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[DUOS-2830][risk=no] Update DAR Data Use translations for V3 #2205

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merged 6 commits into from
Dec 8, 2023
Merged

[DUOS-2830][risk=no] Update DAR Data Use translations for V3 #2205

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27b8857
fixes
rushtong Dec 5, 2023
4a0cdae
cleanup and sonarlint suggestions
rushtong Dec 6, 2023
ccf2991
more cleanup, deprecation, tests
rushtong Dec 6, 2023
cbdfad8
clean up DAR other conditions
rushtong Dec 6, 2023
c5220d8
tests
rushtong Dec 6, 2023
3496610
Update src/main/java/org/broadinstitute/consent/http/service/UseRestr…
rushtong Dec 6, 2023
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40 changes: 34 additions & 6 deletions src/main/java/org/broadinstitute/consent/http/models/DataUse.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,25 +22,39 @@ public class DataUse {
private Boolean hmbResearch;
private List<String> diseaseRestrictions;
private Boolean populationOriginsAncestry;
@Deprecated
private Boolean populationStructure;
private Boolean commercialUse;
private Boolean nonProfitUse;
private Boolean methodsResearch;
@Deprecated
private String aggregateResearch;
@Deprecated
private String controlSetOption;
private boolean controls;
private Boolean controls;
private String gender;
private Boolean pediatric;
private boolean population;
private Boolean population;
@Deprecated
private List<String> populationRestrictions;
@Deprecated
private Boolean otherRestrictions;
private String dateRestriction;
@Deprecated
private Boolean recontactingDataSubjects;
@Deprecated
private String recontactMay;
@Deprecated
private String recontactMust;
@Deprecated
private String genomicPhenotypicData;
@Deprecated
private String cloudStorage;
// Also known as "irb"
private Boolean ethicsApprovalRequired;
@Deprecated
private Boolean collaboratorRequired;
@Deprecated
private String geographicalRestrictions;
private String other;
private String secondaryOther;
Expand All @@ -51,12 +65,17 @@ public class DataUse {
private Boolean vulnerablePopulations;
private Boolean psychologicalTraits;
private Boolean notHealth;
@Deprecated
private Boolean nonBiomedical;
@Deprecated
private Boolean manualReview;
private Boolean geneticStudiesOnly;
private Boolean publicationResults;
@Deprecated
private Boolean genomicResults;
@Deprecated
private String genomicSummaryResults;
@Deprecated
private Boolean collaborationInvestigators;
private String publicationMoratorium;

Expand Down Expand Up @@ -108,6 +127,14 @@ public void setCommercialUse(Boolean commercialUse) {
this.commercialUse = commercialUse;
}

public Boolean getNonProfitUse() {
return nonProfitUse;
}

public void setNonProfitUse(Boolean nonProfitUse) {
this.nonProfitUse = nonProfitUse;
}

public Boolean getMethodsResearch() {
return methodsResearch;
}
Expand Down Expand Up @@ -364,19 +391,19 @@ public void setPublicationMoratorium(String publicationMoratorium) {
this.publicationMoratorium = publicationMoratorium;
}

public boolean getControls() {
public Boolean getControls() {
return controls;
}

public void setControls(boolean controls) {
public void setControls(Boolean controls) {
this.controls = controls;
}

public boolean getPopulation() {
public Boolean getPopulation() {
return population;
}

public void setPopulation(boolean population) {
public void setPopulation(Boolean population) {
this.population = population;
}

Expand Down Expand Up @@ -423,6 +450,7 @@ public boolean equals(Object o) {
&& Objects.equal(getPopulationOriginsAncestry(), dataUse.getPopulationOriginsAncestry())
&& Objects.equal(getPopulationStructure(), dataUse.getPopulationStructure())
&& Objects.equal(getCommercialUse(), dataUse.getCommercialUse())
&& Objects.equal(getNonProfitUse(), dataUse.getNonProfitUse())
&& Objects.equal(getMethodsResearch(), dataUse.getMethodsResearch())
&& Objects.equal(getAggregateResearch(), dataUse.getAggregateResearch())
&& Objects.equal(getControlSetOption(), dataUse.getControlSetOption())
Expand Down
195 changes: 57 additions & 138 deletions src/main/java/org/broadinstitute/consent/http/service/UseRestrictionConverter.java
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Original file line number Diff line number Diff line change
@@ -1,33 +1,23 @@
package org.broadinstitute.consent.http.service;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
import jakarta.ws.rs.InternalServerErrorException;
import jakarta.ws.rs.client.Client;
import jakarta.ws.rs.client.Entity;
import jakarta.ws.rs.client.WebTarget;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
import org.apache.commons.collections4.CollectionUtils;
import org.broadinstitute.consent.http.configurations.ServicesConfiguration;
import org.broadinstitute.consent.http.enumeration.DataUseTranslationType;
import org.broadinstitute.consent.http.models.DataAccessRequest;
import org.broadinstitute.consent.http.models.DataUse;
import org.broadinstitute.consent.http.models.OntologyEntry;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.broadinstitute.consent.http.util.ConsentLogger;

@SuppressWarnings("WeakerAccess")
public class UseRestrictionConverter {
public class UseRestrictionConverter implements ConsentLogger {

private static final Logger LOGGER = LoggerFactory.getLogger("UseRestrictionConverter");
private static final ObjectMapper mapper = new ObjectMapper();
private final ServicesConfiguration servicesConfiguration;
private final Client client;

Expand All @@ -36,82 +26,6 @@ public UseRestrictionConverter(Client client, ServicesConfiguration config) {
this.servicesConfiguration = config;
}

/**
* This method, and its counterpart that processes a DataAccessRequest, translates DAR questions
* to a DataUse
*
* @param json String in json form
* @return DataUse
*/
@SuppressWarnings("unchecked")
public DataUse parseDataUsePurpose(String json) {
Map<String, Object> form = parseAsMap(json);
DataUse dataUse = new DataUse();

//
// Research related entries
//
if (Boolean.parseBoolean(form.getOrDefault("methods", false).toString())) {
dataUse.setMethodsResearch(true);
}
if (Boolean.parseBoolean(form.getOrDefault("population", false).toString())) {
dataUse.setPopulationStructure(true);
}
if (Boolean.parseBoolean(form.getOrDefault("controls", false).toString())) {
dataUse.setControlSetOption("Yes");
}

//
// Diseases related entries
//
ArrayList<HashMap<String, String>> ontologies = (ArrayList<HashMap<String, String>>) form.get(
"ontologies");
if (CollectionUtils.isNotEmpty(ontologies)) {
List<String> restrictions = ontologies
.stream()
.filter(Objects::nonNull)
.filter(hashMap -> hashMap.containsKey("id"))
.map(hashMap -> hashMap.get("id"))
.collect(Collectors.toList());
if (!restrictions.isEmpty()) {
dataUse.setDiseaseRestrictions(restrictions);
}
}

//
// gender, age and commercial status entries
//
boolean forProfitOnly = Boolean.parseBoolean(form.getOrDefault("forProfit", false).toString());
dataUse.setCommercialUse(forProfitOnly);

// limited to one gender + children analysis
boolean oneGenderOnly = Boolean.parseBoolean(form.getOrDefault("onegender", false).toString());
String selectedGender = (String) form.getOrDefault("gender", "X");
boolean pediatricsOnly = Boolean.parseBoolean(form.getOrDefault("pediatric", false).toString());

if (oneGenderOnly) {
if (selectedGender.equalsIgnoreCase("M")) {
dataUse.setGender("Male");
} else if (selectedGender.equalsIgnoreCase("F")) {
dataUse.setGender("Female");
}
}

if (pediatricsOnly) {
dataUse.setPediatric(true);
}

if (Boolean.parseBoolean(form.getOrDefault("poa", false).toString())) {
dataUse.setPopulationOriginsAncestry(true);
}

if (Boolean.parseBoolean(form.getOrDefault("hmb", false).toString())) {
dataUse.setHmbResearch(true);
}

return dataUse;
}

/**
* This method, and its counterpart that processes a map, translates DAR questions to a DataUse
*
Expand All @@ -124,77 +38,91 @@ public DataUse parseDataUsePurpose(DataAccessRequest dar) {
//
// Research related entries
//
if (Objects.nonNull(dar.getData().getMethods())) {
if (Objects.nonNull(dar.getData().getMethods()) && Boolean.TRUE.equals(dar.getData().getMethods())) {
dataUse.setMethodsResearch(dar.getData().getMethods());
}
if (Objects.nonNull(dar.getData().getPopulation())) {
dataUse.setPopulationStructure(dar.getData().getPopulation());
if (Objects.nonNull(dar.getData().getPopulation()) && Boolean.TRUE.equals(dar.getData().getPopulation())) {
dataUse.setPopulation(dar.getData().getPopulation());
}
if (Objects.nonNull(dar.getData().getControls())) {
dataUse.setControlSetOption("Yes");
if (Objects.nonNull(dar.getData().getControls()) && Boolean.TRUE.equals(dar.getData().getControls())) {
dataUse.setControls(dar.getData().getControls());
}

//
// Diseases related entries
//

List<String> ontologies = dar.getData().getOntologies()
.stream().map(OntologyEntry::getId).collect(Collectors.toList());
List<String> ontologies = dar.getData()
.getOntologies()
.stream()
.map(OntologyEntry::getId)
.toList();
if (CollectionUtils.isNotEmpty(ontologies)) {
dataUse.setDiseaseRestrictions(ontologies);
}

//
// gender, age and commercial status entries
//
// commercial status
if (Objects.nonNull(dar.getData().getForProfit())) {
dataUse.setCommercialUse(dar.getData().getForProfit());
Boolean isForProfit = Boolean.TRUE.equals(dar.getData().getForProfit());
dataUse.setCommercialUse(isForProfit);
dataUse.setNonProfitUse(!isForProfit);
}

// limited to one gender + children analysis
if (Objects.nonNull(dar.getData().getOneGender()) && Objects.nonNull(
dar.getData().getGender())) {
boolean oneGenderOnly = dar.getData().getOneGender();
// gender
if (Objects.nonNull(dar.getData().getGender())) {
String selectedGender = dar.getData().getGender();
if (oneGenderOnly) {
if (selectedGender.equalsIgnoreCase("M")) {
dataUse.setGender("Male");
} else if (selectedGender.equalsIgnoreCase("F")) {
dataUse.setGender("Female");
}
if (selectedGender.equalsIgnoreCase("M")) {
dataUse.setGender("Male");
} else if (selectedGender.equalsIgnoreCase("F")) {
dataUse.setGender("Female");
}
}
if (Objects.nonNull(dar.getData().getPediatric())) {
if (dar.getData().getPediatric()) {
// pediatric
if (Objects.nonNull(dar.getData().getPediatric()) && (Boolean.TRUE.equals(dar.getData().getPediatric()))) {
dataUse.setPediatric(true);
}
}

if (Objects.nonNull(dar.getData().getPoa())) {
if (dar.getData().getPoa()) {
dataUse.setPopulationOriginsAncestry(true);
}
}

if (Objects.nonNull(dar.getData().getHmb())) {
if (dar.getData().getHmb()) {
if (Objects.nonNull(dar.getData().getHmb()) && (Boolean.TRUE.equals(dar.getData().getHmb()))) {
dataUse.setHmbResearch(true);
}

}

// Other Conditions
if (Objects.nonNull(dar.getData().getOther())) {
dataUse.setOtherRestrictions(dar.getData().getOther());
}
if (Objects.nonNull(dar.getData().getOtherText())) {
if (Objects.nonNull(dar.getData().getOther())
&& Boolean.TRUE.equals(dar.getData().getOther())
&& Objects.nonNull(dar.getData().getOtherText())) {
dataUse.setOtherRestrictions(true);
dataUse.setOther(dar.getData().getOtherText());
}

if (Objects.nonNull(dar.getData().getNotHealth())) {
if ((Objects.nonNull(dar.getData().getIllegalBehavior())) && Boolean.TRUE.equals(dar.getData()
.getIllegalBehavior())) {
dataUse.setIllegalBehavior(dar.getData().getIllegalBehavior());
}

if ((Objects.nonNull(dar.getData().getSexualDiseases())) && Boolean.TRUE.equals(dar.getData()
.getSexualDiseases())) {
dataUse.setSexualDiseases(dar.getData().getSexualDiseases());
}

if ((Objects.nonNull(dar.getData().getStigmatizedDiseases())) && Boolean.TRUE.equals(dar.getData()
.getStigmatizedDiseases())) {
dataUse.setStigmatizeDiseases(dar.getData().getStigmatizedDiseases());
}

if ((Objects.nonNull(dar.getData().getVulnerablePopulation())) && Boolean.TRUE.equals(dar.getData()
.getVulnerablePopulation())) {
dataUse.setVulnerablePopulations(dar.getData().getVulnerablePopulation());
}

if ((Objects.nonNull(dar.getData().getPsychiatricTraits())) && Boolean.TRUE.equals(dar.getData()
.getPsychiatricTraits())) {
dataUse.setPsychologicalTraits(dar.getData().getPsychiatricTraits());
}

if ((Objects.nonNull(dar.getData().getNotHealth())) && Boolean.TRUE.equals(dar.getData().getNotHealth())) {
dataUse.setNotHealth(dar.getData().getNotHealth());
dataUse.setNonBiomedical(dar.getData().getNotHealth());
}

}
Expand All @@ -210,20 +138,11 @@ public String translateDataUse(DataUse dataUse, DataUseTranslationType type) {
try {
return response.readEntity(String.class);
} catch (Exception e) {
LOGGER.error("Error parsing response from Ontology service: " + e);
logException("Error parsing response from Ontology service", e);
}
}
LOGGER.error("Error response from Ontology service: " + response.readEntity(String.class));
logException("Error response from Ontology service: " + response.readEntity(String.class), new InternalServerErrorException());
return null;
}

public Map<String, Object> parseAsMap(String str) {
ObjectReader reader = mapper.readerFor(Map.class);
try {
return reader.readValue(str);
} catch (IOException e) {
LOGGER.debug("While parsing as a Map ...", e);
}
return null;
}
}
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