Johanna/6723 add destination disease columns upload table (#6857)

* Added two new columns to upload table

* Added cascade to rollback

* Removed not null constraint so the schema changes are backwards compatible

* added manual rollback for the disease_id column

* Implemented insert of new information in table and unit testing partially updated

* Fixed some more test cases

* Updated models and fixed some test suites

* save to DB logic moved back to main thread

* Added mocks for repo_save

* Fixed sonar cloud smells

* Fixed more code smells

* addresses feedback

backend/src/main/java/gov/cdc/usds/simplereport/api/uploads/FileUploadController.java

@@ -14,6 +14,7 @@
 import gov.cdc.usds.simplereport.service.TestResultUploadService;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.List;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -76,7 +77,7 @@ public TestResultUpload handleConditionAgnosticResultsUpload(
   }
 
   @PostMapping(RESULT_UPLOAD)
-  public TestResultUpload handleResultsUpload(@RequestParam("file") MultipartFile file) {
+  public List<TestResultUpload> handleResultsUpload(@RequestParam("file") MultipartFile file) {
     assertCsvFileType(file);
 
     try (InputStream resultsUpload = file.getInputStream()) {

backend/src/main/java/gov/cdc/usds/simplereport/db/model/TestResultUpload.java

@@ -1,8 +1,10 @@
 package gov.cdc.usds.simplereport.db.model;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
+import gov.cdc.usds.simplereport.db.model.auxiliary.Pipeline;
 import gov.cdc.usds.simplereport.db.model.auxiliary.UploadStatus;
 import gov.cdc.usds.simplereport.service.model.reportstream.FeedbackMessage;
+import java.util.List;
 import java.util.UUID;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -11,16 +13,23 @@
 import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
 import javax.persistence.Table;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Getter;
+import lombok.NoArgsConstructor;
 import lombok.Setter;
 import lombok.extern.slf4j.Slf4j;
 import org.hibernate.annotations.Type;
 
-@Getter
-@Setter
 @Entity
 @Slf4j
+@AllArgsConstructor
+@NoArgsConstructor
+@Builder
+@Setter
+@Getter
 @Table(name = "upload")
 public class TestResultUpload extends AuditedEntity {
 
@@ -47,24 +56,13 @@ public class TestResultUpload extends AuditedEntity {
   @Type(type = "jsonb")
   private FeedbackMessage[] errors;
 
-  protected TestResultUpload() {}
+  @Column()
+  @Type(type = "pg_enum")
+  @Enumerated(EnumType.STRING)
+  private Pipeline destination;
 
-  public TestResultUpload(
-      UUID reportId,
-      UUID submissionId,
-      UploadStatus status,
-      int recordsCount,
-      Organization organization,
-      FeedbackMessage[] warnings,
-      FeedbackMessage[] errors) {
-    this.reportId = reportId;
-    this.submissionId = submissionId;
-    this.status = status;
-    this.recordsCount = recordsCount;
-    this.organization = organization;
-    this.warnings = warnings;
-    this.errors = errors;
-  }
+  @OneToMany(mappedBy = "upload")
+  List<UploadDiseaseDetails> uploadDiseaseDetails;
 
   public TestResultUpload(UploadStatus status) {
     this.status = status;

backend/src/main/java/gov/cdc/usds/simplereport/db/model/UploadDiseaseDetails.java

@@ -0,0 +1,27 @@
+package gov.cdc.usds.simplereport.db.model;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.NoArgsConstructor;
+
+@NoArgsConstructor
+@AllArgsConstructor
+@Entity
+@Builder
+public class UploadDiseaseDetails extends AuditedEntity {
+
+  @ManyToOne
+  @JoinColumn(name = "supported_disease_id", nullable = false)
+  private SupportedDisease disease;
+
+  @ManyToOne
+  @JoinColumn(name = "upload_id", nullable = false)
+  private TestResultUpload upload;
+
+  @Column(nullable = false)
+  private int recordsCount;
+}

backend/src/main/java/gov/cdc/usds/simplereport/db/model/auxiliary/CovidSubmissionSummary.java

@@ -0,0 +1,13 @@
+package gov.cdc.usds.simplereport.db.model.auxiliary;
+
+import gov.cdc.usds.simplereport.db.model.Organization;
+import gov.cdc.usds.simplereport.service.model.reportstream.UploadResponse;
+import java.util.HashMap;
+import java.util.UUID;
+
+public record CovidSubmissionSummary(
+    UUID submissionId,
+    Organization org,
+    UploadResponse submissionResponse,
+    Exception processingException,
+    HashMap<String, Integer> reportedDiseases) {}

backend/src/main/java/gov/cdc/usds/simplereport/db/model/auxiliary/FHIRBundleRecord.java

@@ -0,0 +1,6 @@
+package gov.cdc.usds.simplereport.db.model.auxiliary;
+
+import java.util.HashMap;
+import java.util.List;
+
+public record FHIRBundleRecord(List<String> serializedBundle, HashMap<String, Integer> metadata) {}

backend/src/main/java/gov/cdc/usds/simplereport/db/model/auxiliary/Pipeline.java

@@ -0,0 +1,6 @@
+package gov.cdc.usds.simplereport.db.model.auxiliary;
+
+public enum Pipeline {
+  COVID,
+  UNIVERSAL;
+}

backend/src/main/java/gov/cdc/usds/simplereport/db/model/auxiliary/UniversalSubmissionSummary.java

@@ -0,0 +1,12 @@
+package gov.cdc.usds.simplereport.db.model.auxiliary;
+
+import gov.cdc.usds.simplereport.db.model.Organization;
+import gov.cdc.usds.simplereport.service.model.reportstream.UploadResponse;
+import java.util.HashMap;
+import java.util.UUID;
+
+public record UniversalSubmissionSummary(
+    UUID submissionId,
+    Organization org,
+    UploadResponse submissionResponse,
+    HashMap<String, Integer> reportedDiseases) {}

backend/src/main/java/gov/cdc/usds/simplereport/db/repository/UploadDiseaseDetailsRepository.java

@@ -0,0 +1,6 @@
+package gov.cdc.usds.simplereport.db.repository;
+
+import gov.cdc.usds.simplereport.db.model.UploadDiseaseDetails;
+
+public interface UploadDiseaseDetailsRepository
+    extends AuditedEntityRepository<UploadDiseaseDetails> {}