Merge pull request #533 from overture-stack/song-494-remove-analysisIds

Song 494 remove analysis ids
overture-stack · Nov 22, 2019 · 25e4959 · 25e4959
2 parents 513c299 + 5e903ef
commit 25e4959
Show file tree

Hide file tree

Showing 41 changed files with 130 additions and 725 deletions.
diff --git a/song-client/src/main/java/bio/overture/song/client/command/ExportCommand.java b/song-client/src/main/java/bio/overture/song/client/command/ExportCommand.java
@@ -125,12 +125,6 @@ public class ExportCommand extends Command {
       required = true)
   private String outputDir;
 
-  @Parameter(
-      names = {INCLUDE_ANALYSIS_ID_SHORT, INCLUDE_ANALYSIS_ID_LONG},
-      description = "Include the analysisId field when exporting payloads",
-      arity = 1)
-  private boolean includeAnalysisId = true;
-
   /** Dependencies */
   @NonNull private SongApi songApi;
 
@@ -209,7 +203,7 @@ private void checkNumThreads() {
   }
 
   private void processStudyMode() {
-    val exportedPayloads = songApi.exportStudy(studyId, includeAnalysisId);
+    val exportedPayloads = songApi.exportStudy(studyId);
     val exportStatus = exportedPayloadsToDisk("Study(" + studyId + ")", exportedPayloads);
     if (exportStatus.hasErrors()) {
       save(exportStatus);
@@ -267,7 +261,7 @@ private Status processAnalysis(String name, List<String> analysisIds) {
     Status exportStatus = new Status();
     List<ExportedPayload> exportedPayloads = null;
     try {
-      exportedPayloads = songApi.exportAnalyses(analysisIds, includeAnalysisId);
+      exportedPayloads = songApi.exportAnalyses(analysisIds);
     } catch (Throwable t) {
       exportStatus.err("ExportError: %s", t.getMessage());
     }

diff --git a/song-client/src/main/java/bio/overture/song/client/command/FileUpdateCommand.java b/song-client/src/main/java/bio/overture/song/client/command/FileUpdateCommand.java
@@ -17,6 +17,10 @@
 
 package bio.overture.song.client.command;
 
+import static bio.overture.song.core.model.enums.AccessTypes.resolveAccessType;
+import static java.lang.String.format;
+import static java.util.Objects.isNull;
+
 import bio.overture.song.client.config.CustomRestClientConfig;
 import bio.overture.song.core.model.FileUpdateRequest;
 import bio.overture.song.core.model.enums.AccessTypes;
@@ -27,16 +31,11 @@
 import com.beust.jcommander.ParameterException;
 import com.beust.jcommander.Parameters;
 import com.fasterxml.jackson.databind.JsonNode;
+import java.io.IOException;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import lombok.val;
 
-import java.io.IOException;
-
-import static java.lang.String.format;
-import static java.util.Objects.isNull;
-import static bio.overture.song.core.model.enums.AccessTypes.resolveAccessType;
-
 @RequiredArgsConstructor
 @Parameters(separators = "=", commandDescription = "Update a file")
 public class FileUpdateCommand extends Command {

diff --git a/song-client/src/test/java/bio/overture/song/client/HappyPathClientMainTest.java b/song-client/src/test/java/bio/overture/song/client/HappyPathClientMainTest.java
@@ -30,7 +30,6 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertTrue;
-import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyList;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.when;
@@ -480,8 +479,8 @@ public void testExport() {
     val exportedPayload2 = createExportedPayload(DUMMY_STUDY_ID, payloads2);
     val expectedResponse = List.of(exportedPayload1, exportedPayload2);
 
-    when(songApi.exportStudy(eq(DUMMY_STUDY_ID), anyBoolean())).thenReturn(expectedResponse);
-    when(songApi.exportAnalyses(anyList(), anyBoolean())).thenReturn(expectedResponse);
+    when(songApi.exportStudy(eq(DUMMY_STUDY_ID))).thenReturn(expectedResponse);
+    when(songApi.exportAnalyses(anyList())).thenReturn(expectedResponse);
 
     val outputDir = tmp.newFolder().toPath();
     val studyDir = outputDir.resolve(DUMMY_STUDY_ID);

diff --git a/song-core/src/main/java/bio/overture/song/core/exceptions/ServerErrors.java b/song-core/src/main/java/bio/overture/song/core/exceptions/ServerErrors.java
@@ -92,7 +92,6 @@ public enum ServerErrors implements ServerError {
   SPECIMEN_ALREADY_EXISTS(CONFLICT),
   VARIANT_CALL_CORRUPTED_DUPLICATE(INTERNAL_SERVER_ERROR),
   SEQUENCING_READ_CORRUPTED_DUPLICATE(INTERNAL_SERVER_ERROR),
-  DUPLICATE_ANALYSIS_ATTEMPT(CONFLICT),
   STUDY_ALREADY_EXISTS(CONFLICT),
   MISMATCHING_STORAGE_OBJECT_SIZES(CONFLICT),
   MISMATCHING_STORAGE_OBJECT_CHECKSUMS(CONFLICT),

diff --git a/song-java-sdk/src/main/java/bio/overture/song/sdk/SongApi.java b/song-java-sdk/src/main/java/bio/overture/song/sdk/SongApi.java
@@ -16,6 +16,8 @@
  */
 package bio.overture.song.sdk;
 
+import static java.lang.Boolean.parseBoolean;
+
 import bio.overture.song.core.model.Analysis;
 import bio.overture.song.core.model.AnalysisType;
 import bio.overture.song.core.model.ExportedPayload;
@@ -27,16 +29,13 @@
 import bio.overture.song.sdk.model.ListAnalysisTypesRequest;
 import bio.overture.song.sdk.web.Endpoint;
 import bio.overture.song.sdk.web.RestClient;
+import java.util.List;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import lombok.SneakyThrows;
 import lombok.val;
 import org.springframework.web.client.ResourceAccessException;
 
-import java.util.List;
-
-import static java.lang.Boolean.parseBoolean;
-
 @RequiredArgsConstructor
 public class SongApi {
 
@@ -105,14 +104,13 @@ public String unpublish(@NonNull String studyId, @NonNull String analysisId) {
     return restClient.put(url, String.class).getBody();
   }
 
-  public List<ExportedPayload> exportStudy(@NonNull String studyId, boolean includeAnalysisId) {
-    val url = endpoint.exportStudy(studyId, includeAnalysisId);
+  public List<ExportedPayload> exportStudy(@NonNull String studyId) {
+    val url = endpoint.exportStudy(studyId);
     return restClient.getList(url, ExportedPayload.class).getBody();
   }
 
-  public List<ExportedPayload> exportAnalyses(
-      @NonNull List<String> analysisIds, boolean includeAnalysisId) {
-    val url = endpoint.exportAnalysisIds(analysisIds, includeAnalysisId);
+  public List<ExportedPayload> exportAnalyses(@NonNull List<String> analysisIds) {
+    val url = endpoint.exportAnalysisIds(analysisIds);
     return restClient.getList(url, ExportedPayload.class).getBody();
   }
 

diff --git a/song-java-sdk/src/main/java/bio/overture/song/sdk/web/Endpoint.java b/song-java-sdk/src/main/java/bio/overture/song/sdk/web/Endpoint.java
@@ -95,15 +95,12 @@ public String updateFile(@NonNull String studyId, @NonNull String objectId) {
     return format("%s/studies/%s/files/%s", serverUrl, studyId, objectId);
   }
 
-  public String exportAnalysisIds(@NonNull List<String> analysisIds, boolean includeAnalysisId) {
-    return format(
-        "%s/export/analysis/%s?includeAnalysisId=%s",
-        serverUrl, COMMA.join(analysisIds), includeAnalysisId);
+  public String exportAnalysisIds(@NonNull List<String> analysisIds) {
+    return format("%s/export/analysis/%s", serverUrl, COMMA.join(analysisIds));
   }
 
-  public String exportStudy(@NonNull String studyId, boolean includeAnalysisId) {
-    return format(
-        "%s/export/studies/%s?includeAnalysisId=%s", serverUrl, studyId, includeAnalysisId);
+  public String exportStudy(@NonNull String studyId) {
+    return format("%s/export/studies/%s", serverUrl, studyId);
   }
 
   public String suppress(@NonNull String studyId, @NonNull String analysisId) {

diff --git a/song-java-sdk/src/main/java/bio/overture/song/sdk/web/RestClient.java b/song-java-sdk/src/main/java/bio/overture/song/sdk/web/RestClient.java
@@ -19,12 +19,10 @@
 
 import static bio.overture.song.core.utils.Deserialization.deserializeList;
 import static bio.overture.song.core.utils.Deserialization.deserializePage;
-import static bio.overture.song.core.utils.JsonUtils.mapper;
 import static org.springframework.http.ResponseEntity.status;
 
 import bio.overture.song.core.exceptions.ServerException;
 import bio.overture.song.core.model.PageDTO;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import java.util.List;
 import lombok.NonNull;
 import lombok.SneakyThrows;
@@ -33,8 +31,6 @@
 
 public interface RestClient {
 
-  ObjectMapper MAPPER = mapper();
-
   <R> ResponseEntity<R> get(String endpoint, Class<R> responseType) throws ServerException;
 
   <R> ResponseEntity<R> post(String endpoint, Object body, Class<R> responseType)

diff --git a/song-server/src/main/java/bio/overture/song/server/config/IdConfig.java b/song-server/src/main/java/bio/overture/song/server/config/IdConfig.java
@@ -22,7 +22,6 @@
 
 import bio.overture.song.server.properties.IdProperties;
 import bio.overture.song.server.properties.IdProperties.FederatedProperties.AuthProperties.BearerProperties;
-import bio.overture.song.server.repository.AnalysisRepository;
 import bio.overture.song.server.service.auth.StaticTokenService;
 import bio.overture.song.server.service.id.FederatedIdService;
 import bio.overture.song.server.service.id.IdService;
@@ -56,35 +55,26 @@ public class IdConfig {
   /** Dependencies */
   private final IdProperties idProperties;
 
-  private final AnalysisRepository analysisRepository;
   private final RetryTemplate retryTemplate;
 
   @Autowired
-  public IdConfig(
-      @NonNull IdProperties idProperties,
-      @NonNull AnalysisRepository analysisRepository,
-      @NonNull RetryTemplate retryTemplate) {
+  public IdConfig(@NonNull IdProperties idProperties, @NonNull RetryTemplate retryTemplate) {
     this.idProperties = idProperties;
-    this.analysisRepository = analysisRepository;
     this.retryTemplate = retryTemplate;
   }
 
   @Bean
-  public NameBasedGenerator nameBasedGenerator() {
-    return createNameBasedGenerator();
-  }
-
-  @Bean
-  public IdService idService(@Autowired NameBasedGenerator nameBasedGenerator) {
+  public IdService idService() {
+    val localIdService = new LocalIdService(createNameBasedGenerator());
     if (idProperties.isUseLocal()) {
       log.info("Loading LOCAL mode for IdService");
-      return new LocalIdService(nameBasedGenerator, analysisRepository);
+      return localIdService;
     } else {
       log.info("Loading FEDERATED mode for IdService");
       val uriResolver = createUriResolver(idProperties.getFederated().getUriTemplate());
       val restTemplate = restTemplate(idProperties.getFederated().getAuth().getBearer());
       val restClient = new RestClient(restTemplate, retryTemplate);
-      return new FederatedIdService(restClient, uriResolver);
+      return new FederatedIdService(restClient, localIdService, uriResolver);
     }
   }
 

diff --git a/song-server/src/main/java/bio/overture/song/server/controller/ExportController.java b/song-server/src/main/java/bio/overture/song/server/controller/ExportController.java
@@ -27,7 +27,6 @@
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.RestController;
 
@@ -43,10 +42,8 @@ public class ExportController {
   @ApiOperation(value = "ExportStudy", notes = "Exports all the payloads for a study")
   @GetMapping(value = "/studies/{studyId}")
   @ResponseBody
-  public List<ExportedPayload> exportStudy(
-      @PathVariable("studyId") String studyId,
-      @RequestParam(value = "includeAnalysisId", defaultValue = "true") boolean includeAnalysisId) {
-    return exportService.exportPayloadsForStudy(studyId, includeAnalysisId);
+  public List<ExportedPayload> exportStudy(@PathVariable("studyId") String studyId) {
+    return exportService.exportPayloadsForStudy(studyId);
   }
 
   @ApiOperation(value = "ExportAnalysis", notes = "Exports the payload for a list of analysisIds")
@@ -55,8 +52,7 @@ public List<ExportedPayload> exportStudy(
   public List<ExportedPayload> exportAnalysis(
       @PathVariable("analysisIds")
           @ApiParam(value = "Comma separated list of analysisIds", required = true)
-          List<String> analysisIds,
-      @RequestParam(value = "includeAnalysisId", defaultValue = "true") boolean includeAnalysisId) {
-    return exportService.exportPayload(analysisIds, includeAnalysisId);
+          List<String> analysisIds) {
+    return exportService.exportPayload(analysisIds);
   }
 }
diff --git a/song-server/src/main/java/bio/overture/song/server/controller/UploadController.java b/song-server/src/main/java/bio/overture/song/server/controller/UploadController.java
@@ -56,20 +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, false);
-  }
-
-  @ApiOperation(
-      value = "ForceSubmit",
-      notes = "Forcefully submit a json payload, ignoring analysisId collisions")
-  @PostMapping(
-      value = "/{studyId}/force",
-      consumes = {APPLICATION_JSON_VALUE, APPLICATION_JSON_UTF8_VALUE})
-  @PreAuthorize("@systemSecurity.authorize(authentication)")
-  public SubmitResponse forceSubmit(
-      @RequestHeader(value = AUTHORIZATION, required = false) final String accessToken,
-      @PathVariable("studyId") String studyId,
-      @RequestBody @Valid String json_payload) {
-    return uploadService.submit(studyId, json_payload, true);
+    return uploadService.submit(studyId, json_payload);
   }
 }
diff --git a/song-server/src/main/java/bio/overture/song/server/converter/FileConverter.java b/song-server/src/main/java/bio/overture/song/server/converter/FileConverter.java
@@ -19,6 +19,7 @@
 
 import static org.mapstruct.factory.Mappers.getMapper;
 
+import bio.overture.song.core.model.FileDTO;
 import bio.overture.song.core.model.FileData;
 import bio.overture.song.core.model.FileUpdateRequest;
 import bio.overture.song.server.config.ConverterConfig;
@@ -62,6 +63,8 @@ default FileEntity copyFile(FileEntity ref) {
 
   List<FileEntity> copyFiles(List<FileEntity> files);
 
+  FileDTO convertToFileDTO(FileEntity f);
+
   default StorageObject toStorageObject(FileEntity file) {
     return StorageObject.builder()
         .objectId(file.getObjectId())

diff --git a/song-server/src/main/java/bio/overture/song/server/model/dto/Payload.java b/song-server/src/main/java/bio/overture/song/server/model/dto/Payload.java
@@ -23,7 +23,6 @@
 public class Payload extends DynamicData {
 
   private String study;
-  private String analysisId;
   private AnalysisTypeId analysisType;
   private List<CompositeEntity> sample;
   private List<FileEntity> file;

diff --git a/song-server/src/main/java/bio/overture/song/server/properties/IdProperties.java b/song-server/src/main/java/bio/overture/song/server/properties/IdProperties.java
@@ -33,15 +33,6 @@ public static class UriTemplateProperties {
       private String specimen;
       private String sample;
       private String file;
-      private final AnalysisTemplateProperties analysis = new AnalysisTemplateProperties();
-
-      @Getter
-      @Setter
-      public static class AnalysisTemplateProperties {
-        private String existence;
-        private String generate;
-        private String save;
-      }
     }
 
     @Getter