Examples with FINAL org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 36 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method supportsSystem.

@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
    synchronized (lock) {
        if (codeSystems.has(system) && codeSystems.get(system).getContent() != CodeSystemContentMode.NOTPRESENT) {
            return true;
        } else if (supportedCodeSystems.contains(system)) {
            return true;
        } else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com") || system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:")) {
            return false;
        } else {
            if (noTerminologyServer) {
                return false;
            }
            if (txcaps == null) {
                try {
                    logger.logMessage("Terminology server: Check for supported code systems for " + system);
                    final TerminologyCapabilities capabilityStatement = txCache.hasTerminologyCapabilities() ? txCache.getTerminologyCapabilities() : txClient.getTerminologyCapabilities();
                    txCache.cacheTerminologyCapabilities(capabilityStatement);
                    setTxCaps(capabilityStatement);
                } catch (Exception e) {
                    if (canRunWithoutTerminology) {
                        noTerminologyServer = true;
                        logger.logMessage("==============!! Running without terminology server !! ==============");
                        if (txClient != null) {
                            logger.logMessage("txServer = " + txClient.getAddress());
                            logger.logMessage("Error = " + e.getMessage() + "");
                        }
                        logger.logMessage("=====================================================================");
                        return false;
                    } else {
                        e.printStackTrace();
                        throw new TerminologyServiceException(e);
                    }
                }
                if (supportedCodeSystems.contains(system)) {
                    return true;
                }
            }
        }
        return false;
    }
}

Example 37 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class ConceptMapEngineTest method codingTranslate.

@Test
@DisplayName("Coding is translated according to ConceptMap")
void codingTranslate() throws IOException {
    final ConceptMap.SourceElementComponent sourceElementComponent = getSourceElementComponent();
    final ConceptMapEngine conceptMapEngine = getConceptMapEngine(Arrays.asList(sourceElementComponent));
    Coding coding = new Coding(null, SOURCE_CODE_STRING, "Body Weight");
    Coding actual = conceptMapEngine.translate(coding, CONCEPT_MAP_URL);
    assertEquals(TARGET_CODE_STRING, actual.getCode());
}

Example 38 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class DiagnosticReportRenderer method addObservationToTable.

private void addObservationToTable(XhtmlNode tr, ResourceWrapper obs, int i, String ref, boolean refRange, boolean flags, boolean note, boolean effectiveTime, boolean issued, DataType eff, DataType iss) throws UnsupportedEncodingException, FHIRException, IOException {
    // code (+bodysite)
    XhtmlNode td = tr.td();
    PropertyWrapper pw = getProperty(obs, "code");
    if (valued(pw)) {
        render(td.ah(ref), pw.value());
    }
    pw = getProperty(obs, "bodySite");
    if (valued(pw)) {
        td.tx(" (");
        render(td, pw.value());
        td.tx(")");
    }
    // value / dataAbsentReason (in red)
    td = tr.td();
    pw = getProperty(obs, "value[x]");
    if (valued(pw)) {
        render(td, pw.value());
    } else {
        pw = getProperty(obs, "dataAbsentReason");
        if (valued(pw)) {
            XhtmlNode span = td.span("color: maroon", "Error");
            span.tx("Error: ");
            render(span.b(), pw.value());
        }
    }
    if (refRange) {
        // reference range
        td = tr.td();
        pw = getProperty(obs, "referenceRange");
        if (valued(pw)) {
            boolean first = true;
            for (BaseWrapper v : pw.getValues()) {
                if (first)
                    first = false;
                else
                    td.br();
                PropertyWrapper pwr = getProperty(v, "type");
                if (valued(pwr)) {
                    render(td, pwr.value());
                    td.tx(": ");
                }
                PropertyWrapper pwt = getProperty(v, "text");
                if (valued(pwt)) {
                    render(td, pwt.value());
                } else {
                    PropertyWrapper pwl = getProperty(v, "low");
                    PropertyWrapper pwh = getProperty(v, "high");
                    if (valued(pwl) && valued(pwh)) {
                        render(td, pwl.value());
                        td.tx(" - ");
                        render(td, pwh.value());
                    } else if (valued(pwl)) {
                        td.tx(">");
                        render(td, pwl.value());
                    } else if (valued(pwh)) {
                        td.tx("<");
                        render(td, pwh.value());
                    } else {
                        td.tx("??");
                    }
                }
                pwr = getProperty(v, "appliesTo");
                PropertyWrapper pwrA = getProperty(v, "age");
                if (valued(pwr) || valued(pwrA)) {
                    boolean firstA = true;
                    td.tx(" for ");
                    if (valued(pwr)) {
                        for (BaseWrapper va : pwr.getValues()) {
                            if (firstA)
                                firstA = false;
                            else
                                td.tx(", ");
                            render(td, va);
                        }
                    }
                    if (valued(pwrA)) {
                        if (firstA)
                            firstA = false;
                        else
                            td.tx(", ");
                        td.tx("Age ");
                        render(td, pwrA.value());
                    }
                }
            }
        }
    }
    if (flags) {
        // flags (status other than F, interpretation, )
        td = tr.td();
        boolean first = true;
        pw = getProperty(obs, "status");
        if (valued(pw)) {
            if (!pw.value().getBase().primitiveValue().equals("final")) {
                if (first)
                    first = false;
                else
                    td.br();
                render(td, pw.value());
            }
        }
        pw = getProperty(obs, "interpretation");
        if (valued(pw)) {
            for (BaseWrapper v : pw.getValues()) {
                if (first)
                    first = false;
                else
                    td.br();
                render(td, v);
            }
        }
    }
    if (note) {
        td = tr.td();
        pw = getProperty(obs, "note");
        if (valued(pw)) {
            render(td, pw.value());
        }
    }
    if (effectiveTime) {
        // effective if different to DR
        td = tr.td();
        pw = getProperty(obs, "effective[x]");
        if (valued(pw)) {
            if (!Base.compareDeep(pw.value().getBase(), eff, true)) {
                render(td, pw.value());
            }
        }
    }
    if (issued) {
        // issued if different to DR
        td = tr.td();
        pw = getProperty(obs, "issued");
        if (valued(pw)) {
            if (!Base.compareDeep(pw.value().getBase(), eff, true)) {
                render(td, pw.value());
            }
        }
    }
}

Example 39 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class DiagnosticReportRenderer method addObservationToTable.

private void addObservationToTable(XhtmlNode tr, ResourceWrapper obs, int i, String ref, boolean refRange, boolean flags, boolean note, boolean effectiveTime, boolean issued, DataType eff, DataType iss) throws UnsupportedEncodingException, FHIRException, IOException {
    // code (+bodysite)
    XhtmlNode td = tr.td();
    PropertyWrapper pw = getProperty(obs, "code");
    if (valued(pw)) {
        render(td.ah(ref), pw.value());
    }
    pw = getProperty(obs, "bodySite");
    if (valued(pw)) {
        td.tx(" (");
        render(td, pw.value());
        td.tx(")");
    }
    // value / dataAbsentReason (in red)
    td = tr.td();
    pw = getProperty(obs, "value[x]");
    if (valued(pw)) {
        render(td, pw.value());
    } else {
        pw = getProperty(obs, "dataAbsentReason");
        if (valued(pw)) {
            XhtmlNode span = td.span("color: maroon", "Error");
            span.tx("Error: ");
            render(span.b(), pw.value());
        }
    }
    if (refRange) {
        // reference range
        td = tr.td();
        pw = getProperty(obs, "referenceRange");
        if (valued(pw)) {
            boolean first = true;
            for (BaseWrapper v : pw.getValues()) {
                if (first)
                    first = false;
                else
                    td.br();
                PropertyWrapper pwr = getProperty(v, "type");
                if (valued(pwr)) {
                    render(td, pwr.value());
                    td.tx(": ");
                }
                PropertyWrapper pwt = getProperty(v, "text");
                if (valued(pwt)) {
                    render(td, pwt.value());
                } else {
                    PropertyWrapper pwl = getProperty(v, "low");
                    PropertyWrapper pwh = getProperty(v, "high");
                    if (valued(pwl) && valued(pwh)) {
                        render(td, pwl.value());
                        td.tx(" - ");
                        render(td, pwh.value());
                    } else if (valued(pwl)) {
                        td.tx(">");
                        render(td, pwl.value());
                    } else if (valued(pwh)) {
                        td.tx("<");
                        render(td, pwh.value());
                    } else {
                        td.tx("??");
                    }
                }
                pwr = getProperty(v, "appliesTo");
                PropertyWrapper pwrA = getProperty(v, "age");
                if (valued(pwr) || valued(pwrA)) {
                    boolean firstA = true;
                    td.tx(" for ");
                    if (valued(pwr)) {
                        for (BaseWrapper va : pwr.getValues()) {
                            if (firstA)
                                firstA = false;
                            else
                                td.tx(", ");
                            render(td, va);
                        }
                    }
                    if (valued(pwrA)) {
                        if (firstA)
                            firstA = false;
                        else
                            td.tx(", ");
                        td.tx("Age ");
                        render(td, pwrA.value());
                    }
                }
            }
        }
    }
    if (flags) {
        // flags (status other than F, interpretation, )
        td = tr.td();
        boolean first = true;
        pw = getProperty(obs, "status");
        if (valued(pw)) {
            if (!pw.value().getBase().primitiveValue().equals("final")) {
                if (first)
                    first = false;
                else
                    td.br();
                render(td, pw.value());
            }
        }
        pw = getProperty(obs, "interpretation");
        if (valued(pw)) {
            for (BaseWrapper v : pw.getValues()) {
                if (first)
                    first = false;
                else
                    td.br();
                render(td, v);
            }
        }
    }
    if (note) {
        td = tr.td();
        pw = getProperty(obs, "note");
        if (valued(pw)) {
            render(td, pw.value());
        }
    }
    if (effectiveTime) {
        // effective if different to DR
        td = tr.td();
        pw = getProperty(obs, "effective[x]");
        if (valued(pw)) {
            if (!Base.compareDeep(pw.value().getBase(), eff, true)) {
                render(td, pw.value());
            }
        }
    }
    if (issued) {
        // issued if different to DR
        td = tr.td();
        pw = getProperty(obs, "issued");
        if (valued(pw)) {
            if (!Base.compareDeep(pw.value().getBase(), eff, true)) {
                render(td, pw.value());
            }
        }
    }
}

Example 40 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class DiagnosticReportRenderer method scanObsForFlags.

private boolean scanObsForFlags(List<ObservationNode> observations) throws UnsupportedEncodingException, FHIRException, IOException {
    for (ObservationNode o : observations) {
        if (o.obs != null && o.obs.getResource() != null) {
            PropertyWrapper pw = getProperty(o.obs.getResource(), "interpretation");
            if (valued(pw)) {
                return true;
            }
            pw = getProperty(o.obs.getResource(), "status");
            if (valued(pw)) {
                if (!pw.value().getBase().primitiveValue().equals("final")) {
                    return true;
                }
            }
        }
        if (o.contained != null) {
            if (scanObsForFlags(o.contained)) {
                return true;
            }
        }
    }
    return false;
}