Examples with StructureDefinition org.hl7.fhir.dstu3.model.StructureDefinition used on opensource projects

Example 96 with StructureDefinition

use of org.hl7.fhir.dstu3.model.StructureDefinition in project kindling by HL7.

the class ReviewSpreadsheetGenerator method processRows.

private int processRows(HSSFWorkbook workbook, String path, StructureDefinition profile, List<ElementDefinition> list, int i, HSSFSheet sheet, String indent) throws FHIRException {
    ElementDefinition ed = list.get(i);
    HSSFFont font = workbook.createFont();
    font.setFontName("Calibri");
    HSSFCellStyle style = workbook.createCellStyle();
    style.setFont(font);
    while (i < list.size() && ed.getPath().startsWith(path + ".")) {
        HSSFRow row = sheet.createRow(sheet.getPhysicalNumberOfRows());
        int c = 0;
        HSSFRichTextString richString;
        if (ed.getType().size() == 0) {
            richString = new HSSFRichTextString(indent + ed.getPath().substring(path.length() + 1) + " [" + describeCardinality(ed) + "]");
        } else if (ed.getType().size() == 1) {
            richString = new HSSFRichTextString(indent + ed.getPath().substring(path.length() + 1) + " : " + ed.getType().get(0).getWorkingCode() + " [" + describeCardinality(ed) + "]");
            HSSFFont fontBlue = workbook.createFont();
            fontBlue.setFontName("Calibri");
            fontBlue.setColor(IndexedColors.DARK_BLUE.getIndex());
            richString.applyFont(indent.length() + ed.getPath().length() - (path.length() + 1), richString.length() - describeCardinality(ed).length() - 3, fontBlue);
        } else {
            richString = new HSSFRichTextString(indent + ed.getPath().substring(path.length() + 1) + " : * [" + describeCardinality(ed) + "]");
        }
        HSSFCell cell = row.createCell(c++);
        cell.setCellStyle(style);
        cell.setCellValue(richString);
        if (ed.getType().size() == 0) {
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            cell.setCellValue(ed.getSliceName());
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            cell.setCellValue("");
            i++;
            if (i < list.size())
                i = processRows(workbook, ed.getPath(), profile, list, i, sheet, indent + "  ");
        } else if (ed.getType().size() == 1) {
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            if (ed.getType().get(0).hasProfile())
                cell.setCellValue(ed.getType().get(0).getProfile().get(0).getValue());
            if (ed.getType().get(0).hasTargetProfile())
                cell.setCellValue(ed.getType().get(0).getTargetProfile().get(0).getValue());
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            cell.setCellValue(describeBinding(profile, ed));
            i++;
        } else {
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            cell.setCellValue(ed.getSliceName());
            cell = row.createCell(c++);
            cell.setCellStyle(style);
            cell.setCellValue(describeBinding(profile, ed));
            i++;
        }
        cell = row.createCell(c++);
        cell.setCellStyle(style);
        cell = row.createCell(c++);
        cell.setCellStyle(style);
        cell.setCellValue("");
        if (i < list.size())
            ed = list.get(i);
    }
    return i;
}

Example 97 with StructureDefinition

use of org.hl7.fhir.dstu3.model.StructureDefinition in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7EncounterFHIRConversionTest method testEncounterModeOfArrival.

@Test
void testEncounterModeOfArrival() {
    String hl7message = "MSH|^~\\&|PROSOLV|SENTARA|WHIA|IBM|20151008111200|S1|ADT^A01^ADT_A01|MSGID000001|T|2.6|10092|PRPA008|AL|AL|100|8859/1|ENGLISH|ARM|ARM5007\n" + "EVN|A04|20151008111200|20171013152901|O|OID1006|20171013153621|EVN1009\n" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1|1|E|SAN JOSE|A|10089|MILPITAS|2740^Torres^Callie|2913^Grey^Meredith^F|3065^Sloan^Mark^J|CAR|FOSTER CITY|AD|R|1|A4|VI|9052^Shepeard^Derek^|AH|10019181|FIC1002|IC|CC|CR|CO|20161012034052|60000|6|AC|GHBR|20160926054052|AC5678|45000|15000|D|20161016154413|DCD|SAN FRANCISCO|VEG|RE|O|AV|FREMONT|CALIFORNIA|20161013154626|20161014154634|10000|14000|2000|4000|POL8009|V|PHY6007\n" + "PV2|SAN BRUNO|AC4567|vomits|less equipped|purse|SAN MATEO|HO|20171014154626|20171018154634|4|3|DIAHHOREA|RSA456|20161013154626|Y|D|20191026001640|O|Y|1|F|Y|KAISER|AI|2|20161013154626|ED|20171018001900|20161013154626|10000|RR|Y|20171108002129|Y|Y|N|N|C^Car^HL70430\n";
    Encounter encounter = ResourceUtils.getEncounter(ftv, hl7message);
    List<Extension> extensionList = encounter.getExtension();
    assertNotNull(extensionList);
    assertThat(extensionList).hasSize(1);
    boolean extFound = false;
    for (Extension ext : extensionList) {
        if (ext.getUrl().equals("http://hl7.org/fhir/StructureDefinition/encounter-modeOfArrival")) {
            extFound = true;
            assertTrue(ext.getValue() instanceof Coding);
            Coding valueCoding = (Coding) ext.getValue();
            assertThat(valueCoding.getCode()).isEqualTo("C");
            assertThat(valueCoding.getDisplay()).isEqualTo("Car");
            assertThat(valueCoding.getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/v2-0430");
            break;
        }
    }
    assertTrue(extFound, "modeOfArrival extension not found");
}

Example 98 with StructureDefinition

use of org.hl7.fhir.dstu3.model.StructureDefinition in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7EncounterFHIRConversionTest method test_encounter_modeOfarrival_invalid_with_system.

@Test
void test_encounter_modeOfarrival_invalid_with_system() {
    String hl7message = "MSH|^~\\&|WHI_LOAD_GENERATOR|IBM_TORONTO_LAB||IBM|20210330144208|8078780|ADT^A01|MSGID_4e1c575f-6c6d-47b2-ab9f-829f20c96db2|T|2.3\n" + "EVN||20210330144208||ADT_EVENT|007|20210309140700\n" + "PID|1||0a8a1752-e336-43e1-bf7f-0c8f6f437ca3^^^MRN||Patient^Load^Generator||19690720|M|Patient^Alias^Generator|AA|9999^^CITY^STATE^ZIP^CAN|COUNTY|(866)845-0900||ENGLISH^ENGLISH|SIN|NONE|Account_0a8a1752-e336-43e1-bf7f-0c8f6f437ca3|123-456-7890|||N|BIRTH PLACE|N||||||N\n" + "PV1||I|^^^Toronto^^5642 Hilly Av||||2905^Doctor^Attending^M^IV^^M.D|5755^Doctor^Referring^^Sr|770542^Doctor^Consulting^Jr||||||||59367^Doctor^Admitting||Visit_0a3be81e-144b-4885-9b4e-c5cd33c8f038|||||||||||||||||||||||||20210407191342\n" + "PV2||TEL||||X-5546||20210330144208|20210309||||||||||||n|N|South Shore Hosptial Weymouth^SSHW^^^^^^SSH-WEYMOUTH|||||||||N||||||AMB^AMBULATORY^FUNKY\n";
    Encounter encounter = ResourceUtils.getEncounter(ftv, hl7message);
    List<Extension> extensionList = encounter.getExtension();
    assertNotNull(extensionList);
    assertThat(extensionList).isNotEmpty();
    boolean extFound = false;
    for (Extension ext : extensionList) {
        if (ext.getUrl().equals("http://hl7.org/fhir/StructureDefinition/encounter-modeOfArrival")) {
            extFound = true;
            assertTrue(ext.getValue() instanceof Coding);
            Coding valueCoding = (Coding) ext.getValue();
            assertThat(valueCoding.getCode()).isEqualTo("AMB");
            assertThat(valueCoding.getDisplay()).isEqualTo("AMBULATORY");
            assertThat(valueCoding.getSystem()).isEqualTo("urn:id:FUNKY");
            break;
        }
    }
    assertTrue(extFound, "modeOfArrival extension not found");
}

Example 99 with StructureDefinition

use of org.hl7.fhir.dstu3.model.StructureDefinition in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7EncounterFHIRConversionTest method test_encounter_modeOfarrival_invalid_singlevalue.

@Test
void test_encounter_modeOfarrival_invalid_singlevalue() {
    String hl7message = "MSH|^~\\&|WHI_LOAD_GENERATOR|IBM_TORONTO_LAB||IBM|20210330144208|8078780|ADT^A01|MSGID_4e1c575f-6c6d-47b2-ab9f-829f20c96db2|T|2.3\n" + "EVN||20210330144208||ADT_EVENT|007|20210309140700\n" + "PID|1||0a8a1752-e336-43e1-bf7f-0c8f6f437ca3^^^MRN||Patient^Load^Generator||19690720|M|Patient^Alias^Generator|AA|9999^^CITY^STATE^ZIP^CAN|COUNTY|(866)845-0900||ENGLISH^ENGLISH|SIN|NONE|Account_0a8a1752-e336-43e1-bf7f-0c8f6f437ca3|123-456-7890|||N|BIRTH PLACE|N||||||N\n" + "PV1||I|^^^Toronto^^5642 Hilly Av||||2905^Doctor^Attending^M^IV^^M.D|5755^Doctor^Referring^^Sr|770542^Doctor^Consulting^Jr||||||||59367^Doctor^Admitting||Visit_0a3be81e-144b-4885-9b4e-c5cd33c8f038|||||||||||||||||||||||||20210407191342\n" + "PV2||TEL||||X-5546||20210330144208|20210309||||||||||||n|N|South Shore Hosptial Weymouth^SSHW^^^^^^SSH-WEYMOUTH|||||||||N||||||AMBULATORY\n";
    Encounter encounter = ResourceUtils.getEncounter(ftv, hl7message);
    List<Extension> extensionList = encounter.getExtension();
    assertNotNull(extensionList);
    assertThat(extensionList).isNotEmpty();
    boolean extFound = false;
    for (Extension ext : extensionList) {
        if (ext.getUrl().equals("http://hl7.org/fhir/StructureDefinition/encounter-modeOfArrival")) {
            extFound = true;
            assertTrue(ext.getValue() instanceof Coding);
            Coding valueCoding = (Coding) ext.getValue();
            assertThat(valueCoding.getCode()).isEqualTo("AMBULATORY");
            assertThat(valueCoding.getDisplay()).isNull();
            assertThat(valueCoding.getSystem()).isNull();
            break;
        }
    }
    assertTrue(extFound, "modeOfArrival extension not found");
}

Example 100 with StructureDefinition

use of org.hl7.fhir.dstu3.model.StructureDefinition in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7NoteFHIRConverterTest method testMedicationRequestNoteCreation.

// Suppress warnings about too many assertions in a test.  Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@ParameterizedTest
@MethodSource("parmsTestMedicationRequestNoteCreation")
void testMedicationRequestNoteCreation(String message, String medicalRequestSegments) {
    // Minimal valid ORC message.  Requires RXO and RXR segments.
    String hl7message = "MSH|^~\\&||||IBM|20210101000000||" + message + "|MSGID|T|2.6\n" + "PID|||1234||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|OP|1234|1234|0827||||||||||||||||||||\n" + // May be RXO or RXO+RXE values from parmsTestMedicationRequestNoteCreation
    medicalRequestSegments + "NTE|1|O|TEST MedReq NOTE AA line 1||Pract1ID^Pract1Last^Pract1First|\n" + "NTE|2|O|TEST NOTE AA line 2|\n" + "NTE|3|O|TEST NOTE AA line 3|\n" + "OBX|1|NM|17985^GLYCOHEMOGLOBIN HGB A1C^LRR^^^^^^GLYCOHEMOGLOBIN HGB A1C||5.6|%|<6.0||||F||||||||||||||\n" + // GLYCOHEMOGLOBIN Observation NTE has a practitioner reference in NTE.5.  Note in second NTE. The first valid NTE.5 is used.
    "NTE|1|L|TEST OBXa NOTE BB line 1|\n" + "NTE|2|L|TEST NOTE BB line 2||Pract2ID^Pract2Last^Pract2First|\n" + "NTE|3|L|TEST NOTE BB line 3|\n" + "OBX|2|NM|17853^MEAN BLOOD GLUCOSE^LRR^^^^^^MEAN BLOOD GLUCOSE||114.02|mg/dL|||||F||||||||||||||\n" + // Glucose Observation NTE has no practitioner reference in NTE.5
    "NTE|1|L|TEST OBXb NOTE CC line 1|\n" + "NTE|2|L|TEST NOTE CC line 2|\n" + // Test that blank lines are preserved.
    "NTE|3|L| |\n" + "NTE|4|L|TEST NOTE CC line 4|\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Expect MedicationRequest containing NTE for RXO or RXE
    List<Resource> medicationRequests = ResourceUtils.getResourceList(e, ResourceType.MedicationRequest);
    assertThat(medicationRequests).hasSize(1);
    MedicationRequest medicationRequest = ResourceUtils.getResourceMedicationRequest(medicationRequests.get(0), ResourceUtils.context);
    assertThat(medicationRequest.hasNote()).isTrue();
    assertThat(medicationRequest.getNote()).hasSize(1);
    // NOTE: the note contains an Annotation, which contains a MarkdownType that has the string.
    // Must use getTextElement().getValueAsString() to see untrimmed contents.
    assertThat(medicationRequest.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST MedReq NOTE AA line 1  \nTEST NOTE AA line 2  \nTEST NOTE AA line 3");
    assertThat(medicationRequest.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerServReqRefId = medicationRequest.getNote().get(0).getAuthorReference().getReference();
    // Two observations.  One has GLYCOHEMOGLOBIN and notes BB, One has GLUCOSE and notes CC
    List<Resource> observations = ResourceUtils.getResourceList(e, ResourceType.Observation);
    // Should be 2 for ORU and ORM
    assertThat(observations).hasSize(2);
    Observation obsGlucose = ResourceUtils.getResourceObservation(observations.get(0), ResourceUtils.context);
    Observation obsHemoglobin = ResourceUtils.getResourceObservation(observations.get(1), ResourceUtils.context);
    // Figure out which is first and reassign if needed for testing
    if (obsGlucose.getCode().getText() != "MEAN BLOOD GLUCOSE") {
        Observation temp = obsGlucose;
        obsGlucose = obsHemoglobin;
        obsHemoglobin = temp;
    }
    // Validate the note contents and references
    assertThat(obsHemoglobin.hasNote()).isTrue();
    assertThat(obsHemoglobin.getNote()).hasSize(1);
    assertThat(obsHemoglobin.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST OBXa NOTE BB line 1  \nTEST NOTE BB line 2  \nTEST NOTE BB line 3");
    assertThat(obsHemoglobin.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerObsHemoglobinRefId = obsHemoglobin.getNote().get(0).getAuthorReference().getReference();
    assertThat(obsGlucose.hasNote()).isTrue();
    assertThat(obsGlucose.getNote()).hasSize(1);
    assertThat(obsGlucose.getNote().get(0).getTextElement().getValueAsString()).isEqualTo(// Test that blank lines are preserved.
    "TEST OBXb NOTE CC line 1  \nTEST NOTE CC line 2  \n   \nTEST NOTE CC line 4");
    assertThat(obsGlucose.getNote().get(0).hasAuthorReference()).isFalse();
    // Two Practitioners, one for the serviceRequest, one for the GLYCOHEMOGLOBIN Observation
    List<Resource> practitioners = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitioners).hasSize(2);
    Practitioner practitionerServReq = ResourceUtils.getResourcePractitioner(practitioners.get(0), ResourceUtils.context);
    Practitioner practitionerObsHemoglobin = ResourceUtils.getResourcePractitioner(practitioners.get(1), ResourceUtils.context);
    // Adjust to correct practitioner if needed
    if (!practitionerServReq.getIdentifierFirstRep().getValue().contentEquals("Pract1ID")) {
        Practitioner temp = practitionerObsHemoglobin;
        practitionerObsHemoglobin = practitionerServReq;
        practitionerServReq = temp;
    }
    // Check the values for the Practitioners and validate match to references.
    assertThat(practitionerServReq.getIdentifier()).hasSize(1);
    assertThat(practitionerServReq.getIdentifierFirstRep().getValue()).isEqualTo("Pract1ID");
    assertThat(practitionerServReq.getName()).hasSize(1);
    assertThat(practitionerServReq.getNameFirstRep().getText()).isEqualTo("Pract1First Pract1Last");
    // Check the cross-reference
    assertThat(practitionerServReq.getId()).isEqualTo(practitionerServReqRefId);
    // Sanity check to confirm data corruption in meta content has not returned.
    CodeableConcept ccSourceEventTrigger = (CodeableConcept) practitionerServReq.getMeta().getExtensionByUrl("http://ibm.com/fhir/cdm/StructureDefinition/source-event-trigger").getValue();
    assertThat(ccSourceEventTrigger.hasText()).isFalse();
    assertThat(practitionerObsHemoglobin.getIdentifier()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getIdentifierFirstRep().getValue()).isEqualTo("Pract2ID");
    assertThat(practitionerObsHemoglobin.getName()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getNameFirstRep().getText()).isEqualTo("Pract2First Pract2Last");
    // Check the cross-reference
    assertThat(practitionerObsHemoglobin.getId()).isEqualTo(practitionerObsHemoglobinRefId);
}