From eb6cd5a521a317922564313f45c4f8d6375735c8 Mon Sep 17 00:00:00 2001 From: Alex-Nita Date: Thu, 21 Nov 2024 14:12:50 +0000 Subject: [PATCH 1/6] Reformat xml file --- ...ected-xml-with-standalone-observations.xml | 505 +++++++++--------- 1 file changed, 259 insertions(+), 246 deletions(-) diff --git a/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml b/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml index 8a5f1a6c55..6f9d0ced6b 100644 --- a/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml +++ b/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml @@ -1,293 +1,306 @@ - - - + + + - + - - + - - + + - + - - - - - - - Unknown - - - - TEMPLE SOWERBY MEDICAL PRACTICE - - - - - - - - - Unknown - - - - Dr - David - McAvenue - - - - - - - - - - - - -
- - - - - - - - - - - - - - Filed Report - - - -
- - - - - - CommentType:LABORATORY RESULT COMMENT(E141) -CommentDate:20030221115000 + + + + + + Unknown + + + + TEMPLE SOWERBY MEDICAL PRACTICE + + + + + + + + + Unknown + + + + Dr + David + McAvenue + + + + + + + + + + + + +
+ + + + + + + + + + + + + + Filed Report + + + +
+ + + + + + CommentType:LABORATORY RESULT COMMENT(E141) + CommentDate:20030221115000 -Status: unknown - - - - - - - - - - -
- - - - - - - -
- - - UNKNOWN - - - - - - - CommentType:AGGREGATE COMMENT SET - CommentDate:UNK + Status: unknown + + + + + + + + + + + +
+ + + + + + + +
+ + + UNKNOWN + + + + + + + CommentType:AGGREGATE COMMENT SET + CommentDate:UNK - EMPTY REPORT - - - - - - - - - - - -
- - - - - - - -
- - - Blood - - - - - - - CommentType:LAB SPECIMEN COMMENT(E271) -CommentDate:20030109000000 + EMPTY REPORT + + + + + + + + + + + + + +
+ + + + + + + +
+ + + Blood + + + + + + + CommentType:LAB SPECIMEN COMMENT(E271) + CommentDate:20030109000000 -Received Date: 2003-01-09 13:54 - - - - - - - - - CommentType:AGGREGATE COMMENT SET -CommentDate:UNK + Received Date: 2003-01-09 13:54 + + + + + + + + + CommentType:AGGREGATE COMMENT SET + CommentDate:UNK -EMPTY REPORT - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - This is some random free text - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - Mocked code - - -
- - + EMPTY REPORT + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + This is some random free text + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + Mocked code + + + +
+ + - - - - - - + + + + + + - - - - - - - - - + + + + + + + + + - + - - + + From b298406022eddb753101d4d4a798366b4b24a0d1 Mon Sep 17 00:00:00 2001 From: Alex-Nita Date: Thu, 21 Nov 2024 14:16:28 +0000 Subject: [PATCH 2/6] Fixed duplication of test reports during mapping --- .../DiagnosticReportMapper.java | 11 +++- .../diagnosticreport/SpecimenMapperTest.java | 2 +- .../diagnostic-report-with-no-specimen.json | 2 +- .../diagnostic-report-with-no-specimen.xml | 55 +++++-------------- ...ected-xml-with-standalone-observations.xml | 14 +---- 5 files changed, 28 insertions(+), 56 deletions(-) diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java index f2009e4de7..066a06727b 100644 --- a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java +++ b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java @@ -87,7 +87,9 @@ public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnostic specimens); String mappedSpecimens = specimens.stream() - .map(specimen -> specimenMapper.mapSpecimenToCompoundStatement(specimen, observationsExcludingFilingComments, diagnosticReport)) + .map(specimen -> specimenMapper.mapSpecimenToCompoundStatement(specimen, + observationsForSpecimen(specimen, observationsExcludingFilingComments), + diagnosticReport)) .collect(Collectors.joining()); String reportLevelNarrativeStatements = prepareReportLevelNarrativeStatements(diagnosticReport, observations); @@ -113,6 +115,13 @@ public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnostic ); } + private List observationsForSpecimen(Specimen specimen, List observations) { + return observations.stream() + .filter(Observation::hasSpecimen) + .filter(observation -> observation.getSpecimen().getReference().equals(specimen.getId())) + .collect(Collectors.toList()); + } + private String fetchExtensionId(List identifiers) { return identifiers.stream() .filter(DiagnosticReportMapper::isPMIPCodeSystem) diff --git a/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapperTest.java b/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapperTest.java index 452c850362..e30749a61d 100644 --- a/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapperTest.java +++ b/service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapperTest.java @@ -139,7 +139,7 @@ void When_MappingDefaultSpecimenWithObservation_Expect_DefaultSpecimenAndObserva final String actualXml = specimenMapper.mapSpecimenToCompoundStatement( specimen, observations, DIAGNOSTIC_REPORT); - assertThat(actualXml).isEqualTo(expectedXml); + assertThat(actualXml).isEqualToIgnoringWhitespace(expectedXml); } @Test diff --git a/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.json b/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.json index 1d25fa39c2..d1486bc558 100644 --- a/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.json +++ b/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.json @@ -54,7 +54,7 @@ "reference": "Observation/FILING-COMMENT-WITH-NO-COMMENT" }, { - "reference": "Observation/6E30A9E3-FF9A-4868-8FCD-7DAC26A16E78" + "reference": "Observation/TestResult-WithoutSpecimenReference" } ] } \ No newline at end of file diff --git a/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.xml b/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.xml index a32421b9de..9fe37d75a0 100644 --- a/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.xml +++ b/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-no-specimen.xml @@ -68,8 +68,8 @@ - - + + Mocked code @@ -78,46 +78,19 @@
- - - - - Mocked code - - - -
- - - - - mmol/L - - - - - - - - - - - - - - - - - CommentType:USER COMMENT - CommentDate:20201215151713 + + + + + + CommentType:AGGREGATE COMMENT SET + CommentDate:20100223 - (q) - Normal - No Action - - - - - - + This is a test result without a specimen. + + + + diff --git a/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml b/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml index 6f9d0ced6b..5fce2b723a 100644 --- a/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml +++ b/service/src/test/resources/ehr/request/fhir/output/expected-xml-with-standalone-observations.xml @@ -180,21 +180,11 @@ CommentDate:20030109000000 Received Date: 2003-01-09 13:54 - - - - - - - - - CommentType:AGGREGATE COMMENT SET - CommentDate:UNK - EMPTY REPORT + EMPTY SPECIMEN - + From 253fdb05c125e7674d11c245486d21a04a70ec52 Mon Sep 17 00:00:00 2001 From: Steven McCullagh Date: Fri, 22 Nov 2024 14:42:20 +0000 Subject: [PATCH 3/6] Adding medications scenarios from PR 958 --- ...nvestigationsStructuredRecordResponse.json | 1535 +++++++++++++++++ 1 file changed, 1535 insertions(+) create mode 100644 wiremock/stubs/__files/correctPatientInvestigationsStructuredRecordResponse.json diff --git a/wiremock/stubs/__files/correctPatientInvestigationsStructuredRecordResponse.json b/wiremock/stubs/__files/correctPatientInvestigationsStructuredRecordResponse.json new file mode 100644 index 0000000000..6bf579fca4 --- /dev/null +++ b/wiremock/stubs/__files/correctPatientInvestigationsStructuredRecordResponse.json @@ -0,0 +1,1535 @@ +{ + "resourceType": "Bundle", + "id": "54d0ebb9-2d56-471e-9642-74ee55c38981", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/GPConnect-StructuredRecord-Bundle-1" + ] + }, + "type": "collection", + "entry": [ + { + "resource": { + "resourceType": "Patient", + "id": "1", + "meta": { + "versionId": "1521806400000", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Patient-1" + ] + }, + "extension": [ + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-RegistrationDetails-1", + "extension": [ + { + "url": "registrationPeriod", + "valuePeriod": { + "start": "1962-07-13T00:00:00+01:00" + } + } + ] + }, + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSCommunication-1", + "extension": [ + { + "url": "language", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-HumanLanguage-1", + "code": "en", + "display": "English" + } + ] + } + }, + { + "url": "preferred", + "valueBoolean": false + }, + { + "url": "modeOfCommunication", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-LanguageAbilityMode-1", + "code": "RWR", + "display": "Received written" + } + ] + } + }, + { + "url": "communicationProficiency", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-LanguageAbilityProficiency-1", + "code": "E", + "display": "Excellent" + } + ] + } + }, + { + "url": "interpreterRequired", + "valueBoolean": false + } + ] + } + ], + "identifier": [ + { + "extension": [ + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSNumberVerificationStatus-1", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-NHSNumberVerificationStatus-1", + "code": "01", + "display": "Number present and verified" + } + ] + } + } + ], + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "{{jsonPath request.body '$.parameter[0].valueIdentifier.value'}}" + } + ], + "active": true, + "telecom": [ + { + "system": "phone", + "value": "02123636563", + "use": "home" + } + ], + {{^patient}} + "name": [ + { + "use": "official", + "text": "Samuel HESLBY", + "family": "HESLBY", + "given": [ + "Samuel" + ], + "prefix": [ + "MR" + ] + } + ], + "gender": "male", + "birthDate": "1936-03-17", + "address": [ + { + "use": "home", + "type": "physical", + "line": [ + "10 MANOR DRIVE", + "STILLINGTON" + ], + "city": "STOCKTON-ON-TEES", + "district": "CLEVELAND", + "postalCode": "TS21 1JG" + } + ], + {{/patient}} + {{#patient}} + "name": [ + { + "use": "official", + "text": "{{patient.name.0.given.0}} {{patient.name.0.family}}", + "family": "{{patient.name.0.family}}", + "given": [ + "{{patient.name.0.given.0}}" + ], + "prefix": [ + "{{patient.name.0.prefix.0}}" + ] + } + ], + "gender": "{{ patient.gender }}", + "birthDate": "{{ patient.birthDate }}", + "address": [ + { + "use": "home", + "type": "physical", + "line": [ + "{{ patient.address.0.line.0 }}", + "{{ patient.address.0.line.1 }}" + ], + "postalCode": "{{ patient.address.0.postalCode }}" + } + ], + {{/patient}} + "generalPractitioner": [ + { + "reference": "Practitioner/1" + } + ], + "managingOrganization": { + "reference": "Organization/7" + } + } + }, + { + "resource": { + "resourceType": "Practitioner", + "id": "1", + "meta": { + "versionId": "1469444400000", + "lastUpdated": "2016-07-25T12:00:00.000+01:00", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Practitioner-1" + ] + }, + "extension": [ + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSCommunication-1", + "extension": [ + { + "url": "language", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-HumanLanguage-1", + "code": "de", + "display": "German" + } + ] + } + } + ] + }, + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSCommunication-1", + "extension": [ + { + "url": "language", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-HumanLanguage-1", + "code": "en", + "display": "English" + } + ] + } + } + ] + } + ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/sds-user-id", + "value": "G13579135" + } + ], + "name": [ + { + "use": "usual", + "family": "Gilbert", + "given": [ + "Nichole" + ], + "prefix": [ + "Miss" + ] + } + ], + "gender": "female" + } + }, + { + "resource": { + "resourceType": "Practitioner", + "id": "2", + "meta": { + "versionId": "1469444400000", + "lastUpdated": "2016-07-25T12:00:00.000+01:00", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Practitioner-1" + ] + }, + "extension": [ + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSCommunication-1", + "extension": [ + { + "url": "language", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-HumanLanguage-1", + "code": "de", + "display": "German" + } + ] + } + } + ] + }, + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-NHSCommunication-1", + "extension": [ + { + "url": "language", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-HumanLanguage-1", + "code": "en", + "display": "English" + } + ] + } + } + ] + } + ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/sds-user-id", + "value": "G22345655" + }, + { + "system": "https://fhir.nhs.uk/Id/sds-role-profile-id", + "value": "PT1122" + }, + { + "system": "https://fhir.nhs.uk/Id/sds-role-profile-id", + "value": "PT1234" + } + ], + "name": [ + { + "use": "usual", + "family": "Slater", + "given": [ + "Kibo" + ], + "prefix": [ + "Mr" + ] + } + ], + "gender": "male" + } + }, + { + "resource": { + "resourceType": "Organization", + "id": "7", + "meta": { + "versionId": "1469444400000", + "lastUpdated": "2016-07-25T12:00:00.000+01:00", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Organization-1" + ] + }, + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "B82617" + } + ], + "name": "COXWOLD SURGERY", + "telecom": [ + { + "system": "phone", + "value": "12345678", + "use": "work" + } + ], + "address": [ + { + "use": "work", + "line": [ + "NHS NPFIT Test Data Manager", + "Princes Exchange" + ], + "city": "Leeds", + "district": "West Yorkshire", + "postalCode": "LS1 4HY" + } + ] + } + }, + { + "resource": { + "resourceType": "PractitionerRole", + "id": "PT1122", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-PractitionerRole-1" + ] + }, + "practitioner": { + "reference": "Practitioner/2" + }, + "organization": { + "reference": "Organization/1" + }, + "code": [ + { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1", + "code": "R0050", + "display": "Consultant" + } + ] + } + ] + } + }, + { + "resource": { + "resourceType": "PractitionerRole", + "id": "PT1234", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-PractitionerRole-1" + ] + }, + "practitioner": { + "reference": "Practitioner/2" + }, + "organization": { + "reference": "Organization/1" + }, + "code": [ + { + "coding": [ + { + "system": "https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1", + "code": "R0050", + "display": "Consultant" + } + ] + } + ] + } + }, + { + "resource": { + "resourceType": "Organization", + "id": "1", + "meta": { + "versionId": "1469444400000", + "lastUpdated": "2016-07-25T12:00:00.000+01:00", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Organization-1" + ] + }, + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "GPC001" + } + ], + "name": "GP Connect Demonstrator", + "telecom": [ + { + "system": "phone", + "value": "12345678", + "use": "work" + } + ], + "address": [ + { + "use": "work", + "line": [ + "23 Main Street", + "Pudsey" + ], + "city": "Leeds", + "district": "West Yorkshire", + "postalCode": "GPC 111" + } + ] + } + }, + { + "resource": { + "resourceType": "Organization", + "id": "2", + "meta": { + "versionId": "1469444400000", + "lastUpdated": "2016-07-25T12:00:00.000+01:00", + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Organization-1" + ] + }, + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R1A14" + } + ], + "name": "Test GP Care Trust", + "telecom": [ + { + "system": "phone", + "value": "12345678", + "use": "work" + } + ], + "address": [ + { + "use": "work", + "line": [ + "24 Back Lane", + "Farsley" + ], + "city": "Leeds", + "district": "West Yorkshire", + "postalCode": "GPC 113" + } + ] + } + }, + { + "resource": { + "resourceType": "DiagnosticReport", + "id": "NoSpecimen-NoResults", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-DiagnosticReport-1" + ] + }, + "identifier": [ + { + "system": "https://wiremock/", + "value": "NoSpecimen-NoResults" + } + ], + "status": "unknown", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "721981007", + "display": "Diagnostic studies report" + } + ] + }, + "subject": { + "reference": "Patient/1" + }, + "issued": "2001-01-01T09:00:00+00:00" + } + }, + { + "resource": { + "resourceType": "DiagnosticReport", + "id": "NoSpecimen-OneResult", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-DiagnosticReport-1" + ] + }, + "identifier": [ + { + "system": "https://wiremock/", + "value": "NoSpecimen-OneResult" + } + ], + "status": "unknown", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "721981007", + "display": "Diagnostic studies report" + } + ] + }, + "subject": { + "reference": "Patient/1" + }, + "issued": "2001-01-02T09:00:00+00:00", + "result": [ + { + "reference": "Observation/NoSpecimen-OneResult" + } + ] + } + }, + { + "resource": { + "resourceType": "Observation", + "id": "NoSpecimen-OneResult", + "meta": { + "profile": [ + "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-Observation-1" + ] + }, + "identifier": [ + { + "system": "https://wiremock/", + "value": "NoSpecimen-OneResult" + } + ], + "status": "final", + "code": { + "coding": [ + { + "system": "http://read.info/readv2", + "code": "42R5.00", + "display": "Serum TIBC", + "userSelected": true + }, + { + "extension": [ + { + "url": "https://fhir.nhs.uk/STU3/StructureDefinition/Extension-coding-sctdescid", + "extension": [ + { + "url": "descriptionId", + "valueId": "2580111000000118" + } + ] + } + ], + "system": "http://snomed.info/sct", + "code": "1015451000000101", + "display": "Serum total iron binding capacity" + } + ] + }, + "subject": { + "reference": "Patient/1" + }, + "effectiveDateTime": 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