chore: changed stratifier to dktk sample centric search

packages/demo/src/AppCCP.svelte

@@ -9,7 +9,7 @@
         dktkMedicationStatementsMeasure,
         dktkPatientsMeasure,
         dktkProceduresMeasure,
-        dktkSpecimenMeasure,
+        dktkSpecificSpecimenMeasure,
         dktkHistologyMeasure,
     } from "./measures";
 
@@ -65,7 +65,7 @@
             measures: [
                 dktkPatientsMeasure as MeasureItem,
                 dktkDiagnosisMeasure as MeasureItem,
-                dktkSpecimenMeasure as MeasureItem,
+                dktkSpecificSpecimenMeasure as MeasureItem,
                 dktkProceduresMeasure as MeasureItem,
                 dktkMedicationStatementsMeasure as MeasureItem,
                 dktkHistologyMeasure as MeasureItem,

packages/demo/src/backends/ast-to-cql-translator.ts

@@ -110,11 +110,8 @@ const getSingleton = (criterion: AstBottomLayerValue): string => {
         if (myCQL) {
             switch (myCriterion.type) {
                 case "gender":
-                case "BBMRI_gender":
                 case "histology":
                 case "conditionValue":
-                case "BBMRI_conditionValue":
-                case "BBMRI_conditionSampleDiagnosis":
                 case "conditionBodySite":
                 case "conditionLocalization":
                 case "observation":
@@ -125,8 +122,6 @@ const getSingleton = (criterion: AstBottomLayerValue): string => {
                 case "procedureResidualstatus":
                 case "medicationStatement":
                 case "specimen":
-                case "BBMRI_specimen":
-                case "BBMRI_hasSpecimen":
                 case "hasSpecimen":
                 case "Organization":
                 case "observationMolecularMarkerName":

packages/demo/src/backends/cqlquery-mappings.ts

@@ -207,69 +207,6 @@ export const cqltemplate = new Map<string, string>([
         "(exists ([Observation: Code '21908-9' from loinc] O where O.value.coding.code contains '{{C}}')) or (exists ([Observation: Code '21902-2' from loinc] O where O.value.coding.code contains '{{C}}'))",
     ],
     ["histology", "exists from [Observation: Code '59847-4' from loinc] O\n"],
-
-    ["BBMRI_gender", "Patient.gender"],
-    [
-        "BBMRI_conditionSampleDiagnosis",
-        "((exists[Condition: Code '{{C}}' from {{A1}}]) or (exists[Condition: Code '{{C}}' from {{A2}}])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains '{{C}}'))",
-    ],
-    ["BBMRI_conditionValue", "exists [Condition: Code '{{C}}' from {{A1}}]"],
-    [
-        "BBMRI_conditionRangeDate",
-        "exists from [Condition] C\nwhere FHIRHelpers.ToDateTime(C.onset) between {{D1}} and {{D2}}",
-    ],
-    [
-        "BBMRI_conditionRangeAge",
-        "exists from [Condition] C\nwhere AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling({{D1}}) and Ceiling({{D2}})",
-    ],
-    ["BBMRI_age", "AgeInYears() between Ceiling({{D1}}) and Ceiling({{D2}})"],
-    [
-        "BBMRI_observation",
-        "exists from [Observation: Code '{{K}}' from {{A1}}] O\nwhere O.value.coding.code contains '{{C}}'",
-    ],
-    [
-        "BBMRI_observationSmoker",
-        "exists from [Observation: Code '72166-2' from {{A1}}] O\nwhere O.value.coding.code contains '{{C}}'",
-    ],
-    [
-        "BBMRI_observationRange",
-        "exists from [Observation: Code '{{K}}' from {{A1}}] O\nwhere O.value between {{D1}} and {{D2}}",
-    ],
-    [
-        "BBMRI_observationBodyWeight",
-        "exists from [Observation: Code '29463-7' from {{A1}}] O\nwhere ((O.value as Quantity) < {{D1}} 'kg' and (O.value as Quantity) > {{D2}} 'kg')",
-    ],
-    [
-        "BBMRI_observationBMI",
-        "exists from [Observation: Code '39156-5' from {{A1}}] O\nwhere ((O.value as Quantity) < {{D1}} 'kg/m2' and (O.value as Quantity) > {{D2}} 'kg/m2')",
-    ],
-    ["BBMRI_hasSpecimen", "exists [Specimen]"],
-    ["BBMRI_specimen", "exists [Specimen: Code '{{C}}' from {{A1}}]"],
-    ["BBMRI_retrieveSpecimenByType", "(S.type.coding.code contains '{{C}}')"],
-    [
-        "BBMRI_retrieveSpecimenByTemperature",
-        "(S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding.code contains '{{C}}')",
-    ],
-    [
-        "BBMRI_retrieveSpecimenBySamplingDate",
-        "(FHIRHelpers.ToDateTime(S.collection.collected) between {{D1}} and {{D2}})",
-    ],
-    [
-        "BBMRI_retrieveSpecimenByFastingStatus",
-        "(S.collection.fastingStatus.coding.code contains '{{C}}')",
-    ],
-    [
-        "BBMRI_samplingDate",
-        "exists from [Specimen] S\nwhere FHIRHelpers.ToDateTime(S.collection.collected) between {{D1}} and {{D2}}",
-    ],
-    [
-        "BBMRI_fastingStatus",
-        "exists from [Specimen] S\nwhere S.collection.fastingStatus.coding.code contains '{{C}}'",
-    ],
-    [
-        "BBMRI_storageTemperature",
-        "exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code '{{C}}' from {{A1}})",
-    ],
 ]);
 
 export const criterionMap = new Map<string, { type: string; alias?: string[] }>(

packages/demo/src/measures.ts

@@ -913,6 +913,50 @@ DKTK_STRAT_SPECIMEN_STRATIFIER
 `,
 };
 
+export const dktkSpecificSpecimenMeasure = {
+    key: "specimen",
+    measure: {
+        code: {
+            text: "specimen",
+        },
+        extension: [
+            {
+                url: "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-populationBasis",
+                valueCode: "Specimen",
+            },
+        ],
+        population: [
+            {
+                code: {
+                    coding: [
+                        {
+                            system: "http://terminology.hl7.org/CodeSystem/measure-population",
+                            code: "initial-population",
+                        },
+                    ],
+                },
+                criteria: {
+                    language: "text/cql-identifier",
+                    expression: "Specimen",
+                },
+            },
+        ],
+        stratifier: [
+            {
+                code: {
+                    text: "sample_kind",
+                },
+                criteria: {
+                    language: "text/cql",
+                    expression: "SampleType",
+                },
+            },
+        ],
+    },
+    cql: `
+DKTK_REPLACE_SPECIMEN_STRATIFIER`,
+};
+
 export const dktkProceduresMeasure = {
     key: "procedures",
     measure: {
@@ -1044,6 +1088,6 @@ export const dktkHistologyMeasure = {
         ],
     },
     cql: `
-  DKTK_STRAT_HISTOLOGY_STRATIFIER
+  DKTK_REPLACE_HISTOLOGY_STRATIFIER
 `,
 };

packages/lib/src/components/results/ChartComponent.wc.svelte

@@ -271,16 +271,21 @@
                     valueToAccumulate.values,
                     catalogueGroupCode,
                 );
-
-                combinedSubGroupData.data.push(aggregationCount);
-                combinedSubGroupData.labels.push(valueToAccumulate.name);
-
-                for (let i = 0; i < combinedSubGroupData.labels.length; i++) {
-                    const element: string = combinedSubGroupData.labels[i];
-                    if (valueToAccumulate.values.includes(element)) {
-                        combinedSubGroupData.labels.splice(i, 1);
-                        combinedSubGroupData.data.splice(i, 1);
-                        i--;
+                if (aggregationCount > 0) {
+                    combinedSubGroupData.data.push(aggregationCount);
+                    combinedSubGroupData.labels.push(valueToAccumulate.name);
+
+                    for (
+                        let i = 0;
+                        i < combinedSubGroupData.labels.length;
+                        i++
+                    ) {
+                        const element: string = combinedSubGroupData.labels[i];
+                        if (valueToAccumulate.values.includes(element)) {
+                            combinedSubGroupData.labels.splice(i, 1);
+                            combinedSubGroupData.data.splice(i, 1);
+                            i--;
+                        }
                     }
                 }
             });