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[DUOS-2830][risk=no] Update DAR Data Use translations for V3 (#2205)
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Co-authored-by: fboulnois <[email protected]>
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@rushtong @fboulnois
rushtong and fboulnois authored Dec 8, 2023
1 parent d413c3e commit b2489f2
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Showing 3 changed files with 205 additions and 311 deletions.
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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