activated replicon handling and prodigal tf

.kube/dev-deployment.yaml

@@ -64,7 +64,7 @@ spec:
             secretKeyRef:
               key: Token
               name: authhandler
-        image: harbor.computational.bio.uni-giessen.de/bakta/bakta-web-backend:0.2.7
+        image: harbor.computational.bio.uni-giessen.de/bakta/bakta-web-backend:0.2.8
         imagePullPolicy: Always
         name: baktabackend
         ports:

config/local-config.yaml

@@ -1,9 +1,14 @@
 Objectstorage:
   S3:
-    Bucket: baktadata
+    UserBucket: baktauserdata
+    DBBucket: baktadbs
     BaseKey: data/dev
 Database:
   Backend: SQLite
   SQLite:
     Path: /tmp
-K8sNamespace: "bakta-dev"
+K8sNamespace: "bakta-dev"
+UpdateService:
+  Name: baktawebbackend
+  Port: "8081"
+Testing: true

database/handler.go

@@ -169,7 +169,8 @@ func (handler *Handler) CreateJob() (*Job, string, error) {
 //UpdateK8s Updates a job with its k8s id
 func (handler *Handler) UpdateK8s(id string, k8s string, conf string) error {
 	job := Job{
-		JobID: id,
+		JobID:      id,
+		ConfString: conf,
 	}
 
 	getDataResult := handler.DB.First(&job)

endpoints/job.go

@@ -83,7 +83,7 @@ func (apiHandler *BaktaJobAPI) StartJob(ctx context.Context, request *api.StartJ
 		return nil, err
 	}
 
-	k8sJob, err := apiHandler.scheduler.StartJob(request.Job.GetJobID(), request.GetConfig())
+	k8sJob, err := apiHandler.scheduler.StartJob(request.Job.GetJobID(), request.GetConfig(), request.GetJobConfigString())
 	if err != nil {
 		log.Println(err.Error())
 		return nil, err

go.mod

@@ -3,7 +3,7 @@ module github.com/ag-computational-bio/bakta-web-backend
 go 1.16
 
 require (
-	github.com/ag-computational-bio/bakta-web-api-go v0.0.0-20210511164724-debd1af1ed2a
+	github.com/ag-computational-bio/bakta-web-api-go v0.0.0-20210512084259-ad07339c1e85
 	github.com/aws/aws-sdk-go-v2 v1.4.0
 	github.com/aws/aws-sdk-go-v2/config v1.1.7
 	github.com/aws/aws-sdk-go-v2/service/s3 v1.6.0
@@ -31,7 +31,7 @@ require (
 	golang.org/x/term v0.0.0-20210503060354-a79de5458b56 // indirect
 	google.golang.org/appengine v1.6.7 // indirect
 	google.golang.org/genproto v0.0.0-20210510173355-fb37daa5cd7a // indirect
-	google.golang.org/grpc v1.37.0
+	google.golang.org/grpc v1.37.1
 	google.golang.org/protobuf v1.26.0
 	gopkg.in/ini.v1 v1.62.0 // indirect
 	gorm.io/driver/postgres v1.1.0

main.go

@@ -9,7 +9,7 @@ import (
 )
 
 var opts struct {
-	ConfigFile string `short:"c" long:"configfile" description:"File of the config file" default:"./config/config.yaml"`
+	ConfigFile string `short:"c" long:"configfile" description:"File of the config file" default:"./config/local-config.yaml"`
 }
 
 //Version Version tag

monitor/SimpleMonitor.go

@@ -48,7 +48,7 @@ func (monitor *SimpleMonitor) GetJobStatus(jobID string) (JobStatus, error) {
 	if job.Status.Active >= 1 {
 		jobStatus.Status = api.JobStatusEnum_RUNNING
 	} else if job.Status.Succeeded >= 1 && job.Status.Active == 0 {
-		jobStatus.Status = api.JobStatusEnum_SUCCESFULL
+		jobStatus.Status = api.JobStatusEnum_SUCCESSFULL
 	} else if job.Status.Failed >= 1 && job.Status.Active == 0 {
 		jobStatus.Status = api.JobStatusEnum_ERROR
 	} else {

objectStorage/S3ObjectStorageHandler.go

@@ -24,6 +24,7 @@ type UploadLinks struct {
 	GBFF            string `bakta:"gbff"`
 	FNA             string `bakta:"fna"`
 	FAA             string `bakta:"faa"`
+	JSON            string `bakta:"json"`
 	TSVHypothetical string `bakta:"hypotheticals.tsv"`
 	FAAHypothetical string `bakta:"hypotheticals.faa"`
 }

scheduler/JobConfigurator.go

@@ -18,14 +18,17 @@ import (
 //The job has to be provided along with two bools that indicate if a prodigal training file and/or a replicon file are present
 func createDownloadConf(job *database.Job, prodigaltf bool, replicontsv bool) (string, error) {
 	keyString := job.FastaKey
+	bucketString := job.DataBucket
 	if prodigaltf {
 		keyString = fmt.Sprintf(keyString+",%v", job.ProdigalKey)
+		bucketString = fmt.Sprintf(bucketString+",%v", job.DataBucket)
 	}
 	if replicontsv {
 		keyString = fmt.Sprintf(keyString+",%v", job.RepliconKey)
+		bucketString = fmt.Sprintf(bucketString+",%v", job.DataBucket)
 	}
 
-	confString := fmt.Sprintf("download -b %v -k %v -d /data -e s3.computational.bio.uni-giessen.de", job.DataBucket, keyString)
+	confString := fmt.Sprintf("download -b %v -k %v -d /data -e s3.computational.bio.uni-giessen.de", bucketString, keyString)
 
 	return confString, nil
 }
@@ -43,6 +46,14 @@ func createBaktaConf(job *database.Job, conf *api.JobConfig, rawConfString strin
 	confStringElements = append(confStringElements, "--prefix result")
 	confStringElements = append(confStringElements, "-o /output")
 
+	if conf.HasProdigal {
+		confStringElements = append(confStringElements, "--prodigal-tf prodigaltraining.protf")
+	}
+
+	if conf.HasReplicons {
+		confStringElements = append(confStringElements, "--replicons replicons.tsv")
+	}
+
 	if viper.IsSet("Testing") || viper.IsSet("Debug") {
 		confStringElements = append(confStringElements, "--db /db/db-mock")
 	} else {

scheduler/SimpleScheduler.go

@@ -58,20 +58,20 @@ func InitSimpleScheduler(dbHandler *database.Handler) (*SimpleScheduler, error)
 }
 
 //StartJob Starts a bakta job on Kubernetes
-func (scheduler *SimpleScheduler) StartJob(jobID string, jobConfig *api.JobConfig) (*batchv1.Job, error) {
+func (scheduler *SimpleScheduler) StartJob(jobID string, jobConfig *api.JobConfig, baktaConfString string) (*batchv1.Job, error) {
 	job, err := scheduler.databaseHandler.GetJob(jobID)
 	if err != nil {
 		log.Println(err.Error())
 		return nil, err
 	}
 
-	downloadConf, err := createDownloadConf(job, false, false)
+	downloadConf, err := createDownloadConf(job, jobConfig.HasProdigal, jobConfig.HasReplicons)
 	if err != nil {
 		log.Println(err.Error())
 		return nil, err
 	}
 
-	baktaConf, err := createBaktaConf(job, jobConfig, job.ConfString)
+	baktaConf, err := createBaktaConf(job, jobConfig, baktaConfString)
 	if err != nil {
 		log.Println(err.Error())
 		return nil, err

scheduler/startJob.go

@@ -167,7 +167,7 @@ func createBaseJobConf(
 					},
 				},
 			},
-			BackoffLimit: int32Link(4),
+			BackoffLimit: int32Link(1),
 		},
 	}