wdl-engine 0.13.2

Execution engine for Workflow Description Language (WDL) documents.
Documentation
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
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
//! Implements the `join_paths` function from the WDL standard library.

use std::path::Path;

use path_clean::PathClean;
use wdl_analysis::stdlib::STDLIB as ANALYSIS_STDLIB;
use wdl_analysis::types::PrimitiveType;
use wdl_ast::Diagnostic;

use super::CallContext;
use super::Callback;
use super::Function;
use super::Signature;
use crate::PrimitiveValue;
use crate::Value;
use crate::diagnostics::function_call_failed;

/// The name of the function defined in this file for use in diagnostics.
const FUNCTION_NAME: &str = "join_paths";

/// Joins together two paths into an absolute path in the execution
/// environment's filesystem.
///
/// `String join_paths(Directory, String)`: Joins together exactly two paths.
/// The first path may be either absolute or relative and must specify a
/// directory; the second path is relative to the first path and may specify a
/// file or directory.
///
/// https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-join_paths
fn join_paths_simple(context: CallContext<'_>) -> Result<Value, Diagnostic> {
    debug_assert!(context.arguments.len() == 2);
    debug_assert!(context.return_type_eq(PrimitiveType::String));

    let first = context
        .coerce_argument(0, PrimitiveType::Directory)
        .unwrap_directory();

    let second = context
        .coerce_argument(1, PrimitiveType::String)
        .unwrap_string();

    // Join the first argument with the base path as it might be relative
    let first = context.base_dir().join(first.as_str()).map_err(|_| {
        function_call_failed(
            FUNCTION_NAME,
            format!("path `{first}` cannot be joined with the evaluation base path"),
            context.arguments[0].span,
        )
    })?;

    if first.is_local() {
        let path = first.unwrap_local();
        let second = Path::new(second.as_str());
        if !second.is_relative() {
            return Err(function_call_failed(
                FUNCTION_NAME,
                format!(
                    "path `{second}` is not a relative path",
                    second = second.display()
                ),
                context.arguments[1].span,
            ));
        }

        Ok(PrimitiveValue::new_string(
            path.join(second)
                .clean()
                .into_os_string()
                .into_string()
                .expect("should be UTF-8"),
        )
        .into())
    } else {
        let mut url = first.unwrap_remote();
        if second.starts_with('/') || second.contains(":") {
            return Err(function_call_failed(
                FUNCTION_NAME,
                format!("path `{second}` is not a relative path"),
                context.arguments[1].span,
            ));
        }

        // For consistency with `PathBuf::push`, push an empty segment so that we treat
        // the last segment as a directory; otherwise, `Url::join` will treat it as a
        // file.
        if let Ok(mut segments) = url.path_segments_mut() {
            segments.pop_if_empty();
            segments.push("");
        }

        url.join(&second)
            .map(|u| PrimitiveValue::new_string(u.to_string()).into())
            .map_err(|_| {
                function_call_failed(
                    FUNCTION_NAME,
                    format!("path `{second}` cannot be joined with URL `{url}`"),
                    context.arguments[1].span,
                )
            })
    }
}

/// Joins together two or more paths into an absolute path in the execution
/// environment's filesystem.
///
/// `String join_paths(Directory, Array[String]+)`: Joins together any number of
/// relative paths with a base path. The first argument may be either an
/// absolute or a relative path and must specify a directory. The paths in the
/// second array argument must all be relative. The last element may specify a
/// file or directory; all other elements must specify a directory.
///
/// `String join_paths(Array[String]+)`: Joins together any number of paths. The
/// array must not be empty. The first element of the array may be either
/// absolute or relative; subsequent path(s) must be relative. The last element
/// may specify a file or directory; all other elements must specify a
/// directory.
///
/// https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-join_paths
fn join_paths(context: CallContext<'_>) -> Result<Value, Diagnostic> {
    debug_assert!(!context.arguments.is_empty() && context.arguments.len() < 3);
    debug_assert!(context.return_type_eq(PrimitiveType::String));

    // Handle being provided one or two arguments
    let (first, array, skip, array_span) = if context.arguments.len() == 1 {
        let array = context
            .coerce_argument(0, ANALYSIS_STDLIB.array_string_non_empty_type().clone())
            .unwrap_array();

        (
            array.as_slice()[0].clone().unwrap_string(),
            array,
            true,
            context.arguments[0].span,
        )
    } else {
        let first = context
            .coerce_argument(0, PrimitiveType::Directory)
            .unwrap_directory()
            .into();

        let array = context
            .coerce_argument(1, ANALYSIS_STDLIB.array_string_non_empty_type().clone())
            .unwrap_array();

        (first, array, false, context.arguments[1].span)
    };

    // Join the first argument with the base path as it might be relative
    let first = context.base_dir().join(&first).map_err(|_| {
        function_call_failed(
            FUNCTION_NAME,
            format!("path `{first}` cannot be joined with the evaluation base path"),
            context.arguments[0].span,
        )
    })?;

    if first.is_local() {
        let mut path = first.unwrap_local();
        for (i, element) in array
            .as_slice()
            .iter()
            .enumerate()
            .skip(if skip { 1 } else { 0 })
        {
            let next = element.as_string().expect("element should be string");
            let p = Path::new(next.as_str());
            if !p.is_relative() {
                return Err(function_call_failed(
                    FUNCTION_NAME,
                    format!("path `{next}` (array index {i}) is not a relative path"),
                    array_span,
                ));
            }

            path.push(p);
        }

        Ok(PrimitiveValue::new_string(
            path.clean()
                .into_os_string()
                .into_string()
                .expect("should be UTF-8"),
        )
        .into())
    } else {
        let mut url = first.unwrap_remote();
        for (i, element) in array
            .as_slice()
            .iter()
            .enumerate()
            .skip(if skip { 1 } else { 0 })
        {
            let next = element.as_string().expect("element should be string");
            if next.starts_with('/') || next.contains(":") {
                return Err(function_call_failed(
                    FUNCTION_NAME,
                    format!("path `{next}` (array index {i}) is not a relative path"),
                    array_span,
                ));
            }

            // For consistency with `PathBuf::push`, push an empty segment so that we treat
            // the last segment as a directory; otherwise, `Url::join` will treat it as a
            // file.
            if let Ok(mut segments) = url.path_segments_mut() {
                segments.pop_if_empty();
                segments.push("");
            }

            url = url.join(next).map_err(|_| {
                function_call_failed(
                    FUNCTION_NAME,
                    format!("path `{next}` (array index {i}) cannot be joined with URL `{url}`"),
                    context.arguments[1].span,
                )
            })?;
        }

        Ok(PrimitiveValue::new_string(url.to_string()).into())
    }
}

/// Gets the function describing `join_paths`.
pub const fn descriptor() -> Function {
    Function::new(
        const {
            &[
                Signature::new(
                    "(base: Directory, relative: String) -> String",
                    Callback::Sync(join_paths_simple),
                ),
                Signature::new(
                    "(base: Directory, relative: Array[String]+) -> String",
                    Callback::Sync(join_paths),
                ),
                Signature::new(
                    "(paths: Array[String]+) -> String",
                    Callback::Sync(join_paths),
                ),
            ]
        },
    )
}

#[cfg(test)]
mod test {
    use pretty_assertions::assert_eq;
    use wdl_ast::version::V1;

    use crate::v1::test::TestEnv;
    use crate::v1::test::eval_v1_expr;

    #[tokio::test]
    async fn join_paths() {
        let env = TestEnv::default();
        #[cfg(unix)]
        {
            use std::path::Path;

            let value = eval_v1_expr(&env, V1::Two, "join_paths('/usr', ['bin', 'echo'])")
                .await
                .unwrap();
            assert_eq!(value.unwrap_string().as_str(), "/usr/bin/echo");

            let value = eval_v1_expr(&env, V1::Two, "join_paths(['/usr', 'bin', 'echo'])")
                .await
                .unwrap();
            assert_eq!(value.unwrap_string().as_str(), "/usr/bin/echo");

            let value = eval_v1_expr(&env, V1::Two, "join_paths('mydir', 'mydata.txt')")
                .await
                .unwrap();
            assert_eq!(
                Path::new(value.unwrap_string().as_str())
                    .strip_prefix(env.base_dir().as_local().unwrap())
                    .unwrap()
                    .to_str()
                    .unwrap(),
                "mydir/mydata.txt"
            );

            let value = eval_v1_expr(&env, V1::Two, "join_paths('/usr', 'bin/echo')")
                .await
                .unwrap();
            assert_eq!(value.unwrap_string().as_str(), "/usr/bin/echo");

            let diagnostic = eval_v1_expr(&env, V1::Two, "join_paths('/usr', '/bin/echo')")
                .await
                .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `/bin/echo` is not a relative path"
            );

            let diagnostic =
                eval_v1_expr(&env, V1::Two, "join_paths('/usr', ['foo', '/bin/echo'])")
                    .await
                    .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `/bin/echo` (array index 1) is not a \
                 relative path"
            );

            let diagnostic =
                eval_v1_expr(&env, V1::Two, "join_paths(['/usr', 'foo', '/bin/echo'])")
                    .await
                    .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `/bin/echo` (array index 2) is not a \
                 relative path"
            );
        }

        #[cfg(windows)]
        {
            let diagnostic = eval_v1_expr(&env, V1::Two, "join_paths('C:\\usr', 'C:\\bin\\echo')")
                .await
                .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `C:\\bin\\echo` is not a relative path"
            );

            let diagnostic = eval_v1_expr(
                &env,
                V1::Two,
                "join_paths('C:\\usr', ['foo', 'C:\\bin\\echo'])",
            )
            .await
            .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `C:\\bin\\echo` (array index 1) is \
                 not a relative path"
            );

            let diagnostic = eval_v1_expr(
                &env,
                V1::Two,
                "join_paths(['C:\\usr', 'foo', 'C:\\bin\\echo'])",
            )
            .await
            .unwrap_err();
            assert_eq!(
                diagnostic.message(),
                "call to function `join_paths` failed: path `C:\\bin\\echo` (array index 2) is \
                 not a relative path"
            );
        }

        let diagnostic = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com', '/foo/bar')",
        )
        .await
        .unwrap_err();
        assert_eq!(
            diagnostic.message(),
            "call to function `join_paths` failed: path `/foo/bar` is not a relative path"
        );

        let diagnostic = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com', '//wrong.org/foo')",
        )
        .await
        .unwrap_err();
        assert_eq!(
            diagnostic.message(),
            "call to function `join_paths` failed: path `//wrong.org/foo` is not a relative path"
        );

        let diagnostic = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com', 'https://wrong.org/foo')",
        )
        .await
        .unwrap_err();
        assert_eq!(
            diagnostic.message(),
            "call to function `join_paths` failed: path `https://wrong.org/foo` is not a relative \
             path"
        );

        let value = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com', 'foo/bar/baz')",
        )
        .await
        .unwrap();
        assert_eq!(
            value.unwrap_string().as_str(),
            "https://example.com/foo/bar/baz"
        );

        let value = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com/foo/bar/', 'baz')",
        )
        .await
        .unwrap();
        assert_eq!(
            value.unwrap_string().as_str(),
            "https://example.com/foo/bar/baz"
        );

        let value = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com/foo/bar', '../baz')",
        )
        .await
        .unwrap();
        assert_eq!(
            value.unwrap_string().as_str(),
            "https://example.com/foo/baz"
        );

        let value = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com/foo/bar', ['nope', '../baz', 'qux'])",
        )
        .await
        .unwrap();
        assert_eq!(
            value.unwrap_string().as_str(),
            "https://example.com/foo/bar/baz/qux"
        );

        let value = eval_v1_expr(
            &env,
            V1::Two,
            "join_paths('https://example.com/foo/bar?foo=jam', 'baz?foo=qux')",
        )
        .await
        .unwrap();
        assert_eq!(
            value.unwrap_string().as_str(),
            "https://example.com/foo/bar/baz?foo=qux"
        );
    }
}