feat: implement infer schema from single file (#1348)

* feat: implement infer schema from file

* feat: implement compression type

* refactor: remove unnecessary BufReader

* refactor: remove SyncIoBridge and using tokio_util::io::SyncIoBridge instead

* chore: apply suggestions from CR
This commit is contained in:
Weny Xu
2023-04-11 17:59:30 +09:00
committed by GitHub
parent dfc2a45de1
commit fac9c17a9b
18 changed files with 673 additions and 10 deletions

8
Cargo.lock generated
View File

@@ -1561,11 +1561,19 @@ dependencies = [
name = "common-datasource"
version = "0.1.1"
dependencies = [
"arrow",
"arrow-schema",
"async-compression",
"async-trait",
"common-error",
"common-runtime",
"datafusion",
"futures",
"object-store",
"regex",
"snafu",
"tokio",
"tokio-util",
"url",
]

View File

@@ -77,7 +77,7 @@ snafu = { version = "0.7", features = ["backtraces"] }
sqlparser = "0.32"
tempfile = "3"
tokio = { version = "1.24.2", features = ["full"] }
tokio-util = "0.7"
tokio-util = { version = "0.7", features = ["io-util"] }
tonic = { version = "0.8", features = ["tls"] }
uuid = { version = "1", features = ["serde", "v4", "fast-rng"] }

View File

@@ -5,9 +5,24 @@ edition.workspace = true
license.workspace = true
[dependencies]
arrow.workspace = true
arrow-schema.workspace = true
async-compression = { version = "0.3", features = [
"bzip2",
"gzip",
"xz",
"zstd",
"futures-io",
"tokio",
] }
async-trait.workspace = true
common-error = { path = "../error" }
common-runtime = { path = "../runtime" }
datafusion.workspace = true
futures.workspace = true
object-store = { path = "../../object-store" }
regex = "1.7"
snafu.workspace = true
tokio.workspace = true
tokio-util.workspace = true
url = "2.3"

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@@ -0,0 +1,84 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
use std::fmt::Display;
use std::str::FromStr;
use async_compression::tokio::bufread::{BzDecoder, GzipDecoder, XzDecoder, ZstdDecoder};
use tokio::io::{AsyncRead, BufReader};
use crate::error::{self, Error, Result};
#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
pub enum CompressionType {
/// Gzip-ed file
GZIP,
/// Bzip2-ed file
BZIP2,
/// Xz-ed file (liblzma)
XZ,
/// Zstd-ed file,
ZSTD,
/// Uncompressed file
UNCOMPRESSED,
}
impl FromStr for CompressionType {
type Err = Error;
fn from_str(s: &str) -> Result<Self> {
let s = s.to_uppercase();
match s.as_str() {
"GZIP" | "GZ" => Ok(Self::GZIP),
"BZIP2" | "BZ2" => Ok(Self::BZIP2),
"XZ" => Ok(Self::XZ),
"ZST" | "ZSTD" => Ok(Self::ZSTD),
"" => Ok(Self::UNCOMPRESSED),
_ => error::UnsupportedCompressionTypeSnafu {
compression_type: s,
}
.fail(),
}
}
}
impl Display for CompressionType {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
f.write_str(match self {
Self::GZIP => "GZIP",
Self::BZIP2 => "BZIP2",
Self::XZ => "XZ",
Self::ZSTD => "ZSTD",
Self::UNCOMPRESSED => "",
})
}
}
impl CompressionType {
pub const fn is_compressed(&self) -> bool {
!matches!(self, &Self::UNCOMPRESSED)
}
pub fn convert_async_read<T: AsyncRead + Unpin + Send + 'static>(
&self,
s: T,
) -> Box<dyn AsyncRead + Unpin + Send> {
match self {
CompressionType::GZIP => Box::new(GzipDecoder::new(BufReader::new(s))),
CompressionType::BZIP2 => Box::new(BzDecoder::new(BufReader::new(s))),
CompressionType::XZ => Box::new(XzDecoder::new(BufReader::new(s))),
CompressionType::ZSTD => Box::new(ZstdDecoder::new(BufReader::new(s))),
CompressionType::UNCOMPRESSED => Box::new(s),
}
}
}

View File

@@ -21,6 +21,9 @@ use url::ParseError;
#[derive(Debug, Snafu)]
#[snafu(visibility(pub))]
pub enum Error {
#[snafu(display("Unsupported compression type: {}", compression_type))]
UnsupportedCompressionType { compression_type: String },
#[snafu(display("Unsupported backend protocol: {}", protocol))]
UnsupportedBackendProtocol { protocol: String },
@@ -33,12 +36,44 @@ pub enum Error {
#[snafu(display("Invalid url: {}, error :{}", url, source))]
InvalidUrl { url: String, source: ParseError },
#[snafu(display("Failed to decompression, source: {}", source))]
Decompression {
source: object_store::Error,
location: Location,
},
#[snafu(display("Failed to build backend, source: {}", source))]
BuildBackend {
source: object_store::Error,
location: Location,
},
#[snafu(display("Failed to read object from path: {}, source: {}", path, source))]
ReadObject {
path: String,
location: Location,
source: object_store::Error,
},
#[snafu(display("Failed to read parquet source: {}", source))]
ReadParquetSnafu {
location: Location,
source: datafusion::parquet::errors::ParquetError,
},
#[snafu(display("Failed to convert parquet to schema: {}", source))]
ParquetToSchema {
location: Location,
source: datafusion::parquet::errors::ParquetError,
},
#[snafu(display("Failed to infer schema from file: {}, source: {}", path, source))]
InferSchema {
path: String,
location: Location,
source: arrow_schema::ArrowError,
},
#[snafu(display("Failed to list object in path: {}, source: {}", path, source))]
ListObjects {
path: String,
@@ -48,6 +83,12 @@ pub enum Error {
#[snafu(display("Invalid connection: {}", msg))]
InvalidConnection { msg: String },
#[snafu(display("Failed to join handle: {}", source))]
JoinHandle {
location: Location,
source: tokio::task::JoinError,
},
}
pub type Result<T> = std::result::Result<T, Error>;
@@ -56,13 +97,21 @@ impl ErrorExt for Error {
fn status_code(&self) -> StatusCode {
use Error::*;
match self {
BuildBackend { .. } | ListObjects { .. } => StatusCode::StorageUnavailable,
BuildBackend { .. } | ListObjects { .. } | ReadObject { .. } => {
StatusCode::StorageUnavailable
}
UnsupportedBackendProtocol { .. }
| UnsupportedCompressionType { .. }
| InvalidConnection { .. }
| InvalidUrl { .. }
| EmptyHostPath { .. }
| InvalidPath { .. } => StatusCode::InvalidArguments,
| InvalidPath { .. }
| InferSchema { .. }
| ReadParquetSnafu { .. }
| ParquetToSchema { .. } => StatusCode::InvalidArguments,
Decompression { .. } | JoinHandle { .. } => StatusCode::Unexpected,
}
}
@@ -71,14 +120,23 @@ impl ErrorExt for Error {
}
fn location_opt(&self) -> Option<common_error::snafu::Location> {
use Error::*;
match self {
Error::BuildBackend { location, .. } => Some(*location),
Error::ListObjects { location, .. } => Some(*location),
Error::UnsupportedBackendProtocol { .. }
| Error::EmptyHostPath { .. }
| Error::InvalidPath { .. }
| Error::InvalidUrl { .. }
| Error::InvalidConnection { .. } => None,
BuildBackend { location, .. } => Some(*location),
ReadObject { location, .. } => Some(*location),
ListObjects { location, .. } => Some(*location),
InferSchema { location, .. } => Some(*location),
ReadParquetSnafu { location, .. } => Some(*location),
ParquetToSchema { location, .. } => Some(*location),
Decompression { location, .. } => Some(*location),
JoinHandle { location, .. } => Some(*location),
UnsupportedBackendProtocol { .. }
| EmptyHostPath { .. }
| InvalidPath { .. }
| InvalidUrl { .. }
| InvalidConnection { .. }
| UnsupportedCompressionType { .. } => None,
}
}
}

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@@ -0,0 +1,30 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
pub mod csv;
pub mod json;
pub mod parquet;
pub const DEFAULT_SCHEMA_INFER_MAX_RECORD: usize = 1000;
use arrow::datatypes::SchemaRef;
use async_trait::async_trait;
use object_store::ObjectStore;
use crate::error::Result;
#[async_trait]
pub trait FileFormat: Send + Sync + std::fmt::Debug {
async fn infer_schema(&self, store: &ObjectStore, path: String) -> Result<SchemaRef>;
}

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@@ -0,0 +1,158 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
use std::sync::Arc;
use arrow::csv::reader::infer_reader_schema as infer_csv_schema;
use arrow_schema::SchemaRef;
use async_trait::async_trait;
use common_runtime;
use object_store::ObjectStore;
use snafu::ResultExt;
use tokio_util::io::SyncIoBridge;
use crate::compression::CompressionType;
use crate::error::{self, Result};
use crate::file_format::{self, FileFormat};
#[derive(Debug)]
pub struct CsvFormat {
pub has_header: bool,
pub delimiter: u8,
pub schema_infer_max_record: Option<usize>,
pub compression_type: CompressionType,
}
impl Default for CsvFormat {
fn default() -> Self {
Self {
has_header: true,
delimiter: b',',
schema_infer_max_record: Some(file_format::DEFAULT_SCHEMA_INFER_MAX_RECORD),
compression_type: CompressionType::UNCOMPRESSED,
}
}
}
#[async_trait]
impl FileFormat for CsvFormat {
async fn infer_schema(&self, store: &ObjectStore, path: String) -> Result<SchemaRef> {
let reader = store
.reader(&path)
.await
.context(error::ReadObjectSnafu { path: &path })?;
let decoded = self.compression_type.convert_async_read(reader);
let delimiter = self.delimiter;
let schema_infer_max_record = self.schema_infer_max_record;
let has_header = self.has_header;
common_runtime::spawn_blocking_read(move || {
let reader = SyncIoBridge::new(decoded);
let (schema, _records_read) =
infer_csv_schema(reader, delimiter, schema_infer_max_record, has_header)
.context(error::InferSchemaSnafu { path: &path })?;
Ok(Arc::new(schema))
})
.await
.context(error::JoinHandleSnafu)?
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::file_format::FileFormat;
use crate::test_util::{self, format_schema, test_store};
fn test_data_root() -> String {
test_util::get_data_dir("tests/csv").display().to_string()
}
#[tokio::test]
async fn infer_schema_basic() {
let csv = CsvFormat::default();
let store = test_store(&test_data_root());
let schema = csv
.infer_schema(&store, "simple.csv".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(
vec![
"c1: Utf8: NULL",
"c2: Int64: NULL",
"c3: Int64: NULL",
"c4: Int64: NULL",
"c5: Int64: NULL",
"c6: Int64: NULL",
"c7: Int64: NULL",
"c8: Int64: NULL",
"c9: Int64: NULL",
"c10: Int64: NULL",
"c11: Float64: NULL",
"c12: Float64: NULL",
"c13: Utf8: NULL"
],
formatted,
);
}
#[tokio::test]
async fn infer_schema_with_limit() {
let json = CsvFormat {
schema_infer_max_record: Some(3),
..CsvFormat::default()
};
let store = test_store(&test_data_root());
let schema = json
.infer_schema(&store, "schema_infer_limit.csv".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(
vec![
"a: Int64: NULL",
"b: Float64: NULL",
"c: Int64: NULL",
"d: Int64: NULL"
],
formatted
);
let json = CsvFormat::default();
let store = test_store(&test_data_root());
let schema = json
.infer_schema(&store, "schema_infer_limit.csv".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(
vec![
"a: Int64: NULL",
"b: Float64: NULL",
"c: Int64: NULL",
"d: Utf8: NULL"
],
formatted
);
}
}

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@@ -0,0 +1,121 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
use std::io::BufReader;
use std::sync::Arc;
use arrow::datatypes::SchemaRef;
use arrow::json::reader::{infer_json_schema_from_iterator, ValueIter};
use async_trait::async_trait;
use common_runtime;
use object_store::ObjectStore;
use snafu::ResultExt;
use tokio_util::io::SyncIoBridge;
use crate::compression::CompressionType;
use crate::error::{self, Result};
use crate::file_format::{self, FileFormat};
#[derive(Debug)]
pub struct JsonFormat {
pub schema_infer_max_record: Option<usize>,
pub compression_type: CompressionType,
}
impl Default for JsonFormat {
fn default() -> Self {
Self {
schema_infer_max_record: Some(file_format::DEFAULT_SCHEMA_INFER_MAX_RECORD),
compression_type: CompressionType::UNCOMPRESSED,
}
}
}
#[async_trait]
impl FileFormat for JsonFormat {
async fn infer_schema(&self, store: &ObjectStore, path: String) -> Result<SchemaRef> {
let reader = store
.reader(&path)
.await
.context(error::ReadObjectSnafu { path: &path })?;
let decoded = self.compression_type.convert_async_read(reader);
let schema_infer_max_record = self.schema_infer_max_record;
common_runtime::spawn_blocking_read(move || {
let mut reader = BufReader::new(SyncIoBridge::new(decoded));
let iter = ValueIter::new(&mut reader, schema_infer_max_record);
let schema = infer_json_schema_from_iterator(iter)
.context(error::InferSchemaSnafu { path: &path })?;
Ok(Arc::new(schema))
})
.await
.context(error::JoinHandleSnafu)?
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::file_format::FileFormat;
use crate::test_util::{self, format_schema, test_store};
fn test_data_root() -> String {
test_util::get_data_dir("tests/json").display().to_string()
}
#[tokio::test]
async fn infer_schema_basic() {
let json = JsonFormat::default();
let store = test_store(&test_data_root());
let schema = json
.infer_schema(&store, "simple.json".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(
vec![
"a: Int64: NULL",
"b: Float64: NULL",
"c: Boolean: NULL",
"d: Utf8: NULL",
],
formatted
);
}
#[tokio::test]
async fn infer_schema_with_limit() {
let json = JsonFormat {
schema_infer_max_record: Some(3),
..JsonFormat::default()
};
let store = test_store(&test_data_root());
let schema = json
.infer_schema(&store, "schema_infer_limit.json".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(
vec!["a: Int64: NULL", "b: Float64: NULL", "c: Boolean: NULL"],
formatted
);
}
}

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@@ -0,0 +1,78 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
use std::sync::Arc;
use arrow_schema::SchemaRef;
use async_trait::async_trait;
use datafusion::parquet::arrow::async_reader::AsyncFileReader;
use datafusion::parquet::arrow::parquet_to_arrow_schema;
use object_store::ObjectStore;
use snafu::ResultExt;
use crate::error::{self, Result};
use crate::file_format::FileFormat;
#[derive(Debug, Default)]
pub struct ParquetFormat {}
#[async_trait]
impl FileFormat for ParquetFormat {
async fn infer_schema(&self, store: &ObjectStore, path: String) -> Result<SchemaRef> {
let mut reader = store
.reader(&path)
.await
.context(error::ReadObjectSnafu { path: &path })?;
let metadata = reader
.get_metadata()
.await
.context(error::ReadParquetSnafuSnafu)?;
let file_metadata = metadata.file_metadata();
let schema = parquet_to_arrow_schema(
file_metadata.schema_descr(),
file_metadata.key_value_metadata(),
)
.context(error::ParquetToSchemaSnafu)?;
Ok(Arc::new(schema))
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::file_format::FileFormat;
use crate::test_util::{self, format_schema, test_store};
fn test_data_root() -> String {
test_util::get_data_dir("tests/parquet")
.display()
.to_string()
}
#[tokio::test]
async fn infer_schema_basic() {
let json = ParquetFormat::default();
let store = test_store(&test_data_root());
let schema = json
.infer_schema(&store, "basic.parquet".to_string())
.await
.unwrap();
let formatted: Vec<_> = format_schema(schema);
assert_eq!(vec!["num: Int64: NULL", "str: Utf8: NULL"], formatted);
}
}

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@@ -12,7 +12,10 @@
// See the License for the specific language governing permissions and
// limitations under the License.
pub mod compression;
pub mod error;
pub mod file_format;
pub mod lister;
pub mod object_store;
pub mod test_util;
pub mod util;

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@@ -0,0 +1,48 @@
// Copyright 2023 Greptime Team
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
use std::path::PathBuf;
use arrow_schema::SchemaRef;
use object_store::services::Fs;
use object_store::ObjectStore;
pub fn get_data_dir(path: &str) -> PathBuf {
// https://doc.rust-lang.org/cargo/reference/environment-variables.html
let dir = env!("CARGO_MANIFEST_DIR");
PathBuf::from(dir).join(path)
}
pub fn format_schema(schema: SchemaRef) -> Vec<String> {
schema
.fields()
.iter()
.map(|f| {
format!(
"{}: {:?}: {}",
f.name(),
f.data_type(),
if f.is_nullable() { "NULL" } else { "NOT NULL" }
)
})
.collect()
}
pub fn test_store(root: &str) -> ObjectStore {
let mut builder = Fs::default();
builder.root(root);
ObjectStore::new(builder).unwrap().finish()
}

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@@ -0,0 +1,24 @@
### Parquet
The `parquet/basic.parquet` was converted from `csv/basic.csv` via [bdt](https://github.com/andygrove/bdt).
Internal of `parquet/basic.parquet`:
Data:
```
+-----+-------+
| num | str |
+-----+-------+
| 5 | test |
| 2 | hello |
| 4 | foo |
+-----+-------+
```
Schema:
```
+-------------+-----------+-------------+
| column_name | data_type | is_nullable |
+-------------+-----------+-------------+
| num | Int64 | YES |
| str | Utf8 | YES |
+-------------+-----------+-------------+
```

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@@ -0,0 +1,4 @@
num,str
5,test
2,hello
4,foo
1 num str
2 5 test
3 2 hello
4 4 foo

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@@ -0,0 +1,5 @@
a,b,c,d
1,2,3,4
1,2,3,4
1,2.0,3,4
1,2,4,test
1 a b c d
2 1 2 3 4
3 1 2 3 4
4 1 2.0 3 4
5 1 2 4 test

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@@ -0,0 +1,11 @@
c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13
c,2,1,18109,2033001162,-6513304855495910254,25,43062,1491205016,5863949479783605708,0.110830784,0.9294097332465232,6WfVFBVGJSQb7FhA7E0lBwdvjfZnSW
d,5,-40,22614,706441268,-7542719935673075327,155,14337,3373581039,11720144131976083864,0.69632107,0.3114712539863804,C2GT5KVyOPZpgKVl110TyZO0NcJ434
b,1,29,-18218,994303988,5983957848665088916,204,9489,3275293996,14857091259186476033,0.53840446,0.17909035118828576,AyYVExXK6AR2qUTxNZ7qRHQOVGMLcz
a,1,-85,-15154,1171968280,1919439543497968449,77,52286,774637006,12101411955859039553,0.12285209,0.6864391962767343,0keZ5G8BffGwgF2RwQD59TFzMStxCB
b,5,-82,22080,1824882165,7373730676428214987,208,34331,3342719438,3330177516592499461,0.82634634,0.40975383525297016,Ig1QcuKsjHXkproePdERo2w0mYzIqd
b,4,-111,-1967,-4229382,1892872227362838079,67,9832,1243785310,8382489916947120498,0.06563997,0.152498292971736,Sfx0vxv1skzZWT1PqVdoRDdO6Sb6xH
e,3,104,-25136,1738331255,300633854973581194,139,20807,3577318119,13079037564113702254,0.40154034,0.7764360990307122,DuJNG8tufSqW0ZstHqWj3aGvFLMg4A
a,3,13,12613,1299719633,2020498574254265315,191,17835,3998790955,14881411008939145569,0.041445434,0.8813167497816289,Amn2K87Db5Es3dFQO9cw9cvpAM6h35
d,1,38,18384,-335410409,-1632237090406591229,26,57510,2712615025,1842662804748246269,0.6064476,0.6404495093354053,4HX6feIvmNXBN7XGqgO4YVBkhu8GDI
a,4,-38,20744,762932956,308913475857409919,7,45465,1787652631,878137512938218976,0.7459874,0.02182578039211991,ydkwycaISlYSlEq3TlkS2m15I2pcp8
1 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 c11 c12 c13
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