Merge branch 'main' into feature/SNRK-70/dependecy-graph
This commit is contained in:
commit
cfe0f0740f
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package space.kscience.snark.storage.local
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import space.kscience.snark.storage.Directory
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import space.kscience.snark.storage.FileReader
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import space.kscience.snark.storage.FileWriter
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import java.nio.file.Path
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import kotlin.io.path.*
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public fun localStorage(rootPath: Path): Directory {
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return LocalDirectory(rootPath)
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}
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private class LocalFile(private val path: Path) : FileReader, FileWriter {
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override fun close() {}
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override suspend fun readAll(): ByteArray = path.readBytes()
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override suspend fun write(bytes: ByteArray) = path.writeBytes(bytes)
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}
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private class LocalDirectory(private val path: Path) : Directory {
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private fun child(child: String): Path = path / child
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private fun child(child: Path): Path = path / child
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override fun close() {}
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override suspend fun get(filename: String): FileReader = LocalFile(child(filename))
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override suspend fun create(filename: String, ignoreIfExists: Boolean) {
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try {
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child(filename).createFile()
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} catch (ex: FileAlreadyExistsException) {
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if (!ignoreIfExists) {
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throw ex
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}
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}
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}
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override suspend fun put(filename: String): FileWriter = LocalFile(child(filename))
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override suspend fun getSubdir(path: Path): Directory = LocalDirectory(child(path))
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override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory {
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val dir = child(dirname)
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try {
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dir.createDirectory()
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} catch (ex: FileAlreadyExistsException) {
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if (!ignoreIfExists) {
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throw ex
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}
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}
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return LocalDirectory(dir)
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}
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}
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@ -1,35 +0,0 @@
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package space.kscience.snark.storage.local
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import space.kscience.snark.storage.Directory
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import space.kscience.snark.storage.FileReader
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import space.kscience.snark.storage.FileWriter
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import java.io.File
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import java.nio.file.Path
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public class LocalFile(private val path: String) : FileReader, FileWriter {
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override fun close() {}
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override suspend fun readAll(): ByteArray = File(this.path).readBytes()
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override suspend fun write(bytes: ByteArray) = File(this.path).writeBytes(bytes)
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}
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public class LocalDirectory(private val path: String) : Directory {
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override fun close() {}
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override suspend fun get(filename: String): FileReader = LocalFile("${this.path}/$filename")
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override suspend fun create(filename: String, ignoreIfExists: Boolean) {
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if (!File(filename).createNewFile() && !ignoreIfExists) {
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throw UnsupportedOperationException("File already exists")
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}
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}
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override suspend fun put(filename: String): FileWriter = LocalFile("${this.path}/$filename")
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override suspend fun getSubdir(dirpath: Path): Directory = LocalDirectory("${this.path}/$dirpath")
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override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory {
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if (!File(dirname).mkdir() && !ignoreIfExists) {
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throw UnsupportedOperationException("File already exists")
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}
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return this.getSubdir(File(dirname).toPath())
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}
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}
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package space.kscience.snark.storage.s3
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import aws.sdk.kotlin.services.s3.S3Client
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import space.kscience.snark.storage.Directory
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import space.kscience.snark.storage.FileReader
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import space.kscience.snark.storage.FileWriter
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import java.nio.file.Path
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import kotlin.io.path.*
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internal class S3Directory(
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private val client: S3Client,
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private val bucketName: String,
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private val currentDir: Path,
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) : Directory {
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override suspend fun get(filename: String): FileReader =
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S3FileReader(client, bucketName, currentDir / filename)
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override suspend fun create(filename: String, ignoreIfExists: Boolean) {
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if (!ignoreIfExists) {
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TODO("could not check if file exists")
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}
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}
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override suspend fun put(filename: String): FileWriter =
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S3FileWriter(client, bucketName, currentDir / filename)
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override suspend fun getSubdir(path: Path): S3Directory =
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S3Directory(client, bucketName, currentDir / path)
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override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): S3Directory =
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if (!ignoreIfExists) {
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TODO("could not check if directory exists")
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} else {
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S3Directory(client, bucketName, currentDir / dirname)
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}
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override fun close() {
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}
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}
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package space.kscience.snark.storage.s3
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import aws.sdk.kotlin.services.s3.S3Client
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import aws.sdk.kotlin.services.s3.model.GetObjectRequest
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import aws.sdk.kotlin.services.s3.putObject
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import aws.smithy.kotlin.runtime.content.ByteStream
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import aws.smithy.kotlin.runtime.content.toByteArray
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import space.kscience.snark.storage.FileReader
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import space.kscience.snark.storage.FileWriter
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import java.nio.file.Path
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import kotlin.io.path.*
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internal class S3FileReader(private val client: S3Client, private val bucketName: String, private val path: Path) : FileReader {
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override suspend fun readAll(): ByteArray {
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val result = client.getObject(GetObjectRequest{
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bucket = bucketName
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key = path.toString()
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}) {
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it.body?.toByteArray() ?: ByteArray(0)
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}
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return result
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}
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override fun close() {
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}
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}
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internal class S3FileWriter(private val client: S3Client, private val bucketName: String, private val path: Path) : FileWriter {
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override suspend fun write(bytes: ByteArray) {
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client.putObject {
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bucket = bucketName
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key = path.toString()
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body = ByteStream.fromBytes(bytes)
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}
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}
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override fun close() {
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}
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}
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package space.kscience.snark.storage.s3
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import aws.sdk.kotlin.services.s3.*
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import space.kscience.snark.storage.Directory
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import space.kscience.snark.storage.FileReader
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import space.kscience.snark.storage.FileWriter
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import java.lang.Exception
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import java.nio.file.Path
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import kotlin.io.path.*
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public fun s3Storage(client: S3Client): Directory =
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S3Root(client)
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public fun s3Bucket(client: S3Client, bucket: String): Directory =
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S3Directory(client, bucket, Path(""))
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internal fun splitPathIntoBucketAndPath(path: Path): Pair<String, Path> {
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val bucket = path.getName(0)
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val filePath = path.relativize(bucket)
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return Pair(bucket.toString(), filePath)
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}
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internal class S3Root(private val client: S3Client) : Directory {
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override suspend fun get(filename: String): FileReader {
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throw NoSuchFileException(Path(filename).toFile())
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}
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override suspend fun create(filename: String, ignoreIfExists: Boolean) {
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throw NoSuchFileException(Path(filename).toFile())
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}
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override suspend fun put(filename: String): FileWriter {
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throw NoSuchFileException(Path(filename).toFile())
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}
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override suspend fun getSubdir(path: Path): Directory = try {
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val (bucketName, filePath) = splitPathIntoBucketAndPath(path)
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client.headBucket {
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bucket = bucketName
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}
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S3Directory(client, bucketName, filePath)
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} catch (ex: Exception) {
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throw AccessDeniedException(path.toFile(), reason = ex.message)
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}
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override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = try {
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val (bucketName, filePath) = splitPathIntoBucketAndPath(Path(dirname))
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client.createBucket {
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bucket = bucketName
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}
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S3Directory(client, bucketName, filePath)
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} catch (ex: Exception) {
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throw AccessDeniedException(Path(dirname).toFile(), reason = ex.message)
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}
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override fun close() {
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}
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}
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@ -0,0 +1,24 @@
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package space.kscience.snark.storage.unzip
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import space.kscience.snark.storage.Directory
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import java.io.FileInputStream
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import java.util.zip.ZipInputStream
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public suspend fun unzip(source_path: String, target: Directory) {
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val zis = ZipInputStream(FileInputStream(source_path))
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var zipEntry = zis.nextEntry
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while (zipEntry != null) {
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if (!zipEntry.isDirectory) {
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val filename = zipEntry.name
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target.create(filename, true)
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val fos = target.put(filename)
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val buffer = ByteArray(zipEntry.size.toInt())
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zis.read(buffer)
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fos.write(buffer)
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fos.close()
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}
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zipEntry = zis.nextEntry
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}
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zis.closeEntry()
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zis.close()
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}
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