactoryImpl implements VepMetadataServiceFactory {
 
     @Override
     public FieldMetadataService create() {
-        return new VepMetadataService(new EmptyFieldMetadataService());
-    }
-
-    /**
-     * vip-inheritance-matcher does not require knowledge of custom VEP metadata
-     */
-    static class EmptyFieldMetadataService extends AbstractFieldMetadataService {
-        private static final String EMPTY_METADATA_JSON = """
-                {
-                  "format": {
-                  },
-                  "info": {
-                    "CSQ": {
-                      "nestedFields": {
-                      }
-                    }
-                  }
-                }
-                """;
-
-        @Override
-        public FieldMetadata load(VCFInfoHeaderLine vcfInfoHeaderLine) {
-            return this.load(new ByteArrayInputStream(EMPTY_METADATA_JSON.getBytes(UTF_8)), vcfInfoHeaderLine);
+        File json;
+        try {
+            json = ResourceUtils.getFile("classpath:metadata.json");
+        } catch (FileNotFoundException e) {
+            throw new UncheckedIOException(e);
         }
+        return new FieldMetadataServiceImpl(json);
     }
 }

src/main/java/org/molgenis/vcf/inheritance/matcher/vcf/meta/MissingVepMetadataException.java

@@ -0,0 +1,14 @@
+package org.molgenis.vcf.inheritance.matcher.vcf.meta;
+
+import java.io.Serial;
+
+import static java.lang.String.format;
+
+public class MissingVepMetadataException extends RuntimeException {
+        @Serial
+        private static final long serialVersionUID = 1L;
+
+  public MissingVepMetadataException(String field) {
+            super(format("VEP metadata is missing in metadata json, vep id: '%s'.", field));
+        }
+}

src/main/java/org/molgenis/vcf/inheritance/matcher/vcf/meta/VepMetadata.java

@@ -5,9 +5,12 @@
 import java.util.Map;
 
 import lombok.Getter;
+import org.molgenis.vcf.utils.metadata.FieldIdentifier;
 import org.molgenis.vcf.utils.metadata.FieldMetadataService;
-import org.molgenis.vcf.utils.model.FieldMetadata;
-import org.molgenis.vcf.utils.model.NestedField;
+import org.molgenis.vcf.utils.metadata.NestedAttributes;
+import org.molgenis.vcf.utils.model.metadata.FieldMetadata;
+import org.molgenis.vcf.utils.model.metadata.FieldMetadatas;
+import org.molgenis.vcf.utils.model.metadata.NestedFieldMetadata;
 
 public class VepMetadata {
 
@@ -50,21 +53,28 @@ private void init() {
     for (VCFInfoHeaderLine vcfInfoHeaderLine : vcfHeader.getInfoHeaderLines()) {
       if (canMap(vcfInfoHeaderLine)) {
         this.vepFieldId = vcfInfoHeaderLine.getID();
-        FieldMetadata fieldMetadata = fieldMetadataService.load(
-            vcfInfoHeaderLine);
-        Map<String, NestedField> nestedFields = fieldMetadata.getNestedFields();
-        geneIndex = getIndex(nestedFields, GENE);
-        geneSourceIndex = getIndex(nestedFields, SYMBOL_SOURCE);
-        inheritanceIndex = getIndex(nestedFields, INHERITANCE);
-        alleleNumIndex = getIndex(nestedFields, ALLELE_NUM);
-        classIndex = getIndex(nestedFields, VIP_CLASS);
+        FieldMetadatas fieldMetadatas = fieldMetadataService.load(vcfHeader, Map.of(FieldIdentifier.builder()
+                .type(org.molgenis.vcf.utils.metadata.FieldType.INFO).name(vepFieldId).build(), NestedAttributes.builder().prefix(INFO_DESCRIPTION_PREFIX).seperator("|").build()));
+        FieldMetadata vepField = fieldMetadatas.getInfo().get(vepFieldId);
+        if (vepField == null) {
+          throw new MissingInfoException(vepFieldId);
+        }
+        Map<String, NestedFieldMetadata> nestedFieldsMeta = vepField.getNestedFields();
+        if (nestedFieldsMeta == null) {
+          throw new MissingVepMetadataException(vepFieldId);
+        }
+        geneIndex = getIndex(nestedFieldsMeta, GENE);
+        geneSourceIndex = getIndex(nestedFieldsMeta, SYMBOL_SOURCE);
+        inheritanceIndex = getIndex(nestedFieldsMeta, INHERITANCE);
+        alleleNumIndex = getIndex(nestedFieldsMeta, ALLELE_NUM);
+        classIndex = getIndex(nestedFieldsMeta, VIP_CLASS);
         return;
       }
     }
     throw new MissingInfoException("VEP");
   }
 
-  private static int getIndex(Map<String, NestedField> nestedFields, String fieldName) {
+  private static int getIndex(Map<String, NestedFieldMetadata> nestedFields, String fieldName) {
     return nestedFields.get(fieldName) != null ? nestedFields.get(fieldName).getIndex() : -1;
   }
 }

src/main/resources/metadata.json

@@ -0,0 +1,10 @@
+{
+  "format": {
+  },
+  "info": {
+    "CSQ": {
+      "nestedFields": {
+      }
+    }
+  }
+}

src/test/java/org/molgenis/vcf/inheritance/matcher/MissingVepMetadataExceptionTest.java

@@ -0,0 +1,16 @@
+package org.molgenis.vcf.inheritance.matcher;
+
+import org.junit.jupiter.api.Test;
+import org.molgenis.vcf.inheritance.matcher.vcf.meta.MissingVepMetadataException;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+class MissingVepMetadataExceptionTest {
+
+  @Test
+  void getMessage() {
+    assertEquals(
+        "VEP metadata is missing in metadata json, vep id: 'CSQ'.",
+        new MissingVepMetadataException("CSQ").getMessage());
+  }
+}