From b51845793e4ed37d226597b44e9485f1b6af8b88 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 07:55:46 +0200 Subject: [PATCH 1/7] chore:bump spring-boot-starter-parent 3.0.5 to 3.1.3 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 4eb19b2..a311d96 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.springframework.boot spring-boot-starter-parent - 3.0.5 + 3.1.3 From b3090162b13c15fff3353f862ed02ee12d6c184e Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 07:56:20 +0200 Subject: [PATCH 2/7] chore:bump samtools.htsjdk 3.0.5 to 4.0.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a311d96..561cda5 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ 17 1.5.0 - 3.0.5 + 4.0.1 0.8.9 1.4.0 From d8e338bee6177fa8f5ed64dd41964fbc0d6d7f06 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 07:56:43 +0200 Subject: [PATCH 3/7] chore:bump jacoco-maven-plugin 0.8.9 to 0.8.10 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 561cda5..7309d34 100644 --- a/pom.xml +++ b/pom.xml @@ -42,7 +42,7 @@ 17 1.5.0 4.0.1 - 0.8.9 + 0.8.10 1.4.0 From 11026517b90992ac049264de50686b5c6f49ec30 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 07:57:00 +0200 Subject: [PATCH 4/7] chore:bump vip-utils 1.4.0 to 1.4.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 7309d34..7f2c914 100644 --- a/pom.xml +++ b/pom.xml @@ -43,7 +43,7 @@ 1.5.0 4.0.1 0.8.10 - 1.4.0 + 1.4.1 From eb253733c63b2d85cc7f3b03a76c6235abdad575 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 07:57:22 +0200 Subject: [PATCH 5/7] chore:bump version 3.7.0 to 3.7.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 7f2c914..4827b10 100644 --- a/pom.xml +++ b/pom.xml @@ -13,7 +13,7 @@ org.molgenis vip-decision-tree - 3.7.0 + 3.7.1 vip-decision-tree Decision tree module for filtering and labelling VCF files From 15741295b4efcb4e4f3fd790fd676f58e720ee22 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 08:01:51 +0200 Subject: [PATCH 6/7] chore:resolve NonNull on primitive warnings --- src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java | 2 +- .../org/molgenis/vcf/decisiontree/filter/model/NestedField.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java index 04505f6..d2ffc27 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java @@ -11,5 +11,5 @@ public class Allele { @NonNull String bases; - @NonNull int index; + int index; } diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/model/NestedField.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/model/NestedField.java index 65bb47a..86263d1 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/model/NestedField.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/model/NestedField.java @@ -11,7 +11,6 @@ @NonFinal public class NestedField extends FieldImpl implements Comparable { - @NonNull final int index; @NonNull final Field parent; From 14ab0091060fee45f4b75d876321126d1c5295c5 Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Mon, 11 Sep 2023 08:07:42 +0200 Subject: [PATCH 7/7] fix: add serialVersionUID to exceptions, remove unneeded toString() --- .../vcf/decisiontree/filter/EvaluationException.java | 5 ++++- .../vcf/decisiontree/filter/FlagListException.java | 5 ++++- .../filter/InvalidNumberOfTokensException.java | 4 +++- .../decisiontree/filter/MissingPhenotypesException.java | 5 ++++- .../vcf/decisiontree/filter/UnknownFieldException.java | 5 ++++- .../vcf/decisiontree/filter/UnsupportedFieldException.java | 5 ++++- .../filter/UnsupportedFormatFieldException.java | 5 ++++- .../filter/UnsupportedNestedFieldException.java | 5 ++++- .../loader/ConfigDecisionTreeValidationException.java | 5 ++++- .../vcf/decisiontree/runner/CountMismatchException.java | 7 +++++-- .../decisiontree/runner/FileValueNotAllowedException.java | 5 ++++- .../vcf/decisiontree/runner/MissingProbandsException.java | 4 +++- .../decisiontree/runner/UnsupportedOperatorException.java | 5 ++++- .../runner/UnsupportedValueCountException.java | 5 ++++- .../runner/UnsupportedValueCountTypeException.java | 5 ++++- .../decisiontree/runner/UnsupportedValueTypeException.java | 5 ++++- .../runner/info/InvalidHeaderLineException.java | 4 ++++ .../runner/info/MissingRequiredNestedValueException.java | 4 ++++ .../vcf/decisiontree/runner/info/MissingVepException.java | 5 ++++- .../vcf/decisiontree/utils/TypeConversionException.java | 5 ++++- 20 files changed, 79 insertions(+), 19 deletions(-) diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/EvaluationException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/EvaluationException.java index 9dc1bc2..2667b62 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/EvaluationException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/EvaluationException.java @@ -4,8 +4,11 @@ import org.molgenis.vcf.decisiontree.filter.model.Node; -public class EvaluationException extends RuntimeException { +import java.io.Serial; +public class EvaluationException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public EvaluationException(Node node, Variant variant, String message) { super( format( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/FlagListException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/FlagListException.java index 4a5c0bc..eeafe6e 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/FlagListException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/FlagListException.java @@ -1,9 +1,12 @@ package org.molgenis.vcf.decisiontree.filter; +import java.io.Serial; + import static java.lang.String.format; public class FlagListException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "INFO field '%s' of type FLAG cannot contain a list of values."; private final String field; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/InvalidNumberOfTokensException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/InvalidNumberOfTokensException.java index aa95a06..9b9ea91 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/InvalidNumberOfTokensException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/InvalidNumberOfTokensException.java @@ -2,11 +2,13 @@ import static java.lang.String.format; +import java.io.Serial; import java.util.List; import org.molgenis.vcf.decisiontree.filter.model.FieldType; public class InvalidNumberOfTokensException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "Unsupported number of tokens for input '%s' expecting %d tokens for fieldtype '%s'."; private final List fieldTokens; private final FieldType type; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/MissingPhenotypesException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/MissingPhenotypesException.java index 05c6425..da088ed 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/MissingPhenotypesException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/MissingPhenotypesException.java @@ -1,10 +1,13 @@ package org.molgenis.vcf.decisiontree.filter; +import java.io.Serial; + import static java.lang.String.format; public class MissingPhenotypesException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "Attempting to filter on phenotypes without specifying phenotypes for smaple '%s'."; private final String sample; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnknownFieldException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnknownFieldException.java index d63b952..785cd03 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnknownFieldException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnknownFieldException.java @@ -5,9 +5,12 @@ import org.molgenis.vcf.decisiontree.filter.model.FieldType; +import java.io.Serial; + public class UnknownFieldException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "Unknown '%s' field '%s'."; private final String field; private final FieldType type; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFieldException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFieldException.java index eb5a969..5a04d7b 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFieldException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFieldException.java @@ -1,10 +1,13 @@ package org.molgenis.vcf.decisiontree.filter; +import java.io.Serial; + import static java.lang.String.format; public class UnsupportedFieldException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "Unsupported field '%s'."; private final String rootField; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFormatFieldException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFormatFieldException.java index 8cec150..ab58a27 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFormatFieldException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFormatFieldException.java @@ -1,10 +1,13 @@ package org.molgenis.vcf.decisiontree.filter; +import java.io.Serial; + import static java.util.Objects.requireNonNull; public class UnsupportedFormatFieldException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private final Class clazz; public UnsupportedFormatFieldException(Class clazz) { diff --git a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedNestedFieldException.java b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedNestedFieldException.java index 04b1e99..7de8071 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedNestedFieldException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedNestedFieldException.java @@ -1,8 +1,11 @@ package org.molgenis.vcf.decisiontree.filter; +import java.io.Serial; + public class UnsupportedNestedFieldException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; private final String field; public UnsupportedNestedFieldException(String field) { diff --git a/src/main/java/org/molgenis/vcf/decisiontree/loader/ConfigDecisionTreeValidationException.java b/src/main/java/org/molgenis/vcf/decisiontree/loader/ConfigDecisionTreeValidationException.java index d8436e6..0a60db7 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/loader/ConfigDecisionTreeValidationException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/loader/ConfigDecisionTreeValidationException.java @@ -1,7 +1,10 @@ package org.molgenis.vcf.decisiontree.loader; -public class ConfigDecisionTreeValidationException extends RuntimeException { +import java.io.Serial; +public class ConfigDecisionTreeValidationException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public ConfigDecisionTreeValidationException(String message) { super(message); } diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/CountMismatchException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/CountMismatchException.java index 5ca957a..dd93861 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/CountMismatchException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/CountMismatchException.java @@ -4,10 +4,13 @@ import org.molgenis.vcf.decisiontree.loader.model.ConfigBoolQuery; -public class CountMismatchException extends RuntimeException { +import java.io.Serial; +public class CountMismatchException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public CountMismatchException(ConfigBoolQuery query) { super( - format("Query value for field '%s' should be a collection for query '%s'.", query.getField(), query.toString())); + format("Query value for field '%s' should be a collection for query '%s'.", query.getField(), query)); } } diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/FileValueNotAllowedException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/FileValueNotAllowedException.java index 9fcd357..2219afc 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/FileValueNotAllowedException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/FileValueNotAllowedException.java @@ -4,8 +4,11 @@ import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator; -public class FileValueNotAllowedException extends RuntimeException { +import java.io.Serial; +public class FileValueNotAllowedException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public FileValueNotAllowedException(ConfigOperator operator, String allowedFileOperators, String field) { super( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/MissingProbandsException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/MissingProbandsException.java index 3ff8ea0..6665732 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/MissingProbandsException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/MissingProbandsException.java @@ -2,10 +2,12 @@ import static java.lang.String.format; +import java.io.Serial; import java.util.List; public class MissingProbandsException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; public MissingProbandsException(List probands) { super( format( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedOperatorException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedOperatorException.java index 34fa434..ceee49f 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedOperatorException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedOperatorException.java @@ -6,8 +6,11 @@ import org.molgenis.vcf.decisiontree.filter.model.Field; import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator; -public class UnsupportedOperatorException extends RuntimeException { +import java.io.Serial; +public class UnsupportedOperatorException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public UnsupportedOperatorException(ConfigOperator operator, Field field, DecisionType decisionType) { super( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java index 708311e..940c735 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java @@ -5,8 +5,11 @@ import org.molgenis.vcf.decisiontree.filter.model.DecisionType; import org.molgenis.vcf.decisiontree.filter.model.Field; -public class UnsupportedValueCountException extends RuntimeException { +import java.io.Serial; +public class UnsupportedValueCountException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public UnsupportedValueCountException(Field field, DecisionType decisionType) { super( format( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java index 697b9dd..98dbd2e 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java @@ -5,8 +5,11 @@ import org.molgenis.vcf.decisiontree.filter.model.DecisionType; import org.molgenis.vcf.decisiontree.filter.model.Field; -public class UnsupportedValueCountTypeException extends RuntimeException { +import java.io.Serial; +public class UnsupportedValueCountTypeException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public UnsupportedValueCountTypeException(Field field, DecisionType decisionType) { super( format( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueTypeException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueTypeException.java index c50b22f..ce3f9d7 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueTypeException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueTypeException.java @@ -5,8 +5,11 @@ import org.molgenis.vcf.decisiontree.filter.model.DecisionType; import org.molgenis.vcf.decisiontree.filter.model.Field; -public class UnsupportedValueTypeException extends RuntimeException { +import java.io.Serial; +public class UnsupportedValueTypeException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; public UnsupportedValueTypeException(Field field, DecisionType decisionType) { super( format( diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/InvalidHeaderLineException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/InvalidHeaderLineException.java index 736902c..75e615e 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/InvalidHeaderLineException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/InvalidHeaderLineException.java @@ -1,9 +1,13 @@ package org.molgenis.vcf.decisiontree.runner.info; +import java.io.Serial; + import static java.lang.String.format; public class InvalidHeaderLineException extends RuntimeException { + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "VCF header with id '%s' is not a SnpEff header."; public InvalidHeaderLineException(String id) { diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingRequiredNestedValueException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingRequiredNestedValueException.java index 91ecd4c..1712d46 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingRequiredNestedValueException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingRequiredNestedValueException.java @@ -1,8 +1,12 @@ package org.molgenis.vcf.decisiontree.runner.info; +import java.io.Serial; + import static java.lang.String.format; public class MissingRequiredNestedValueException extends RuntimeException{ + @Serial + private static final long serialVersionUID = 1L; private static final String MESSAGE = "For '%s' annotations the '%s' field is expected to be present."; public MissingRequiredNestedValueException(String fieldName, String nestedFieldName) { diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingVepException.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingVepException.java index 889fe17..2691b5c 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingVepException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingVepException.java @@ -1,8 +1,11 @@ package org.molgenis.vcf.decisiontree.runner.info; +import java.io.Serial; + public class MissingVepException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; @Override public String getMessage() { return "Input VCF is missing required VEP annotation."; diff --git a/src/main/java/org/molgenis/vcf/decisiontree/utils/TypeConversionException.java b/src/main/java/org/molgenis/vcf/decisiontree/utils/TypeConversionException.java index daf47b1..ed8ef41 100644 --- a/src/main/java/org/molgenis/vcf/decisiontree/utils/TypeConversionException.java +++ b/src/main/java/org/molgenis/vcf/decisiontree/utils/TypeConversionException.java @@ -1,9 +1,12 @@ package org.molgenis.vcf.decisiontree.utils; +import java.io.Serial; + import static java.lang.String.format; public class TypeConversionException extends RuntimeException { - + @Serial + private static final long serialVersionUID = 1L; public TypeConversionException(Object value, Class thatClass) { super( format(