link up WDS record with cbas submission

add columns to piplines table
add FK between impuation_jobs and pipelines table
rename pipeline_id to name (and subsequent changes in code/comments)

common/openapi.yml

@@ -53,9 +53,9 @@ paths:
           $ref: '#/components/responses/ServerError'
 
 
-  /api/pipelines/v1alpha1/{pipelineId}:
+  /api/pipelines/v1alpha1/{pipelineName}:
     parameters:
-      - $ref: '#/components/parameters/PipelineId'
+      - $ref: '#/components/parameters/PipelineName'
     get:
       summary: Return info about the specified pipeline
       operationId: getPipeline
@@ -103,9 +103,9 @@ paths:
         500:
           $ref: '#/components/responses/ServerError'
 
-  /api/pipelines/v1alpha1/{pipelineId}/jobs:
+  /api/pipelines/v1alpha1/{pipelineName}/jobs:
     parameters:
-      - $ref: '#/components/parameters/PipelineId'
+      - $ref: '#/components/parameters/PipelineName'
       - $ref: '#/components/parameters/Limit'
       - $ref: '#/components/parameters/PageToken'
     get:
@@ -210,8 +210,8 @@ components:
       schema:
         type: string
 
-    PipelineId:
-      name: pipelineId
+    PipelineName:
+      name: pipelineName
       in: path
       description: A string identifier to used to identify a pipeline in the service.
       required: true
@@ -434,12 +434,12 @@ components:
 
     Pipeline:
       description: |
-        Object containing the id, display name, and description of a Pipeline.
+        Object containing the pipeline identifier, display name, and description of a Pipeline.
       type: object
-      required: [ pipelineId, displayName, description ]
+      required: [ pipelineName, displayName, description ]
       properties:
-        pipelineId:
-          $ref: "#/components/schemas/PipelineId"
+        pipelineName:
+          $ref: "#/components/schemas/PipelineName"
         displayName:
           $ref: "#/components/schemas/PipelineDisplayName"
         description:
@@ -457,7 +457,7 @@ components:
       type: string
       format: string
 
-    PipelineId:
+    PipelineName:
       description: |
         The identifier string for the Pipeline.
       type: string

scripts/write-config.sh

@@ -91,8 +91,9 @@ case $target in
         ;;
 
     local)
-        # for local development we will use the QA environment stuff for now to mimic our BEEs
-        fcenv=qa
+        # for local development we will use the dev environment configuration because our app is currently set up to work
+        # with the dev environment by default
+        fcenv=dev
         ;;
 
     dev)

service/src/main/java/bio/terra/pipelines/app/controller/PipelinesApiController.java

@@ -1,6 +1,6 @@
 package bio.terra.pipelines.app.controller;
 
-import static bio.terra.pipelines.common.utils.PipelinesEnum.IMPUTATION;
+import static bio.terra.pipelines.common.utils.PipelinesEnum.IMPUTATION_MINIMAC4;
 
 import bio.terra.common.exception.ApiException;
 import bio.terra.common.iam.SamUser;
@@ -74,8 +74,9 @@ public ResponseEntity<ApiGetPipelinesResult> getPipelines() {
   }
 
   @Override
-  public ResponseEntity<ApiPipeline> getPipeline(@PathVariable("pipelineId") String pipelineId) {
-    PipelinesEnum validatedPipelineId = validatePipelineId(pipelineId);
+  public ResponseEntity<ApiPipeline> getPipeline(
+      @PathVariable("pipelineName") String pipelineName) {
+    PipelinesEnum validatedPipelineId = validatePipelineName(pipelineName);
     Pipeline pipelineInfo = pipelinesService.getPipeline(validatedPipelineId);
     ApiPipeline result = pipelineToApi(pipelineInfo);
 
@@ -94,7 +95,7 @@ static ApiGetPipelinesResult pipelinesToApi(List<Pipeline> pipelineList) {
 
   static ApiPipeline pipelineToApi(Pipeline pipelineInfo) {
     return new ApiPipeline()
-        .pipelineId(pipelineInfo.getPipelineId())
+        .pipelineName(pipelineInfo.getName())
         .displayName(pipelineInfo.getDisplayName())
         .description(pipelineInfo.getDescription());
   }
@@ -108,15 +109,16 @@ static ApiPipeline pipelineToApi(Pipeline pipelineInfo) {
    * <p>For now, the job will be created with a random UUID. In the future (TSPS-136), we will
    * require the user to provide a job UUID.
    *
-   * @param pipelineId the pipeline to run
+   * @param pipelineName the pipeline to run
    * @param body the inputs for the pipeline
    * @return the created job response, which includes a job report containing the job ID,
    *     description, status, status code, submitted timestamp, completed timestamp (if completed),
    *     and result URL. The response also includes an error report if the job failed.
    */
   @Override
   public ResponseEntity<ApiCreateJobResponse> createJob(
-      @PathVariable("pipelineId") String pipelineId, @RequestBody ApiCreateJobRequestBody body) {
+      @PathVariable("pipelineName") String pipelineName,
+      @RequestBody ApiCreateJobRequestBody body) {
     final SamUser userRequest = getAuthenticatedInfo();
     String userId = userRequest.getSubjectId();
     UUID jobId = body.getJobControl().getId();
@@ -125,36 +127,34 @@ public ResponseEntity<ApiCreateJobResponse> createJob(
     String pipelineVersion = body.getPipelineVersion();
     Object pipelineInputs = body.getPipelineInputs();
 
-    PipelinesEnum validatedPipelineId = validatePipelineId(pipelineId);
+    PipelinesEnum validatedPipelineName = validatePipelineName(pipelineName);
 
     logger.info(
         "Creating {} pipeline (version {}) job (id {}) for user {} with inputs {}",
-        pipelineId,
+        pipelineName,
         pipelineVersion,
         jobId,
         userId,
         pipelineInputs);
 
-    // TSPS-136 will require that the user provide the job UUID
-    UUID createdJobUuid;
-    if (validatedPipelineId == IMPUTATION) {
+    if (validatedPipelineName == IMPUTATION_MINIMAC4) {
+      Pipeline pipeline = pipelinesService.getPipeline(IMPUTATION_MINIMAC4);
       // eventually we'll expand this out to kick off the imputation pipeline flight but for
       // now this is good enough.
-      imputationService.queryForWorkspaceApps();
+      imputationService.queryForWorkspaceApps(pipeline);
 
-      createdJobUuid =
-          imputationService.createImputationJob(
-              jobId, userId, description, pipelineVersion, pipelineInputs);
+      imputationService.createImputationJob(
+          jobId, userId, description, pipeline.getId(), pipelineInputs);
     } else {
-      logger.error("Unknown validatedPipelineId {}", validatedPipelineId);
+      logger.error("Unknown validatedPipelineName {}", validatedPipelineName);
       throw new ApiException("An internal error occurred.");
     }
 
-    logger.info("Created {} job {}", validatedPipelineId.getValue(), createdJobUuid);
+    logger.info("Created {} job {}", validatedPipelineName.getValue(), jobId);
 
-    MetricsUtils.incrementPipelineRun(validatedPipelineId);
+    MetricsUtils.incrementPipelineRun(validatedPipelineName);
 
-    FlightState flightState = jobService.retrieveJob(createdJobUuid, userId);
+    FlightState flightState = jobService.retrieveJob(jobId, userId);
     ApiJobReport jobReport = JobApiUtils.mapFlightStateToApiJobReport(flightState);
     ApiCreateJobResponse createdJobResponse = new ApiCreateJobResponse().jobReport(jobReport);
 
@@ -164,35 +164,36 @@ public ResponseEntity<ApiCreateJobResponse> createJob(
   /** Retrieves job reports for all jobs of the specified pipeline that the user has access to. */
   @Override
   public ResponseEntity<ApiGetJobsResponse> getPipelineJobs(
-      @PathVariable("pipelineId") String pipelineId, Integer limit, String pageToken) {
+      @PathVariable("pipelineName") String pipelineName, Integer limit, String pageToken) {
     final SamUser userRequest = getAuthenticatedInfo();
     String userId = userRequest.getSubjectId();
-    PipelinesEnum validatedPipelineId = validatePipelineId(pipelineId);
+    PipelinesEnum validatedPipelineName = validatePipelineName(pipelineName);
     EnumeratedJobs enumeratedJobs =
-        jobService.enumerateJobs(userId, limit, pageToken, validatedPipelineId);
+        jobService.enumerateJobs(userId, limit, pageToken, validatedPipelineName);
 
     ApiGetJobsResponse result = JobApiUtils.mapEnumeratedJobsToApi(enumeratedJobs);
 
     return new ResponseEntity<>(result, HttpStatus.OK);
   }
 
   /**
-   * Validates that the pipelineId is a valid pipelineId and returns the Enum value for the
-   * pipelineId
+   * Validates that the pipelineName is a valid pipelineName and returns the Enum value for the
+   * pipelineName
    *
    * <p>Note that in PipelinesServiceTest, we check that all the pipelines in the enum exist in the
    * pipelines table
    *
-   * @param pipelineId the pipelineId to validate
-   * @return the Enum value for the pipelineId
-   * @throws InvalidPipelineException if the pipelineId is not valid
+   * @param pipelineName the pipelineName to validate
+   * @return the Enum value for the pipelineName
+   * @throws InvalidPipelineException if the pipelineName is not valid
    */
-  public PipelinesEnum validatePipelineId(String pipelineId) {
+  public PipelinesEnum validatePipelineName(String pipelineName) {
     try {
-      return PipelinesEnum.valueOf(pipelineId.toUpperCase());
+      return PipelinesEnum.valueOf(pipelineName.toUpperCase());
     } catch (IllegalArgumentException e) {
-      logger.error("Unknown pipeline id {}", pipelineId);
-      throw new InvalidPipelineException(String.format("%s is not a valid pipelineId", pipelineId));
+      logger.error("Unknown pipeline name {}", pipelineName);
+      throw new InvalidPipelineException(
+          String.format("%s is not a valid pipelineName", pipelineName));
     }
   }
 }

service/src/main/java/bio/terra/pipelines/common/utils/PipelinesEnum.java

@@ -1,7 +1,7 @@
 package bio.terra.pipelines.common.utils;
 
 public enum PipelinesEnum {
-  IMPUTATION("imputation");
+  IMPUTATION_MINIMAC4("imputation_minimac4");
 
   private final String value;
 

service/src/main/java/bio/terra/pipelines/db/entities/ImputationJob.java

@@ -23,12 +23,12 @@ public class ImputationJob {
   @Column(name = "user_id", nullable = false)
   private String userId;
 
-  @Column(name = "pipeline_version", nullable = false)
-  private String pipelineVersion;
+  @Column(name = "pipeline_id", nullable = false)
+  private Long pipelineId;
 
-  public ImputationJob(UUID jobId, String userId, String pipelineVersion) {
+  public ImputationJob(UUID jobId, String userId, Long pipelineId) {
     this.jobId = jobId;
     this.userId = userId;
-    this.pipelineVersion = pipelineVersion;
+    this.pipelineId = pipelineId;
   }
 }

service/src/main/java/bio/terra/pipelines/db/entities/Pipeline.java

@@ -14,15 +14,15 @@
 @NoArgsConstructor
 @Table(
     name = "pipelines",
-    uniqueConstraints = {@UniqueConstraint(columnNames = {"pipeline_id", "version"})})
+    uniqueConstraints = {@UniqueConstraint(columnNames = {"name", "version"})})
 public class Pipeline {
   @Id
   @Column(name = "id", nullable = false)
   @GeneratedValue(strategy = GenerationType.IDENTITY)
   private Long id;
 
-  @Column(name = "pipeline_id", nullable = false)
-  private String pipelineId;
+  @Column(name = "name", nullable = false)
+  private String name;
 
   @Column(name = "version", nullable = false)
   private String version;
@@ -33,20 +33,42 @@ public class Pipeline {
   @Column(name = "description")
   private String description;
 
-  public Pipeline(String pipelineId, String version, String displayName, String description) {
-    this.pipelineId = pipelineId;
+  @Column(name = "pipeline_type")
+  private String pipelineType;
+
+  @Column(name = "wdl_url")
+  private String wdlUrl;
+
+  @Column(name = "wdl_method_name")
+  private String wdlMethodName;
+
+  public Pipeline(
+      String name,
+      String version,
+      String displayName,
+      String description,
+      String pipelineType,
+      String wdlUrl,
+      String wdlMethodName) {
+    this.name = name;
     this.version = version;
     this.displayName = displayName;
     this.description = description;
+    this.pipelineType = pipelineType;
+    this.wdlUrl = wdlUrl;
+    this.wdlMethodName = wdlMethodName;
   }
 
   @Override
   public String toString() {
     return new StringJoiner(", ", Pipeline.class.getSimpleName() + "[", "]")
-        .add("pipelineId=" + pipelineId)
+        .add("pipelineName=" + name)
         .add("version=" + version)
         .add("displayName=" + displayName)
         .add("description=" + description)
+        .add("pipelineType=" + pipelineType)
+        .add("wdlUrl=" + wdlUrl)
+        .add("wdlMethodName=" + wdlMethodName)
         .toString();
   }
 
@@ -61,10 +83,13 @@ public int hashCode() {
         // two randomly chosen prime numbers
         // if deriving: appendSuper(super.hashCode()).
         .append(id)
-        .append(pipelineId)
+        .append(name)
         .append(version)
         .append(displayName)
         .append(description)
+        .append(pipelineType)
+        .append(wdlUrl)
+        .append(wdlMethodName)
         .toHashCode();
   }
 
@@ -76,10 +101,13 @@ public boolean equals(Object obj) {
     Pipeline otherObject = (Pipeline) obj;
     return new EqualsBuilder()
         .append(id, otherObject.id)
-        .append(pipelineId, otherObject.pipelineId)
+        .append(name, otherObject.name)
         .append(version, otherObject.version)
         .append(displayName, otherObject.displayName)
         .append(description, otherObject.description)
+        .append(pipelineType, otherObject.pipelineType)
+        .append(wdlUrl, otherObject.wdlUrl)
+        .append(wdlMethodName, otherObject.wdlMethodName)
         .isEquals();
   }
 }

service/src/main/java/bio/terra/pipelines/db/repositories/PipelinesRepository.java

@@ -11,7 +11,7 @@ public interface PipelinesRepository extends CrudRepository<Pipeline, Long> {
   @Override
   List<Pipeline> findAll();
 
-  Boolean existsByPipelineId(String pipelineId);
+  Boolean existsByName(String name);
 
-  Pipeline findByPipelineId(String pipelineId);
+  Pipeline findByName(String name);
 }

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasService.java

@@ -1,8 +1,7 @@
 package bio.terra.pipelines.dependencies.cbas;
 
 import bio.terra.cbas.client.ApiException;
-import bio.terra.cbas.model.MethodListResponse;
-import bio.terra.cbas.model.SystemStatus;
+import bio.terra.cbas.model.*;
 import bio.terra.pipelines.dependencies.common.HealthCheckWorkspaceApps;
 import org.springframework.retry.support.RetryTemplate;
 import org.springframework.stereotype.Service;
@@ -17,10 +16,26 @@ public CbasService(CbasClient cbasClient, RetryTemplate listenerResetRetryTempla
     this.listenerResetRetryTemplate = listenerResetRetryTemplate;
   }
 
-  public MethodListResponse getAllMethods(String cbasBaseUri, String accesstoken) {
+  public MethodListResponse getAllMethods(String cbasBaseUri, String accessToken) {
     return executionWithRetryTemplate(
         listenerResetRetryTemplate,
-        () -> cbasClient.methodsApi(cbasBaseUri, accesstoken).getMethods(null, null, null));
+        () -> cbasClient.methodsApi(cbasBaseUri, accessToken).getMethods(null, null, null));
+  }
+
+  // method used to create a method programtically
+  public PostMethodResponse createMethod(
+      String cbasBaseUri, String accessToken, PostMethodRequest postMethodRequest) {
+    return executionWithRetryTemplate(
+        listenerResetRetryTemplate,
+        () -> cbasClient.methodsApi(cbasBaseUri, accessToken).postMethod(postMethodRequest));
+  }
+
+  public RunSetStateResponse createRunset(
+      String cbasBaseUri, String accessToken, RunSetRequest runSetRequest) {
+
+    return executionWithRetryTemplate(
+        listenerResetRetryTemplate,
+        () -> cbasClient.runSetsApi(cbasBaseUri, accessToken).postRunSet(runSetRequest));
   }
 
   @Override