Examples with Source org.hl7.fhir.utilities.validation.ValidationMessage.Source used on opensource projects

Example 86 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeImplementationGuideImplementationGuidePackageResourceComponent.

protected void composeImplementationGuideImplementationGuidePackageResourceComponent(Complex parent, String parentType, String name, ImplementationGuide.ImplementationGuidePackageResourceComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "resource", name, element, index);
    if (element.hasExampleElement())
        composeBoolean(t, "ImplementationGuide", "example", element.getExampleElement(), -1);
    if (element.hasNameElement())
        composeString(t, "ImplementationGuide", "name", element.getNameElement(), -1);
    if (element.hasDescriptionElement())
        composeString(t, "ImplementationGuide", "description", element.getDescriptionElement(), -1);
    if (element.hasAcronymElement())
        composeString(t, "ImplementationGuide", "acronym", element.getAcronymElement(), -1);
    if (element.hasSource())
        composeType(t, "ImplementationGuide", "source", element.getSource(), -1);
    if (element.hasExampleFor())
        composeReference(t, "ImplementationGuide", "exampleFor", element.getExampleFor(), -1);
}

Example 87 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeMessageHeader.

protected void composeMessageHeader(Complex parent, String parentType, String name, MessageHeader element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "MessageHeader", name, element, index);
    if (element.hasTimestampElement())
        composeInstant(t, "MessageHeader", "timestamp", element.getTimestampElement(), -1);
    if (element.hasEvent())
        composeCoding(t, "MessageHeader", "event", element.getEvent(), -1);
    if (element.hasResponse())
        composeMessageHeaderMessageHeaderResponseComponent(t, "MessageHeader", "response", element.getResponse(), -1);
    if (element.hasSource())
        composeMessageHeaderMessageSourceComponent(t, "MessageHeader", "source", element.getSource(), -1);
    for (int i = 0; i < element.getDestination().size(); i++) composeMessageHeaderMessageDestinationComponent(t, "MessageHeader", "destination", element.getDestination().get(i), i);
    if (element.hasEnterer())
        composeReference(t, "MessageHeader", "enterer", element.getEnterer(), -1);
    if (element.hasAuthor())
        composeReference(t, "MessageHeader", "author", element.getAuthor(), -1);
    if (element.hasReceiver())
        composeReference(t, "MessageHeader", "receiver", element.getReceiver(), -1);
    if (element.hasResponsible())
        composeReference(t, "MessageHeader", "responsible", element.getResponsible(), -1);
    if (element.hasReason())
        composeCodeableConcept(t, "MessageHeader", "reason", element.getReason(), -1);
    for (int i = 0; i < element.getData().size(); i++) composeReference(t, "MessageHeader", "data", element.getData().get(i), i);
}

Example 88 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method getProfile.

// private static String listStructures(StructureDefinition p) {
// StringBuilder b = new StringBuilder();
// boolean first = true;
// for (ProfileStructureComponent s : p.getStructure()) {
// if (first)
// first = false;
// else
// b.append(", ");
// if (pkp != null && pkp.hasLinkFor(s.getType()))
// b.append("<a href=\""+pkp.getLinkFor(s.getType())+"\">"+s.getType()+"</a>");
// else
// b.append(s.getType());
// }
// return b.toString();
// }
public StructureDefinition getProfile(StructureDefinition source, String url) {
    StructureDefinition profile;
    String code;
    if (url.startsWith("#")) {
        profile = source;
        code = url.substring(1);
    } else {
        String[] parts = url.split("\\#");
        profile = context.fetchResource(StructureDefinition.class, parts[0]);
        code = parts.length == 1 ? null : parts[1];
    }
    if (profile == null)
        return null;
    if (code == null)
        return profile;
    for (Resource r : profile.getContained()) {
        if (r instanceof StructureDefinition && r.getId().equals(code))
            return (StructureDefinition) r;
    }
    return null;
}

Example 89 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method genTypes.

private Cell genTypes(HierarchicalTableGenerator gen, Row r, ElementDefinition e, String profileBaseFileName, StructureDefinition profile, String corePath) {
    Cell c = gen.new Cell();
    r.getCells().add(c);
    List<TypeRefComponent> types = e.getType();
    if (!e.hasType()) {
        if (e.hasContentReference()) {
            return c;
        } else {
            ElementDefinition d = (ElementDefinition) e.getUserData(DERIVATION_POINTER);
            if (d != null && d.hasType()) {
                types = new ArrayList<ElementDefinition.TypeRefComponent>();
                for (TypeRefComponent tr : d.getType()) {
                    TypeRefComponent tt = tr.copy();
                    tt.setUserData(DERIVATION_EQUALS, true);
                    types.add(tt);
                }
            } else
                return c;
        }
    }
    boolean first = true;
    // either all types are the same, or we don't consider any of them the same
    Element source = types.get(0);
    boolean allReference = ADD_REFERENCE_TO_TABLE && !types.isEmpty();
    for (TypeRefComponent t : types) {
        if (!(t.getCode().equals("Reference") && t.hasProfile()))
            allReference = false;
    }
    if (allReference) {
        c.getPieces().add(gen.new Piece(corePath + "references.html", "Reference", null));
        c.getPieces().add(gen.new Piece(null, "(", null));
    }
    TypeRefComponent tl = null;
    for (TypeRefComponent t : types) {
        if (first)
            first = false;
        else if (allReference)
            c.addPiece(checkForNoChange(tl, gen.new Piece(null, " | ", null)));
        else
            c.addPiece(checkForNoChange(tl, gen.new Piece(null, ", ", null)));
        tl = t;
        if (t.getCode().equals("Reference") || (t.getCode().equals("Resource") && t.hasProfile())) {
            if (ADD_REFERENCE_TO_TABLE && !allReference) {
                c.getPieces().add(gen.new Piece(corePath + "references.html", "Reference", null));
                c.getPieces().add(gen.new Piece(null, "(", null));
            }
            if (t.hasProfile() && t.getProfile().get(0).getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
                StructureDefinition sd = context.fetchResource(StructureDefinition.class, t.getProfile().get(0).getValue());
                if (sd != null) {
                    String disp = sd.hasDisplay() ? sd.getDisplay() : sd.getName();
                    c.addPiece(checkForNoChange(t, gen.new Piece(corePath + sd.getUserString("path"), disp, null)));
                } else {
                    String rn = t.getProfile().get(0).getValue().substring(40);
                    c.addPiece(checkForNoChange(t, gen.new Piece(corePath + pkp.getLinkFor(rn), rn, null)));
                }
            } else if (t.getProfile().size() == 0) {
                c.addPiece(checkForNoChange(t, gen.new Piece(null, t.getCode(), null)));
            } else if (t.getProfile().get(0).getValue().startsWith("#"))
                c.addPiece(checkForNoChange(t, gen.new Piece(corePath + profileBaseFileName + "." + t.getProfile().get(0).getValue().substring(1).toLowerCase() + ".html", t.getProfile().get(0).getValue(), null)));
            else
                c.addPiece(checkForNoChange(t, gen.new Piece(corePath + t.getProfile().get(0).getValue(), t.getProfile().get(0).getValue(), null)));
            if (ADD_REFERENCE_TO_TABLE && !allReference) {
                c.getPieces().add(gen.new Piece(null, ")", null));
            }
        } else if (t.hasProfile()) {
            // a profiled type
            String ref;
            ref = pkp.getLinkForProfile(profile, t.getProfile().get(0).getValue());
            if (ref != null) {
                String[] parts = ref.split("\\|");
                c.addPiece(checkForNoChange(t, gen.new Piece(corePath + parts[0], parts[1], t.getCode())));
            } else
                c.addPiece(checkForNoChange(t, gen.new Piece(corePath + ref, t.getCode(), null)));
        } else if (pkp.hasLinkFor(t.getCode())) {
            c.addPiece(checkForNoChange(t, gen.new Piece(corePath + pkp.getLinkFor(t.getCode()), t.getCode(), null)));
        } else
            c.addPiece(checkForNoChange(t, gen.new Piece(null, t.getCode(), null)));
    }
    if (allReference) {
        c.getPieces().add(gen.new Piece(null, ")", null));
    }
    return c;
}

Example 90 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method updateFromDefinition.

private void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl) throws DefinitionException, FHIRException {
    // we start with a clone of the base profile ('dest') and we copy from the profile ('source')
    // over the top for anything the source has
    ElementDefinition base = dest;
    ElementDefinition derived = source;
    derived.setUserData(DERIVATION_POINTER, base);
    if (derived != null) {
        boolean isExtension = checkExtensionDoco(base);
        if (derived.hasShortElement()) {
            if (!Base.compareDeep(derived.getShortElement(), base.getShortElement(), false))
                base.setShortElement(derived.getShortElement().copy());
            else if (trimDifferential)
                derived.setShortElement(null);
            else if (derived.hasShortElement())
                derived.getShortElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasDefinitionElement()) {
            if (derived.getDefinition().startsWith("..."))
                base.setDefinition(base.getDefinition() + "\r\n" + derived.getDefinition().substring(3));
            else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false))
                base.setDefinitionElement(derived.getDefinitionElement().copy());
            else if (trimDifferential)
                derived.setDefinitionElement(null);
            else if (derived.hasDefinitionElement())
                derived.getDefinitionElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasCommentsElement()) {
            if (derived.getComments().startsWith("..."))
                base.setComments(base.getComments() + "\r\n" + derived.getComments().substring(3));
            else if (!Base.compareDeep(derived.getCommentsElement(), base.getCommentsElement(), false))
                base.setCommentsElement(derived.getCommentsElement().copy());
            else if (trimDifferential)
                base.setCommentsElement(derived.getCommentsElement().copy());
            else if (derived.hasCommentsElement())
                derived.getCommentsElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasLabelElement()) {
            if (derived.getLabel().startsWith("..."))
                base.setLabel(base.getLabel() + "\r\n" + derived.getLabel().substring(3));
            else if (!Base.compareDeep(derived.getLabelElement(), base.getLabelElement(), false))
                base.setLabelElement(derived.getLabelElement().copy());
            else if (trimDifferential)
                base.setLabelElement(derived.getLabelElement().copy());
            else if (derived.hasLabelElement())
                derived.getLabelElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasRequirementsElement()) {
            if (derived.getRequirements().startsWith("..."))
                base.setRequirements(base.getRequirements() + "\r\n" + derived.getRequirements().substring(3));
            else if (!Base.compareDeep(derived.getRequirementsElement(), base.getRequirementsElement(), false))
                base.setRequirementsElement(derived.getRequirementsElement().copy());
            else if (trimDifferential)
                base.setRequirementsElement(derived.getRequirementsElement().copy());
            else if (derived.hasRequirementsElement())
                derived.getRequirementsElement().setUserData(DERIVATION_EQUALS, true);
        }
        // sdf-9
        if (derived.hasRequirements() && !base.getPath().contains("."))
            derived.setRequirements(null);
        if (base.hasRequirements() && !base.getPath().contains("."))
            base.setRequirements(null);
        if (derived.hasAlias()) {
            if (!Base.compareDeep(derived.getAlias(), base.getAlias(), false))
                for (StringType s : derived.getAlias()) {
                    if (!base.hasAlias(s.getValue()))
                        base.getAlias().add(s.copy());
                }
            else if (trimDifferential)
                derived.getAlias().clear();
            else
                for (StringType t : derived.getAlias()) t.setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMinElement()) {
            if (!Base.compareDeep(derived.getMinElement(), base.getMinElement(), false)) {
                if (derived.getMin() < base.getMin())
                    messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived min  (" + Integer.toString(derived.getMin()) + ") cannot be less than base min (" + Integer.toString(base.getMin()) + ")", IssueSeverity.ERROR));
                base.setMinElement(derived.getMinElement().copy());
            } else if (trimDifferential)
                derived.setMinElement(null);
            else
                derived.getMinElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMaxElement()) {
            if (!Base.compareDeep(derived.getMaxElement(), base.getMaxElement(), false)) {
                if (isLargerMax(derived.getMax(), base.getMax()))
                    messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived max (" + derived.getMax() + ") cannot be greater than base max (" + base.getMax() + ")", IssueSeverity.ERROR));
                base.setMaxElement(derived.getMaxElement().copy());
            } else if (trimDifferential)
                derived.setMaxElement(null);
            else
                derived.getMaxElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasFixed()) {
            if (!Base.compareDeep(derived.getFixed(), base.getFixed(), true)) {
                base.setFixed(derived.getFixed().copy());
            } else if (trimDifferential)
                derived.setFixed(null);
            else
                derived.getFixed().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasPattern()) {
            if (!Base.compareDeep(derived.getPattern(), base.getPattern(), false)) {
                base.setPattern(derived.getPattern().copy());
            } else if (trimDifferential)
                derived.setPattern(null);
            else
                derived.getPattern().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasExample()) {
            if (!Base.compareDeep(derived.getExample(), base.getExample(), false))
                base.setExample(derived.getExample().copy());
            else if (trimDifferential)
                derived.setExample(null);
            else
                derived.getExample().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMaxLengthElement()) {
            if (!Base.compareDeep(derived.getMaxLengthElement(), base.getMaxLengthElement(), false))
                base.setMaxLengthElement(derived.getMaxLengthElement().copy());
            else if (trimDifferential)
                derived.setMaxLengthElement(null);
            else
                derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMaxValue()) {
            if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
                base.setMaxValue(derived.getMaxValue().copy());
            else if (trimDifferential)
                derived.setMaxValue(null);
            else
                derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMinValue()) {
            if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
                base.setMinValue(derived.getMinValue().copy());
            else if (trimDifferential)
                derived.setMinValue(null);
            else
                derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMustSupportElement()) {
            if (!Base.compareDeep(derived.getMustSupportElement(), base.getMustSupportElement(), false))
                base.setMustSupportElement(derived.getMustSupportElement().copy());
            else if (trimDifferential)
                derived.setMustSupportElement(null);
            else
                derived.getMustSupportElement().setUserData(DERIVATION_EQUALS, true);
        }
        // but extensions can change isModifier
        if (isExtension) {
            if (!Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false))
                base.setIsModifierElement(derived.getIsModifierElement().copy());
            else if (trimDifferential)
                derived.setIsModifierElement(null);
            else
                derived.getIsModifierElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasBinding()) {
            if (!Base.compareDeep(derived.getBinding(), base.getBinding(), false)) {
                if (base.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && derived.getBinding().getStrength() != BindingStrength.REQUIRED)
                    messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "illegal attempt to change a binding from " + base.getBinding().getStrength().toCode() + " to " + derived.getBinding().getStrength().toCode(), IssueSeverity.ERROR));
                else // throw new DefinitionException("StructureDefinition "+pn+" at "+derived.getPath()+": illegal attempt to change a binding from "+base.getBinding().getStrength().toCode()+" to "+derived.getBinding().getStrength().toCode());
                if (base.hasBinding() && derived.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && base.getBinding().hasValueSetReference() && derived.getBinding().hasValueSetReference()) {
                    ValueSetExpansionOutcome expBase = context.expandVS(context.fetchResource(ValueSet.class, base.getBinding().getValueSetReference().getReference()), true);
                    ValueSetExpansionOutcome expDerived = context.expandVS(context.fetchResource(ValueSet.class, derived.getBinding().getValueSetReference().getReference()), true);
                    if (expBase.getValueset() == null)
                        messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + base.getPath(), "Binding " + base.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
                    else if (expDerived.getValueset() == null)
                        messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
                    else if (!isSubset(expBase.getValueset(), expDerived.getValueset()))
                        messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " is not a subset of binding " + base.getBinding().getValueSetReference().getReference(), IssueSeverity.ERROR));
                }
                base.setBinding(derived.getBinding().copy());
            } else if (trimDifferential)
                derived.setBinding(null);
            else
                derived.getBinding().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasIsSummaryElement()) {
            if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false))
                base.setIsSummaryElement(derived.getIsSummaryElement().copy());
            else if (trimDifferential)
                derived.setIsSummaryElement(null);
            else
                derived.getIsSummaryElement().setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasType()) {
            if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
                if (base.hasType()) {
                    for (TypeRefComponent ts : derived.getType()) {
                        boolean ok = false;
                        CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
                        for (TypeRefComponent td : base.getType()) {
                            b.append(td.getCode());
                            if (td.hasCode() && (td.getCode().equals(ts.getCode()) || td.getCode().equals("Extension") || td.getCode().equals("Element") || td.getCode().equals("*") || ((td.getCode().equals("Resource") || (td.getCode().equals("DomainResource")) && pkp.isResource(ts.getCode())))))
                                ok = true;
                        }
                        if (!ok)
                            throw new DefinitionException("StructureDefinition " + pn + " at " + derived.getPath() + ": illegal constrained type " + ts.getCode() + " from " + b.toString());
                    }
                }
                base.getType().clear();
                for (TypeRefComponent t : derived.getType()) {
                    TypeRefComponent tt = t.copy();
                    // tt.setUserData(DERIVATION_EQUALS, true);
                    base.getType().add(tt);
                }
            } else if (trimDifferential)
                derived.getType().clear();
            else
                for (TypeRefComponent t : derived.getType()) t.setUserData(DERIVATION_EQUALS, true);
        }
        if (derived.hasMapping()) {
            // todo: mappings are not cumulative - one replaces another
            if (!Base.compareDeep(derived.getMapping(), base.getMapping(), false)) {
                for (ElementDefinitionMappingComponent s : derived.getMapping()) {
                    boolean found = false;
                    for (ElementDefinitionMappingComponent d : base.getMapping()) {
                        found = found || (d.getIdentity().equals(s.getIdentity()) && d.getMap().equals(s.getMap()));
                    }
                    if (!found)
                        base.getMapping().add(s);
                }
            } else if (trimDifferential)
                derived.getMapping().clear();
            else
                for (ElementDefinitionMappingComponent t : derived.getMapping()) t.setUserData(DERIVATION_EQUALS, true);
        }
        // todo: constraints are cumulative. there is no replacing
        for (ElementDefinitionConstraintComponent s : base.getConstraint()) s.setUserData(IS_DERIVED, true);
        if (derived.hasConstraint()) {
            for (ElementDefinitionConstraintComponent s : derived.getConstraint()) {
                base.getConstraint().add(s.copy());
            }
        }
    }
}