protected void populateSearch(String[] input, ExampleSearch exampleSearch) {
ArrayDesignSearch search = (ArrayDesignSearch) exampleSearch;
ArrayDesign example = new ArrayDesign();
if (headerIndexMap.get(API) < input.length && !input[headerIndexMap.get(API)].equals("")) {
search.setApi(input[headerIndexMap.get(API)].trim());
}
if (headerIndexMap.get(NAME) < input.length && !input[headerIndexMap.get(NAME)].equals(""))
example.setName(input[headerIndexMap.get(NAME)].trim());
if (headerIndexMap.get(LSID) < input.length && !input[headerIndexMap.get(LSID)].equals(""))
example.setLsid(input[headerIndexMap.get(LSID)].trim());
if (headerIndexMap.get(PROVIDER) < input.length
&& !input[headerIndexMap.get(PROVIDER)].equals("")) {
/*ArrayProvider provider = new ArrayProvider();
provider.setName(input[headerIndexMap.get(PROVIDER)]);
example.setArrayProvider(provider);*/
ArrayProvider provider = null;
try {
provider = apiFacade.getArrayProvider(search.getApi(), input[headerIndexMap.get(PROVIDER)]);
} catch (Exception e) {
log.error("Error retrieving ArrayProvider for ArrayDesign search", e);
provider = new ArrayProvider();
provider.setName(input[headerIndexMap.get(PROVIDER)]);
}
if (provider != null) {
example.setArrayProvider(provider);
}
}
if (headerIndexMap.get(ASSAY_TYPE) < input.length
&& !input[headerIndexMap.get(ASSAY_TYPE)].equals("")) {
example.getAssayTypes().add(new AssayType(input[headerIndexMap.get(ASSAY_TYPE)]));
}
if (headerIndexMap.get(NULL) < input.length && !input[headerIndexMap.get(NULL)].equals("")) {
example = null;
}
search.setArrayDesign(example);
if (headerIndexMap.get(TEST_CASE) < input.length
&& !input[headerIndexMap.get(TEST_CASE)].equals(""))
search.setTestCase(Float.parseFloat(input[headerIndexMap.get(TEST_CASE)].trim()));
if (headerIndexMap.get(EXPECTED_RESULTS) < input.length
&& !input[headerIndexMap.get(EXPECTED_RESULTS)].equals(""))
search.setExpectedResults(
Integer.parseInt(input[headerIndexMap.get(EXPECTED_RESULTS)].trim()));
if (headerIndexMap.get(MIN_RESULTS) < input.length
&& !input[headerIndexMap.get(MIN_RESULTS)].equals(""))
search.setMinResults(Integer.parseInt(input[headerIndexMap.get(MIN_RESULTS)].trim()));
if (headerIndexMap.get(EXPECTED_PROVIDER) < input.length
&& !input[headerIndexMap.get(EXPECTED_PROVIDER)].equals(""))
search.setExpectedProvider(input[headerIndexMap.get(EXPECTED_PROVIDER)].trim());
if (headerIndexMap.get(EXPECTED_ORGANISM) < input.length
&& !input[headerIndexMap.get(EXPECTED_ORGANISM)].equals(""))
search.setExpectedOrganism(input[headerIndexMap.get(EXPECTED_ORGANISM)]);
}
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);
}
}
}
}