biors 0.23.0

Command-line tools for bio-rs biological AI model input workflows.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156

use serde_json::Value;
use std::process::{Command, Stdio};

mod common;
use common::ChildInputExt;

#[test]
fn human_errors_include_stable_error_code() {
    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("tokenize")
        .arg("-")
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn biors tokenize")
        .tap_stdin("ACDE\n");

    assert_eq!(output.status.code(), Some(2));
    assert!(output.stdout.is_empty());

    let stderr = String::from_utf8(output.stderr).expect("stderr is UTF-8");
    assert!(stderr.contains("error[fasta.missing_header]:"));
    assert!(stderr.contains("FASTA input must start with a header line"));
}

#[test]
fn help_snapshot_lists_commands_and_global_json_flag() {
    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("--help")
        .output()
        .expect("run biors help");

    assert!(output.status.success());
    assert!(output.stderr.is_empty());

    let stdout = String::from_utf8(output.stdout).expect("help is UTF-8");
    for expected in [
        "Usage: biors [OPTIONS] <COMMAND>",
        "--json",
        "doctor",
        "completions",
        "fasta",
        "inspect",
        "model-input",
        "package",
        "seq",
        "tokenizer",
        "tokenize",
    ] {
        assert!(stdout.contains(expected), "help output missing {expected}");
    }
}

#[test]
fn completions_command_outputs_shell_script() {
    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("completions")
        .arg("bash")
        .output()
        .expect("run biors completions");

    assert!(output.status.success());
    assert!(output.stderr.is_empty());

    let stdout = String::from_utf8(output.stdout).expect("completion output is UTF-8");
    assert!(stdout.contains("_biors"));
    assert!(stdout.contains("COMPREPLY"));
}

#[test]
fn malformed_json_input_fails_without_panic() {
    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("--json")
        .arg("package")
        .arg("validate")
        .arg("-")
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn biors package validate")
        .tap_stdin("{not valid json");

    assert_eq!(output.status.code(), Some(2));
    assert!(output.stderr.is_empty());

    let value: Value = serde_json::from_slice(&output.stdout).expect("valid JSON error");
    assert_eq!(value["error"]["code"], "json.invalid");
}

#[test]
fn invalid_utf8_fasta_fails_without_panic() {
    let mut child = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("--json")
        .arg("tokenize")
        .arg("-")
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn biors tokenize");

    use std::io::Write;
    child
        .stdin
        .as_mut()
        .expect("stdin pipe")
        .write_all(b">seq1\nAC\xffDE\n")
        .expect("write stdin");

    let output = child.wait_with_output().expect("wait for biors");
    assert_eq!(output.status.code(), Some(1));
    assert!(output.stderr.is_empty());

    let value: Value = serde_json::from_slice(&output.stdout).expect("valid JSON error");
    assert_eq!(value["error"]["code"], "io.read_failed");
    assert!(value["error"]["message"]
        .as_str()
        .expect("message")
        .contains("invalid UTF-8"));
}

#[test]
fn manifest_path_traversal_fails_without_panic() {
    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("--json")
        .arg("package")
        .arg("validate")
        .arg("-")
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn biors package validate")
        .tap_stdin(
            r#"{
              "schema_version": "biors.package.v0",
              "name": "bad-path",
              "model": { "format": "onnx", "path": "../escape.onnx" },
              "preprocessing": [],
              "postprocessing": [],
              "runtime": {
                "backend": "onnx-webgpu",
                "target": "browser-wasm-webgpu"
              },
              "fixtures": []
            }"#,
        );

    assert_eq!(output.status.code(), Some(2));
    assert!(output.stderr.is_empty());

    let value: Value = serde_json::from_slice(&output.stdout).expect("valid JSON error");
    assert_eq!(value["error"]["code"], "package.invalid_asset_path");
}