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Changes to enable update of H2 to version 2.2.x
Update H2 version 1.4.200 -> 2.2.224 Update Flyway version 8.2.1 -> 10.6.0 to support H2 update Add new ProtobufDataType Update ClinVarDataType, AlleleKeyDataType and AllelePropertiesDataType to extend ProtobufDataType Delete static data from exomiser-spring-boot-autoconfigure/test/resources Add new TestDataDirectories class to dynamically create test data for the exomiser-spring-boot-autoconfigure module to allow for simpler updating of H2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -20,25 +20,23 @@ | |
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| package org.monarchinitiative.exomiser.core.genome.dao.serialisers; | ||
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| import com.google.protobuf.InvalidProtocolBufferException; | ||
| import org.h2.mvstore.DataUtils; | ||
| import org.h2.mvstore.WriteBuffer; | ||
| import com.google.protobuf.Parser; | ||
| import org.h2.mvstore.type.DataType; | ||
| import org.h2.util.Utils; | ||
| import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey; | ||
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| import java.nio.ByteBuffer; | ||
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| /** | ||
| * Specialised {@link DataType} for (de)serialising {@link AlleleKey} objects into and out of | ||
| * the {@link org.h2.mvstore.MVStore}. | ||
| * | ||
| * @author Jules Jacobsen <[email protected]> | ||
| */ | ||
| public class AlleleKeyDataType implements DataType { | ||
| public class AlleleKeyDataType extends ProtobufDataType<AlleleKey> { | ||
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| public static final AlleleKeyDataType INSTANCE = new AlleleKeyDataType(); | ||
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| private AlleleKeyDataType() { | ||
| } | ||
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| /** | ||
| * Sorts variants according to their natural ordering of genome position. Variants are sorted according to | ||
| * chromosome number, chromosome position, reference sequence then alternative sequence. | ||
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@@ -47,59 +45,26 @@ public class AlleleKeyDataType implements DataType { | |
| * @return comparator score consistent with equals. | ||
| */ | ||
| @Override | ||
| public int compare(Object a, Object b) { | ||
| AlleleKey keyA = (AlleleKey) a; | ||
| AlleleKey keyB = (AlleleKey) b; | ||
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| if (keyA.getChr() != keyB.getChr()) { | ||
| return Integer.compare(keyA.getChr(), keyB.getChr()); | ||
| public int compare(AlleleKey a, AlleleKey b) { | ||
| if (a.getChr() != b.getChr()) { | ||
| return Integer.compare(a.getChr(), b.getChr()); | ||
| } | ||
| if (keyA.getPosition() != keyB.getPosition()) { | ||
| return Integer.compare(keyA.getPosition(), keyB.getPosition()); | ||
| if (a.getPosition() != b.getPosition()) { | ||
| return Integer.compare(a.getPosition(), b.getPosition()); | ||
| } | ||
| if (!keyA.getRef().equals(keyB.getRef())) { | ||
| return keyA.getRef().compareTo(keyB.getRef()); | ||
| if (!a.getRef().equals(b.getRef())) { | ||
| return a.getRef().compareTo(b.getRef()); | ||
| } | ||
| return keyA.getAlt().compareTo(keyB.getAlt()); | ||
| return a.getAlt().compareTo(b.getAlt()); | ||
| } | ||
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| @Override | ||
| public int getMemory(Object obj) { | ||
| AlleleKey key = (AlleleKey) obj; | ||
| return key.getSerializedSize(); | ||
| public Parser<AlleleKey> messageParser() { | ||
| return AlleleKey.parser(); | ||
| } | ||
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| @Override | ||
| public void read(ByteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| obj[i] = read(buff); | ||
| } | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| write(buff, obj[i]); | ||
| } | ||
| public AlleleKey[] createStorage(int size) { | ||
| return new AlleleKey[size]; | ||
| } | ||
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| @Override | ||
| public AlleleKey read(ByteBuffer buff) { | ||
| int len = DataUtils.readVarInt(buff); | ||
| byte[] data = Utils.newBytes(len); | ||
| buff.get(data); | ||
| try { | ||
| return AlleleKey.parseFrom(data); | ||
| } catch (InvalidProtocolBufferException e) { | ||
| throw new InvalidAlleleProtoException(e); | ||
| } | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object obj) { | ||
| AlleleKey key = (AlleleKey) obj; | ||
| byte[] data = key.toByteArray(); | ||
| buff.putVarInt(data.length).put(data); | ||
| } | ||
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| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -20,66 +20,38 @@ | |
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| package org.monarchinitiative.exomiser.core.genome.dao.serialisers; | ||
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| import com.google.protobuf.InvalidProtocolBufferException; | ||
| import org.h2.mvstore.DataUtils; | ||
| import org.h2.mvstore.WriteBuffer; | ||
| import com.google.protobuf.Parser; | ||
| import org.h2.mvstore.type.DataType; | ||
| import org.h2.util.Utils; | ||
| import org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties; | ||
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| import java.nio.ByteBuffer; | ||
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| /** | ||
| * Specialised {@link DataType} for (de)serialising {@link AlleleProperties} objects into and out of | ||
| * the {@link org.h2.mvstore.MVStore}. | ||
| * | ||
| * @author Jules Jacobsen <[email protected]> | ||
| */ | ||
| public class AllelePropertiesDataType implements DataType { | ||
| public class AllelePropertiesDataType extends ProtobufDataType<AlleleProperties> { | ||
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| public static final AllelePropertiesDataType INSTANCE = new AllelePropertiesDataType(); | ||
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| @Override | ||
| public int compare(Object a, Object b) { | ||
| return -1; | ||
| } | ||
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| @Override | ||
| public int getMemory(Object obj) { | ||
| AlleleProperties props = (AlleleProperties) obj; | ||
| return props.getSerializedSize(); | ||
| } | ||
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| @Override | ||
| public void read(ByteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| obj[i] = read(buff); | ||
| } | ||
| private AllelePropertiesDataType() { | ||
| } | ||
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| @Override | ||
| public AlleleProperties read(ByteBuffer buff) { | ||
| int len = DataUtils.readVarInt(buff); | ||
| byte[] data = Utils.newBytes(len); | ||
| buff.get(data); | ||
| try { | ||
| return AlleleProperties.parseFrom(data); | ||
| } catch (InvalidProtocolBufferException e) { | ||
| throw new InvalidAlleleProtoException(e); | ||
| public int compare(AlleleProperties a, AlleleProperties b) { | ||
| if (a.equals(b)) { | ||
| return 0; | ||
| } | ||
| throw new UnsupportedOperationException("Unable to compare " + a + " with " + b); | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| write(buff, obj[i]); | ||
| } | ||
| public AlleleProperties[] createStorage(int size) { | ||
| return new AlleleProperties[size]; | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object obj) { | ||
| AlleleProperties props = (AlleleProperties) obj; | ||
| byte[] data = props.toByteArray(); | ||
| buff.putVarInt(data.length).put(data); | ||
| public Parser<AlleleProperties> messageParser() { | ||
| return AlleleProperties.parser(); | ||
| } | ||
| } | ||
56 changes: 12 additions & 44 deletions
56
...main/java/org/monarchinitiative/exomiser/core/genome/dao/serialisers/ClinVarDataType.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,60 +1,28 @@ | ||
| package org.monarchinitiative.exomiser.core.genome.dao.serialisers; | ||
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| import com.google.protobuf.InvalidProtocolBufferException; | ||
| import org.h2.mvstore.DataUtils; | ||
| import org.h2.mvstore.WriteBuffer; | ||
| import org.h2.mvstore.type.DataType; | ||
| import org.h2.util.Utils; | ||
| import org.monarchinitiative.exomiser.core.proto.AlleleProto; | ||
| import com.google.protobuf.Parser; | ||
| import org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar; | ||
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| import java.nio.ByteBuffer; | ||
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| public class ClinVarDataType extends ProtobufDataType<ClinVar> { | ||
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| public enum ClinVarDataType implements DataType { | ||
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| INSTANCE; | ||
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| @Override | ||
| public int compare(Object a, Object b) { | ||
| return -1; | ||
| } | ||
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| @Override | ||
| public int getMemory(Object obj) { | ||
| AlleleProto.ClinVar clinVar = (AlleleProto.ClinVar) obj; | ||
| return clinVar.getSerializedSize(); | ||
| } | ||
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| @Override | ||
| public void read(ByteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| obj[i] = read(buff); | ||
| } | ||
| } | ||
| public static final ClinVarDataType INSTANCE = new ClinVarDataType(); | ||
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| @Override | ||
| public AlleleProto.ClinVar read(ByteBuffer buff) { | ||
| int len = DataUtils.readVarInt(buff); | ||
| byte[] data = Utils.newBytes(len); | ||
| buff.get(data); | ||
| try { | ||
| return AlleleProto.ClinVar.parseFrom(data); | ||
| } catch (InvalidProtocolBufferException e) { | ||
| throw new InvalidAlleleProtoException(e); | ||
| public int compare(ClinVar a, ClinVar b) { | ||
| if (a.equals(b)) { | ||
| return 0; | ||
| } | ||
| throw new UnsupportedOperationException("Unable to compare " + a + " with " + b); | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object[] obj, int len, boolean key) { | ||
| for (int i = 0; i < len; i++) { | ||
| write(buff, obj[i]); | ||
| } | ||
| public ClinVar[] createStorage(int size) { | ||
| return new ClinVar[size]; | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, Object obj) { | ||
| AlleleProto.ClinVar clinVar = (AlleleProto.ClinVar) obj; | ||
| byte[] data = clinVar.toByteArray(); | ||
| buff.putVarInt(data.length).put(data); | ||
| public Parser<ClinVar> messageParser() { | ||
| return ClinVar.parser(); | ||
| } | ||
| } |
40 changes: 40 additions & 0 deletions
40
...ain/java/org/monarchinitiative/exomiser/core/genome/dao/serialisers/ProtobufDataType.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| package org.monarchinitiative.exomiser.core.genome.dao.serialisers; | ||
|
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| import com.google.protobuf.InvalidProtocolBufferException; | ||
| import com.google.protobuf.Message; | ||
| import com.google.protobuf.Parser; | ||
| import org.h2.mvstore.DataUtils; | ||
| import org.h2.mvstore.WriteBuffer; | ||
| import org.h2.mvstore.type.BasicDataType; | ||
| import org.h2.util.Utils; | ||
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| import java.nio.ByteBuffer; | ||
|
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| public abstract class ProtobufDataType<T extends Message> extends BasicDataType<T> { | ||
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| @Override | ||
| public int getMemory(T obj) { | ||
| return obj.getSerializedSize(); | ||
| } | ||
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| @Override | ||
| public void write(WriteBuffer buff, T obj) { | ||
| byte[] data = obj.toByteArray(); | ||
| buff.putVarInt(data.length).put(data); | ||
| } | ||
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| @Override | ||
| public T read(ByteBuffer buff) { | ||
| int len = DataUtils.readVarInt(buff); | ||
| byte[] data = Utils.newBytes(len); | ||
| buff.get(data); | ||
| try { | ||
| return messageParser().parseFrom(data); | ||
| } catch (InvalidProtocolBufferException e) { | ||
| throw new InvalidAlleleProtoException(e); | ||
| } | ||
| } | ||
|
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| public abstract Parser<T> messageParser(); | ||
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| } |
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