diff --git a/src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java b/src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java index 544fd3c..c3446f2 100644 --- a/src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java +++ b/src/main/java/de/numcodex/sq2cql/model/structured_query/AbstractCriterion.java @@ -71,7 +71,7 @@ static Container 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); diff --git a/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java b/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java index 98e143d..8efc183 100644 --- a/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java +++ b/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java @@ -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; @@ -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; @@ -78,41 +81,14 @@ private static Bundle createBundle(Library library, Measure measure) { } public static List 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 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(); } } diff --git a/src/test/java/de/numcodex/sq2cql/MedicationAdministrationTest.java b/src/test/java/de/numcodex/sq2cql/MedicationAdministrationTest.java index 7f6cc7c..7b174e7 100644 --- a/src/test/java/de/numcodex/sq2cql/MedicationAdministrationTest.java +++ b/src/test/java/de/numcodex/sq2cql/MedicationAdministrationTest.java @@ -43,7 +43,7 @@ public void translateMedicationAdministration() throws Exception { context Unfiltered - define HeparinB01AB01Ref: + define B01AB01Ref: from [Medication: Code 'B01AB01' from atc] M return 'Medication/' + M.id @@ -51,7 +51,7 @@ public void translateMedicationAdministration() throws Exception { define Criterion: exists (from [MedicationAdministration] M - where M.medication.reference in HeparinB01AB01Ref) + where M.medication.reference in B01AB01Ref) define InInitialPopulation: Criterion @@ -74,7 +74,7 @@ public void translateMedicationAdministrationTimeRestriction() throws Exception context Unfiltered - define HeparinB01AB01Ref: + define B01AB01Ref: from [Medication: Code 'B01AB01' from atc] M return 'Medication/' + M.id @@ -82,7 +82,7 @@ public void translateMedicationAdministrationTimeRestriction() throws Exception 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])) @@ -107,7 +107,7 @@ public void translateMedicationAdministrationDoubleCriteria() throws Exception { context Unfiltered - define HeparinB01AB01Ref: + define B01AB01Ref: from [Medication: Code 'B01AB01' from atc] M return 'Medication/' + M.id @@ -115,13 +115,13 @@ public void translateMedicationAdministrationDoubleCriteria() throws Exception { 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])) @@ -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" diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient.zip b/src/test/resources/de/numcodex/sq2cql/returningOnePatient.zip deleted file mode 100644 index 23a9807..0000000 Binary files a/src/test/resources/de/numcodex/sq2cql/returningOnePatient.zip and /dev/null differ diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/Diagnose-f728b4fa-4248-5e3a-0a5d-2f346baa9455 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/Diagnose-f728b4fa-4248-5e3a-0a5d-2f346baa9455 new file mode 100644 index 0000000..cc10a80 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/Diagnose-f728b4fa-4248-5e3a-0a5d-2f346baa9455 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/MedicationAdministration-aedab7b5-e2aa-55a7-4951-03edfd05a5f5 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/MedicationAdministration-aedab7b5-e2aa-55a7-4951-03edfd05a5f5 new file mode 100644 index 0000000..c17b868 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/MedicationAdministration-aedab7b5-e2aa-55a7-4951-03edfd05a5f5 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00183cfe-ceb0-9220-7984-f33f61c61ae4 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00183cfe-ceb0-9220-7984-f33f61c61ae4 new file mode 100644 index 0000000..cfdf0eb --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00183cfe-ceb0-9220-7984-f33f61c61ae4 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0021b632-3246-b7d9-bb29-66398e4a295d b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0021b632-3246-b7d9-bb29-66398e4a295d new file mode 100644 index 0000000..eebe873 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0021b632-3246-b7d9-bb29-66398e4a295d @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-002f9cc4-096b-faff-f5b7-751f497e28aa b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-002f9cc4-096b-faff-f5b7-751f497e28aa new file mode 100644 index 0000000..d9f890d --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-002f9cc4-096b-faff-f5b7-751f497e28aa @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00d3d1af-353e-0c86-24ae-ba79e4b82987 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00d3d1af-353e-0c86-24ae-ba79e4b82987 new file mode 100644 index 0000000..a6be833 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00d3d1af-353e-0c86-24ae-ba79e4b82987 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f24603-8295-1fe0-52c5-53b5d2f74429 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f24603-8295-1fe0-52c5-53b5d2f74429 new file mode 100644 index 0000000..b96636b --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f24603-8295-1fe0-52c5-53b5d2f74429 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f520f4-9ef1-c846-1dbc-24fd0a8aa1e4 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f520f4-9ef1-c846-1dbc-24fd0a8aa1e4 new file mode 100644 index 0000000..d5d028a --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-00f520f4-9ef1-c846-1dbc-24fd0a8aa1e4 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-01847803-d840-fccb-2446-eceecaa0a679 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-01847803-d840-fccb-2446-eceecaa0a679 new file mode 100644 index 0000000..7683ce2 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-01847803-d840-fccb-2446-eceecaa0a679 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-025b7c5f-1284-b9d7-8d4e-2753ef26a5b7 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-025b7c5f-1284-b9d7-8d4e-2753ef26a5b7 new file mode 100644 index 0000000..4a9f29e --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-025b7c5f-1284-b9d7-8d4e-2753ef26a5b7 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0262a5aa-edec-31ef-5762-762620379089 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0262a5aa-edec-31ef-5762-762620379089 new file mode 100644 index 0000000..f46e75f --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0262a5aa-edec-31ef-5762-762620379089 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027752fe-61f6-8c6e-689c-0559bf4fa4a3 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027752fe-61f6-8c6e-689c-0559bf4fa4a3 new file mode 100644 index 0000000..0e5e73a --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027752fe-61f6-8c6e-689c-0559bf4fa4a3 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027c013f-3801-8399-ee6a-8e2f9c19ed34 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027c013f-3801-8399-ee6a-8e2f9c19ed34 new file mode 100644 index 0000000..e3b1bf6 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-027c013f-3801-8399-ee6a-8e2f9c19ed34 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0361524c-2cc0-f859-aa65-24ab713b7e05 b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0361524c-2cc0-f859-aa65-24ab713b7e05 new file mode 100644 index 0000000..0e077a4 --- /dev/null +++ b/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-0361524c-2cc0-f859-aa65-24ab713b7e05 @@ -0,0 +1 @@ +{"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#"} \ No newline at end of file diff --git a/src/test/resources/de/numcodex/sq2cql/returningOnePatient/ObservationLab-03a89879-36a9-8d74-00de-59f550f0fc2b 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