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Feat/bbmri cql #93

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May 13, 2024
Merged

Feat/bbmri cql #93

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5 changes: 5 additions & 0 deletions packages/lib/src/cql-translator-service/ast-to-cql-translator.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -119,8 +119,11 @@ 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":
Expand All @@ -131,6 +134,8 @@ const getSingleton = (criterion: AstBottomLayerValue): string => {
case "procedureResidualstatus":
case "medicationStatement":
case "specimen":
case "BBMRI_specimen":
case "BBMRI_hasSpecimen":
case "hasSpecimen":
case "Organization":
case "observationMolecularMarkerName":
Expand Down
116 changes: 116 additions & 0 deletions packages/lib/src/cql-translator-service/cqlquery-mappings.ts
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Expand Up @@ -63,6 +63,21 @@ export const alias = new Map<string, string>([
"http://dktk.dkfz.de/fhir/onco/core/CodeSystem/TNMmSymbolCS",
],
["molecularMarker", "http://www.genenames.org"],

["BBMRI_icd10", "http://hl7.org/fhir/sid/icd-10"],
["BBMRI_icd10gm", "http://fhir.de/CodeSystem/dimdi/icd-10-gm"],
[
"BBMRI_SampleMaterialType",
"https://fhir.bbmri.de/CodeSystem/SampleMaterialType",
], //specimentype
[
"BBMRI_StorageTemperature",
"https://fhir.bbmri.de/CodeSystem/StorageTemperature",
],
[
"BBMRI_SmokingStatus",
"http://hl7.org/fhir/uv/ips/ValueSet/current-smoking-status-uv-ips",
],
]);

export const cqltemplate = new Map<string, string>([
Expand Down Expand Up @@ -192,6 +207,69 @@ 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[] }>(
Expand Down Expand Up @@ -309,5 +387,43 @@ export const criterionMap = new Map<string, { type: string; alias?: string[] }>(
["75186-7", { type: "observation", alias: ["loinc", "vitalstatuscs"] }], //Vitalstatus
//["Organization", {type: "Organization"}],
["Organization", { type: "department" }],

["BBMRI_gender", { type: "BBMRI_gender" }],
[
"BBMRI_diagnosis",
{
type: "BBMRI_conditionSampleDiagnosis",
alias: ["BBMRI_icd10", "BBMRI_icd10gm"],
},
],
[
"BBMRI_body_weight",
{ type: "BBMRI_observationBodyWeight", alias: ["loinc"] },
], //Body weight
["BBMRI_bmi", { type: "BBMRI_observationBMI", alias: ["loinc"] }], //BMI
[
"BBMRI_smoking_status",
{ type: "BBMRI_observationSmoker", alias: ["loinc"] },
], //Smoking habit
["BBMRI_donor_age", { type: "BBMRI_age" }],
["BBMRI_date_of_diagnosis", { type: "BBMRI_conditionRangeDate" }],
[
"BBMRI_sample_kind",
{ type: "BBMRI_specimen", alias: ["BBMRI_SampleMaterialType"] },
],
[
"BBMRI_storage_temperature",
{
type: "BBMRI_storageTemperature",
alias: ["BBMRI_StorageTemperature"],
},
],
["BBMRI_pat_with_samples", { type: "BBMRI_hasSpecimen" }],
["BBMRI_diagnosis_age_donor", { type: "BBMRI_conditionRangeAge" }],
[
"BBMRI_fasting_status",
{ type: "BBMRI_fastingStatus", alias: ["loinc"] },
],
["BBMRI_sampling_date", { type: "BBMRI_samplingDate" }],
],
);
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