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IBP-3322-ImportExperimentDesignValues #868

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e0950ca
Resolve projectprop value from GeolocationProperty
gelli-leafnode Aug 24, 2020
60a9069
Code cleanup
gelli-leafnode Aug 24, 2020
daf211d
Set Role of Experimental Design Variables to TRIAL_ENVIRONMENT during…
gelli-leafnode Aug 26, 2020
67344bb
Code cleanup
gelli-leafnode Aug 26, 2020
1786509
Merge branch 'master' of https://github.com/IntegratedBreedingPlatfor…
gelli-leafnode Sep 14, 2020
c9501a6
Fix RMAP value for single sheet and with description
gelli-leafnode Sep 21, 2020
810082c
Fix failing unit test: Adding null pointer check
gelli-leafnode Sep 21, 2020
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37 changes: 19 additions & 18 deletions src/main/java/org/generationcp/middleware/operation/builder/StandardVariableBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ public class StandardVariableBuilder extends Builder {

public StandardVariableBuilder(final HibernateSessionProvider sessionProviderForLocal) {
super(sessionProviderForLocal);
daoFactory = new DaoFactory(sessionProviderForLocal);
this.daoFactory = new DaoFactory(sessionProviderForLocal);
}

public StandardVariable create(final int standardVariableId, final String programUUID) {
Expand Down Expand Up @@ -127,7 +127,7 @@ private void specialProcessing(final List<StandardVariableSummary> summaries) {
// Now this relationship is linked to the "Property" of the standard variable. (facepalm).
if (summary.getProperty() != null) {
final List<CVTermRelationship> propertyCvTermRelationships =
daoFactory.getCvTermRelationshipDao().getBySubject(summary.getProperty().getId());
this.daoFactory.getCvTermRelationshipDao().getBySubject(summary.getProperty().getId());
final Term isAOfProperty = this.createTerm(propertyCvTermRelationships, TermId.IS_A);
if (isAOfProperty != null) {
summary.setIsA(new TermSummary(isAOfProperty.getId(), isAOfProperty.getName(), isAOfProperty.getDefinition()));
Expand All @@ -150,7 +150,7 @@ public String getCropOntologyId(final Term term) {
}

final CVTermProperty property =
daoFactory.getCvTermPropertyDao().getOneByCvTermAndType(term.getId(), TermId.CROP_ONTOLOGY_ID.getId());
this.daoFactory.getCvTermPropertyDao().getOneByCvTermAndType(term.getId(), TermId.CROP_ONTOLOGY_ID.getId());
if (property != null) {
cropOntologyId = property.getValue();
}
Expand Down Expand Up @@ -192,7 +192,7 @@ public List<TermProperty> createTermProperties(final int cvTermId) {
}

private CVTerm getCvTerm(final int id) {
return daoFactory.getCvTermDao().getById(id);
return this.daoFactory.getCvTermDao().getById(id);
}

public StandardVariable findOrSave(
Expand Down Expand Up @@ -287,7 +287,7 @@ public VariableType mapPhenotypicTypeToDefaultVariableType(final PhenotypicType
}

public StandardVariable getByName(final String name, final String programUUID) {
final CVTerm cvTerm = daoFactory.getCvTermDao().getByNameAndCvId(name, CvId.VARIABLES.getId());
final CVTerm cvTerm = this.daoFactory.getCvTermDao().getByNameAndCvId(name, CvId.VARIABLES.getId());
if (cvTerm != null && cvTerm.getCvTermId() != null) {
return this.getStandardVariableBuilder().create(cvTerm.getCvTermId(), programUUID);
}
Expand Down Expand Up @@ -319,8 +319,7 @@ public StandardVariable getByPropertyScaleMethodRole(
}

public Integer getIdByPropertyScaleMethod(final Integer propertyId, final Integer scaleId, final Integer methodId) {
Integer stdVariableId = null;
stdVariableId = daoFactory.getCvTermDao().getStandadardVariableIdByPropertyScaleMethod(propertyId, scaleId, methodId, "DESC");
final Integer stdVariableId = this.daoFactory.getCvTermDao().getStandadardVariableIdByPropertyScaleMethod(propertyId, scaleId, methodId, "DESC");
return stdVariableId;
}

Expand All @@ -333,7 +332,7 @@ public Map<String, List<StandardVariable>> getStandardVariablesInProjects(final
// Trim all header names
final List<String> headerNamesTrimmed = new ArrayList<>(Lists.transform(headerNames, new Function<String, String>() {

public String apply(String s) {
public String apply(final String s) {
// Transform header names to uppercase; header names can be in lowercase or combination when defined in file
return s.toUpperCase().trim();
}
Expand Down Expand Up @@ -407,7 +406,11 @@ private void removeHeaderNamesWithMatch(
protected void setRoleOfVariables(final List<StandardVariable> variables, final Map<Integer, VariableType> varIdsWithType) {
for (final StandardVariable standardVariable : variables) {
final VariableType type = varIdsWithType.get(standardVariable.getId());
if (type != null) {
// Experimental Design Variables will have Trial_Environment phenotypic type
final int standardVarialbeId = standardVariable.getId();
if (WorkbookBuilder.EXPERIMENTAL_DESIGN_VARIABLES.contains(standardVarialbeId)) {
standardVariable.setPhenotypicType(PhenotypicType.TRIAL_ENVIRONMENT);
} else if(type != null) {
standardVariable.setPhenotypicType(type.getRole());
}
}
Expand Down Expand Up @@ -435,39 +438,37 @@ public Map<String, Map<Integer, VariableType>> getStandardVariableIdsWithTypeByA

public Map<String, Map<Integer, VariableType>> getStandardVariableIdsWithTypeForTerms(final List<String> termNames) {
if (!termNames.isEmpty()) {
return daoFactory.getCvTermDao().getTermIdsWithTypeByNameOrSynonyms(termNames, CvId.VARIABLES.getId());
return this.daoFactory.getCvTermDao().getTermIdsWithTypeByNameOrSynonyms(termNames, CvId.VARIABLES.getId());
}
return new HashMap<>();
}

public Map<String, Map<Integer, VariableType>> getStandardVariableIdsForTraits(final List<String> traitNames) {
if (!traitNames.isEmpty()) {
return daoFactory.getCvTermDao().getStandardVariableIdsWithTypeByProperties(traitNames);
return this.daoFactory.getCvTermDao().getStandardVariableIdsWithTypeByProperties(traitNames);
}
return new HashMap<>();
}

public Integer getIdByTermId(final int cvTermId, final TermId termId) {
Integer stdVariableId = null;
stdVariableId = daoFactory.getCvTermDao().getStandardVariableIdByTermId(cvTermId, termId);
final Integer stdVariableId = this.daoFactory.getCvTermDao().getStandardVariableIdByTermId(cvTermId, termId);
return stdVariableId;
}

public CVTerm getCvTerm(final String name, final int cvId) {
return daoFactory.getCvTermDao().getByNameAndCvId(name, cvId);
return this.daoFactory.getCvTermDao().getByNameAndCvId(name, cvId);
}

public Integer getIdByPropertyScaleMethodRole(
final Integer propertyId, final Integer scaleId, final Integer methodId,
final PhenotypicType role) {
Integer stdVariableId = null;
stdVariableId = daoFactory.getCvTermDao().getStandadardVariableIdByPropertyScaleMethodRole(propertyId, scaleId, methodId, role);
final Integer stdVariableId = this.daoFactory.getCvTermDao().getStandadardVariableIdByPropertyScaleMethodRole(propertyId, scaleId, methodId, role);
return stdVariableId;
}

public boolean validateEnumerationUsage(final int standardVariableId, final int enumerationId) {
final Integer storedInId =
daoFactory.getCvTermRelationshipDao().getObjectIdByTypeAndSubject(TermId.STORED_IN.getId(), standardVariableId).get(0);
this.daoFactory.getCvTermRelationshipDao().getObjectIdByTypeAndSubject(TermId.STORED_IN.getId(), standardVariableId).get(0);
final String value = String.valueOf(enumerationId);
if (storedInId == TermId.STUDY_INFO_STORAGE.getId() || storedInId == TermId.DATASET_INFO_STORAGE.getId()) {
return !this.isExistsPropertyByTypeAndValue(standardVariableId, value);
Expand Down Expand Up @@ -512,6 +513,6 @@ private boolean isExistsPhenotypeByTypeAndValue(final Integer variateId, final S
}

public List<StandardVariableReference> findAllByProperty(final int propertyId) {
return new ArrayList<>(daoFactory.getCvTermDao().getStandardVariablesOfProperty(propertyId));
return new ArrayList<>(this.daoFactory.getCvTermDao().getStandardVariablesOfProperty(propertyId));
}
}
9 changes: 8 additions & 1 deletion src/main/java/org/generationcp/middleware/operation/builder/WorkbookBuilder.java
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Expand Up @@ -372,7 +372,13 @@ public Workbook createStudyVariableSettings(final int id) {
if (PhenotypicType.TRIAL_ENVIRONMENT == varType.getRole()) {
value = projectProperty.getValue();
if (value == null) {
value = StringUtils.EMPTY;
// During import of study, experiment design values are not set in ProjectProperty so we resolve them from GeolocationProperty
if (VariableType.ENVIRONMENT_DETAIL.equals(varType)) {
final GeolocationPropertyDao geolocationPropertyDao = this.daoFactory.getGeolocationPropertyDao();
value = geolocationPropertyDao.getGeolocationPropValue(stdVariable.getId(), id);
} else {
value = StringUtils.EMPTY;
}
}
} else if (PhenotypicType.VARIATE == varType.getRole()) {// TODO traits
// constants, no need to retrieve the value if it's a trial study
Expand Down Expand Up @@ -735,6 +741,7 @@ private List<MeasurementVariable> removeConstantsFromVariates(
for (final MeasurementVariable constant : constants) {
if (variate.getTermId() == constant.getTermId()) {
found = true;
break;
}
}
}
Expand Down
48 changes: 48 additions & 0 deletions src/main/java/org/generationcp/middleware/operation/saver/WorkbookSaver.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import org.apache.commons.lang3.StringUtils;
import org.generationcp.middleware.dao.LocationDAO;
import org.generationcp.middleware.domain.dms.*;
import org.generationcp.middleware.domain.dms.Enumeration;
import org.generationcp.middleware.domain.etl.MeasurementData;
import org.generationcp.middleware.domain.etl.MeasurementRow;
import org.generationcp.middleware.domain.etl.MeasurementVariable;
Expand All @@ -25,6 +26,7 @@
import org.generationcp.middleware.hibernate.HibernateSessionProvider;
import org.generationcp.middleware.manager.DaoFactory;
import org.generationcp.middleware.manager.Operation;
import org.generationcp.middleware.manager.api.OntologyDataManager;
import org.generationcp.middleware.manager.api.StudyDataManager;
import org.generationcp.middleware.operation.builder.WorkbookBuilder;
import org.generationcp.middleware.operation.transformer.etl.ExperimentValuesTransformer;
Expand Down Expand Up @@ -76,6 +78,9 @@ public class WorkbookSaver extends Saver {
@Resource
private StudyDataManager studyDataManager;

@Resource
private OntologyDataManager ontologyDataManager;

public WorkbookSaver() {

}
Expand Down Expand Up @@ -136,6 +141,8 @@ public Map saveVariables(final Workbook workbook, final String programUUID) {
variableTypeMap.put(WorkbookSaver.TRIALVARIABLES, trialVariables);
variableTypeMap.put(WorkbookSaver.EFFECTVARIABLE, effectVariables);
// -- measurementVariables

this.setRMAPValueIfNecessary(trialMV, programUUID);
measurementVariableMap.put(WorkbookSaver.TRIALMV, trialMV);

final List<MeasurementVariable> effectMV = workbook.getMeasurementDatasetVariables();
Expand Down Expand Up @@ -520,6 +527,10 @@ private int createLocationsAndSetToObservations(
if (geolocationId == 0) {
// if geolocationId does not exist, create the geolocation
// and set to row.locationId

//Set RMAP Value if Necessary
this.setRMAPValueObservationIfNecessary(row.getDataList(), programUUID);

final TimerWatch watch = new TimerWatch("transformTrialEnvironment in createLocationsAndSetToObservations");
final VariableList geolocation =
this.getVariableListTransformer().transformTrialEnvironment(row, trialFactors, trialHeaders);
Expand Down Expand Up @@ -1346,5 +1357,42 @@ private void createMeansExperiments(
}
}

private void setRMAPValueIfNecessary(final List<MeasurementVariable> mvarList, final String programUUID) {
final List<MeasurementVariable> catVar = mvarList.stream().filter(variable -> variable.getTermId() == TermId.REPLICATIONS_MAP
.getId()).collect(Collectors.toList());
if (catVar != null) {
for (final MeasurementVariable mVar : catVar) {
final StandardVariable strdVariable = this.ontologyDataManager.findStandardVariableByTraitScaleMethodNames(mVar.getProperty(), mVar.getScale(), mVar.getMethod(), programUUID);
if (strdVariable != null && strdVariable.getEnumerations() !=null) {
final List<Enumeration> possibleValues = strdVariable.getEnumerations().stream().filter(enumeration -> enumeration.getName().equals(mVar.getValue())).collect(
Collectors.toList());
if (possibleValues != null && possibleValues.size() > 0) {
mVar.setValue(String.valueOf(possibleValues.get(0).getId()));
}
}
}
}
}

private void setRMAPValueObservationIfNecessary(final List<MeasurementData> mvarList, final String programUUID) {
final List<MeasurementData> catVar = mvarList.stream().filter(variable -> variable.getMeasurementVariable() != null && variable.getMeasurementVariable().getTermId() == TermId.REPLICATIONS_MAP
.getId()).collect(Collectors.toList());
if (catVar != null) {
for (final MeasurementData mData : catVar) {
final MeasurementVariable mVar = mData.getMeasurementVariable();
final StandardVariable strdVariable;
strdVariable =
this.ontologyDataManager.findStandardVariableByTraitScaleMethodNames(mVar.getProperty(), mVar.getScale(), mVar.getMethod(), programUUID);
if (strdVariable != null && strdVariable.getEnumerations() !=null) {
final List<Enumeration> possibleValues = strdVariable.getEnumerations().stream().filter(enumeration -> enumeration.getName().equals(mData.getValue())).collect(
Collectors.toList());
if (possibleValues != null && possibleValues.size() > 0) {
mVar.setValue(String.valueOf(possibleValues.get(0).getId()));
mData.setValue(String.valueOf(possibleValues.get(0).getId()));
}
}
}
}
}

}
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