Add reference descriptions and make them and names updateable [AS-512]

build.gradle

@@ -15,7 +15,7 @@ sourceCompatibility = JavaVersion.VERSION_11
 
 allprojects {
 	group = "bio.terra"
-	version = "0.9.0-SNAPSHOT"
+	version = "0.10.0-SNAPSHOT"
 	ext {
 		artifactGroup = "${group}.workspace"
 		swaggerOutputDir = "${buildDir}/swagger-code"

src/main/java/bio/terra/workspace/app/controller/WorkspaceApiController.java

@@ -4,6 +4,7 @@
 import bio.terra.workspace.generated.controller.WorkspaceApi;
 import bio.terra.workspace.generated.model.*;
 import bio.terra.workspace.service.datareference.DataReferenceService;
+import bio.terra.workspace.service.datareference.exception.InvalidDataReferenceException;
 import bio.terra.workspace.service.datareference.model.CloningInstructions;
 import bio.terra.workspace.service.datareference.model.DataReference;
 import bio.terra.workspace.service.datareference.model.DataReferenceRequest;
@@ -157,6 +158,7 @@ public ResponseEntity<DataReferenceDescription> createDataReference(
         DataReferenceRequest.builder()
             .workspaceId(id)
             .name(body.getName())
+            .referenceDescription(body.getReferenceDescription())
             .referenceType(referenceType)
             .cloningInstructions(CloningInstructions.fromApiModel(body.getCloningInstructions()))
             .referenceObject(snapshot)
@@ -209,6 +211,36 @@ public ResponseEntity<DataReferenceDescription> getDataReferenceByName(
     return new ResponseEntity<>(ref.toApiModel(), HttpStatus.OK);
   }
 
+  @Override
+  public ResponseEntity<Void> updateDataReference(
+      @PathVariable("id") UUID id,
+      @PathVariable("referenceId") UUID referenceId,
+      @RequestBody UpdateDataReferenceRequestBody body) {
+    AuthenticatedUserRequest userReq = getAuthenticatedInfo();
+
+    if (body.getName() == null && body.getReferenceDescription() == null) {
+      throw new InvalidDataReferenceException(
+          "Must specify name or referenceDescription to update.");
+    }
+
+    if (body.getName() != null) {
+      DataReferenceValidationUtils.validateReferenceName(body.getName());
+    }
+
+    logger.info(
+        String.format(
+            "Updating data reference by id %s in workspace %s for %s with body %s",
+            referenceId.toString(), id.toString(), userReq.getEmail(), body.toString()));
+
+    dataReferenceService.updateDataReference(id, referenceId, body, userReq);
+    logger.info(
+        String.format(
+            "Updating data reference by id %s in workspace %s for %s with body %s",
+            referenceId.toString(), id.toString(), userReq.getEmail(), body.toString()));
+
+    return new ResponseEntity<>(HttpStatus.NO_CONTENT);
+  }
+
   @Override
   public ResponseEntity<Void> deleteDataReference(
       @PathVariable("id") UUID workspaceId, @PathVariable("referenceId") UUID referenceId) {

src/main/java/bio/terra/workspace/db/DataReferenceDao.java

@@ -2,6 +2,7 @@
 
 import bio.terra.workspace.common.exception.DataReferenceNotFoundException;
 import bio.terra.workspace.common.exception.DuplicateDataReferenceException;
+import bio.terra.workspace.db.exception.InvalidDaoRequestException;
 import bio.terra.workspace.service.datareference.model.CloningInstructions;
 import bio.terra.workspace.service.datareference.model.DataReference;
 import bio.terra.workspace.service.datareference.model.DataReferenceRequest;
@@ -10,6 +11,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.util.List;
 import java.util.Optional;
+import java.util.StringJoiner;
 import java.util.UUID;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -43,14 +45,15 @@ public DataReferenceDao(NamedParameterJdbcTemplate jdbcTemplate) {
   public String createDataReference(DataReferenceRequest request, UUID referenceId)
       throws DuplicateDataReferenceException {
     String sql =
-        "INSERT INTO workspace_data_reference (workspace_id, reference_id, name, cloning_instructions, reference_type, reference) VALUES "
-            + "(:workspace_id, :reference_id, :name, :cloning_instructions, :reference_type, cast(:reference AS json))";
+        "INSERT INTO workspace_data_reference (workspace_id, reference_id, name, reference_description, cloning_instructions, reference_type, reference) VALUES "
+            + "(:workspace_id, :reference_id, :name, :reference_description, :cloning_instructions, :reference_type, cast(:reference AS json))";
 
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("workspace_id", request.workspaceId().toString())
             .addValue("reference_id", referenceId.toString())
             .addValue("name", request.name())
+            .addValue("reference_description", request.referenceDescription())
             .addValue("cloning_instructions", request.cloningInstructions().toSql())
             .addValue("reference_type", request.referenceType().toSql())
             .addValue("reference", request.referenceObject().toJson());
@@ -71,7 +74,7 @@ public String createDataReference(DataReferenceRequest request, UUID referenceId
   /** Retrieve a data reference by ID from the DB. */
   public DataReference getDataReference(UUID workspaceId, UUID referenceId) {
     String sql =
-        "SELECT workspace_id, reference_id, name, cloning_instructions, reference_type, reference from workspace_data_reference where workspace_id = :workspace_id AND reference_id = :reference_id";
+        "SELECT workspace_id, reference_id, name, reference_description, cloning_instructions, reference_type, reference from workspace_data_reference where workspace_id = :workspace_id AND reference_id = :reference_id";
 
     MapSqlParameterSource params =
         new MapSqlParameterSource()
@@ -97,7 +100,7 @@ public DataReference getDataReference(UUID workspaceId, UUID referenceId) {
   public DataReference getDataReferenceByName(
       UUID workspaceId, DataReferenceType type, String name) {
     String sql =
-        "SELECT workspace_id, reference_id, name, cloning_instructions, reference_type, reference from workspace_data_reference where workspace_id = :id AND reference_type = :type AND name = :name";
+        "SELECT workspace_id, reference_id, name, reference_description, cloning_instructions, reference_type, reference from workspace_data_reference where workspace_id = :id AND reference_type = :type AND name = :name";
 
     MapSqlParameterSource params =
         new MapSqlParameterSource()
@@ -135,6 +138,49 @@ public boolean isControlled(UUID workspaceId, UUID referenceId) {
     }
   }
 
+  public boolean updateDataReference(
+      UUID workspaceId, UUID referenceId, String name, String referenceDescription) {
+    if (name == null && referenceDescription == null) {
+      throw new InvalidDaoRequestException("Must specify name or referenceDescription to update.");
+    }
+
+    MapSqlParameterSource params =
+        new MapSqlParameterSource()
+            .addValue("id", referenceId.toString())
+            .addValue("workspace_id", workspaceId.toString())
+            .addValue("name", name)
+            .addValue("reference_description", referenceDescription);
+
+    StringJoiner updateStatement =
+        new StringJoiner(
+            ", ",
+            "UPDATE workspace_data_reference SET ",
+            " WHERE reference_id = :id AND workspace_id = :workspace_id");
+
+    if (name != null) {
+      updateStatement.add("name = :name");
+    }
+    if (referenceDescription != null) {
+      updateStatement.add("reference_description = :reference_description");
+    }
+
+    int rowsAffected = jdbcTemplate.update(updateStatement.toString(), params);
+    boolean updated = rowsAffected > 0;
+
+    if (updated)
+      logger.info(
+          String.format(
+              "Updated record for data reference %s in workspace %s",
+              referenceId.toString(), workspaceId.toString()));
+    else
+      logger.info(
+          String.format(
+              "Failed to update record for data reference %s in workspace %s",
+              referenceId.toString(), workspaceId.toString()));
+
+    return updated;
+  }
+
   public boolean deleteDataReference(UUID workspaceId, UUID referenceId) {
     MapSqlParameterSource params =
         new MapSqlParameterSource()
@@ -164,7 +210,7 @@ public boolean deleteDataReference(UUID workspaceId, UUID referenceId) {
   // should consider joining and listing those entries here.
   public List<DataReference> enumerateDataReferences(UUID workspaceId, int offset, int limit) {
     String sql =
-        "SELECT workspace_id, reference_id, name, cloning_instructions, reference_type, reference"
+        "SELECT workspace_id, reference_id, name, reference_description, cloning_instructions, reference_type, reference"
             + " FROM workspace_data_reference"
             + " WHERE workspace_id = :id"
             + " ORDER BY reference_id"
@@ -189,6 +235,7 @@ public List<DataReference> enumerateDataReferences(UUID workspaceId, int offset,
             .workspaceId(UUID.fromString(rs.getString("workspace_id")))
             .referenceId(UUID.fromString(rs.getString("reference_id")))
             .name(rs.getString("name"))
+            .referenceDescription(rs.getString("reference_description"))
             .referenceType(referenceType)
             .cloningInstructions(CloningInstructions.fromSql(rs.getString("cloning_instructions")))
             .referenceObject(deserializedReferenceObject)

src/main/java/bio/terra/workspace/db/exception/InvalidDaoRequestException.java

@@ -0,0 +1,10 @@
+package bio.terra.workspace.db.exception;
+
+import bio.terra.common.exception.InternalServerErrorException;
+
+public class InvalidDaoRequestException extends InternalServerErrorException {
+
+  public InvalidDaoRequestException(String message) {
+    super(message);
+  }
+}

src/main/java/bio/terra/workspace/service/datareference/DataReferenceService.java

@@ -2,6 +2,7 @@
 
 import bio.terra.workspace.common.exception.*;
 import bio.terra.workspace.db.DataReferenceDao;
+import bio.terra.workspace.generated.model.UpdateDataReferenceRequestBody;
 import bio.terra.workspace.service.datareference.exception.ControlledResourceNotImplementedException;
 import bio.terra.workspace.service.datareference.flight.CreateDataReferenceFlight;
 import bio.terra.workspace.service.datareference.flight.DataReferenceFlightMapKeys;
@@ -98,6 +99,9 @@ public DataReference createDataReference(
                 userReq)
             .addParameter(DataReferenceFlightMapKeys.WORKSPACE_ID, referenceRequest.workspaceId())
             .addParameter(DataReferenceFlightMapKeys.NAME, referenceRequest.name())
+            .addParameter(
+                DataReferenceFlightMapKeys.REFERENCE_DESCRIPTION,
+                referenceRequest.referenceDescription())
             .addParameter(
                 DataReferenceFlightMapKeys.REFERENCE_TYPE, referenceRequest.referenceType())
             .addParameter(
@@ -128,6 +132,24 @@ public List<DataReference> enumerateDataReferences(
     return dataReferenceDao.enumerateDataReferences(workspaceId, offset, limit);
   }
 
+  @Traced
+  public void updateDataReference(
+      UUID workspaceId,
+      UUID referenceId,
+      UpdateDataReferenceRequestBody updateRequest,
+      AuthenticatedUserRequest userReq) {
+    workspaceService.validateWorkspaceAndAction(
+        userReq, workspaceId, SamConstants.SAM_WORKSPACE_WRITE_ACTION);
+
+    if (!dataReferenceDao.updateDataReference(
+        workspaceId,
+        referenceId,
+        updateRequest.getName(),
+        updateRequest.getReferenceDescription())) {
+      throw new DataReferenceNotFoundException("Data Reference not found.");
+    }
+  }
+
   /**
    * Delete a data reference, or throw an exception if the specified reference does not exist.
    * Verifies workspace existence and write permission before deleting the reference.

src/main/java/bio/terra/workspace/service/datareference/flight/CreateDataReferenceStep.java

@@ -32,6 +32,8 @@ public StepResult doStep(FlightContext flightContext) throws RetryException {
     UUID referenceId = workingMap.get(DataReferenceFlightMapKeys.REFERENCE_ID, UUID.class);
     UUID workspaceId = inputMap.get(DataReferenceFlightMapKeys.WORKSPACE_ID, UUID.class);
     String name = inputMap.get(DataReferenceFlightMapKeys.NAME, String.class);
+    String referenceDescription =
+        inputMap.get(DataReferenceFlightMapKeys.REFERENCE_DESCRIPTION, String.class);
     DataReferenceType type =
         inputMap.get(DataReferenceFlightMapKeys.REFERENCE_TYPE, DataReferenceType.class);
     CloningInstructions cloningInstructions =
@@ -43,6 +45,7 @@ public StepResult doStep(FlightContext flightContext) throws RetryException {
         DataReferenceRequest.builder()
             .workspaceId(workspaceId)
             .name(name)
+            .referenceDescription(referenceDescription)
             .referenceType(type)
             .cloningInstructions(cloningInstructions)
             .referenceObject(referenceObject)

src/main/java/bio/terra/workspace/service/datareference/flight/DataReferenceFlightMapKeys.java

@@ -4,6 +4,7 @@ public final class DataReferenceFlightMapKeys {
   public static final String REFERENCE_ID = "referenceId";
   public static final String WORKSPACE_ID = "workspaceId";
   public static final String NAME = "name";
+  public static final String REFERENCE_DESCRIPTION = "referenceDescription";
   public static final String REFERENCE_TYPE = "referenceType";
   public static final String CLONING_INSTRUCTIONS = "cloningInstructions";
   public static final String REFERENCE_OBJECT = "referenceObject";

src/main/java/bio/terra/workspace/service/datareference/model/DataReference.java

@@ -3,6 +3,7 @@
 import bio.terra.workspace.generated.model.DataReferenceDescription;
 import com.google.auto.value.AutoValue;
 import java.util.UUID;
+import javax.annotation.Nullable;
 
 /**
  * Internal representation of an uncontrolled data reference.
@@ -21,6 +22,10 @@ public abstract class DataReference {
   /** Name of the reference. Names are unique per workspace, per reference type. */
   public abstract String name();
 
+  /** Description of the data reference. */
+  @Nullable
+  public abstract String referenceDescription();
+
   /** Type of this data reference. */
   public abstract DataReferenceType referenceType();
 
@@ -35,6 +40,7 @@ public DataReferenceDescription toApiModel() {
     return new DataReferenceDescription()
         .referenceId(referenceId())
         .name(name())
+        .referenceDescription(referenceDescription())
         .workspaceId(workspaceId())
         .referenceType(referenceType().toApiModel())
         .reference(((SnapshotReference) referenceObject()).toApiModel())
@@ -53,6 +59,8 @@ public abstract static class Builder {
 
     public abstract DataReference.Builder name(String value);
 
+    public abstract DataReference.Builder referenceDescription(String value);
+
     public abstract DataReference.Builder referenceType(DataReferenceType value);
 
     public abstract DataReference.Builder cloningInstructions(CloningInstructions value);

src/main/java/bio/terra/workspace/service/datareference/model/DataReferenceRequest.java

@@ -2,6 +2,7 @@
 
 import com.google.auto.value.AutoValue;
 import java.util.UUID;
+import javax.annotation.Nullable;
 
 /**
  * This is an internal representation of a request to create a data reference.
@@ -22,6 +23,10 @@ public abstract class DataReferenceRequest {
    */
   public abstract String name();
 
+  /** Description of the reference. */
+  @Nullable
+  public abstract String referenceDescription();
+
   /** Type of this data reference. */
   public abstract DataReferenceType referenceType();
 
@@ -41,6 +46,8 @@ public abstract static class Builder {
 
     public abstract DataReferenceRequest.Builder name(String value);
 
+    public abstract DataReferenceRequest.Builder referenceDescription(String value);
+
     public abstract DataReferenceRequest.Builder referenceType(DataReferenceType value);
 
     public abstract DataReferenceRequest.Builder cloningInstructions(CloningInstructions value);

src/main/resources/api/service_openapi.yaml

@@ -158,6 +158,25 @@ paths:
           $ref: '#/components/responses/NotFound'
         '500':
           $ref: '#/components/responses/ServerError'
+    patch:
+      summary: Update name or description of a data reference in a workspace.
+      operationId: updateDataReference
+      tags: [Workspace]
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/UpdateDataReferenceRequestBody'
+      responses:
+        '204':
+          description: OK
+        '403':
+          $ref: '#/components/responses/PermissionDenied'
+        '404':
+          $ref: '#/components/responses/NotFound'
+        '500':
+          $ref: '#/components/responses/ServerError'
     delete:
       summary: Deletes a data reference from a workspace.
       operationId: deleteDataReference
@@ -606,6 +625,8 @@ components:
       properties:
         name:
           $ref: "#/components/schemas/Name"
+        referenceDescription:
+          type: string
         resourceId:
           description: The ID of the resource
           type: string
@@ -617,6 +638,14 @@ components:
         cloningInstructions:
           $ref: '#/components/schemas/CloningInstructionsEnum'
 
+    UpdateDataReferenceRequestBody:
+      type: object
+      properties:
+        name:
+          $ref: "#/components/schemas/Name"
+        referenceDescription:
+          type: string
+
     DataReferenceDescription:
       type: object
       required: [referenceId, name, workspaceId, cloningInstructions]
@@ -628,6 +657,8 @@ components:
         name:
           description: The name of the data reference; used to refer to the reference
           type: string
+        referenceDescription:
+          type: string
         workspaceId:
           description: The ID of the workspace containing the reference
           type: string

src/main/resources/db/changelog.xml

@@ -6,4 +6,5 @@
     <include file="changesets/20201028_feature_toggle.yaml" relativeToChangelogFile="true"/>
     <include file="changesets/20201104_reference_index.yaml" relativeToChangelogFile="true"/>
     <include file="changesets/20201204_json_to_jsonb.yaml" relativeToChangelogFile="true"/>
+    <include file="changesets/20210205_add_description.yaml" relativeToChangelogFile="true"/>
 </databaseChangeLog>