helios-sof 0.1.47

This crate provides a complete implementation of the SQL-on-FHIR specification for Rust, enabling the transformation of FHIR resources into tabular data using declarative ViewDefinitions. It supports all major FHIR versions (R4, R4B, R5, R6) through a version-agnostic abstraction layer.
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
//! Tests for header parameter in the request body

use axum::http::StatusCode;
use serde_json::json;

mod common;

#[tokio::test]
async fn test_header_parameter_boolean_true() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",
                "valueBoolean": true
            },
            {
                "name": "_format",
                "valueCode": "text/csv"
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"},
                            {"name": "gender", "path": "gender"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-1",
                    "gender": "male"
                }
            }
        ]
    });

    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .json(&request_body)
        .await;

    assert_eq!(response.status_code(), StatusCode::OK);
    assert_eq!(
        response.header("content-type").to_str().unwrap(),
        "text/csv"
    );

    let csv_text = response.text();
    let lines: Vec<&str> = csv_text.lines().collect();

    // Should have column headers when valueBoolean is true
    assert_eq!(lines.len(), 2);
    assert!(lines[0].contains("id") && lines[0].contains("gender"));
    assert!(lines[1].contains("test-1") && lines[1].contains("male"));
}

#[tokio::test]
async fn test_header_parameter_boolean_false() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",  // Test without underscore
                "valueBoolean": false
            },
            {
                "name": "_format",
                "valueCode": "text/csv"
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"},
                            {"name": "birthDate", "path": "birthDate"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-2",
                    "birthDate": "1990-01-01"
                }
            }
        ]
    });

    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .json(&request_body)
        .await;

    assert_eq!(response.status_code(), StatusCode::OK);
    assert_eq!(
        response.header("content-type").to_str().unwrap(),
        "text/csv"
    );

    let csv_text = response.text();
    let lines: Vec<&str> = csv_text.lines().collect();

    // Should NOT have column headers when valueBoolean is false
    assert_eq!(lines.len(), 1);
    assert!(!lines[0].contains("id,birthDate")); // No column header row
    assert!(lines[0].contains("test-2") && lines[0].contains("1990-01-01"));
}

#[tokio::test]
async fn test_header_parameter_overrides_query() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",
                "valueBoolean": false  // Body says no header
            },
            {
                "name": "_format",
                "valueCode": "text/csv"
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-3"
                }
            }
        ]
    });

    // Query parameter says true, but body should override
    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .add_query_param("header", "true")
        .json(&request_body)
        .await;

    assert_eq!(response.status_code(), StatusCode::OK);

    let csv_text = response.text();
    let lines: Vec<&str> = csv_text.lines().collect();

    // Body parameter (false) should override query parameter (true)
    assert_eq!(lines.len(), 1);
    assert!(!lines[0].contains("id")); // No column headers
    assert!(lines[0].contains("test-3"));
}

#[tokio::test]
async fn test_header_parameter_without_format() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",
                "valueBoolean": true
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-4"
                }
            }
        ]
    });

    // No format specified, should default to JSON
    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .json(&request_body)
        .await;

    // header parameter only applies to CSV, should get error with JSON format
    assert_eq!(response.status_code(), StatusCode::BAD_REQUEST);

    let json: serde_json::Value = response.json();
    assert_eq!(json["resourceType"], "OperationOutcome");
    assert!(
        json["issue"][0]["details"]["text"]
            .as_str()
            .unwrap()
            .contains("Header parameter only applies to CSV format")
    );
}

#[tokio::test]
async fn test_header_parameter_with_csv_accept() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",
                "valueBoolean": false
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-5"
                }
            }
        ]
    });

    // Accept header requests CSV
    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .add_header("Accept", "text/csv")
        .json(&request_body)
        .await;

    assert_eq!(response.status_code(), StatusCode::OK);
    assert_eq!(
        response.header("content-type").to_str().unwrap(),
        "text/csv"
    );

    let csv_text = response.text();
    let lines: Vec<&str> = csv_text.lines().collect();

    // header parameter false should remove column headers even with CSV accept
    assert_eq!(lines.len(), 1);
    assert!(!lines[0].contains("id"));
    assert!(lines[0].contains("test-5"));
}

#[tokio::test]
async fn test_invalid_header_parameter_type() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "header",
                "valueString": "yes"  // Should be boolean, not string
            },
            {
                "name": "_format",
                "valueCode": "text/csv"
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-6"
                }
            }
        ]
    });

    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .json(&request_body)
        .await;

    // Should get bad request for non-boolean header value
    let status = response.status_code();
    let json: serde_json::Value = response.json();

    if status != StatusCode::BAD_REQUEST {
        // Debug output to understand what happened
        eprintln!("Unexpected response status: {}", status);
        eprintln!(
            "Response body: {}",
            serde_json::to_string_pretty(&json).unwrap()
        );
    }
    assert_eq!(status, StatusCode::BAD_REQUEST);

    assert_eq!(json["resourceType"], "OperationOutcome");
    assert!(
        json["issue"][0]["details"]["text"]
            .as_str()
            .unwrap()
            .contains("Header parameter must be a boolean value")
    );
}

#[tokio::test]
async fn test_both_format_and_header_in_body() {
    let server = common::test_server().await;

    let request_body = json!({
        "resourceType": "Parameters",
        "parameter": [
            {
                "name": "_format",
                "valueCode": "text/csv"
            },
            {
                "name": "header",
                "valueBoolean": true
            },
            {
                "name": "viewResource",
                "resource": {
                    "resourceType": "ViewDefinition",
                    "status": "active",
                    "resource": "Patient",
                    "select": [{
                        "column": [
                            {"name": "id", "path": "id"},
                            {"name": "active", "path": "active"}
                        ]
                    }]
                }
            },
            {
                "name": "resource",
                "resource": {
                    "resourceType": "Patient",
                    "id": "test-7",
                    "active": true
                }
            }
        ]
    });

    let response = server
        .post("/ViewDefinition/$viewdefinition-run")
        .json(&request_body)
        .await;

    assert_eq!(response.status_code(), StatusCode::OK);
    assert_eq!(
        response.header("content-type").to_str().unwrap(),
        "text/csv"
    );

    let csv_text = response.text();
    let lines: Vec<&str> = csv_text.lines().collect();

    // Both format and header specified in body
    assert_eq!(lines.len(), 2);
    assert!(lines[0].contains("id") && lines[0].contains("active"));
    assert!(lines[1].contains("test-7") && lines[1].contains("true"));
}