Merge pull request #62 from molgenis/fix/require_metadata

Add metadata json as a required parameter

README.md

@@ -63,9 +63,10 @@ contain the following:
 
 ## Usage
 ```
-usage: java -jar vcf-inheritance-matcher.jar -i <arg> [-o <arg>] [-pd
+usage: java -jar vcf-inheritance-matcher.jar -i <arg> -m <arg> [-o <arg>] [-pd
        <arg>] [-pb <arg>] [-np <arg>] [-c] [-f] [-d]
  -i,--input <arg>            Input VCF file (.vcf or .vcf.gz).
+ -m,--metadata <arg>         VCF metadata file (.json).
  -o,--output <arg>           Output VCF file (.vcf or .vcf.gz).
  -pd,--pedigree <arg>        Comma-separated list of pedigree files
                              (.ped).

pom.xml

@@ -12,7 +12,7 @@
 
   <groupId>org.molgenis</groupId>
   <artifactId>vip-inheritance-matcher</artifactId>
-  <version>3.3.1</version>
+  <version>3.3.2</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/AppCommandLineOptions.java

@@ -14,6 +14,8 @@ class AppCommandLineOptions {
   static final String OPT_INPUT_LONG = "input";
   static final String OPT_OUTPUT = "o";
   static final String OPT_OUTPUT_LONG = "output";
+  static final String OPT_METADATA = "m";
+  static final String OPT_METADATA_LONG = "metadata";
   static final String OPT_PED = "pd";
   static final String OPT_PED_LONG = "pedigree";
   static final String OPT_PROBANDS = "pb";
@@ -44,6 +46,13 @@ class AppCommandLineOptions {
             .longOpt(OPT_OUTPUT_LONG)
             .desc("Output VCF file (.vcf or .vcf.gz).")
             .build());
+    appOptions.addOption(
+        Option.builder(OPT_METADATA)
+            .hasArg(true)
+            .required()
+            .longOpt(OPT_METADATA_LONG)
+            .desc("VCF metadata file (.json).")
+            .build());
     appOptions.addOption(
         Option.builder(OPT_PED)
             .hasArg(true)
@@ -97,6 +106,7 @@ static Options getAppVersionOptions() {
   static void validateCommandLine(CommandLine commandLine) {
     validateInput(commandLine);
     validateOutput(commandLine);
+    validateMetadata(commandLine);
   }
 
   private static void validateInput(CommandLine commandLine) {
@@ -132,4 +142,25 @@ private static void validateOutput(CommandLine commandLine) {
           format("Output file '%s' already exists", outputPath));
     }
   }
+
+  private static void validateMetadata(CommandLine commandLine) {
+    Path metadataPath = Path.of(commandLine.getOptionValue(OPT_METADATA));
+    if (!Files.exists(metadataPath)) {
+      throw new IllegalArgumentException(
+              format("Metadata file '%s' does not exist.", metadataPath));
+    }
+    if (Files.isDirectory(metadataPath)) {
+      throw new IllegalArgumentException(
+              format("Metadata file '%s' is a directory.", metadataPath));
+    }
+    if (!Files.isReadable(metadataPath)) {
+      throw new IllegalArgumentException(
+              format("Metadata file '%s' is not readable.", metadataPath));
+    }
+    String inputPathStr = metadataPath.toString();
+    if (!inputPathStr.endsWith(".json")) {
+      throw new IllegalArgumentException(
+              format("Metadata file '%s' is not a .json file.", inputPathStr));
+    }
+  }
 }

src/main/java/org/molgenis/vcf/inheritance/matcher/AppCommandLineRunner.java

@@ -76,6 +76,7 @@ public void run(String... args) {
   private Settings mapSettings(CommandLine commandLine) {
     String inputPathValue = commandLine.getOptionValue(OPT_INPUT);
     Path inputPath = Path.of(inputPathValue);
+    Path metadataPath = Path.of(commandLine.getOptionValue(OPT_METADATA));
 
     Path outputPath;
     if (commandLine.hasOption(OPT_OUTPUT)) {
@@ -111,7 +112,7 @@ private Settings mapSettings(CommandLine commandLine) {
 
     return Settings.builder().inputVcfPath(inputPath).inputPedPaths(pedPaths)
         .outputPath(outputPath).probands(probandNames).overwrite(overwriteOutput).
-            pathogenicClasses(pathogenicClasses).debug(debugMode)
+            pathogenicClasses(pathogenicClasses).metadataPath(metadataPath).debug(debugMode)
         .build();
   }
 

src/main/java/org/molgenis/vcf/inheritance/matcher/model/Settings.java

@@ -13,6 +13,7 @@ public class Settings {
   Path inputVcfPath;
   List<Path> inputPedPaths;
   Path outputPath;
+  Path metadataPath;
   List<String> probands;
   Set<String> pathogenicClasses;
   boolean overwrite;

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

@@ -1,7 +1,8 @@
 package org.molgenis.vcf.inheritance.matcher.util;
 
+import org.molgenis.vcf.inheritance.matcher.model.Settings;
 import org.molgenis.vcf.utils.metadata.FieldMetadataService;
 
 public interface VepMetadataServiceFactory {
-    FieldMetadataService create();
+    FieldMetadataService create(Settings settings);
 }

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

@@ -1,45 +1,19 @@
 package org.molgenis.vcf.inheritance.matcher.util;
 
+import org.molgenis.vcf.inheritance.matcher.model.Settings;
 import org.molgenis.vcf.utils.metadata.FieldMetadataService;
 import org.molgenis.vcf.utils.metadata.FieldMetadataServiceImpl;
 import org.springframework.stereotype.Component;
 
-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 {
-            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);
+    public FieldMetadataService create(Settings settings) {
+        return new FieldMetadataServiceImpl(settings.getMetadataPath().toFile());
     }
 }

src/main/java/org/molgenis/vcf/inheritance/matcher/vcf/VcfReaderFactoryImpl.java

@@ -20,7 +20,7 @@ public VcfReaderFactoryImpl(VepMetadataServiceFactoryImpl vepMetadataServiceFact
     public VcfReader create(Settings settings) {
         Path inputVcfPath = settings.getInputVcfPath();
         VCFFileReader vcfFileReader = new VCFFileReader(inputVcfPath.toFile(), false);
-        VepMetadata vepMetadata = new VepMetadata(vcfFileReader.getFileHeader(), vepMetadataServiceFactoryImpl.create());
+        VepMetadata vepMetadata = new VepMetadata(vcfFileReader.getFileHeader(), vepMetadataServiceFactoryImpl.create(settings));
         return new VcfReader(vcfFileReader, new VcfRecordFactoryImpl(vepMetadata), settings.getPathogenicClasses());
     }
 }

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

@@ -18,10 +18,11 @@ class AppIT {
   @Test
   void testNoVep() throws IOException {
     String inputFile = ResourceUtils.getFile("classpath:integration_noVEPinheritance.vcf").toString();
+    String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
     String pedigree = ResourceUtils.getFile("classpath:pedigree_complex.ped").toString();
     String outputFile = sharedTempDir.resolve("actual.vcf").toString();
 
-    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree};
+    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-m", metadataFile};
     SpringApplication.run(App.class, args);
 
     String outputVcf = Files.readString(Path.of(outputFile));
@@ -35,9 +36,10 @@ void testNoVep() throws IOException {
   @Test
   void testNoPed() throws IOException {
     String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
+    String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
     String outputFile = sharedTempDir.resolve("actual.vcf").toString();
 
-    String[] args = {"-i", inputFile, "-o", outputFile, "-c", "P"};
+    String[] args = {"-i", inputFile, "-o", outputFile, "-c", "P", "-m", metadataFile};
     SpringApplication.run(App.class, args);
 
     String outputVcf = Files.readString(Path.of(outputFile));
@@ -51,10 +53,11 @@ void testNoPed() throws IOException {
   @Test
   void testProband() throws IOException {
     String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
+    String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
     String pedigree = ResourceUtils.getFile("classpath:pedigree_complex.ped").toString();
     String outputFile = sharedTempDir.resolve("actual.vcf").toString();
 
-    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force" ,"-c","P,B"};
+    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force" ,"-c","P,B", "-m", metadataFile};
     SpringApplication.run(App.class, args);
 
     String outputVcf = Files.readString(Path.of(outputFile));
@@ -68,10 +71,11 @@ void testProband() throws IOException {
   @Test
   void testNoParents() throws IOException {
     String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
+    String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
     String pedigree = ResourceUtils.getFile("classpath:pedigree_fam_no_parents.ped").toString();
     String outputFile = sharedTempDir.resolve("actual.vcf").toString();
 
-    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force"};
+    String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force", "-m", metadataFile};
     SpringApplication.run(App.class, args);
 
     String outputVcf = Files.readString(Path.of(outputFile));

src/test/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImplTest.java

@@ -2,6 +2,12 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.molgenis.vcf.inheritance.matcher.model.Settings;
+
+import java.nio.file.Path;
+
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 class VepMetadataServiceFactoryImplTest {
     private VepMetadataServiceFactoryImpl vepMetadataServiceFactoryImpl;
@@ -13,7 +19,9 @@ void setUp() {
 
     @Test
     void create() {
+        Settings settings = mock(Settings.class);
+        when(settings.getMetadataPath()).thenReturn(Path.of("TEST"));
         // test that no exception is thrown
-        vepMetadataServiceFactoryImpl.create();
+        vepMetadataServiceFactoryImpl.create(settings);
     }
 }