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

Example 56 with Enumeration

use of org.hl7.fhir.r5.model.Enumeration 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.getWorkingCode() + (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 57 with Enumeration

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

the class ProfileDrivenRenderer method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        return;
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType) {
        renderDateTime(x, e);
    } else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.r5.model.DateType) {
        org.hl7.fhir.r5.model.DateType dt = ((org.hl7.fhir.r5.model.DateType) e);
        renderDate(x, dt);
    } else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType) {
        x.addText(((BooleanType) e).getValue().toString());
    } else if (e instanceof CodeableConcept) {
        renderCodeableConcept(x, (CodeableConcept) e, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding(x, (Coding) e, showCodeDetails);
    } else if (e instanceof CodeableReference) {
        renderCodeableReference(x, (CodeableReference) e, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation(x, (Annotation) e);
    } else if (e instanceof Identifier) {
        renderIdentifier(x, (Identifier) e);
    } else if (e instanceof org.hl7.fhir.r5.model.IntegerType) {
        if (((org.hl7.fhir.r5.model.IntegerType) e).hasValue()) {
            x.addText(Integer.toString(((org.hl7.fhir.r5.model.IntegerType) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
        if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
            x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
        x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName(x, (HumanName) e);
    } else if (e instanceof SampledData) {
        renderSampledData(x, (SampledData) e);
    } else if (e instanceof Address) {
        renderAddress(x, (Address) e);
    } else if (e instanceof ContactPoint) {
        renderContactPoint(x, (ContactPoint) e);
    } else if (e instanceof Expression) {
        renderExpression(x, (Expression) e);
    } else if (e instanceof Money) {
        renderMoney(x, (Money) e);
    } else if (e instanceof ContactDetail) {
        ContactDetail cd = (ContactDetail) e;
        if (cd.hasName()) {
            x.tx(cd.getName() + ": ");
        }
        boolean first = true;
        for (ContactPoint c : cd.getTelecom()) {
            if (first)
                first = false;
            else
                x.tx(",");
            renderContactPoint(x, c);
        }
    } else if (e instanceof UriType) {
        renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
    } else if (e instanceof Timing) {
        renderTiming(x, (Timing) e);
    } else if (e instanceof Range) {
        renderRange(x, (Range) e);
    } else if (e instanceof Quantity) {
        renderQuantity(x, (Quantity) e, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(x, ((Ratio) e).getNumerator(), showCodeDetails);
        x.tx("/");
        renderQuantity(x, ((Ratio) e).getDenominator(), showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        renderPeriod(x, p);
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        if (r.getReference() != null && r.getReference().contains("#")) {
            if (containedIds.contains(r.getReference().substring(1))) {
                x.ah(r.getReference()).tx("See " + r.getReference());
            } else {
                // in this case, we render the resource in line
                ResourceWrapper rw = null;
                for (ResourceWrapper t : res.getContained()) {
                    if (r.getReference().substring(1).equals(t.getId())) {
                        rw = t;
                    }
                }
                if (rw == null) {
                    renderReference(res, x, r);
                } else {
                    x.an(rw.getId());
                    ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
                    rr.render(parent.blockquote(), rw);
                }
            }
        } else {
            renderReference(res, x, r);
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof DataRequirement) {
        DataRequirement p = (DataRequirement) e;
        renderDataRequirement(x, p);
    } else if (e instanceof PrimitiveType) {
        x.tx(((PrimitiveType) e).primitiveValue());
    } else if (e instanceof ElementDefinition) {
        x.tx("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled - should not be here");
    }
}

Example 58 with Enumeration

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

the class SearchParameterRenderer method render.

public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
    x.h2().addText(spd.getName());
    XhtmlNode p = x.para();
    p.tx("Parameter ");
    p.code().tx(spd.getCode());
    p.tx(":");
    p.code().tx(spd.getType().toCode());
    addMarkdown(x, spd.getDescription());
    XhtmlNode tbl = x.table("grid");
    XhtmlNode tr = tbl.tr();
    tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
    XhtmlNode td = tr.td();
    for (CodeType t : spd.getBase()) {
        StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
        if (sd != null && sd.hasUserData("path")) {
            td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
        } else {
            td.sep(", ").tx(t.getCode());
        }
    }
    tr = tbl.tr();
    tr.td().tx("Expression");
    if (spd.hasExpression()) {
        tr.td().code().tx(spd.getExpression());
    } else {
        tr.td().tx("(none)");
    }
    if (spd.hasXpathUsage()) {
        tr = tbl.tr();
        tr.td().tx("Usage");
        tr.td().tx(spd.getXpathUsage().getDisplay());
    }
    if (spd.hasXpath()) {
        tr = tbl.tr();
        tr.td().tx("XPath");
        tr.td().code().tx(spd.getXpath());
    }
    if (spd.hasTarget()) {
        tr = tbl.tr();
        tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
        td = tr.td();
        for (CodeType t : spd.getTarget()) {
            StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
            if (sd != null && sd.hasUserData("path")) {
                td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
            } else {
                td.sep(", ").tx(t.getCode());
            }
        }
    }
    tr = tbl.tr();
    tr.td().tx("Multiples");
    if (spd.getMultipleAnd() && spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
    } else if (spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
    } else if (spd.getMultipleAnd()) {
        tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
    } else {
        tr.td().tx("The parameter cannot repeat or have multiple values");
    }
    if (spd.hasComparator()) {
        tr = tbl.tr();
        tr.td().tx("Comparators");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchComparator> t : spd.getComparator()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasModifier()) {
        tr = tbl.tr();
        tr.td().tx("Modifiers");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasChain()) {
        tr = tbl.tr();
        tr.td().tx("Chains");
        td = tr.td().tx("Allowed: ");
        for (StringType t : spd.getChain()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasComponent()) {
        x.para().b().tx("Components");
        tbl = x.table("grid");
        for (SearchParameterComponentComponent t : spd.getComponent()) {
            tr = tbl.tr();
            SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
            if (tsp != null && tsp.hasUserData("path")) {
                tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
            } else {
                tr.td().tx(t.getDefinition());
            }
            tr.td().code().tx(t.getExpression());
        }
    }
    return false;
}

Example 59 with Enumeration

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

the class DataRenderer method displayTiming.

private String displayTiming(Timing s) throws FHIRException {
    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
    if (s.hasCode())
        b.append("Code: " + displayCodeableConcept(s.getCode()));
    if (s.getEvent().size() > 0) {
        CommaSeparatedStringBuilder c = new CommaSeparatedStringBuilder();
        for (DateTimeType p : s.getEvent()) {
            if (p.hasValue()) {
                c.append(displayDateTime(p));
            } else if (!renderExpression(c, p)) {
                c.append("??");
            }
        }
        b.append("Events: " + c.toString());
    }
    if (s.hasRepeat()) {
        TimingRepeatComponent rep = s.getRepeat();
        if (rep.hasBoundsPeriod() && rep.getBoundsPeriod().hasStart())
            b.append("Starting " + displayDateTime(rep.getBoundsPeriod().getStartElement()));
        if (rep.hasCount())
            b.append("Count " + Integer.toString(rep.getCount()) + " times");
        if (rep.hasDuration())
            b.append("Duration " + rep.getDuration().toPlainString() + displayTimeUnits(rep.getPeriodUnit()));
        if (rep.hasWhen()) {
            String st = "";
            if (rep.hasOffset()) {
                st = Integer.toString(rep.getOffset()) + "min ";
            }
            b.append("Do " + st);
            for (Enumeration<EventTiming> wh : rep.getWhen()) b.append(displayEventCode(wh.getValue()));
        } else {
            String st = "";
            if (!rep.hasFrequency() || (!rep.hasFrequencyMax() && rep.getFrequency() == 1))
                st = "Once";
            else {
                st = Integer.toString(rep.getFrequency());
                if (rep.hasFrequencyMax())
                    st = st + "-" + Integer.toString(rep.getFrequency());
            }
            if (rep.hasPeriod()) {
                st = st + " per " + rep.getPeriod().toPlainString();
                if (rep.hasPeriodMax())
                    st = st + "-" + rep.getPeriodMax().toPlainString();
                st = st + " " + displayTimeUnits(rep.getPeriodUnit());
            }
            b.append("Do " + st);
        }
        if (rep.hasBoundsPeriod() && rep.getBoundsPeriod().hasEnd())
            b.append("Until " + displayDateTime(rep.getBoundsPeriod().getEndElement()));
    }
    return b.toString();
}

Example 60 with Enumeration

use of org.hl7.fhir.r5.model.Enumeration in project redmatch by aehrc.

the class FhirExporter method getValue.

/**
 * Resolves a value.
 *
 * @param value The value specified in the transformation rules.
 * @param fhirType The type of the FHIR attribute where this value will be set.
 * @param vertex A vertex with patient data.
 * @param recordId The id of this record. Used to create the references to FHIR ids.
 * @param enumFactory If the type is an enumeration, this is the factory to create an instance.
 * @param fhirPackage The target FHIR package.
 * @return The value or null if the value cannot be determined. This can also be a list.
 */
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
    // If this is a field-based value then make sure that there is a value and if not return null
    if (value instanceof FieldBasedValue) {
        FieldBasedValue fbv = (FieldBasedValue) value;
        // Account for field ids of the form xx___y
        String fieldId = fbv.getFieldId();
        String shortFieldId = null;
        String regex = "(?<fieldId>.*)___\\d+$";
        Pattern pattern = Pattern.compile(regex);
        Matcher matcher = pattern.matcher(fieldId);
        if (matcher.find()) {
            shortFieldId = matcher.group("fieldId");
            log.debug("Transformed fieldId into '" + fieldId + "'");
        }
        boolean hasValue = false;
        JsonElement jsonElement = vertex.get(fieldId);
        if (jsonElement != null) {
            String rawValue = jsonElement.getAsString();
            if (!rawValue.isEmpty()) {
                hasValue = true;
            }
        }
        if (!hasValue && shortFieldId != null) {
            jsonElement = vertex.get(shortFieldId);
            if (jsonElement != null) {
                String rawValue = jsonElement.getAsString();
                if (!rawValue.isEmpty()) {
                    hasValue = true;
                }
            }
        }
        if (!hasValue) {
            return null;
        }
    }
    if (value instanceof BooleanValue) {
        return new BooleanType(((BooleanValue) value).getValue());
    } else if (value instanceof CodeLiteralValue) {
        String code = ((CodeLiteralValue) value).getCode();
        return getCode(code, enumFactory);
    } else if (value instanceof ConceptLiteralValue) {
        ConceptLiteralValue clv = (ConceptLiteralValue) value;
        String system = clv.getSystem();
        String code = clv.getCode();
        String display = clv.getDisplay() != null ? clv.getDisplay() : "";
        return getConcept(system, code, display, fhirType);
    } else if (value instanceof DoubleValue) {
        return new DecimalType(((DoubleValue) value).getValue());
    } else if (value instanceof IntegerValue) {
        return new IntegerType(((IntegerValue) value).getValue());
    } else if (value instanceof ReferenceValue) {
        ReferenceValue rv = (ReferenceValue) value;
        Reference ref = new Reference();
        String resourceType = rv.getResourceType();
        String resourceId = rv.getResourceId();
        boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
        CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
        if (codeInfo.isProfile()) {
            resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
        }
        if (unique) {
            // This is a reference to a unique resource - no need to append row id
            if (fhirResourceMap.containsKey(resourceId)) {
                ref.setReference("/" + resourceType + "/" + resourceId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId);
            }
        } else {
            if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
                ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
            }
        }
        return ref;
    } else if (value instanceof StringValue) {
        if (fhirType.equals(StringType.class)) {
            return new StringType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(MarkdownType.class)) {
            return new MarkdownType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(IdType.class)) {
            return new IdType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UriType.class)) {
            return new UriType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(OidType.class)) {
            return new OidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UuidType.class)) {
            return new UuidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(CanonicalType.class)) {
            return new CanonicalType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UrlType.class)) {
            return new UrlType(((StringValue) value).getStringValue());
        } else {
            throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
        }
    } else if (value instanceof CodeSelectedValue) {
        CodeSelectedValue csv = (CodeSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        return getTarget(m).getCodeElement();
    } else if (value instanceof ConceptSelectedValue) {
        ConceptSelectedValue csv = (ConceptSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        if (fhirType.isAssignableFrom(Coding.class)) {
            return getTarget(m);
        } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
            return new CodeableConcept().addCoding(getTarget(m));
        } else {
            throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
        }
    } else if (value instanceof ConceptValue) {
        // Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
        ConceptValue cv = (ConceptValue) value;
        String fieldId = cv.getFieldId();
        Mapping m = getMapping(fieldId);
        if (m != null) {
            if (fhirType.isAssignableFrom(Coding.class)) {
                return getTarget(m);
            } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                return new CodeableConcept().addCoding(getTarget(m));
            } else {
                throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
            }
        } else {
            au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
            Coding c = field.getCoding(vertex);
            if (c != null) {
                if (fhirType.isAssignableFrom(Coding.class)) {
                    return c;
                } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                    return new CodeableConcept().addCoding(c);
                } else {
                    throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
                }
            }
        }
        throw new TransformationException("Could not get concept for field " + fieldId + ".");
    } else if (value instanceof FieldValue) {
        FieldValue fv = (FieldValue) value;
        String fieldId = fv.getFieldId();
        FieldValue.DatePrecision pr = fv.getDatePrecision();
        au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
        return field.getValue(vertex, fhirType, pr);
    } else {
        throw new TransformationException("Unable to get VALUE for " + value);
    }
}