From a4220d62a35517e3e13c6ec344ff60879fef4cbc Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Wed, 27 Nov 2024 09:41:50 +0100 Subject: [PATCH 1/6] Fix inheritance matcher broken when running as jar --- .../util/VepMetadataServiceFactoryImpl.java | 22 ++++++++++++++++--- src/main/resources/metadata.json | 10 --------- 2 files changed, 19 insertions(+), 13 deletions(-) delete mode 100644 src/main/resources/metadata.json diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java index 89eee2a..a09aa83 100644 --- a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java +++ b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java @@ -3,22 +3,38 @@ import org.molgenis.vcf.utils.metadata.FieldMetadataService; import org.molgenis.vcf.utils.metadata.FieldMetadataServiceImpl; import org.springframework.stereotype.Component; -import org.springframework.util.ResourceUtils; import java.io.*; +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 public FieldMetadataService create() { File json; try { - json = ResourceUtils.getFile("classpath:metadata.json"); - } catch (FileNotFoundException e) { + Path path = Files.createTempFile("metadata", ".json"); + byte[] buf = EMPTY_METADATA_JSON.getBytes(); + Files.write(path, buf); + json = path.toFile(); + } catch (IOException e) { throw new UncheckedIOException(e); } return new FieldMetadataServiceImpl(json); diff --git a/src/main/resources/metadata.json b/src/main/resources/metadata.json deleted file mode 100644 index 7d0e490..0000000 --- a/src/main/resources/metadata.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "format": { - }, - "info": { - "CSQ": { - "nestedFields": { - } - } - } -} \ No newline at end of file From 58124da59eede3ad7914fe32c2ae9aba59ca043b Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Wed, 27 Nov 2024 09:43:16 +0100 Subject: [PATCH 2/6] bump version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a59b0de..ad31fd7 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.molgenis vip-inheritance-matcher - 3.2.1 + 3.3.1 vip-inheritance-matcher Annotates VCF samples with mendelian violation and possible compound flags and From e3fd5a2dfefe1d66bf1cfc2c09cda52674021d4e Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Wed, 27 Nov 2024 09:55:06 +0100 Subject: [PATCH 3/6] delete file on exit --- .../inheritance/matcher/util/VepMetadataServiceFactoryImpl.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java index 5dd8288..833f4bf 100644 --- a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java +++ b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java @@ -35,6 +35,7 @@ public FieldMetadataService create() { byte[] buf = EMPTY_METADATA_JSON.getBytes(); Files.write(path, buf); json = path.toFile(); + json.deleteOnExit(); } catch (IOException e) { throw new UncheckedIOException(e); } From b3fd54a6fb534c06e2538ea976553a8c03d8ad1d Mon Sep 17 00:00:00 2001 From: Bart Charbon Date: Wed, 27 Nov 2024 09:55:33 +0100 Subject: [PATCH 4/6] Update src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java Co-authored-by: Dennis Hendriksen --- .../inheritance/matcher/util/VepMetadataServiceFactoryImpl.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java index 833f4bf..43eff04 100644 --- a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java +++ b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java @@ -32,7 +32,7 @@ public FieldMetadataService create() { File json; try { Path path = Files.createTempFile("metadata", ".json"); - byte[] buf = EMPTY_METADATA_JSON.getBytes(); + byte[] buf = EMPTY_METADATA_JSON.getBytes(StandardCharsets.UTF_8); Files.write(path, buf); json = path.toFile(); json.deleteOnExit(); From 85330316e8d9f5dd726f81301fde9cd622184603 Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Wed, 27 Nov 2024 09:56:32 +0100 Subject: [PATCH 5/6] fix pom --- pom.xml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pom.xml b/pom.xml index ad31fd7..41ddb1a 100644 --- a/pom.xml +++ b/pom.xml @@ -115,6 +115,14 @@ maven-failsafe-plugin org.apache.maven.plugins + + + org.apache.maven.plugins + maven-surefire-plugin + + -XX:+EnableDynamicAgentLoading + + From ab0f516e4073ae5703a00db04eca5a2b18b9bc57 Mon Sep 17 00:00:00 2001 From: "bart.charbon" Date: Wed, 27 Nov 2024 10:01:49 +0100 Subject: [PATCH 6/6] Fix --- .../inheritance/matcher/util/VepMetadataServiceFactoryImpl.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java index 43eff04..35f847d 100644 --- a/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java +++ b/src/main/java/org/molgenis/vcf/inheritance/matcher/util/VepMetadataServiceFactoryImpl.java @@ -5,6 +5,7 @@ import org.springframework.stereotype.Component; import java.io.*; +import java.nio.charset.StandardCharsets; import java.nio.file.Files; import java.nio.file.Path;