Examples with Base org.hl7.fhir.dstu2.model.Base used on opensource projects

Example 61 with Base

use of org.hl7.fhir.dstu2.model.Base in project drug-formulary-ri by HL7-DaVinci.

the class ExampleServerDstu3IT method testCreateAndRead.

@Test
public void testCreateAndRead() {
    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
    String methodName = "testCreateResourceConditional";
    Patient pt = new Patient();
    pt.addName().setFamily(methodName);
    IIdType id = ourClient.create().resource(pt).execute().getId();
    Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
    assertEquals(methodName, pt2.getName().get(0).getFamily());
}

Example 62 with Base

use of org.hl7.fhir.dstu2.model.Base in project org.hl7.fhir.core by hapifhir.

the class ICD11Generator method execute.

private void execute(String base, String dest) throws IOException {
    CodeSystem cs = makeMMSCodeSystem();
    JsonObject version = fetchJson(Utilities.pathURL(base, "/icd/release/11/mms"));
    String[] p = version.get("latestRelease").getAsString().split("\\/");
    cs.setVersion(p[6]);
    JsonObject root = fetchJson(url(base, version.get("latestRelease").getAsString()));
    cs.setDateElement(new DateTimeType(root.get("releaseDate").getAsString()));
    for (JsonElement child : root.getAsJsonArray("child")) {
        processMMSEntity(cs, base, child.getAsString(), cs.addConcept(), dest);
        System.out.println();
    }
    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
    makeFullVs(dest, cs);
    cs = makeEntityCodeSystem();
    root = fetchJson(Utilities.pathURL(base, "/icd/entity"));
    cs.setVersion(root.get("releaseId").getAsString());
    cs.setDateElement(new DateTimeType(root.get("releaseDate").getAsString()));
    cs.setTitle(readString(root, "title"));
    Set<String> ids = new HashSet<>();
    for (JsonElement child : root.getAsJsonArray("child")) {
        processEntity(cs, ids, base, tail(child.getAsString()), dest);
        System.out.println();
    }
    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-foundation.xml")), cs);
    makeFullVs2(dest, cs);
    System.out.println("finished");
}

Example 63 with Base

use of org.hl7.fhir.dstu2.model.Base in project org.hl7.fhir.core by hapifhir.

the class ICD11Generator method processMMSEntity.

private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
    System.out.print(".");
    JsonObject entity = fetchJson(url(base, ref));
    cc.setId(tail(ref));
    if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
        cc.setCode(entity.get("code").getAsString());
    } else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
        cc.setCode(entity.get("blockId").getAsString());
    } else {
        cc.setCode(cc.getId());
        cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
    }
    if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
        cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
    }
    cc.setDisplay(readString(entity, "title"));
    StringBuilder defn = new StringBuilder();
    String d = readString(entity, "definition");
    if (d != null) {
        defn.append(d);
    }
    if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
        defn.append(cc.getDisplay());
    }
    if (entity.has("inclusion")) {
        defn.append(". Includes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("inclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            defn.append(readString((JsonObject) child, "label"));
        }
    }
    if (entity.has("exclusion")) {
        defn.append(". Excludes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("exclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            JsonObject co = (JsonObject) child;
            String v = readString(co, "label");
            if (v != null) {
                defn.append(v);
                if (co.has("linearizationReference")) {
                    cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
                }
            }
        }
    }
    cc.setDefinition(defn.toString());
    addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
    addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
    addProperty(readString(entity, "codingNote"), cc, "codingNote");
    if (entity.has("indexTerm")) {
        // }
        for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
            processIndexTerm(cc, (JsonObject) child);
        }
    }
    if (entity.has("postcoordinationScale")) {
        for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
            JsonObject o = (JsonObject) child;
            String name = tail(o.get("axisName").getAsString());
            ConceptPropertyComponent prop = cc.addProperty();
            prop.setCode("postcoordinationScale");
            prop.setValue(new CodeType(name));
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
            if (o.has("scaleEntity")) {
                ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
            }
        }
    }
    if (entity.has("child")) {
        for (JsonElement child : entity.getAsJsonArray("child")) {
            processMMSEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
        }
    }
}

Example 64 with Base

use of org.hl7.fhir.dstu2.model.Base in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints) throws FHIRException, UnsupportedEncodingException, IOException {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        x.addText("Extensions: Todo");
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType)
        x.addText(((DateTimeType) e).toHumanDisplay());
    else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.dstu2.model.DateType)
        x.addText(((org.hl7.fhir.dstu2.model.DateType) e).toHumanDisplay());
    else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType)
        x.addText(((BooleanType) e).getValue().toString());
    else if (e instanceof CodeableConcept) {
        renderCodeableConcept((CodeableConcept) e, x, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding((Coding) e, x, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation((Annotation) e, x);
    } else if (e instanceof Identifier) {
        renderIdentifier((Identifier) e, x);
    } else if (e instanceof org.hl7.fhir.dstu2.model.IntegerType) {
        x.addText(Integer.toString(((org.hl7.fhir.dstu2.model.IntegerType) e).getValue()));
    } else if (e instanceof org.hl7.fhir.dstu2.model.DecimalType) {
        x.addText(((org.hl7.fhir.dstu2.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName((HumanName) e, x);
    } else if (e instanceof SampledData) {
        renderSampledData((SampledData) e, x);
    } else if (e instanceof Address) {
        renderAddress((Address) e, x);
    } else if (e instanceof ContactPoint) {
        renderContactPoint((ContactPoint) e, x);
    } else if (e instanceof UriType) {
        renderUri((UriType) e, x);
    } else if (e instanceof Timing) {
        renderTiming((Timing) e, x);
    } else if (e instanceof Range) {
        renderRange((Range) e, x);
    } else if (e instanceof Quantity) {
        renderQuantity((Quantity) e, x, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(((Ratio) e).getNumerator(), x, showCodeDetails);
        x.addText("/");
        renderQuantity(((Ratio) e).getDenominator(), x, showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        x.addText(!p.hasStart() ? "??" : p.getStartElement().toHumanDisplay());
        x.addText(" --> ");
        x.addText(!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        XhtmlNode c = x;
        ResourceWithReference tr = null;
        if (r.hasReferenceElement()) {
            tr = resolveReference(res, r.getReference());
            if (!r.getReference().startsWith("#")) {
                if (tr != null && tr.getReference() != null)
                    c = x.addTag("a").attribute("href", tr.getReference());
                else
                    c = x.addTag("a").attribute("href", r.getReference());
            }
        }
        // what to display: if text is provided, then that. if the reference was resolved, then show the generated narrative
        if (r.hasDisplayElement()) {
            c.addText(r.getDisplay());
            if (tr != null) {
                c.addText(". Generated Summary: ");
                generateResourceSummary(c, tr.getResource(), true, r.getReference().startsWith("#"));
            }
        } else if (tr != null) {
            generateResourceSummary(c, tr.getResource(), r.getReference().startsWith("#"), r.getReference().startsWith("#"));
        } else {
            c.addText(r.getReference());
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof ElementDefinition) {
        x.addText("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta))
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled yet");
}

Example 65 with Base

use of org.hl7.fhir.dstu2.model.Base in project org.hl7.fhir.core by hapifhir.

the class BatchLoader method main.

public static void main(String[] args) throws IOException, Exception {
    if (args.length < 4) {
        System.out.println("Batch uploader takes 4 parameters in order: server base url, file/folder to upload, xml/json, and batch size");
    } else {
        String server = args[0];
        String file = args[1];
        // args[2].equals("json") ? new JsonParser() : new XmlParser();
        IParser p = new JsonParser();
        int size = Integer.parseInt(args[3]);
        size = 500;
        if (file.endsWith(".xml")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".json")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".zip")) {
            LoadZipFile(server, file, p, size, 0, -1);
        } else if (new File(file).isDirectory()) {
            LoadDirectory(server, file, p, size);
        } else
            throw new FHIRException("Unknown file type " + file);
    }
}