Examples with TerminologyServiceException org.hl7.fhir.exceptions.TerminologyServiceException used on opensource projects

Example 16 with TerminologyServiceException

use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method expandVS.

@Override
public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean heirachical) throws TerminologyServiceException {
    ValueSet vs = new ValueSet();
    vs.setCompose(new ValueSetComposeComponent());
    vs.getCompose().getInclude().add(inc);
    CacheToken cacheToken = txCache.generateExpandToken(vs, heirachical);
    ValueSetExpansionOutcome res;
    res = txCache.getExpansion(cacheToken);
    if (res != null)
        return res;
    Parameters p = expParameters.copy();
    p.setParameter("includeDefinition", false);
    p.setParameter("excludeNested", !heirachical);
    if (noTerminologyServer)
        return new ValueSetExpansionOutcome("Error expanding ValueSet: running without terminology services", TerminologyServiceErrorClass.NOSERVICE);
    Map<String, String> params = new HashMap<String, String>();
    params.put("_limit", Integer.toString(expandCodesLimit));
    params.put("_incomplete", "true");
    tlog("$expand on " + txCache.summary(vs));
    try {
        ValueSet result = txClient.expandValueset(vs, p, params);
        res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
    } catch (Exception e) {
        res = new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
        if (txLog != null)
            res.setTxLink(txLog.getLastId());
    }
    txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
    return res;
}

Example 17 with TerminologyServiceException

use of org.hl7.fhir.exceptions.TerminologyServiceException in project fhir-bridge by ehrbase.

the class TerminologyService method getDisplay.

@Cacheable(cacheNames = "terminologyDisplays", key = "#system + '_' + #code")
public String getDisplay(String system, String code) {
    Parameters in = new Parameters();
    in.addParameter(CodeSystem.SP_URL, new UriType(system));
    in.addParameter(CodeSystem.SP_CODE, new StringType(code));
    Parameters out = client.operation().onType(CodeSystem.class).named("validate-code").withParameters(in).execute();
    StringType display = (StringType) out.getParameter("display");
    if (display == null) {
        throw new TerminologyServiceException("Cannot find display for coding: system=" + system + ", code=" + code);
    }
    return display.getValue();
}

Example 18 with TerminologyServiceException

use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkCode.

// public API
private boolean checkCode(List<ValidationMessage> errors, Element element, String path, String code, String system, String version, String display, boolean checkDisplay, NodeStack stack) throws TerminologyServiceException {
    long t = System.nanoTime();
    boolean ss = context.supportsSystem(system);
    timeTracker.tx(t, "ss " + system);
    if (ss) {
        t = System.nanoTime();
        ValidationResult s = checkCodeOnServer(stack, code, system, version, display, checkDisplay);
        timeTracker.tx(t, "vc " + system + "#" + code + " '" + display + "'");
        if (s == null)
            return true;
        if (s.isOk()) {
            if (s.getMessage() != null)
                txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, I18nConstants.TERMINOLOGY_PASSTHROUGH_TX_MESSAGE, s.getMessage(), system, code);
            return true;
        }
        if (s.getErrorClass() != null && s.getErrorClass().isInfrastructure())
            txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else if (s.getSeverity() == IssueSeverity.INFORMATION)
            txHint(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else if (s.getSeverity() == IssueSeverity.WARNING)
            txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else
            return txRule(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, I18nConstants.TERMINOLOGY_PASSTHROUGH_TX_MESSAGE, s.getMessage(), system, code);
        return true;
    } else if (system.startsWith("http://build.fhir.org") || system.startsWith("https://build.fhir.org")) {
        rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_WRONG_BUILD, system, suggestSystemForBuild(system));
        return false;
    } else if (system.startsWith("http://hl7.org/fhir") || system.startsWith("https://hl7.org/fhir") || system.startsWith("http://www.hl7.org/fhir") || system.startsWith("https://www.hl7.org/fhir")) {
        if (SIDUtilities.isknownCodeSystem(system)) {
            // else don't check these (for now)
            return true;
        } else if (system.startsWith("http://hl7.org/fhir/test")) {
            // we don't validate these
            return true;
        } else if (system.endsWith(".html")) {
            rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_WRONG_HTML, system, suggestSystemForPage(system));
            return false;
        } else {
            CodeSystem cs = getCodeSystem(system);
            if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs != null, I18nConstants.TERMINOLOGY_TX_SYSTEM_UNKNOWN, system)) {
                ConceptDefinitionComponent def = getCodeDefinition(cs, code);
                if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, def != null, I18nConstants.TERMINOLOGY_TX_CODE_UNKNOWN, system, code))
                    return warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, display == null || display.equals(def.getDisplay()), I18nConstants.TERMINOLOGY_TX_DISPLAY_WRONG, def.getDisplay());
            }
            return false;
        }
    } else if (context.isNoTerminologyServer() && Utilities.existsInList(system, "http://loinc.org", "http://unitsofmeasure.org", "http://hl7.org/fhir/sid/icd-9-cm", "http://snomed.info/sct", "http://www.nlm.nih.gov/research/umls/rxnorm")) {
        // no checks in this case
        return true;
    } else if (startsWithButIsNot(system, "http://snomed.info/sct", "http://loinc.org", "http://unitsofmeasure.org", "http://www.nlm.nih.gov/research/umls/rxnorm")) {
        rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_INVALID, system);
        return false;
    } else {
        try {
            if (context.fetchResourceWithException(ValueSet.class, system) != null) {
                rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_VALUESET, system);
            // Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur.  Please talk to me before changing the code back.
            }
            boolean done = false;
            if (system.startsWith("https:") && system.length() > 7) {
                String ns = "http:" + system.substring(6);
                CodeSystem cs = getCodeSystem(ns);
                if (cs != null || Utilities.existsInList(system, "https://loinc.org", "https://unitsofmeasure.org", "https://snomed.info/sct", "https://www.nlm.nih.gov/research/umls/rxnorm")) {
                    rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_HTTPS, system);
                    done = true;
                }
            }
            hint(errors, IssueType.UNKNOWN, element.line(), element.col(), path, done, I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system);
            return true;
        } catch (Exception e) {
            return true;
        }
    }
}

Example 19 with TerminologyServiceException

use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method doInternalIncludeCodes.

public void doInternalIncludeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> imports, CodeSystem cs) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
    if (cs == null) {
        if (context.isNoTerminologyServer())
            throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
        else
            throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
    }
    cs.checkNoModifiers("Code System", "expanding");
    if (cs.getContent() != CodeSystemContentMode.COMPLETE)
        throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
    if (cs.hasVersion())
        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
            params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
    if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
        // special case - add all the code system
        for (ConceptDefinitionComponent def : cs.getConcept()) {
            addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
        }
    }
    if (!inc.getConcept().isEmpty()) {
        canBeHeirarchy = false;
        for (ConceptReferenceComponent c : inc.getConcept()) {
            c.checkNoModifiers("Code in Code System", "expanding");
            addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
        }
    }
    if (inc.getFilter().size() > 1) {
        // which will bt the case if we get around to supporting this
        canBeHeirarchy = false;
        // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
        throw new TerminologyServiceException("Multiple filters not handled yet");
    }
    if (inc.getFilter().size() == 1) {
        ConceptSetFilterComponent fc = inc.getFilter().get(0);
        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
            // special: all codes in the target code system under the value
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
            // special: all codes in the target code system that are not under the value
            ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
            if (defEx == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent def : cs.getConcept()) {
                addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx);
            }
        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
            // special: all codes in the target code system under the value
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null);
        } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
            // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
            canBeHeirarchy = false;
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def != null) {
                if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
                    if (def.getDisplay().contains(fc.getValue())) {
                        addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports);
                    }
                }
            }
        } else
            throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
    }
}

Example 20 with TerminologyServiceException

use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method importValueSet.

private ValueSet importValueSet(String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive, ValueSet valueSet) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
    if (value == null)
        throw fail("unable to find value set with no identity");
    ValueSet vs = context.fetchResource(ValueSet.class, value);
    if (vs == null) {
        if (context.fetchResource(CodeSystem.class, value) != null) {
            throw fail("Cannot include value set " + value + " because it's actually a code system");
        } else {
            throw fail("Unable to find imported value set " + value);
        }
    }
    if (noInactive) {
        expParams = expParams.copy();
        expParams.addParameter("activeOnly", true);
    }
    ValueSetExpansionOutcome vso = new ValueSetExpanderSimple(context, allErrors).expand(vs, expParams);
    if (vso.getError() != null) {
        addErrors(vso.getAllErrors());
        throw fail("Unable to expand imported value set " + vs.getUrl() + ": " + vso.getError());
    }
    if (vs.hasVersion())
        if (!existsInParams(exp.getParameter(), "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
            exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
    for (Extension ex : vso.getValueset().getExpansion().getExtension()) {
        if (ex.getUrl().equals(ToolingExtensions.EXT_EXP_TOOCOSTLY)) {
            if (ex.getValue() instanceof BooleanType) {
                exp.getExtension().add(new Extension(ToolingExtensions.EXT_EXP_TOOCOSTLY).setValue(new UriType(value)));
            } else {
                exp.getExtension().add(ex);
            }
        }
    }
    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
        if (!existsInParams(exp.getParameter(), p.getName(), p.getValue()))
            exp.getParameter().add(p);
    }
    if (isValueSetUnionImports(valueSet)) {
        copyExpansion(vso.getValueset().getExpansion().getContains());
    }
    // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
    canBeHeirarchy = false;
    return vso.getValueset();
}