From a97a99d138cc36e433f00050c67b80e4aff259f9 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 17 Apr 2023 17:28:34 +0300
Subject: [PATCH 01/15] SNRK-48: Add s3 implementation

Use common s3 api and '/'-separated keys to simulate directories
---
 .../kscience/snark/storage/s3/Directory.kt    | 41 +++++++++++++++++
 .../space/kscience/snark/storage/s3/File.kt   | 38 +++++++++++++++
 .../space/kscience/snark/storage/s3/Root.kt   | 46 +++++++++++++++++++
 3 files changed, 125 insertions(+)
 create mode 100644 snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt
 create mode 100644 snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt
 create mode 100644 snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt
new file mode 100644
index 0000000..27ece3b
--- /dev/null
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt
@@ -0,0 +1,41 @@
+package space.kscience.snark.storage.s3
+
+import aws.sdk.kotlin.services.s3.S3Client
+import space.kscience.snark.storage.Directory as Dir
+import space.kscience.snark.storage.FileReader
+import space.kscience.snark.storage.FileWriter
+import java.nio.file.Path
+
+public class Directory(
+    private val client: S3Client,
+    private val bucketName: String,
+    private val currentDir: String,
+) : Dir {
+    override suspend fun get(filename: String): FileReader = run {
+        S3FileReader(client, bucketName, "$currentDir/$filename")
+    }
+
+    override suspend fun create(filename: String, ignoreIfExists: Boolean) {
+        if (!ignoreIfExists) {
+            throw IllegalArgumentException("could not check if file exists")
+        }
+    }
+
+    override suspend fun put(filename: String): FileWriter = run {
+        S3FileWriter(client, bucketName, "$currentDir/$filename")
+    }
+
+    override suspend fun getSubdir(path: Path): Directory = run {
+        Directory(client, bucketName, "$currentDir/$path")
+    }
+
+    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = run {
+        if (!ignoreIfExists) {
+            throw IllegalArgumentException("could not check if directory exists")
+        }
+        Directory(client, bucketName, "$currentDir/$dirname")
+    }
+
+    override fun close() {
+    }
+}
\ No newline at end of file
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt
new file mode 100644
index 0000000..43e872f
--- /dev/null
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt
@@ -0,0 +1,38 @@
+package space.kscience.snark.storage.s3
+
+import aws.sdk.kotlin.services.s3.S3Client
+import aws.sdk.kotlin.services.s3.model.GetObjectRequest
+import aws.sdk.kotlin.services.s3.putObject
+import aws.smithy.kotlin.runtime.content.ByteStream
+import aws.smithy.kotlin.runtime.content.toByteArray
+import space.kscience.snark.storage.FileReader
+import space.kscience.snark.storage.FileWriter
+
+public class S3FileReader(private val client: S3Client, private val bucketName: String, private val fullQualifiedPath: String) : FileReader {
+    override suspend fun readAll(): ByteArray {
+        val result = client.getObject(GetObjectRequest{
+            bucket = bucketName
+            key = fullQualifiedPath
+        }) {
+            it.body?.toByteArray() ?: ByteArray(0)
+        }
+        return result
+    }
+
+    override fun close() {
+    }
+}
+
+public class S3FileWriter(private val client: S3Client, private val bucketName: String, private val fullQualifiedPath: String) : FileWriter {
+    override suspend fun write(bytes: ByteArray) {
+        client.putObject {
+            bucket = bucketName
+            key = fullQualifiedPath
+            body = ByteStream.fromBytes(bytes)
+        }
+    }
+
+    override fun close() {
+    }
+
+}
\ No newline at end of file
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt
new file mode 100644
index 0000000..de51731
--- /dev/null
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt
@@ -0,0 +1,46 @@
+package space.kscience.snark.storage.s3
+
+import aws.sdk.kotlin.services.s3.*
+import space.kscience.snark.storage.Directory as Dir
+import space.kscience.snark.storage.FileReader
+import space.kscience.snark.storage.FileWriter
+import java.io.File
+import java.lang.Exception
+import java.nio.file.Path
+
+public class Root(private val client: S3Client) : Dir {
+    override suspend fun get(filename: String): FileReader {
+        throw NoSuchFileException(File(filename))
+    }
+
+    override suspend fun create(filename: String, ignoreIfExists: Boolean) {
+        throw IllegalCallerException()
+    }
+
+    override suspend fun put(filename: String): FileWriter {
+        throw NoSuchFileException(File(filename))
+    }
+
+    override suspend fun getSubdir(path: Path): Directory = try {
+        val bucketName = path.toString()
+        client.headBucket {
+            bucket = bucketName
+        }
+        Directory(client, bucketName, "")
+    } catch (ex: Exception) {
+        throw java.nio.file.AccessDeniedException(path.toString()).initCause(ex)
+    }
+
+    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = try {
+        client.createBucket {
+            bucket = dirname
+        }
+        Directory(client, dirname, "")
+    } catch (ex: Exception) {
+        throw java.nio.file.AccessDeniedException(dirname).initCause(ex)
+    }
+
+    override fun close() {
+    }
+
+}
\ No newline at end of file

From 9651ad1cd9a7052a0dc99fe5c05fd51b89911494 Mon Sep 17 00:00:00 2001
From: Anton Belyi <anton.8938575@gmail.com>
Date: Mon, 24 Apr 2023 15:32:29 +0300
Subject: [PATCH 02/15] SNRK-60: slightly changed local driver and added unzip
 function

---
 .../snark/storage/local/localDriver.kt        | 10 ++++----
 .../kscience/snark/storage/unzip/Unzip.kt     | 24 +++++++++++++++++++
 2 files changed, 29 insertions(+), 5 deletions(-)
 create mode 100644 snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/unzip/Unzip.kt

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt
index 554faf0..04c78f2 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt
@@ -15,19 +15,19 @@ public class LocalFile(private val path: String) : FileReader, FileWriter {
 
 public class LocalDirectory(private val path: String) : Directory {
     override fun close() {}
-    override suspend fun get(filename: String): FileReader = LocalFile("${this.path}/$filename")
+    override suspend fun get(filename: String): FileReader = LocalFile("${this.path}${File.separator}$filename")
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
-        if (!File(filename).createNewFile() && !ignoreIfExists) {
+        if (!File("${this.path}${File.separator}$filename").createNewFile() && !ignoreIfExists) {
             throw UnsupportedOperationException("File already exists")
         }
     }
 
-    override suspend fun put(filename: String): FileWriter = LocalFile("${this.path}/$filename")
+    override suspend fun put(filename: String): FileWriter = LocalFile("${this.path}${File.separator}$filename")
 
-    override suspend fun getSubdir(dirpath: Path): Directory = LocalDirectory("${this.path}/$dirpath")
+    override suspend fun getSubdir(dirpath: Path): Directory = LocalDirectory("${this.path}${File.separator}$dirpath")
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory {
-        if (!File(dirname).mkdir() && !ignoreIfExists) {
+        if (!File("${this.path}${File.separator}$dirname").mkdir() && !ignoreIfExists) {
             throw UnsupportedOperationException("File already exists")
         }
         return this.getSubdir(File(dirname).toPath())
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/unzip/Unzip.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/unzip/Unzip.kt
new file mode 100644
index 0000000..e7aff9c
--- /dev/null
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/unzip/Unzip.kt
@@ -0,0 +1,24 @@
+package space.kscience.snark.storage.unzip
+
+import space.kscience.snark.storage.Directory
+import java.io.FileInputStream
+import java.util.zip.ZipInputStream
+
+public suspend fun unzip(source_path: String, target: Directory) {
+    val zis = ZipInputStream(FileInputStream(source_path))
+    var zipEntry = zis.nextEntry
+    while (zipEntry != null) {
+        if (!zipEntry.isDirectory) {
+            val filename = zipEntry.name
+            target.create(filename, true)
+            val fos = target.put(filename)
+            val buffer = ByteArray(zipEntry.size.toInt())
+            zis.read(buffer)
+            fos.write(buffer)
+            fos.close()
+        }
+        zipEntry = zis.nextEntry
+    }
+    zis.closeEntry()
+    zis.close()
+}
\ No newline at end of file

From 88510dbba80874e2dd13193220303415fadda715 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 00:27:24 +0300
Subject: [PATCH 03/15] SNRK-67: Fix pathes

---
 .../local/{localDriver.kt => LocalDriver.kt}  | 20 ++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)
 rename snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/{localDriver.kt => LocalDriver.kt} (64%)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
similarity index 64%
rename from snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt
rename to snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
index 04c78f2..bb76118 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/localDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
@@ -13,23 +13,29 @@ public class LocalFile(private val path: String) : FileReader, FileWriter {
     override suspend fun write(bytes: ByteArray) = File(this.path).writeBytes(bytes)
 }
 
-public class LocalDirectory(private val path: String) : Directory {
+public class LocalDirectory(private val root: String, private val path: String) : Directory {
+    private val current = "$root/$path"
+
+    private fun child(child: String): String = "$current/$child"
+
     override fun close() {}
-    override suspend fun get(filename: String): FileReader = LocalFile("${this.path}${File.separator}$filename")
+
+    override suspend fun get(filename: String): FileReader = LocalFile(child(filename))
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
-        if (!File("${this.path}${File.separator}$filename").createNewFile() && !ignoreIfExists) {
+        if (!File(child(filename)).createNewFile() && !ignoreIfExists) {
             throw UnsupportedOperationException("File already exists")
         }
     }
 
-    override suspend fun put(filename: String): FileWriter = LocalFile("${this.path}${File.separator}$filename")
+    override suspend fun put(filename: String): FileWriter = LocalFile(child(filename))
 
-    override suspend fun getSubdir(dirpath: Path): Directory = LocalDirectory("${this.path}${File.separator}$dirpath")
+    override suspend fun getSubdir(path: Path): Directory = LocalDirectory(root, child(path.toString()))
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory {
-        if (!File("${this.path}${File.separator}$dirname").mkdir() && !ignoreIfExists) {
+        val dir = child(dirname)
+        if (!File(dir).mkdir() && !ignoreIfExists) {
             throw UnsupportedOperationException("File already exists")
         }
-        return this.getSubdir(File(dirname).toPath())
+        return this.getSubdir(File(dir).toPath())
     }
 }

From 8069ea2f0b441351f761b283a8dc7bc9fd734f61 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 00:36:33 +0300
Subject: [PATCH 04/15] SNRK-67: Add top-level function

---
 .../space/kscience/snark/storage/local/LocalDriver.kt       | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
index bb76118..d75db16 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
@@ -6,6 +6,10 @@ import space.kscience.snark.storage.FileWriter
 import java.io.File
 import java.nio.file.Path
 
+public fun localStorage(rootPath: Path): Directory {
+    return LocalDirectory(rootPath, ".")
+}
+
 public class LocalFile(private val path: String) : FileReader, FileWriter {
     override fun close() {}
     override suspend fun readAll(): ByteArray = File(this.path).readBytes()
@@ -13,7 +17,7 @@ public class LocalFile(private val path: String) : FileReader, FileWriter {
     override suspend fun write(bytes: ByteArray) = File(this.path).writeBytes(bytes)
 }
 
-public class LocalDirectory(private val root: String, private val path: String) : Directory {
+public class LocalDirectory(private val root: Path, path: String) : Directory {
     private val current = "$root/$path"
 
     private fun child(child: String): String = "$current/$child"

From b543735628584d689705c26a3145e57cd5563066 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 00:37:14 +0300
Subject: [PATCH 05/15] SNRK-67: Make implementation private

---
 .../kotlin/space/kscience/snark/storage/local/LocalDriver.kt  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
index d75db16..324267c 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
@@ -10,14 +10,14 @@ public fun localStorage(rootPath: Path): Directory {
     return LocalDirectory(rootPath, ".")
 }
 
-public class LocalFile(private val path: String) : FileReader, FileWriter {
+private class LocalFile(private val path: String) : FileReader, FileWriter {
     override fun close() {}
     override suspend fun readAll(): ByteArray = File(this.path).readBytes()
 
     override suspend fun write(bytes: ByteArray) = File(this.path).writeBytes(bytes)
 }
 
-public class LocalDirectory(private val root: Path, path: String) : Directory {
+private class LocalDirectory(private val root: Path, path: String) : Directory {
     private val current = "$root/$path"
 
     private fun child(child: String): String = "$current/$child"

From 7c6157be96f2a5a3dd247defce596e58398cf0ad Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 16:35:50 +0300
Subject: [PATCH 06/15] SNRK-67: Use system-specific path separator

---
 .../kotlin/space/kscience/snark/storage/local/LocalDriver.kt  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
index 324267c..de6708b 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
@@ -18,9 +18,9 @@ private class LocalFile(private val path: String) : FileReader, FileWriter {
 }
 
 private class LocalDirectory(private val root: Path, path: String) : Directory {
-    private val current = "$root/$path"
+    private val current = "$root${File.separator}$path"
 
-    private fun child(child: String): String = "$current/$child"
+    private fun child(child: String): String = "$current${File.separator}$child"
 
     override fun close() {}
 

From e9eaa0f8c27501432aa5b210e32e0152f2636dc9 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 16:53:48 +0300
Subject: [PATCH 07/15] SNRK-67: Use kotlin.io.Path

---
 .../snark/storage/local/LocalDriver.kt        | 37 +++++++++++--------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
index de6708b..28e9487 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/local/LocalDriver.kt
@@ -3,43 +3,50 @@ package space.kscience.snark.storage.local
 import space.kscience.snark.storage.Directory
 import space.kscience.snark.storage.FileReader
 import space.kscience.snark.storage.FileWriter
-import java.io.File
 import java.nio.file.Path
+import kotlin.io.path.*
 
 public fun localStorage(rootPath: Path): Directory {
-    return LocalDirectory(rootPath, ".")
+    return LocalDirectory(rootPath)
 }
 
-private class LocalFile(private val path: String) : FileReader, FileWriter {
+private class LocalFile(private val path: Path) : FileReader, FileWriter {
     override fun close() {}
-    override suspend fun readAll(): ByteArray = File(this.path).readBytes()
+    override suspend fun readAll(): ByteArray = path.readBytes()
 
-    override suspend fun write(bytes: ByteArray) = File(this.path).writeBytes(bytes)
+    override suspend fun write(bytes: ByteArray) = path.writeBytes(bytes)
 }
 
-private class LocalDirectory(private val root: Path, path: String) : Directory {
-    private val current = "$root${File.separator}$path"
-
-    private fun child(child: String): String = "$current${File.separator}$child"
+private class LocalDirectory(private val path: Path) : Directory {
+    private fun child(child: String): Path = path / child
+    private fun child(child: Path): Path = path / child
 
     override fun close() {}
 
     override suspend fun get(filename: String): FileReader = LocalFile(child(filename))
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
-        if (!File(child(filename)).createNewFile() && !ignoreIfExists) {
-            throw UnsupportedOperationException("File already exists")
+        try {
+            child(filename).createFile()
+        } catch (ex: FileAlreadyExistsException) {
+            if (!ignoreIfExists) {
+                throw ex
+            }
         }
     }
 
     override suspend fun put(filename: String): FileWriter = LocalFile(child(filename))
 
-    override suspend fun getSubdir(path: Path): Directory = LocalDirectory(root, child(path.toString()))
+    override suspend fun getSubdir(path: Path): Directory = LocalDirectory(child(path))
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory {
         val dir = child(dirname)
-        if (!File(dir).mkdir() && !ignoreIfExists) {
-            throw UnsupportedOperationException("File already exists")
+        try {
+            dir.createDirectory()
+        } catch (ex: FileAlreadyExistsException) {
+            if (!ignoreIfExists) {
+                throw ex
+            }
         }
-        return this.getSubdir(File(dir).toPath())
+        return LocalDirectory(dir)
     }
 }

From d292abc816d0c2f3c803db3386cc9a05b2cfacbd Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 21:12:21 +0300
Subject: [PATCH 08/15] SNRK-57: Fix internals

---
 .../s3/{Directory.kt => S3Directory.kt}       | 25 ++++++++--------
 .../snark/storage/s3/{File.kt => S3File.kt}   | 10 ++++---
 .../snark/storage/s3/{Root.kt => S3Root.kt}   | 30 ++++++++++++++-----
 3 files changed, 41 insertions(+), 24 deletions(-)
 rename snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/{Directory.kt => S3Directory.kt} (58%)
 rename snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/{File.kt => S3File.kt} (69%)
 rename snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/{Root.kt => S3Root.kt} (55%)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
similarity index 58%
rename from snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt
rename to snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
index 27ece3b..d972fed 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Directory.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
@@ -1,18 +1,19 @@
 package space.kscience.snark.storage.s3
 
 import aws.sdk.kotlin.services.s3.S3Client
-import space.kscience.snark.storage.Directory as Dir
+import space.kscience.snark.storage.Directory
 import space.kscience.snark.storage.FileReader
 import space.kscience.snark.storage.FileWriter
 import java.nio.file.Path
+import kotlin.io.path.*
 
-public class Directory(
+internal class S3Directory(
     private val client: S3Client,
     private val bucketName: String,
-    private val currentDir: String,
-) : Dir {
+    private val currentDir: Path,
+) : Directory {
     override suspend fun get(filename: String): FileReader = run {
-        S3FileReader(client, bucketName, "$currentDir/$filename")
+        S3FileReader(client, bucketName, currentDir / filename)
     }
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
@@ -21,19 +22,17 @@ public class Directory(
         }
     }
 
-    override suspend fun put(filename: String): FileWriter = run {
-        S3FileWriter(client, bucketName, "$currentDir/$filename")
-    }
+    override suspend fun put(filename: String): FileWriter =
+        S3FileWriter(client, bucketName, currentDir / filename)
 
-    override suspend fun getSubdir(path: Path): Directory = run {
-        Directory(client, bucketName, "$currentDir/$path")
-    }
+    override suspend fun getSubdir(path: Path): S3Directory =
+        S3Directory(client, bucketName, currentDir / path)
 
-    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = run {
+    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): S3Directory = run {
         if (!ignoreIfExists) {
             throw IllegalArgumentException("could not check if directory exists")
         }
-        Directory(client, bucketName, "$currentDir/$dirname")
+        S3Directory(client, bucketName, currentDir / dirname)
     }
 
     override fun close() {
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3File.kt
similarity index 69%
rename from snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt
rename to snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3File.kt
index 43e872f..8255519 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/File.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3File.kt
@@ -7,12 +7,14 @@ import aws.smithy.kotlin.runtime.content.ByteStream
 import aws.smithy.kotlin.runtime.content.toByteArray
 import space.kscience.snark.storage.FileReader
 import space.kscience.snark.storage.FileWriter
+import java.nio.file.Path
+import kotlin.io.path.*
 
-public class S3FileReader(private val client: S3Client, private val bucketName: String, private val fullQualifiedPath: String) : FileReader {
+internal class S3FileReader(private val client: S3Client, private val bucketName: String, private val path: Path) : FileReader {
     override suspend fun readAll(): ByteArray {
         val result = client.getObject(GetObjectRequest{
             bucket = bucketName
-            key = fullQualifiedPath
+            key = path.toString()
         }) {
             it.body?.toByteArray() ?: ByteArray(0)
         }
@@ -23,11 +25,11 @@ public class S3FileReader(private val client: S3Client, private val bucketName:
     }
 }
 
-public class S3FileWriter(private val client: S3Client, private val bucketName: String, private val fullQualifiedPath: String) : FileWriter {
+internal class S3FileWriter(private val client: S3Client, private val bucketName: String, private val path: Path) : FileWriter {
     override suspend fun write(bytes: ByteArray) {
         client.putObject {
             bucket = bucketName
-            key = fullQualifiedPath
+            key = path.toString()
             body = ByteStream.fromBytes(bytes)
         }
     }
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
similarity index 55%
rename from snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt
rename to snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
index de51731..4625a8c 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/Root.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
@@ -1,20 +1,35 @@
 package space.kscience.snark.storage.s3
 
 import aws.sdk.kotlin.services.s3.*
-import space.kscience.snark.storage.Directory as Dir
+import space.kscience.snark.storage.Directory
 import space.kscience.snark.storage.FileReader
 import space.kscience.snark.storage.FileWriter
 import java.io.File
 import java.lang.Exception
 import java.nio.file.Path
+import kotlin.io.path.*
 
-public class Root(private val client: S3Client) : Dir {
+public fun s3Storage(client: S3Client): Directory {
+    return S3Root(client)
+}
+
+public fun s3Bucket(client: S3Client, bucket: String): Directory {
+    return S3Directory(client, bucket, Path(""))
+}
+
+internal fun splitPathIntoBucketAndPath(path: Path): Pair<String, Path> {
+    val bucket = path.getName(0)
+    val recent = path.relativize(bucket)
+    return Pair(bucket.toString(), recent)
+}
+
+internal class S3Root(private val client: S3Client) : Directory {
     override suspend fun get(filename: String): FileReader {
         throw NoSuchFileException(File(filename))
     }
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
-        throw IllegalCallerException()
+        throw NoSuchFileException(File(filename))
     }
 
     override suspend fun put(filename: String): FileWriter {
@@ -22,20 +37,21 @@ public class Root(private val client: S3Client) : Dir {
     }
 
     override suspend fun getSubdir(path: Path): Directory = try {
-        val bucketName = path.toString()
+        val (bucketName, recentPath) = splitPathIntoBucketAndPath(path)
         client.headBucket {
             bucket = bucketName
         }
-        Directory(client, bucketName, "")
+        S3Directory(client, bucketName, recentPath)
     } catch (ex: Exception) {
         throw java.nio.file.AccessDeniedException(path.toString()).initCause(ex)
     }
 
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = try {
+        val (bucketName, recentPath) = splitPathIntoBucketAndPath(Path(dirname))
         client.createBucket {
-            bucket = dirname
+            bucket = bucketName
         }
-        Directory(client, dirname, "")
+        S3Directory(client, bucketName, recentPath)
     } catch (ex: Exception) {
         throw java.nio.file.AccessDeniedException(dirname).initCause(ex)
     }

From 256fb167483172b13eef2c694997bb9c26b3b014 Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Mon, 24 Apr 2023 21:45:42 +0300
Subject: [PATCH 09/15] SNRK-57: Pretty exceptions

---
 .../space/kscience/snark/storage/s3/S3Directory.kt |  8 ++++----
 .../space/kscience/snark/storage/s3/S3Root.kt      | 14 ++++++--------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
index d972fed..4ca0587 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
@@ -28,12 +28,12 @@ internal class S3Directory(
     override suspend fun getSubdir(path: Path): S3Directory =
         S3Directory(client, bucketName, currentDir / path)
 
-    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): S3Directory = run {
+    override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): S3Directory =
         if (!ignoreIfExists) {
-            throw IllegalArgumentException("could not check if directory exists")
+            TODO("could not check if directory exists")
+        } else {
+            S3Directory(client, bucketName, currentDir / dirname)
         }
-        S3Directory(client, bucketName, currentDir / dirname)
-    }
 
     override fun close() {
     }
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
index 4625a8c..14f18bd 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
@@ -9,13 +9,11 @@ import java.lang.Exception
 import java.nio.file.Path
 import kotlin.io.path.*
 
-public fun s3Storage(client: S3Client): Directory {
-    return S3Root(client)
-}
+public fun s3Storage(client: S3Client): Directory =
+    S3Root(client)
 
-public fun s3Bucket(client: S3Client, bucket: String): Directory {
-    return S3Directory(client, bucket, Path(""))
-}
+public fun s3Bucket(client: S3Client, bucket: String): Directory =
+    S3Directory(client, bucket, Path(""))
 
 internal fun splitPathIntoBucketAndPath(path: Path): Pair<String, Path> {
     val bucket = path.getName(0)
@@ -43,7 +41,7 @@ internal class S3Root(private val client: S3Client) : Directory {
         }
         S3Directory(client, bucketName, recentPath)
     } catch (ex: Exception) {
-        throw java.nio.file.AccessDeniedException(path.toString()).initCause(ex)
+        throw AccessDeniedException(path.toFile(), reason = ex.message)
     }
 
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = try {
@@ -53,7 +51,7 @@ internal class S3Root(private val client: S3Client) : Directory {
         }
         S3Directory(client, bucketName, recentPath)
     } catch (ex: Exception) {
-        throw java.nio.file.AccessDeniedException(dirname).initCause(ex)
+        throw AccessDeniedException(File(dirname), reason = ex.message)
     }
 
     override fun close() {

From 52772cde7d3459857715aebbdbfe9b201d7043fe Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Fri, 28 Apr 2023 16:59:11 +0300
Subject: [PATCH 10/15] SNRK-57: Remove `run`

---
 .../main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
index 4ca0587..2cdc8fd 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
@@ -12,9 +12,8 @@ internal class S3Directory(
     private val bucketName: String,
     private val currentDir: Path,
 ) : Directory {
-    override suspend fun get(filename: String): FileReader = run {
+    override suspend fun get(filename: String): FileReader =
         S3FileReader(client, bucketName, currentDir / filename)
-    }
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
         if (!ignoreIfExists) {

From f71e5a3f1ababf8b12c34c589f28b036daf2a29b Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Fri, 28 Apr 2023 17:07:54 +0300
Subject: [PATCH 11/15] SNRK-57: Format file

---
 .../space/kscience/snark/storage/s3/S3Directory.kt   |  2 +-
 .../kotlin/space/kscience/snark/storage/s3/S3Root.kt | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
index 2cdc8fd..ed2c743 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Directory.kt
@@ -17,7 +17,7 @@ internal class S3Directory(
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
         if (!ignoreIfExists) {
-            throw IllegalArgumentException("could not check if file exists")
+            TODO("could not check if file exists")
         }
     }
 
diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
index 14f18bd..3ab1a68 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
@@ -17,8 +17,8 @@ public fun s3Bucket(client: S3Client, bucket: String): Directory =
 
 internal fun splitPathIntoBucketAndPath(path: Path): Pair<String, Path> {
     val bucket = path.getName(0)
-    val recent = path.relativize(bucket)
-    return Pair(bucket.toString(), recent)
+    val filePath = path.relativize(bucket)
+    return Pair(bucket.toString(), filePath)
 }
 
 internal class S3Root(private val client: S3Client) : Directory {
@@ -35,21 +35,21 @@ internal class S3Root(private val client: S3Client) : Directory {
     }
 
     override suspend fun getSubdir(path: Path): Directory = try {
-        val (bucketName, recentPath) = splitPathIntoBucketAndPath(path)
+        val (bucketName, filePath) = splitPathIntoBucketAndPath(path)
         client.headBucket {
             bucket = bucketName
         }
-        S3Directory(client, bucketName, recentPath)
+        S3Directory(client, bucketName, filePath)
     } catch (ex: Exception) {
         throw AccessDeniedException(path.toFile(), reason = ex.message)
     }
 
     override suspend fun createSubdir(dirname: String, ignoreIfExists: Boolean): Directory = try {
-        val (bucketName, recentPath) = splitPathIntoBucketAndPath(Path(dirname))
+        val (bucketName, filePath) = splitPathIntoBucketAndPath(Path(dirname))
         client.createBucket {
             bucket = bucketName
         }
-        S3Directory(client, bucketName, recentPath)
+        S3Directory(client, bucketName, filePath)
     } catch (ex: Exception) {
         throw AccessDeniedException(File(dirname), reason = ex.message)
     }

From a672db082f25814a9157c8e54aa2610d81fd545c Mon Sep 17 00:00:00 2001
From: Kirill Grachev <grachev.ka@phystech.edu>
Date: Fri, 28 Apr 2023 17:37:39 +0300
Subject: [PATCH 12/15] SNRK-57: Remove `File` from sources

---
 .../kotlin/space/kscience/snark/storage/s3/S3Root.kt     | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
index 3ab1a68..3f0037c 100644
--- a/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
+++ b/snark-storage-driver/src/main/kotlin/space/kscience/snark/storage/s3/S3Root.kt
@@ -4,7 +4,6 @@ import aws.sdk.kotlin.services.s3.*
 import space.kscience.snark.storage.Directory
 import space.kscience.snark.storage.FileReader
 import space.kscience.snark.storage.FileWriter
-import java.io.File
 import java.lang.Exception
 import java.nio.file.Path
 import kotlin.io.path.*
@@ -23,15 +22,15 @@ internal fun splitPathIntoBucketAndPath(path: Path): Pair<String, Path> {
 
 internal class S3Root(private val client: S3Client) : Directory {
     override suspend fun get(filename: String): FileReader {
-        throw NoSuchFileException(File(filename))
+        throw NoSuchFileException(Path(filename).toFile())
     }
 
     override suspend fun create(filename: String, ignoreIfExists: Boolean) {
-        throw NoSuchFileException(File(filename))
+        throw NoSuchFileException(Path(filename).toFile())
     }
 
     override suspend fun put(filename: String): FileWriter {
-        throw NoSuchFileException(File(filename))
+        throw NoSuchFileException(Path(filename).toFile())
     }
 
     override suspend fun getSubdir(path: Path): Directory = try {
@@ -51,7 +50,7 @@ internal class S3Root(private val client: S3Client) : Directory {
         }
         S3Directory(client, bucketName, filePath)
     } catch (ex: Exception) {
-        throw AccessDeniedException(File(dirname), reason = ex.message)
+        throw AccessDeniedException(Path(dirname).toFile(), reason = ex.message)
     }
 
     override fun close() {

From 6c9a08a14a1acc031fd42c6220c3224597bcf72e Mon Sep 17 00:00:00 2001
From: "liubar.pa" <liubar.pa@phystech.edu>
Date: Thu, 4 May 2023 02:18:37 +0300
Subject: [PATCH 13/15] SNRK-70: better test naming

---
 snark-document-builder/src/test/kotlin/DocumentBuilder.kt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/snark-document-builder/src/test/kotlin/DocumentBuilder.kt b/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
index bc019e3..6c16cc9 100644
--- a/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
+++ b/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
@@ -5,7 +5,7 @@ import kotlinx.coroutines.runBlocking
 
 class SomeTest {
     @Test
-    fun testEssential() = runBlocking {
+    fun justWorks() = runBlocking {
         buildDocument("../example")
     }
 }

From 5458bd367740773e0a25f24d638fb679c88ddc23 Mon Sep 17 00:00:00 2001
From: "liubar.pa" <liubar.pa@phystech.edu>
Date: Thu, 4 May 2023 02:30:03 +0300
Subject: [PATCH 14/15] SNRK-70: better arguments in buildDocument

---
 snark-document-builder/src/main/kotlin/DocumentBuilder.kt | 4 +---
 snark-document-builder/src/test/kotlin/DocumentBuilder.kt | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/snark-document-builder/src/main/kotlin/DocumentBuilder.kt b/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
index 551ba70..1b1ebe5 100644
--- a/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
+++ b/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
@@ -2,13 +2,11 @@ package documentBuilder
 
 import com.fasterxml.jackson.core.io.BigDecimalParser
 import space.kscience.snark.storage.*
-import space.kscience.snark.storage.local.LocalDirectory
 import java.nio.file.Path
 
 val DEFAULT_DOCUMENT_ROOT = "main.md"
 
-public suspend fun buildDocument(documentPath: String) {
-    val documentDirectory: Directory = LocalDirectory(documentPath)
+public suspend fun buildDocument(documentDirectory: Directory) {
     val documentRoot = documentDirectory.get(DEFAULT_DOCUMENT_ROOT)
 
     TODO()
diff --git a/snark-document-builder/src/test/kotlin/DocumentBuilder.kt b/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
index 6c16cc9..95c6002 100644
--- a/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
+++ b/snark-document-builder/src/test/kotlin/DocumentBuilder.kt
@@ -6,6 +6,6 @@ import kotlinx.coroutines.runBlocking
 class SomeTest {
     @Test
     fun justWorks() = runBlocking {
-        buildDocument("../example")
+        // buildDocument(Directory("../example"))
     }
 }

From dee40ecdcc699f33fa64e4bc7c92b0251845f264 Mon Sep 17 00:00:00 2001
From: "liubar.pa" <liubar.pa@phystech.edu>
Date: Thu, 4 May 2023 02:33:58 +0300
Subject: [PATCH 15/15] SNRK-70: visibility of DEFAULT_DICUMENT_ROOT is
 specified

---
 snark-document-builder/src/main/kotlin/DocumentBuilder.kt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/snark-document-builder/src/main/kotlin/DocumentBuilder.kt b/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
index 1b1ebe5..fe96f5e 100644
--- a/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
+++ b/snark-document-builder/src/main/kotlin/DocumentBuilder.kt
@@ -4,7 +4,7 @@ import com.fasterxml.jackson.core.io.BigDecimalParser
 import space.kscience.snark.storage.*
 import java.nio.file.Path
 
-val DEFAULT_DOCUMENT_ROOT = "main.md"
+private val DEFAULT_DOCUMENT_ROOT = "main.md"
 
 public suspend fun buildDocument(documentDirectory: Directory) {
     val documentRoot = documentDirectory.get(DEFAULT_DOCUMENT_ROOT)