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Remove dependency on field_metadata.json (#49)
* chore:remove dependency on field_metadata.json * chore:bump vip-utils 1.4.5 to 1.4.6, bump version 3.0.1 to 3.0.2 * fix VepMetadataServiceFactoryImpl
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7 changes: 7 additions & 0 deletions
7
src/main/java/org/molgenis/vcf/inheritance/matcher/util/InheritanceServiceFactory.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| import org.molgenis.vcf.inheritance.matcher.InheritanceService; | ||
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| public interface InheritanceServiceFactory { | ||
| InheritanceService create(); | ||
| } |
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src/main/java/org/molgenis/vcf/inheritance/matcher/util/InheritanceServiceFactoryImpl.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| import org.molgenis.vcf.inheritance.matcher.Annotator; | ||
| import org.molgenis.vcf.inheritance.matcher.InheritanceService; | ||
| import org.molgenis.vcf.inheritance.matcher.PedigreeInheritanceChecker; | ||
| import org.springframework.stereotype.Component; | ||
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| import static java.util.Objects.requireNonNull; | ||
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| /** | ||
| * Quirky class to enable use of local {@link org.molgenis.vcf.utils.vep.VepMetadataService} | ||
| */ | ||
| @Component | ||
| public class InheritanceServiceFactoryImpl implements InheritanceServiceFactory { | ||
| private final Annotator annotator; | ||
| private final VepMetadataServiceFactory vepMetadataServiceFactory; | ||
| private final PedigreeInheritanceChecker pedigreeInheritanceChecker; | ||
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| public InheritanceServiceFactoryImpl(Annotator annotator, VepMetadataServiceFactory vepMetadataServiceFactory, PedigreeInheritanceChecker pedigreeInheritanceChecker) { | ||
| this.annotator = requireNonNull(annotator); | ||
| this.vepMetadataServiceFactory = requireNonNull(vepMetadataServiceFactory); | ||
| this.pedigreeInheritanceChecker = requireNonNull(pedigreeInheritanceChecker); | ||
| } | ||
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| @Override | ||
| public InheritanceService create() { | ||
| return new InheritanceService(annotator, vepMetadataServiceFactory.create(), pedigreeInheritanceChecker); | ||
| } | ||
| } |
7 changes: 7 additions & 0 deletions
7
src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactory.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| import org.molgenis.vcf.utils.metadata.FieldMetadataService; | ||
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| public interface VepMetadataServiceFactory { | ||
| FieldMetadataService create(); | ||
| } |
47 changes: 47 additions & 0 deletions
47
src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| 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.springframework.stereotype.Component; | ||
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| import java.io.ByteArrayInputStream; | ||
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| import static java.nio.charset.StandardCharsets.UTF_8; | ||
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| /** | ||
| * Quirky class to enable reuse of {@link VepMetadataService} from vip-utils | ||
| */ | ||
| @Component | ||
| public class VepMetadataServiceFactoryImpl implements VepMetadataServiceFactory { | ||
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| @Override | ||
| public FieldMetadataService create() { | ||
| return new VepMetadataService(new EmptyFieldMetadataService()); | ||
| } | ||
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| /** | ||
| * 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": { | ||
| } | ||
| } | ||
| } | ||
| } | ||
| """; | ||
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| @Override | ||
| public FieldMetadata load(VCFInfoHeaderLine vcfInfoHeaderLine) { | ||
| return this.load(new ByteArrayInputStream(EMPTY_METADATA_JSON.getBytes(UTF_8)), vcfInfoHeaderLine); | ||
| } | ||
| } | ||
| } |
31 changes: 31 additions & 0 deletions
31
...est/java/org/molgenis/vcf/inheritance/matcher/util/InheritanceServiceFactoryImplTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.junit.jupiter.api.extension.ExtendWith; | ||
| import org.mockito.Mock; | ||
| import org.mockito.junit.jupiter.MockitoExtension; | ||
| import org.molgenis.vcf.inheritance.matcher.Annotator; | ||
| import org.molgenis.vcf.inheritance.matcher.PedigreeInheritanceChecker; | ||
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| import static org.mockito.Mockito.verify; | ||
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| @ExtendWith(MockitoExtension.class) | ||
| class InheritanceServiceFactoryImplTest { | ||
| @Mock | ||
| private Annotator annotator; | ||
| @Mock | ||
| private VepMetadataServiceFactory vepMetadataServiceFactory; | ||
| @Mock | ||
| private PedigreeInheritanceChecker pedigreeInheritanceChecker; | ||
| private InheritanceServiceFactoryImpl inheritanceServiceFactoryImpl; | ||
| @BeforeEach | ||
| void setUp() { | ||
| inheritanceServiceFactoryImpl = new InheritanceServiceFactoryImpl(annotator, vepMetadataServiceFactory, pedigreeInheritanceChecker); | ||
| } | ||
| @Test | ||
| void create() { | ||
| inheritanceServiceFactoryImpl.create(); | ||
| verify(vepMetadataServiceFactory).create(); | ||
| } | ||
| } |
19 changes: 19 additions & 0 deletions
19
...est/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImplTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| package org.molgenis.vcf.inheritance.matcher.util; | ||
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| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
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| class VepMetadataServiceFactoryImplTest { | ||
| private VepMetadataServiceFactoryImpl vepMetadataServiceFactoryImpl; | ||
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| @BeforeEach | ||
| void setUp() { | ||
| vepMetadataServiceFactoryImpl = new VepMetadataServiceFactoryImpl(); | ||
| } | ||
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| @Test | ||
| void create() { | ||
| // test that no exception is thrown | ||
| vepMetadataServiceFactoryImpl.create(); | ||
| } | ||
| } |