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Merge pull request #37 from samply/feature/addCqlTemplatesNNGM
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Added CQL Templates for nNGM
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@torbrenner
torbrenner committed Dec 12, 2023
2 parents 66538a2 + 3285704 commit fd02b5b
Showing 1 changed file with 45 additions and 25 deletions.
70 changes: 45 additions & 25 deletions core/cql/src/cql-translator.service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,14 +25,23 @@ export class CqlTranslatorService implements QueryTranslator {
alias = new Map<string, string>([
['icd10', 'http://fhir.de/CodeSystem/bfarm/icd-10-gm'],
['loinc', 'http://loinc.org'],
["snomed", "http://snomed.info/sct"],
['gradingcs', 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GradingCS'],
["gradingcsnngm", "urn:oid:2.16.840.1.113883.15.16"],
["tnmtnngm", "urn:oid:2.16.840.1.113883.15.16"],
["tnmnnngm", "urn:oid:2.16.840.1.113883.15.16"],
["tnmmnngm", "urn:oid:2.16.840.1.113883.15.16"],
["tnmrynngm", "urn:oid:2.16.840.1.113883.15.16"],
['ops', 'http://fhir.de/CodeSystem/bfarm/ops'],
['morph', 'urn:oid:2.16.840.1.113883.6.43.1'],
['lokalisation_icd_o_3', 'urn:oid:2.16.840.1.113883.6.43.1'],
[
'bodySite',
'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS',
],
["bodySiteNNGM", "http://terminology.hl7.org/CodeSystem/icd-o-3"],
["uicc8nNGM", "http://uk-koeln.de/fhir/CodeSystem/nNGM/uiccStagingV8"],
["uicc7nNGM", "http://uk-koeln.de/fhir/CodeSystem/nNGM/uiccStagingV7"],
[
'Therapieart',
'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SYSTTherapieartCS',
Expand Down Expand Up @@ -66,6 +75,9 @@ export class CqlTranslatorService implements QueryTranslator {
'vitalstatuscs',
'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/VitalstatusCS',
],
["vitalstatuscsnngm", "http://uk-koeln.de/fhir/nNGM/Vitalstatus"],
["raucherstatuscsnngm", "http://uk-koeln.de/fhir/StructureDefinition/Observation/nNGM/raucherstatus"],
["ecogcsnngm", "http://uk-koeln.de/fhir/StructureDefinition/Observation/nNGM/ecog"],
['jnucs', 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS'],
[
'fmlokalisationcs',
Expand Down Expand Up @@ -106,6 +118,8 @@ export class CqlTranslatorService implements QueryTranslator {
["conditionRangeAge", "exists [Condition] C\nwhere AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between {{D1}} and {{D2}}"],
["conditionLowerThanAge", "exists [Condition] C\nwhere AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) <= {{D2}}"],
["conditionGreaterThanAge", "exists [Condition] C\nwhere AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) >= {{D1}}"],
//UICC Anfrage auf Erstdiagnose (V7+V8) sowie auf Condition
["conditionUicc", "(exists from [Condition] C\nwhere (C.stage.summary.coding contains Code '{{C}}' from {{A1}})) or (exists from [Condition] C\nwhere (C.stage.summary.coding contains Code '{{C}}' from {{A2}})) or (exists from [Observation: Code '260879005' from {{A3}}] O\nwhere O.value.coding.code contains '{{C}}')"],
//TODO Revert to first expression if https://github.com/samply/blaze/issues/808 is solved
// ["observation", "exists from [Observation: Code '{{K}}' from {{A1}}] O\nwhere O.value.coding contains Code '{{C}}' from {{A2}}"],
[
Expand Down Expand Up @@ -140,6 +154,11 @@ export class CqlTranslatorService implements QueryTranslator {
'observationMolecularMarkerEnsemblID',
"exists from [Observation: Code '69548-6' from {{A1}}] O\nwhere O.component.where(code.coding contains Code '{{K}}' from {{A1}}).value = '{{C}}'",
],
[
"observationGradingNNGM",
"exists from [Observation: Code '59847-4' from {{A1}}] O\nwhere O.component.where(code.coding contains Code '59542-1' from {{A1}}).value.coding.code = '{{C}}'"
],
["observationTnmNNGM", "exists from [Observation: Code '260879005' from {{A1}}] O\nwhere O.component.where(code.coding contains Code '{{K}}' from {{A1}}).value.coding.code = '{{C}}'"],
['procedure', "exists [Procedure: category in Code '{{K}}' from {{A1}}]"],
[
'procedureResidualstatus',
Expand Down Expand Up @@ -169,12 +188,20 @@ export class CqlTranslatorService implements QueryTranslator {
['gender', { type: 'gender' }],
['samplingDate', { type: 'samplingDate' }],
['diagnosis', { type: 'conditionValue', alias: ['icd10'] }],
['nngmDiagnosis', { type: 'conditionValue', alias: ['lokalisation_icd_o_3'] }],
["uicc", {type: "conditionUicc", alias: ["uicc8","uicc7","snomed"]}],
['bodySite', { type: 'conditionBodySite', alias: ['bodySite'] }],
['bodySiteNNGM', { type: 'conditionBodySite', alias: ['bodySiteNNGM'] }],
[
'urn:oid:2.16.840.1.113883.6.43.1',
{ type: 'conditionLocalization', alias: ['lokalisation_icd_o_3'] },
],
['59542-1', { type: 'observation', alias: ['loinc', 'gradingcs'] }], //grading
["59542-1-nNGM", {type: "observationGradingNNGM", alias: ["loinc", "gradingcsnngm"]}], //grading
["78873005", {type: "observationTnmNNGM", alias: ["snomed", "tnmtnngm"]}], //tnmt
["277206009", {type: "observationTnmNNGM", alias: ["snomed", "tnmnnngm"]}], //tnmn
["277208005", {type: "observationTnmNNGM", alias: ["snomed", "tnmmnngm"]}], //tnmm
["399566009", {type: "observationTnmNNGM", alias: ["snomed", "tnmrynngm"]}], //tnmm
[
'metastases_present',
{ type: 'observationMetastasis', alias: ['loinc', 'jnucs'] },
Expand Down Expand Up @@ -264,6 +291,9 @@ export class CqlTranslatorService implements QueryTranslator {
['75186-7', { type: 'observation', alias: ['loinc', 'vitalstatuscs'] }], //Vitalstatus
//["Organization", {type: "Organization"}],
['Organization', { type: 'department' }],
["67162-8", {type: "observation", alias: ["loinc", "vitalstatuscsnngm"]}], //Vitalstatus
["72166-2", {type: "observation", alias: ["loinc", "raucherstatuscs"]}], //Raucherstatus
["89247-1", {type: "observation", alias: ["loinc", "ecogcs"]}], //ecog
]);

criteria!: Criteria;
Expand Down Expand Up @@ -330,41 +360,19 @@ export class CqlTranslatorService implements QueryTranslator {
break;
}

case "conditionUicc":
case 'conditionValue':
case 'conditionBodySite':
case 'conditionLocalization':
case 'observation':
case "observationGradingNNGM":
case "observationTnmNNGM":
case 'observationMetastasis':
case 'observationMetastasisBodySite':
case 'procedure':
case 'procedureResidualstatus':
case 'medicationStatement':
case 'specimen':
case 'samplingDate':
{
if (
typeof criterion.value == 'object' &&
!(criterion.value instanceof Array) &&
(criterion.value.min instanceof Date &&
criterion.value.max instanceof Date)
)
{
expression = expression.slice(0, -1);
expression += " and ("

expression +=
this.substituteCQLExpressionDate(
criterion.key,
myCriterion.alias,
myCQL,
'',
criterion.value.min as Date,
criterion.value.max as Date
) + ') and\n';
}
break;

}
case 'hasSpecimen':
case 'Organization':
case 'observationMolecularMarkerName':
Expand Down Expand Up @@ -539,10 +547,14 @@ export class CqlTranslatorService implements QueryTranslator {
let cqlString: string;
if (value) {
cqlString = cql.replace(new RegExp('{{C}}'), value);
while (cqlString.search('{{C}}') != -1) {
cqlString = cqlString.replace(new RegExp('{{C}}'), value);
}
} else {
cqlString = cql;
}
cqlString = cqlString.replace(new RegExp('{{K}}'), key);
// TODO: Write this with a loop for future A4 ...
if (alias && alias[0]) {
cqlString = cqlString.replace(new RegExp('{{A1}}', 'g'), alias[0]);
const systemExpression =
Expand All @@ -559,6 +571,14 @@ export class CqlTranslatorService implements QueryTranslator {
this.codesystems.push(systemExpression);
}
}
if (alias && alias[2]) {
cqlString = cqlString.replace(new RegExp('{{A3}}', 'g'), alias[2]);
const systemExpression =
'codesystem ' + alias[2] + ": '" + this.alias.get(alias[2]) + "'";
if (!this.codesystems.includes(systemExpression)) {
this.codesystems.push(systemExpression);
}
}
if (min != undefined) {
cqlString = cqlString.replace(new RegExp("{{D1}}"), min.toString())
}
Expand Down

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