Examples with Quantity org.hl7.fhir.dstu2.model.Quantity used on opensource projects

Example 11 with Quantity

use of org.hl7.fhir.dstu2.model.Quantity in project kindling by HL7.

the class SpreadSheetReloader method parseType.

private void parseType(ElementDefinition ed, String value, String hierarchy) throws Exception {
    ed.getType().clear();
    ed.setContentReferenceElement(null);
    if (ed.getPath().equals("Resource.id")) {
        ed.addType().setCode("http://hl7.org/fhirpath/System.String").addExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", new UriType("id"));
    } else {
        if (Utilities.noString(value)) {
            if (ed.getPath().contains(".")) {
                ed.addType().setCode("BackboneElement");
            }
        } else if (value.startsWith("#")) {
            ed.setContentReference(value);
        } else {
            List<TypeRef> tl = new TypeParser(version).parse(value, false, null, context, false);
            for (TypeRef tr : tl) {
                TypeRefComponent t = ed.addType().setCode(tr.getName());
                if ("SimpleQuantity".equals(t.getCode())) {
                    t.setCode("Quantity");
                    t.addProfile("http://hl7.org/fhir/StructureDefinition/SimpleQuantity");
                }
                for (String p : tr.getParams()) {
                    if (p.equals("Definition")) {
                        t.addExtension(BuildExtensions.EXT_PATTERN, new CanonicalType("http://hl7.org/fhir/StructureDefinition/Definition"));
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/ActivityDefinition");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/EventDefinition");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/EvidenceVariable");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/Measure");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/OperationDefinition");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/PlanDefinition");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/Questionnaire");
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/SubscriptionTopic");
                    } else {
                        t.addTargetProfile("http://hl7.org/fhir/StructureDefinition/" + p);
                    }
                }
                if (Utilities.existsInList(tr.getName(), "canonical", "Reference") && !Utilities.noString(hierarchy)) {
                    t.addExtension(BuildExtensions.EXT_HIERARCHY, new BooleanType(Utilities.existsInList(hierarchy, "true", "True", "TRUE", "1", "y", "Y")));
                }
            }
        }
    }
}

Example 12 with Quantity

use of org.hl7.fhir.dstu2.model.Quantity in project kindling by HL7.

the class ResourceParser method parseED.

private void parseED(ProfileUtilities pu, ElementDefn ed, ElementDefinition focus, StructureDefinition sd, String parentName) throws IOException {
    ed.setMinCardinality(focus.getMin());
    ed.setMaxCardinality("*".equals(focus.getMax()) ? Integer.MAX_VALUE : Integer.parseInt(focus.getMax()));
    ed.setIsModifier(focus.getIsModifier());
    ed.setModifierReason(focus.getIsModifierReason());
    ed.setMustSupport(focus.getMustSupport());
    ed.setSummaryItem(focus.getIsSummary());
    ed.setRegex(ToolingExtensions.readStringExtension(focus, ToolingExtensions.EXT_REGEX));
    ed.setXmlAttribute(focus.hasRepresentation(PropertyRepresentation.XMLATTR));
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_DIR)) {
        ed.setUmlDir(ToolingExtensions.readStringExtension(focus, BuildExtensions.EXT_UML_DIR));
    }
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_BREAK)) {
        ed.setUmlBreak(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_UML_BREAK));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_SVG)) {
        String svg = BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_SVG);
        if (svg.contains("w=")) {
            ed.setSvgWidth(Integer.parseInt(svg.substring(svg.indexOf("w=") + 2)));
            svg = svg.substring(0, svg.indexOf(";"));
        }
        ed.setSvgLeft(Integer.parseInt(svg.substring(0, svg.indexOf(","))));
        ed.setSvgTop(Integer.parseInt(svg.substring(svg.indexOf(",") + 1)));
    }
    ed.setName(tail(focus.getPath()));
    ed.setShortDefn(focus.getShort());
    ed.setDefinition(focus.getDefinition());
    ed.setRequirements(focus.getRequirements());
    ed.setComments(focus.getComment());
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_TODO)) {
        ed.setTodo(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_TODO));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES)) {
        ed.setCommitteeNotes(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_HINT)) {
        ed.setDisplayHint(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_HINT));
    }
    if (focus.hasExtension(BuildExtensions.EXT_NO_BINDING)) {
        ed.setNoBindingAllowed(focus.getExtensionString(BuildExtensions.EXT_NO_BINDING).equals("true"));
    }
    for (StringType t : focus.getAlias()) {
        ed.getAliases().add(t.getValue());
    }
    if (focus.hasMaxLength()) {
        ed.setMaxLength(Integer.toString(focus.getMaxLength()));
    }
    ed.setExample(focus.getExampleFirstRep().getValue());
    ed.setMeaningWhenMissing(focus.getMeaningWhenMissing());
    if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_TRANSLATABLE)) {
        ed.setTranslatable(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_TRANSLATABLE));
    }
    ed.setOrderMeaning(focus.getOrderMeaning());
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)) {
        ed.setStandardsStatus(StandardsStatus.fromCode(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)));
    }
    if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION)) {
        ed.setNormativeVersion(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION));
    }
    for (ElementDefinitionConstraintComponent cst : focus.getConstraint()) {
        Invariant inv = new Invariant();
        inv.setContext(focus.getPath());
        inv.setEnglish(cst.getHuman());
        if (cst.hasExtension(BuildExtensions.EXT_OCL)) {
            inv.setOcl(cst.getExtensionString(BuildExtensions.EXT_OCL));
        }
        inv.setXpath(cst.getXpath());
        inv.setId(cst.getKey());
        if (cst.hasExtension(BuildExtensions.EXT_FIXED_NAME)) {
            inv.setFixedName(cst.getExtensionString(BuildExtensions.EXT_FIXED_NAME));
        }
        inv.setSeverity(cst.getSeverity().toCode());
        if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE)) {
            inv.setSeverity("best-practice");
        }
        if (cst.hasExtension(BuildExtensions.EXT_TURTLE)) {
            inv.setTurtle(cst.getExtensionString(BuildExtensions.EXT_TURTLE));
        }
        inv.setRequirements(cst.getRequirements());
        inv.setExpression(cst.getExpression());
        if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION)) {
            inv.setExplanation(cst.getExtensionString(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION));
        }
        ed.getInvariants().put(inv.getId(), inv);
        invariants.put(inv.getId(), inv);
    }
    for (IdType cnd : focus.getCondition()) {
        Invariant inv = invariants.get(cnd.primitiveValue());
        if (inv == null) {
            System.out.println("Unable to find invariant " + cnd.primitiveValue());
        } else {
            ed.getStatedInvariants().add(inv);
        }
    }
    for (ElementDefinitionMappingComponent map : focus.getMapping()) {
        String uri = getMappingUri(sd, map.getIdentity());
        if ("http://hl7.org/fhir/fivews".equals(uri)) {
            ed.setW5(reverseW5(map.getMap()));
        } else {
            ed.getMappings().put(uri, map.getMap());
        }
    }
    if (focus.hasContentReference()) {
        ed.getTypes().add(new TypeRef("@" + focus.getContentReference().substring(1)));
    } else {
        for (TypeRefComponent tr : focus.getType()) {
            if (!Utilities.existsInList(tr.getCode(), "Element", "BackboneElement")) {
                TypeRef t = new TypeRef();
                ed.getTypes().add(t);
                if (tr.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type")) {
                    t.setName(tr.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"));
                } else {
                    t.setName(tr.getCode());
                }
                if (ToolingExtensions.hasExtension(tr, BuildExtensions.EXT_HIERARCHY)) {
                    ed.setHierarchy(ToolingExtensions.readBoolExtension(tr, BuildExtensions.EXT_HIERARCHY));
                }
                for (CanonicalType u : tr.getProfile()) {
                    t.setProfile(u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", ""));
                }
                for (CanonicalType u : tr.getTargetProfile()) {
                    String s = u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", "");
                    if ("Resource".equals(s)) {
                        t.getParams().add("Any");
                    } else {
                        t.getParams().add(s);
                    }
                }
                if (t.getName().equals("Quantity") && "SimpleQuantity".equals(t.getProfile())) {
                    t.setName("SimpleQuantity");
                    t.setProfile(null);
                }
                if ("Resource".equals(t.getProfile())) {
                    t.setProfile("Any");
                }
                if (t.getParams().toString().equals("[ActivityDefinition, EventDefinition, EvidenceVariable, Measure, OperationDefinition, PlanDefinition, Questionnaire, SubscriptionTopic]")) {
                    t.getParams().clear();
                    t.getParams().add("Definition");
                }
            }
        }
        if (ed.getTypes().size() == STAR_TYPES_COUNT) {
            ed.getTypes().clear();
            ed.getTypes().add(new TypeRef("*"));
        }
    }
    String name = parentName + Utilities.capitalize(ed.getName());
    if (focus.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name")) {
        ed.setStatedType(focus.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name"));
        ed.setDeclaredTypeName(ed.getStatedType());
    } else if (ed.getTypes().isEmpty() && !focus.hasContentReference()) {
        ed.setDeclaredTypeName(name + "Component");
    }
    if (focus.hasBinding()) {
        ed.setBinding(parseBinding(focus.getBinding()));
    }
    for (ElementDefinition child : pu.getChildList(sd, focus, true, false)) {
        ElementDefn c = new ElementDefn();
        ed.getElements().add(c);
        parseED(pu, c, child, sd, name);
    }
// todo:
// private ElementDefinition derivation;
}

Example 13 with Quantity

use of org.hl7.fhir.dstu2.model.Quantity in project kindling by HL7.

the class FhirTurtleGenerator method processTypes.

private void processTypes(String baseResourceName, FHIRResource baseResource, ElementDefn td, String predicateBase, boolean innerIsBackbone) throws Exception {
    for (ElementDefn ed : td.getElements()) {
        String predicateName = predicateBase + "." + (ed.getName().endsWith("[x]") ? ed.getName().substring(0, ed.getName().length() - 3) : ed.getName());
        FHIRResource predicateResource;
        if (ed.getName().endsWith("[x]")) {
            predicateResource = fact.fhir_objectProperty(predicateName);
            // Choice entry
            if (ed.typeCode().equals("*")) {
                // Wild card -- any element works (probably should be more restrictive but...)
                Resource targetResource = RDFNamespace.FHIR.resourceRef("Element");
                baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, targetResource, ed.getMinCardinality(), ed.getMaxCardinality()));
                predicateResource.domain(baseResource);
                predicateResource.range(targetResource);
            } else {
                // Create a restriction on the union of possible types
                List<Resource> typeOpts = new ArrayList<Resource>();
                for (TypeRef tr : ed.getTypes()) {
                    // TODO: Figure out how to get the type reference code
                    String trName = tr.getName();
                    if (trName.equals("SimpleQuantity"))
                        trName = "Quantity";
                    String qualifiedPredicateName = predicateName + Utilities.capitalize(trName);
                    Resource targetRes = fact.fhir_class(tr.getName()).resource;
                    FHIRResource qualifiedPredicate = fact.fhir_objectProperty(qualifiedPredicateName, predicateResource.resource).domain(baseResource).range(targetRes);
                    typeOpts.add(fact.fhir_cardinality_restriction(qualifiedPredicate.resource, targetRes, ed.getMinCardinality(), ed.getMaxCardinality()));
                }
                baseResource.restriction(fact.fhir_union(typeOpts));
            }
        } else {
            FHIRResource baseDef;
            if (ed.getTypes().isEmpty()) {
                predicateResource = fact.fhir_objectProperty(predicateName);
                String targetClassName = mapComponentName(baseResourceName, ed.getDeclaredTypeName());
                baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition());
                processTypes(targetClassName, baseDef, ed, predicateName, innerIsBackbone);
            } else {
                TypeRef targetType = ed.getTypes().get(0);
                String targetName = targetType.getName();
                if (targetName.startsWith("@")) {
                    // Link to earlier definition
                    ElementDefn targetRef = getElementForPath(targetName.substring(1));
                    String targetRefName = targetRef.getName();
                    String targetClassName = baseResourceName + Character.toUpperCase(targetRefName.charAt(0)) + targetRefName.substring(1);
                    baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition()).addTitle(ed.getShortDefn());
                    if (!processing.contains(targetRefName)) {
                        processing.add(targetRefName);
                        processTypes(targetClassName, baseDef, targetRef, predicateName, innerIsBackbone);
                        processing.remove(targetRefName);
                    }
                } else {
                    // A placeholder entry.  The rest of the information will be supplied elsewhere
                    baseDef = fact.fhir_class(targetName);
                }
                // XHTML the exception, in that the html doesn't derive from Primitive
                if (targetName.equals("xhtml"))
                    predicateResource = fact.fhir_dataProperty(predicateName);
                else
                    predicateResource = fact.fhir_objectProperty(predicateName);
            }
            predicateResource.addTitle(ed.getShortDefn()).addDefinition(ed.getDefinition()).domain(baseResource);
            baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, baseDef.resource, ed.getMinCardinality(), ed.getMaxCardinality()));
            predicateResource.range(baseDef.resource);
            if (!Utilities.noString(ed.getW5()))
                predicateResource.addObjectProperty(RDFS.subPropertyOf, RDFNamespace.W5.resourceRef(ed.getW5()));
        }
    }
}

Example 14 with Quantity

use of org.hl7.fhir.dstu2.model.Quantity in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method testObservationSN_valueQuantity_missing_comparator_result.

@Test
void testObservationSN_valueQuantity_missing_comparator_result() throws IOException {
    String hl7message = baseMessage + "OBX|1|SN|1554-5^GLUCOSE||^182|mg/dl|70_105||||F";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    // Check valueQuantity
    assertNotNull(obs.getValueQuantity());
    Quantity q = obs.getValueQuantity();
    // code only set if system exists
    assertNull(q.getCode());
    assertEquals("mg/dl", q.getUnit());
    assertNull(q.getSystem());
    assertEquals(182, q.getValue().floatValue());
    // no comparator passed in
    assertNull(q.getComparator());
    // Check referenceRange
    assertTrue(obs.hasReferenceRange());
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertNotNull(range);
    assertTrue(range.hasHigh());
    assertTrue(range.hasLow());
    Quantity high = range.getHigh();
    // uses OBX.6.1 for units not text in string
    assertEquals("mg/dl", high.getUnit());
    assertEquals(105f, high.getValue().floatValue());
    Quantity low = range.getLow();
    // uses OBX.6.1 for units not text in string
    assertEquals("mg/dl", low.getUnit());
    assertEquals(70f, low.getValue().floatValue());
    assertEquals("70_105", range.getText());
}

Example 15 with Quantity

use of org.hl7.fhir.dstu2.model.Quantity in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MedicationRequestFHIRConversionTest method dosageInstructionTestRateQuantityRXO.

@Test
void dosageInstructionTestRateQuantityRXO() {
    // Test dosageInstruction.rateQuantity where RXO.21 exists and RXO.17 does not exist -> use RXO segment, no range
    String hl7message = "MSH|^~\\\\&|||||20210101000000||OMP^O09|MSGID|T|2.6\n" + "PID|||1234||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|OP||||||||||||||||||||||\n" + // RXO.22.3 purposely empty to check that default system is used
    "RXO|00054418425^Dexamethasone 4 MG Oral Tablet^NDC||||||||||||||||||||6|PC||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> medicationRequestList = ResourceUtils.getResourceList(e, ResourceType.MedicationRequest);
    // Confirm that one medicationRequest was created.
    assertThat(medicationRequestList).hasSize(1);
    MedicationRequest medicationRequest = ResourceUtils.getResourceMedicationRequest(medicationRequestList.get(0), ResourceUtils.context);
    Quantity rateQuantity = medicationRequest.getDosageInstructionFirstRep().getDoseAndRateFirstRep().getRateQuantity();
    // dosageInstruction.doseAndRate.rateQuantity RXO.21
    // RXO.21
    assertThat(rateQuantity.getValue()).hasToString("6.0");
    // RXO.22.1
    assertThat(rateQuantity.getUnit()).isEqualTo("PC");
    // default
    assertThat(rateQuantity.getSystem()).isEqualTo("http://unitsofmeasure.org");
    // Verify no extraneous resources
    // Expect MedicationRequest, and Patient
    assertThat(e).hasSize(2);
}