Examples with FINAL org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 41 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method sortDifferential.

public void sortDifferential(StructureDefinition base, StructureDefinition diff, String name, List<String> errors) throws FHIRException {
    final List<ElementDefinition> diffList = diff.getDifferential().getElement();
    int lastCount = diffList.size();
    // first, we move the differential elements into a tree
    if (diffList.isEmpty())
        return;
    ElementDefinitionHolder edh = null;
    int i = 0;
    if (diffList.get(0).getPath().contains(".")) {
        String newPath = diffList.get(0).getPath().split("\\.")[0];
        ElementDefinition e = new ElementDefinition(new StringType(newPath));
        edh = new ElementDefinitionHolder(e, true);
    } else {
        edh = new ElementDefinitionHolder(diffList.get(0));
        i = 1;
    }
    boolean hasSlicing = false;
    // in a differential, slicing may not be stated explicitly
    List<String> paths = new ArrayList<String>();
    for (ElementDefinition elt : diffList) {
        if (elt.hasSlicing() || paths.contains(elt.getPath())) {
            hasSlicing = true;
            break;
        }
        paths.add(elt.getPath());
    }
    if (!hasSlicing) {
        // if Differential does not have slicing then safe to pre-sort the list
        // so elements and subcomponents are together
        Collections.sort(diffList, new ElementNameCompare());
    }
    processElementsIntoTree(edh, i, diff.getDifferential().getElement());
    // now, we sort the siblings throughout the tree
    ElementDefinitionComparer cmp = new ElementDefinitionComparer(true, base.getSnapshot().getElement(), "", 0, name);
    sortElements(edh, cmp, errors);
    // now, we serialise them back to a list
    diffList.clear();
    writeElements(edh, diffList);
    if (lastCount != diffList.size())
        errors.add("Sort failed: counts differ; at least one of the paths in the differential is illegal");
}

Example 42 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpansionCache method loadCache.

private void loadCache() throws FHIRFormatError, IOException {
    File[] files = new File(cacheFolder).listFiles();
    for (File f : files) {
        if (f.getName().endsWith(".xml")) {
            final FileInputStream is = new FileInputStream(f);
            try {
                Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
                if (r instanceof OperationOutcome) {
                    OperationOutcome oo = (OperationOutcome) r;
                    expansions.put(ToolingExtensions.getExtension(oo, VS_ID_EXT).getValue().toString(), new ValueSetExpansionOutcome(new XhtmlComposer(XhtmlComposer.XML, false).composePlainText(oo.getText().getDiv()), TerminologyServiceErrorClass.UNKNOWN));
                } else if (r instanceof ValueSet) {
                    ValueSet vs = (ValueSet) r;
                    if (vs.hasExpansion())
                        expansions.put(vs.getUrl(), new ValueSetExpansionOutcome(vs));
                    else {
                        canonicals.put(vs.getUrl(), vs);
                        if (vs.hasVersion())
                            canonicals.put(vs.getUrl() + "|" + vs.getVersion(), vs);
                    }
                } else if (r instanceof CanonicalResource) {
                    CanonicalResource md = (CanonicalResource) r;
                    canonicals.put(md.getUrl(), md);
                    if (md.hasVersion())
                        canonicals.put(md.getUrl() + "|" + md.getVersion(), md);
                }
            } finally {
                IOUtils.closeQuietly(is);
            }
        }
    }
}

Example 43 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class TerminologyCacheTests method testExtractedUnder1000.

@ParameterizedTest
@MethodSource("under1000IntParams")
public void testExtractedUnder1000(int max) throws IOException {
    TerminologyCache cache = createTerminologyCache();
    ValueSet vs = new ValueSet();
    List<ValueSet.ValueSetExpansionContainsComponent> list = createContainsArray(max);
    vs.setUrl("http://dummy.org");
    vs.getExpansion().setContains(list);
    org.hl7.fhir.r5.formats.JsonParser json = new org.hl7.fhir.r5.formats.JsonParser();
    json.setOutputStyle(IParser.OutputStyle.PRETTY);
    String extracted = cache.extracted(json, vs);
    JsonElement element = jsonParser.parse(extracted);
    final int expansionSize = element.getAsJsonObject().has("expansion") ? element.getAsJsonObject().getAsJsonObject("expansion").getAsJsonArray("contains").size() : 0;
    assertEquals(max, expansionSize);
}

Example 44 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class XhtmlParser method parseLiteral.

private void parseLiteral(StringBuilder s) throws IOException, FHIRFormatError {
    // UInt16 w;
    readChar();
    String c = readUntil(";&'\"><");
    if (c.isEmpty())
        throw new FHIRFormatError("Invalid literal declaration following text: " + s);
    else if (c.charAt(0) == '#') {
        if (isInteger(c.substring(1), 10))
            s.append((char) Integer.parseInt(c.substring(1)));
        else if (c.charAt(1) == 'x' && isInteger(c.substring(2), 16))
            s.append((char) Integer.parseInt(c.substring(2), 16));
    } else if (entities.containsKey(c)) {
        s.append(entities.get(c));
    // what's going on here?
    // the contents that follow already existed, and then I added the routine to populate the entities
    // which was generated from other code. The code that follows is probably redundant, but I haven't
    // cross checked it. some is welcome to do so... (GG 8-Nov 2021)
    } else if (c.equals("apos"))
        s.append('\'');
    else if (c.equals("quot"))
        s.append('"');
    else if (c.equals("nbsp"))
        s.append(XhtmlNode.NBSP);
    else if (c.equals("amp"))
        s.append('&');
    else if (c.equals("lsquo"))
        // right single quotation, U+2019 ISOnum
        s.append((char) 8216);
    else if (c.equals("rsquo"))
        // right single quotation, U+2019 ISOnum
        s.append((char) 8217);
    else if (c.equals("gt"))
        s.append('>');
    else if (c.equals("lt"))
        s.append('<');
    else if (c.equals("copy"))
        s.append((char) 169);
    else if (c.equals("reg"))
        s.append((char) 174);
    else if (c.equals("sect"))
        s.append((char) 0xA7);
    else if (c.equals("fnof"))
        // latin small f with hook = function = florin, U+0192 ISOtech -->
        s.append((char) 402);
    else if (c.equals("Alpha"))
        // greek capital letter alpha, U+0391
        s.append((char) 913);
    else if (c.equals("Beta"))
        // greek capital letter beta, U+0392
        s.append((char) 914);
    else if (c.equals("Gamma"))
        // greek capital letter gamma, U+0393 ISOgrk3
        s.append((char) 915);
    else if (c.equals("Delta"))
        // greek capital letter delta, U+0394 ISOgrk3
        s.append((char) 916);
    else if (c.equals("Epsilon"))
        // greek capital letter epsilon, U+0395
        s.append((char) 917);
    else if (c.equals("Zeta"))
        // greek capital letter zeta, U+0396
        s.append((char) 918);
    else if (c.equals("Eta"))
        // greek capital letter eta, U+0397
        s.append((char) 919);
    else if (c.equals("Theta"))
        // greek capital letter theta, U+0398 ISOgrk3
        s.append((char) 920);
    else if (c.equals("Iota"))
        // greek capital letter iota, U+0399
        s.append((char) 921);
    else if (c.equals("Kappa"))
        // greek capital letter kappa, U+039A
        s.append((char) 922);
    else if (c.equals("Lambda"))
        // greek capital letter lambda, U+039B ISOgrk3
        s.append((char) 923);
    else if (c.equals("Mu"))
        // greek capital letter mu, U+039C
        s.append((char) 924);
    else if (c.equals("Nu"))
        // greek capital letter nu, U+039D
        s.append((char) 925);
    else if (c.equals("Xi"))
        // greek capital letter xi, U+039E ISOgrk3
        s.append((char) 926);
    else if (c.equals("Omicron"))
        // greek capital letter omicron, U+039F
        s.append((char) 927);
    else if (c.equals("Pi"))
        // greek capital letter pi, U+03A0 ISOgrk3
        s.append((char) 928);
    else if (c.equals("Rho"))
        // greek capital letter rho, U+03A1
        s.append((char) 929);
    else if (c.equals("Sigma"))
        // greek capital letter sigma, U+03A3 ISOgrk3
        s.append((char) 931);
    else if (c.equals("Tau"))
        // greek capital letter tau, U+03A4
        s.append((char) 932);
    else if (c.equals("Upsilon"))
        // greek capital letter upsilon, U+03A5 ISOgrk3
        s.append((char) 933);
    else if (c.equals("Phi"))
        // greek capital letter phi, U+03A6 ISOgrk3
        s.append((char) 934);
    else if (c.equals("Chi"))
        // greek capital letter chi, U+03A7
        s.append((char) 935);
    else if (c.equals("Psi"))
        // greek capital letter psi, U+03A8 ISOgrk3
        s.append((char) 936);
    else if (c.equals("Omega"))
        // greek capital letter omega, U+03A9 ISOgrk3
        s.append((char) 937);
    else if (c.equals("alpha"))
        // greek small letter alpha, U+03B1 ISOgrk3
        s.append((char) 945);
    else if (c.equals("beta"))
        // greek small letter beta, U+03B2 ISOgrk3
        s.append((char) 946);
    else if (c.equals("gamma"))
        // greek small letter gamma, U+03B3 ISOgrk3
        s.append((char) 947);
    else if (c.equals("delta"))
        // greek small letter delta, U+03B4 ISOgrk3
        s.append((char) 948);
    else if (c.equals("epsilon"))
        // greek small letter epsilon, U+03B5 ISOgrk3
        s.append((char) 949);
    else if (c.equals("zeta"))
        // greek small letter zeta, U+03B6 ISOgrk3
        s.append((char) 950);
    else if (c.equals("eta"))
        // greek small letter eta, U+03B7 ISOgrk3
        s.append((char) 951);
    else if (c.equals("theta"))
        // greek small letter theta, U+03B8 ISOgrk3
        s.append((char) 952);
    else if (c.equals("iota"))
        // greek small letter iota, U+03B9 ISOgrk3
        s.append((char) 953);
    else if (c.equals("kappa"))
        // greek small letter kappa, U+03BA ISOgrk3
        s.append((char) 954);
    else if (c.equals("lambda"))
        // greek small letter lambda, U+03BB ISOgrk3
        s.append((char) 955);
    else if (c.equals("mu"))
        // greek small letter mu, U+03BC ISOgrk3
        s.append((char) 956);
    else if (c.equals("nu"))
        // greek small letter nu, U+03BD ISOgrk3
        s.append((char) 957);
    else if (c.equals("xi"))
        // greek small letter xi, U+03BE ISOgrk3
        s.append((char) 958);
    else if (c.equals("omicron"))
        // greek small letter omicron, U+03BF NEW
        s.append((char) 959);
    else if (c.equals("pi"))
        // greek small letter pi, U+03C0 ISOgrk3
        s.append((char) 960);
    else if (c.equals("rho"))
        // greek small letter rho, U+03C1 ISOgrk3
        s.append((char) 961);
    else if (c.equals("sigmaf"))
        // greek small letter final sigma, U+03C2 ISOgrk3
        s.append((char) 962);
    else if (c.equals("sigma"))
        // greek small letter sigma, U+03C3 ISOgrk3
        s.append((char) 963);
    else if (c.equals("tau"))
        // greek small letter tau, U+03C4 ISOgrk3
        s.append((char) 964);
    else if (c.equals("upsilon"))
        // greek small letter upsilon, U+03C5 ISOgrk3
        s.append((char) 965);
    else if (c.equals("phi"))
        // greek small letter phi, U+03C6 ISOgrk3
        s.append((char) 966);
    else if (c.equals("chi"))
        // greek small letter chi, U+03C7 ISOgrk3
        s.append((char) 967);
    else if (c.equals("psi"))
        // greek small letter psi, U+03C8 ISOgrk3
        s.append((char) 968);
    else if (c.equals("omega"))
        // greek small letter omega, U+03C9 ISOgrk3
        s.append((char) 969);
    else if (c.equals("thetasym"))
        // greek small letter theta symbol, U+03D1 NEW
        s.append((char) 977);
    else if (c.equals("upsih"))
        // greek upsilon with hook symbol, U+03D2 NEW
        s.append((char) 978);
    else if (c.equals("piv"))
        // greek pi symbol, U+03D6 ISOgrk3
        s.append((char) 982);
    else if (c.equals("bull"))
        // bullet = black small circle, U+2022 ISOpub
        s.append((char) 8226);
    else if (c.equals("hellip"))
        // horizontal ellipsis = three dot leader, U+2026 ISOpub
        s.append((char) 8230);
    else if (c.equals("prime"))
        // prime = minutes = feet, U+2032 ISOtech
        s.append((char) 8242);
    else if (c.equals("Prime"))
        // double prime = seconds = inches, U+2033 ISOtech
        s.append((char) 8243);
    else if (c.equals("oline"))
        // overline = spacing overscore, U+203E NEW
        s.append((char) 8254);
    else if (c.equals("frasl"))
        // fraction slash, U+2044 NEW
        s.append((char) 8260);
    else if (c.equals("weierp"))
        // script capital P = power set = Weierstrass p, U+2118 ISOamso
        s.append((char) 8472);
    else if (c.equals("image"))
        // blackletter capital I = imaginary part, U+2111 ISOamso
        s.append((char) 8465);
    else if (c.equals("real"))
        // blackletter capital R = real part symbol, U+211C ISOamso
        s.append((char) 8476);
    else if (c.equals("trade"))
        // trade mark sign, U+2122 ISOnum
        s.append((char) 8482);
    else if (c.equals("alefsym"))
        // alef symbol = first transfinite cardinal, U+2135 NEW
        s.append((char) 8501);
    else if (c.equals("larr"))
        // leftwards arrow, U+2190 ISOnum
        s.append((char) 8592);
    else if (c.equals("uarr"))
        // upwards arrow, U+2191 ISOnum
        s.append((char) 8593);
    else if (c.equals("rarr"))
        // rightwards arrow, U+2192 ISOnum
        s.append((char) 8594);
    else if (c.equals("darr"))
        // downwards arrow, U+2193 ISOnum
        s.append((char) 8595);
    else if (c.equals("harr"))
        // left right arrow, U+2194 ISOamsa
        s.append((char) 8596);
    else if (c.equals("crarr"))
        // downwards arrow with corner leftwards = carriage return, U+21B5 NEW
        s.append((char) 8629);
    else if (c.equals("lArr"))
        // leftwards double arrow, U+21D0 ISOtech
        s.append((char) 8656);
    else if (c.equals("uArr"))
        // upwards double arrow, U+21D1 ISOamsa
        s.append((char) 8657);
    else if (c.equals("rArr"))
        // rightwards double arrow, U+21D2 ISOtech
        s.append((char) 8658);
    else if (c.equals("dArr"))
        // downwards double arrow, U+21D3 ISOamsa
        s.append((char) 8659);
    else if (c.equals("hArr"))
        // left right double arrow, U+21D4 ISOamsa
        s.append((char) 8660);
    else if (c.equals("forall"))
        // for all, U+2200 ISOtech
        s.append((char) 8704);
    else if (c.equals("part"))
        // partial differential, U+2202 ISOtech
        s.append((char) 8706);
    else if (c.equals("exist"))
        // there exists, U+2203 ISOtech
        s.append((char) 8707);
    else if (c.equals("empty"))
        // empty set = null set = diameter, U+2205 ISOamso
        s.append((char) 8709);
    else if (c.equals("nabla"))
        // nabla = backward difference, U+2207 ISOtech
        s.append((char) 8711);
    else if (c.equals("isin"))
        // element of, U+2208 ISOtech
        s.append((char) 8712);
    else if (c.equals("notin"))
        // not an element of, U+2209 ISOtech
        s.append((char) 8713);
    else if (c.equals("ni"))
        // contains as member, U+220B ISOtech
        s.append((char) 8715);
    else if (c.equals("prod"))
        // n-ary product = product sign, U+220F ISOamsb
        s.append((char) 8719);
    else if (c.equals("sum"))
        // n-ary sumation, U+2211 ISOamsb
        s.append((char) 8721);
    else if (c.equals("minus"))
        // minus sign, U+2212 ISOtech
        s.append((char) 8722);
    else if (c.equals("lowast"))
        // asterisk operator, U+2217 ISOtech
        s.append((char) 8727);
    else if (c.equals("radic"))
        // square root = radical sign, U+221A ISOtech
        s.append((char) 8730);
    else if (c.equals("prop"))
        // proportional to, U+221D ISOtech
        s.append((char) 8733);
    else if (c.equals("infin"))
        // infinity, U+221E ISOtech -->
        s.append((char) 8734);
    else if (c.equals("ang"))
        // angle, U+2220 ISOamso
        s.append((char) 8736);
    else if (c.equals("and"))
        // logical and = wedge, U+2227 ISOtech
        s.append((char) 8743);
    else if (c.equals("or"))
        // logical or = vee, U+2228 ISOtech
        s.append((char) 8744);
    else if (c.equals("cap"))
        // intersection = cap, U+2229 ISOtech
        s.append((char) 8745);
    else if (c.equals("cup"))
        // union = cup, U+222A ISOtech
        s.append((char) 8746);
    else if (c.equals("int"))
        // integral, U+222B ISOtech
        s.append((char) 8747);
    else if (c.equals("there4"))
        // therefore, U+2234 ISOtech
        s.append((char) 8756);
    else if (c.equals("sim"))
        // tilde operator = varies with = similar t U+223C ISOtech
        s.append((char) 8764);
    else if (c.equals("cong"))
        // approximately equal to, U+2245 ISOtec
        s.append((char) 8773);
    else if (c.equals("asymp"))
        // almost equal to = asymptotic to, U+2248 ISOamsr
        s.append((char) 8776);
    else if (c.equals("ne"))
        // not equal to, U+2260 ISOtech
        s.append((char) 8800);
    else if (c.equals("equiv"))
        // identical to, U+2261 ISOtech
        s.append((char) 8801);
    else if (c.equals("le"))
        // less-than or equal to, U+2264 ISOtech
        s.append((char) 8804);
    else if (c.equals("ge"))
        // greater-than or equal to, U+2265 ISOtech
        s.append((char) 8805);
    else if (c.equals("sub"))
        // subset of, U+2282 ISOtech
        s.append((char) 8834);
    else if (c.equals("sup"))
        // superset of, U+2283 ISOtech
        s.append((char) 8835);
    else if (c.equals("nsub"))
        // not a subset of, U+2284 ISOamsn
        s.append((char) 8836);
    else if (c.equals("sube"))
        // subset of or equal to, U+2286 ISOtech
        s.append((char) 8838);
    else if (c.equals("supe"))
        // superset of or equal to, U+2287 ISOtech
        s.append((char) 8839);
    else if (c.equals("oplus"))
        // circled plus = direct sum, U+2295 ISOamsb
        s.append((char) 8853);
    else if (c.equals("otimes"))
        // circled times = vector product, U+2297 ISOamsb -->
        s.append((char) 8855);
    else if (c.equals("perp"))
        // up tack = orthogonal to = perpendicular, U+22A5 ISOtech
        s.append((char) 8869);
    else if (c.equals("sdot"))
        // dot operator, U+22C5 ISOamsb
        s.append((char) 8901);
    else if (c.equals("lceil"))
        // left ceiling = apl upstile, U+2308 ISOamsc
        s.append((char) 8968);
    else if (c.equals("rceil"))
        // right ceiling, U+2309 ISOamsc
        s.append((char) 8969);
    else if (c.equals("lfloor"))
        // left floor = apl downstile, U+230A ISOamsc
        s.append((char) 8970);
    else if (c.equals("rfloor"))
        // right floor, U+230B ISOamsc
        s.append((char) 8971);
    else if (c.equals("lang"))
        // left-pointing angle bracket = bra, U+2329 ISOtech
        s.append((char) 9001);
    else if (c.equals("rang"))
        // right-pointing angle bracket = ket, U+232A ISOtech
        s.append((char) 9002);
    else if (c.equals("loz"))
        // lozenge, U+25CA ISOpub
        s.append((char) 9674);
    else if (c.equals("spades"))
        // black spade suit, U+2660 ISOpub
        s.append((char) 9824);
    else if (c.equals("clubs"))
        // black club suit = shamrock, U+2663 ISOpub
        s.append((char) 9827);
    else if (c.equals("hearts"))
        // black heart suit = valentine, U+2665 ISOpub
        s.append((char) 9829);
    else if (c.equals("diams"))
        // black diamond suit, U+2666 ISOpub --
        s.append((char) 9830);
    else if (c.equals("ndash"))
        s.append((char) 8211);
    else if (c.equals("mdash"))
        s.append((char) 8212);
    else if (c.equals("ldquo"))
        s.append((char) 8221);
    else if (c.equals("rdquo"))
        s.append((char) 201D);
    else if (c.equals("frac14"))
        s.append((char) 188);
    else if (!mustBeWellFormed) {
        // we guess that this is an accidentally unescaped &
        s.append("&" + c);
    } else {
        throw new FHIRFormatError("unable to parse character reference '" + c + "'' (last text = '" + lastText + "'" + descLoc());
    }
}

Example 45 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project org.hl7.fhir.core by hapifhir.

the class CachingPackageClientTests method testExists.

// private static final String SERVER2 = "http://local.fhir.org:8080/packages";
@Test
public void testExists() throws IOException {
    CachingPackageClient client = new CachingPackageClient(CachingPackageClientTests.SERVER1);
    Assertions.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
    Assertions.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
    Assertions.assertTrue(client.exists("HL7.fhir.r4.core", "4.0.1"));
    Assertions.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
}