Merge pull request #20 from molgenis/chore/bump_deps

chore:bump dependencies, resolve warnings, small PanelMapper fix

pom.xml

@@ -7,13 +7,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.0.5</version>
+    <version>3.1.3</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>org.molgenis</groupId>
   <artifactId>vip-utils</artifactId>
-  <version>1.4.0</version>
+  <version>1.4.1</version>
 
   <name>vip-utils</name>
   <description>Shared classes and tools between VIP repo's</description>
@@ -47,9 +47,9 @@
 
   <properties>
     <java.version>17</java.version>
-    <samtools.htsjdk.version>3.0.5</samtools.htsjdk.version>
-    <jacoco-maven-plugin.version>0.8.9</jacoco-maven-plugin.version>
-    <opencsv.version>5.7.1</opencsv.version>
+    <samtools.htsjdk.version>4.0.1</samtools.htsjdk.version>
+    <jacoco-maven-plugin.version>0.8.10</jacoco-maven-plugin.version>
+    <opencsv.version>5.8</opencsv.version>
     <commons.cli.version>1.4</commons.cli.version>
   </properties>
 

src/main/java/org/molgenis/vcf/utils/InvalidPedException.java

@@ -1,8 +1,12 @@
 package org.molgenis.vcf.utils;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class InvalidPedException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "Invalid PED line, expected 6 columns on line: %s";
   private final String argument;
 

src/main/java/org/molgenis/vcf/utils/InvalidSamplePhenotypesException.java

@@ -1,9 +1,12 @@
 package org.molgenis.vcf.utils;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class InvalidSamplePhenotypesException extends RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE =
       "Invalid phenotype argument: '%s', valid example: 'sample1/phenotype1;phenotype2,sample2/phenotype1'";
   private final String argument;

src/main/java/org/molgenis/vcf/utils/MixedPhenotypesException.java

@@ -1,6 +1,10 @@
 package org.molgenis.vcf.utils;
 
+import java.io.Serial;
+
 public class MixedPhenotypesException extends IllegalArgumentException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE =
       "Mixing general phenotypes for all samples and phenotypes per sample is not allowed.";
 

src/main/java/org/molgenis/vcf/utils/UnexpectedEnumException.java

@@ -1,5 +1,7 @@
 package org.molgenis.vcf.utils;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 import static java.util.Objects.requireNonNull;
 
@@ -8,7 +10,8 @@
  * strategy.
  */
 public class UnexpectedEnumException extends RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String UNEXPECTED_ENUM_CONSTANT_FORMAT =
       "Unexpected enum constant '%s' for type '%s'";
 

src/main/java/org/molgenis/vcf/utils/metadata/UnknownFieldException.java

@@ -3,8 +3,11 @@
 
 import org.springframework.lang.NonNull;
 
-public class UnknownFieldException extends RuntimeException {
+import java.io.Serial;
 
+public class UnknownFieldException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "No known nested metadata for identifier '%s'.";
   private final String id;
 

src/main/java/org/molgenis/vcf/utils/model/NestedField.java

@@ -5,7 +5,6 @@
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 import lombok.NoArgsConstructor;
-import lombok.NonNull;
 import lombok.ToString;
 import lombok.experimental.SuperBuilder;
 
@@ -16,6 +15,5 @@
 @AllArgsConstructor
 @ToString(callSuper=true)
 public class NestedField extends Field {
-  @NonNull
   @Default int index = -1;
 }

src/main/java/org/molgenis/vcf/utils/panelmapper/PanelMapper.java

@@ -86,7 +86,6 @@ private static Path getOutput(CommandLine commandLine) {
     } else {
       outputPath = Path.of(commandLine
             .getOptionValue(OPT_INPUT)
-            .replace(" ", "_")
             .replace(".txt", "_mapped.tsv"));
     }
     return outputPath;

src/main/java/org/molgenis/vcf/utils/sample/UnsupportedPedException.java

@@ -1,8 +1,12 @@
 package org.molgenis.vcf.utils.sample;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class UnsupportedPedException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE =
       "Phenotype value '%s' that is not an affection status (-9, 0, 1 or 2) is unsupported";
   private final String token;

src/main/java/org/molgenis/vcf/utils/sample/mapper/IllegalPhenotypeArgumentException.java

@@ -1,9 +1,13 @@
 package org.molgenis.vcf.utils.sample.mapper;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 import static java.util.Objects.requireNonNull;
 
 public class IllegalPhenotypeArgumentException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE =
       "Illegal phenotype '%s' phenotypes must be specified in CURIE (prefix:reference) format.";
   private final String argument;

src/main/java/org/molgenis/vcf/utils/sample/mapper/VcfParseException.java

@@ -1,7 +1,10 @@
 package org.molgenis.vcf.utils.sample.mapper;
 
-public class VcfParseException extends RuntimeException {
+import java.io.Serial;
 
+public class VcfParseException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public VcfParseException(String message) {
     super(message);
   }

src/main/java/org/molgenis/vcf/utils/sample/model/Sample.java

@@ -17,10 +17,8 @@ public class Sample {
 
   // index of the sample in the VCF, -1 means the sample is not available in the file.
   @JsonProperty("index")
-  @NonNull
   int index;
 
   @JsonProperty("proband")
-  @NonNull
   boolean proband;
 }

src/test/java/org/molgenis/vcf/utils/panelmapper/AppIT.java

@@ -32,7 +32,7 @@ void test() throws IOException {
     assertEquals(expected, output);
   }
   @Test
-  void testNoOuputParam() throws IOException {
+  void testNoOutputParam() throws IOException {
     File inputFile = ResourceUtils.getFile("classpath:panel.txt");
     String inputPath = inputFile.toString();
     String mappingFile = ResourceUtils.getFile("classpath:mapping.txt").toString();
@@ -43,7 +43,6 @@ void testNoOuputParam() throws IOException {
     Path expectedPath = ResourceUtils.getFile("classpath:expected.tsv").toPath();
     String expected = Files.readString(expectedPath).replaceAll("\\R", "\n");
     Path outputPath = Path.of(inputFile.getPath()
-            .replace(" ", "_")
             .replace(".txt", "_mapped.tsv"));
     String output = Files.readString(outputPath).replaceAll("\\R", "\n");
     assertEquals(expected, output);