Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Replace toPath().toString() with getURIString() #1719

Merged
merged 2 commits into from
Oct 7, 2024
Merged

Replace toPath().toString() with getURIString() #1719

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
de2ec4c
Use full path with scheme in beta VCFDecoder
lbergelson Oct 4, 2024
58d48b6
Refactor optional handling for clarity
lbergelson Oct 4, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 9 additions & 13 deletions src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,10 @@
import htsjdk.variant.vcf.VCFHeader;

import java.io.IOException;
import java.nio.channels.SeekableByteChannel;
import java.util.List;
import java.util.Optional;
import java.util.function.Function;

/**
* InternalAPII
Expand Down Expand Up @@ -197,7 +199,7 @@ private static FeatureReader<VariantContext> getVCFReader(
"The provided %s resource (%s) must be a readable/input resource",
BundleResourceType.CT_VARIANT_CONTEXTS,
variantsResource));
} else if (!variantsResource.getIOPath().isPresent()) {
} else if (variantsResource.getIOPath().isEmpty()) {
throw new HtsjdkUnsupportedOperationException("VCF reader from stream not implemented");
}
final IOPath variantsIOPath = variantsResource.getIOPath().get();
Expand All @@ -206,25 +208,19 @@ private static FeatureReader<VariantContext> getVCFReader(
//TODO: this resolves the index automatically. it should check to make sure the provided index
// matches the one that is automatically resolved, otherwise throw since the request will not be honored
return AbstractFeatureReader.getFeatureReader(
variantsIOPath.toPath().toString(),
indexIOPath.isPresent() ?
indexIOPath.get().toPath().toString() :
null,
variantsIOPath.getURIString(),
indexIOPath.map(IOPath::getURIString).orElse(null),
vcfCodec,
indexIOPath.isPresent(),
decoderOptions.getVariantsChannelTransformer().isPresent() ?
decoderOptions.getVariantsChannelTransformer().get() :
null,
decoderOptions.getIndexChannelTransformer().isPresent() ?
decoderOptions.getIndexChannelTransformer().get() :
null
decoderOptions.getVariantsChannelTransformer().orElse(null),
decoderOptions.getIndexChannelTransformer().orElse(null)
);
}

// the underlying readers can't handle index streams, so for now we can only handle IOPaths
private static Optional<IOPath> getIndexIOPath(final Bundle inputBundle) {
final Optional<BundleResource> optIndexResource = inputBundle.get(BundleResourceType.CT_VARIANTS_INDEX);
if (!optIndexResource.isPresent()) {
if (optIndexResource.isEmpty()) {
return Optional.empty();
}
final BundleResource indexResource = optIndexResource.get();
Expand All @@ -234,7 +230,7 @@ private static Optional<IOPath> getIndexIOPath(final Bundle inputBundle) {
BundleResourceType.CT_VARIANTS_INDEX,
indexResource));
}
if (!indexResource.getIOPath().isPresent()) {
if (indexResource.getIOPath().isEmpty()) {
throw new HtsjdkUnsupportedOperationException("Reading a VCF index from a stream not implemented");
}
return indexResource.getIOPath();
Expand Down
24 changes: 23 additions & 1 deletion src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
package htsjdk.beta.codecs.variants.vcf;

import com.google.common.jimfs.Configuration;
import com.google.common.jimfs.Jimfs;
import com.google.common.jimfs.SystemJimfsFileSystemProvider;
import htsjdk.HtsjdkTest;
import htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2;
import htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3;
Expand All @@ -26,6 +29,7 @@
import htsjdk.beta.plugin.variants.VariantsEncoder;
import htsjdk.beta.plugin.variants.VariantsFormats;
import htsjdk.samtools.util.IOUtil;
import htsjdk.tribble.TestUtils;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFHeader;
import org.testng.Assert;
Expand All @@ -36,6 +40,9 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.FileSystem;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collections;
import java.util.function.Function;
Expand All @@ -60,11 +67,26 @@ private Object[][] vcfReadWriteTests() {
};
}

@Test
public void testRoundTripNio() throws IOException {
try(FileSystem fs = Jimfs.newFileSystem("test", Configuration.unix())){
final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");
Path tribbleFileInJimfs = TestUtils.getTribbleFileInJimfs(TEST_VCF_WITH_INDEX.getRawInputString(), TEST_VCF_INDEX.getRawInputString(), fs);
HtsPath vcf = new HtsPath(tribbleFileInJimfs.toUri().toString());
checkCodecAndReadWriteVcf( vcf , VCFCodecV4_0.VCF_V40_VERSION , outputPath);
}
}

@Test(dataProvider = "vcfReadWriteTests")
public void testRoundTripVCFThroughPath(final IOPath inputPath, final HtsVersion expectedCodecVersion) {
final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");

checkCodecAndReadWriteVcf(inputPath, expectedCodecVersion, outputPath);
}

private void checkCodecAndReadWriteVcf(IOPath inputPath, HtsVersion expectedCodecVersion, IOPath outputPath) {
// some test files require "AllowMissingFields" options for writing
final VariantsEncoderOptions variantsEncoderOptions = new VariantsEncoderOptions().setAllowFieldsMissingFromHeader(true);
final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");

try (final VariantsDecoder variantsDecoder = HtsDefaultRegistry.getVariantsResolver().getVariantsDecoder(inputPath);
final VariantsEncoder variantsEncoder = HtsDefaultRegistry.getVariantsResolver().getVariantsEncoder(
Expand Down
Loading