CVE-2018-18074

Advisory

Onecodex 0.10.0 updates its dependency 'requests' to v2.27.1 to include a security fix.

Affected package

Affected versions

Fixed versions

Vulnerability changelog

Added

- Adds `download_samples()` function and `onecodex download samples` CLI command for downloading batches of samples as FASTA/Q files
- Adds support for Python 3.9 and 3.10
- Adds support for Apple M1 processors

Changed

- Improves `SampleCollection._collate_results()` runtime by at least 20x
- Improves missing value coercion in `SampleCollection._collate_results()`
- Updates some dependency versions to address security vulnerabilities, performance enhancements, expanded environment support, and easier installation
- `numpy` is no longer required to be installed prior to installing the `onecodex` package
- Relaxes `filelock` dependency version pin
- Changes `helponecodex.com` to `supportonecodex.com` in user messaging

Fixed

- Fixes PCoA/MDS plot URL bug
- Fixes `metric` parameter behavior in `SampleCollection` constructor (it is no longer ignored)

Removed

- Removes Python 2 support
- Removes bash completion
- Removes `Classifications._append_abundance_rollups()` in favor of retrieving `abundance_w_children` metric from One Codex API

Resources

• https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-18074