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BI-2045 (Failure to report error when uploading duplicated experiment name) #333

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Merged
davedrp merged 7 commits into from
Mar 5, 2024
Merged

BI-2045 (Failure to report error when uploading duplicated experiment name) #333

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1651611
[BI-2045] added error for 'Experiment Title already exist'
davedrp Feb 15, 2024
ec74194
[BI-2045] improved variable name
davedrp Feb 19, 2024
52a5655
[BI-2045] WIP (improve unit testing)
davedrp Feb 22, 2024
d7e3dcd
[BI-2045] Check for existing Env when validating for 'Experiment Titl…
davedrp Mar 4, 2024
1a2ff09
[BI-2045] fixed test
davedrp Mar 4, 2024
1102222
[BI-2045] fixed test name
davedrp Mar 4, 2024
1ae021c
[BI-2046] address PR comments
davedrp Mar 4, 2024
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16 changes: 11 additions & 5 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@ public class ExperimentProcessor implements Processor {

private static final String NAME = "Experiment";
private static final String MISSING_OBS_UNIT_ID_ERROR = "Experimental entities are missing ObsUnitIDs";
private static final String PREEXISTING_EXPERIMENT_TITLE = "Experiment Title already exists";
private static final String MULTIPLE_EXP_TITLES = "File contains more than one Experiment Title";
private static final String MIDNIGHT = "T00:00:00-00:00";
private static final String TIMESTAMP_PREFIX = "TS:";
Expand Down Expand Up @@ -1174,9 +1175,14 @@ private void fetchOrCreateLocationPIO(ExperimentObservation importRow) {
}

private PendingImportObject<BrAPITrial> fetchOrCreateTrialPIO(Program program, User user, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) throws UnprocessableEntityException {
PendingImportObject<BrAPITrial> pio;
PendingImportObject<BrAPITrial> trialPio;
if (trialByNameNoScope.containsKey(importRow.getExpTitle())) {
pio = trialByNameNoScope.get(importRow.getExpTitle());
PendingImportObject<BrAPIStudy> envPio;
trialPio = trialByNameNoScope.get(importRow.getExpTitle());
envPio = this.studyByNameNoScope.get(importRow.getEnv());
if (trialPio!=null && ImportObjectState.EXISTING==trialPio.getState() && (StringUtils.isBlank( importRow.getObsUnitID() )) && (envPio!=null && ImportObjectState.EXISTING==envPio.getState() ) ){
throw new UnprocessableEntityException(PREEXISTING_EXPERIMENT_TITLE);
}
} else if (!trialByNameNoScope.isEmpty()) {
throw new UnprocessableEntityException(MULTIPLE_EXP_TITLES);
} else {
Expand All @@ -1186,10 +1192,10 @@ private PendingImportObject<BrAPITrial> fetchOrCreateTrialPIO(Program program, U
expSeqValue = expNextVal.get().toString();
}
BrAPITrial newTrial = importRow.constructBrAPITrial(program, user, commit, BRAPI_REFERENCE_SOURCE, id, expSeqValue);
pio = new PendingImportObject<>(ImportObjectState.NEW, newTrial, id);
this.trialByNameNoScope.put(importRow.getExpTitle(), pio);
trialPio = new PendingImportObject<>(ImportObjectState.NEW, newTrial, id);
this.trialByNameNoScope.put(importRow.getExpTitle(), trialPio);
}
return pio;
return trialPio;
}

private void updateObservationDependencyValues(Program program) {
Expand Down
124 changes: 79 additions & 45 deletions src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,7 @@ public void importNewExpNewLocNoObsSuccess() {

@Test
@SneakyThrows
public void importNewExpMultiNewEnvNoObsSuccess() {
public void importNewExpMultiNewEnvSuccess() {
Program program = createProgram("New Exp and Multi New Env", "MULENV", "MULENV", BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);
Map<String, Object> firstEnv = new HashMap<>();
firstEnv.put(Columns.GERMPLASM_GID, "1");
Expand Down Expand Up @@ -282,15 +282,15 @@ public void importNewExpMultiNewEnvNoObsSuccess() {

@Test
@SneakyThrows
public void importNewEnvExistingExpNoObsSuccess() {
Program program = createProgram("New Env Existing Exp", "NEWENV", "NEWENV", BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);
public void importExistingExpAndEnvErrorMessage() {
Program program = createProgram("New Env Existing Exp", "DUPENV", "DUPENV", BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);
Map<String, Object> newExp = new HashMap<>();
newExp.put(Columns.GERMPLASM_GID, "1");
newExp.put(Columns.TEST_CHECK, "T");
newExp.put(Columns.EXP_TITLE, "Test Exp");
newExp.put(Columns.EXP_UNIT, "Plot");
newExp.put(Columns.EXP_TYPE, "Phenotyping");
newExp.put(Columns.ENV, "New Env");
newExp.put(Columns.ENV, "Existing Env");
newExp.put(Columns.ENV_LOCATION, "Location A");
newExp.put(Columns.ENV_YEAR, "2023");
newExp.put(Columns.EXP_UNIT_ID, "a-1");
Expand All @@ -301,6 +301,38 @@ public void importNewEnvExistingExpNoObsSuccess() {

JsonObject expResult = importTestUtils.uploadAndFetch(importTestUtils.writeExperimentDataToFile(List.of(newExp), null), null, true, client, program, mappingId);

Map<String, Object> dupExp = new HashMap<>();
dupExp.put(Columns.GERMPLASM_GID, "1");
dupExp.put(Columns.TEST_CHECK, "T");
dupExp.put(Columns.EXP_TITLE, "Test Exp");
dupExp.put(Columns.EXP_UNIT, "Plot");
dupExp.put(Columns.EXP_TYPE, "Phenotyping");
dupExp.put(Columns.ENV, "Existing Env");
dupExp.put(Columns.ENV_LOCATION, "Location A");
dupExp.put(Columns.ENV_YEAR, "2023");
dupExp.put(Columns.EXP_UNIT_ID, "a-1");
dupExp.put(Columns.REP_NUM, "1");
dupExp.put(Columns.BLOCK_NUM, "1");
dupExp.put(Columns.ROW, "1");
dupExp.put(Columns.COLUMN, "1");

Flowable<HttpResponse<String>> call = importTestUtils.uploadDataFile(importTestUtils.writeExperimentDataToFile(List.of(dupExp), null), null, false, client, program, mappingId);
HttpResponse<String> response = call.blockingFirst();
assertEquals(HttpStatus.ACCEPTED, response.getStatus());

String importId = JsonParser.parseString(response.body()).getAsJsonObject().getAsJsonObject("result").get("importId").getAsString();

HttpResponse<String> upload = importTestUtils.getUploadedFile(importId, client, program, mappingId);
JsonObject result = JsonParser.parseString(upload.body()).getAsJsonObject().getAsJsonObject("result");
assertEquals(422, result.getAsJsonObject("progress").get("statuscode").getAsInt(), "Returned data: " + result);
assertTrue(result.getAsJsonObject("progress").get("message").getAsString().startsWith("Experiment Title already exists"));
}

@Test
@SneakyThrows
public void importNewEnvNoObsSuccess() {
Program program = createProgram("New Env", "NEWENV", "NEWENV", BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);

Map<String, Object> newEnv = new HashMap<>();
newEnv.put(Columns.GERMPLASM_GID, "1");
newEnv.put(Columns.TEST_CHECK, "T");
Expand All @@ -322,13 +354,14 @@ public void importNewEnvExistingExpNoObsSuccess() {
assertEquals(1, previewRows.size());
JsonObject row = previewRows.get(0).getAsJsonObject();

assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
assertEquals("NEW", row.getAsJsonObject("trial").get("state").getAsString());
assertEquals("NEW", row.getAsJsonObject("location").get("state").getAsString());
assertEquals("NEW", row.getAsJsonObject("study").get("state").getAsString());
assertEquals("NEW", row.getAsJsonObject("observationUnit").get("state").getAsString());
assertRowSaved(newEnv, program, null);
}


@ParameterizedTest
@ValueSource(booleans = {true, false})
@SneakyThrows
Expand Down Expand Up @@ -566,45 +599,46 @@ public void verifyFailureImportNewExpWithInvalidObs(boolean commit) {
uploadAndVerifyFailure(program, importTestUtils.writeExperimentDataToFile(List.of(newExp), traits), traits.get(0).getObservationVariableName(), commit);
}

@ParameterizedTest
@ValueSource(booleans = {true, false})
@SneakyThrows
public void verifyFailureNewOuExistingEnv(boolean commit) {
Program program = createProgram("New OU Exising Env "+(commit ? "C" : "P"), "FLOU"+(commit ? "C" : "P"), "FLOU"+(commit ? "C" : "P"), BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);
Map<String, Object> newExp = new HashMap<>();
newExp.put(Columns.GERMPLASM_GID, "1");
newExp.put(Columns.TEST_CHECK, "T");
newExp.put(Columns.EXP_TITLE, "Test Exp");
newExp.put(Columns.EXP_UNIT, "Plot");
newExp.put(Columns.EXP_TYPE, "Phenotyping");
newExp.put(Columns.ENV, "New Env");
newExp.put(Columns.ENV_LOCATION, "Location A");
newExp.put(Columns.ENV_YEAR, "2023");
newExp.put(Columns.EXP_UNIT_ID, "a-1");
newExp.put(Columns.REP_NUM, "1");
newExp.put(Columns.BLOCK_NUM, "1");
newExp.put(Columns.ROW, "1");
newExp.put(Columns.COLUMN, "1");

importTestUtils.uploadAndFetch(importTestUtils.writeExperimentDataToFile(List.of(newExp), null), null, true, client, program, mappingId);

Map<String, Object> newOU = new HashMap<>(newExp);
newOU.put(Columns.EXP_UNIT_ID, "a-2");
newOU.put(Columns.ROW, "1");
newOU.put(Columns.COLUMN, "2");

Flowable<HttpResponse<String>> call = importTestUtils.uploadDataFile(importTestUtils.writeExperimentDataToFile(List.of(newOU), null), null, commit, client, program, mappingId);
HttpResponse<String> response = call.blockingFirst();
assertEquals(HttpStatus.ACCEPTED, response.getStatus());

String importId = JsonParser.parseString(response.body()).getAsJsonObject().getAsJsonObject("result").get("importId").getAsString();

HttpResponse<String> upload = importTestUtils.getUploadedFile(importId, client, program, mappingId);
JsonObject result = JsonParser.parseString(upload.body()).getAsJsonObject().getAsJsonObject("result");
assertEquals(422, result.getAsJsonObject("progress").get("statuscode").getAsInt(), "Returned data: " + result);

assertTrue(result.getAsJsonObject("progress").get("message").getAsString().startsWith("Experimental entities are missing ObsUnitIDs"));
}
// NO Longer needed, but may be needed in the future.
// @ParameterizedTest
// @ValueSource(booleans = {true, false})
// @SneakyThrows
// public void verifyFailureNewOuExistingEnv(boolean commit) {
// Program program = createProgram("New OU Exising Env "+(commit ? "C" : "P"), "FLOU"+(commit ? "C" : "P"), "FLOU"+(commit ? "C" : "P"), BRAPI_REFERENCE_SOURCE, createGermplasm(1), null);
// Map<String, Object> newExp = new HashMap<>();
// newExp.put(Columns.GERMPLASM_GID, "1");
// newExp.put(Columns.TEST_CHECK, "T");
// newExp.put(Columns.EXP_TITLE, "Test Exp");
// newExp.put(Columns.EXP_UNIT, "Plot");
// newExp.put(Columns.EXP_TYPE, "Phenotyping");
// newExp.put(Columns.ENV, "New Env");
// newExp.put(Columns.ENV_LOCATION, "Location A");
// newExp.put(Columns.ENV_YEAR, "2023");
// newExp.put(Columns.EXP_UNIT_ID, "a-1");
// newExp.put(Columns.REP_NUM, "1");
// newExp.put(Columns.BLOCK_NUM, "1");
// newExp.put(Columns.ROW, "1");
// newExp.put(Columns.COLUMN, "1");
//
// importTestUtils.uploadAndFetch(importTestUtils.writeExperimentDataToFile(List.of(newExp), null), null, true, client, program, mappingId);
//
// Map<String, Object> newOU = new HashMap<>(newExp);
// newOU.put(Columns.EXP_UNIT_ID, "a-2");
// newOU.put(Columns.ROW, "1");
// newOU.put(Columns.COLUMN, "2");
//
// Flowable<HttpResponse<String>> call = importTestUtils.uploadDataFile(importTestUtils.writeExperimentDataToFile(List.of(newOU), null), null, commit, client, program, mappingId);
// HttpResponse<String> response = call.blockingFirst();
// assertEquals(HttpStatus.ACCEPTED, response.getStatus());
//
// String importId = JsonParser.parseString(response.body()).getAsJsonObject().getAsJsonObject("result").get("importId").getAsString();
//
// HttpResponse<String> upload = importTestUtils.getUploadedFile(importId, client, program, mappingId);
// JsonObject result = JsonParser.parseString(upload.body()).getAsJsonObject().getAsJsonObject("result");
// assertEquals(422, result.getAsJsonObject("progress").get("statuscode").getAsInt(), "Returned data: " + result);
//
// assertTrue(result.getAsJsonObject("progress").get("message").getAsString().startsWith("Experimental entities are missing ObsUnitIDs"));
// }

@Test
@SneakyThrows
Expand Down