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

Example 71 with ProfileUtilities

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

the class Publisher method getSnapShotForProfile.

public StructureDefinition getSnapShotForProfile(String base) throws Exception {
    String[] parts = base.split("#");
    if (parts[0].startsWith("http://hl7.org/fhir/StructureDefinition/") && parts.length == 1) {
        String name = base.substring(40);
        if (page.getDefinitions().hasResource(name))
            return page.getDefinitions().getSnapShotForType(name);
        else if (page.getDefinitions().hasType(name)) {
            TypeDefn t = page.getDefinitions().getElementDefn(name);
            if (t.getProfile().hasSnapshot())
                return t.getProfile();
            throw new Exception("unable to find snapshot for " + name);
        }
    // else
    // throw new Exception("unable to find base definition for "+name);
    }
    StructureDefinition p = new ProfileUtilities(page.getWorkerContext(), page.getValidationErrors(), page).getProfile(null, parts[0]);
    if (p == null)
        throw new Exception("unable to find base definition for " + base);
    if (parts.length == 1) {
        if (p.getSnapshot() == null)
            // or else we could fill it in?
            throw new Exception("StructureDefinition " + base + " has no snapshot");
        return p;
    }
    for (Resource r : p.getContained()) {
        if (r instanceof StructureDefinition && r.getId().equals(parts[1])) {
            StructureDefinition pc = (StructureDefinition) r;
            if (pc.getSnapshot() == null) {
                StructureDefinition ps = getSnapShotForProfile(pc.getBaseDefinition());
                processProfile(pc);
            }
            return pc;
        }
    }
    throw new Exception("Unable to find snapshot for " + base);
}

Example 72 with ProfileUtilities

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

the class Publisher method processProfile.

private void processProfile(StructureDefinition ae) throws Exception {
    if (ae.getDate() == null)
        ae.setDate(page.getGenDate().getTime());
    if (ae.hasBaseDefinition() && ae.hasSnapshot()) {
        // cause it probably doesn't, coming from the profile directly
        StructureDefinition base = getIgProfile(ae.getBaseDefinition());
        if (base == null)
            base = new ProfileUtilities(page.getWorkerContext(), page.getValidationErrors(), page).getProfile(null, ae.getBaseDefinition());
        new ProfileUtilities(page.getWorkerContext(), page.getValidationErrors(), page).generateSnapshot(base, ae, ae.getBaseDefinition().split("#")[0], "http://hl7.org/fhir", ae.getName());
        if (page.getProfiles().has(ae.getUrl()))
            throw new Exception("Duplicate Profile URL " + ae.getUrl());
        page.getProfiles().see(ae, page.packageInfo());
    }
}

Example 73 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class R2016MayToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2016may = null;
    if (isJson)
        r2016may = new JsonParser().parse(stream);
    else
        r2016may = new XmlParser().parse(stream);
    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_14_50.convertResource(r2016may, advisor);
    Bundle b;
    if (r5 instanceof Bundle)
        b = (Bundle) r5;
    else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
    }
    for (CodeSystem cs : advisor.getCslist()) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    for (BundleEntryComponent be : b.getEntry()) {
        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
            StructureDefinition sd = (StructureDefinition) be.getResource();
            new ProfileUtilities(null, null, null).setIds(sd, false);
            if (patchUrls) {
                sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2016MAY));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
            }
        }
    }
    return b;
}

Example 74 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class R2016MayToR4Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2016may = null;
    if (isJson)
        r2016may = new JsonParser().parse(stream);
    else
        r2016may = new XmlParser().parse(stream);
    org.hl7.fhir.r4.model.Resource r4 = VersionConvertorFactory_14_40.convertResource(r2016may, advisor);
    Bundle b;
    if (r4 instanceof Bundle)
        b = (Bundle) r4;
    else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r4).setFullUrl(r4 instanceof MetadataResource ? ((MetadataResource) r4).getUrl() : null);
    }
    for (CodeSystem cs : advisor.getCslist()) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    for (BundleEntryComponent be : b.getEntry()) {
        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
            StructureDefinition sd = (StructureDefinition) be.getResource();
            new ProfileUtilities(null, null, null).setIds(sd, false);
            if (patchUrls) {
                sd.setUrl(sd.getUrl().replace(URL_BASE, "http://hl7.org/fhir/2016May/"));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
            }
        }
    }
    return b;
}

Example 75 with ProfileUtilities

use of org.hl7.fhir.r5.conformance.ProfileUtilities in project org.hl7.fhir.core by hapifhir.

the class SimpleWorkerContext method generateSnapshot.

public void generateSnapshot(StructureDefinition p) throws DefinitionException, FHIRException {
    if (!p.hasSnapshot() && 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);
        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 ((!ignoreProfileErrors && 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;
    }
}