Examples with ProfileUtilities org.hl7.fhir.r5.conformance.ProfileUtilities used on opensource projects

Example 6 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project kindling by HL7.

the class CDAGenerator method processDataType.

private void processDataType(Element dt, String n, String p) throws FileNotFoundException, IOException, FHIRFormatError, DefinitionException {
    if (!Utilities.existsInList(n, "TYPE", "BN", "BIN", "CO", "UID", "OID", "UUID", "RUID", "URL", "ADXP", "ENXP", "PN", "TN", "ON", "RTO", "CAL", "CLCY", "SET", "LIST", "GLIST", "SLIST", "BAG", "HXIT", "HIST", "UVP", "NPPD", "PPD")) {
        if (n.equals("GTS"))
            n = "SXCM_TS";
        System.out.print(" " + n);
        StructureDefinition sd = new StructureDefinition();
        sd.setId(fix(n));
        sd.setUrl("http://hl7.org/fhir/cda/StructureDefinition/" + fix(n));
        library.put(sd.getUrl(), sd);
        sd.setName("V3 Data type " + n + " (" + dt.getAttribute("title") + ")");
        sd.setTitle(sd.getName());
        sd.setStatus(PublicationStatus.ACTIVE);
        sd.setExperimental(false);
        sd.setPublisher("HL7");
        sd.setDescription(getDefinition(dt));
        sd.setType(sd.getUrl());
        sd.setKind(StructureDefinitionKind.LOGICAL);
        sd.setAbstract("true".equals(dt.getAttribute("isAbstract")));
        sd.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("urn:hl7-org:v3"));
        Element derived = XMLUtil.getNamedChild(dt, "mif:derivedFrom");
        if (Utilities.existsInList(n, "ST", "ED", "TEL", "AD", "EN", "IVL_PQ", "IVL_INT", "TS")) {
            sd.setBaseDefinition("http://hl7.org/fhir/cda/StructureDefinition/ANY");
        } else if (Utilities.existsInList(n, "SXCM_TS")) {
            sd.setBaseDefinition("http://hl7.org/fhir/cda/StructureDefinition/TS");
        } else if (n.equals("PIVL_TS") || n.equals("EIVL_TS") || n.equals("IVL_TS")) {
            sd.setBaseDefinition("http://hl7.org/fhir/cda/StructureDefinition/SXCM_TS");
        } else if (derived != null) {
            sd.setBaseDefinition("http://hl7.org/fhir/cda/StructureDefinition/" + XMLUtil.getNamedChildAttribute(derived, "mif:targetDatatype", "name"));
        } else
            sd.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Element");
        sd.setDerivation(TypeDerivationRule.SPECIALIZATION);
        ElementDefinition edb = new ElementDefinition();
        edb.setPath(sd.getId());
        seePath(edb);
        edb.setMin(1);
        edb.setMax("*");
        edb.addType().setCode("Element");
        sd.getDifferential().getElement().add(edb);
        if (n.equals("ED"))
            addEDElements(sd.getDifferential().getElement());
        if (n.equals("SC"))
            copyAttributes(sd, getDefinition("CV"), "code", "codeSystem", "codeSystemVersion", "displayName");
        if (primitiveTypes.containsKey(n))
            addValueAttribute(sd.getDifferential().getElement(), n, primitiveTypes.get(n));
        if (n.equals("TS"))
            edb.addExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-timeformat", new CodeType("YYYYMMDDHHMMSS.UUUU[+|-ZZzz]"));
        if (n.equals("TEL"))
            addValueAttribute(sd.getDifferential().getElement(), n, "uri");
        if (n.equals("SXCM_TS")) {
            addOperatorAttribute(sd.getDifferential().getElement(), "SXCM_TS");
            sd.setAbstract(true);
        }
        if (n.equals("AD")) {
            addParts(sd.getDifferential().getElement(), n, "delimiter", "country", "state", "county", "city", "postalCode", "streetAddressLine", "houseNumber", "houseNumberNumeric", "direction", "streetName", "streetNameBase", "streetNameType", "additionalLocator", "unitID", "unitType", "careOf", "censusTract", "deliveryAddressLine", "deliveryInstallationType", "deliveryInstallationArea", "deliveryInstallationQualifier", "deliveryMode", "deliveryModeIdentifier", "buildingNumberSuffix", "postBox", "precinct");
            addTextItem(sd.getDifferential().getElement(), n);
        }
        if (n.equals("EN")) {
            addParts(sd.getDifferential().getElement(), n, "delimiter", "family", "given", "prefix", "suffix");
            addTextItem(sd.getDifferential().getElement(), n);
        }
        List<Element> props = new ArrayList<Element>();
        XMLUtil.getNamedChildren(dt, "mif:property", props);
        for (Element prop : props) {
            processProperty(sd.getDifferential().getElement(), n, prop, p);
        }
        if (n.equals("TS") || n.equals("PQ"))
            addInclusiveAttribute(sd.getDifferential().getElement(), n);
        if (n.equals("CE") || n.equals("CV") || n.equals("CD"))
            addCDExtensions(sd.getDifferential().getElement(), n);
        new ProfileUtilities(null, null, null).setIds(sd, true);
        structures.add(sd);
    }
}

Example 7 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project kindling by HL7.

the class LogicalModelProcessor method genLogicalModelTable.

private String genLogicalModelTable(StructureDefinition sd, String prefix) throws Exception {
    ProfileUtilities pu = new ProfileUtilities(page.getWorkerContext(), null, this);
    XhtmlNode x = pu.generateTable(sd.getId() + "-definitions.html", sd, sd.hasSnapshot() ? false : true, page.getFolders().dstDir, false, sd.getId(), true, prefix, prefix, true, false, null, true, false);
    return new XhtmlComposer(XhtmlComposer.HTML).compose(x);
}

Example 8 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project kindling by HL7.

the class SourceParser method loadConformancePackage.

private void loadConformancePackage(Profile ap, List<ValidationMessage> issues, WorkGroup wg) throws FileNotFoundException, IOException, Exception {
    if (ap.getSourceType() == ConformancePackageSourceType.Spreadsheet) {
        OldSpreadsheetParser sparser = new OldSpreadsheetParser(ap.getCategory(), new CSFileInputStream(ap.getSource()), Utilities.noString(ap.getId()) ? ap.getSource() : ap.getId(), ap.getSource(), definitions, srcDir, logger, registry, version, context, genDate, false, page, false, ini, wg, definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
        sparser.setFolder(Utilities.getDirectoryForFile(ap.getSource()));
        sparser.parseConformancePackage(ap, definitions, Utilities.getDirectoryForFile(ap.getSource()), ap.getCategory(), issues, wg);
        errors.addAll(sparser.getErrors());
    } else if (ap.getSourceType() == ConformancePackageSourceType.StructureDefinition) {
        Resource rf;
        try {
            rf = new XmlParser().parse(new CSFileInputStream(ap.getSource()));
        } catch (Exception e) {
            throw new Exception("Error parsing " + ap.getSource() + ": " + e.getMessage(), e);
        }
        if (!(rf instanceof StructureDefinition))
            throw new Exception("Error parsing Profile: not a structure definition");
        StructureDefinition sd = (StructureDefinition) rf;
        sd.setVersion(version.toCode());
        ap.putMetadata("id", sd.getId() + "-pack");
        ap.putMetadata("date", sd.getDateElement().asStringValue());
        ap.putMetadata("title", sd.getTitle());
        ap.putMetadata("status", sd.getStatus().toCode());
        ap.putMetadata("description", new XhtmlComposer(XhtmlComposer.HTML).compose(sd.getText().getDiv()));
        if (ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg")) {
            wg = definitions.getWorkgroups().get(ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"));
            ap.putMetadata("workgroup", wg.getCode());
        }
        ap.setTitle(sd.getTitle());
        new ProfileUtilities(page.getWorkerContext(), null, null).setIds(sd, false);
        ap.getProfiles().add(new ConstraintStructure(sd, definitions.getUsageIG(ap.getCategory(), "Parsing " + ap.getSource()), wg == null ? wg(sd) : wg, fmm(sd), sd.getExperimental()));
    } else if (ap.getSource() != null) {
        parseConformanceDocument(ap, ap.getId(), new CSFile(ap.getSource()), ap.getCategory(), wg);
    }
}

Example 9 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project kindling by HL7.

the class ResourceParser method parseResource.

private ResourceDefn parseResource(String t) throws FHIRFormatError, FileNotFoundException, IOException {
    StructureDefinition sd = (StructureDefinition) parseXml("structuredefinition-" + t + ".xml");
    sdList.put(sd.getUrl(), sd);
    sd.setVersion(version);
    ResourceDefn r = new ResourceDefn();
    r.setName(sd.getName());
    r.setEnteredInErrorStatus(ToolingExtensions.readStringExtension(sd, BuildExtensions.EXT_ENTERED_IN_ERROR_STATUS));
    r.setStatus(StandardsStatus.fromCode(ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_STANDARDS_STATUS)));
    r.setAbstract(sd.getAbstract());
    r.setInterface(ToolingExtensions.readBoolExtension(sd, BuildExtensions.EXT_RESOURCE_INTERFACE));
    r.setWg(definitions.getWorkgroups().get(ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_WORKGROUP)));
    r.setFmmLevel(ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_FMM_LEVEL));
    r.setProposedOrder(ToolingExtensions.readStringExtension(sd, BuildExtensions.EXT_PROPOSED_ORDER));
    r.setSecurityCategorization(SecurityCategorization.fromCode(ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category")));
    r.setRequirements(sd.getPurpose());
    r.setDefinition(sd.getDescription());
    if (sd.hasExtension(BuildExtensions.EXT_TEMPLATE)) {
        String tname = BuildExtensions.readStringExtension(sd, BuildExtensions.EXT_TEMPLATE);
        ResourceDefn template = definitions.getResourceByName(tname);
        r.setTemplate(template.getRoot());
    }
    // private long timestamp; only set in regenerator...?
    // todo:
    // private List<InheritedMapping> inheritedMappings = new ArrayList<InheritedMapping>();
    // private ElementDefn template;
    // private Map<String, PointSpec> layout = new HashMap<String, PointSpec>();
    ProfileUtilities pu = new ProfileUtilities(context, null, null);
    r.setRoot(parseTypeDefinition(pu, sd.getDifferential().getElementFirstRep(), sd));
    r.getRoot().setFmmLevel(r.getFmmLevel());
    r.getRoot().setRequirements(r.getRequirements());
    if (r.isAbstract()) {
        r.getRoot().setAbstractType(true);
    }
    if (sd.hasBaseDefinition()) {
        r.getRoot().getTypes().add(new TypeRef(sd.getBaseDefinition().replace("http://hl7.org/fhir/StructureDefinition/", "")));
    }
    return r;
}

Example 10 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities 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;
}