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Extract Zip and Update Tests
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Also removed display from criterion reference name
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@bastianschaffer
bastianschaffer committed Sep 4, 2024
1 parent b239112 commit d0c80c8
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Showing 798 changed files with 830 additions and 60 deletions.
2 changes: 1 addition & 1 deletion src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java
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Expand Up @@ -71,7 +71,7 @@ static Container<RetrieveExpression> retrieveExpr(MappingContext mappingContext,
}

private static String referenceName(TermCode termCode) {
return "%s".formatted(termCode.display() + termCode.code() + "Ref");
return termCode.code() + "Ref";
}

public abstract T appendAttributeFilter(AttributeFilter attributeFilter);
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52 changes: 14 additions & 38 deletions src/test/java/de/numcodex/sq2cql/AcceptanceTest.java
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Expand Up @@ -7,7 +7,11 @@
import com.fasterxml.jackson.databind.ObjectMapper;
import de.numcodex.sq2cql.model.structured_query.StructuredQuery;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Library;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.Parameters;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
Expand All @@ -32,9 +36,8 @@
import java.nio.file.Paths;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.UUID;
import java.util.zip.ZipFile;
import java.util.stream.Stream;

import static de.numcodex.sq2cql.Util.createTranslator;
import static java.lang.String.format;
Expand Down Expand Up @@ -78,41 +81,14 @@ private static Bundle createBundle(Library library, Measure measure) {
}

public static List<StructuredQuery> getTestQueriesReturningOnePatient() throws URISyntaxException, IOException {
var exclusions = Set.of("new_testdata/1-age.json",
// Blaze can't parse the unit [arb'U]/mL https://github.com/samply/blaze/issues/1234
"new_testdata/ObservationLab-38dfe76b-ae35-8290-6d80-ab08c963d148",
"new_testdata/ObservationLab-16408169-a38d-8afc-fdd2-ed7af97ccc57",
"new_testdata/ObservationLab-0fa07a3f-2e29-5065-6fa2-31e959acdd98",
"new_testdata/ObservationLab-43eb280e-7901-7990-64e3-22cfa51de78b",
"new_testdata/ObservationLab-09c67417-306a-a871-feef-71cbc915d113",
"new_testdata/ObservationLab-26184c80-edf6-b1e0-ee8f-0e0999755cb9",
"new_testdata/ObservationLab-9d44c93e-7799-a8e2-b368-c5539c30ceaa",
"new_testdata/ObservationLab-755a3ac1-32ae-2a20-1ac9-02ee25777cf0",
"new_testdata/ObservationLab-8ec9ea98-6581-f934-9bcf-b1c4f87e3560",
"new_testdata/ObservationLab-315e8080-7425-f4e9-3891-aef5ebe0572c",
"new_testdata/ObservationLab-44c8fd00-1a0f-f218-9eb8-83257add8fed",
"new_testdata/ObservationLab-7a2be049-40d2-d16f-3db6-12f46df2fc82",
"new_testdata/ObservationLab-78c5a976-1786-72e8-006b-8fd6af157ed9",
"new_testdata/ObservationLab-254bf7ae-1d0a-b994-f20b-575d4e28e674",
"new_testdata/ObservationLab-4bf41e10-1c62-2f82-d081-3d923aca43f2",
// Blaze can't parse the unit /[HPF]
"new_testdata/ObservationLab-bf7b68ae-1f89-41b6-e6a1-a40bf031f4b9",
"new_testdata/ObservationLab-b080e003-5e7f-503c-4b13-47f601d6d903",
"new_testdata/ObservationLab-3dd0c866-0649-def5-0fb2-de1ea0b976c2",
"new_testdata/ObservationLab-98b33c6e-0a14-b90a-7795-e98680ee526e",
// Blaze can't parse the unit /100{WBCs}
"new_testdata/ObservationLab-d2d07223-0b20-ee0f-8505-0a17d2e1ed4d"
);
try (var zipFile = new ZipFile(resourcePath("returningOnePatient.zip").toString())) {
return zipFile.stream()
.filter(entry -> !exclusions.contains(entry.toString()))
.map(entry -> {
try {
return new ObjectMapper().readValue(zipFile.getInputStream(entry), StructuredQuery.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}).toList();
try (Stream<Path> paths = Files.list(resourcePath("returningOnePatient"))) {
return paths.map(path -> {
try {
return new ObjectMapper().readValue(Files.readString(path), StructuredQuery.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}).toList();
}
}

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42 changes: 21 additions & 21 deletions src/test/java/de/numcodex/sq2cql/MedicationAdministrationTest.java
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Expand Up @@ -43,15 +43,15 @@ public void translateMedicationAdministration() throws Exception {
context Unfiltered
define HeparinB01AB01Ref:
define B01AB01Ref:
from [Medication: Code 'B01AB01' from atc] M
return 'Medication/' + M.id
context Patient
define Criterion:
exists (from [MedicationAdministration] M
where M.medication.reference in HeparinB01AB01Ref)
where M.medication.reference in B01AB01Ref)
define InInitialPopulation:
Criterion
Expand All @@ -74,15 +74,15 @@ public void translateMedicationAdministrationTimeRestriction() throws Exception
context Unfiltered
define HeparinB01AB01Ref:
define B01AB01Ref:
from [Medication: Code 'B01AB01' from atc] M
return 'Medication/' + M.id
context Patient
define Criterion:
exists (from [MedicationAdministration] M
where M.medication.reference in HeparinB01AB01Ref and
where M.medication.reference in B01AB01Ref and
(ToDate(M.effective as dateTime) in Interval[@2024-01-01, @2024-02-01] or
M.effective overlaps Interval[@2024-01-01, @2024-02-01]))
Expand All @@ -107,21 +107,21 @@ public void translateMedicationAdministrationDoubleCriteria() throws Exception {
context Unfiltered
define HeparinB01AB01Ref:
define B01AB01Ref:
from [Medication: Code 'B01AB01' from atc] M
return 'Medication/' + M.id
context Patient
define "Criterion 1":
exists (from [MedicationAdministration] M
where M.medication.reference in HeparinB01AB01Ref and
where M.medication.reference in B01AB01Ref and
(ToDate(M.effective as dateTime) in Interval[@2024-01-01, @2024-02-01] or
M.effective overlaps Interval[@2024-01-01, @2024-02-01]))
define "Criterion 2":
exists (from [MedicationAdministration] M
where M.medication.reference in HeparinB01AB01Ref and
where M.medication.reference in B01AB01Ref and
(ToDate(M.effective as dateTime) in Interval[@2023-01-01, @2023-02-01] or
M.effective overlaps Interval[@2023-01-01, @2023-02-01]))
Expand All @@ -142,29 +142,29 @@ public void translateMedicationAdministrationTwoCriteria() throws Exception {
library Retrieve version '1.0.0'
using FHIR version '4.0.0'
include FHIRHelpers version '4.0.0'
codesystem atc: 'http://fhir.de/CodeSystem/bfarm/atc'
context Unfiltered
define "AcetylsalicylsäureB01AC06Ref":
from [Medication: Code 'B01AC06' from atc] M
return 'Medication/' + M.id
define HeparinB01AB01Ref:
define B01AB01Ref:
from [Medication: Code 'B01AB01' from atc] M
return 'Medication/' + M.id
define B01AC06Ref:
from [Medication: Code 'B01AC06' from atc] M
return 'Medication/' + M.id
context Patient
define "Criterion 1":
exists (from [MedicationAdministration] M
where M.medication.reference in HeparinB01AB01Ref)
where M.medication.reference in B01AB01Ref)
define "Criterion 2":
exists (from [MedicationAdministration] M
where M.medication.reference in "AcetylsalicylsäureB01AC06Ref")
where M.medication.reference in B01AC06Ref)
define InInitialPopulation:
"Criterion 1" and
"Criterion 2"
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Binary file removed src/test/resources/de/numcodex/sq2cql/returningOnePatient.zip
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1 change: 1 addition & 0 deletions ...rces/de/numcodex/sq2cql/returningOnePatient/Diagnose-f728b4fa-4248-5e3a-0a5d-2f346baa9455
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "I08.0", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm"}], "context": {"code": "Diagnose", "display": "Diagnose", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
1 change: 1 addition & 0 deletions .../sq2cql/returningOnePatient/MedicationAdministration-aedab7b5-e2aa-55a7-4951-03edfd05a5f5
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "P01CA", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/atc"}], "context": {"code": "Medikamentenverabreichung", "display": "Verabreichung von Medikamenten", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
1 change: 1 addition & 0 deletions ...e/numcodex/sq2cql/returningOnePatient/ObservationLab-00183cfe-ceb0-9220-7984-f33f61c61ae4
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "46128-5", "display": "", "system": "http://loinc.org"}], "valueFilter": {"selectedConcepts": [{"code": "260373001", "display": "", "system": "http://snomed.info/sct"}], "type": "concept"}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "734-4", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "10*3/uL", "display": "10*3/uL"}, "value": 22.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
1 change: 1 addition & 0 deletions ...e/numcodex/sq2cql/returningOnePatient/ObservationLab-002f9cc4-096b-faff-f5b7-751f497e28aa
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "32207-3", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "fL", "display": "fL"}, "value": -14.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
1 change: 1 addition & 0 deletions ...e/numcodex/sq2cql/returningOnePatient/ObservationLab-00d3d1af-353e-0c86-24ae-ba79e4b82987
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "40569-6", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "10*3/uL", "display": "10*3/uL"}, "value": 67.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
1 change: 1 addition & 0 deletions ...e/numcodex/sq2cql/returningOnePatient/ObservationLab-00f24603-8295-1fe0-52c5-53b5d2f74429
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "2705-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mm[Hg]", "display": "mm[Hg]"}, "value": -80.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "4542-7", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mg/dL", "display": "mg/dL"}, "value": 17.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "20483-4", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "{titer}", "display": "{titer}"}, "value": -22.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "728-6", "display": "", "system": "http://loinc.org"}], "valueFilter": {"selectedConcepts": [{"code": "260373001", "display": "", "system": "http://snomed.info/sct"}], "type": "concept"}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "30433-7", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "10*3/uL", "display": "10*3/uL"}, "value": 1.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "26465-5", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "/uL", "display": "/uL"}, "value": 61.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "2069-3", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mmol/L", "display": "mmol/L"}, "value": 38.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "19234-4", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mmol/L", "display": "mmol/L"}, "value": 58.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "1961-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mmol/L", "display": "mmol/L"}, "value": 87.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "2871-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "g/dL", "display": "g/dL"}, "value": -45.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "5235-7", "display": "", "system": "http://loinc.org"}], "valueFilter": {"selectedConcepts": [{"code": "260415000", "display": "", "system": "http://snomed.info/sct"}], "type": "concept"}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "2164-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mL/min", "display": "mL/min"}, "value": 7.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "13983-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "%", "display": "%"}, "value": -48.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "15152-2", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mg/dL", "display": "mg/dL"}, "value": 46.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "2704-5", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "mm[Hg]", "display": "mm[Hg]"}, "value": 77.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "26511-6", "display": "", "system": "http://loinc.org"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "%", "display": "%"}, "value": 66.0}, "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
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