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

Example 41 with TypeRefComponent

use of org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent in project org.hl7.fhir.core by hapifhir.

the class CSVWriter method itemList.

private String itemList(List l) {
    StringBuilder s = new StringBuilder();
    for (int i = 0; i < l.size(); i++) {
        Object o = l.get(i);
        String val = "";
        if (o instanceof StringType) {
            val = ((StringType) o).getValue();
        } else if (o instanceof UriType) {
            val = ((UriType) o).getValue();
        } else if (o instanceof IdType) {
            val = ((IdType) o).getValue();
        } else if (o instanceof Enumeration<?>) {
            val = o.toString();
        } else if (o instanceof TypeRefComponent) {
            TypeRefComponent t = (TypeRefComponent) o;
            val = t.getCode() + (t.getProfile() == null ? "" : " {" + t.getProfile() + "}") + (t.getTargetProfile() == null ? "" : " {" + t.getTargetProfile() + "}") + (t.getAggregation() == null || t.getAggregation().isEmpty() ? "" : " (" + itemList(t.getAggregation()) + ")");
        } else if (o instanceof Coding) {
            Coding t = (Coding) o;
            val = (t.getSystem() == null ? "" : t.getSystem()) + (t.getCode() == null ? "" : "#" + t.getCode()) + (t.getDisplay() == null ? "" : " (" + t.getDisplay() + ")");
        } else if (o instanceof ElementDefinitionConstraintComponent) {
            ElementDefinitionConstraintComponent c = (ElementDefinitionConstraintComponent) o;
            val = c.getKey() + ":" + c.getHuman() + " {" + c.getExpression() + "}";
        } else if (o instanceof ElementDefinitionSlicingDiscriminatorComponent) {
            ElementDefinitionSlicingDiscriminatorComponent c = (ElementDefinitionSlicingDiscriminatorComponent) o;
            val = c.getType().toCode() + ":" + c.getPath() + "}";
        } else {
            val = o.toString();
            val = val.substring(val.indexOf("[") + 1);
            val = val.substring(0, val.indexOf("]"));
        }
        s = s.append(val);
        if (i == 0)
            s.append("\n");
    }
    return s.toString();
}

Example 42 with TypeRefComponent

use of org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent in project org.hl7.fhir.core by hapifhir.

the class FHIRPathEngine method getChildTypesByName.

private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr) throws PathEngineException, DefinitionException {
    if (Utilities.noString(type))
        throw new PathEngineException("No type provided in BuildToolPathEvaluator.getChildTypesByName", expr.getStart(), expr.toString());
    if (type.equals("http://hl7.org/fhir/StructureDefinition/xhtml"))
        return;
    if (type.startsWith(Constants.NS_SYSTEM_TYPE))
        return;
    if (type.equals(TypeDetails.FP_SimpleTypeInfo)) {
        getSimpleTypeChildTypesByName(name, result);
    } else if (type.equals(TypeDetails.FP_ClassInfo)) {
        getClassInfoChildTypesByName(name, result);
    } else {
        String url = null;
        if (type.contains("#")) {
            url = type.substring(0, type.indexOf("#"));
        } else {
            url = type;
        }
        String tail = "";
        StructureDefinition sd = worker.fetchResource(StructureDefinition.class, url);
        if (sd == null)
            // this really is an error, because we can only get to here if the internal infrastrucgture is wrong
            throw new DefinitionException("Unknown type " + type);
        List<StructureDefinition> sdl = new ArrayList<StructureDefinition>();
        ElementDefinitionMatch m = null;
        if (type.contains("#"))
            m = getElementDefinition(sd, type.substring(type.indexOf("#") + 1), false, expr);
        if (m != null && hasDataType(m.definition)) {
            if (m.fixedType != null) {
                StructureDefinition dt = worker.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(m.fixedType, worker.getOverrideVersionNs()));
                if (dt == null)
                    throw new DefinitionException("unknown data type " + m.fixedType);
                sdl.add(dt);
            } else
                for (TypeRefComponent t : m.definition.getType()) {
                    StructureDefinition dt = worker.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(t.getCode(), worker.getOverrideVersionNs()));
                    if (dt == null)
                        throw new DefinitionException("unknown data type " + t.getCode());
                    sdl.add(dt);
                }
        } else {
            sdl.add(sd);
            if (type.contains("#")) {
                tail = type.substring(type.indexOf("#") + 1);
                tail = tail.substring(tail.indexOf("."));
            }
        }
        for (StructureDefinition sdi : sdl) {
            String path = sdi.getSnapshot().getElement().get(0).getPath() + tail + ".";
            if (name.equals("**")) {
                assert (result.getCollectionStatus() == CollectionStatus.UNORDERED);
                for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
                    if (ed.getPath().startsWith(path))
                        for (TypeRefComponent t : ed.getType()) {
                            if (t.hasCode() && t.getCodeElement().hasValue()) {
                                String tn = null;
                                if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                                    tn = sdi.getType() + "#" + ed.getPath();
                                else
                                    tn = t.getCode();
                                if (t.getCode().equals("Resource")) {
                                    for (String rn : worker.getResourceNames()) {
                                        if (!result.hasType(worker, rn)) {
                                            getChildTypesByName(result.addType(rn), "**", result, expr);
                                        }
                                    }
                                } else if (!result.hasType(worker, tn)) {
                                    getChildTypesByName(result.addType(tn), "**", result, expr);
                                }
                            }
                        }
                }
            } else if (name.equals("*")) {
                assert (result.getCollectionStatus() == CollectionStatus.UNORDERED);
                for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
                    if (ed.getPath().startsWith(path) && !ed.getPath().substring(path.length()).contains("."))
                        for (TypeRefComponent t : ed.getType()) {
                            if (// Element.id or Extension.url
                            Utilities.noString(t.getCode()))
                                result.addType("System.string");
                            else if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                                result.addType(sdi.getType() + "#" + ed.getPath());
                            else if (t.getCode().equals("Resource"))
                                result.addTypes(worker.getResourceNames());
                            else
                                result.addType(t.getCode());
                        }
                }
            } else {
                path = sdi.getSnapshot().getElement().get(0).getPath() + tail + "." + name;
                ElementDefinitionMatch ed = getElementDefinition(sdi, path, false, expr);
                if (ed != null) {
                    if (!Utilities.noString(ed.getFixedType()))
                        result.addType(ed.getFixedType());
                    else
                        for (TypeRefComponent t : ed.getDefinition().getType()) {
                            if (Utilities.noString(t.getCode())) {
                                if (Utilities.existsInList(ed.getDefinition().getId(), "Element.id", "Extension.url") || Utilities.existsInList(ed.getDefinition().getBase().getPath(), "Resource.id", "Element.id", "Extension.url"))
                                    result.addType(TypeDetails.FP_NS, "string");
                                // throw new PathEngineException("Illegal reference to primitive value attribute @ "+path);
                                break;
                            }
                            ProfiledType pt = null;
                            if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement"))
                                pt = new ProfiledType(sdi.getUrl() + "#" + path);
                            else if (t.getCode().equals("Resource"))
                                result.addTypes(worker.getResourceNames());
                            else
                                pt = new ProfiledType(t.getCode());
                            if (pt != null) {
                                if (t.hasProfile())
                                    pt.addProfiles(t.getProfile());
                                if (ed.getDefinition().hasBinding())
                                    pt.addBinding(ed.getDefinition().getBinding());
                                result.addType(pt);
                            }
                        }
                }
            }
        }
    }
}

Example 43 with TypeRefComponent

use of org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent in project org.hl7.fhir.core by hapifhir.

the class GraphQLSchemaGenerator method generateProperties.

private void generateProperties(List<StringBuilder> list, StringBuilder b, String typeName, StructureDefinition sd, ElementDefinition ed, String mode, String suffix) throws IOException {
    List<ElementDefinition> children = ProfileUtilities.getChildList(sd, ed);
    for (ElementDefinition child : children) {
        if (child.hasContentReference()) {
            ElementDefinition ref = resolveContentReference(sd, child.getContentReference());
            generateProperty(list, b, typeName, sd, child, ref.getType().get(0), false, ref, mode, suffix);
        } else if (child.getType().size() == 1) {
            generateProperty(list, b, typeName, sd, child, child.getType().get(0), false, null, mode, suffix);
        } else {
            boolean ref = false;
            for (TypeRefComponent t : child.getType()) {
                if (!t.hasTarget())
                    generateProperty(list, b, typeName, sd, child, t, true, null, mode, suffix);
                else if (!ref) {
                    ref = true;
                    generateProperty(list, b, typeName, sd, child, t, true, null, mode, suffix);
                }
            }
        }
    }
}

Example 44 with TypeRefComponent

use of org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method generateSnapshot.

/**
 * Given a base (snapshot) profile structure, and a differential profile, generate a new snapshot profile
 *
 * @param base - the base structure on which the differential will be applied
 * @param differential - the differential to apply to the base
 * @param url - where the base has relative urls for profile references, these need to be converted to absolutes by prepending this URL (e.g. the canonical URL)
 * @param webUrl - where the base has relative urls in markdown, these need to be converted to absolutes by prepending this URL (this is not the same as the canonical URL)
 * @param trimDifferential - if this is true, then the snap short generator will remove any material in the element definitions that is not different to the base
 * @return
 * @throws FHIRException
 * @throws DefinitionException
 * @throws Exception
 */
public void generateSnapshot(StructureDefinition base, StructureDefinition derived, String url, String webUrl, String profileName) throws DefinitionException, FHIRException {
    if (base == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_BASE_PROFILE_PROVIDED));
    }
    if (derived == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_DERIVED_STRUCTURE_PROVIDED));
    }
    checkNotGenerating(base, "Base for generating a snapshot for the profile " + derived.getUrl());
    checkNotGenerating(derived, "Focus for generating a snapshot");
    if (!base.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE_PROFILE__HAS_NO_TYPE, base.getUrl()));
    }
    if (!derived.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_TYPE, derived.getUrl()));
    }
    if (!derived.hasDerivation()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_DERIVATION_VALUE_AND_SO_CANT_BE_PROCESSED, derived.getUrl()));
    }
    if (!base.getType().equals(derived.getType()) && derived.getDerivation() == TypeDerivationRule.CONSTRAINT) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE__DERIVED_PROFILES_HAVE_DIFFERENT_TYPES____VS___, base.getUrl(), base.getType(), derived.getUrl(), derived.getType()));
    }
    if (snapshotStack.contains(derived.getUrl())) {
        throw new DefinitionException(context.formatMessage(I18nConstants.CIRCULAR_SNAPSHOT_REFERENCES_DETECTED_CANNOT_GENERATE_SNAPSHOT_STACK__, snapshotStack.toString()));
    }
    derived.setUserData("profileutils.snapshot.generating", true);
    snapshotStack.add(derived.getUrl());
    try {
        if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
            webUrl = webUrl + '/';
        if (defWebRoot == null)
            defWebRoot = webUrl;
        derived.setSnapshot(new StructureDefinitionSnapshotComponent());
        try {
            checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
            checkDifferentialBaseType(derived);
            // so we have two lists - the base list, and the differential list
            // the differential list is only allowed to include things that are in the base list, but
            // is allowed to include them multiple times - thereby slicing them
            // our approach is to walk through the base list, and see whether the differential
            // says anything about them.
            int baseCursor = 0;
            // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
            int diffCursor = 0;
            for (ElementDefinition e : derived.getDifferential().getElement()) e.clearUserData(GENERATED_IN_SNAPSHOT);
            // we actually delegate the work to a subroutine so we can re-enter it with a different cursors
            // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
            StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential());
            StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                String derivedType = derived.getType();
                if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
                    derivedType = derivedType.substring(derivedType.lastIndexOf("/") + 1);
                }
                baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
            }
            // if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
            // debug = true;
            // }
            processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size() - 1, derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size() - 1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
            checkGroupConstraints(derived);
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition e : diff.getElement()) {
                    if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                        ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
                        e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
                        derived.getSnapshot().addElement(outcome);
                    }
                }
            }
            if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
                throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
            updateMaps(base, derived);
            setIds(derived, false);
            if (debug) {
                System.out.println("Differential: ");
                for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                System.out.println("Snapshot: ");
                for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
            }
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            // Check that all differential elements have a corresponding snapshot element
            int ce = 0;
            for (ElementDefinition e : diff.getElement()) {
                if (!e.hasUserData("diff-source"))
                    throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
                else {
                    if (e.hasUserData(DERIVATION_EQUALS))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
                    if (e.hasUserData(DERIVATION_POINTER))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
                }
                if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                    b.append(e.hasId() ? "id: " + e.getId() : "path: " + e.getPath());
                    ce++;
                    if (e.hasId()) {
                        String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
                    }
                }
            }
            if (!Utilities.noString(b.toString())) {
                String msg = "The profile " + derived.getUrl() + " has " + ce + " " + Utilities.pluralize("element", ce) + " in the differential (" + b.toString() + ") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
                System.out.println("Error in snapshot generation: " + msg);
                if (!debug) {
                    System.out.println("Differential: ");
                    for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                    System.out.println("Snapshot: ");
                    for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                }
                if (exception)
                    throw new DefinitionException(msg);
                else
                    messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
            }
            // hack around a problem in R4 definitions (somewhere?)
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
                    if (mm.hasMap()) {
                        mm.setMap(mm.getMap().trim());
                    }
                }
                for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
                    if (s.hasSource()) {
                        String ref = s.getSource();
                        if (!Utilities.isAbsoluteUrl(ref)) {
                            if (ref.contains(".")) {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref.substring(0, ref.indexOf(".")) + "#" + ref);
                            } else {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref);
                            }
                        }
                    }
                }
            }
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                    if (!ed.hasBase()) {
                        ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
                    }
                }
            }
            // last, check for wrong profiles or target profiles
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (TypeRefComponent t : ed.getType()) {
                    for (UriType u : t.getProfile()) {
                        StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
                        if (sd == null) {
                            if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
                                sd = xver.makeDefinition(u.getValue());
                            }
                        }
                        if (sd == null) {
                            if (messages != null) {
                                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), "The type of profile " + u.getValue() + " cannot be checked as the profile is not known", IssueSeverity.WARNING));
                            }
                        } else {
                            String wt = t.getWorkingCode();
                            if (ed.getPath().equals("Bundle.entry.response.outcome")) {
                                wt = "OperationOutcome";
                            }
                            if (!sd.getType().equals(wt)) {
                                boolean ok = isCompatibleType(wt, sd);
                                if (!ok) {
                                    String smsg = "The profile " + u.getValue() + " has type " + sd.getType() + " which is not consistent with the stated type " + wt;
                                    if (exception)
                                        throw new DefinitionException(smsg);
                                    else
                                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), smsg, IssueSeverity.ERROR));
                                }
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
            // if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
            derived.setSnapshot(null);
            derived.clearUserData("profileutils.snapshot.generating");
            throw e;
        }
    } finally {
        derived.clearUserData("profileutils.snapshot.generating");
        snapshotStack.remove(derived.getUrl());
    }
}

Example 45 with TypeRefComponent

use of org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method typeCode.

public static String typeCode(List<TypeRefComponent> types) {
    StringBuilder b = new StringBuilder();
    boolean first = true;
    for (TypeRefComponent type : types) {
        if (first)
            first = false;
        else
            b.append(", ");
        b.append(type.getWorkingCode());
        if (type.hasTargetProfile())
            b.append("{" + type.getTargetProfile() + "}");
        else if (type.hasProfile())
            b.append("{" + type.getProfile() + "}");
    }
    return b.toString();
}