rust-lang / rust-lang/libz-sys

Problems reading GZIPPED file with libz-sys > 1.1.5 and zlib-ng-compat

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Dominant language
Rust
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Forks
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Description

Problems reading GZIPPED file with libz-sys > 1.1.5 withzlib-ng-compat.
With zlib and it works fine. With libz-sys == 1.1.5andzlib-ng-compat` it also works fine.

See: https://github.com/pola-rs/polars/issues/3895

Problematic gzipped CSV file: https://temp.aertslab.org/.tsv/atac_fragments.head40000000.tsv.gz

import polars as pl

df = pl.read_csv(
    'atac_fragments.head40000000.tsv.gz',
    skip_rows=52,
    has_headers=False, 
    sep="\t",
    use_pyarrow=False
)

Cargo.toml

[package]
name = "polars_read_csv"
version = "0.1.0"
edition = "2021"


[dependencies]
polars-core = { path = "../polars/polars/polars-core", default-features = false }

[features]


[dependencies.polars]
path = "../polars/polars"
default-features = false
features = [
  "simd",
  "strings",
  "csv-file",
  "performant",
  "decompress-fast",
]


[profile.release]
target-cpu = "native"
debug = 1

src/main.rs

use polars::prelude::*;

fn main() -> Result<()> {
    let df = CsvReader::from_path(
        "atac_fragments.head40000000.tsv.gz",
    )?
    .with_delimiter(b'\t')
    .with_skip_rows(52)
    .finish()?;

    println!("{:?}", df.shape());
    println!("{}", df.tail(Some(30)));

    Ok(())
}

Get polars:

cd ..
git clone --maxdepth 100 https://github.com/pola-rs/polars

Ttry dffirent flate2 backends in polars-core by changing: decompress-fast

❯ git diff polars/polars-io/Cargo.toml
diff --git a/polars/polars-io/Cargo.toml b/polars/polars-io/Cargo.toml
index 3461c37e7d..a39b89b06c 100644
--- a/polars/polars-io/Cargo.toml
+++ b/polars/polars-io/Cargo.toml
@@ -28,7 +28,9 @@ dtype-categorical = ["polars-core/dtype-categorical"]
 csv-file = ["csv-core", "memmap", "lexical", "polars-core/rows", "lexical-core"]
 fmt = ["polars-core/fmt"]
 decompress = ["flate2/miniz_oxide"]
-decompress-fast = ["flate2/zlib-ng-compat"]
+#decompress-fast = ["flate2/zlib"]
+#decompress-fast = ["flate2/zlib-ng"]
 temporal = ["dtype-datetime", "dtype-date", "dtype-time"]
 partition = ["polars-core/partition_by"]
 # don't use this
# Compile each version with differnt decompress-fast settings:
cargo build --release

# with "flate2/zlib-ng-compat"
$ target/release/polars_read_csv 
Error: ComputeError("invalid utf8 data in csv")

# with "flate2/zlib-ng"
$ target/release/polars_read_csv 
Error: ComputeError("invalid utf8 data in csv")

# with "flate2/zlib"
$ target/release/polars_read_csv
(39999947, 5)

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Cargo.toml feature configuration and src/main.rs reproduction, using the linked gzipped TSV file. Build with each flate2 backend and compare the reported CSV error or resulting shape; done means the problematic file reads correctly without invalid UTF-8 data.

Written by the indexing model from the issue text.

Assessment

Tech stack
rust
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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