Skip to content

Commit

Permalink
Dss/evsrestapi 999 fhir r4 testing (#317)
Browse files Browse the repository at this point in the history
  • Loading branch information
@shapirod2
shapirod2 authored Feb 4, 2025
1 parent 35a15c7 commit 4e90551
Show file tree
Hide file tree
Showing 19 changed files with 4,000 additions and 1,311 deletions.
80 changes: 42 additions & 38 deletions src/main/java/gov/nih/nci/evs/api/fhir/R4/CodeSystemProviderR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,23 +130,22 @@ public Parameters lookupImplicit(
termUtils.getIndexedTerminology(codeSys.getTitle(), esQueryService);
final Concept conc =
esQueryService.getConcept(codeToLookup, term, new IncludeParam("children")).get();
params.addParameter("code", "code");
params.addParameter("system", codeSys.getUrl());
params.addParameter("code", codeSys.getName());
params.addParameter("version", codeSys.getVersion());
// required in the specification
params.addParameter("name", codeSys.getName());
params.addParameter("display", conc.getName());
params.addParameter("active", true);
// optional in the specification
params.addParameter("version", codeSys.getVersion());
// properties
params.addParameter(FhirUtilityR4.createProperty("active", conc.getActive(), false));
for (final Concept parent : conc.getParents()) {
params.addParameter(FhirUtilityR4.createProperty("parent", parent.getCode(), true));
}
for (final Concept child : conc.getChildren()) {
params.addParameter(FhirUtilityR4.createProperty("child", child.getCode(), true));
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("system", (system == null ? new UriType("<null>") : system));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

Expand Down Expand Up @@ -221,29 +220,28 @@ public Parameters lookupInstance(
termUtils.getIndexedTerminology(codeSys.getTitle(), esQueryService);
final Concept conc =
esQueryService.getConcept(codeToLookup, term, new IncludeParam("children")).get();
params.addParameter("code", "code");
params.addParameter("system", codeSys.getUrl());
params.addParameter("code", codeSys.getName());
params.addParameter("version", codeSys.getVersion());
// required in the specification
params.addParameter("name", codeSys.getName());
params.addParameter("display", conc.getName());
params.addParameter("active", true);
// optional in the specification
params.addParameter("version", codeSys.getVersion());
params.addParameter(FhirUtilityR4.createProperty("active", conc.getActive(), false));
for (final Concept parent : conc.getParents()) {
params.addParameter(FhirUtilityR4.createProperty("parent", parent.getCode(), true));
}
for (final Concept child : conc.getChildren()) {
params.addParameter(FhirUtilityR4.createProperty("child", child.getCode(), true));
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("system", (system == null ? new UriType("<null>") : system));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

} catch (final FHIRServerResponseException e) {
throw e;
} catch (final Exception e) {
e.printStackTrace();
throw FhirUtilityR4.exception(
"Failed to lookup code", OperationOutcome.IssueType.EXCEPTION, 500);
}
Expand Down Expand Up @@ -318,10 +316,11 @@ public Parameters validateCodeImplicit(
if (check.isPresent()) {
final Concept conc =
esQueryService.getConcept(codeToValidate, term, new IncludeParam("children")).get();
params.addParameter("result", true);
if (display == null || conc.getName().equals(display.getValue())) {
params.addParameter("result", true);
params.addParameter("code", conc.getCode());
} else {
params.addParameter("result", false);
params.addParameter(
"message",
"The code "
Expand All @@ -340,10 +339,8 @@ public Parameters validateCodeImplicit(
params.addParameter("version", codeSys.getVersion());
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("url", (url == null ? new UriType("<null>") : url));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

Expand Down Expand Up @@ -421,10 +418,11 @@ public Parameters validateCodeInstance(
if (check.isPresent()) {
final Concept conc =
esQueryService.getConcept(codeToValidate, term, new IncludeParam("children")).get();
params.addParameter("result", true);
if (display == null || conc.getName().equals(display.getValue())) {
params.addParameter("code", conc.getCode());
params.addParameter("result", true);
} else {
params.addParameter("result", false);
params.addParameter(
"message",
"The code "
Expand All @@ -443,10 +441,8 @@ public Parameters validateCodeInstance(
params.addParameter("version", codeSys.getVersion());
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("url", (url == null ? new UriType("<null>") : url));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

Expand Down Expand Up @@ -513,6 +509,12 @@ public Parameters subsumesImplicit(
} else if (codingA != null && codingB != null) {
code1 = codingA.getCode();
code2 = codingB.getCode();
} else if (codeA == null) {
throw FhirUtilityR4.exception(
"No codeA parameter provided in request", OperationOutcome.IssueType.EXCEPTION, 400);
} else if (codeB == null) {
throw FhirUtilityR4.exception(
"No codeB parameter provided in request", OperationOutcome.IssueType.EXCEPTION, 400);
}
final CodeSystem codeSys = cs.get(0);
final Terminology term =
Expand All @@ -533,10 +535,8 @@ public Parameters subsumesImplicit(
}
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("system", (system == null ? new UriType("<null>") : system));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

Expand Down Expand Up @@ -605,6 +605,12 @@ public Parameters subsumesInstance(
} else if (codingA != null && codingB != null) {
code1 = codingA.getCode();
code2 = codingB.getCode();
} else if (codeA == null) {
throw FhirUtilityR4.exception(
"No codeA parameter provided in request", OperationOutcome.IssueType.EXCEPTION, 400);
} else if (codeB == null) {
throw FhirUtilityR4.exception(
"No codeB parameter provided in request", OperationOutcome.IssueType.EXCEPTION, 400);
}
final CodeSystem codeSys = cs.get(0);
final Terminology term =
Expand All @@ -616,19 +622,17 @@ public Parameters subsumesInstance(
if (checkA.get() != null && checkB.get() != null) {
params.addParameter("system", codeSys.getUrl());
params.addParameter("version", codeSys.getVersion());
if (esQueryService.getPathsToParent(code1, code2, term).getCt() > 0) {
if (esQueryService.getPathsToParent(code1, code2, term).getPathCount() > 0) {
params.addParameter("outcome", "subsumes");
} else if (esQueryService.getPathsToParent(code2, code1, term).getCt() > 0) {
} else if (esQueryService.getPathsToParent(code2, code1, term).getPathCount() > 0) {
params.addParameter("outcome", "subsumed-by");
} else {
params.addParameter("outcome", "no-subsumption-relationship");
}
}
} else {
params.addParameter("result", false);
params.addParameter("message", "Unable to find matching code system");
params.addParameter("system", (system == null ? new UriType("<null>") : system));
params.addParameter("version", version);
throw FhirUtilityR4.exception(
"Unable to find matching code system", OperationOutcome.IssueType.NOTFOUND, 400);
}
return params;

Expand Down
47 changes: 37 additions & 10 deletions src/main/java/gov/nih/nci/evs/api/fhir/R4/ValueSetProviderR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionParameterComponent;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
Expand Down Expand Up @@ -173,7 +174,9 @@ public ValueSet expandImplicit(
final List<ValueSet> vsList = findPossibleValueSets(null, null, url, version);
if (vsList.size() == 0) {
throw FhirUtilityR4.exception(
"Value set " + url + " not found", OperationOutcome.IssueType.EXCEPTION, 500);
"Value set " + url.getValueAsString() + " not found",
OperationOutcome.IssueType.EXCEPTION,
500);
}
final ValueSet vs = vsList.get(0);
List<Concept> subsetMembers = new ArrayList<Concept>();
Expand Down Expand Up @@ -225,6 +228,15 @@ public ValueSet expandImplicit(
vsContains.setCode(subset.getCode());
vsContains.setDisplay(subset.getName());
vsExpansion.addContains(vsContains);
ValueSetExpansionParameterComponent vsParameter =
new ValueSetExpansionParameterComponent();
vsParameter.setName("url");
vsParameter.setValue(url);
vsExpansion.addParameter(vsParameter);
vsParameter = new ValueSetExpansionParameterComponent();
vsParameter.setName("version");
vsParameter.setValue(version);
vsExpansion.addParameter(vsParameter);
}
}
vs.setExpansion(vsExpansion);
Expand Down Expand Up @@ -294,8 +306,8 @@ public ValueSet expandInstance(
@OperationParam(name = "contextDirection") final CodeType contextDirection,
@OperationParam(name = "filter") final StringType filter,
@OperationParam(name = "date") final DateTimeType date,
@OperationParam(name = "offset") final IntegerType offset,
@OperationParam(name = "count") final IntegerType count,
@ca.uhn.fhir.rest.annotation.Offset final Integer offset,
@ca.uhn.fhir.rest.annotation.Count final Integer count,
@OperationParam(name = "includeDesignations") final BooleanType includeDesignations,
@OperationParam(name = "designation") final StringType designation,
@OperationParam(name = "includeDefinition") final BooleanType includeDefinition,
Expand All @@ -319,7 +331,7 @@ public ValueSet expandInstance(
try {
// URL is not required because "id" is provided
// FhirUtilityR4.required("url", url);
FhirUtilityR4.notSupported("valueSet", valueSet);
FhirUtilityR4.notSupported("valueSet", null);
FhirUtilityR4.notSupported("context", context);
FhirUtilityR4.notSupported("contextDirection", contextDirection);
FhirUtilityR4.notSupported("date", date);
Expand All @@ -337,7 +349,9 @@ public ValueSet expandInstance(
final List<ValueSet> vsList = findPossibleValueSets(id, null, url, version);
if (vsList.size() == 0) {
throw FhirUtilityR4.exception(
"Value set " + url + " not found", OperationOutcome.IssueType.EXCEPTION, 500);
"Value set " + url.getValueAsString() + " not found",
OperationOutcome.IssueType.EXCEPTION,
500);
}
final ValueSet vs = vsList.get(0);
List<Concept> subsetMembers = new ArrayList<Concept>();
Expand Down Expand Up @@ -366,8 +380,8 @@ public ValueSet expandInstance(
final List<Terminology> terminologies = new ArrayList<>();
terminologies.add(termUtils.getIndexedTerminology(vs.getTitle(), esQueryService));
final SearchCriteria sc = new SearchCriteria();
sc.setPageSize(count != null ? count.getValue() : 10);
sc.setFromRecord(offset != null ? offset.getValue() : 0);
sc.setPageSize(count != null ? count : 10);
sc.setFromRecord(offset != null ? offset : 0);
sc.setTerm(filter != null ? filter.getValue() : null);
sc.setType("contains");
sc.setTerminology(
Expand All @@ -376,7 +390,7 @@ public ValueSet expandInstance(
}
final ValueSetExpansionComponent vsExpansion = new ValueSetExpansionComponent();
vsExpansion.setTimestamp(new Date());
vsExpansion.setOffset(offset != null ? offset.getValue() : 0);
vsExpansion.setOffset(offset != null ? offset : 0);
vsExpansion.setTotal(subsetMembers.size());
if (subsetMembers.size() > 0) {
for (final Concept subset : subsetMembers) {
Expand All @@ -389,6 +403,15 @@ public ValueSet expandInstance(
vsContains.setCode(subset.getCode());
vsContains.setDisplay(subset.getName());
vsExpansion.addContains(vsContains);
ValueSetExpansionParameterComponent vsParameter =
new ValueSetExpansionParameterComponent();
vsParameter.setName("url");
vsParameter.setValue(url);
vsExpansion.addParameter(vsParameter);
vsParameter = new ValueSetExpansionParameterComponent();
vsParameter.setName("version");
vsParameter.setValue(version);
vsExpansion.addParameter(vsParameter);
}
}
vs.setExpansion(vsExpansion);
Expand Down Expand Up @@ -492,16 +515,18 @@ public Parameters validateCodeImplicit(
final List<Terminology> terms = Arrays.asList(term);
final List<Concept> conc = searchService.findConcepts(terms, sc).getConcepts();
if (conc.size() > 0) {
params.addParameter("result", true);
params.addParameter("display", conc.get(0).getName());
if (display != null && !display.getValue().equals(conc.get(0).getName())) {
params.addParameter("result", false);
params.addParameter(
"message",
"The code '"
+ code
+ "' was found in this value set, however the display '"
+ display
+ "' did not match any designations.");
} else {
params.addParameter("result", true);
}
} else {
params.addParameter("result", false);
Expand Down Expand Up @@ -612,16 +637,18 @@ public Parameters validateCodeInstance(
final List<Terminology> terms = Arrays.asList(term);
final List<Concept> conc = searchService.findConcepts(terms, sc).getConcepts();
if (conc.size() > 0) {
params.addParameter("result", true);
params.addParameter("display", conc.get(0).getName());
if (display != null && !display.getValue().equals(conc.get(0).getName())) {
params.addParameter("result", false);
params.addParameter(
"message",
"The code '"
+ code
+ "' was found in this value set, however the display '"
+ display
+ "' did not match any designations.");
} else {
params.addParameter("result", true);
}
} else {
params.addParameter("result", false);
Expand Down
Loading

0 comments on commit 4e90551

Please sign in to comment.