use of org.hl7.elm.r1.Time in project kindling by HL7.
the class OldSpreadsheetParser method readSearchParams.
/* for profiles that have a "search" tab not tied to a structure */
private void readSearchParams(Profile pack, Sheet sheet, String prefix) throws Exception {
for (int row = 0; row < sheet.rows.size(); row++) {
if (!sheet.hasColumn(row, "Name"))
throw new Exception("Search Param has no name " + getLocation(row));
String n = sheet.getColumn(row, "Name");
if (!n.startsWith("!")) {
SearchParameter sp = new SearchParameter();
if (!sheet.hasColumn(row, "Type"))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no type " + getLocation(row));
if (n.endsWith("-before") || n.endsWith("-after"))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " includes relative time " + getLocation(row));
// if (!n.toLowerCase().equals(n))
// throw new Exception("Search Param "+pack.getTitle()+"/"+n+" must be all lowercase "+ getLocation(row));
sp.setVersion(version.toCode());
sp.setName(n);
sp.setCode(n);
if (pack.getProfiles().size() > 0 && pack.getProfiles().get(0).getResource() != null) {
sp.setStatus(pack.getProfiles().get(0).getResource().getStatus());
sp.setExperimental(pack.getProfiles().get(0).getResource().getExperimental());
} else {
// we just guess
sp.setStatus(PublicationStatus.DRAFT);
sp.setExperimental(true);
}
String d = sheet.getColumn(row, "Description");
sp.setType(SearchParamType.fromCode(sheet.getColumn(row, "Type")));
List<String> pn = new ArrayList<String>();
String path = sheet.getColumn(row, "Path");
if (Utilities.noString(path))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no path");
if (!path.contains(".") && !path.startsWith("#"))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path: " + path);
ResourceDefn root2 = null;
if (!path.startsWith("#")) {
path = path.substring(0, path.indexOf('.'));
if (!pkp.isResource(path))
throw new Exception("Ilegal Search Parameter path " + sheet.getColumn(row, "Path"));
sp.addBase(path);
sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
if (definitions != null) {
// igtodo (and below)
root2 = definitions.getResourceByName(path);
if (root2 == null)
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path (resource not found)");
if (!pkp.isResource(root2.getName()))
throw new Exception("Ilegal Search Parameter path " + sheet.getColumn(row, "Path"));
sp.getBase().clear();
sp.addBase(root2.getName());
sp.setId(pack.getId() + "-" + (root2 == null ? "all" : root2.getName()) + "-" + sp.getName());
}
}
if (!Utilities.noString(sheet.getColumn(row, "Target Types")))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has manually specified targets (not allowed)");
if (root2 != null && root2.getSearchParams().containsKey(n))
throw new Exception("Search Param " + root2.getName() + "/" + n + ": duplicate name " + getLocation(row));
if (sp.getType() == SearchParamType.COMPOSITE) {
throw new Exception("not supported");
} else {
String[] pl = sheet.getColumn(row, "Path").split("\\|");
String xp = sheet.getColumn(row, "XPath");
for (String pi : pl) {
String p = pi.trim();
ElementDefn e = null;
if (Utilities.noString(p))
throw new Exception("Search Param " + root2.getName() + "/" + n + ": empty path " + getLocation(row));
if (p.startsWith("#")) {
// root less extension search parameter
StructureDefinition ex = pack.getExtension(prefix + p.substring(1));
if (ex == null)
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to unknown extension '" + p + "' " + getLocation(row));
e = definitions.getElementDefn("Extension");
if (ex.getContext().size() != 1 || ex.getContext().get(0).getType() != ExtensionContextType.ELEMENT)
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to an extension with multiple contexts, not not an element context - not supported '" + p + "' " + getLocation(row));
path = ex.getContext().get(0).getExpression();
if (Utilities.noString(path))
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has no path");
if (path.contains("."))
path = path.substring(0, path.indexOf('.'));
sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
root2 = definitions.getResourceByName(path);
if (root2 == null)
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " has an invalid path (resource not found)");
if (root2 != null && root2.getSearchParams().containsKey(n))
throw new Exception("Search Param " + root2.getName() + "/" + n + ": duplicate name " + getLocation(row));
sp.setId(pack.getId() + "-" + path + "-" + sp.getName());
pn.add(ex.getContext().get(0).getExpression() + ".extension{" + ex.getUrl() + "}");
} else if (p.contains(".extension{")) {
String url = extractExtensionUrl(p);
// not created yet?
StructureDefinition ex = context.fetchResource(StructureDefinition.class, url);
if (ex == null)
ex = context.getExtensionStructure(null, url);
if (ex == null)
throw new Exception("Search Param " + pack.getTitle() + "/" + n + " refers to unknown extension '" + url + "' " + getLocation(row));
if (Utilities.noString(d))
d = ex.getDescription();
if (definitions != null)
e = definitions.getElementDefn("Extension");
pn.add(p);
} else if (!p.startsWith("!") && !p.startsWith("Extension{") && root2 != null) {
e = root2.getRoot().getElementForPath(p, definitions, "search param", true, true);
}
if (e == null && Utilities.noString(d))
throw new Exception("unable to resolve sarch param " + p);
if (e == null)
sp.setExpression(p);
if (Utilities.noString(d) && e != null)
d = e.getShortDefn();
if (d == null)
throw new Exception("Search Param " + root2.getName() + "/" + n + " has no description " + getLocation(row));
if (e != null)
pn.add(p);
if (sp.getType() == SearchParamType.REFERENCE) {
// no check?
} else if (e != null && e.typeCode().startsWith("Reference("))
throw new Exception("Search Param " + root2.getName() + "/" + n + " wrong type. The search type is " + sp.getType().toCode() + ", but the element type is " + e.typeCode());
sp.setDescription(d);
}
sp.setXpath(Utilities.noString(xp) ? new XPathQueryGenerator(definitions, log, null).generateXpath(pn, null) : xp);
sp.setXpathUsage(readSearchXPathUsage(sheet.getColumn(row, "Path Usage"), row));
}
sp.setUrl("http://hl7.org/fhir/SearchParameter/" + sp.getId());
if (definitions != null)
definitions.addNs(sp.getUrl(), "Search Parameter " + sp.getName(), pack.getId() + ".html#search");
if (context.getSearchParameter(sp.getUrl()) != null)
throw new Exception("Duplicated Search Parameter " + sp.getUrl());
context.cacheResource(sp);
pack.getSearchParameters().add(sp);
}
}
}
use of org.hl7.elm.r1.Time in project hl7v2-fhir-converter by LinuxForHealth.
the class HL7ConditionFHIRConversionTest method validateProblemWithOnsetDateTimeWithNoOnsetString.
// Tests that onset[x] is set to PRB.16 if it is present AND
// Tests that onset[x] is set to PRB.16 if it is present and PRB.17 is present.
@ParameterizedTest
@ValueSource(strings = { // PRB.17 purposely empty
"PRB|AD|20170110074000|K80.00^Cholelithiasis^I10|53956||||||||||||20180310074000||\r", // PRB.17 present
"PRB|AD|20170110074000|K80.00^Cholelithiasis^I10|53956||||||||||||20180310074000|textual representation of the time when the problem began|\r" })
void validateProblemWithOnsetDateTimeWithNoOnsetString(String segmentPRB) {
String hl7message = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\r" + "PID||||||||||||||||||||||||||||||\r" + segmentPRB;
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Find the condition from the FHIR bundle.
List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
// Get the condition Resource
Condition condition = (Condition) conditionResource.get(0);
// Verify onset is set correctly to PRB.16
// PRB.16
assertThat(condition.getOnset().toString()).containsPattern("2018-03-10T07:40:00");
}
use of org.hl7.elm.r1.Time in project hl7v2-fhir-converter by LinuxForHealth.
the class HL7ConditionFHIRConversionTest method validateDiagnosis.
// --------------------- DIAGNOSIS UNIT TESTS (DG1) ---------------------
// Tests the DG1 segment (diagnosis) with all supported message types.
// This tests all the fields in the happy path.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@ParameterizedTest
@ValueSource(strings = { "MSH|^~\\&|||||||ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r", // "MSH|^~\\&|||||||ADT^A04|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r",
"MSH|^~\\&|||||||ADT^A08|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r" // "MSH|^~\\&|||||||ADT^A28^ADT^A28|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r",
// "MSH|^~\\&|||||||ADT^A31|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r",
// "MSH|^~\\&|||||||ORM^O01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r"
// PPR_PC1, PPR_PC2, and PPR_PC3 create Conditions but they don't have a DG1 segment so they are tested in a different testcase.
})
void validateDiagnosis(String msh) {
String hl7message = msh + "PID||||||||||||||||||||||||||||||\r" + "PV1||I|||||||||||||||||1400|||||||||||||||||||||||||\r" + // DG1.20 to Identifier
"DG1|1||C56.9^Ovarian Cancer^I10||20210322154449|A|||||||||1|123^DOE^JOHN^A^|||20210322154326|V45|||||\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify no extraneous resources
// Expect encounter, patient, practitioner, condition
assertThat(e).hasSize(4);
// --- CONDITION TESTS ---
// Find the condition from the FHIR bundle.
List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
Condition condition = (Condition) conditionResource.get(0);
// Verify we have 3 identifiers
// NOTE: The other identifiers, not related to condition, are tested deeply in the
// identifier suite of unit tests.
assertThat(condition.getIdentifier()).hasSize(3);
// First identifier is the Visit Number, and is a codeable concept
DatatypeUtils.checkCommonCodeableConceptAssertions(condition.getIdentifier().get(0).getType(), "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// Second identifier
assertThat(condition.getIdentifier().get(1).getSystem()).isEqualTo("urn:id:extID");
assertThat(condition.getIdentifier().get(1).getValue()).isEqualTo("C56.9-I10");
// The 3rd identifier value should be from DG1.20
// DG1.20
assertThat(condition.getIdentifier().get(2).getValue()).isEqualTo("V45");
// Verify asserter reference to Practitioner exists
assertThat(condition.getAsserter().getReference().substring(0, 13)).isEqualTo("Practitioner/");
// Verify recorded date is set correctly.
// DG1.19
assertThat(condition.getRecordedDateElement().toString()).containsPattern("2021-03-22T15:43:26");
// Verify onset date time is set correctly.
// DG1.5
assertThat(condition.getOnset().toString()).containsPattern("2021-03-22T15:44:49");
// Verify code text and coding are set correctly.
DatatypeUtils.checkCommonCodeableConceptAssertions(condition.getCode(), "C56.9", "Ovarian Cancer", "http://hl7.org/fhir/sid/icd-10-cm", // DG1.3
"Ovarian Cancer");
// Verify encounter reference exists
assertThat(condition.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
// Verify subject reference to Patient exists
assertThat(condition.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
// Verify category text and coding are set correctly.
assertThat(condition.getCategory()).hasSize(1);
DatatypeUtils.checkCommonCodeableConceptAssertions(condition.getCategoryFirstRep(), "encounter-diagnosis", "Encounter Diagnosis", "http://terminology.hl7.org/CodeSystem/condition-category", // DG1.3
"Encounter Diagnosis");
// --- ENCOUNTER TESTS ---
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
Encounter encounter = (Encounter) encounterResource.get(0);
// Encounter should have a reference to the conditions (only 1 in this unit test)
assertThat(encounter.getReasonReference()).hasSize(1);
assertThat(encounter.getReasonReference().get(0).getReference().substring(0, 10)).isEqualTo("Condition/");
// Verify encounter diagnosis condition, use, and rank are set correctly
assertThat(encounter.getDiagnosis()).hasSize(1);
assertThat(encounter.getDiagnosisFirstRep().getCondition().getReference().substring(0, 10)).isEqualTo("Condition/");
DatatypeUtils.checkCommonCodeableConceptAssertions(encounter.getDiagnosisFirstRep().getUse(), "AD", "Admission diagnosis", "http://terminology.hl7.org/CodeSystem/diagnosis-role", // DG1.6
null);
// DG1.15
assertThat(encounter.getDiagnosisFirstRep().getRank()).isEqualTo(1);
// --- PRACTIONER TESTS ---
// Find the asserter (practitioner) resource from the FHIR bundle.
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(1);
Practitioner practitioner = (Practitioner) practitionerResource.get(0);
// Verify name text, family, and given are set correctly.
assertThat(practitioner.getName()).hasSize(1);
// DG1.16
assertThat(practitioner.getNameFirstRep().getText()).isEqualTo("JOHN A DOE");
// DG1.16.2
assertThat(practitioner.getNameFirstRep().getFamily()).isEqualTo("DOE");
// DG1.16.3
assertThat(practitioner.getNameFirstRep().getGivenAsSingleString()).isEqualTo("JOHN A");
// Verify asserter (practitioner) identifier is set correctly.
assertThat(practitioner.getIdentifier()).hasSize(1);
// DG1.16.1
assertThat(practitioner.getIdentifierFirstRep().getValue()).isEqualTo("123");
}
use of org.hl7.elm.r1.Time in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ObservationFHIRConversionTest method testObservationStNullResult.
@Test
void testObservationStNullResult() throws IOException {
String hl7message = baseMessage + "OBX|1|ST|14151-5^HCO3 BldCo-sCnc^LN|TEST|||||||F|||20210311122016|||||20210311122153||||";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
Observation obs = (Observation) obsResource.get(0);
assertThat(obs.getValueStringType()).isNotNull();
StringType q = obs.getValueStringType();
assertThat(q.asStringValue()).isNull();
// Check the coding (OBX.3)
assertThat(obs.hasCode()).isTrue();
DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getCode(), "14151-5", "HCO3 BldCo-sCnc", "http://loinc.org", "HCO3 BldCo-sCnc");
// Check the effective Date Time (OBX 14)
assertThat(obs.hasEffective()).isTrue();
assertThat(obs.hasEffectiveDateTimeType()).isTrue();
assertThat(obs.getEffectiveDateTimeType().asStringValue()).isEqualTo("2021-03-11T12:20:16+08:00");
}
use of org.hl7.elm.r1.Time in project hl7v2-fhir-converter by LinuxForHealth.
the class InputTimeZoneIdTest method validateTimeZoneIdSettingViaOption.
@Test
void validateTimeZoneIdSettingViaOption() {
// NOTE: This simple Condition (PRB) segment is used for testing time because it has both
// standard DateTime conversions (abatementDateTime, recordedDate) and value conversions (extension).
String hl7message = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\r" + "PID||||||||||||||||||||||||||||||\r" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\r" + // PRB.16 to onsetDateTime (check time ZoneId)
"PRB|AD|20020202020000|K80.00^Cholelithiasis^I10|53956|||20070707070000||20090909090000|||||||20160616160000\r";
// FIRST test with city based ZoneId passed through options
ConverterOptions customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("America/Chicago").build();
// "America/Chicago" will become -06:00 in winter (CST) -05:00 in spring/summer/fall (CDT). This is expected.
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
Condition condition = (Condition) conditionResource.get(0);
// PRB.2 Chicago Central STANDARD Time
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00-06:00");
// PRB.9 Chicago Central DAYLIGHT Time
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00-05:00");
// PRB.16 Chicago CDT
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00-05:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7 Chicago CDT
"2007-07-07T07:00:00-05:00");
// SECOND test with fixed ZoneId passed through options
customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("+03:00").build();
e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
condition = (Condition) conditionResource.get(0);
// PRB.2 fixed ZoneId
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+03:00");
// PRB.9
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+03:00");
// PRB.16
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+03:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
"2007-07-07T07:00:00+03:00");
// THIRD test with no ZoneId passed through options, so it uses the config.properties ZoneId
customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().build();
e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
// Find the condition from the FHIR bundle.
conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
assertThat(conditionResource).hasSize(1);
condition = (Condition) conditionResource.get(0);
// PRB.2 config.properties ZoneId
assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+08:00");
// PRB.9
assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+08:00");
// PRB.16
assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+08:00");
assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
"2007-07-07T07:00:00+08:00");
}
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