Merge pull request #153 from samply/fix/value_quantity

another type of extension in MR model

resources/test/measure_report_bbmri_new_extension.json

@@ -0,0 +1 @@
+{"date": "2023-03-03T15:54:21.740195064Z", "extension": [{"url": "https://samply.github.io/blaze/fhir/StructureDefinition/eval-duration", "valueQuantity": {"code": "s", "system": "http://unitsofmeasure.org", "unit": "s", "value": 0.050495759}}, {"url":"https://samply.github.io/blaze/fhir/StructureDefinition/bloom-filter-ratio","valueRatio":{"denominator":{"value":0},"numerator":{"value":0}}}], "group": [{"code": {"text": "patients"}, "population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 74}], "stratifier": [{"code": [{"text": "Gender"}], "stratum": [{"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 31}], "value": {"text": "female"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 43}], "value": {"text": "male"}}]}, {"code": [{"text": "Age"}], "stratum": [{"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 5}], "value": {"text": "40"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 4}], "value": {"text": "50"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 14}], "value": {"text": "60"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 4}], "value": {"text": "80"}}]}, {"code": [{"text": "Custodian"}], "stratum": [{"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 31}], "value": {"text": "bbmri-eric:ID:CZ_CUNI_PILS:collection:serum_plasma"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 43}], "value": {"text": "null"}}]}]}, {"code": {"text": "diagnosis"}, "population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 324}], "stratifier": [{"code": [{"text": "diagnosis"}], "stratum": [{"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 26}], "value": {"text": "C34.0"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 28}], "value": {"text": "C34.2"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 25}], "value": {"text": "C34.8"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 27}], "value": {"text": "C78.0"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 25}], "value": {"text": "D38.6"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 25}], "value": {"text": "R91"}}]}]}, {"code": {"text": "specimen"}, "population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 124}], "stratifier": [{"code": [{"text": "sample_kind"}], "stratum": [{"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 62}], "value": {"text": "blood-plasma"}}, {"population": [{"code": {"coding": [{"code": "initial-population", "system": "http://terminology.hl7.org/CodeSystem/measure-population"}]}, "count": 62}], "value": {"text": "blood-serum"}}]}]}], "measure": "urn:uuid:fe7e5bf7-d792-4368-b1d2-5798930db13e", "period": {"end": "2030", "start": "2000"}, "resourceType": "MeasureReport", "status": "complete", "type": "summary", "meta": {"lastUpdated": "2023-06-27T13:12:56.719Z", "versionId": "11"}, "id": "DCH47RNHPKH6TC3W"}

src/util.rs

@@ -8,7 +8,7 @@ use serde_json::{json, Value};
 use std::collections::HashMap;
 use std::fs::File;
 use std::io::{self, BufRead, BufReader};
-use std::path::{Path, PathBuf};
+use std::path::{Path};
 use tracing::warn;
 
 #[derive(Debug, Deserialize, Serialize)]
@@ -25,11 +25,18 @@ struct ValueQuantity {
     value: f64,
 }
 
+#[derive(Debug, Deserialize, Serialize)]
+struct ValueRatio {
+    denominator: Value,
+    numerator: Value,
+}
+
 #[derive(Debug, Deserialize, Serialize)]
 #[serde(rename_all = "camelCase")]
 struct Extension {
     url: String,
-    value_quantity: ValueQuantity,
+    value_quantity: Option<ValueQuantity>,
+    value_ratio: Option<ValueRatio>,
 }
 
 #[derive(Debug, Deserialize, Serialize)]
@@ -351,6 +358,8 @@ mod test {
     const QUERY_BBMRI: &str = include_str!("../resources/test/query_bbmri.cql");
     const EXAMPLE_MEASURE_REPORT_BBMRI: &str =
         include_str!("../resources/test/measure_report_bbmri.json");
+        const EXAMPLE_MEASURE_REPORT_BBMRI_NEW_EXTENSION: &str =
+        include_str!("../resources/test/measure_report_bbmri_new_extension.json");
     const EXAMPLE_MEASURE_REPORT_DKTK: &str =
         include_str!("../resources/test/measure_report_dktk.json");
     const EXAMPLE_MEASURE_REPORT_EXLIQUID: &str =
@@ -453,6 +462,52 @@ mod test {
         pretty_assertions::assert_eq!(replace_cql(decoded_library), expected_result);
     }
 
+    #[test]
+    fn test_obfuscate_counts_bbmri_new_extension() {
+        let mut obf_cache = ObfCache {
+            cache: HashMap::new(),
+        };
+        let obfuscated_json = obfuscate_counts_mr(
+            EXAMPLE_MEASURE_REPORT_BBMRI_NEW_EXTENSION,
+            &mut obf_cache,
+            false,
+            1,
+            DELTA_PATIENT,
+            DELTA_SPECIMEN,
+            DELTA_DIAGNOSIS,
+            DELTA_PROCEDURES,
+            DELTA_MEDICATION_STATEMENTS,
+            DELTA_HISTO,
+            EPSILON,
+            ROUNDING_STEP,
+        )
+        .unwrap();
+
+        // Check that the obfuscated JSON can be parsed and has the same structure as the original JSON
+        let _: MeasureReport = serde_json::from_str(&obfuscated_json).unwrap();
+
+        // Check that the obfuscated JSON is different from the original JSON
+        assert_ne!(obfuscated_json, EXAMPLE_MEASURE_REPORT_BBMRI_NEW_EXTENSION);
+
+        // Check that obfuscating the same JSON twice with the same obfuscation cache gives the same result
+        let obfuscated_json_2 = obfuscate_counts_mr(
+            EXAMPLE_MEASURE_REPORT_BBMRI_NEW_EXTENSION,
+            &mut obf_cache,
+            false,
+            1,
+            DELTA_PATIENT,
+            DELTA_SPECIMEN,
+            DELTA_DIAGNOSIS,
+            DELTA_PROCEDURES,
+            DELTA_MEDICATION_STATEMENTS,
+            DELTA_HISTO,
+            EPSILON,
+            ROUNDING_STEP,
+        )
+        .unwrap();
+        pretty_assertions::assert_eq!(obfuscated_json, obfuscated_json_2);
+    }
+
     #[test]
     fn test_obfuscate_counts_bbmri() {
         let mut obf_cache = ObfCache {
@@ -499,6 +554,7 @@ mod test {
         pretty_assertions::assert_eq!(obfuscated_json, obfuscated_json_2);
     }
 
+
     #[test]
     fn test_obfuscate_counts_dktk() {
         let mut obf_cache = ObfCache {