Merge pull request #86 from samply/develop

Helpful error message when deserialization in obfuscation method fails
samply · Dec 8, 2023 · 719c6e4 · 719c6e4
2 parents 5113864 + d455cfa
commit 719c6e4
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Showing 2 changed files with 149 additions and 3 deletions.
diff --git a/resources/test/measure_report_exliquid.json b/resources/test/measure_report_exliquid.json
@@ -0,0 +1,117 @@
+{
+    "date": "2023-12-08T14:37:25.66727986Z",
+    "group": [
+        {
+            "stratifier": [
+                {
+                    "code": [
+                        {
+                            "coding": [
+                                {
+                                    "system": "https://dktk.dkfz.de/fhir/CodeSystem/exliquid-stratifier",
+                                    "code": "diagnosis"
+                                }
+                            ]
+                        }
+                    ]
+                }
+            ],
+            "population": [
+                {
+                    "subjectResults": {
+                        "reference": "List/DDCJ3SRU5DPLO4N3"
+                    },
+                    "count": 0,
+                    "code": {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                                "code": "initial-population"
+                            }
+                        ]
+                    }
+                }
+            ],
+            "code": {
+                "coding": [
+                    {
+                        "system": "https://dktk.dkfz.de/fhir/CodeSystem/exliquid-measure-group",
+                        "code": "patient"
+                    }
+                ]
+            }
+        },
+        {
+            "stratifier": [
+                {
+                    "code": [
+                        {
+                            "coding": [
+                                {
+                                    "system": "https://dktk.dkfz.de/fhir/CodeSystem/exliquid-stratifier",
+                                    "code": "sample-diagnosis"
+                                }
+                            ]
+                        },
+                        {
+                            "coding": [
+                                {
+                                    "system": "https://dktk.dkfz.de/fhir/CodeSystem/exliquid-stratifier",
+                                    "code": "sample-type"
+                                }
+                            ]
+                        }
+                    ]
+                }
+            ],
+            "population": [
+                {
+                    "subjectResults": {
+                        "reference": "List/DDCJ3SRU5DPLO4N4"
+                    },
+                    "count": 0,
+                    "code": {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                                "code": "initial-population"
+                            }
+                        ]
+                    }
+                }
+            ],
+            "code": {
+                "coding": [
+                    {
+                        "system": "https://dktk.dkfz.de/fhir/CodeSystem/exliquid-measure-group",
+                        "code": "specimen"
+                    }
+                ]
+            }
+        }
+    ],
+    "meta": {
+        "versionId": "615",
+        "lastUpdated": "2023-12-08T14:37:25.775Z"
+    },
+    "type": "subject-list",
+    "resourceType": "MeasureReport",
+    "measure": "urn:uuid:7ff542ad-69e4-48ed-a2d3-2efafb609f61",
+    "extension": [
+        {
+            "url": "https://samply.github.io/blaze/fhir/StructureDefinition/eval-duration",
+            "valueQuantity": {
+                "value": 0.027764815,
+                "unit": "s",
+                "system": "http://unitsofmeasure.org",
+                "code": "s"
+            }
+        }
+    ],
+    "status": "complete",
+    "id": "DDCJ3SRWUBLWIFTI",
+    "period": {
+        "start": "2000",
+        "end": "2030"
+    }
+}
diff --git a/src/util.rs b/src/util.rs
@@ -150,7 +150,7 @@ pub fn obfuscate_counts_mr(
         _ => ObfuscateBelow10Mode::Obfuscate,
     };
     let mut measure_report: MeasureReport = serde_json::from_str(&json_str)
-        .map_err(|e| FocusError::DeserializationError(e.to_string()))?;
+        .map_err(|e| FocusError::DeserializationError(format!(r#"{}. Is obfuscation turned on when it shouldn't be? Is the metadata in the task formatted correctly, like this {{"project": "name"}}? Are there any other projects stated in the projects_no_obfuscation parameter in the bridgehead?"#, e)))?;
     for g in &mut measure_report.group {
         match &g.code.text[..] {
             "patients" => {
@@ -346,8 +346,11 @@ mod test {
     use super::*;
     use serde_json::json;
 
-    const EXAMPLE_MEASURE_REPORT_BBMRI: &str = include_str!("../resources/measure_report_bbmri.json");
+    const EXAMPLE_MEASURE_REPORT_BBMRI: &str =
+        include_str!("../resources/measure_report_bbmri.json");
     const EXAMPLE_MEASURE_REPORT_DKTK: &str = include_str!("../resources/measure_report_dktk.json");
+    const EXAMPLE_MEASURE_REPORT_EXLIQUID: &str =
+        include_str!("../resources/test/measure_report_exliquid.json");
 
     const DELTA_PATIENT: f64 = 1.;
     const DELTA_SPECIMEN: f64 = 20.;
@@ -482,7 +485,8 @@ mod test {
         assert_eq!(replace_cql(decoded_library), expected_result);
 
         let decoded_library = "EXLIQUID_STRAT_W_ALIQUOTS";
-        let expected_result = "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n\n";
+        let expected_result =
+            "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n\n";
 
         assert_eq!(replace_cql(decoded_library), expected_result);
 
@@ -587,4 +591,29 @@ mod test {
         .unwrap();
         assert_eq!(obfuscated_json, obfuscated_json_2);
     }
+
+    #[test]
+    fn test_obfuscate_counts_bad_measure() {
+        let mut obf_cache = ObfCache {
+            cache: HashMap::new(),
+        };
+        let obfuscated_json = obfuscate_counts_mr(
+            EXAMPLE_MEASURE_REPORT_EXLIQUID,
+            &mut obf_cache,
+            false,
+            1,
+            DELTA_PATIENT,
+            DELTA_SPECIMEN,
+            DELTA_DIAGNOSIS,
+            DELTA_PROCEDURES,
+            DELTA_MEDICATION_STATEMENTS,
+            EPSILON,
+            ROUNDING_STEP,
+        );
+
+        assert_eq!(
+            obfuscated_json.unwrap_err().to_string(),
+            r#"Deserialization error: missing field `text` at line 42 column 13. Is obfuscation turned on when it shouldn't be? Is the metadata in the task formatted correctly, like this {"project": "name"}? Are there any other projects stated in the projects_no_obfuscation parameter in the bridgehead?"#
+        );
+    }
 }