Examples with Property org.hl7.fhir.r5.model.Property used on opensource projects

Example 56 with Property

use of org.hl7.fhir.r5.model.Property in project org.hl7.fhir.core by hapifhir.

the class SHCParser method parse.

public List<NamedElement> parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
    List<NamedElement> res = new ArrayList<>();
    String src = TextFile.streamToString(stream).trim();
    List<String> list = new ArrayList<>();
    String pfx = null;
    if (src.startsWith("{")) {
        JsonObject json = JsonTrackingParser.parseJson(src);
        if (checkProperty(json, "$", "verifiableCredential", true, "Array")) {
            pfx = "verifiableCredential";
            JsonArray arr = json.getAsJsonArray("verifiableCredential");
            int i = 0;
            for (JsonElement e : arr) {
                if (!(e instanceof JsonPrimitive)) {
                    logError(line(e), col(e), "$.verifiableCredential[" + i + "]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found " + JSONUtil.type(e), IssueSeverity.ERROR);
                } else {
                    list.add(e.getAsString());
                }
                i++;
            }
        } else {
            return res;
        }
    } else {
        list.add(src);
    }
    int c = 0;
    for (String ssrc : list) {
        String prefix = pfx == null ? "" : pfx + "[" + Integer.toString(c) + "].";
        c++;
        JWT jwt = null;
        try {
            jwt = decodeJWT(ssrc);
        } catch (Exception e) {
            logError(1, 1, prefix + "JWT", IssueType.INVALID, "Unable to decode JWT token", IssueSeverity.ERROR);
            return res;
        }
        map = jwt.map;
        checkNamedProperties(jwt.getPayload(), prefix + "payload", "iss", "nbf", "vc");
        checkProperty(jwt.getPayload(), prefix + "payload", "iss", true, "String");
        logError(1, 1, prefix + "JWT", IssueType.INFORMATIONAL, "The FHIR Validator does not check the JWT signature " + "(see https://demo-portals.smarthealth.cards/VerifierPortal.html or https://github.com/smart-on-fhir/health-cards-dev-tools) (Issuer = '" + jwt.getPayload().get("iss").getAsString() + "')", IssueSeverity.INFORMATION);
        checkProperty(jwt.getPayload(), prefix + "payload", "nbf", true, "Number");
        JsonObject vc = jwt.getPayload().getAsJsonObject("vc");
        if (vc == null) {
            logError(1, 1, "JWT", IssueType.STRUCTURE, "Unable to find property 'vc' in the payload", IssueSeverity.ERROR);
            return res;
        }
        String path = prefix + "payload.vc";
        checkNamedProperties(vc, path, "type", "credentialSubject");
        if (!checkProperty(vc, path, "type", true, "Array")) {
            return res;
        }
        JsonArray type = vc.getAsJsonArray("type");
        int i = 0;
        for (JsonElement e : type) {
            if (!(e instanceof JsonPrimitive)) {
                logError(line(e), col(e), path + ".type[" + i + "]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found " + JSONUtil.type(e), IssueSeverity.ERROR);
            } else {
                types.add(e.getAsString());
            }
            i++;
        }
        if (!types.contains("https://smarthealth.cards#health-card")) {
            logError(line(vc), col(vc), path, IssueType.STRUCTURE, "Card does not claim to be of type https://smarthealth.cards#health-card, cannot validate", IssueSeverity.ERROR);
            return res;
        }
        if (!checkProperty(vc, path, "credentialSubject", true, "Object")) {
            return res;
        }
        JsonObject cs = vc.getAsJsonObject("credentialSubject");
        path = path + ".credentialSubject";
        if (!checkProperty(cs, path, "fhirVersion", true, "String")) {
            return res;
        }
        JsonElement fv = cs.get("fhirVersion");
        if (!VersionUtilities.versionsCompatible(context.getVersion(), fv.getAsString())) {
            logError(line(fv), col(fv), path + ".fhirVersion", IssueType.STRUCTURE, "Card claims to be of version " + fv.getAsString() + ", cannot be validated against version " + context.getVersion(), IssueSeverity.ERROR);
            return res;
        }
        if (!checkProperty(cs, path, "fhirBundle", true, "Object")) {
            return res;
        }
        // ok. all checks passed, we can now validate the bundle
        Element e = jsonParser.parse(cs.getAsJsonObject("fhirBundle"), map);
        if (e != null) {
            res.add(new NamedElement(path, e));
        }
    }
    return res;
}

Example 57 with Property

use of org.hl7.fhir.r5.model.Property in project org.hl7.fhir.core by hapifhir.

the class TurtleParser method parse.

private Element parse(Turtle src, TTLComplex cmp) throws FHIRException {
    TTLObject type = cmp.getPredicates().get("http://www.w3.org/2000/01/rdf-schema#type");
    if (type == null) {
        logError(cmp.getLine(), cmp.getCol(), "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.UNKNOWN_RESOURCE_TYPE_MISSING_RDFSTYPE), IssueSeverity.FATAL);
        return null;
    }
    if (type instanceof TTLList) {
        // this is actually broken - really we have to look through the structure definitions at this point
        for (TTLObject obj : ((TTLList) type).getList()) {
            if (obj instanceof TTLURL && ((TTLURL) obj).getUri().startsWith(FHIR_URI_BASE)) {
                type = obj;
                break;
            }
        }
    }
    if (!(type instanceof TTLURL)) {
        logError(cmp.getLine(), cmp.getCol(), "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.UNEXPECTED_DATATYPE_FOR_RDFSTYPE), IssueSeverity.FATAL);
        return null;
    }
    String name = ((TTLURL) type).getUri();
    String ns = name.substring(0, name.lastIndexOf("/"));
    name = name.substring(name.lastIndexOf("/") + 1);
    String path = "/" + name;
    StructureDefinition sd = getDefinition(cmp.getLine(), cmp.getCol(), ns, name);
    if (sd == null)
        return null;
    Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd));
    result.markLocation(cmp.getLine(), cmp.getCol());
    result.setType(name);
    parseChildren(src, path, cmp, result, false);
    result.numberChildren();
    return result;
}

Example 58 with Property

use of org.hl7.fhir.r5.model.Property in project org.hl7.fhir.core by hapifhir.

the class TurtleParser method parseResource.

private void parseResource(Turtle src, String npath, TTLComplex object, Element element, Property property, String name, TTLObject e) throws FHIRException {
    TTLComplex obj;
    if (e instanceof TTLComplex)
        obj = (TTLComplex) e;
    else if (e instanceof TTLURL) {
        String url = ((TTLURL) e).getUri();
        obj = src.getObject(url);
        if (obj == null) {
            logError(e.getLine(), e.getCol(), npath, IssueType.INVALID, context.formatMessage(I18nConstants.REFERENCE_TO__CANNOT_BE_RESOLVED, url), IssueSeverity.FATAL);
            return;
        }
    } else
        throw new FHIRFormatError(context.formatMessage(I18nConstants.WRONG_TYPE_FOR_RESOURCE));
    TTLObject type = obj.getPredicates().get("http://www.w3.org/2000/01/rdf-schema#type");
    if (type == null) {
        logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, context.formatMessage(I18nConstants.UNKNOWN_RESOURCE_TYPE_MISSING_RDFSTYPE), IssueSeverity.FATAL);
        return;
    }
    if (type instanceof TTLList) {
        // this is actually broken - really we have to look through the structure definitions at this point
        for (TTLObject tobj : ((TTLList) type).getList()) {
            if (tobj instanceof TTLURL && ((TTLURL) tobj).getUri().startsWith(FHIR_URI_BASE)) {
                type = tobj;
                break;
            }
        }
    }
    if (!(type instanceof TTLURL)) {
        logError(object.getLine(), object.getCol(), npath, IssueType.INVALID, context.formatMessage(I18nConstants.UNEXPECTED_DATATYPE_FOR_RDFSTYPE), IssueSeverity.FATAL);
        return;
    }
    String rt = ((TTLURL) type).getUri();
    String ns = rt.substring(0, rt.lastIndexOf("/"));
    rt = rt.substring(rt.lastIndexOf("/") + 1);
    StructureDefinition sd = getDefinition(object.getLine(), object.getCol(), ns, rt);
    if (sd == null)
        return;
    Element n = new Element(tail(name), property).markLocation(object.getLine(), object.getCol());
    element.getChildren().add(n);
    n.updateProperty(new Property(this.context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(n.getProperty()), property);
    n.setType(rt);
    parseChildren(src, npath, obj, n, false);
}

Example 59 with Property

use of org.hl7.fhir.r5.model.Property in project org.hl7.fhir.core by hapifhir.

the class JsonParser method parse.

public Element parse(JsonObject object) throws FHIRException {
    JsonElement rt = object.get("resourceType");
    if (rt == null) {
        logError(line(object), col(object), "$", IssueType.INVALID, context.formatMessage(I18nConstants.UNABLE_TO_FIND_RESOURCETYPE_PROPERTY), IssueSeverity.FATAL);
        return null;
    } else {
        String name = rt.getAsString();
        String path = name;
        StructureDefinition sd = getDefinition(line(object), col(object), name);
        if (sd == null)
            return null;
        Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities));
        checkObject(object, path);
        result.markLocation(line(object), col(object));
        result.setType(name);
        result.setPath(result.fhirType());
        parseChildren(path, object, result, true);
        result.numberChildren();
        return result;
    }
}

Example 60 with Property

use of org.hl7.fhir.r5.model.Property 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");
        }
    }
}