Song 559 change base schema

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

@@ -270,7 +270,7 @@ public void testAnalysisSearch() {
             .analysisId(DUMMY_ANALYSIS_ID)
             .analysisState(UNPUBLISHED)
             .analysisType(ANALYSIS_TYPE_ID1)
-            .study(DUMMY_STUDY_ID)
+            .studyId(DUMMY_STUDY_ID)
             .build();
     when(songApi.getAnalysis(DUMMY_STUDY_ID, DUMMY_ANALYSIS_ID)).thenReturn(expectedAnalysis);
     assertOutputJson(objectToTree(expectedAnalysis), "search", "-a", DUMMY_ANALYSIS_ID);
@@ -289,7 +289,7 @@ public void testIdSearch() {
                 .analysisId(DUMMY_ANALYSIS_ID)
                 .analysisState(UNPUBLISHED)
                 .analysisType(ANALYSIS_TYPE_ID1)
-                .study(DUMMY_STUDY_ID)
+                .studyId(DUMMY_STUDY_ID)
                 .build());
 
     when(songApi.idSearch(DUMMY_STUDY_ID, expectedSample.getSampleId(), null, null, null))

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

@@ -18,9 +18,9 @@
 public class Analysis extends DynamicData {
 
   private String analysisId;
-  private String study;
+  private String studyId;
   private AnalysisStates analysisState;
   private AnalysisTypeId analysisType;
-  private List<CompositeSample> sample;
-  private List<FileDTO> file;
+  private List<CompositeSample> samples;
+  private List<FileDTO> files;
 }

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

@@ -17,6 +17,6 @@ public class Donor extends Metadata {
 
   private String donorId;
   private String studyId;
-  private String donorSubmitterId;
-  private String donorGender;
+  private String submitterDonorId;
+  private String gender;
 }

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

@@ -28,4 +28,6 @@ public interface File extends FileMetadata, FileContent {
   String getFileName();
 
   String getFileType();
+
+  String getDataType();
 }

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

@@ -19,4 +19,5 @@ public class FileDTO extends Metadata implements File {
   private String fileMd5sum;
   private Long fileSize;
   private String fileAccess;
+  private String dataType;
 }

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

@@ -39,7 +39,7 @@
 @AllArgsConstructor
 @EqualsAndHashCode
 @ToString
-@JsonInclude(JsonInclude.Include.NON_ABSENT)
+@JsonInclude(JsonInclude.Include.NON_EMPTY)
 public class Metadata {
 
   private final Map<String, Object> info = new TreeMap<>();
@@ -59,6 +59,7 @@ public void setInfo(String info) {
   }
 
   @JsonGetter
+  @JsonInclude(JsonInclude.Include.NON_EMPTY)
   public JsonNode getInfo() {
     return JsonUtils.toJsonNode(info);
   }

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

@@ -17,6 +17,7 @@ public class Sample extends Metadata {
 
   private String sampleId;
   private String specimenId;
-  private String sampleSubmitterId;
+  private String submitterSampleId;
   private String sampleType;
+  private String matchedNormalSubmitterSampleId;
 }

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

@@ -17,7 +17,8 @@ public class Specimen extends Metadata {
 
   private String specimenId;
   private String donorId;
-  private String specimenSubmitterId;
-  private String specimenClass;
+  private String submitterSpecimenId;
+  private String tumourNormalDesignation;
+  private String specimenTissueSource;
   private String specimenType;
 }

song-java-sdk/src/main/java/bio/overture/song/sdk/SongApi.java

@@ -88,11 +88,6 @@ public boolean isAlive() {
     }
   }
 
-  /**
-   * TODO: [DCC-5641] the ResponseEntity from AnalysisController is not returned, since
-   * RestTemplate.put is a void method. need to find RestTemplate implementation that returns a
-   * response
-   */
   public String publish(
       @NonNull String studyId, @NonNull String analysisId, boolean ignoreUndefinedMd5) {
     val url = endpoint.publish(studyId, analysisId, ignoreUndefinedMd5);

song-java-sdk/src/main/java/bio/overture/song/sdk/web/Endpoint.java

@@ -37,7 +37,7 @@ public Endpoint() {
   }
 
   public String submit(@NonNull String studyId) {
-    return format("%s/upload/%s", serverUrl, studyId);
+    return format("%s/submit/%s", serverUrl, studyId);
   }
 
   public String getAnalysisFiles(@NonNull String studyId, @NonNull String analysisId) {

song-java-sdk/src/test/java/bio/overture/song/sdk/RestClientTest.java

@@ -67,15 +67,15 @@ public class RestClientTest {
   private static final Sample EXAMPLE_SAMPLE1 =
       Sample.builder()
           .sampleId("someSampleId_1")
-          .sampleSubmitterId("someSampleSubmitterId_1")
+          .submitterSampleId("someSampleSubmitterId_1")
           .sampleType("someSampleType_1")
           .specimenId("someSpecimenId_1")
           .build();
   private static final JsonNode EXAMPLE_SAMPLE1_JSON = objectToTree(EXAMPLE_SAMPLE1);
   private static final Sample EXAMPLE_SAMPLE2 =
       Sample.builder()
           .sampleId("someSampleId_2")
-          .sampleSubmitterId("someSampleSubmitterId_2")
+          .submitterSampleId("someSampleSubmitterId_2")
           .sampleType("someSampleType_2")
           .specimenId("someSpecimenId_2")
           .build();

song-server/src/main/java/bio/overture/song/server/config/ValidationConfig.java

@@ -16,8 +16,6 @@
  */
 package bio.overture.song.server.config;
 
-import static bio.overture.song.server.model.enums.Constants.SEQUENCING_READ_TYPE;
-import static bio.overture.song.server.model.enums.Constants.VARIANT_CALL_TYPE;
 import static bio.overture.song.server.utils.ParameterChecker.createParameterChecker;
 
 import bio.overture.song.core.utils.JsonDocUtils;
@@ -28,7 +26,6 @@
 import bio.overture.song.server.utils.ParameterChecker;
 import bio.overture.song.server.validation.SchemaValidator;
 import com.fasterxml.jackson.databind.JsonNode;
-import com.google.common.collect.ImmutableMap;
 import com.networknt.schema.JsonSchema;
 import java.util.HashMap;
 import java.util.Map;
@@ -47,10 +44,7 @@
 public class ValidationConfig {
 
   private static String[] schemaList = {
-    "schemas/sequencingRead.json",
-    "schemas/variantCall.json",
-    "schemas/fileUpdateRequest.json",
-    "schemas/storageDownloadResponse.json"
+    "schemas/fileUpdateRequest.json", "schemas/storageDownloadResponse.json"
   };
 
   @Value("${validation.delayMs:500}")
@@ -88,12 +82,4 @@ public Map<String, JsonSchema> schemaCache() {
     }
     return cache;
   }
-
-  @Bean
-  public Map<String, String> jsonSchemaMap() {
-    return ImmutableMap.<String, String>builder()
-        .put(SEQUENCING_READ_TYPE, "schemas/sequencingRead.json")
-        .put(VARIANT_CALL_TYPE, "schemas/variantCall.json")
-        .build();
-  }
 }

song-server/src/main/java/bio/overture/song/server/controller/DonorController.java

@@ -51,20 +51,6 @@ public Donor read(@PathVariable("studyId") String studyId, @PathVariable("id") S
     return donorService.securedRead(studyId, id);
   }
 
-  /**
-   * [DCC-5726] - updates disabled until back propagation updates due to business key updates is
-   * implemented
-   */
-  //  @PutMapping(value = "/donors/{id}", consumes = { APPLICATION_JSON_VALUE,
-  // APPLICATION_JSON_UTF8_VALUE })
-  //  @ResponseBody
-  //  @PreAuthorize("@studySecurity.authorize(authentication, #studyId)")
-  //  public String update(@PathVariable("study") String studyId, @PathVariable("id") String id,
-  // @RequestBody Donor donor) {
-  //    // TODO: [DCC-5642] Add checkRequest between path ID and Entity's ID
-  //    return donorService.update(donor);
-  //  }
-
   @ApiOperation(
       value = "DeleteDonors",
       notes = "Deletes donor data and all dependent specimens and samples for donorIds")

song-server/src/main/java/bio/overture/song/server/controller/SampleController.java

@@ -51,20 +51,6 @@ public Sample read(@PathVariable("studyId") String studyId, @PathVariable("id")
     return sampleService.securedRead(studyId, id);
   }
 
-  /**
-   * [DCC-5726] - updates disabled until back propagation updates due to business key updates is
-   * implemented
-   */
-  //  @PutMapping(value = "/samples/{id}", consumes = { APPLICATION_JSON_VALUE,
-  // APPLICATION_JSON_UTF8_VALUE })
-  //  @ResponseBody
-  //  @PreAuthorize("@studySecurity.authorize(authentication, #studyId)")
-  //  public String update(@PathVariable("studyId") String studyId, @PathVariable("id") String id,
-  //                       @RequestBody Sample sample) {
-  //    // TODO: [DCC-5642] Add checkRequest between path ID and Entity's ID
-  //    return sampleService.update(sample);
-  //  }
-
   @ApiOperation(value = "DeleteSamples", notes = "Deletes sample data for sampleIds")
   @DeleteMapping(value = "/samples/{ids}")
   @ResponseBody

song-server/src/main/java/bio/overture/song/server/controller/SpecimenController.java

@@ -51,20 +51,6 @@ public Specimen read(@PathVariable("studyId") String studyId, @PathVariable("id"
     return specimenService.securedRead(studyId, id);
   }
 
-  /**
-   * [DCC-5726] - updates disabled until back propagation updates due to business key updates is
-   * implemented
-   */
-  //  @PutMapping(value = "/specimens/{id}", consumes = { APPLICATION_JSON_VALUE,
-  // APPLICATION_JSON_UTF8_VALUE })
-  //  @ResponseBody
-  //  @PreAuthorize("@studySecurity.authorize(authentication, #studyId)")
-  //  public String update(@PathVariable("studyId") String studyId, @PathVariable("id") String id,
-  //                       @RequestBody Specimen specimen) {
-  //    // TODO: [DCC-5642] Add checkRequest between path ID and Entity's ID
-  //    return specimenService.update(specimen);
-  //  }
-
   @ApiOperation(
       value = "DeleteSpecimens",
       notes = "Deletes specimen data and all dependent samples for specimenIds")

song-server/src/main/java/bio/overture/song/server/controller/UploadController.java → song-server/src/main/java/bio/overture/song/server/controller/SubmitController.java

@@ -22,7 +22,7 @@
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 
 import bio.overture.song.core.model.SubmitResponse;
-import bio.overture.song.server.service.UploadService;
+import bio.overture.song.server.service.SubmitService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import javax.validation.Valid;
@@ -39,13 +39,13 @@
 
 @Slf4j
 @RestController
-@RequestMapping(path = "/upload")
+@RequestMapping(path = "/submit")
 @RequiredArgsConstructor
-@Api(tags = "Upload", description = "Submit and validate json metadata")
-public class UploadController {
+@Api(tags = "Submit", description = "Submit and validate json metadata")
+public class SubmitController {
 
   /** Dependencies */
-  @Autowired private final UploadService uploadService;
+  @Autowired private final SubmitService submitService;
 
   @ApiOperation(value = "Submit", notes = "Synchronously submit a json payload")
   @PostMapping(
@@ -56,6 +56,6 @@ public SubmitResponse submit(
       @RequestHeader(value = AUTHORIZATION, required = false) final String accessToken,
       @PathVariable("studyId") String studyId,
       @RequestBody @Valid String json_payload) {
-    return uploadService.submit(studyId, json_payload);
+    return submitService.submit(studyId, json_payload);
   }
 }

song-server/src/main/java/bio/overture/song/server/converter/FileConverter.java

@@ -44,6 +44,7 @@ public interface FileConverter {
   FileUpdateRequest fileEntityToFileUpdateRequest(FileEntity file);
 
   @Mapping(target = "fileType", ignore = true)
+  @Mapping(target = "dataType", ignore = true)
   @Mapping(target = "objectId", ignore = true)
   @Mapping(target = "studyId", ignore = true)
   @Mapping(target = "analysisId", ignore = true)

song-server/src/main/java/bio/overture/song/server/converter/PayloadConverter.java

@@ -62,6 +62,7 @@ public interface PayloadConverter {
   @Mapping(target = "objectId", ignore = true)
   @Mapping(target = "studyId", ignore = true)
   @Mapping(target = "info", ignore = true)
+  @Mapping(target = "dataType", nullValuePropertyMappingStrategy = SET_TO_DEFAULT)
   @Mapping(target = "fileType", nullValuePropertyMappingStrategy = SET_TO_DEFAULT)
   @Mapping(target = "fileAccess", nullValuePropertyMappingStrategy = SET_TO_DEFAULT)
   void updateFile(FileEntity ref, @MappingTarget FileEntity entityToUpdate);

song-server/src/main/java/bio/overture/song/server/model/analysis/Analysis.java

@@ -64,7 +64,7 @@ public class Analysis {
   private String analysisId;
 
   @Column(name = TableAttributeNames.STUDY_ID, nullable = false)
-  private String study;
+  private String studyId;
 
   @Column(name = TableAttributeNames.STATE, nullable = false)
   private String analysisState = UNPUBLISHED.name();
@@ -82,9 +82,9 @@ public class Analysis {
   @JsonIgnore
   private AnalysisData analysisData;
 
-  @Transient private List<CompositeEntity> sample;
+  @Transient private List<CompositeEntity> samples;
 
-  @Transient private List<FileEntity> file;
+  @Transient private List<FileEntity> files;
 
   // TODO: need to remove this, and replace anything that needs this with Payload object
   public AnalysisTypeId getAnalysisType() {