protected Platform getPlatform(Hybridization hybridization) throws DataRetrievalException {
ArrayDesign arrayDesign = hybridization.getArrayDesign();
if (arrayDesign == null) {
throw new DataRetrievalException(
"There is no array design associated with the array for the hybridization "
+ hybridization.getName()
+ ", unable to load array data");
}
Platform platform = getDao().getPlatform(arrayDesign.getName());
if (platform == null) {
throw new DataRetrievalException(
"The platform named " + arrayDesign.getName() + " hasn't been loaded into the system");
}
return platform;
}
@Override
protected void evaluateResults(
List<? extends AbstractCaArrayEntity> resultsList,
ExampleSearch search,
TestResult testResult) {
ArrayDesignSearch adSearch = (ArrayDesignSearch) search;
List<ArrayDesign> adResults = (List<ArrayDesign>) resultsList;
if (adSearch.getExpectedResults() != null || adSearch.getMinResults() != null) {
int namedResults = 0;
for (ArrayDesign arrayDesign : adResults) {
if (arrayDesign.getName() != null) namedResults++;
}
if (adSearch.getExpectedResults() != null && namedResults != adSearch.getExpectedResults()) {
testResult.setPassed(false);
String detail =
"Failed with unexpected number of results, ArrayDesign:"
+ adSearch.getArrayDesign().getName()
+ "- expected number of results: "
+ adSearch.getExpectedResults()
+ ", actual number of results: "
+ namedResults;
testResult.addDetail(detail);
} else {
String detail = "Found expected number of results: " + namedResults;
testResult.addDetail(detail);
}
if (adSearch.getMinResults() != null && namedResults < adSearch.getMinResults()) {
testResult.setPassed(false);
String detail =
"Failed with unexpected minimum number of results, ArrayDesign:"
+ adSearch.getArrayDesign().getName()
+ "- expected number of results: "
+ adSearch.getMinResults()
+ ", actual number of results: "
+ namedResults;
testResult.addDetail(detail);
}
}
if (adSearch.getExample() == null) {
if (adSearch.getExceptionClass() != null) {
if (!adSearch.getExceptionClass().equals(InvalidInputException.class.toString())
&& !adSearch.getExceptionClass().equals(InvalidInputFault.class.toString())) {
testResult.setPassed(false);
String detail = "Failed with unexpected exception class: " + adSearch.getExceptionClass();
testResult.addDetail(detail);
} else {
testResult.addDetail("Found expected exception " + adSearch.getExceptionClass());
}
}
}
for (ArrayDesign arrayDesign : adResults) {
if (adSearch.getExpectedProvider() != null) {
if (arrayDesign.getArrayProvider() == null
|| !arrayDesign.getArrayProvider().getName().equals(adSearch.getExpectedProvider())) {
testResult.setPassed(false);
String detail =
"Failed with unexpected array provider: "
+ (arrayDesign.getArrayProvider() == null
? "null"
: arrayDesign.getArrayProvider().getName())
+ ", expected provider: "
+ adSearch.getExpectedProvider();
testResult.addDetail(detail);
} else {
String detail = "Found expected provider: " + adSearch.getExpectedProvider();
testResult.addDetail(detail);
}
}
if (adSearch.getExpectedOrganism() != null) {
if (arrayDesign.getOrganism() == null
|| !arrayDesign
.getOrganism()
.getCommonName()
.equalsIgnoreCase(adSearch.getExpectedOrganism())) {
testResult.setPassed(false);
String detail =
"Failed with unexpected organism common name: "
+ (arrayDesign.getOrganism() == null
? "null"
: arrayDesign.getOrganism().getCommonName())
+ ", expected name: "
+ adSearch.getExpectedOrganism();
testResult.addDetail(detail);
} else {
String detail = "Found expected organism: " + adSearch.getExpectedOrganism();
testResult.addDetail(detail);
}
}
}
}