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

Example 61 with UriType

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

the class ValueSetExpanderSimple method includeCodes.

private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, boolean heirarchical) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
    inc.checkNoModifiers("Compose.include", "expanding");
    List<ValueSet> imports = new ArrayList<ValueSet>();
    for (UriType imp : inc.getValueSet()) {
        imports.add(importValueSet(imp.getValue(), params, expParams));
    }
    if (!inc.hasSystem()) {
        if (// though this is not supposed to be the case
        imports.isEmpty())
            return;
        ValueSet base = imports.get(0);
        imports.remove(0);
        base.checkNoModifiers("Imported ValueSet", "expanding");
        copyImportContains(base.getExpansion().getContains(), null, expParams, imports);
    } else {
        CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
        if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE)) {
            doServerIncludeCodes(inc, heirarchical, params, imports, expParams);
        } else {
            doInternalIncludeCodes(inc, params, expParams, imports, cs);
        }
    }
}

Example 62 with UriType

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

the class ValueSetCheckerSimple method inComponent.

private boolean inComponent(ConceptSetComponent vsi, String system, String code, boolean only) throws FHIRException {
    for (UriType uri : vsi.getValueSet()) {
        if (inImport(uri.getValue(), system, code))
            return true;
    }
    if (!vsi.hasSystem())
        return false;
    if (only && system == null) {
        // whether we know the system or not, we'll accept the stated codes at face value
        for (ConceptReferenceComponent cc : vsi.getConcept()) if (cc.getCode().equals(code))
            return true;
    }
    if (!system.equals(vsi.getSystem()))
        return false;
    if (vsi.hasFilter()) {
        boolean ok = true;
        for (ConceptSetFilterComponent f : vsi.getFilter()) if (!codeInFilter(system, f, code)) {
            ok = false;
            break;
        }
        if (ok)
            return true;
    }
    CodeSystem def = context.fetchCodeSystem(system);
    if (def.getContent() != CodeSystemContentMode.COMPLETE)
        throw new FHIRException("Unable to resolve system " + vsi.getSystem() + " - system is not complete");
    List<ConceptDefinitionComponent> list = def.getConcept();
    boolean ok = validateCodeInConceptList(code, def, list);
    if (ok && vsi.hasConcept()) {
        for (ConceptReferenceComponent cc : vsi.getConcept()) if (cc.getCode().equals(code))
            return true;
        return false;
    } else
        return ok;
}

Example 63 with UriType

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

the class TerminologyCache method getIncSummary.

private String getIncSummary(ConceptSetComponent cc) {
    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
    for (UriType vs : cc.getValueSet()) b.append(vs.asStringValue());
    String vsd = b.length() > 0 ? " where the codes are in the value sets (" + b.toString() + ")" : "";
    String system = cc.getSystem();
    if (cc.hasConcept())
        return Integer.toString(cc.getConcept().size()) + " codes from " + system + vsd;
    if (cc.hasFilter()) {
        String s = "";
        for (ConceptSetFilterComponent f : cc.getFilter()) {
            if (!Utilities.noString(s))
                s = s + " & ";
            s = s + f.getProperty() + " " + (f.hasOp() ? f.getOp().toCode() : "?") + " " + f.getValue();
        }
        return "from " + system + " where " + s + vsd;
    }
    return "All codes from " + system + vsd;
}

Example 64 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());
    }
}

Example 65 with UriType

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

the class ProfileUtilities method generateExtensionTable.

public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker, RenderingContext rc) throws IOException, FHIRException {
    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
    gen.setTranslator(getTranslator());
    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId() + (full ? "f" : "n"), true);
    boolean deep = false;
    String m = "";
    boolean vdeep = false;
    if (ed.getSnapshot().getElementFirstRep().getIsModifier())
        m = "modifier_";
    for (ElementDefinition eld : ed.getSnapshot().getElement()) {
        deep = deep || eld.getPath().contains("Extension.extension.");
        vdeep = vdeep || eld.getPath().contains("Extension.extension.extension.");
    }
    Row r = gen.new Row();
    model.getRows().add(r);
    String en;
    if (!full)
        en = ed.getName();
    else if (ed.getSnapshot().getElement().get(0).getIsModifier())
        en = "modifierExtension";
    else
        en = "extension";
    r.getCells().add(gen.new Cell(null, defFile == null ? "" : defFile + "-definitions.html#extension." + ed.getName(), en, null, null));
    r.getCells().add(gen.new Cell());
    r.getCells().add(gen.new Cell(null, null, describeCardinality(ed.getSnapshot().getElement().get(0), null, new UnusedTracker()), null, null));
    ElementDefinition ved = null;
    if (full || vdeep) {
        r.getCells().add(gen.new Cell("", "", "Extension", null, null));
        r.setIcon(deep ? "icon_" + m + "extension_complex.png" : "icon_extension_simple.png", deep ? HierarchicalTableGenerator.TEXT_ICON_EXTENSION_COMPLEX : HierarchicalTableGenerator.TEXT_ICON_EXTENSION_SIMPLE);
        List<ElementDefinition> children = getChildren(ed.getSnapshot().getElement(), ed.getSnapshot().getElement().get(0));
        for (ElementDefinition child : children) if (!child.getPath().endsWith(".id")) {
            List<StructureDefinition> sdl = new ArrayList<>();
            sdl.add(ed);
            genElement(defFile == null ? "" : defFile + "-definitions.html#extension.", gen, r.getSubRows(), child, ed.getSnapshot().getElement(), sdl, true, defFile, true, full, corePath, imagePath, true, false, false, false, null, false, rc);
        }
    } else if (deep) {
        List<ElementDefinition> children = new ArrayList<ElementDefinition>();
        for (ElementDefinition ted : ed.getSnapshot().getElement()) {
            if (ted.getPath().equals("Extension.extension"))
                children.add(ted);
        }
        r.getCells().add(gen.new Cell("", "", "Extension", null, null));
        r.setIcon("icon_" + m + "extension_complex.png", HierarchicalTableGenerator.TEXT_ICON_EXTENSION_COMPLEX);
        for (ElementDefinition c : children) {
            ved = getValueFor(ed, c);
            ElementDefinition ued = getUrlFor(ed, c);
            if (ved != null && ued != null) {
                Row r1 = gen.new Row();
                r.getSubRows().add(r1);
                r1.getCells().add(gen.new Cell(null, defFile == null ? "" : defFile + "-definitions.html#extension." + ed.getName(), ((UriType) ued.getFixed()).getValue(), null, null));
                r1.getCells().add(gen.new Cell());
                r1.getCells().add(gen.new Cell(null, null, describeCardinality(c, null, new UnusedTracker()), null, null));
                genTypes(gen, r1, ved, defFile, ed, corePath, imagePath, false, false);
                Cell cell = gen.new Cell();
                cell.addMarkdown(c.getDefinition());
                r1.getCells().add(cell);
                r1.setIcon("icon_" + m + "extension_simple.png", HierarchicalTableGenerator.TEXT_ICON_EXTENSION_SIMPLE);
            }
        }
    } else {
        for (ElementDefinition ted : ed.getSnapshot().getElement()) {
            if (ted.getPath().startsWith("Extension.value"))
                ved = ted;
        }
        genTypes(gen, r, ved, defFile, ed, corePath, imagePath, false, false);
        r.setIcon("icon_" + m + "extension_simple.png", HierarchicalTableGenerator.TEXT_ICON_EXTENSION_SIMPLE);
    }
    Cell c = gen.new Cell("", "", "URL = " + ed.getUrl(), null, null);
    Piece cc = gen.new Piece(null, ed.getName() + ": ", null);
    c.addPiece(gen.new Piece("br")).addPiece(cc);
    c.addMarkdown(ed.getDescription());
    if (!full && !(deep || vdeep) && ved != null && ved.hasBinding()) {
        c.addPiece(gen.new Piece("br"));
        BindingResolution br = pkp.resolveBinding(ed, ved.getBinding(), ved.getPath());
        c.getPieces().add(checkForNoChange(ved.getBinding(), gen.new Piece(null, translate("sd.table", "Binding") + ": ", null).addStyle("font-weight:bold")));
        c.getPieces().add(checkForNoChange(ved.getBinding(), gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath + br.url, br.display, null)));
        if (ved.getBinding().hasStrength()) {
            c.getPieces().add(checkForNoChange(ved.getBinding(), gen.new Piece(null, " (", null)));
            c.getPieces().add(checkForNoChange(ved.getBinding(), gen.new Piece(corePath + "terminologies.html#" + ved.getBinding().getStrength().toCode(), egt(ved.getBinding().getStrengthElement()), ved.getBinding().getStrength().getDefinition())));
            c.getPieces().add(gen.new Piece(null, ")", null));
        }
        if (ved.getBinding().hasDescription() && MarkDownProcessor.isSimpleMarkdown(ved.getBinding().getDescription())) {
            c.getPieces().add(gen.new Piece(null, ": ", null));
            c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, ved.getBinding().getDescriptionElement()).asStringValue());
        }
    }
    c.addPiece(gen.new Piece("br")).addPiece(gen.new Piece(null, describeExtensionContext(ed), null));
    r.getCells().add(c);
    try {
        return gen.generate(model, corePath, 0, outputTracker);
    } catch (org.hl7.fhir.exceptions.FHIRException e) {
        throw new FHIRException(e.getMessage(), e);
    }
}