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

Example 11 with Observation

use of org.hl7.fhir.r4.model.Observation in project kindling by HL7.

the class PageProcessor method generateToc.

private String generateToc() throws Exception {
    // return breadCrumbManager.makeToc();
    List<String> entries = new ArrayList<String>();
    entries.addAll(toc.keySet());
    Collections.sort(entries, new SectionSorter());
    Set<String> pages = new HashSet<String>();
    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(folders.dstDir, false, true);
    TableModel model = gen.new TableModel("toc", true);
    model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Table of Contents", "Table of Contents", null, 0));
    Deque<TocItem> stack = new ArrayDeque<TocItem>();
    for (String s : entries) {
        TocEntry t = toc.get(s);
        if (!t.isIg() && !s.startsWith("?")) {
            String nd = s;
            while (nd.endsWith(".0")) nd = nd.substring(0, nd.length() - 2);
            int d = Utilities.charCount(nd, '.');
            if (d < 4 && !pages.contains(t.getLink())) {
                String np = getNormativePackageForPage(t.getLink());
                pages.add(t.getLink());
                while (!stack.isEmpty() && stack.getFirst().depth >= d) stack.pop();
                Row row = gen.new Row();
                row.setIcon("icon_page.gif", null);
                String td = t.getText();
                if (!stack.isEmpty()) {
                    if (td.startsWith(stack.getFirst().entry.getText() + " - "))
                        td = td.substring(stack.getFirst().entry.getText().length() + 3);
                    else if (td.startsWith(stack.getFirst().entry.getText()))
                        td = td.substring(stack.getFirst().entry.getText().length());
                }
                Cell cell = gen.new Cell(null, t.getLink(), nd + " " + td, t.getText() + " ", null);
                row.getCells().add(cell);
                if (np != null) {
                    cell.addPiece(gen.new Piece(null, " ", null));
                    cell.addPiece(gen.new Piece("versions.html#std-process", "basic".equals(np) ? "(Normative)" : "(Normative / " + Utilities.capitalize(np) + ")", null).addStyle("color: #008000"));
                    if (np.equals("infrastructure"))
                        row.setIcon("icon_page_n_i.gif", null);
                    else if (np.equals("conformance"))
                        row.setIcon("icon_page_n_c.gif", null);
                    else if (np.equals("patient"))
                        row.setIcon("icon_page_n_p.gif", null);
                    else if (np.equals("observation"))
                        row.setIcon("icon_page_n_o.gif", null);
                    else
                        row.setIcon("icon_page_n.gif", null);
                } else {
                    cell.addPiece(gen.new Piece(null, " ", null));
                    cell.addPiece(gen.new Piece("versions.html#std-process", "(Trial Use)", null).addStyle("color: #b3b3b3"));
                }
                if (stack.isEmpty())
                    model.getRows().add(row);
                else
                    stack.getFirst().row.getSubRows().add(row);
                stack.push(new TocItem(t, row, d));
            }
        }
    }
    return new XhtmlComposer(XhtmlComposer.HTML).compose(gen.generate(model, "", 0, null));
}

Example 12 with Observation

use of org.hl7.fhir.r4.model.Observation in project kindling by HL7.

the class PageProcessor method profileDictionaryLink.

private String profileDictionaryLink(ConstraintStructure profile) {
    String uri = ToolingExtensions.readStringExtension(profile.getResource(), "http://hl7.org/fhir/StructureDefinition/datadictionary");
    if (Utilities.noString(uri))
        return "<!-- no uri -->";
    Dictionary dict = definitions.getDictionaries().get(uri);
    if (dict == null)
        return "<p>This profile specifies that the value of the " + profile.getResource().getSnapshot().getElement().get(0).getPath() + " resource must be a valid Observation as defined in the data dictionary (Unknown? - " + uri + ").</p>";
    else
        return "<p>This profile specifies that the value of the " + profile.getResource().getSnapshot().getElement().get(0).getPath() + " resource must be a valid Observation as defined in the data dictionary <a href=\"" + uri + ".html\">" + dict.getName() + "</a>.</p>";
}

Example 13 with Observation

use of org.hl7.fhir.r4.model.Observation in project kindling by HL7.

the class ADLImporter method execute.

private void execute() throws Exception {
    // load config
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
    // load ADL
    builder = factory.newDocumentBuilder();
    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
    check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
    check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
    check("root", XMLUtil.getNamedChild(adl, "adl_version").getTextContent(), "1.4", "unsupported ADL version");
    String id = XMLUtil.getFirstChild(XMLUtil.getNamedChild(adl, "archetype_id")).getTextContent().split("\\.")[1];
    String baseType = XMLUtil.getNamedChild(XMLUtil.getNamedChild(adl, "definition"), "rm_type_name").getTextContent();
    if (!baseType.equals("OBSERVATION"))
        return;
    // load texts from ontology
    List<Element> set = new ArrayList<Element>();
    Element ontology = XMLUtil.getNamedChild(adl, "ontology");
    Element term_definitions = XMLUtil.getNamedChild(ontology, "term_definitions");
    set.clear();
    XMLUtil.getNamedChildren(term_definitions, "items", set);
    for (Element item : set) {
        processTextItem(item);
    }
    // create structure definition
    StructureDefinition sd = new StructureDefinition();
    sd.setId("netha-" + id);
    sd.setUrl("http://hl7.org/fhir/StructureDefinition/" + sd.getId());
    sd.setKind(StructureDefinitionKind.LOGICAL);
    populateMetadata(set, sd);
    // load data and protocol
    Element definition = XMLUtil.getNamedChild(adl, "definition");
    NodeTreeEntry root = new NodeTreeEntry();
    root.typeName = XMLUtil.getNamedChild(definition, "rm_type_name").getTextContent();
    root.atCode = XMLUtil.getNamedChild(definition, "node_id").getTextContent();
    root.name = generateToken(root.atCode, true);
    sd.setName(root.name);
    root.cardinality = readCardinality("root", XMLUtil.getNamedChild(definition, "occurrences"));
    set.clear();
    XMLUtil.getNamedChildren(definition, "attributes", set);
    for (Element item : set) {
        // we're actually skipping this level - we don't care about data protocol etc.
        // XMLUtil.getNamedChild(XMLUtil.getNamedChild(item, "children"), "attributes");
        Element attributes = item;
        loadChildren(root.atCode, root, attributes);
    }
    dumpChildren("", root);
    genElements(sd, root.name, root);
    // save
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
    System.out.println("done. saved as " + dest);
}

Example 14 with Observation

use of org.hl7.fhir.r4.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7EncounterFHIRConversionTest method testEncounterReferencesObservationAndDiagnosis.

/**
 * Testing Encounter correctly references Observation AND Diagnosis when both are present.
 */
@Test
void testEncounterReferencesObservationAndDiagnosis() throws IOException {
    String hl7message = "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A01|||2.6|\n" + "PID|||1234^^^^MR||DOE^JANE^|||F|||||||||||||||||||||\n" + "PV1|1|O|Location||||||||||||||||261938_6_201306171546|||||||||||||||||||||||||20130617134644|||||||||\n" + "OBX|1|SN|24467-3^CD3+CD4+ (T4 helper) cells [#/volume] in Blood^LN||=^440|{Cells}/uL^cells per microliter^UCUM|649-1346 cells/mcL|L|||F\r" + "DG1|1|ICD10|^Ovarian Cancer|||||||||||||||||||||\r";
    String json = ftv.convert(hl7message, OPTIONS);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
    assertThat(encounterResource).hasSize(1);
    Encounter enc = (Encounter) encounterResource.get(0);
    List<Reference> reasonRefs = enc.getReasonReference();
    assertEquals(2, reasonRefs.size());
    // Guess at the order of the references
    Reference refObservation = reasonRefs.get(0);
    Reference refCondition = reasonRefs.get(1);
    // If guessed wrong, reverse them
    if (!refObservation.getReference().contains("Observation")) {
        refObservation = reasonRefs.get(1);
        refCondition = reasonRefs.get(0);
    }
    assertTrue(refObservation.getReference().contains("Observation"));
    assertTrue(refCondition.getReference().contains("Condition"));
}

Example 15 with Observation

use of org.hl7.fhir.r4.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_content_test.

@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_content_test(String segment) {
    String documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // Next three lines create an attachment
    "OBX|1|TX|||ECHOCARDIOGRAPHIC REPORT||||||F|||202101010000|||\n" + "OBX|2|TX|||NORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH||||||F|||202101010000|||\n" + "OBX|3|TX|||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%||||||F|||202101010000|||\n";
    DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    DocumentReference.DocumentReferenceContentComponent content = report.getContentFirstRep();
    // Future TXA.3, currently always defaults to text/plain
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // TXA.7 date
    assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
    assertThat(content.getAttachment().hasData()).isTrue();
    String decodedData = new String(Base64.getDecoder().decode(content.getAttachment().getDataElement().getValueAsString()));
    assertThat(decodedData).isEqualTo("ECHOCARDIOGRAPHIC REPORT\nNORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH\nHYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%");
    // TODO: Determine if we need to look at anything other than OBX.2 when it is TX
    // Leave this test in place as a reminder
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // TODO: find better code for this test which is to see that OBX.2 is the fallback.
    "OBX|1|SN|||||||||F";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    content = report.getContentFirstRep();
    // Because the OBX is not TX, the content is put in an Observation
    // FHIR requires a Content element, so only a minimal one is created.
    // Future OBX.2 is the backup for content type, but currently always defaults to text/plain
    assertThat(content.getAttachment().hasContentType()).isTrue();
    // Currently always defaults to text/plain
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // TXA.7 date
    assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
    assertThat(content.getAttachment().hasData()).isFalse();
    // Test that content is created even if TXA.7 is empty
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + // Ensure that empty TXA.7 still works
    "TXA|1||||||||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + "OBX|1|SN|||||||||F";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    content = report.getContentFirstRep();
    // Because the OBX is not TX, the content is put in an Observation
    // FHIR requires a Content element, so only a minimal one is created.
    // Currently always defaults to text/plain
    assertThat(content.getAttachment().hasContentType()).isTrue();
    // Currently always defaults to text/plain, even if not data for content
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // No TXA.7 date
    assertThat(content.getAttachment().hasCreationElement()).isFalse();
    assertThat(content.getAttachment().hasData()).isFalse();
}