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fix a lot of bugs
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@Dert1129
Dert1129 committed Nov 11, 2024
1 parent 58b04df commit d3c1a87
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Showing 13 changed files with 240 additions and 135 deletions.
4 changes: 2 additions & 2 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerDatasetDisplay.java
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Expand Up @@ -58,7 +58,7 @@ public SpatialViewerDatasetDisplay(SpatialViewerFileDataset svFile){
configType = svFile.getConfigType();
imageType = svFile.getImageType();
dataType = svFile.getDataType();
dlFileId = svFile.getId().getDlFileId();
dlFileId = svFile.getDlFileId();
fileName = svFile.getFileName();
packageId = svFile.getPackageId();
fileSize = svFile.getFileSize();
Expand Down Expand Up @@ -86,7 +86,7 @@ public SpatialViewerDatasetDisplay(SpatialViewerFileDataset svFile){
race = new HashSet<String>();


redcapId.add(svFile.getId().getRedcapId());
redcapId.add(svFile.getRedcapId());
if(shouldAdd(svFile.getAge())){
age.add(svFile.getAge());
}
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17 changes: 11 additions & 6 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerDatasetService.java
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Expand Up @@ -74,9 +74,9 @@ public List<SpatialViewerDataset> getSpatialViewerDataset() throws Exception {
Map<String, SpatialViewerDatasetDisplay> displayFiles = new HashMap<>();
Map<String, SpatialViewerExternalLinkDatasetDisplay> displayLinks = new HashMap<>();
for(SpatialViewerFileDataset spatialViewerFileDataset : datasetFiles){
if(displayFiles.containsKey(spatialViewerFileDataset.getId().getDlFileId())){
if(displayFiles.containsKey(spatialViewerFileDataset.getDlFileId())){
// update all of the list items in that display file
SpatialViewerDatasetDisplay displayFile = displayFiles.get(spatialViewerFileDataset.getId().getDlFileId());
SpatialViewerDatasetDisplay displayFile = displayFiles.get(spatialViewerFileDataset.getDlFileId());
displayFile.addA1c(spatialViewerFileDataset.getA1c());
displayFile.addAge(spatialViewerFileDataset.getAge());
displayFile.addAlbuminuria(spatialViewerFileDataset.getAlbuminuria());
Expand All @@ -92,30 +92,35 @@ public List<SpatialViewerDataset> getSpatialViewerDataset() throws Exception {
displayFile.addProteinuria(spatialViewerFileDataset.getProteinuria());
displayFile.addProtocol(spatialViewerFileDataset.getProtocol());
displayFile.addRace(spatialViewerFileDataset.getRace());
displayFile.addRedcapId(spatialViewerFileDataset.getId().getRedcapId());
displayFile.addRedcapId(spatialViewerFileDataset.getRedcapId());
displayFile.addSampleType(spatialViewerFileDataset.getSampleType());
displayFile.addSex(spatialViewerFileDataset.getSex());
displayFile.addTissueSource(spatialViewerFileDataset.getTissueSource());
displayFiles.put(spatialViewerFileDataset.getId().getDlFileId(), displayFile);
displayFiles.put(spatialViewerFileDataset.getDlFileId(), displayFile);
}else{
SpatialViewerDatasetDisplay displayFile = new SpatialViewerDatasetDisplay(spatialViewerFileDataset);
if(Double.compare(spatialViewerFileDataset.getReleaseVersion(), maxReleaseVersion) == EQUALITY_OPERATOR){
displayFile.setReleaseVersion("Recently Released - " + recentlyReleasedDate);
}else {
displayFile.setReleaseVersion(null);
}
displayFiles.put(spatialViewerFileDataset.getId().getDlFileId(), displayFile);
displayFiles.put(spatialViewerFileDataset.getDlFileId(), displayFile);
}

}
for(SpatialViewerExternalLinkDataset spatialViewerExternalLinkDataset : datasetLinks){
if(displayLinks.containsKey(spatialViewerExternalLinkDataset.getDlFileId())){
// update all of the list items in that display link
SpatialViewerExternalLinkDatasetDisplay displayLink = displayLinks.get(spatialViewerExternalLinkDataset.getDlFileId());
// do adders
}
SpatialViewerExternalLinkDatasetDisplay displayLink = new SpatialViewerExternalLinkDatasetDisplay(spatialViewerExternalLinkDataset);
if(Double.compare(spatialViewerExternalLinkDataset.getReleaseVersion(), maxLinkReleaseVersion) == EQUALITY_OPERATOR){
displayLink.setReleaseVersion("Recently Released - " + recentlyReleasedDate);
}else{
displayLink.setReleaseVersion(null);
}
displayLinks.put(spatialViewerExternalLinkDataset.getId().getDlFileId(), displayLink);
displayLinks.put(spatialViewerExternalLinkDataset.getId().getRedcapId(), displayLink);
}
datasetsFinal.addAll(displayFiles.values());
datasetsFinal.addAll(displayLinks.values());
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11 changes: 1 addition & 10 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerExternalLinkDataset.java
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Expand Up @@ -24,7 +24,6 @@ public class SpatialViewerExternalLinkDataset {
private String imageType;
private String dataType;
private String spectrackSampleId;
private String redcapId;
private int participantId;
private String age;
private String protocol;
Expand All @@ -33,6 +32,7 @@ public class SpatialViewerExternalLinkDataset {
private String tissueSource;
private String enrollmentCategory;
private Double releaseVersion;
@Column(name = "primary_adjudicated_cat")
private String primaryAdjudicatedCategory;
private String kdigoStage;
private String baselineEgfr;
Expand Down Expand Up @@ -196,15 +196,6 @@ public void setSpectrackSampleId(String spectrackSampleId) {
}


public String getRedcapId() {
return redcapId;
}

public void setRedcapId(String redcapId) {
this.redcapId = redcapId;
}


public int getParticipantId() {
return participantId;
}
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32 changes: 1 addition & 31 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerExternalLinkId.java
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Expand Up @@ -2,23 +2,11 @@

import java.io.Serializable;

import jakarta.persistence.Column;
// import jakarta.persistence.Column;
import jakarta.persistence.Embeddable;
@Embeddable
public class SpatialViewerExternalLinkId implements Serializable{
private String dlFileId;
private String redcapId;
private String experimentalStrategy;
private String doi;

@Column(name = "dl_file_id")
public String getDlFileId() {
return this.dlFileId;
}

public void setDlFileId(String dlFileId) {
this.dlFileId = dlFileId;
}

public String getRedcapId() {
return this.redcapId;
Expand All @@ -27,22 +15,4 @@ public String getRedcapId() {
public void setRedcapId(String redcapId) {
this.redcapId = redcapId;
}

public String getExperimentalStrategy() {
return this.experimentalStrategy;
}

public void setExperimentalStrategy(String experimentalStrategy) {
this.experimentalStrategy = experimentalStrategy;
}

public String getDoi() {
return this.doi;
}

public void setDoi(String doi) {
if (doi != null && !doi.isEmpty()){
this.doi = doi;
}
}
}
13 changes: 0 additions & 13 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerFileDataset.java
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Expand Up @@ -20,10 +20,6 @@
@Table(name = "sv_file_v")
public class SpatialViewerFileDataset {



@EmbeddedId
private SpatialViewerFileDatasetId id;
@Id
@Column(name = "file_id")
private int fileId;
Expand Down Expand Up @@ -69,15 +65,6 @@ public class SpatialViewerFileDataset {
)
@ManyToMany(fetch = FetchType.EAGER)
private List<File> relatedFiles;

public SpatialViewerFileDatasetId getId(){
return this.id;
}

public void setId(SpatialViewerFileDatasetId id){
this.id = id;
}


public int getFileId() {
return fileId;
Expand Down
20 changes: 0 additions & 20 deletions src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerFileDatasetId.java
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Expand Up @@ -8,8 +8,6 @@
public class SpatialViewerFileDatasetId implements Serializable{
private String dlFileId;
private String redcapId;
private String experimentalStrategy;
private String doi;

@Column(name = "dl_file_id")
public String getDlFileId() {
Expand All @@ -27,22 +25,4 @@ public String getRedcapId() {
public void setRedcapId(String redcapId) {
this.redcapId = redcapId;
}

public String getExperimentalStrategy() {
return this.experimentalStrategy;
}

public void setExperimentalStrategy(String experimentalStrategy) {
this.experimentalStrategy = experimentalStrategy;
}

public String getDoi() {
return this.doi;
}

public void setDoi(String doi) {
if (doi != null && !doi.isEmpty()){
this.doi = doi;
}
}
}
46 changes: 35 additions & 11 deletions src/main/resources/graphql/knowledge_environment.graphqls
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,13 @@ type SpatialViewerDataset {
configType: String
imageType: String
dataType: String
redcapId: String
age: String
protocol: String
redcapId: [String]
age: [String]
protocol: [String]
sampleType: String
sex: String
tissueSource: String
enrollmentCategory: String
sex: [String]
tissueSource: [String]
enrollmentCategory: [String]
spectrackSampleId: String
level: String # may be null
relatedFiles: [File] # may be null
Expand All @@ -34,6 +34,18 @@ type SpatialViewerDataset {
fileNameSort: String
participantIdSort: Int
imageTypeSort: String
primaryAdjudicatedCategory: String
kdigoStage: String
baselineEgfr: String
proteinuria: String
a1c: String
albuminuria: String
diabetesDuration: String
diabetesHistory: String
hypertensionDuration: String
hypertensionHistory: String
race: String
onRaasBlockade: String
}

type SpatialViewerExternalLink {
Expand All @@ -42,15 +54,27 @@ type SpatialViewerExternalLink {
imageType: String
dataType: String
spectrackSampleId: String
redcapId: String
redcapId: [String]
participantId: Int
age: String
protocol: String
protocol: [String]
sampleType: String
sex: String
tissueSource: String
enrollmentCategory: String
sex: [String]
tissueSource: [String]
enrollmentCategory: [String]
participantIdSort: Int
imageTypeSort: String
releaseVersion: String
primaryAdjudicatedCategory: String
kdigoStage: String
baselineEgfr: String
proteinuria: String
a1c: String
albuminuria: String
diabetesDuration: String
diabetesHistory: String
hypertensionDuration: String
hypertensionHistory: String
race: String
onRaasBlockade: String
}
1 change: 0 additions & 1 deletion src/test/java/org/kpmp/spatialViewerDataset/SpatialViewerDatasetDisplayTest.java
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Expand Up @@ -28,7 +28,6 @@ public class SpatialViewerDatasetDisplayTest {
public void setUp() throws Exception {
MockitoAnnotations.openMocks(this);

when(spatialViewerFileDataset.getId()).thenReturn(spatialViewerFileDatasetId);
spatialViewerDatasetDisplay = new SpatialViewerDatasetDisplay(spatialViewerFileDataset);
}

Expand Down
35 changes: 14 additions & 21 deletions src/test/java/org/kpmp/spatialViewerDataset/SpatialViewerDatasetServiceTest.java
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Expand Up @@ -5,6 +5,7 @@
import static org.mockito.Mockito.when;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.json.JSONException;
import org.junit.jupiter.api.AfterEach;
Expand Down Expand Up @@ -68,38 +69,30 @@ public void testGetSpatialViewerFileDataset() throws JSONException, Exception {
assertEquals(expectedResult, service.getSpatialViewerFileDataset());
}

@Test
@SuppressWarnings("unchecked")
@Test
public void testLoadEnterpriseSearch() throws JSONException, Exception {
when(env.getProperty("ES_API_TOKEN")).thenReturn("TOKEN");
HttpHeaders headers = new HttpHeaders();
headers.set("Authorization", "Bearer "+ "TOKEN");
headers.setContentType(MediaType.APPLICATION_JSON);

ArrayList<SpatialViewerDataset> results = new ArrayList<>();
List<SpatialViewerExternalLinkDataset> expectedResult1 = new ArrayList<>();
List<SpatialViewerFileDataset> expectedResult2 = new ArrayList<>();
SpatialViewerExternalLinkDataset spatialViewerDataset1 = new SpatialViewerExternalLinkDataset();
SpatialViewerExternalLinkDataset spatialViewerDataset2 = new SpatialViewerExternalLinkDataset();
SpatialViewerFileDataset spatialViewerDataset3 = new SpatialViewerFileDataset();
spatialViewerDataset3.setDlFileId("DlFileId");
spatialViewerDataset3.setReleaseVersion(45.0);
SpatialViewerFileDataset spatialViewerDataset4 = new SpatialViewerFileDataset();
spatialViewerDataset4.setReleaseVersion(34.0);
spatialViewerDataset4.setDlFileId("DlFileId2");
expectedResult1.add(spatialViewerDataset1);
expectedResult1.add(spatialViewerDataset2);
expectedResult2.add(spatialViewerDataset3);
expectedResult2.add(spatialViewerDataset4);
when(fileRepo.max()).thenReturn(34.0);
when(externalLinkRepo.findAll()).thenReturn(expectedResult1);
when(fileRepo.findAll()).thenReturn(expectedResult2);
results.addAll(expectedResult1);
results.addAll(expectedResult2);
ArrayList<SpatialViewerDataset> results = new ArrayList<>();
List<SpatialViewerFileDataset> datasetFiles = new ArrayList<>();
List<SpatialViewerExternalLinkDataset> datasetLinks = new ArrayList<>();
SpatialViewerFileDataset spatialViewerFileDataset = new SpatialViewerFileDataset();
SpatialViewerExternalLinkDataset spatialViewerExternalLinkDataset = new SpatialViewerExternalLinkDataset();
datasetFiles.add(spatialViewerFileDataset);
datasetLinks.add(spatialViewerExternalLinkDataset);
when(fileRepo.findAll()).thenReturn(datasetFiles);
when(externalLinkRepo.findAll()).thenReturn(datasetLinks);


HttpEntity<Object> entity = new HttpEntity<>(results, headers);
SpatialViewerDatasetService.ESResponse[] esResponses = {new SpatialViewerDatasetService.ESResponse()};
when(restTemplate.postForObject("host/api/as/v1/engines/search-engine/documents", entity, SpatialViewerDatasetService.ESResponse[].class)).thenReturn(esResponses);
service.loadEnterpriseSearch();
verify(restTemplate).postForObject("host/api/as/v1/engines/search-engine/documents", entity, SpatialViewerDatasetService.ESResponse[].class);
}

}
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