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

Example 71 with UriType

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

the class XLSXWriter 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.getWorkingCode();
            if (val == null)
                val = "";
            if (val.startsWith("http://hl7.org/fhir/StructureDefinition/"))
                val = val.substring(40);
            if (t.hasTargetProfile())
                val = val + "(" + canonicalList(t.getTargetProfile()) + ")";
            if (t.hasProfile())
                val = val + " {" + canonicalList(t.getProfile()) + "}";
            if (t.hasAggregation())
                val = val + " <<" + aggList(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 72 with UriType

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

the class QuestionnaireBuilder method selectTypes.

private void selectTypes(StructureDefinition profile, QuestionnaireItemComponent sub, TypeRefComponent t, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> source, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> dest) throws FHIRFormatError {
    List<QuestionnaireResponse.QuestionnaireResponseItemComponent> temp = new ArrayList<QuestionnaireResponse.QuestionnaireResponseItemComponent>();
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : source) if (instanceOf(t, (Element) g.getUserData("object")))
        temp.add(g);
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) source.remove(g);
    for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) {
        // it should be empty
        assert (g.getItem().size() == 0);
        QuestionnaireResponse.QuestionnaireResponseItemComponent q = g.addItem();
        q.setLinkId(g.getLinkId() + "._type");
        q.setText("type");
        QuestionnaireResponseItemAnswerComponent a = q.addAnswer();
        if (t.hasTarget()) {
            for (UriType u : t.getTargetProfile()) {
                if (u.getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                    Coding cc = new Coding();
                    a.setValue(cc);
                    cc.setCode(u.getValue().substring(40));
                    cc.setSystem("http://hl7.org/fhir/resource-types");
                }
            }
        } else {
            Coding cc = new Coding();
            a.setValue(cc);
            ProfileUtilities pu = new ProfileUtilities(context, null, null);
            StructureDefinition ps = null;
            if (t.hasProfile())
                ps = pu.getProfile(profile, t.getProfile().get(0).getValue());
            if (ps != null) {
                cc.setCode(t.getProfile().get(0).getValue());
                cc.setSystem("http://hl7.org/fhir/resource-types");
            } else {
                cc.setCode(t.getWorkingCode());
                cc.setSystem("http://hl7.org/fhir/data-types");
            }
        }
        // 1st: create the subgroup
        QuestionnaireResponse.QuestionnaireResponseItemComponent subg = a.addItem();
        dest.add(subg);
        subg.setLinkId(sub.getLinkId());
        subg.setText(sub.getText());
        subg.setUserData("object", g.getUserData("object"));
    }
}

Example 73 with UriType

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

the class QuestionnaireBuilder method makeTypeList.

private ValueSet makeTypeList(StructureDefinition profile, List<TypeRefComponent> types, String path) {
    ValueSet vs = new ValueSet();
    vs.setName("Type options for " + path);
    vs.setDescription(vs.present());
    vs.setStatus(PublicationStatus.ACTIVE);
    vs.setExpansion(new ValueSetExpansionComponent());
    vs.getExpansion().setIdentifier(Factory.createUUID());
    vs.getExpansion().setTimestampElement(DateTimeType.now());
    for (TypeRefComponent t : types) {
        if (t.hasTarget()) {
            for (UriType u : t.getTargetProfile()) {
                if (u.getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                    ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
                    cc.setCode(u.getValue().substring(40));
                    cc.setSystem("http://hl7.org/fhir/resource-types");
                    cc.setDisplay(cc.getCode());
                }
            }
        } else if (!t.hasProfile()) {
            ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
            cc.setCode(t.getWorkingCode());
            cc.setDisplay(t.getWorkingCode());
            cc.setSystem("http://hl7.org/fhir/data-types");
        } else
            for (UriType u : t.getProfile()) {
                ProfileUtilities pu = new ProfileUtilities(context, null, null);
                StructureDefinition ps = pu.getProfile(profile, u.getValue());
                if (ps != null) {
                    ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
                    cc.setCode(u.getValue());
                    cc.setDisplay(ps.getType());
                    cc.setSystem("http://hl7.org/fhir/resource-types");
                }
            }
    }
    return vs;
}

Example 74 with UriType

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

the class StructureMapUtilities method parseConceptMap.

private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
    lexer.token("conceptmap");
    ConceptMap map = new ConceptMap();
    String id = lexer.readConstant("map id");
    if (id.startsWith("#")) {
        throw lexer.error("Concept Map identifier must start with #");
    }
    map.setId(id);
    // todo: how to add this to the text format
    map.setStatus(PublicationStatus.DRAFT);
    result.getContained().add(map);
    lexer.token("{");
    // lexer.token("source");
    // map.setSource(new UriType(lexer.readConstant("source")));
    // lexer.token("target");
    // map.setSource(new UriType(lexer.readConstant("target")));
    Map<String, String> prefixes = new HashMap<String, String>();
    while (lexer.hasToken("prefix")) {
        lexer.token("prefix");
        String n = lexer.take();
        lexer.token("=");
        String v = lexer.readConstant("prefix url");
        prefixes.put(n, v);
    }
    while (lexer.hasToken("unmapped")) {
        lexer.token("unmapped");
        lexer.token("for");
        String n = readPrefix(prefixes, lexer);
        ConceptMapGroupComponent g = getGroup(map, n, null);
        lexer.token("=");
        String v = lexer.take();
        if (v.equals("provided")) {
            g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
        } else {
            throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
        }
    }
    while (!lexer.hasToken("}")) {
        String srcs = readPrefix(prefixes, lexer);
        lexer.token(":");
        String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
        ConceptMapEquivalence eq = readEquivalence(lexer);
        String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
        ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
        SourceElementComponent e = g.addElement();
        e.setCode(sc);
        if (e.getCode().startsWith("\"")) {
            e.setCode(lexer.processConstant(e.getCode()));
        }
        TargetElementComponent tgt = e.addTarget();
        tgt.setEquivalence(eq);
        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
            lexer.token(":");
            tgt.setCode(lexer.take());
            if (tgt.getCode().startsWith("\"")) {
                tgt.setCode(lexer.processConstant(tgt.getCode()));
            }
        }
        tgt.setComment(lexer.getFirstComment());
    }
    lexer.token("}");
}

Example 75 with UriType

use of org.hl7.fhir.r5.model.UriType 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());
    }
}