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Update based on GATK usage and rebase.
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@cmnbroad
cmnbroad committed Aug 19, 2024
1 parent cced91e commit b01d2e5
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45 changes: 44 additions & 1 deletion src/main/java/htsjdk/beta/io/IOPathUtils.java
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Expand Up @@ -3,14 +3,16 @@
import htsjdk.beta.exception.HtsjdkIOException;
import htsjdk.io.HtsPath;
import htsjdk.io.IOPath;
import htsjdk.utils.ValidationUtils;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Optional;
import java.util.function.Function;

public class IOPathUtils {

Expand Down Expand Up @@ -69,4 +71,45 @@ public static void writeStringToPath(final IOPath ioPath, final String contents)
e);
}
}

/**
* Takes an IOPath and returns a new IOPath object that keeps the same basename as the original but has
* a new extension. If append is set to false, only the last component of an extension will be replaced.
* e.g. "my.fasta.gz" -> "my.fasta.tmp"
*
* If the input IOPath was created from a rawInputString that specifies a relative local path, the new path will
* have a rawInputString that specifies an absolute path.
*
* Examples:
* - (test_na12878.bam, .bai) -> test_na12878.bai (append = false)
* - (test_na12878.bam, .md5) -> test_na12878.bam.md5 (append = true)
*
* @param path The original path
* @param newExtension A new file extension. Must include the leading dot e.g. ".txt", ".bam"
* @param append If set to true, append the new extension to the original basename. If false, replace the original extension
* with the new extension. If append = false and the original name has no extension, an exception will be thrown.
* @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type <T>
* @return A new IOPath object with the new extension
*/
public static <T extends IOPath> T replaceExtension(
final IOPath path,
final String newExtension,
final boolean append,
final Function<String, T> ioPathConstructor){
ValidationUtils.validateArg(newExtension.startsWith("."), "newExtension must start with a dot '.'");

final String oldFileName = path.toPath().getFileName().toString();

String newFileName;
if (append){
newFileName = oldFileName + newExtension;
} else {
final Optional<String> oldExtension = path.getExtension();
if (oldExtension.isEmpty()){
throw new RuntimeException("The original path must have an extension when append = false: " + path.getURIString());
}
newFileName = oldFileName.replaceAll(oldExtension.get() + "$", newExtension);
}
return ioPathConstructor.apply(path.toPath().resolveSibling(newFileName).toUri().toString());
}
}
3 changes: 3 additions & 0 deletions src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
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Expand Up @@ -46,6 +46,9 @@ public class BundleJSON {
* @throws IllegalArgumentException if any resource in bundle is not an IOPathResources.
*/
public static String toJSON(final Bundle bundle) {
ValidationUtils.validateArg(
!bundle.getPrimaryContentType().equals(JSON_PROPERTY_PRIMARY),
"Primary content type cannot be named 'primary'");
final JSONObject outerJSON = new JSONObject()
.put(JSON_PROPERTY_SCHEMA_NAME, JSON_SCHEMA_NAME)
.put(JSON_PROPERTY_SCHEMA_VERSION, JSON_SCHEMA_VERSION)
Expand Down
115 changes: 58 additions & 57 deletions src/main/java/htsjdk/beta/plugin/variants/VariantsBundle.java
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Expand Up @@ -4,17 +4,14 @@
import htsjdk.beta.io.bundle.*;
import htsjdk.io.HtsPath;
import htsjdk.io.IOPath;
import htsjdk.samtools.SamFiles;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Tuple;
import htsjdk.utils.ValidationUtils;

import java.io.Serializable;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collection;
import java.util.Optional;
import java.nio.file.Files;
import java.util.*;
import java.util.function.Function;

/**
Expand All @@ -26,57 +23,51 @@
* Note that this class is merely a convenience class for the case where the variants are backed by files on disk.
* A bundle that contains variants and related resources can be created manually using the {@link Bundle} class.
* This class provides convenient constructors, and validation for JSON interconversions. To create a VariantsBundle
* for variants sources that are backed by streams or otherv{@link BundleResource} types, the {@link Bundle} and
* for variants sources that are backed by streams or other {@link BundleResource} types, the {@link Bundle} and
* {@link BundleBuilder} classes can be used to construct such bundles directly.
*
* @param <T> The type to use when creating a new IOPathResource for a {@link htsjdk.beta.plugin.variants.VariantsBundle}.
* Note that any resources that are manually inserted into a {@link htsjdk.beta.plugin.variants.VariantsBundle}
* using the {@link #VariantsBundle(Collection)} constructor may have IOPathResources that do not conform to
* this type.
*/
public class VariantsBundle<T extends IOPath> extends Bundle implements Serializable {
public class VariantsBundle extends Bundle implements Serializable {
private static final long serialVersionUID = 1L;
private static final Log LOG = Log.getInstance(htsjdk.beta.plugin.variants.VariantsBundle.class);

private static final Log LOG = Log.getInstance(VariantsBundle.class);
/**
* Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing only a variants resource.
*
* @param vcfPath An {@link IOPath}-derived object that represents a source of variants.
*/
public VariantsBundle(final T vcfPath) {
this(Arrays.asList(toInputResource(
BundleResourceType.VARIANT_CONTEXTS,
ValidationUtils.nonNull(vcfPath, BundleResourceType.VARIANTS_VCF))));
public VariantsBundle(final IOPath vcfPath) {
this(Arrays.asList(
new IOPathResource(
ValidationUtils.nonNull(vcfPath, "IOPath must not be null"),
BundleResourceType.VARIANT_CONTEXTS)));
}

/**
* Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing only variants and an index.
*
* @param vcfPath An {@link IOPath}-derived object that represents a source of variants.
* @param indexPath An {@link IOPath}-derived object that represents the companion index for {@code vcfPath}.
*/
public VariantsBundle(final T vcfPath, final T indexPath) {
public VariantsBundle(final IOPath vcfPath, final IOPath indexPath) {
this(Arrays.asList(
toInputResource(BundleResourceType.VARIANT_CONTEXTS,
ValidationUtils.nonNull(vcfPath, BundleResourceType.VARIANTS_VCF)),
toInputResource(
BundleResourceType.VARIANTS_INDEX,
ValidationUtils.nonNull(indexPath, BundleResourceType.VARIANTS_INDEX))));
new IOPathResource(
ValidationUtils.nonNull(vcfPath, "IOPath must not be null"),
BundleResourceType.VARIANT_CONTEXTS),
new IOPathResource(ValidationUtils.nonNull(
indexPath, "IOPath must not be null"),
BundleResourceType.VARIANTS_INDEX)));
}

/**
* Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} using the resources in an existing bundle. A
* resource with content type {@link BundleResourceType#VARIANTS_VCF} must be present in the resources, or
* this constructor will throw.
*
* Note that this constructor allows existing {@link IOPathResource}s that do not conform to the type
* {@link T} to be included in the resulting {@link htsjdk.beta.plugin.variants.VariantsBundle}.
*
* @param resources collection of {@link BundleResource}. the collection must include a resource with
* content type {@link BundleResourceType#VARIANTS_VCF}.
* @throws IllegalArgumentException if no resource with content type {@link BundleResourceType#VARIANTS_VCF} is
* included in the input {@link BundleResource} collection
*/
protected VariantsBundle(final Collection<BundleResource> resources) {
public VariantsBundle(final Collection<BundleResource> resources) {
super(BundleResourceType.VARIANT_CONTEXTS, resources);
}

Expand All @@ -93,7 +84,7 @@ public BundleResource getVariants() {
* Get the optional {@link BundleResourceType#VARIANTS_INDEX} resource for this {@link htsjdk.beta.plugin.variants.VariantsBundle}.
*
* @return the optional {@link BundleResourceType#VARIANTS_INDEX} resrouce for this {@link htsjdk.beta.plugin.variants.VariantsBundle},
* or Optional.empty if no index resource is present in the bundle.
* or Optional.empty() if no index resource is present in the bundle.
*/
public Optional<BundleResource> getIndex() {
return get(BundleResourceType.VARIANTS_INDEX);
Expand All @@ -106,33 +97,47 @@ public Optional<BundleResource> getIndex() {
* must contain a resource with content type VARIANT_CONTEXTS.
* @return a {@link VariantsBundle} created from jsonPath
*/
public static VariantsBundle<IOPath> getVariantsBundleFromPath(final IOPath jsonPath) {
public static VariantsBundle getVariantsBundleFromPath(final IOPath jsonPath) {
return getVariantsBundleFromString(IOPathUtils.getStringFromPath(jsonPath));
}

/**
* Create a {@link VariantsBundle} from a JSON string contained in jsonPath.
*
* @param <T> the IOPath-derived type of the IOPathResources to be used in the new bundle
* @param jsonPath the path to a file that contains a {@link Bundle} serialized to JSON. The bundle
* must contain a resource with content type VARIANT_CONTEXTS.
* @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type {@code T}
* @return a {@link VariantsBundle} created from jsonPath
*/
public static <T extends IOPath> VariantsBundle getVariantsBundleFromPath(final IOPath jsonPath,
final Function<String, T> ioPathConstructor) {
return getVariantsBundleFromString(IOPathUtils.getStringFromPath(jsonPath), ioPathConstructor);
}

/**
* Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} from a JSON string.
*
* @param jsonString the jsonString to use to create the {@link htsjdk.beta.plugin.variants.VariantsBundle}
* @return a {@link htsjdk.beta.plugin.variants.VariantsBundle}
*/
public static VariantsBundle<IOPath> getVariantsBundleFromString(final String jsonString) {
public static VariantsBundle getVariantsBundleFromString(final String jsonString) {
return getVariantsBundleFromString(jsonString, HtsPath::new);
}

/**
* Create a {@link htsjdk.beta.plugin.variants.VariantsBundle} from a JSON string with all IOPathResources using
* an IOPath-derived class of type {@code T}.
*
* @param <T> the IOPath-derived type of the IOPathResources to be used in the new bundle
* @param jsonString the string to use to create the {@link htsjdk.beta.plugin.variants.VariantsBundle}
* @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type {@code T}
* @param <T> the type of
* @return a newly created {@link htsjdk.beta.plugin.variants.VariantsBundle}
*/
public static <T extends IOPath> VariantsBundle<T> getVariantsBundleFromString(
public static <T extends IOPath> VariantsBundle getVariantsBundleFromString(
final String jsonString,
final Function<String, T> ioPathConstructor) {
return new VariantsBundle<>(BundleJSON.toBundle(jsonString, ioPathConstructor).getResources());
return new VariantsBundle(BundleJSON.toBundle(jsonString, ioPathConstructor).getResources());
}

/**
Expand All @@ -143,39 +148,36 @@ public static <T extends IOPath> VariantsBundle<T> getVariantsBundleFromString(
* @return a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing variants and companion index, if it can
* be found.
*/
public static VariantsBundle<IOPath> resolveIndex(final IOPath variants) {
public static Optional<IOPath> resolveIndex(final IOPath variants) {
return resolveIndex(variants, HtsPath::new);
}

/**
* Find the companion index for a variants source, and create a new {@link htsjdk.beta.plugin.variants.VariantsBundle} containing the
* variants and the companion index, if one can be found.
* Attempts to find the companion index for a variants source based on commonly used file extensions, and
* create a new {@link htsjdk.beta.plugin.variants.VariantsBundle} containing the variants and the companion
* index, if one can be found.
*
* An index can only be resolved for an IOPath that represents on a file system for which an NIO
* An index can only be resolved for an IOPath that represents a file on a file system for which an NIO
* provider is installed. Remote paths that use a protocol scheme for which no NIO file system is
* available will (silently) not be resolved.
*
* @param variants the variants source to use
* @param <T> the IOPath-derived type of the IOPath to be returned
* @param variantsHtsPath the IOPath-derived object representing the variants source to use
* @param ioPathConstructor a function that takes a string and returns an IOPath-derived class of type <T>
* @param <T> the IOPath-derived type of the IOPathResources in the new bundle
* @return a {@link htsjdk.beta.plugin.variants.VariantsBundle} containing variants and companion index, if it can be found
* @return a {@link IOPath}-derived object of type T containing the companion index for {@code variantsPath},
* if it can be found
*/
public static <T extends IOPath> VariantsBundle<T> resolveIndex(
final T variants,
public static <T extends IOPath> Optional<T> resolveIndex(
final T variantsHtsPath,
final Function<String, T> ioPathConstructor) {
if (variants.hasFileSystemProvider()) {
final Path index = SamFiles.findIndex(variants.toPath());
if (index == null) {
return new VariantsBundle<>(variants);
} else {
return new VariantsBundle<T>(variants, ioPathConstructor.apply(index.toUri().toString()));
final Set<String> indexExtensions = Set.of(FileExtensions.TRIBBLE_INDEX, FileExtensions.TABIX_INDEX);
for (final String extension : indexExtensions) {
final T putativeIndexPath = IOPathUtils.replaceExtension(variantsHtsPath, extension, true, ioPathConstructor);
if (Files.exists(putativeIndexPath.toPath())) {
return Optional.of(putativeIndexPath);
}
}
return new VariantsBundle<>(variants);
}

public static boolean looksLikeAVariantsBundle(final IOPath rawVCFPath) {
return rawVCFPath.getURI().getPath().endsWith(BundleJSON.BUNDLE_EXTENSION);
return Optional.empty();
}

private static <T extends IOPath> IOPathResource toInputResource(final String providedContentType, final T ioPath) {
Expand Down Expand Up @@ -206,12 +208,11 @@ private static <T extends IOPath> Optional<Tuple<String, String>> getInferredCon
if (extension.isPresent()) {
final String ext = extension.get();
if (ext.equals(FileExtensions.VCF)) {
return Optional.of(new Tuple<>(BundleResourceType.VARIANT_CONTEXTS, BundleResourceType.VARIANTS_VCF));
return Optional.of(new Tuple<>(BundleResourceType.VARIANT_CONTEXTS, "VCF"));
} else if (ext.equals(FileExtensions.COMPRESSED_VCF)) {
return Optional.of(new Tuple<>(BundleResourceType.VARIANT_CONTEXTS, BundleResourceType.VARIANTS_VCF));
return Optional.of(new Tuple<>(BundleResourceType.VARIANT_CONTEXTSS, "VCF"));
} //TODO...finish this
}
return Optional.empty();
}

}
8 changes: 8 additions & 0 deletions src/main/java/htsjdk/io/IOPath.java
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Expand Up @@ -77,6 +77,14 @@ default String getScheme() {
return getURI().getScheme();
}

// default String resolveSibling(final String sibling) {
// return getSiblingPath(sibling).toString();
// }
//
// default String getSiblingPath(final String sibling) {
// return toPath().resolveSibling(sibling).toString();
// }

/**
* @return an {@link Optional} containing the extension of the last component of the hierarchical part of the
* scheme-specific part of the URI, if any, including the ".", or Optional.empty() if the hierarchical name ends
Expand Down
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