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Add metadata json as a required parameter
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3 changes: 2 additions & 1 deletion
3
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 |
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@@ -1,7 +1,8 @@ | ||
package org.molgenis.vcf.inheritance.matcher.util; | ||
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import org.molgenis.vcf.inheritance.matcher.model.Settings; | ||
import org.molgenis.vcf.utils.metadata.FieldMetadataService; | ||
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public interface VepMetadataServiceFactory { | ||
FieldMetadataService create(); | ||
FieldMetadataService create(Settings settings); | ||
} |
32 changes: 3 additions & 29 deletions
32
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 |
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@@ -1,45 +1,19 @@ | ||
package org.molgenis.vcf.inheritance.matcher.util; | ||
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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; | ||
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import java.io.*; | ||
import java.nio.charset.StandardCharsets; | ||
import java.nio.file.Files; | ||
import java.nio.file.Path; | ||
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/** | ||
* 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": { | ||
} | ||
} | ||
} | ||
} | ||
"""; | ||
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@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()); | ||
} | ||
} |
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