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Description: a few changes to calls to JsonFormat methods have to be changed
when building against protobuf-java-format 1.3 instead of 1.2
Author: Pierre Gruet <pgt@debian.org>
Forwarded: https://github.com/GenomicsDB/GenomicsDB/issues/229
Last-Update: 2022-07-26
--- a/src/main/java/org/genomicsdb/importer/extensions/JsonFileExtensions.java
+++ b/src/main/java/org/genomicsdb/importer/extensions/JsonFileExtensions.java
@@ -35,7 +35,7 @@
*/
default File dumpTemporaryLoaderJSONFile(final GenomicsDBImportConfiguration.ImportConfiguration importConfiguration,
final String filename) throws IOException {
- String loaderJSONString = JsonFormat.printToString(importConfiguration);
+ String loaderJSONString = new JsonFormat().printToString(importConfiguration);
File tempLoaderJSONFile = (filename.isEmpty()) ?
File.createTempFile("loader_", ".json") :
@@ -61,7 +61,7 @@
default void writeCallsetMapJSONFile(final String outputCallsetMapJSONFilePath,
final GenomicsDBCallsetsMapProto.CallsetMappingPB callsetMappingPB)
{
- String callsetMapJSONString = printToString(callsetMappingPB);
+ String callsetMapJSONString = new JsonFormat().printToString(callsetMappingPB);
if (GenomicsDBUtils.writeToFile(outputCallsetMapJSONFilePath, callsetMapJSONString) != 0) {
throw new GenomicsDBException(String.format("Could not write callset map json file : %s", outputCallsetMapJSONFilePath));
}
@@ -79,7 +79,7 @@
default void writeVidMapJSONFile(final String outputVidMapJSONFilePath,
final GenomicsDBVidMapProto.VidMappingPB vidMappingPB)
{
- String vidMapJSONString = printToString(vidMappingPB);
+ String vidMapJSONString = new JsonFormat().printToString(vidMappingPB);
if (GenomicsDBUtils.writeToFile(outputVidMapJSONFilePath, vidMapJSONString) != 0) {
throw new GenomicsDBException(String.format("Could not write vid map json file : %s", outputVidMapJSONFilePath));
}
@@ -124,7 +124,12 @@
String existingVidJson = GenomicsDBUtils.readEntireFile(vidFile);
GenomicsDBVidMapProto.VidMappingPB.Builder vidMapBuilder =
GenomicsDBVidMapProto.VidMappingPB.newBuilder();
- merge(existingVidJson, vidMapBuilder);
+ try {
+ new JsonFormat().merge(new ByteArrayInputStream(existingVidJson.getBytes()), vidMapBuilder);
+ } catch (IOException e) {
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
return vidMapBuilder.build();
}
@@ -157,7 +162,12 @@
static String getProtobufAsBase64StringFromFile(Message.Builder builder,
String file) throws com.googlecode.protobuf.format.JsonFormat.ParseException {
String jsonString = GenomicsDBUtils.readEntireFile(file);
- JsonFormat.merge(jsonString, builder);
+ try {
+ new JsonFormat().merge(new ByteArrayInputStream(jsonString.getBytes()), builder);
+ } catch (IOException e) {
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
byte[] pb = builder.build().toByteArray();
return Base64.getEncoder().encodeToString(pb);
}
--- a/src/main/java/org/genomicsdb/importer/extensions/CallSetMapExtensions.java
+++ b/src/main/java/org/genomicsdb/importer/extensions/CallSetMapExtensions.java
@@ -1,5 +1,6 @@
package org.genomicsdb.importer.extensions;
+import com.googlecode.protobuf.format.JsonFormat;
import htsjdk.tribble.FeatureReader;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeader;
@@ -7,6 +8,8 @@
import org.genomicsdb.GenomicsDBUtils;
import org.genomicsdb.exception.GenomicsDBException;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
import java.net.URI;
import java.util.*;
@@ -232,7 +235,12 @@
GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder callsetMapBuilder =
newCallsetMapPB.toBuilder();
checkDuplicateCallsetsForIncrementalImport(existingCallsetsJSON, inputSampleNameToPath);
- merge(existingCallsetsJSON, callsetMapBuilder);
+ try {
+ new JsonFormat().merge(new ByteArrayInputStream(existingCallsetsJSON.getBytes()), callsetMapBuilder);
+ } catch (IOException e) {
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
return callsetMapBuilder.build();
}
@@ -253,7 +261,12 @@
// iterate through the existing callset
GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder callsetMapBuilder =
GenomicsDBCallsetsMapProto.CallsetMappingPB.newBuilder();
- merge(existingCallsetsJSON, callsetMapBuilder);
+ try {
+ new JsonFormat().merge(new ByteArrayInputStream(existingCallsetsJSON.getBytes()), callsetMapBuilder);
+ } catch (IOException e) {
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
GenomicsDBCallsetsMapProto.CallsetMappingPB existingCallsetsPB = callsetMapBuilder.build();
int callsetsCount = existingCallsetsPB.getCallsetsCount();
for (int i=0; i<callsetsCount; i++) {
--- a/example/java/TestGenomicsDB.java
+++ b/example/java/TestGenomicsDB.java
@@ -39,6 +39,7 @@
import org.genomicsdb.model.GenomicsDBExportConfiguration;
import org.genomicsdb.reader.GenomicsDBFeatureReader;
+import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
@@ -55,7 +56,12 @@
private static GenomicsDBExportConfiguration.ExportConfiguration resolveExportConfigurationFromJsonString(String jsonString) throws JsonFormat.ParseException {
GenomicsDBExportConfiguration.ExportConfiguration.Builder exportConfigurationBuilder =
GenomicsDBExportConfiguration.ExportConfiguration.newBuilder();
- JsonFormat.merge(jsonString, exportConfigurationBuilder);
+ try {
+ new JsonFormat().merge(new ByteArrayInputStream(jsonString.getBytes()), exportConfigurationBuilder);
+ } catch(IOException e) {
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
return exportConfigurationBuilder.build();
}
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