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

Example 1 with NoTerminologyServiceException

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

the class BaseWorkerContext method expandVS.

@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical) {
    try {
        if (vs.hasExpansion()) {
            return new ValueSetExpansionOutcome(vs.copy());
        }
        String cacheFn = null;
        if (cache != null) {
            cacheFn = Utilities.path(cache, determineCacheId(vs, heirarchical) + ".json");
            if (new File(cacheFn).exists()) {
                return loadFromCache(vs.copy(), cacheFn);
            }
        }
        if (cacheOk && vs.hasUrl()) {
            if (expProfile == null) {
                throw new Exception("No ExpansionProfile provided");
            }
            ValueSetExpansionOutcome vse = expansionCache.getExpander().expand(vs, expProfile.setExcludeNested(!heirarchical));
            if (vse.getValueset() != null) {
                if (cache != null) {
                    FileOutputStream s = new FileOutputStream(cacheFn);
                    newJsonParser().compose(new FileOutputStream(cacheFn), vse.getValueset());
                    s.close();
                }
            }
            return vse;
        } else {
            ValueSetExpansionOutcome res = expandOnServer(vs, cacheFn);
            if (cacheFn != null) {
                if (res.getValueset() != null) {
                    saveToCache(res.getValueset(), cacheFn);
                } else {
                    OperationOutcome oo = new OperationOutcome();
                    oo.addIssue().getDetails().setText(res.getError());
                    saveToCache(oo, cacheFn);
                }
            }
            return res;
        }
    } catch (NoTerminologyServiceException e) {
        return new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(), TerminologyServiceErrorClass.NOSERVICE);
    } catch (Exception e) {
        return new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
    }
}

Example 2 with NoTerminologyServiceException

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

the class BaseWorkerContext method validateCode.

@Override
public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
    CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
    ValidationResult res = txCache.getValidation(cacheToken);
    if (res != null) {
        return res;
    }
    for (Coding c : code.getCoding()) {
        if (c.hasSystem()) {
            codeSystemsUsed.add(c.getSystem());
        }
    }
    if (options.isUseClient()) {
        // ok, first we try to validate locally
        try {
            ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
            res = vsc.validateCode(code);
            txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
            return res;
        } catch (Exception e) {
            if (e instanceof NoTerminologyServiceException) {
                return new ValidationResult(IssueSeverity.ERROR, "No Terminology Service", TerminologyServiceErrorClass.NOSERVICE);
            }
        }
    }
    if (!options.isUseServer()) {
        return new ValidationResult(IssueSeverity.WARNING, "Unable to validate code without using server", TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS);
    }
    // if that failed, we try to validate on the server
    if (noTerminologyServer) {
        return new ValidationResult(IssueSeverity.ERROR, "Error validating code: running without terminology services", TerminologyServiceErrorClass.NOSERVICE);
    }
    tlog("$validate " + txCache.summary(code) + " for " + txCache.summary(vs));
    try {
        Parameters pIn = new Parameters();
        pIn.addParameter().setName("codeableConcept").setValue(code);
        setTerminologyOptions(options, pIn);
        res = validateOnServer(vs, pIn, options);
    } catch (Exception e) {
        res = new ValidationResult(IssueSeverity.ERROR, e.getMessage() == null ? e.getClass().getName() : e.getMessage()).setTxLink(txLog.getLastId());
    }
    txCache.cacheValidation(cacheToken, res, TerminologyCache.PERMANENT);
    return res;
}

Example 3 with NoTerminologyServiceException

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

the class BaseWorkerContext method validateCode.

@Override
public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
    CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
    ValidationResult res = txCache.getValidation(cacheToken);
    if (res != null) {
        return res;
    }
    for (Coding c : code.getCoding()) {
        if (c.hasSystem()) {
            codeSystemsUsed.add(c.getSystem());
        }
    }
    if (options.isUseClient()) {
        // ok, first we try to validate locally
        try {
            ValueSetCheckerSimple vsc = constructValueSetCheckerSimple(options, vs);
            res = vsc.validateCode(code);
            txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
            return res;
        } catch (Exception e) {
            if (e instanceof NoTerminologyServiceException) {
                return new ValidationResult(IssueSeverity.ERROR, "No Terminology Service", TerminologyServiceErrorClass.NOSERVICE);
            }
        }
    }
    if (!options.isUseServer()) {
        return new ValidationResult(IssueSeverity.WARNING, "Unable to validate code without using server", TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS);
    }
    // if that failed, we try to validate on the server
    if (noTerminologyServer) {
        return new ValidationResult(IssueSeverity.ERROR, "Error validating code: running without terminology services", TerminologyServiceErrorClass.NOSERVICE);
    }
    txLog("$validate " + txCache.summary(code) + " for " + txCache.summary(vs));
    try {
        Parameters pIn = constructParameters(options, code);
        res = validateOnServer(vs, pIn, options);
    } catch (Exception e) {
        res = new ValidationResult(IssueSeverity.ERROR, e.getMessage() == null ? e.getClass().getName() : e.getMessage()).setTxLink(txLog.getLastId());
    }
    txCache.cacheValidation(cacheToken, res, TerminologyCache.PERMANENT);
    return res;
}

Example 4 with NoTerminologyServiceException

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

the class ValueSetExpanderSimple method doInternalIncludeCodes.

public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
    if (cs == null) {
        if (context.isNoTerminologyServer())
            throw failTSE("Unable to find code system " + inc.getSystem().toString());
        else
            throw failTSE("Unable to find code system " + inc.getSystem().toString());
    }
    cs.checkNoModifiers("Code System", "expanding");
    if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)
        throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete");
    if (cs.hasVersion())
        if (!existsInParams(exp.getParameter(), "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
            exp.getParameter().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, new AllConceptsFilter(), noInactive);
        }
        if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
            addFragmentWarning(exp, cs);
        }
        if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
            addExampleWarning(exp, cs);
        }
    }
    if (!inc.getConcept().isEmpty()) {
        canBeHeirarchy = false;
        for (ConceptReferenceComponent c : inc.getConcept()) {
            c.checkNoModifiers("Code in Code System", "expanding");
            ConceptDefinitionComponent def = CodeSystemUtilities.findCode(cs.getConcept(), c.getCode());
            // default is true if we're a fragment and
            Boolean inactive = false;
            if (def == null) {
                if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
                    addFragmentWarning(exp, cs);
                } else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
                    addExampleWarning(exp, cs);
                } else {
                    if (checkCodesWhenExpanding) {
                        throw failTSE("Unable to find code '" + c.getCode() + "' in code system " + cs.getUrl());
                    }
                }
            } else {
                inactive = CodeSystemUtilities.isInactive(cs, def);
            }
            addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, inactive, imports, noInactive);
        }
    }
    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 failTSE("Multiple filters not handled yet");
    }
    if (inc.getFilter().size() == 1) {
        if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
            addFragmentWarning(exp, cs);
        }
        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 failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
        } 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 failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent def : cs.getConcept()) {
                addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(), noInactive);
            }
        } 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 failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
            if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
                List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
                for (ConceptDefinitionComponent c : children) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
            }
        } 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, noInactive);
                    }
                }
            }
        } else if (isDefinedProperty(cs, fc.getProperty())) {
            for (ConceptDefinitionComponent def : cs.getConcept()) {
                addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())), noInactive);
            }
        } else {
            throw fail("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
        }
    }
}

Example 5 with NoTerminologyServiceException

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

the class ValueSetExpanderSimple method includeCodes.

private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
    List<ValueSet> imports = new ArrayList<ValueSet>();
    for (UriType imp : inc.getValueSet()) imports.add(importValueSet(imp.getValue(), params, profile));
    if (!inc.hasSystem()) {
        if (// though this is not supposed to be the case
        imports.isEmpty())
            return;
        ValueSet base = imports.get(0);
        imports.remove(0);
        copyImportContains(base.getExpansion().getContains(), null, profile, imports);
    } else {
        CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
        if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
            addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
            return;
        }
        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());
        }
        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, profile, imports);
            }
        }
        if (!inc.getConcept().isEmpty()) {
            canBeHeirarchy = false;
            for (ConceptReferenceComponent c : inc.getConcept()) {
                addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, 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, profile, imports);
            } 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, profile, imports);
            } 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(), profile, 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");
        }
    }
}