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

Example 61 with ProfileUtilities

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

the class BuildWorkerContext method generateSnapshot.

public void generateSnapshot(StructureDefinition p, boolean ifLogical) throws DefinitionException, FHIRException {
    if (!p.hasSnapshot() && (ifLogical || p.getKind() != StructureDefinitionKind.LOGICAL)) {
        if (!p.hasBaseDefinition())
            throw new DefinitionException("Profile " + p.getName() + " (" + p.getUrl() + ") has no base and no snapshot");
        StructureDefinition sd = fetchResource(StructureDefinition.class, p.getBaseDefinition());
        if (sd == null)
            throw new DefinitionException("Profile " + p.getName() + " (" + p.getUrl() + ") base " + p.getBaseDefinition() + " could not be resolved");
        List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();
        List<String> errors = new ArrayList<String>();
        ProfileUtilities pu = new ProfileUtilities(this, msgs, this);
        pu.setThrowException(false);
        pu.sortDifferential(sd, p, p.getUrl(), errors, true);
        for (String err : errors) msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: " + err, ValidationMessage.IssueSeverity.ERROR));
        pu.generateSnapshot(sd, p, p.getUrl(), Utilities.extractBaseUrl(sd.getUserString("path")), p.getName());
        for (ValidationMessage msg : msgs) {
            if ((msg.getLevel() == ValidationMessage.IssueSeverity.ERROR) || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
                throw new DefinitionException("Profile " + p.getName() + " (" + p.getUrl() + "). Error generating snapshot: " + msg.getMessage());
        }
        if (!p.hasSnapshot())
            throw new FHIRException("Profile " + p.getName() + " (" + p.getUrl() + "). Error generating snapshot");
        pu = null;
    }
}

Example 62 with ProfileUtilities

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

the class CDAGenerator method processClass.

private void processClass(List<Element> classes, List<Element> associations, String className, Element parentTarget) throws FHIRFormatError, DefinitionException {
    Element cclass = null;
    for (Element cclss : classes) {
        String cname = XMLUtil.getNamedChildAttribute(cclss, "class", "name");
        if (cname.equals(className)) {
            cclass = cclss;
            break;
        }
    }
    if (cclass == null)
        throw new Error("Unable to find class " + className);
    processed.add(className);
    waiting.removeIf((WaitingEntry entry) -> entry.className.equals(className));
    StructureDefinition sd = new StructureDefinition();
    sd.setId(className);
    sd.setUrl("http://hl7.org/fhir/cda/StructureDefinition/" + className);
    library.put(sd.getUrl(), sd);
    sd.setName("CDAR2." + className);
    sd.setTitle("FHIR Definition for CDA R2 Class " + className);
    sd.setStatus(PublicationStatus.ACTIVE);
    sd.setExperimental(false);
    sd.setPublisher("HL7");
    sd.setType(sd.getUrl());
    sd.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("urn:hl7-org:v3"));
    if ("ClinicalDocument".equals(className)) {
        sd.setDescription("This is a generated StructureDefinition that describes CDA - that is, CDA as it actually is for R2. " + "The intent of this StructureDefinition is to enable CDA to be a FHIR resource. That enables the FHIR infrastructure " + "- API, conformance, query - to be used directly against CDA");
    }
    sd.setKind(StructureDefinitionKind.LOGICAL);
    sd.setAbstract(false);
    sd.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Element");
    ElementDefinition ed = new ElementDefinition();
    ed.setPath(className);
    seePath(ed);
    ed.setMin(1);
    ed.setMax("1");
    sd.getDifferential().getElement().add(ed);
    sd.getSnapshot().getElement().add(popBase(ed));
    processClassAttributes(classes, associations, sd.getDifferential().getElement(), sd.getSnapshot().getElement(), cclass, className, parentTarget);
    new ProfileUtilities(null, null, null).setIds(sd, true);
    structures.add(sd);
}

Example 63 with ProfileUtilities

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

the class MarkDownPreProcessor method process.

public static String process(Definitions definitions, BuildWorkerContext workerContext, List<ValidationMessage> validationErrors, String text, String location, String prefix) throws Exception {
    if (Utilities.noString(text))
        return "";
    text = text.replace("||", "\r\n\r\n");
    while (text.contains("[[[")) {
        String left = text.substring(0, text.indexOf("[[["));
        if (text.indexOf("]]]") < 0)
            throw new Error(location + ": Missing closing ]]] in markdown text: " + text);
        String linkText = text.substring(text.indexOf("[[[") + 3, text.indexOf("]]]"));
        String right = text.substring(text.indexOf("]]]") + 3);
        if (linkText.startsWith("valueset:")) {
            String vsid = linkText.substring(9);
            ValueSet vs = workerContext.fetchResource(ValueSet.class, "http://hl7.org/fhir/ValueSet/" + vsid);
            ValueSetExpansionOutcome exp = workerContext.expandVS(vs, true, false);
            if (exp.getValueset() != null)
                text = left + presentExpansion(exp.getValueset().getExpansion().getContains(), workerContext) + right;
            else
                text = left + "[" + vs.getName() + "](" + vs.getUserData("path") + ")" + right;
        } else {
            String url = "";
            String[] parts = linkText.split("\\#");
            if (parts[0].contains("/StructureDefinition/")) {
                StructureDefinition ed = workerContext.getExtensionStructure(null, parts[0]);
                if (ed == null)
                    throw new Error(location + ": Unable to find extension " + parts[0]);
                url = ed.getUserString("path");
                if (url == null && ed.hasUserData("filename")) {
                    url = ed.getUserData("filename") + ".html";
                }
                if (url == null) {
                    System.out.println("Broken link for " + ed.getUrl());
                }
            }
            if (Utilities.noString(url)) {
                String[] paths = parts[0].split("\\.");
                StructureDefinition p = new ProfileUtilities(workerContext, null, null).getProfile(null, paths[0]);
                if (p != null) {
                    String suffix = (paths.length > 1) ? "-definitions.html#" + parts[0] : ".html";
                    if (p.getUserData("filename") == null)
                        url = paths[0].toLowerCase() + suffix;
                    else
                        url = p.getUserData("filename") + suffix;
                } else if (definitions.hasResource(linkText)) {
                    url = linkText.toLowerCase() + ".html#";
                } else if (definitions.hasResource(paths[0])) {
                    url = paths[0].toLowerCase() + "-definitions.html#" + linkText;
                } else if (definitions.hasElementDefn(linkText)) {
                    url = definitions.getSrcFile(linkText) + ".html#" + linkText;
                } else if (definitions.hasPrimitiveType(linkText)) {
                    url = "datatypes.html#" + linkText;
                } else if (definitions.getPageTitles().containsKey(linkText)) {
                    url = definitions.getPageTitles().get(linkText);
                } else if (definitions.getLogicalModel(linkText.toLowerCase()) != null) {
                    url = definitions.getLogicalModel(linkText.toLowerCase()).getId() + ".html";
                } else if (validationErrors != null) {
                    validationErrors.add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, -1, -1, location, "Unresolved logical URL '" + linkText + "'", IssueSeverity.WARNING));
                // throw new Exception("Unresolved logical URL "+url);
                } else
                    url = "??";
            }
            text = left + "[" + linkText + "](" + url + ")" + right;
        }
    }
    // 1. if prefix <> "", then check whether we need to insert the prefix
    if (!Utilities.noString(prefix)) {
        int i = text.length() - 3;
        while (i > 0) {
            if (text.substring(i, i + 2).equals("](")) {
                if (!text.substring(i, i + 7).equals("](http:")) {
                    // && !text.substring(i, i+8).equals("](https:"));
                    text = text.substring(0, i) + "](" + prefix + text.substring(i + 2);
                }
            }
            i--;
        }
    }
    return text;
}

Example 64 with ProfileUtilities

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

the class CDAGenerator method buildSXPR.

private void buildSXPR() throws DefinitionException {
    StructureDefinition sd = new StructureDefinition();
    sd.setId(fix("SXPR_TS"));
    sd.setUrl("http://hl7.org/fhir/cda/StructureDefinition/" + fix("SXPR_TS"));
    library.put(sd.getUrl(), sd);
    sd.setName("V3 Data type SXPR_TS (A set-component that is itself made up of set-components that are evaluated as one value)");
    sd.setTitle("SXPR_TS - Component part of GTS");
    sd.setStatus(PublicationStatus.ACTIVE);
    sd.setExperimental(false);
    sd.setPublisher("HL7");
    sd.setDescription("A set-component that is itself made up of set-components that are evaluated as one value");
    sd.setKind(StructureDefinitionKind.LOGICAL);
    sd.setAbstract(false);
    sd.setType(sd.getUrl());
    sd.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("urn:hl7-org:v3"));
    sd.setBaseDefinition("http://hl7.org/fhir/cda/StructureDefinition/SXCM_TS");
    sd.setDerivation(TypeDerivationRule.SPECIALIZATION);
    ElementDefinition edb = new ElementDefinition();
    edb.setPath(sd.getId());
    edb.setMin(1);
    edb.setMax("*");
    edb.addType().setCode("Element");
    sd.getDifferential().getElement().add(edb);
    ElementDefinition ed = new ElementDefinition();
    ed.setPath("SXPR_TS.comp");
    seePath(ed);
    ed.setMin(1);
    ed.setMax("*");
    ed.addRepresentation(PropertyRepresentation.TYPEATTR);
    ed.addType().setCode("http://hl7.org/fhir/cda/StructureDefinition/IVL_TS");
    ed.addType().setCode("http://hl7.org/fhir/cda/StructureDefinition/EIVL_TS");
    ed.addType().setCode("http://hl7.org/fhir/cda/StructureDefinition/PIVL_TS");
    ed.addType().setCode("http://hl7.org/fhir/cda/StructureDefinition/SXPR_TS");
    sd.getDifferential().getElement().add(ed);
    new ProfileUtilities(null, null, null).setIds(sd, true);
    structures.add(sd);
}

Example 65 with ProfileUtilities

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

the class ProfileGenerator method generate.

public StructureDefinition generate(Profile pack, ConstraintStructure profile, ResourceDefn resource, String id, String html, ImplementationGuideDefn usage, List<ValidationMessage> issues, ResourceDefn baseResource) throws Exception {
    if (profile.getResource() != null)
        return profile.getResource();
    StructureDefinition p = new StructureDefinition();
    p.setId(FormatUtilities.makeId(id));
    p.setUrl("http://hl7.org/fhir/StructureDefinition/" + id);
    if (usage != null && !usage.isCore()) {
        if (!id.startsWith(usage.getCode() + "-"))
            throw new Exception("Error: " + id + " must start with " + usage.getCode() + "-");
    }
    if (!resource.getRoot().getTypes().isEmpty() && (resource.getRoot().getTypes().get(0).getProfile() != null))
        p.setBaseDefinition(resource.getRoot().getTypes().get(0).getProfile());
    else
        p.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/" + resource.getName());
    if (definitions.hasType(resource.getName()))
        p.setKind(StructureDefinitionKind.COMPLEXTYPE);
    else
        p.setKind(StructureDefinitionKind.RESOURCE);
    p.setType(resource.getName());
    p.setDerivation(TypeDerivationRule.CONSTRAINT);
    p.setAbstract(false);
    p.setUserData("filename", id);
    p.setUserData("path", ((usage == null || usage.isCore()) ? "" : usage.getCode() + File.separator) + id + ".html");
    p.setTitle(pack.metadata("display"));
    p.setFhirVersion(version);
    p.setVersion(version.toCode());
    if (pack.hasMetadata("summary-" + profile.getTitle()))
        ToolingExtensions.addMarkdownExtension(p, "http://hl7.org/fhir/StructureDefinition/structuredefinition-summary", pack.metadata("summary-" + profile.getTitle()));
    ToolResourceUtilities.updateUsage(p, usage.getCode());
    p.setName(pack.metadata("name"));
    p.setPublisher(pack.metadata("author.name"));
    if (pack.hasMetadata("author.reference"))
        p.addContact().getTelecom().add(Factory.newContactPoint(ContactPointSystem.URL, pack.metadata("author.reference")));
    // <code> opt Zero+ Coding assist with indexing and finding</code>
    p.setDescription(resource.getRoot().getShortDefn());
    if (!p.hasDescriptionElement() && pack.hasMetadata("description"))
        p.setDescription(preProcessMarkdown(pack.metadata("description"), "pack.description"));
    p.setPurpose(resource.getRoot().getRequirements());
    if (!p.hasPurpose() && pack.hasMetadata("requirements"))
        p.setPurpose(pack.metadata("requirements"));
    p.setExperimental(Utilities.existsInList(pack.metadata("Experimental"), "y", "Y", "true", "TRUE", "1"));
    if (pack.hasMetadata("date"))
        p.setDateElement(Factory.newDateTime(pack.metadata("date").substring(0, 10)));
    else
        p.setDate(genDate.getTime());
    if (pack.hasMetadata("fmm-level"))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(pack.getFmmLevel()));
    else if (pack.hasMetadata("fmm"))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(pack.metadata("fmm")));
    else if (!Utilities.noString(resource.getFmmLevel()))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(resource.getFmmLevel()));
    else if (baseResource != null && !Utilities.noString(baseResource.getFmmLevel()))
        ToolingExtensions.addIntegerExtension(p, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(baseResource.getFmmLevel()));
    if (pack.hasMetadata("workgroup"))
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, pack.getWg());
    else if (resource.getWg() != null)
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, resource.getWg().getCode());
    else if (baseResource != null && baseResource.getWg() != null)
        ToolingExtensions.setCodeExtension(p, ToolingExtensions.EXT_WORKGROUP, baseResource.getWg().getCode());
    if (pack.hasMetadata("Standards-Status"))
        ToolingExtensions.setStandardsStatus(p, StandardsStatus.fromCode(pack.metadata("Standards-Status")), null);
    else
        ToolingExtensions.setStandardsStatus(p, resource.getStatus(), null);
    if (pack.hasMetadata("status"))
        p.setStatus(PublicationStatus.fromCode(pack.metadata("status")));
    if (pack.getMetadata().containsKey("code"))
        for (String s : pack.getMetadata().get("code")) if (!Utilities.noString(s))
            p.getKeyword().add(Factory.makeCoding(s));
    if (pack.hasMetadata("datadictionary"))
        ToolingExtensions.setStringExtension(p, "http://hl7.org/fhir/StructureDefinition/datadictionary", pack.metadata("datadictionary"));
    Set<String> containedSlices = new HashSet<String>();
    p.setDifferential(new StructureDefinitionDifferentialComponent());
    defineElement(pack, p, p.getDifferential().getElement(), resource.getRoot(), resource.getName(), containedSlices, new ArrayList<ProfileGenerator.SliceHandle>(), SnapShotMode.None, true, null, null, false);
    List<String> names = new ArrayList<String>();
    names.addAll(resource.getSearchParams().keySet());
    Collections.sort(names);
    for (String pn : names) {
        pack.getSearchParameters().add(makeSearchParam(p, pack.getId() + "-" + resource.getName() + "-" + pn, resource.getName(), resource.getSearchParams().get(pn), resource));
    }
    StructureDefinition base = definitions.getSnapShotForBase(p.getBaseDefinition());
    List<String> errors = new ArrayList<String>();
    new ProfileUtilities(context, null, pkp).sortDifferential(base, p, p.getName(), errors, false);
    for (String s : errors) issues.add(new ValidationMessage(Source.ProfileValidator, IssueType.STRUCTURE, -1, -1, p.getUrl(), s, IssueSeverity.WARNING));
    reset();
    // ok, c is the differential. now we make the snapshot
    new ProfileUtilities(context, issues, pkp).generateSnapshot(base, p, "http://hl7.org/fhir/StructureDefinition/" + p.getType(), "http://hl7.org/fhir", p.getName());
    reset();
    p.getDifferential().getElement().get(0).getType().clear();
    p.getSnapshot().getElement().get(0).getType().clear();
    addElementConstraintToSnapshot(p);
    XhtmlNode div = new XhtmlNode(NodeType.Element, "div");
    div.addText("to do");
    p.setText(new Narrative());
    p.getText().setStatus(NarrativeStatus.GENERATED);
    p.getText().setDiv(div);
    new ProfileUtilities(context, issues, pkp).setIds(p, false);
    checkHasTypes(p);
    return p;
}