biors 0.33.0

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

use serde_json::Value;
use std::fs;
use std::process::Command;

mod common;
use common::TempDir;

#[test]
fn batch_validate_accepts_multiple_input_files() {
    let temp = TempDir::new("biors-batch-files");
    let dna = temp.write("dna.fasta", ">dna\nACGN\n");
    let protein = temp.write("protein.fasta", ">protein\nMEEPQSDPSV\n");

    let output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("batch")
        .arg("validate")
        .arg("--kind")
        .arg("auto")
        .arg(&dna)
        .arg(&protein)
        .output()
        .expect("run biors batch validate");

    assert!(
        output.status.success(),
        "stderr: {}",
        String::from_utf8_lossy(&output.stderr)
    );
    assert!(output.stderr.is_empty());

    let value: Value = serde_json::from_slice(&output.stdout).expect("valid JSON output");
    assert_eq!(value["data"]["inputs"], 2);
    assert_eq!(value["data"]["summary"]["files"], 2);
    assert_eq!(value["data"]["summary"]["records"], 2);
    assert_eq!(value["data"]["summary"]["kind_counts"]["dna"], 1);
    assert_eq!(value["data"]["summary"]["kind_counts"]["protein"], 1);
    assert_eq!(value["data"]["files"][0]["records"], 1);
    assert_eq!(value["data"]["files"][0]["path"], dna.display().to_string());
    assert!(value["data"]["files"][0]["input_hash"]
        .as_str()
        .expect("input hash")
        .starts_with("fnv1a64:"));
}

#[test]
fn batch_validate_expands_directories_and_quoted_globs() {
    let temp = TempDir::new("biors-batch-globs");
    temp.write("a.fasta", ">a\nACGN\n");
    temp.write("b.fasta", ">b\nACGU\n");
    temp.write("notes.txt", "not fasta\n");

    let dir_output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("batch")
        .arg("validate")
        .arg("--kind")
        .arg("auto")
        .arg(temp.path())
        .output()
        .expect("run biors batch validate dir");

    assert!(dir_output.status.success());
    let dir_value: Value = serde_json::from_slice(&dir_output.stdout).expect("valid JSON output");
    assert_eq!(dir_value["data"]["summary"]["files"], 2);
    assert_eq!(dir_value["data"]["summary"]["records"], 2);

    let glob = temp.path().join("*.fasta").display().to_string();
    let glob_output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("batch")
        .arg("validate")
        .arg("--kind")
        .arg("auto")
        .arg(glob)
        .output()
        .expect("run biors batch validate glob");

    assert!(glob_output.status.success());
    let glob_value: Value = serde_json::from_slice(&glob_output.stdout).expect("valid JSON output");
    assert_eq!(glob_value["data"]["summary"], dir_value["data"]["summary"]);
    assert_eq!(
        glob_value["data"]["files"][0]["path"],
        dir_value["data"]["files"][0]["path"]
    );
}

#[test]
fn batch_validate_recurses_directories_and_reports_empty_globs() {
    let temp = TempDir::new("biors-batch-recursive");
    temp.write("root.fasta", ">root\nACGN\n");
    fs::create_dir_all(temp.path().join("nested/deeper")).expect("create nested dir");
    fs::write(
        temp.path().join("nested/deeper/protein.faa"),
        ">protein\nMEEPQSDPSV\n",
    )
    .expect("write nested FASTA");
    fs::write(temp.path().join("nested/notes.txt"), "not fasta\n").expect("write notes");

    let dir_output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("batch")
        .arg("validate")
        .arg("--kind")
        .arg("auto")
        .arg(temp.path())
        .output()
        .expect("run recursive biors batch validate");

    assert!(
        dir_output.status.success(),
        "stderr: {}",
        String::from_utf8_lossy(&dir_output.stderr)
    );
    let dir_value: Value = serde_json::from_slice(&dir_output.stdout).expect("valid JSON output");
    assert_eq!(dir_value["data"]["summary"]["files"], 2);
    assert_eq!(dir_value["data"]["summary"]["records"], 2);

    let missing_glob = temp.path().join("*.missing").display().to_string();
    let glob_output = Command::new(env!("CARGO_BIN_EXE_biors"))
        .arg("--json")
        .arg("batch")
        .arg("validate")
        .arg("--kind")
        .arg("auto")
        .arg(missing_glob)
        .output()
        .expect("run empty-glob biors batch validate");

    assert_eq!(glob_output.status.code(), Some(2));
    assert!(glob_output.stderr.is_empty());
    let error: Value = serde_json::from_slice(&glob_output.stdout).expect("valid JSON error");
    assert_eq!(error["error"]["code"], "batch.no_inputs");
}