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

Example 6 with UrlType

use of org.hl7.fhir.r4.model.UrlType in project redmatch by aehrc.

the class FhirExporter method getValue.

/**
 * Resolves a value.
 *
 * @param value The value specified in the transformation rules.
 * @param fhirType The type of the FHIR attribute where this value will be set.
 * @param vertex A vertex with patient data.
 * @param recordId The id of this record. Used to create the references to FHIR ids.
 * @param enumFactory If the type is an enumeration, this is the factory to create an instance.
 * @param fhirPackage The target FHIR package.
 * @return The value or null if the value cannot be determined. This can also be a list.
 */
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
    // If this is a field-based value then make sure that there is a value and if not return null
    if (value instanceof FieldBasedValue) {
        FieldBasedValue fbv = (FieldBasedValue) value;
        // Account for field ids of the form xx___y
        String fieldId = fbv.getFieldId();
        String shortFieldId = null;
        String regex = "(?<fieldId>.*)___\\d+$";
        Pattern pattern = Pattern.compile(regex);
        Matcher matcher = pattern.matcher(fieldId);
        if (matcher.find()) {
            shortFieldId = matcher.group("fieldId");
            log.debug("Transformed fieldId into '" + fieldId + "'");
        }
        boolean hasValue = false;
        JsonElement jsonElement = vertex.get(fieldId);
        if (jsonElement != null) {
            String rawValue = jsonElement.getAsString();
            if (!rawValue.isEmpty()) {
                hasValue = true;
            }
        }
        if (!hasValue && shortFieldId != null) {
            jsonElement = vertex.get(shortFieldId);
            if (jsonElement != null) {
                String rawValue = jsonElement.getAsString();
                if (!rawValue.isEmpty()) {
                    hasValue = true;
                }
            }
        }
        if (!hasValue) {
            return null;
        }
    }
    if (value instanceof BooleanValue) {
        return new BooleanType(((BooleanValue) value).getValue());
    } else if (value instanceof CodeLiteralValue) {
        String code = ((CodeLiteralValue) value).getCode();
        return getCode(code, enumFactory);
    } else if (value instanceof ConceptLiteralValue) {
        ConceptLiteralValue clv = (ConceptLiteralValue) value;
        String system = clv.getSystem();
        String code = clv.getCode();
        String display = clv.getDisplay() != null ? clv.getDisplay() : "";
        return getConcept(system, code, display, fhirType);
    } else if (value instanceof DoubleValue) {
        return new DecimalType(((DoubleValue) value).getValue());
    } else if (value instanceof IntegerValue) {
        return new IntegerType(((IntegerValue) value).getValue());
    } else if (value instanceof ReferenceValue) {
        ReferenceValue rv = (ReferenceValue) value;
        Reference ref = new Reference();
        String resourceType = rv.getResourceType();
        String resourceId = rv.getResourceId();
        boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
        CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
        if (codeInfo.isProfile()) {
            resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
        }
        if (unique) {
            // This is a reference to a unique resource - no need to append row id
            if (fhirResourceMap.containsKey(resourceId)) {
                ref.setReference("/" + resourceType + "/" + resourceId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId);
            }
        } else {
            if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
                ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
            }
        }
        return ref;
    } else if (value instanceof StringValue) {
        if (fhirType.equals(StringType.class)) {
            return new StringType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(MarkdownType.class)) {
            return new MarkdownType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(IdType.class)) {
            return new IdType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UriType.class)) {
            return new UriType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(OidType.class)) {
            return new OidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UuidType.class)) {
            return new UuidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(CanonicalType.class)) {
            return new CanonicalType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UrlType.class)) {
            return new UrlType(((StringValue) value).getStringValue());
        } else {
            throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
        }
    } else if (value instanceof CodeSelectedValue) {
        CodeSelectedValue csv = (CodeSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        return getTarget(m).getCodeElement();
    } else if (value instanceof ConceptSelectedValue) {
        ConceptSelectedValue csv = (ConceptSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        if (fhirType.isAssignableFrom(Coding.class)) {
            return getTarget(m);
        } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
            return new CodeableConcept().addCoding(getTarget(m));
        } else {
            throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
        }
    } else if (value instanceof ConceptValue) {
        // Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
        ConceptValue cv = (ConceptValue) value;
        String fieldId = cv.getFieldId();
        Mapping m = getMapping(fieldId);
        if (m != null) {
            if (fhirType.isAssignableFrom(Coding.class)) {
                return getTarget(m);
            } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                return new CodeableConcept().addCoding(getTarget(m));
            } else {
                throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
            }
        } else {
            au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
            Coding c = field.getCoding(vertex);
            if (c != null) {
                if (fhirType.isAssignableFrom(Coding.class)) {
                    return c;
                } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                    return new CodeableConcept().addCoding(c);
                } else {
                    throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
                }
            }
        }
        throw new TransformationException("Could not get concept for field " + fieldId + ".");
    } else if (value instanceof FieldValue) {
        FieldValue fv = (FieldValue) value;
        String fieldId = fv.getFieldId();
        FieldValue.DatePrecision pr = fv.getDatePrecision();
        au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
        return field.getValue(vertex, fhirType, pr);
    } else {
        throw new TransformationException("Unable to get VALUE for " + value);
    }
}

Example 7 with UrlType

use of org.hl7.fhir.r4.model.UrlType in project pathling by aehrc.

the class ImportExecutor method readStringsFromUrl.

@Nonnull
private Dataset<String> readStringsFromUrl(@Nonnull final ParametersParameterComponent urlParam) {
    final String url = ((UrlType) urlParam.getValue()).getValueAsString();
    final String decodedUrl = URLDecoder.decode(url, StandardCharsets.UTF_8);
    final String convertedUrl = PersistenceScheme.convertS3ToS3aUrl(decodedUrl);
    final Dataset<String> jsonStrings;
    try {
        // Check that the user is authorized to execute the operation.
        accessRules.ifPresent(ar -> ar.checkCanImportFrom(convertedUrl));
        final FilterFunction<String> nonBlanks = s -> !s.isBlank();
        jsonStrings = spark.read().textFile(convertedUrl).filter(nonBlanks);
    } catch (final SecurityError e) {
        throw new InvalidUserInputError("Not allowed to import from URL: " + convertedUrl, e);
    } catch (final Exception e) {
        throw new InvalidUserInputError("Error reading from URL: " + convertedUrl, e);
    }
    return jsonStrings;
}

Example 8 with UrlType

use of org.hl7.fhir.r4.model.UrlType in project pathling by aehrc.

the class ImportTest method buildImportParameters.

@SuppressWarnings("SameParameterValue")
@Nonnull
Parameters buildImportParameters(@Nonnull final URL jsonURL, @Nonnull final ResourceType resourceType) {
    final Parameters parameters = new Parameters();
    final ParametersParameterComponent sourceParam = parameters.addParameter().setName("source");
    sourceParam.addPart().setName("resourceType").setValue(new CodeType(resourceType.toCode()));
    sourceParam.addPart().setName("url").setValue(new UrlType(jsonURL.toExternalForm()));
    return parameters;
}

Example 9 with UrlType

use of org.hl7.fhir.r4.model.UrlType in project pathling by aehrc.

the class ExtractTest method extract.

@Test
void extract() throws URISyntaxException, MalformedURLException {
    TestHelpers.mockResource(database, spark, ResourceType.DIAGNOSTICREPORT);
    final String uri = "http://localhost:" + port + "/fhir/DiagnosticReport/$extract?column=id";
    final ResponseEntity<String> response = restTemplate.exchange(uri, HttpMethod.GET, RequestEntity.get(new URI(uri)).build(), String.class);
    assertTrue(response.getStatusCode().is2xxSuccessful());
    final Parameters result = (Parameters) jsonParser.parseResource(response.getBody());
    final URL url = new URL(((UrlType) result.getParameter("url")).getValueAsString());
    final String actual;
    try {
        final InputStream expectedStream = url.openStream();
        final StringWriter writer = new StringWriter();
        IOUtils.copy(expectedStream, writer, UTF_8);
        actual = writer.toString();
    } catch (final IOException e) {
        throw new RuntimeException("Problem retrieving extract result", e);
    }
    final String expected = getResourceAsString("responses/ExtractTest/extract.csv");
    assertEquals(expected, actual);
}

Example 10 with UrlType

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

the class OldSpreadsheetParser method processValue.

private DataType processValue(Sheet sheet, int row, String column, String source, ElementDefn e) throws Exception {
    if (Utilities.noString(source))
        return null;
    if (e.getTypes().size() != 1)
        throw new Exception("Unable to process " + column + " unless a single type is specified (types = " + e.typeCode() + ") " + getLocation(row) + ", column = " + column);
    String type = e.typeCode();
    if (definitions != null) {
        if (definitions.getConstraints().containsKey(type))
            type = definitions.getConstraints().get(type).getBaseType();
    } else {
        StructureDefinition sd = context.fetchTypeDefinition(type);
        if (// not loaded yet?
        sd != null)
            type = sd.getType();
        if (type.equals("SimpleQuantity"))
            type = "Quantity";
    }
    if (source.startsWith("{")) {
        JsonParser json = new JsonParser();
        return json.parseType(source, type);
    } else if (source.startsWith("<")) {
        XmlParser xml = new XmlParser();
        return xml.parseType(source, type);
    } else {
        if (source.startsWith("\"") && source.endsWith("\""))
            source = source.substring(1, source.length() - 1);
        if (type.equals("string"))
            return new StringType(source);
        if (type.equals("boolean"))
            return new BooleanType(Boolean.valueOf(source));
        if (type.equals("integer"))
            return new IntegerType(Integer.valueOf(source));
        if (type.equals("integer64"))
            return new Integer64Type(Long.valueOf(source));
        if (type.equals("unsignedInt"))
            return new UnsignedIntType(Integer.valueOf(source));
        if (type.equals("positiveInt"))
            return new PositiveIntType(Integer.valueOf(source));
        if (type.equals("decimal"))
            return new DecimalType(new BigDecimal(source));
        if (type.equals("base64Binary"))
            return new Base64BinaryType(Base64.decode(source.toCharArray()));
        if (type.equals("instant"))
            return new InstantType(source);
        if (type.equals("uri"))
            return new UriType(source);
        if (type.equals("url"))
            return new UrlType(source);
        if (type.equals("canonical"))
            return new CanonicalType(source);
        if (type.equals("date"))
            return new DateType(source);
        if (type.equals("dateTime"))
            return new DateTimeType(source);
        if (type.equals("time"))
            return new TimeType(source);
        if (type.equals("code"))
            return new CodeType(source);
        if (type.equals("oid"))
            return new OidType(source);
        if (type.equals("uuid"))
            return new UuidType(source);
        if (type.equals("id"))
            return new IdType(source);
        if (type.startsWith("Reference(")) {
            Reference r = new Reference();
            r.setReference(source);
            return r;
        }
        if (type.equals("Period")) {
            if (source.contains("->")) {
                String[] parts = source.split("\\-\\>");
                Period p = new Period();
                p.setStartElement(new DateTimeType(parts[0].trim()));
                if (parts.length > 1)
                    p.setEndElement(new DateTimeType(parts[1].trim()));
                return p;
            } else
                throw new Exception("format not understood parsing " + source + " into a period");
        }
        if (type.equals("CodeableConcept")) {
            CodeableConcept cc = new CodeableConcept();
            if (source.contains(":")) {
                String[] parts = source.split("\\:");
                String system = "";
                if (parts[0].equalsIgnoreCase("SCT"))
                    system = "http://snomed.info/sct";
                else if (parts[0].equalsIgnoreCase("LOINC"))
                    system = "http://loinc.org";
                else if (parts[0].equalsIgnoreCase("AMTv2"))
                    system = "http://nehta.gov.au/amtv2";
                else
                    system = "http://hl7.org/fhir/" + parts[0];
                String code = parts[1];
                String display = parts.length > 2 ? parts[2] : null;
                cc.addCoding().setSystem(system).setCode(code).setDisplay(display);
            } else
                throw new Exception("format not understood parsing " + source + " into a codeable concept");
            return cc;
        }
        if (type.equals("Identifier")) {
            Identifier id = new Identifier();
            id.setSystem("urn:ietf:rfc:3986");
            id.setValue(source);
            return id;
        }
        if (type.equals("Quantity")) {
            int s = 0;
            if (source.startsWith("<=") || source.startsWith("=>"))
                s = 2;
            else if (source.startsWith("<") || source.startsWith(">"))
                s = 1;
            int i = s;
            while (i < source.length() && Character.isDigit(source.charAt(i))) i++;
            Quantity q = new Quantity();
            if (s > 0)
                q.setComparator(QuantityComparator.fromCode(source.substring(0, s)));
            if (i > s)
                q.setValue(new BigDecimal(source.substring(s, i)));
            if (i < source.length())
                q.setUnit(source.substring(i).trim());
            return q;
        }
        throw new Exception("Unable to process primitive value '" + source + "' provided for " + column + " - unhandled type " + type + " @ " + getLocation(row));
    }
}