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Merge pull request #41 from KPMP/KPMP-5569_add-clinical-data-to-ES-index
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add clinical information with endpoint
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@zwright
zwright authored Nov 5, 2024
2 parents f5f652d + 3ee637b commit cb0c2dc
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Showing 9 changed files with 707 additions and 17 deletions.
1 change: 1 addition & 0 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ dependencies {
implementation 'org.springframework.boot:spring-boot-starter-web'
implementation 'org.springframework.boot:spring-boot-starter-data-jpa'
implementation 'com.mysql:mysql-connector-j:8.3.0'
implementation 'org.apache.commons:commons-text:1.12.0'

implementation 'com.graphql-java:graphql-spring-boot-starter:5.0.2'
implementation 'com.graphql-java:graphiql-spring-boot-starter:5.0.2'
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320 changes: 310 additions & 10 deletions src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetDisplay.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,32 +2,47 @@

import java.util.HashSet;
import java.util.TreeSet;

import org.apache.commons.text.WordUtils;

import java.util.Set;
import com.fasterxml.jackson.annotation.JsonProperty;

public class RepositoryDatasetDisplay {
private static final int UUID_LENGTH = 37;
private String dlFileId;
private Set<String> redcapId;
private Set<String> sampleType;
private Set<String> enrollmentCategory;
private Set<String> ageBinned;
private Set<String> sex;
private Set<String> doi;
private String access;
private String platform;
private String releaseVersion;
private Set<String> protocol;
private Set<String> tissueSource;
private Set<String> experimentalStrategy;
private Set<String> workflowType;
private String dataFormat;
private String dataCategory;
private String dataType;
private Long fileSize;
private String fileName;
private String packageId;
private String fileNameSort;
private Set<String> protocol;
private Set<String> tissueSource;
private Set<String> experimentalStrategy;
private Set<String> workflowType;
private Set<String> redcapId;
private Set<String> sampleType;
private Set<String> enrollmentCategory;
private Set<String> ageBinned;
private Set<String> sex;
private Set<String> doi;
private Set<String> primaryAdjudicatedCategory;
private Set<String> kdigoStage;
private Set<String> baselineEgfr;
private Set<String> proteinuria;
private Set<String> a1c;
private Set<String> albuminuria;
private Set<String> diabetesDuration;
private Set<String> diabetesHistory;
private Set<String> hypertensionHistory;
private Set<String> hypertensionDuration;
private Set<String> race;
private Set<String> onRaasBlockade;

public RepositoryDatasetDisplay(RepositoryFileDataset repositoryFile) {
dlFileId = repositoryFile.getId().getDlFileId();
Expand All @@ -41,6 +56,19 @@ public RepositoryDatasetDisplay(RepositoryFileDataset repositoryFile) {
tissueSource = new HashSet<String>();
experimentalStrategy = new TreeSet<String>();
workflowType = new HashSet<String>();
a1c = new HashSet<String>();
albuminuria = new HashSet<String>();
baselineEgfr = new HashSet<String>();
diabetesDuration = new HashSet<String>();
diabetesHistory = new HashSet<String>();
primaryAdjudicatedCategory = new HashSet<String>();
kdigoStage = new HashSet<String>();
proteinuria = new HashSet<String>();
hypertensionDuration = new HashSet<String>();
hypertensionHistory = new HashSet<String>();
race = new HashSet<String>();
onRaasBlockade = new HashSet<String>();

redcapId.add(repositoryFile.getId().getRedcapId());
if (shouldAdd(repositoryFile.getSampleType())) {
sampleType.add(repositoryFile.getSampleType());
Expand Down Expand Up @@ -69,6 +97,42 @@ public RepositoryDatasetDisplay(RepositoryFileDataset repositoryFile) {
if(shouldAdd(repositoryFile.getWorkflowType())){
workflowType.add(repositoryFile.getWorkflowType());
}
if(shouldAdd(repositoryFile.getA1c())){
a1c.add(repositoryFile.getA1c());
}
if(shouldAdd(repositoryFile.getAlbuminuria())){
albuminuria.add(repositoryFile.getAlbuminuria());
}
if(shouldAdd(repositoryFile.getBaselineEgfr())){
baselineEgfr.add(repositoryFile.getBaselineEgfr());
}
if(shouldAdd(repositoryFile.getDiabetesDuration())){
diabetesDuration.add(repositoryFile.getDiabetesDuration());
}
if(shouldAdd(repositoryFile.getDiabetesHistory())){
diabetesHistory.add(repositoryFile.getDiabetesHistory());
}
if(shouldAdd(repositoryFile.getPrimaryAdjudicatedCategory())){
primaryAdjudicatedCategory.add(repositoryFile.getPrimaryAdjudicatedCategory());
}
if(shouldAdd(repositoryFile.getKdigoStage())){
kdigoStage.add(repositoryFile.getKdigoStage());
}
if(shouldAdd(repositoryFile.getProteinuria())){
proteinuria.add(repositoryFile.getProteinuria());
}
if(shouldAdd(repositoryFile.getHypertensionDuration())){
hypertensionDuration.add(repositoryFile.getHypertensionDuration());
}
if(shouldAdd(repositoryFile.getHypertensionHistory())){
hypertensionHistory.add(repositoryFile.getHypertensionHistory());
}
if(shouldAdd(repositoryFile.getRace())){
race.add(repositoryFile.getRace());
}
if(shouldAdd(repositoryFile.getOnRaasBlockade())){
onRaasBlockade.add(repositoryFile.getOnRaasBlockade());
}
access = repositoryFile.getAccess();
dataFormat = repositoryFile.getDataFormat();
platform = repositoryFile.getPlatform();
Expand Down Expand Up @@ -463,4 +527,240 @@ private boolean shouldAdd(String value) {
return true;
}

@JsonProperty("primary_adjudicated_category")
public Set<String> getPrimaryAdjudicatedCategory() {
if(this.primaryAdjudicatedCategory.isEmpty() ){
return null;
}else{
return this.primaryAdjudicatedCategory;
}
}

public void addPrimaryAdjudicatedCategory(String primaryAdjudicatedCategory) {
if(primaryAdjudicatedCategory != null && !primaryAdjudicatedCategory.isEmpty()){
this.primaryAdjudicatedCategory.add(primaryAdjudicatedCategory);
}
}

public void setPrimaryAdjudicatedCat(Set<String> primaryAdjudicatedCategory) {
this.primaryAdjudicatedCategory = primaryAdjudicatedCategory;
}

@JsonProperty("kdigo_stage")
public Set<String> getKdigoStage() {
if(this.kdigoStage.isEmpty()){
return null;
}else{
return this.kdigoStage;
}
}

public void addKdigoStage(String kdigoStage) {
if(kdigoStage != null && !kdigoStage.isEmpty()){
this.kdigoStage.add(kdigoStage);
}
}

public void setKdigoStage(Set<String> kdigoStage) {
this.kdigoStage = kdigoStage;
}

@JsonProperty("baseline_egfr")
public Set<String> getBaselineEgfr() {
if(this.baselineEgfr.isEmpty()){
return null;
}else{
return this.baselineEgfr;
}
}

public void addBaselineEgfr(String baselineEgfr) {
if(baselineEgfr != null && !baselineEgfr.isEmpty()){
this.baselineEgfr.add(baselineEgfr);
}
}

public void setBaselineEgfr(Set<String> baselineEgfr) {
this.baselineEgfr = baselineEgfr;
}

@JsonProperty("proteinuria")
public Set<String> getProteinuria() {
if(this.proteinuria.isEmpty()){
return null;
}else{
return this.proteinuria;
}
}

public void addProteinuria(String proteinuria) {
if(proteinuria != null && !proteinuria.isEmpty()){
this.proteinuria.add(proteinuria);
}
}

public void setProteinuria(Set<String> proteinuria) {
this.proteinuria = proteinuria;
}

@JsonProperty("a1c")
public Set<String> getA1c() {
if(this.a1c.isEmpty()){
return null;
}else{
return this.a1c;
}
}

public void addA1c(String a1c) {
if(a1c != null && !a1c.isEmpty()){
this.a1c.add(a1c);
}
}

public void setA1c(Set<String> a1c) {
this.a1c = a1c;
}

@JsonProperty("albuminuria")
public Set<String> getAlbuminuria() {
if(this.albuminuria.isEmpty()){
return null;
}else{
return this.albuminuria;
}
}

public void addAlbuminuria(String albuminuria) {
if(albuminuria != null && !albuminuria.isEmpty()){
this.albuminuria.add(albuminuria);
}
}

public void setAlbuminuria(Set<String> albuminuria) {
this.albuminuria = albuminuria;
}

@JsonProperty("diabetes_duration")
public Set<String> getDiabetesDuration() {
if(this.diabetesDuration.isEmpty()){
return null;
}else{
return this.diabetesDuration;
}
}

public void addDiabetesDuration(String diabetesDuration) {
if(diabetesDuration != null && !diabetesDuration.isEmpty()){
this.diabetesDuration.add(diabetesDuration);
}
}

public void setDiabetesDuration(Set<String> diabetesDuration) {
this.diabetesDuration = diabetesDuration;
}

@JsonProperty("diabetes_history")
public Set<String> getDiabetesHistory() {
if(this.diabetesHistory.isEmpty()){
return null;
}else{
return fixCapitalization(this.diabetesHistory);
}
}

public void addDiabetesHistory(String diabetesHistory) {
if(diabetesHistory != null && !diabetesHistory.isEmpty()){
this.diabetesHistory.add(diabetesHistory);
}
}

public void setDiabetesHistory(Set<String> diabetesHistory) {
this.diabetesHistory = diabetesHistory;
}

@JsonProperty("hypertension_history")
public Set<String> getHypertensionHistory() {
if(this.hypertensionHistory.isEmpty()){
return null;
}else{
return fixCapitalization(this.hypertensionHistory);
}
}

public void addHypertensionHistory(String hypertensionHistory) {
if(hypertensionHistory != null && !hypertensionHistory.isEmpty()){
this.hypertensionHistory.add(hypertensionHistory);
}
}

public void setHypertensionHistory(Set<String> hypertensionHistory) {
this.hypertensionHistory = hypertensionHistory;
}

@JsonProperty("hypertension_duration")
public Set<String> getHypertensionDuration() {
if(this.hypertensionDuration.isEmpty()){
return null;
}else{
return this.hypertensionDuration;
}
}

public void addHypertensionDuration(String hypertensionDuration) {
if(hypertensionDuration != null && !hypertensionDuration.isEmpty()){
this.hypertensionDuration.add(hypertensionDuration);
}
}

public void setHypertensionDuration(Set<String> hypertensionDuration) {
this.hypertensionDuration = hypertensionDuration;
}

@JsonProperty("ethnicity")
public Set<String> getRace() {
if(this.race.isEmpty()){
return null;
}else{
return this.race;
}
}

public void addRace(String race) {
if(race != null && !race.isEmpty()){
this.race.add(race);
}
}

public void setRace(Set<String> race) {
this.race = race;
}

@JsonProperty("on_raas_blockade")
public Set<String> getOnRaasBlockade() {
if(this.onRaasBlockade.isEmpty()){
return null;
}else{
return this.onRaasBlockade;
}
}

public void addOnRaasBlockade(String onRaasBlockade) {
if(onRaasBlockade != null && !onRaasBlockade.isEmpty()){
this.onRaasBlockade.add(onRaasBlockade);
}
}

public void setOnRaasBlockade(Set<String> onRaasBlockade) {
this.onRaasBlockade = onRaasBlockade;
}

public Set<String> fixCapitalization(Set<String> input){
Set<String> wordList = new HashSet<String>();
for (String string : input) {
String updatedInput = WordUtils.capitalizeFully(string);
wordList.add(updatedInput);
}
return wordList;
}
}
12 changes: 12 additions & 0 deletions src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetService.java
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Expand Up @@ -79,6 +79,18 @@ public List<RepositoryDatasetDisplay> getRepositoryDataset() throws Exception {
displayFile.addExperimentalStrategy(repositoryDataset.getId().getExperimentalStrategy());
displayFile.addDoi(repositoryDataset.getId().getDoi());
displayFile.addWorkflowType(repositoryDataset.getWorkflowType());
displayFile.addA1c(repositoryDataset.getA1c());
displayFile.addAlbuminuria(repositoryDataset.getAlbuminuria());
displayFile.addBaselineEgfr(repositoryDataset.getBaselineEgfr());
displayFile.addDiabetesDuration(repositoryDataset.getDiabetesDuration());
displayFile.addDiabetesHistory(repositoryDataset.getDiabetesHistory());
displayFile.addPrimaryAdjudicatedCategory(repositoryDataset.getPrimaryAdjudicatedCategory());
displayFile.addKdigoStage(repositoryDataset.getKdigoStage());
displayFile.addProteinuria(repositoryDataset.getProteinuria());
displayFile.addHypertensionDuration(repositoryDataset.getHypertensionDuration());
displayFile.addHypertensionHistory(repositoryDataset.getHypertensionHistory());
displayFile.addRace(repositoryDataset.getRace());
displayFile.addOnRaasBlockade(repositoryDataset.getOnRaasBlockade());
displayFile.setAccess(repositoryDataset.getAccess());
displayFiles.put(repositoryDataset.getId().getDlFileId(), displayFile);
} else {
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