Merge pull request #869 from overture-stack/refactor/remove-donor-specimen-sample-from-analysis

Remove Donor, Specimen, and Sample from Analysis Data Classes in SONG

Author: Azher2Ali

song-client/src/main/java/bio/overture/song/client/command/SearchCommand.java

@@ -54,31 +54,13 @@ public class SearchCommand extends Command {
   /** Long Switch Constants */
   private static final String FILE_ID_SWITCH = "--file-id";
 
-  private static final String SAMPLE_ID_SWITCH = "--sample-id";
-  private static final String SPECIMEN_ID_SWITCH = "--specimen-id";
-  private static final String DONOR_ID_SWITCH = "--donor-id";
   private static final String ANALYSIS_ID_SWITCH = "--analysis-id";
 
   @Parameter(
       names = {F_SWITCH, FILE_ID_SWITCH},
       required = false)
   private String fileId;
 
-  @Parameter(
-      names = {SA_SWITCH, SAMPLE_ID_SWITCH},
-      required = false)
-  private String sampleId;
-
-  @Parameter(
-      names = {SP_SWITCH, SPECIMEN_ID_SWITCH},
-      required = false)
-  private String specimenId;
-
-  @Parameter(
-      names = {D_SWITCH, DONOR_ID_SWITCH},
-      required = false)
-  private String donorId;
-
   @Parameter(
       names = {A_SWITCH, ANALYSIS_ID_SWITCH},
       required = false)
@@ -92,8 +74,7 @@ public void run() throws IOException {
     val status = checkRules();
     if (!status.hasErrors()) {
       if (isIdSearchMode()) {
-        status.outputPrettyJson(
-            songApi.idSearch(config.getStudyId(), sampleId, specimenId, donorId, fileId));
+        status.outputPrettyJson(songApi.idSearch(config.getStudyId(), fileId));
       } else if (isAnalysisSearchMode()) {
         status.outputPrettyJson(songApi.getAnalysis(config.getStudyId(), analysisId));
       } else {
@@ -108,18 +89,15 @@ private boolean isAnalysisSearchMode() {
   }
 
   private boolean isIdSearchMode() {
-    return nonNull(fileId) || nonNull(sampleId) || nonNull(specimenId) || nonNull(donorId);
+    return nonNull(fileId);
   }
 
   private Status checkRules() {
     val fileTerm = createParamTerm(F_SWITCH, FILE_ID_SWITCH, fileId, Objects::nonNull);
-    val sampleTerm = createParamTerm(SA_SWITCH, SAMPLE_ID_SWITCH, sampleId, Objects::nonNull);
-    val specimenTerm = createParamTerm(SP_SWITCH, SPECIMEN_ID_SWITCH, specimenId, Objects::nonNull);
-    val donorTerm = createParamTerm(D_SWITCH, DONOR_ID_SWITCH, donorId, Objects::nonNull);
     val analysisIdTerm =
         createParamTerm(A_SWITCH, ANALYSIS_ID_SWITCH, analysisId, Objects::nonNull);
 
-    val idSearchMode = createModeRule(ID_MODE, fileTerm, sampleTerm, specimenTerm, donorTerm);
+    val idSearchMode = createModeRule(ID_MODE, fileTerm);
     val analysisSearchMode = createModeRule(ANALYSIS_MODE, analysisIdTerm);
     val ruleProcessor = createRuleProcessor(idSearchMode, analysisSearchMode);
     return ruleProcessor.check();

song-client/src/test/java/bio/overture/song/client/HappyPathClientMainTest.java

@@ -39,13 +39,10 @@
 import bio.overture.song.core.model.Analysis;
 import bio.overture.song.core.model.AnalysisType;
 import bio.overture.song.core.model.AnalysisTypeId;
-import bio.overture.song.core.model.Donor;
 import bio.overture.song.core.model.FileDTO;
 import bio.overture.song.core.model.FileUpdateRequest;
 import bio.overture.song.core.model.FileUpdateResponse;
 import bio.overture.song.core.model.PageDTO;
-import bio.overture.song.core.model.Sample;
-import bio.overture.song.core.model.Specimen;
 import bio.overture.song.core.model.SubmitResponse;
 import bio.overture.song.core.utils.RandomGenerator;
 import bio.overture.song.sdk.ManifestClient;
@@ -280,9 +277,6 @@ public void testAnalysisSearch() {
   @Test
   public void testIdSearch() {
     val expectedFile = new FileDTO().setObjectId("FI1");
-    val expectedSample = Sample.builder().sampleId("SA1").build();
-    val expectedSpecimen = Specimen.builder().specimenId("SP1").build();
-    val expectedDonor = Donor.builder().donorId("DO1").build();
     val expectedAnalyses =
         List.of(
             Analysis.builder()
@@ -292,27 +286,7 @@ public void testIdSearch() {
                 .studyId(DUMMY_STUDY_ID)
                 .build());
 
-    when(songApi.idSearch(DUMMY_STUDY_ID, expectedSample.getSampleId(), null, null, null))
-        .thenReturn(expectedAnalyses);
-    when(songApi.idSearch(DUMMY_STUDY_ID, null, expectedSpecimen.getSpecimenId(), null, null))
-        .thenReturn(expectedAnalyses);
-    when(songApi.idSearch(DUMMY_STUDY_ID, null, null, expectedDonor.getDonorId(), null))
-        .thenReturn(expectedAnalyses);
-    when(songApi.idSearch(DUMMY_STUDY_ID, null, null, null, expectedFile.getObjectId()))
-        .thenReturn(expectedAnalyses);
-    assertOutputJson(objectToTree(expectedAnalyses), "search", "-d", expectedDonor.getDonorId());
-    assertOutputJson(
-        objectToTree(expectedAnalyses), "search", "--donor-id", expectedDonor.getDonorId());
-    assertOutputJson(
-        objectToTree(expectedAnalyses), "search", "-sp", expectedSpecimen.getSpecimenId());
-    assertOutputJson(
-        objectToTree(expectedAnalyses),
-        "search",
-        "--specimen-id",
-        expectedSpecimen.getSpecimenId());
-    assertOutputJson(objectToTree(expectedAnalyses), "search", "-sa", expectedSample.getSampleId());
-    assertOutputJson(
-        objectToTree(expectedAnalyses), "search", "--sample-id", expectedSample.getSampleId());
+    when(songApi.idSearch(DUMMY_STUDY_ID, expectedFile.getObjectId())).thenReturn(expectedAnalyses);
     assertOutputJson(objectToTree(expectedAnalyses), "search", "-f", expectedFile.getObjectId());
     assertOutputJson(
         objectToTree(expectedAnalyses), "search", "--file-id", expectedFile.getObjectId());

song-core/src/main/java/bio/overture/song/core/model/Analysis.java

@@ -23,7 +23,6 @@ public class Analysis extends DynamicData {
   private String studyId;
   private AnalysisStates analysisState;
   private AnalysisTypeId analysisType;
-  private List<CompositeSample> samples;
   private List<FileDTO> files;
 
   private LocalDateTime createdAt;

song-core/src/main/java/bio/overture/song/core/model/CompositeSample.java

@@ -135,9 +135,8 @@ public FileUpdateResponse updateFile(
     return restClient.put(url, fileUpdateRequest, FileUpdateResponse.class).getBody();
   }
 
-  public List<Analysis> idSearch(
-      String studyId, String sampleId, String specimenId, String donorId, String fileId) {
-    val url = endpoint.idSearch(studyId, sampleId, specimenId, donorId, fileId);
+  public List<Analysis> idSearch(String studyId, String fileId) {
+    val url = endpoint.idSearch(studyId, fileId);
     return restClient.getList(url, Analysis.class).getBody();
   }
 

song-core/src/main/java/bio/overture/song/core/model/Donor.java

@@ -111,12 +111,8 @@ public String suppress(@NonNull String studyId, @NonNull String analysisId) {
     return format("%s/studies/%s/analysis/suppress/%s", serverUrl, studyId, analysisId);
   }
 
-  public String idSearch(
-      @NonNull String studyId, String sampleId, String specimenId, String donorId, String fileId) {
+  public String idSearch(@NonNull String studyId, String fileId) {
     return new RequestParamBuilder()
-        .optionalQuerySingleParam("sampleId", sampleId)
-        .optionalQuerySingleParam("specimenId", specimenId)
-        .optionalQuerySingleParam("donorId", donorId)
         .optionalQuerySingleParam("fileId", fileId)
         .build(format("%s/studies/%s/analysis/search/id", serverUrl, studyId));
   }