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

Example 46 with CanonicalType

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

the class ProfileUtilities method processPaths.

/**
 * @param trimDifferential
 * @param srcSD
 * @throws DefinitionException, FHIRException
 * @throws Exception
 */
private ElementDefinition processPaths(String indent, StructureDefinitionSnapshotComponent result, StructureDefinitionSnapshotComponent base, StructureDefinitionDifferentialComponent differential, int baseCursor, int diffCursor, int baseLimit, int diffLimit, String url, String webUrl, String profileName, String contextPathSrc, String contextPathDst, boolean trimDifferential, String contextName, String resultPathBase, boolean slicingDone, List<ElementRedirection> redirector, StructureDefinition srcSD) throws DefinitionException, FHIRException {
    if (debug)
        System.out.println(indent + "PP @ " + resultPathBase + " / " + contextPathSrc + " : base = " + baseCursor + " to " + baseLimit + ", diff = " + diffCursor + " to " + diffLimit + " (slicing = " + slicingDone + ", redirector = " + (redirector == null ? "null" : redirector.toString()) + ")");
    ElementDefinition res = null;
    List<TypeSlice> typeList = new ArrayList<>();
    // just repeat processing entries until we run out of our allowed scope (1st entry, the allowed scope is all the entries)
    while (baseCursor <= baseLimit) {
        // get the current focus of the base, and decide what to do
        ElementDefinition currentBase = base.getElement().get(baseCursor);
        String cpath = fixedPathSource(contextPathSrc, currentBase.getPath(), redirector);
        if (debug)
            System.out.println(indent + " - " + cpath + ": base = " + baseCursor + " (" + descED(base.getElement(), baseCursor) + ") to " + baseLimit + " (" + descED(base.getElement(), baseLimit) + "), diff = " + diffCursor + " (" + descED(differential.getElement(), diffCursor) + ") to " + diffLimit + " (" + descED(differential.getElement(), diffLimit) + ") " + "(slicingDone = " + slicingDone + ") (diffpath= " + (differential.getElement().size() > diffCursor ? differential.getElement().get(diffCursor).getPath() : "n/a") + ")");
        // get a list of matching elements in scope
        List<ElementDefinition> diffMatches = getDiffMatches(differential, cpath, diffCursor, diffLimit, profileName);
        // in the simple case, source is not sliced.
        if (!currentBase.hasSlicing()) {
            if (diffMatches.isEmpty()) {
                // the differential doesn't say anything about this item
                // so we just copy it in
                ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
                outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                updateFromBase(outcome, currentBase);
                markDerived(outcome);
                if (resultPathBase == null)
                    resultPathBase = outcome.getPath();
                else if (!outcome.getPath().startsWith(resultPathBase))
                    throw new DefinitionException("Adding wrong path");
                result.getElement().add(outcome);
                if (hasInnerDiffMatches(differential, cpath, diffCursor, diffLimit, base.getElement(), true)) {
                    // did we implicitly step into a new type?
                    if (baseHasChildren(base, currentBase)) {
                        // not a new type here
                        processPaths(indent + "  ", result, base, differential, baseCursor + 1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, redirector, srcSD);
                        baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor + 1, baseLimit);
                    } else {
                        if (outcome.getType().size() == 0) {
                            throw new DefinitionException(diffMatches.get(0).getPath() + " has no children (" + differential.getElement().get(diffCursor).getPath() + ") and no types in profile " + profileName);
                        }
                        if (outcome.getType().size() > 1) {
                            for (TypeRefComponent t : outcome.getType()) {
                                if (!t.getWorkingCode().equals("Reference"))
                                    throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") and multiple types (" + typeCode(outcome.getType()) + ") in profile " + profileName);
                            }
                        }
                        StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
                        if (dt == null)
                            throw new DefinitionException("Unknown type " + outcome.getType().get(0) + " at " + diffMatches.get(0).getPath());
                        contextName = dt.getUrl();
                        int start = diffCursor;
                        while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath + ".")) diffCursor++;
                        processPaths(indent + "  ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
                        start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, webUrl, profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, redirector, srcSD);
                    }
                }
                baseCursor++;
            } else if (diffMatches.size() == 1 && (slicingDone || (!isImplicitSlicing(diffMatches.get(0), cpath) && !(diffMatches.get(0).hasSlicing() || (isExtension(diffMatches.get(0)) && diffMatches.get(0).hasSliceName()))))) {
                // one matching element in the differential
                ElementDefinition template = null;
                if (diffMatches.get(0).hasType() && diffMatches.get(0).getType().size() == 1 && diffMatches.get(0).getType().get(0).hasProfile() && !"Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode())) {
                    CanonicalType p = diffMatches.get(0).getType().get(0).getProfile().get(0);
                    StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue());
                    if (sd != null) {
                        if (!sd.hasSnapshot()) {
                            StructureDefinition sdb = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
                            if (sdb == null)
                                throw new DefinitionException("no base for " + sd.getBaseDefinition());
                            generateSnapshot(sdb, sd, sd.getUrl(), (sdb.hasUserData("path")) ? Utilities.extractBaseUrl(sdb.getUserString("path")) : webUrl, sd.getName());
                        }
                        ElementDefinition src;
                        if (p.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) {
                            src = null;
                            String eid = p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT);
                            for (ElementDefinition t : sd.getSnapshot().getElement()) {
                                if (eid.equals(t.getId()))
                                    src = t;
                            }
                            if (src == null)
                                throw new DefinitionException("Unable to find element " + eid + " in " + p.getValue());
                        } else
                            src = sd.getSnapshot().getElement().get(0);
                        template = src.copy().setPath(currentBase.getPath());
                        template.setSliceName(null);
                        // temporary work around
                        if (!"Extension".equals(diffMatches.get(0).getType().get(0).getCode())) {
                            template.setMin(currentBase.getMin());
                            template.setMax(currentBase.getMax());
                        }
                    }
                }
                if (template == null)
                    template = currentBase.copy();
                else
                    // some of what's in currentBase overrides template
                    template = overWriteWithCurrent(template, currentBase);
                ElementDefinition outcome = updateURLs(url, webUrl, template);
                outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                if (res == null)
                    res = outcome;
                updateFromBase(outcome, currentBase);
                if (diffMatches.get(0).hasSliceName())
                    outcome.setSliceName(diffMatches.get(0).getSliceName());
                updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url, srcSD);
                removeStatusExtensions(outcome);
                // if (outcome.getPath().endsWith("[x]") && outcome.getType().size() == 1 && !outcome.getType().get(0).getCode().equals("*") && !diffMatches.get(0).hasSlicing()) // if the base profile allows multiple types, but the profile only allows one, rename it
                // outcome.setPath(outcome.getPath().substring(0, outcome.getPath().length()-3)+Utilities.capitalize(outcome.getType().get(0).getCode()));
                outcome.setSlicing(null);
                if (resultPathBase == null)
                    resultPathBase = outcome.getPath();
                else if (!outcome.getPath().startsWith(resultPathBase))
                    throw new DefinitionException("Adding wrong path");
                result.getElement().add(outcome);
                baseCursor++;
                diffCursor = differential.getElement().indexOf(diffMatches.get(0)) + 1;
                if (differential.getElement().size() > diffCursor && outcome.getPath().contains(".") && (isDataType(outcome.getType()) || outcome.hasContentReference())) {
                    // don't want to do this for the root, since that's base, and we're already processing it
                    if (pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".") && !baseWalksInto(base.getElement(), baseCursor)) {
                        if (outcome.getType().size() > 1) {
                            if (outcome.getPath().endsWith("[x]") && !diffMatches.get(0).getPath().endsWith("[x]")) {
                                String en = tail(outcome.getPath());
                                String tn = tail(diffMatches.get(0).getPath());
                                String t = tn.substring(en.length() - 3);
                                if (isPrimitive(Utilities.uncapitalize(t)))
                                    t = Utilities.uncapitalize(t);
                                // keep any additional information
                                List<TypeRefComponent> ntr = getByTypeName(outcome.getType(), t);
                                if (ntr.isEmpty())
                                    ntr.add(new TypeRefComponent().setCode(t));
                                outcome.getType().clear();
                                outcome.getType().addAll(ntr);
                            }
                            if (outcome.getType().size() > 1)
                                for (TypeRefComponent t : outcome.getType()) {
                                    if (!t.getCode().equals("Reference")) {
                                        boolean nonExtension = false;
                                        for (ElementDefinition ed : diffMatches) if (ed != diffMatches.get(0) && !ed.getPath().endsWith(".extension"))
                                            nonExtension = true;
                                        if (nonExtension)
                                            throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") and multiple types (" + typeCode(outcome.getType()) + ") in profile " + profileName);
                                    }
                                }
                        }
                        int start = diffCursor;
                        while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
                        if (outcome.hasContentReference()) {
                            ElementDefinition tgt = getElementById(base.getElement(), outcome.getContentReference());
                            if (tgt == null)
                                throw new DefinitionException("Unable to resolve reference to " + outcome.getContentReference());
                            replaceFromContentReference(outcome, tgt);
                            int nbc = base.getElement().indexOf(tgt) + 1;
                            int nbl = nbc;
                            while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getPath() + ".")) nbl++;
                            processPaths(indent + "  ", result, base, differential, nbc, start - 1, nbl - 1, diffCursor - 1, url, webUrl, profileName, tgt.getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, redirectorStack(redirector, outcome, cpath), srcSD);
                        } else {
                            StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
                            if (dt == null)
                                throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") for type " + typeCode(outcome.getType()) + " in profile " + profileName + ", but can't find type");
                            contextName = dt.getUrl();
                            processPaths(indent + "  ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
                            start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, webUrl, profileName + pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, new ArrayList<ElementRedirection>(), srcSD);
                        }
                    }
                }
            } else if (diffsConstrainTypes(diffMatches, cpath, typeList)) {
                int start = 0;
                int nbl = findEndOfElement(base, baseCursor);
                int ndc = differential.getElement().indexOf(diffMatches.get(0));
                ElementDefinition elementToRemove = null;
                // we come here whether they are sliced in the diff, or whether the short cut is used.
                if (typeList.get(0).type != null) {
                    // in R3 (and unpatched R4, as a workaround right now...
                    if (!FHIRVersion.isR4Plus(context.getVersion()) || !newSlicingProcessing) {
                        // newSlicingProcessing is a work around for editorial loop dependency
                        // we insert a cloned element with the right types at the start of the diffMatches
                        ElementDefinition ed = new ElementDefinition();
                        ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
                        for (TypeSlice ts : typeList) ed.addType().setCode(ts.type);
                        ed.setSlicing(new ElementDefinitionSlicingComponent());
                        ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
                        ed.getSlicing().setRules(SlicingRules.CLOSED);
                        ed.getSlicing().setOrdered(false);
                        diffMatches.add(0, ed);
                        differential.getElement().add(ndc, ed);
                        elementToRemove = ed;
                    } else {
                        // as of R4, this changed; if there's no slice, there's no constraint on the slice types, only one the type.
                        // so the element we insert specifies no types (= all types) allowed in the base, not just the listed type.
                        // see also discussion here: https://chat.fhir.org/#narrow/stream/179177-conformance/topic/Slicing.20a.20non-repeating.20element
                        ElementDefinition ed = new ElementDefinition();
                        ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
                        ed.setSlicing(new ElementDefinitionSlicingComponent());
                        ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
                        ed.getSlicing().setRules(SlicingRules.CLOSED);
                        ed.getSlicing().setOrdered(false);
                        diffMatches.add(0, ed);
                        differential.getElement().add(ndc, ed);
                        elementToRemove = ed;
                    }
                }
                int ndl = findEndOfElement(differential, ndc);
                // the first element is setting up the slicing
                if (diffMatches.get(0).getSlicing().hasRules())
                    if (diffMatches.get(0).getSlicing().getRules() != SlicingRules.CLOSED)
                        throw new FHIRException("Error at path " + contextPathSrc + ": Type slicing with slicing.rules != closed");
                if (diffMatches.get(0).getSlicing().hasOrdered())
                    if (diffMatches.get(0).getSlicing().getOrdered())
                        throw new FHIRException("Error at path " + contextPathSrc + ": Type slicing with slicing.ordered = true");
                if (diffMatches.get(0).getSlicing().hasDiscriminator()) {
                    if (diffMatches.get(0).getSlicing().getDiscriminator().size() != 1)
                        throw new FHIRException("Error at path " + contextPathSrc + ": Type slicing with slicing.discriminator.count() > 1");
                    if (!"$this".equals(diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getPath()))
                        throw new FHIRException("Error at path " + contextPathSrc + ": Type slicing with slicing.discriminator.path != '$this'");
                    if (diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getType() != DiscriminatorType.TYPE)
                        throw new FHIRException("Error at path " + contextPathSrc + ": Type slicing with slicing.discriminator.type != 'type'");
                }
                // check the slice names too while we're at it...
                for (TypeSlice ts : typeList) if (ts.type != null) {
                    String tn = rootName(cpath) + Utilities.capitalize(ts.type);
                    if (!ts.defn.hasSliceName())
                        ts.defn.setSliceName(tn);
                    else if (!ts.defn.getSliceName().equals(tn))
                        throw new FHIRException("Error at path " + (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath) + ": Slice name must be '" + tn + "' but is '" + ts.defn.getSliceName() + "'");
                    if (!ts.defn.hasType())
                        ts.defn.addType().setCode(ts.type);
                    else if (ts.defn.getType().size() > 1)
                        throw new FHIRException("Error at path " + (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath) + ": Slice for type '" + tn + "' has more than one type '" + ts.defn.typeSummary() + "'");
                    else if (!ts.defn.getType().get(0).getCode().equals(ts.type))
                        throw new FHIRException("Error at path " + (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath) + ": Slice for type '" + tn + "' has wrong type '" + ts.defn.typeSummary() + "'");
                }
                // ok passed the checks.
                // copy the root diff, and then process any children it has
                ElementDefinition e = processPaths(indent + "  ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, redirector, srcSD);
                if (e == null)
                    throw new FHIRException("Did not find type root: " + diffMatches.get(0).getPath());
                // now set up slicing on the e (cause it was wiped by what we called.
                e.setSlicing(new ElementDefinitionSlicingComponent());
                e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
                e.getSlicing().setRules(SlicingRules.CLOSED);
                e.getSlicing().setOrdered(false);
                start++;
                // now we process the base scope repeatedly for each instance of the item in the differential list
                for (int i = start; i < diffMatches.size(); i++) {
                    // our processing scope for the differential is the item in the list, and all the items before the next one in the list
                    ndc = differential.getElement().indexOf(diffMatches.get(i));
                    ndl = findEndOfElement(differential, ndc);
                    processPaths(indent + "  ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, redirector, srcSD);
                }
                if (elementToRemove != null) {
                    differential.getElement().remove(elementToRemove);
                    ndl--;
                }
                // ok, done with that - next in the base list
                baseCursor = nbl + 1;
                diffCursor = ndl + 1;
            } else {
                // ok, the differential slices the item. Let's check our pre-conditions to ensure that this is correct
                if (!unbounded(currentBase) && !isSlicedToOneOnly(diffMatches.get(0)))
                    // (but you might do that in order to split up constraints by type)
                    throw new DefinitionException("Attempt to a slice an element that does not repeat: " + currentBase.getPath() + "/" + currentBase.getPath() + " from " + contextName + " in " + url);
                if (// well, the diff has set up a slice, but hasn't defined it. this is an error
                !diffMatches.get(0).hasSlicing() && !isExtension(currentBase))
                    throw new DefinitionException("Differential does not have a slice: " + currentBase.getPath() + "/ (b:" + baseCursor + " of " + baseLimit + " / " + diffCursor + "/ " + diffLimit + ") in profile " + url);
                // well, if it passed those preconditions then we slice the dest.
                int start = 0;
                int nbl = findEndOfElement(base, baseCursor);
                // if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0))+1) {
                if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && (nbl > baseCursor || differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0)) + 1)) {
                    // there's a default set before the slices
                    int ndc = differential.getElement().indexOf(diffMatches.get(0));
                    int ndl = findEndOfElement(differential, ndc);
                    ElementDefinition e = processPaths(indent + "  ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, redirector, srcSD);
                    if (e == null)
                        throw new FHIRException("Did not find single slice: " + diffMatches.get(0).getPath());
                    e.setSlicing(diffMatches.get(0).getSlicing());
                    start++;
                } else {
                    // we're just going to accept the differential slicing at face value
                    ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
                    outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                    updateFromBase(outcome, currentBase);
                    if (!diffMatches.get(0).hasSlicing())
                        outcome.setSlicing(makeExtensionSlicing());
                    else
                        outcome.setSlicing(diffMatches.get(0).getSlicing().copy());
                    if (!outcome.getPath().startsWith(resultPathBase))
                        throw new DefinitionException("Adding wrong path");
                    result.getElement().add(outcome);
                    // differential - if the first one in the list has a name, we'll process it. Else we'll treat it as the base definition of the slice.
                    if (!diffMatches.get(0).hasSliceName()) {
                        updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url, srcSD);
                        removeStatusExtensions(outcome);
                        if (!outcome.hasContentReference() && !outcome.hasType()) {
                            throw new DefinitionException("not done yet");
                        }
                        start++;
                    // result.getElement().remove(result.getElement().size()-1);
                    } else
                        checkExtensionDoco(outcome);
                }
                // now, for each entry in the diff matches, we're going to process the base item
                // our processing scope for base is all the children of the current path
                int ndc = diffCursor;
                int ndl = diffCursor;
                for (int i = start; i < diffMatches.size(); i++) {
                    // our processing scope for the differential is the item in the list, and all the items before the next one in the list
                    ndc = differential.getElement().indexOf(diffMatches.get(i));
                    ndl = findEndOfElement(differential, ndc);
                    /*            if (skipSlicingElement && i == 0) {
              ndc = ndc + 1;
              if (ndc > ndl)
                continue;
            }*/
                    // now we process the base scope repeatedly for each instance of the item in the differential list
                    processPaths(indent + "  ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, redirector, srcSD);
                }
                // ok, done with that - next in the base list
                baseCursor = nbl + 1;
                diffCursor = ndl + 1;
            }
        } else {
            // the item is already sliced in the base profile.
            // here's the rules
            // 1. irrespective of whether the slicing is ordered or not, the definition order must be maintained
            // 2. slice element names have to match.
            // 3. new slices must be introduced at the end
            // corallory: you can't re-slice existing slices. is that ok?
            // we're going to need this:
            String path = currentBase.getPath();
            ElementDefinition original = currentBase;
            if (diffMatches.isEmpty()) {
                // copy across the currentbase, and all of its children and siblings
                while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path)) {
                    ElementDefinition outcome = updateURLs(url, webUrl, base.getElement().get(baseCursor).copy());
                    outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                    if (!outcome.getPath().startsWith(resultPathBase))
                        throw new DefinitionException("Adding wrong path in profile " + profileName + ": " + outcome.getPath() + " vs " + resultPathBase);
                    // so we just copy it in
                    result.getElement().add(outcome);
                    baseCursor++;
                }
            } else {
                // first - check that the slicing is ok
                boolean closed = currentBase.getSlicing().getRules() == SlicingRules.CLOSED;
                int diffpos = 0;
                boolean isExtension = cpath.endsWith(".extension") || cpath.endsWith(".modifierExtension");
                if (diffMatches.get(0).hasSlicing()) {
                    // it might be null if the differential doesn't want to say anything about slicing
                    // if (!isExtension)
                    // diffpos++; // if there's a slice on the first, we'll ignore any content it has
                    ElementDefinitionSlicingComponent dSlice = diffMatches.get(0).getSlicing();
                    ElementDefinitionSlicingComponent bSlice = currentBase.getSlicing();
                    if (dSlice.hasOrderedElement() && bSlice.hasOrderedElement() && !orderMatches(dSlice.getOrderedElement(), bSlice.getOrderedElement()))
                        throw new DefinitionException("Slicing rules on differential (" + summarizeSlicing(dSlice) + ") do not match those on base (" + summarizeSlicing(bSlice) + ") - order @ " + path + " (" + contextName + ")");
                    if (!discriminatorMatches(dSlice.getDiscriminator(), bSlice.getDiscriminator()))
                        throw new DefinitionException("Slicing rules on differential (" + summarizeSlicing(dSlice) + ") do not match those on base (" + summarizeSlicing(bSlice) + ") - disciminator @ " + path + " (" + contextName + ")");
                    if (!ruleMatches(dSlice.getRules(), bSlice.getRules()))
                        throw new DefinitionException("Slicing rules on differential (" + summarizeSlicing(dSlice) + ") do not match those on base (" + summarizeSlicing(bSlice) + ") - rule @ " + path + " (" + contextName + ")");
                }
                ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
                outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                updateFromBase(outcome, currentBase);
                if (diffMatches.get(0).hasSlicing() || !diffMatches.get(0).hasSliceName()) {
                    updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing());
                    // if there's no slice, we don't want to update the unsliced description
                    updateFromDefinition(outcome, diffMatches.get(0), profileName, closed, url, srcSD);
                    removeStatusExtensions(outcome);
                } else if (!diffMatches.get(0).hasSliceName())
                    // because of updateFromDefinition isn't called
                    diffMatches.get(0).setUserData(GENERATED_IN_SNAPSHOT, outcome);
                result.getElement().add(outcome);
                if (!diffMatches.get(0).hasSliceName()) {
                    // it's not real content, just the slice
                    diffpos++;
                }
                if (hasInnerDiffMatches(differential, cpath, diffpos, diffLimit, base.getElement(), false)) {
                    int nbl = findEndOfElement(base, baseCursor);
                    int ndc = differential.getElement().indexOf(diffMatches.get(0)) + 1;
                    int ndl = findEndOfElement(differential, ndc);
                    processPaths(indent + "  ", result, base, differential, baseCursor + 1, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, srcSD);
                // throw new Error("Not done yet");
                // } else if (currentBase.getType().get(0).getCode().equals("BackboneElement") && diffMatches.size() > 0 && diffMatches.get(0).hasSliceName()) {
                } else if (currentBase.getType().get(0).getCode().equals("BackboneElement")) {
                    // We need to copy children of the backbone element before we start messing around with slices
                    int nbl = findEndOfElement(base, baseCursor);
                    for (int i = baseCursor + 1; i <= nbl; i++) {
                        outcome = updateURLs(url, webUrl, base.getElement().get(i).copy());
                        result.getElement().add(outcome);
                    }
                }
                // now, we have two lists, base and diff. we're going to work through base, looking for matches in diff.
                List<ElementDefinition> baseMatches = getSiblings(base.getElement(), currentBase);
                for (ElementDefinition baseItem : baseMatches) {
                    baseCursor = base.getElement().indexOf(baseItem);
                    outcome = updateURLs(url, webUrl, baseItem.copy());
                    updateFromBase(outcome, currentBase);
                    outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                    outcome.setSlicing(null);
                    if (!outcome.getPath().startsWith(resultPathBase))
                        throw new DefinitionException("Adding wrong path");
                    if (diffpos < diffMatches.size() && diffMatches.get(diffpos).getSliceName().equals(outcome.getSliceName())) {
                        // if there's a diff, we update the outcome with diff
                        // no? updateFromDefinition(outcome, diffMatches.get(diffpos), profileName, closed, url);
                        // then process any children
                        int nbl = findEndOfElement(base, baseCursor);
                        int ndc = differential.getElement().indexOf(diffMatches.get(diffpos));
                        int ndl = findEndOfElement(differential, ndc);
                        // now we process the base scope repeatedly for each instance of the item in the differential list
                        processPaths(indent + "  ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, diffpos), contextPathSrc, contextPathDst, closed, contextName, resultPathBase, true, redirector, srcSD);
                        // ok, done with that - now set the cursors for if this is the end
                        baseCursor = nbl;
                        diffCursor = ndl + 1;
                        diffpos++;
                    } else {
                        result.getElement().add(outcome);
                        baseCursor++;
                        // just copy any children on the base
                        while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path) && !base.getElement().get(baseCursor).getPath().equals(path)) {
                            outcome = updateURLs(url, webUrl, base.getElement().get(baseCursor).copy());
                            outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                            if (!outcome.getPath().startsWith(resultPathBase))
                                throw new DefinitionException("Adding wrong path");
                            result.getElement().add(outcome);
                            baseCursor++;
                        }
                        // Lloyd - add this for test T15
                        baseCursor--;
                    }
                }
                // finally, we process any remaining entries in diff, which are new (and which are only allowed if the base wasn't closed
                if (closed && diffpos < diffMatches.size())
                    throw new DefinitionException("The base snapshot marks a slicing as closed, but the differential tries to extend it in " + profileName + " at " + path + " (" + cpath + ")");
                if (diffpos == diffMatches.size()) {
                // Lloyd This was causing problems w/ Telus
                // diffCursor++;
                } else {
                    while (diffpos < diffMatches.size()) {
                        ElementDefinition diffItem = diffMatches.get(diffpos);
                        for (ElementDefinition baseItem : baseMatches) if (baseItem.getSliceName().equals(diffItem.getSliceName()))
                            throw new DefinitionException("Named items are out of order in the slice");
                        outcome = updateURLs(url, webUrl, currentBase.copy());
                        // outcome = updateURLs(url, diffItem.copy());
                        outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
                        updateFromBase(outcome, currentBase);
                        outcome.setSlicing(null);
                        if (!outcome.getPath().startsWith(resultPathBase))
                            throw new DefinitionException("Adding wrong path");
                        result.getElement().add(outcome);
                        updateFromDefinition(outcome, diffItem, profileName, trimDifferential, url, srcSD);
                        removeStatusExtensions(outcome);
                        // --- LM Added this
                        diffCursor = differential.getElement().indexOf(diffItem) + 1;
                        if (!outcome.getType().isEmpty() && (/*outcome.getType().get(0).getCode().equals("Extension") || */
                        differential.getElement().size() > diffCursor) && outcome.getPath().contains(".") && isDataType(outcome.getType())) {
                            // don't want to do this for the root, since that's base, and we're already processing it
                            if (!baseWalksInto(base.getElement(), baseCursor)) {
                                if (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) {
                                    if (outcome.getType().size() > 1)
                                        for (TypeRefComponent t : outcome.getType()) {
                                            if (!t.getCode().equals("Reference"))
                                                throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") and multiple types (" + typeCode(outcome.getType()) + ") in profile " + profileName);
                                        }
                                    TypeRefComponent t = outcome.getType().get(0);
                                    if (t.getCode().equals("BackboneElement")) {
                                        int baseStart = base.getElement().indexOf(currentBase) + 1;
                                        int baseMax = baseStart + 1;
                                        while (baseMax < base.getElement().size() && base.getElement().get(baseMax).getPath().startsWith(currentBase.getPath() + ".")) baseMax++;
                                        int start = diffCursor;
                                        while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
                                        processPaths(indent + "  ", result, base, differential, baseStart, start - 1, baseMax - 1, diffCursor - 1, url, webUrl, profileName + pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, redirector, srcSD);
                                    } else {
                                        StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
                                        // }
                                        if (dt == null)
                                            throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") for type " + typeCode(outcome.getType()) + " in profile " + profileName + ", but can't find type");
                                        contextName = dt.getUrl();
                                        int start = diffCursor;
                                        while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
                                        processPaths(indent + "  ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
                                        start - 1, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, webUrl, profileName + pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, redirector, srcSD);
                                    }
                                } else if (outcome.getType().get(0).getCode().equals("Extension")) {
                                    // Force URL to appear if we're dealing with an extension.  (This is a kludge - may need to drill down in other cases where we're slicing and the type has a profile declaration that could be setting the fixed value)
                                    StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
                                    for (ElementDefinition extEd : dt.getSnapshot().getElement()) {
                                        // We only want the children that aren't the root
                                        if (extEd.getPath().contains(".")) {
                                            ElementDefinition extUrlEd = updateURLs(url, webUrl, extEd.copy());
                                            extUrlEd.setPath(fixedPathDest(outcome.getPath(), extUrlEd.getPath(), redirector, null));
                                            // updateFromBase(extUrlEd, currentBase);
                                            markDerived(extUrlEd);
                                            result.getElement().add(extUrlEd);
                                        }
                                    }
                                }
                            }
                        }
                        // ---
                        diffpos++;
                    }
                }
                baseCursor++;
            }
        }
    }
    int i = 0;
    for (ElementDefinition e : result.getElement()) {
        i++;
        if (e.hasMinElement() && e.getMinElement().getValue() == null)
            throw new Error("null min");
    }
    return res;
}

Example 47 with CanonicalType

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

the class GraphQLEngine method processCanonicalReference.

private void processCanonicalReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
    if (!(source instanceof CanonicalType))
        throw new EGraphQLException("Not done yet");
    if (services == null)
        throw new EGraphQLException("Resource Referencing services not provided");
    Reference ref = new Reference(source.primitiveValue());
    ReferenceResolution res = services.lookup(appInfo, context, ref);
    if (res != null) {
        if (targetTypeOk(field.getArguments(), res.getTarget())) {
            Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
            ObjectValue obj = new ObjectValue();
            arg.addValue(obj);
            processObject((Resource) res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
        }
    } else if (!hasArgument(field.getArguments(), "optional", "true"))
        throw new EGraphQLException("Unable to resolve reference to " + ref.getReference());
}

Example 48 with CanonicalType

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

the class CanonicalTypeNullTest method equalsShallow.

@Test
@DisplayName("Test null value equalsShallow()")
void equalsShallow() {
    CanonicalType nullCanonical = new CanonicalType();
    CanonicalType validCanonical = new CanonicalType("theValue");
    Assertions.assertFalse(nullCanonical.equalsShallow(validCanonical));
}

Example 49 with CanonicalType

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

the class CanonicalTypeNullTest method copy.

@Test
@DisplayName("Test null value copy()")
void copy() {
    CanonicalType nullCanonical = new CanonicalType();
    CanonicalType copyCanonical = nullCanonical.copy();
    Assertions.assertNull(copyCanonical.getValue());
}

Example 50 with CanonicalType

use of org.hl7.fhir.r5.model.CanonicalType in project pathling by aehrc.

the class ValueSetMapping method toIntersection.

/**
 * Constructs a {@link ValueSet} representing the intersection of a set of codings and a server
 *
 * @param valueSetUri the server defined value set.
 * @param codings the set of codings to intersect.
 * @return the intersection value set.
 */
@Nonnull
public static ValueSet toIntersection(@Nonnull final String valueSetUri, @Nonnull final Collection<SimpleCoding> codings) {
    final Set<CodeSystemReference> validCodeSystems = codings.stream().filter(SimpleCoding::isDefined).map(coding -> new CodeSystemReference(Optional.ofNullable(coding.getSystem()), Optional.ofNullable(coding.getVersion()))).collect(Collectors.toUnmodifiableSet());
    // Create a ValueSet to represent the intersection of the input codings and the ValueSet
    // described by the URI in the argument.
    final ValueSet intersection = new ValueSet();
    final ValueSetComposeComponent compose = new ValueSetComposeComponent();
    final List<ConceptSetComponent> includes = new ArrayList<>();
    // Create an include section for each unique code system present within the input codings.
    for (final CodeSystemReference codeSystem : validCodeSystems) {
        final ConceptSetComponent include = new ConceptSetComponent();
        include.setValueSet(Collections.singletonList(new CanonicalType(valueSetUri)));
        // noinspection OptionalGetWithoutIsPresent
        include.setSystem(codeSystem.getSystem().get());
        codeSystem.getVersion().ifPresent(include::setVersion);
        // Add the codings that match the current code system.
        final List<ConceptReferenceComponent> concepts = codings.stream().filter(codeSystem::matchesCoding).map(SimpleCoding::getCode).filter(Objects::nonNull).distinct().map(code -> {
            final ConceptReferenceComponent concept = new ConceptReferenceComponent();
            concept.setCode(code);
            return concept;
        }).collect(Collectors.toList());
        if (!concepts.isEmpty()) {
            include.setConcept(concepts);
            includes.add(include);
        }
    }
    compose.setInclude(includes);
    intersection.setCompose(compose);
    return intersection;
}