Examples with Group org.hl7.fhir.r4.model.Group used on opensource projects

Example 21 with Group

use of org.hl7.fhir.r4.model.Group in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7FinancialInsuranceTest method testForDataBleedFromPatientToOrganization.

@Test
// Ensure that Patient data does not bleed into Organizations created for the Patient's insurance
void testForDataBleedFromPatientToOrganization() throws IOException {
    String hl7message = "MSH|^~\\&|TEST|TEST|||20220101120000||ADT^A01^ADT_A01|1234|P|2.6\n" + // PID.12 Used for district calculation
    "PID|1|103456|MR12345678^^^^MR||DOE^JANE^|||F|||19 Raymond St^Route3^Albany^NY^56321^USA^P|12||||||||||||||||||||||||||\n" + // PD1.4 Used for org creation to check for bleed of districts
    "PD1|||Mayo|123456^Walt^^^^Dr||||||||||||||||||\n" + // IN1 Broadly populated to create organization
    "IN1|1|GLOBAL|7776664|Blue Cross Blue Shield|456 Blue Cross Lane||||Blue|987123|IBM||||||NON||||||||||||20210322145350|Dr Disney|S|GOOD|200|12|B6543|H789456|||17|||1|M|123 IBM way|True|NONE|B|NO|J321456|M|20210322145605|London|YES\n" + // IN2 Broadly populated to create organizations
    "IN2|A23456|222001111|IBM 1345|EMPLOYEED|E|N23497234|R3294809|S234234|Army|U439823|SGT SCHULTZ|Army|Fort Wayne|USA|E1... E9|ACT|20300402145954|N|N|N|Yes|Grey Duck|Goose|T34941341232|D123123123|C435435345|2|SPR|2ANC|1234.00|O|A0|USA|EN|F|F|Y|N|COG|Stanley|DUTCH|N|M|20170322150208||Software Engineer|8|P|Mr Blue|1-555-333-4444|SURGERY|Jim Stanley|1-555-222-3333|FIRST|20170202150409|20210322150400|3|1-222-333-4444|GLOBAL|GROUP|B14456789|OTH|1-444-777-8888|1-444-555-3333|NONE|N|Y|N|GVH 123456|CDP 98765|2106-3|9\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> patients = ResourceUtils.getResourceList(e, ResourceType.Patient);
    // From PID
    assertThat(patients).hasSize(1);
    Patient patient = (Patient) patients.get(0);
    assertThat(patient.getAddressFirstRep().getDistrict()).hasToString("12");
    List<Resource> organizations = ResourceUtils.getResourceList(e, ResourceType.Organization);
    // From Payor created by IN1
    assertThat(organizations).hasSize(3);
    Organization org = (Organization) organizations.get(0);
    assertThat(org.getAddressFirstRep().hasDistrict()).isFalse();
    org = (Organization) organizations.get(1);
    assertThat(org.hasAddress()).isFalse();
    org = (Organization) organizations.get(2);
    assertThat(org.hasAddress()).isFalse();
    List<Resource> coverages = ResourceUtils.getResourceList(e, ResourceType.Coverage);
    // From IN1 segment
    assertThat(coverages).hasSize(1);
    Coverage coverage = (Coverage) coverages.get(0);
    // Confirm Coverage Identifiers
    assertThat(coverage.getIdentifier()).hasSize(6);
    // Coverage Identifiers deep check in testBasicInsuranceCoverageFields
    // Because the relationship is NON, no subscriber is created
    assertThat(coverage.hasSubscriber()).isFalse();
    // Expect no RelatedPerson because IN1.17 is NON
    List<Resource> relatedPersons = ResourceUtils.getResourceList(e, ResourceType.RelatedPerson);
    // No related person should be created because IN1.17 was an unknown code
    assertThat(relatedPersons).isEmpty();
    // Confirm there are no unaccounted for resources
    // Expected: Coverage, Organization (3), Patient, Practitioner
    assertThat(e).hasSize(6);
}

Example 22 with Group

use of org.hl7.fhir.r4.model.Group in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ORUMessageTest method test_oru_with_multiple_reports.

// 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")
@Test
void test_oru_with_multiple_reports() throws IOException {
    String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|112^Final Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3068^JOHN^Paul^J|\r" + "OBX|1|ST|TS-F-01-007^Endocrine Disorders 7^L||obs report||||||F\r" + "OBX|2|ST|TS-F-01-008^Endocrine Disorders 8^L||ECHOCARDIOGRAPHIC REPORT||||||F\r" + "OBR|1||98^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|113^Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^2.33^^result1|1|27268008^Salmonella^SCT^^^^20090731^^Salmonella species|||A^A^HL70078^^^^2.5|||P|||20120301|||^^^^^^^^Bacterial Culture||201203140957||||||\r" + "OBX|2|ST|TS-F-01-002^Endocrine Disorders^L||ECHOCARDIOGRAPHIC REPORT Group 2||||||F\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Verify that the right resources are being created
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(4);
    List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitionerResource).hasSize(2);
    List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReport).hasSize(2);
    List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(servReqResource).hasSize(2);
    // Expecting only the above resources, no extras!
    assertThat(e).hasSize(11);
    // /////////////////////////////////////////
    // Now confirm content of the FIRST diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
    // Verify status from OBR.25
    assertThat(diag.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag.getCategory()).isEmpty();
    // Verify code from OBR.4
    assertThat(diag.hasCode()).isTrue();
    List<Coding> codings = diag.getCode().getCoding();
    assertThat(codings).hasSize(1);
    Coding coding = codings.get(0);
    assertThat(coding.hasDisplay()).isTrue();
    assertThat(coding.getDisplay()).hasToString("Final Echocardiogram Report");
    assertThat(coding.hasCode()).isTrue();
    assertThat(coding.getCode()).hasToString("112");
    assertThat(coding.hasSystem()).isFalse();
    // Verify encounter reference
    assertThat(diag.getEncounter().isEmpty()).isTrue();
    // Verify subject reference
    assertThat(diag.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    // This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
    // Verify issued from OBR.22
    assertThat(diag.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag.getResultsInterpreter()).hasSize(1);
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    assertThat(diag.getSpecimen()).isEmpty();
    // Verify result reference
    List<Reference> obsRef = diag.getResult();
    assertThat(obsRef).hasSize(2);
    assertThat(obsRef.get(0).isEmpty()).isFalse();
    // Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not of type TX.
    List<Attachment> attachments = diag.getPresentedForm();
    Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
    // /////////////////////////////////////////
    // Now confirm content of the SECOND diagnosticReport because we don't have separate tests for DiagnosticReport
    // /////////////////////////////////////////
    DiagnosticReport diag2 = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
    // Verify status from OBR.25
    assertThat(diag2.getStatus().toCode()).isEqualTo("final");
    // Verify category from OBR.24
    assertThat(diag2.getCategory()).isEmpty();
    // Verify code from OBR.4
    assertThat(diag2.hasCode()).isTrue();
    List<Coding> codings2 = diag2.getCode().getCoding();
    assertThat(codings2).hasSize(1);
    Coding coding2 = codings.get(0);
    assertThat(coding2.hasDisplay()).isTrue();
    assertThat(coding2.getDisplay()).hasToString("Final Echocardiogram Report");
    assertThat(coding2.hasCode()).isTrue();
    assertThat(coding2.getCode()).hasToString("112");
    assertThat(coding2.hasSystem()).isFalse();
    // Verify encounter reference
    assertThat(diag2.getEncounter().isEmpty()).isTrue();
    // Verify subject reference
    assertThat(diag2.getSubject().isEmpty()).isFalse();
    // Verify effectiveDateTime from OBR.7 and OBR.8
    // This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
    assertThat(diag2.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
    // Verify issued from OBR.22
    assertThat(diag2.getIssued()).isNull();
    // Verify resultsInterpreter from OBR.32
    assertThat(diag2.getResultsInterpreter()).hasSize(1);
    // Verify basedOn is ref to the ServiceRequest created for ORC or OBR
    assertThat(diag.getBasedOn()).hasSize(1);
    assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
    // Verify specimen reference
    assertThat(diag2.getSpecimen()).isEmpty();
    // Verify result reference
    List<Reference> obsRef2 = diag2.getResult();
    assertThat(obsRef2).hasSize(2);
    assertThat(obsRef2.get(0).isEmpty()).isFalse();
    // Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not type TX.
    List<Attachment> attachments2 = diag2.getPresentedForm();
    Assertions.assertEquals(0, attachments2.size(), "Unexpected number of attachments");
    // //////////////////////////////////
    for (Resource res : obsResource) {
        // Verify encounter reference is not set
        Observation obs = (Observation) res;
        assertThat(obs.getEncounter().isEmpty()).isTrue();
        // Verify subject reference to Patient exists
        Base subject = ResourceUtils.getValue(obs, "subject");
        assertThat(ResourceUtils.getValueAsString(subject, "reference").substring(0, 8)).isEqualTo("Patient/");
    }
}

Example 23 with Group

use of org.hl7.fhir.r4.model.Group in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7DataExtractor method getAllStructures.

public ParsingResult<Structure> getAllStructures(String group, int groupRep, String segment) {
    LOGGER.debug("Fetching segment: {} {} {} ", group, groupRep, segment);
    try {
        ParsingResult<Structure> parsingResult = null;
        Preconditions.checkArgument(StringUtils.isNotBlank(group), "group cannot be null or empty");
        Preconditions.checkArgument(StringUtils.isNotBlank(segment), SEGMENT_CANNOT_BE_NULL_OR_EMPTY);
        Preconditions.checkArgument(groupRep >= 0, "groupRep should be greater than or equal to 0");
        Structure groupStr = message.get(group, groupRep);
        if (groupStr instanceof Group) {
            Group gp = (Group) groupStr;
            Structure[] s = gp.getAll(segment);
            List<Structure> list = Lists.newArrayList(s);
            list.removeIf(isEmpty());
            parsingResult = new Hl7ParsingStructureResult(Lists.newArrayList(list));
        } else {
            parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
        }
        return parsingResult;
    } catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
        String spec = group + " " + groupRep + " " + segment;
        LOGGER.debug("Cannot extract value for {} ", spec, e);
        LOGGER.warn("Cannot extract value for {} ", spec);
        return new Hl7ParsingStructureResult(new ArrayList<>());
    }
}

Example 24 with Group

use of org.hl7.fhir.r4.model.Group in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7DataExtractor method getAllStructures.

public ParsingResult<Structure> getAllStructures(Structure struct, String segment) {
    LOGGER.debug("Fetching segment: {} {}  ", struct, segment);
    try {
        ParsingResult<Structure> parsingResult = null;
        Preconditions.checkArgument(struct != null, "struct cannot be null ");
        Preconditions.checkArgument(StringUtils.isNotBlank(segment), SEGMENT_CANNOT_BE_NULL_OR_EMPTY);
        if (struct instanceof Group) {
            Group gp = (Group) struct;
            Structure[] s = gp.getAll(segment);
            List<Structure> list = Lists.newArrayList(s);
            list.removeIf(isEmpty());
            parsingResult = new Hl7ParsingStructureResult(list);
        } else {
            parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
        }
        return parsingResult;
    } catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
        LOGGER.debug("Cannot extract value for Structure {} Segment {} ", struct, segment, e);
        LOGGER.warn("Cannot extract value for Structure {} Segment {} ", struct, segment);
        return new Hl7ParsingStructureResult(new ArrayList<>());
    }
}

Example 25 with Group

use of org.hl7.fhir.r4.model.Group in project manifoldcf by apache.

the class ConfluenceClient method getUserAuthorities.

/**
 * @param username
 * @return
 * @throws Exception
 */
public ConfluenceUser getUserAuthorities(final String username) throws Exception {
    final List<String> authorities = Lists.<String>newArrayList();
    final List<Group> groups = getUserGroups(username);
    groups.forEach(group -> {
        authorities.add("group-" + group.getName());
    });
    final User user = getConfluenceUser(username);
    authorities.add("user-" + user.getUserKey());
    final List<Space> spaces = getSpaces();
    for (final Space space : spaces) {
        final List<String> permissions = getSpacePermissionsForUser(space, username);
        if (permissions.contains(VIEW_PERMISSION)) {
            authorities.add("space-" + space.getKey());
        }
    }
    return new ConfluenceUser(username, authorities);
}