From 290028b6756f18167f3994d1402a8982ad3ccf20 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Thu, 18 Jul 2024 15:00:51 +0200 Subject: [PATCH 01/10] chore: Move to Rust Backend --- .gitignore | 1 + Cargo.lock | 7 + Cargo.toml | 6 + README.md | 39 +- config/config.yaml | 31 - config/local-config.yaml | 17 - database/handler.go | 406 -------- database/handler_integration_test.go | 125 --- database/models.go | 25 - endpoints/job.go | 243 ----- endpoints/job_integration_test.go | 116 --- endpoints/server.go | 153 --- endpoints/server_integration_test.go | 13 - endpoints/update.go | 87 -- endpoints/update_integration_test.go | 9 - go.mod | 38 - go.sum | 961 ------------------ kube/dev-deployment.yaml | 113 -- main.go | 37 - monitor/simple_monitor.go | 174 ---- monitor/simple_monitor_test.go | 1 - objectStorage/s3_object_storage_handler.go | 108 -- .../s3_object_storage_handler_test.go | 8 - scheduler/job_configurator.go | 146 --- scheduler/job_configurator_test.go | 1 - scheduler/simple_scheduler.go | 159 --- scheduler/simple_scheduler_test.go | 46 - scheduler/start_job.go | 206 ---- src/main.rs | 6 + tests/docker-compose.test.yml | 45 - 30 files changed, 22 insertions(+), 3305 deletions(-) create mode 100644 Cargo.lock create mode 100644 Cargo.toml delete mode 100644 config/config.yaml delete mode 100644 config/local-config.yaml delete mode 100644 database/handler.go delete mode 100644 database/handler_integration_test.go delete mode 100644 database/models.go delete mode 100644 endpoints/job.go delete mode 100644 endpoints/job_integration_test.go delete mode 100644 endpoints/server.go delete mode 100644 endpoints/server_integration_test.go delete mode 100644 endpoints/update.go delete mode 100644 endpoints/update_integration_test.go delete mode 100644 go.mod delete mode 100644 go.sum delete mode 100644 kube/dev-deployment.yaml delete mode 100644 main.go delete mode 100644 monitor/simple_monitor.go delete mode 100644 monitor/simple_monitor_test.go delete mode 100644 objectStorage/s3_object_storage_handler.go delete mode 100644 objectStorage/s3_object_storage_handler_test.go delete mode 100644 scheduler/job_configurator.go delete mode 100644 scheduler/job_configurator_test.go delete mode 100644 scheduler/simple_scheduler.go delete mode 100644 scheduler/simple_scheduler_test.go delete mode 100644 scheduler/start_job.go create mode 100644 src/main.rs delete mode 100644 tests/docker-compose.test.yml diff --git a/.gitignore b/.gitignore index 66fd13c..7fe85ef 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,7 @@ # Test binary, built with `go test -c` *.test +/target # Output of the go coverage tool, specifically when used with LiteIDE *.out diff --git a/Cargo.lock b/Cargo.lock new file mode 100644 index 0000000..ccf88e6 --- /dev/null +++ b/Cargo.lock @@ -0,0 +1,7 @@ +# This file is automatically @generated by Cargo. +# It is not intended for manual editing. +version = 3 + +[[package]] +name = "bakta-web-backend" +version = "0.2.0" diff --git a/Cargo.toml b/Cargo.toml new file mode 100644 index 0000000..30cd22c --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,6 @@ +[package] +name = "bakta-web-backend" +version = "0.2.0" +edition = "2021" + +[dependencies] diff --git a/README.md b/README.md index 90eedb2..0e0dce7 100644 --- a/README.md +++ b/README.md @@ -2,50 +2,15 @@

Backend to schedule Bakta jobs on a Kubernetes cluster.

-

 go version license

+

  license

# Concept The Bakta-Web backend implements a simple job scheduling system for the Bakta-Web UI. It requires an S3 compatible object storage, a MongoDB and a Kubernetes cluster to run the jobs. Jobs can be submitted via an API. The API is defined using [gRPC](https://grpc.io/) and pregenerated builds are available for Golang. In addition the API can be queried using a JSON-over-REST API that is generated from the gRPC definitions using [grpc-gateway](https://github.com/grpc-ecosystem/grpc-gateway). The corresponding repositories can be found here: - [Bakta](https://github.com/oschwengers/bakta) - [UI](https://github.com/ag-computational-bio/bakta-web-ui) -- [API](https://github.com/ag-computational-bio/bakta-web-api) -- [Go-API](https://github.com/ag-computational-bio/bakta-web-api-go) -- [JSON-over-REST Gateway](https://github.com/ag-computational-bio/bakta-web-gateway) # Deployment ## Requirements - S3-compatible object storage -- MongoDB - Kubernetes-Cluster - -## Configuration -The backend is configured mainly via a config file that needs to be mounted into the running pod of the application using a config map. The secrets for accessing the MongoDB and the object storage are mounted as environment variables via Kubernetes secrets. In addition a properly configured service-account is required. An example configuration file can be found in `config/config.yaml`, kubernetes deployments files for the deployment can be found in the `kube` directory. The service-account requires basic CRUD rights on the batch/Job resource. - - - -### Configuration file - -| Parameter | Description | -|------------------------------|-------------------------------------------------| -| `Objectstorage.S3.UserBucket`| Bucket to store the input and output data | -| `Objectstorage.S3.DBBucket` | Bucket to store the bakta database | -| `Objectstorage.S3.BaseKey` | Key prefix to store the input and output data | -| `Database.MongoHost` | Hostname of the used MongoDB | -| `Database.MongoDBName` | Name of the used database inside MongoDB | -| `Database.MongoUser` | Username for MongoDB authentication | -| `Database.MongoAuthSource` | Authentication database | -| `Database.MongoPort` | Port of the MongoDB | -| `UpdateService.Name` | Servicename that handles the job status updates | -| `UpdateService.Port` | Serviceport that handles the job status updates | -| `ExpiryTime` | Defines how long a job should be kept around | -| `JobContainer` | Registry link to the job container | -| `InCluster` | Indicates if the app is running inside a cluster| -| `Testing` | Indicates if the bakta test db should be used | - - -### Environment variables -| Parameter | Description | -|------------------------------|-------------------------------------------------| -| `MongoPassword` | Password for the MongoDB user | -| `AWS_ACCESS_KEY_ID` | S3 access key | -| `AWS_SECRET_ACCESS_KEY` | S3 secret key | \ No newline at end of file +- Argo Workflows diff --git a/config/config.yaml b/config/config.yaml deleted file mode 100644 index 55d645f..0000000 --- a/config/config.yaml +++ /dev/null @@ -1,31 +0,0 @@ -Objectstorage: - S3: - UserBucket: baktauserdata2 - DBBucket: baktadbs - BaseKey: data/dev -Database: - MongoHost: mongo-mongodb.mongo - MongoDBName: bakta - MongoUser: bakta - MongoAuthSource: bakta - MongoPort: 27017 -K8sNamespace: "bakta" -UpdateService: - Name: bakta - Port: "8081" -Testing: true -Version: - Tool: "1.1.1" - DB: "3.0.0" -ExpiryTime: 34560 -JobContainer: "harbor.computational.bio.uni-giessen.de/bakta/bakta-web-job:0.1.0-beta.11" -InCluster: true -BaktaDatabasePVCName: bakta-web -Job: - CPU: - Limit: 4 - Request: 4 - Memory: - Limit: "4000Mi" - Request: "4000Mi" - \ No newline at end of file diff --git a/config/local-config.yaml b/config/local-config.yaml deleted file mode 100644 index 5f280c7..0000000 --- a/config/local-config.yaml +++ /dev/null @@ -1,17 +0,0 @@ -Objectstorage: - S3: - UserBucket: baktauserdata - DBBucket: baktadbs - BaseKey: data/dev -Database: - MongoHost: localhost - MongoDBName: bakta - MongoUser: root - MongoUserAuthSource: admin - MongoPort: 27017 -K8sNamespace: "bakta-dev" -UpdateService: - Name: baktawebbackend - Port: "8081" -Testing: true -ExpiryTime: 345600 \ No newline at end of file diff --git a/database/handler.go b/database/handler.go deleted file mode 100644 index 97924e0..0000000 --- a/database/handler.go +++ /dev/null @@ -1,406 +0,0 @@ -package database - -import ( - "context" - "crypto/rand" - "crypto/sha256" - "encoding/base64" - "errors" - "fmt" - "log" - "os" - "path" - "time" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/google/uuid" - "github.com/spf13/viper" - "go.mongodb.org/mongo-driver/bson" - "go.mongodb.org/mongo-driver/bson/primitive" - "go.mongodb.org/mongo-driver/mongo" - "go.mongodb.org/mongo-driver/mongo/options" - "go.mongodb.org/mongo-driver/mongo/readpref" -) - -// BackendType The type of the database backend to use -type BackendType string - -//UploadFileType type of file to upload -type UploadFileType string - -const ( - //Fasta fasta file - Fasta UploadFileType = "fasta" - //Replicon replicon file as tsv, see bakta documentation for further details - RepliconCSV UploadFileType = "repliconcsv" - RepliconTSV UploadFileType = "replicontsv" - //Prodigal Prodigal training file, see bakta documentation for further details - Prodigal UploadFileType = "prodigal" -) - -const RESULTFILENAME = "results.tar.gz" -const COLLECTIONNAME = "jobs" - -//Handler Wraps the database with convinence methods -type Handler struct { - DB *mongo.Client - Collection *mongo.Collection - BaseKey string - UserDataBucket string - DBBucket string - ExpiryTime int64 -} - -// InitDatabaseHandler Initializes the database to store the Job -func InitDatabaseHandler() (*Handler, error) { - host := viper.GetString("Database.MongoHost") - dbName := viper.GetString("Database.MongoDBName") - dbUser := viper.GetString("Database.MongoUser") - dbAuthSource := viper.GetString("Database.MongoAuthSource") - dbPassword := os.Getenv("MongoPassword") - dbPort := viper.GetString("Database.MongoPort") - - if dbPassword == "" { - return nil, fmt.Errorf("password for mongodb required, can be set with env var MongoPassword") - } - - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - client, err := mongo.Connect(ctx, options.Client().ApplyURI(fmt.Sprintf("mongodb://%v:%v", host, dbPort)).SetAuth( - options.Credential{ - AuthSource: dbAuthSource, - Username: dbUser, - Password: dbPassword, - }, - )) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - err = client.Ping(ctx, readpref.Primary()) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - collection := client.Database(dbName).Collection(COLLECTIONNAME) - - userBucket := viper.GetString("Objectstorage.S3.UserBucket") - baseKey := viper.GetString("Objectstorage.S3.BaseKey") - expiryTime := viper.GetInt64("ExpiryTime") - - dbHandler := Handler{ - DB: client, - Collection: collection, - UserDataBucket: userBucket, - BaseKey: baseKey, - ExpiryTime: expiryTime, - } - - err = dbHandler.createExpiryIndex() - if err != nil { - log.Println(err.Error()) - return nil, err - } - - return &dbHandler, nil -} - -//CreateJob Creates a new bakta job in init mode -func (handler *Handler) CreateJob(repliconTypeAPI api.RepliconTableType, jobname string) (*Job, string, error) { - jobID := uuid.New() - secretID, err := randStringBytes(50) - if err != nil { - log.Println(err.Error()) - return nil, "", err - } - - secretSHA := sha256.Sum256([]byte(secretID)) - secretSHABase64 := base64.StdEncoding.EncodeToString(secretSHA[:]) - - repliconType := RepliconTSV - - switch repliconTypeAPI { - case api.RepliconTableType_CSV: - repliconType = RepliconCSV - case api.RepliconTableType_TSV: - repliconType = RepliconTSV - } - - job := Job{ - JobID: jobID.String(), - Secret: secretSHABase64, - DataBucket: handler.UserDataBucket, - FastaKey: handler.createUploadStoreKey(jobID.String(), Fasta), - ProdigalKey: handler.createUploadStoreKey(jobID.String(), Prodigal), - RepliconKey: handler.createUploadStoreKey(jobID.String(), repliconType), - ResultKey: handler.createResultStoreKey(jobID.String()), - Status: api.JobStatusEnum_INIT.String(), - ExpiryDate: primitive.Timestamp{T: uint32(time.Now().AddDate(0, 0, 10).Unix())}, - Created: primitive.Timestamp{T: uint32(time.Now().Unix())}, - Updated: primitive.Timestamp{T: uint32(time.Now().Unix())}, - Jobname: jobname, - } - - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - inserted, err := handler.Collection.InsertOne(ctx, job) - if err != nil { - log.Println(err.Error()) - return nil, "", err - } - - inserted_query := bson.M{ - "_id": inserted.InsertedID, - } - - result := handler.Collection.FindOne(ctx, inserted_query) - if result.Err() != nil { - log.Println(result.Err().Error()) - return nil, "", result.Err() - } - - inserted_Job := Job{} - - err = result.Decode(&inserted_Job) - if err != nil { - log.Println(err.Error()) - return nil, "", err - } - - return &inserted_Job, secretID, nil -} - -//UpdateK8s Updates a job with its k8s id -func (handler *Handler) UpdateK8s(id string, k8s string) error { - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - update_filter := bson.M{ - "jobid": id, - } - - update := bson.M{ - "$set": bson.M{ - "k8sid": k8s, - "status": api.JobStatusEnum_INIT.String(), - }, - } - - result, err := handler.Collection.UpdateOne(ctx, update_filter, update) - if err != nil { - log.Println(err.Error()) - return err - } - - if result.MatchedCount != 1 { - err := fmt.Errorf("wrong number of updated job entries found when updating job: %v", id) - log.Println(err.Error()) - return err - } - - return nil -} - -//UpdateStatus Updates the status of a job -func (handler *Handler) UpdateStatus(id string, status api.JobStatusEnum, errorMsg string, isDeleted bool) error { - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - update_filter := bson.M{ - "jobid": id, - } - - update := bson.M{ - "$set": bson.M{ - "error": errorMsg, - "status": status.String(), - "updated": primitive.Timestamp{T: uint32(time.Now().Unix())}, - }, - } - - result, err := handler.Collection.UpdateOne(ctx, update_filter, update) - if err != nil { - log.Println(err.Error()) - return err - } - - if result.MatchedCount != 1 { - err := fmt.Errorf("wrong number of updated job entries found when updating job: %v", id) - log.Println(err.Error()) - return err - } - - return nil -} - -//GetJob Returns the stored config of a job -func (handler *Handler) GetJob(id string) (*Job, error) { - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - find_query := bson.M{ - "jobid": id, - } - - result := handler.Collection.FindOne(ctx, find_query) - if result.Err() != nil { - log.Println(result.Err().Error()) - return nil, result.Err() - } - - job := Job{} - - err := result.Decode(&job) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - return &job, nil -} - -//CheckSecret Compares the provided secret/JobID with a job in the database -func (handler *Handler) CheckSecret(id string, secretKey string) error { - job, err := handler.GetJob(id) - if err != nil { - log.Println(err.Error()) - return err - } - - secretSHA := sha256.Sum256([]byte(secretKey)) - secretSHABase64 := base64.StdEncoding.EncodeToString(secretSHA[:]) - - if secretSHABase64 != job.Secret { - return errors.New("wrong secret provided") - } - - return nil -} - -// GetJobsStatus Returns the status of a list of jobs -func (handler *Handler) GetJobs(jobIDs []*api.JobAuth) ([]Job, error) { - var ids []string - var jobs []Job - - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - for _, id := range jobIDs { - ids = append(ids, id.JobID) - } - - find_query := bson.M{ - "jobid": bson.M{ - "$in": ids, - }, - } - - csr, err := handler.Collection.Find(ctx, find_query) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - if err = csr.All(ctx, &jobs); err != nil { - log.Println(err.Error()) - return nil, err - } - - return jobs, nil -} - -// GetJobStatus Returns the status of an individual job -func (handler *Handler) GetJobStatus(jobID string) (*Job, error) { - job, err := handler.GetJob(jobID) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - return job, nil -} - -func (handler *Handler) GetRunningJobs() ([]*Job, error) { - var runningJobs []*Job - running_jobs_query := bson.M{ - "Status": api.JobStatusEnum_RUNNING.String(), - } - - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - csr, err := handler.Collection.Find(ctx, running_jobs_query) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - if err = csr.All(ctx, &runningJobs); err != nil { - log.Println(err.Error()) - return nil, err - } - - return runningJobs, nil -} - -func (handler *Handler) DeleteJob(id string) error { - query := bson.M{ - "JobID": id, - } - - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - _, err := handler.Collection.DeleteOne(ctx, query) - if err != nil { - log.Println(err.Error()) - return err - } - - return nil -} - -func (handler *Handler) createUploadStoreKey(id string, uploadFileType UploadFileType) string { - var filename string - switch uploadFileType { - case Fasta: - filename = "fastadata.fasta" - case RepliconTSV: - filename = "replicons.tsv" - case RepliconCSV: - filename = "replicons.tsv" - case Prodigal: - filename = "prodigaltraining.tf" - } - - resultKey := path.Join(handler.BaseKey, "uploaddata", id, filename) - return resultKey -} - -func (handler *Handler) createResultStoreKey(id string) string { - resultKey := path.Join(handler.BaseKey, "results", id) - return resultKey -} - -func randStringBytes(n int) (string, error) { - b := make([]byte, n) - _, err := rand.Read(b) - if err != nil { - log.Println(err.Error()) - return "", err - } - - data := base64.StdEncoding.EncodeToString(b) - - return data, nil -} - -func (handler *Handler) createExpiryIndex() error { - ctx, _ := context.WithTimeout(context.Background(), 1*time.Second) - - index := bson.M{ - "ExpiryDate": 1, - } - - _, err := handler.Collection.Indexes().CreateOne(ctx, mongo.IndexModel{Keys: index, Options: options.Index().SetExpireAfterSeconds(0)}, nil) - if err != nil { - log.Println(err.Error()) - return err - } - - return nil -} diff --git a/database/handler_integration_test.go b/database/handler_integration_test.go deleted file mode 100644 index 3a8cc50..0000000 --- a/database/handler_integration_test.go +++ /dev/null @@ -1,125 +0,0 @@ -// +build integration - -package database - -import ( - "fmt" - "github.com/spf13/viper" - "os" - "testing" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" -) - -func TestHandler_CreateJob(t *testing.T) { - - viper.SetConfigFile("../config/config.yaml") - err := viper.ReadInConfig() - if err != nil { - t.Errorf(err.Error()) - } - - db, err := InitDatabaseHandler() - if err != nil { - t.Errorf(err.Error()) - } - - job, s, err := db.CreateJob(api.RepliconTableType_TSV, "test") - - if err != nil { - t.Errorf(err.Error()) - } - - if job == nil || s == "" { - t.Errorf("empty job response") - } - -} - -func TestHandler_GetJob(t *testing.T) { - - os.Setenv("MongoPassword", "testpw1") - - viper.SetConfigFile("../config/config.yaml") - err := viper.ReadInConfig() - if err != nil { - t.Errorf(err.Error()) - } - - db, err := InitDatabaseHandler() - if err != nil { - t.Errorf(err.Error()) - } - - job, s, err := db.CreateJob(api.RepliconTableType_TSV, "test2") - - if err != nil { - t.Errorf(err.Error()) - } - - if job == nil || s == "" { - t.Errorf("empty job response") - } - - getJob, err := db.GetJob(job.JobID) - - if err != nil { - t.Errorf(err.Error()) - } - - if *getJob != *job { - t.Errorf("created and requested job are not equal") - } - -} - -func TestHandler_UpdateStatus(t *testing.T) { - - os.Setenv("MongoPassword", "testpw1") - - viper.SetConfigFile("../config/config.yaml") - err := viper.ReadInConfig() - if err != nil { - t.Errorf(err.Error()) - } - - db, err := InitDatabaseHandler() - if err != nil { - t.Errorf(err.Error()) - } - - job, s, err := db.CreateJob(api.RepliconTableType_TSV, "test2") - - if err != nil { - t.Errorf(err.Error()) - } - - if job == nil || s == "" { - t.Errorf("empty job response") - } - - err = db.UpdateStatus(job.JobID, api.JobStatusEnum_RUNNING, "", false) - - if err != nil { - t.Errorf(err.Error()) - } - - ret_job, err := db.GetJobStatus(job.JobID) - - if err != nil { - t.Errorf(err.Error()) - } - - fmt.Println(ret_job.Status) - if ret_job.Status != "RUNNING" { - t.Errorf("Status update failed") - } - -} - -func TestRndBytes(t *testing.T) { - _, err := randStringBytes(50) - if err != nil { - t.Errorf(err.Error()) - } -} diff --git a/database/models.go b/database/models.go deleted file mode 100644 index 552dcc8..0000000 --- a/database/models.go +++ /dev/null @@ -1,25 +0,0 @@ -package database - -import ( - "go.mongodb.org/mongo-driver/bson/primitive" -) - -// Job The database model for a bakta job -type Job struct { - JobID string - Secret string - K8sID string - Updated primitive.Timestamp - Created primitive.Timestamp - Status string - DataBucket string - FastaKey string - ProdigalKey string - RepliconKey string - ResultKey string - Error string - ExpiryDate primitive.Timestamp - ConfString string - IsDeleted bool - Jobname string -} diff --git a/endpoints/job.go b/endpoints/job.go deleted file mode 100644 index 68bcc14..0000000 --- a/endpoints/job.go +++ /dev/null @@ -1,243 +0,0 @@ -package endpoints - -import ( - "context" - "crypto/sha256" - "encoding/base64" - "encoding/json" - "fmt" - "github.com/spf13/viper" - "log" - "os" - "time" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/monitor" - "github.com/ag-computational-bio/bakta-web-backend/objectStorage" - "google.golang.org/protobuf/types/known/structpb" - "google.golang.org/protobuf/types/known/timestamppb" - - "github.com/ag-computational-bio/bakta-web-backend/database" - "github.com/ag-computational-bio/bakta-web-backend/scheduler" -) - -//BaktaJobAPI implements the job endpoints of the bakta-web-api -type BaktaJobAPI struct { - dbHandler *database.Handler - scheduler *scheduler.SimpleScheduler - s3Handler *objectStorage.S3ObjectStorageHandler - monitor *monitor.SimpleMonitor -} - -//InitBaktaAPI Initiates the Bakta API handler -func InitBaktaAPI(dbHandler *database.Handler, scheduler *scheduler.SimpleScheduler, s3Handler *objectStorage.S3ObjectStorageHandler, monitor *monitor.SimpleMonitor) *BaktaJobAPI { - api := &BaktaJobAPI{ - dbHandler: dbHandler, - scheduler: scheduler, - s3Handler: s3Handler, - monitor: monitor, - } - - return api -} - -//InitJob Initiates a bakta job and returns upload links for the fasta, prodigal training and replicon file -func (apiHandler *BaktaJobAPI) InitJob(ctx context.Context, request *api.InitJobRequest) (*api.InitJobResponse, error) { - job, secret, err := apiHandler.dbHandler.CreateJob(request.RepliconTableType, request.GetName()) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - fastaUploadKey, err := apiHandler.s3Handler.CreateUploadLink(job.DataBucket, job.FastaKey) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - prodigalUploadKey, err := apiHandler.s3Handler.CreateUploadLink(job.DataBucket, job.ProdigalKey) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - repliconsUploadKey, err := apiHandler.s3Handler.CreateUploadLink(job.DataBucket, job.RepliconKey) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - initJobResp := api.InitJobResponse{ - Job: &api.JobAuth{ - JobID: job.JobID, - Secret: secret, - }, - UploadLinkFasta: fastaUploadKey, - UploadLinkProdigal: prodigalUploadKey, - UploadLinkReplicons: repliconsUploadKey, - } - - return &initJobResp, nil -} - -//StartJob Starts a job based on the provided configuration -func (apiHandler *BaktaJobAPI) StartJob(ctx context.Context, request *api.StartJobRequest) (*api.Empty, error) { - err := apiHandler.dbHandler.CheckSecret(request.GetJob().GetJobID(), request.GetJob().GetSecret()) - if err != nil { - err = fmt.Errorf("JobID does not match secret ID") - return nil, err - } - - k8sJob, err := apiHandler.scheduler.StartJob(request.Job.GetJobID(), request.GetConfig()) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - err = apiHandler.dbHandler.UpdateK8s(request.Job.GetJobID(), string(k8sJob.GetUID())) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - return &api.Empty{}, nil -} - -//GetJobsStatus Get the job status of the provided list of jobs -func (apiHandler *BaktaJobAPI) JobsStatus(ctx context.Context, request *api.JobStatusRequestList) (*api.JobStatusReponseList, error) { - var failedJobs []*api.FailedJob - var jobsStatus []*api.JobStatusResponse - - jobs, err := apiHandler.dbHandler.GetJobs(request.GetJobs()) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - foundJobs := make(map[string]database.Job) - for _, job := range jobs { - foundJobs[job.JobID] = job - - } - - for _, expectedJob := range request.GetJobs() { - job, ok := foundJobs[expectedJob.JobID] - if !ok { - failedJobs = append(failedJobs, &api.FailedJob{ - JobID: expectedJob.JobID, - JobStatus: api.JobFailedStatus_NOT_FOUND, - }) - continue - } - - secretSHA := sha256.Sum256([]byte(expectedJob.Secret)) - secretSHABase64 := base64.StdEncoding.EncodeToString(secretSHA[:]) - - if secretSHABase64 != job.Secret { - failedJobs = append(failedJobs, &api.FailedJob{ - JobID: expectedJob.JobID, - JobStatus: api.JobFailedStatus_UNAUTHORIZED, - }) - continue - } - - statusNumber, ok := api.JobStatusEnum_value[job.Status] - if !ok { - err = fmt.Errorf("%v not a valid status", job.Status) - return nil, err - } - - statusEnum := api.JobStatusEnum(statusNumber) - - created_time := timestamppb.New(time.Unix(int64(job.Created.T), 0)) - updated_time := timestamppb.New(time.Unix(int64(job.Updated.T), 0)) - - statusResponse := api.JobStatusResponse{ - JobID: job.JobID, - JobStatus: statusEnum, - Started: created_time, - Updated: updated_time, - Name: job.Jobname, - } - - jobsStatus = append(jobsStatus, &statusResponse) - } - - response := api.JobStatusReponseList{ - Jobs: jobsStatus, - FailedJobs: failedJobs, - } - - return &response, nil -} - -//GetJobResult Returns the results for a specific jobs -func (apiHandler *BaktaJobAPI) JobResult(ctx context.Context, request *api.JobAuth) (*api.JobResultResponse, error) { - err := apiHandler.dbHandler.CheckSecret(request.GetJobID(), request.GetSecret()) - if err != nil { - err = fmt.Errorf("JobID does not match secret ID") - return nil, err - } - - job, err := apiHandler.dbHandler.GetJobStatus(request.GetJobID()) - if err != nil { - log.Println(err.Error()) - return nil, fmt.Errorf("could not read job result for job: %v", request.GetJobID()) - } - - results, err := apiHandler.s3Handler.CreateDownloadLinks(job.DataBucket, job.ResultKey, "result") - if err != nil { - log.Println(err.Error()) - return nil, fmt.Errorf("could not create download url for job: %v", request.GetJobID()) - } - - intermediateByteData, err := json.Marshal(results) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - var structData structpb.Struct - err = structData.UnmarshalJSON(intermediateByteData) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - created_time := timestamppb.New(time.Unix(int64(job.Created.T), 0)) - updated_time := timestamppb.New(time.Unix(int64(job.Updated.T), 0)) - - jobResponse := api.JobResultResponse{ - JobID: job.JobID, - ResultFiles: &structData, - Started: created_time, - Updated: updated_time, - Name: job.Jobname, - } - - return &jobResponse, nil -} - -func (apiHandler *BaktaJobAPI) Version(ctx context.Context, request *api.Empty) (*api.VersionResponse, error) { - shaVersion := os.Getenv("GITHUB_SHA") - - version := api.VersionResponse{ - ToolVersion: viper.GetString("Version.Tool"), - DbVersion: viper.GetString("Version.DB"), - BackendVersion: shaVersion, - } - - return &version, nil -} - -func (apiHandler *BaktaJobAPI) Delete(context.Context, *api.JobAuth) (*api.Empty, error) { - return &api.Empty{}, nil -} - -func pretty(value interface{}) { - empJSON, err := json.MarshalIndent(value, "", " ") - if err != nil { - log.Fatalf(err.Error()) - } - fmt.Printf("%s\n", string(empJSON)) -} diff --git a/endpoints/job_integration_test.go b/endpoints/job_integration_test.go deleted file mode 100644 index 22f8f67..0000000 --- a/endpoints/job_integration_test.go +++ /dev/null @@ -1,116 +0,0 @@ -// +/build integration - -package endpoints - -import ( - "context" - proto_api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/database" - "github.com/ag-computational-bio/bakta-web-backend/monitor" - "github.com/ag-computational-bio/bakta-web-backend/objectStorage" - "github.com/ag-computational-bio/bakta-web-backend/scheduler" - "github.com/spf13/viper" - "testing" -) - -func InitAPI() (api *BaktaJobAPI, err error) { - dbHandler, err := database.InitDatabaseHandler() - if err != nil { - return nil, err - } - - clientset, err := scheduler.CreateClientSet() - - if err != nil { - return nil, err - } - - sched, err := scheduler.InitSimpleScheduler(dbHandler, clientset) - if err != nil { - return nil, err - } - - bucket := viper.GetString("Objectstorage.S3.Bucket") - - s3Handler, err := objectStorage.InitS3ObjectStorageHandler(bucket) - if err != nil { - return nil, err - } - - updateMonitor := monitor.New(sched.GetK8sClient(), sched.GetNamespace(), dbHandler) - - return InitBaktaAPI(dbHandler, sched, s3Handler, &updateMonitor), nil - -} - -func TestBaktaJobAPI_InitJob(t *testing.T) { - api, err := InitAPI() - if err != nil { - t.Fatal(err) - } - response, err := api.InitJob(context.Background(), &proto_api.InitJobRequest{ - RepliconTableType: 1, - Name: "test", - }) - - if err != nil { - t.Fatal(err) - } - - if response != nil { - t.Fatal("nil response") - } - -} - -func TestBaktaJobAPI_StartJob(t *testing.T) { - api, err := InitAPI() - if err != nil { - - t.Fatal(err) - } - response, err := api.InitJob(context.Background(), &proto_api.InitJobRequest{ - RepliconTableType: 0, - Name: "", - }) - if err != nil { - - t.Fatal(err) - } - - api.StartJob(context.Background(), &proto_api.StartJobRequest{ - Job: response.Job, - Config: &proto_api.JobConfig{ - HasProdigal: false, - HasReplicons: false, - TranslationalTable: 0, - CompleteGenome: false, - KeepContigHeaders: false, - MinContigLength: 0, - DermType: 0, - Genus: "", - Species: "", - Strain: "", - Plasmid: "", - Locus: "", - LocusTag: "", - }, - }) - -} - -func TestBaktaJobAPI_JobsStatus(t *testing.T) { - api, err := InitAPI() - if err != nil { - t.Fatal(err) - } - _, err = api.InitJob(context.Background(), &proto_api.InitJobRequest{ - RepliconTableType: 0, - Name: "", - }) - if err != nil { - - t.Fatal(err) - } - -} diff --git a/endpoints/server.go b/endpoints/server.go deleted file mode 100644 index 75cf9aa..0000000 --- a/endpoints/server.go +++ /dev/null @@ -1,153 +0,0 @@ -package endpoints - -import ( - "context" - "fmt" - "log" - "net" - "os" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/monitor" - "github.com/ag-computational-bio/bakta-web-backend/objectStorage" - "github.com/ag-computational-bio/bakta-web-backend/scheduler" - "github.com/spf13/viper" - - "github.com/ag-computational-bio/bakta-web-backend/database" - - "golang.org/x/sync/errgroup" - "google.golang.org/grpc" - "google.golang.org/grpc/metadata" -) - -//AuthHandler Simple auth handler to check if a grpc call has a token -//Only for testing purposes -type AuthHandler struct { - token string -} - -//InitAuthHandler Initiates a simple auth handler -func InitAuthHandler() (*AuthHandler, error) { - apiToken := os.Getenv("ApiToken") - if apiToken == "" { - return nil, fmt.Errorf("invalid API Token") - } - - authHandler := AuthHandler{ - token: apiToken, - } - - return &authHandler, nil -} - -//RunGrpcJobServer Runs the Grpc server -func RunGrpcJobServer() error { - authHandler, err := InitAuthHandler() - if err != nil { - log.Fatalln(err.Error()) - } - - dbHandler, err := database.InitDatabaseHandler() - if err != nil { - log.Fatalln(err.Error()) - } - - clientset, err := scheduler.CreateClientSet() - - if err != nil { - log.Fatalln(err.Error()) - } - - sched, err := scheduler.InitSimpleScheduler(dbHandler, clientset) - if err != nil { - log.Fatalln(err.Error()) - } - - jobListener, err := net.Listen("tcp", fmt.Sprintf("localhost:%v", "8080")) - if err != nil { - log.Println(fmt.Sprintf("failed to listen: %v", err)) - return err - } - - updateListener, err := net.Listen("tcp", fmt.Sprintf("localhost:%v", "8081")) - if err != nil { - log.Println(fmt.Sprintf("failed to listen: %v", err)) - return err - } - - bucket := viper.GetString("Objectstorage.S3.Bucket") - - s3Handler, err := objectStorage.InitS3ObjectStorageHandler(bucket) - if err != nil { - log.Println(fmt.Sprintf("failed to listen: %v", err)) - return err - } - - updateMonitor := monitor.New(sched.GetK8sClient(), sched.GetNamespace(), dbHandler) - - //TODO: write tests before activating - //updateMonitor.RunFindStragglersLoop() - - jobServer := initGrpcJobServer(dbHandler, sched, authHandler, s3Handler, &updateMonitor) - - updateHandler := BaktaUpdateAPI{ - dbHandler: dbHandler, - updateMonitor: &updateMonitor, - scheduler: sched, - } - - updateServer := initGrpcUpdateServer(&updateHandler) - - serverErrGrp, _ := errgroup.WithContext(context.Background()) - - serverErrGrp.Go(func() error { - return jobServer.Serve(jobListener) - }) - - serverErrGrp.Go(func() error { - return updateServer.Serve(updateListener) - }) - - log.Println("Started grpc server") - - return serverErrGrp.Wait() -} - -// initGrpcServer Initializes a new GRPC server that handles bakta-web-api endpoints -func initGrpcJobServer(dbHandler *database.Handler, sched *scheduler.SimpleScheduler, authHandler *AuthHandler, s3Handler *objectStorage.S3ObjectStorageHandler, updateMonitor *monitor.SimpleMonitor) *grpc.Server { - baktaJobsEndpoints := InitBaktaAPI(dbHandler, sched, s3Handler, updateMonitor) - - var opts []grpc.ServerOption - //opts = append(opts, grpc.UnaryInterceptor(authHandler.unaryInterceptor)) - - grpcServer := grpc.NewServer(opts...) - api.RegisterBaktaJobsServer(grpcServer, baktaJobsEndpoints) - - return grpcServer -} - -// initGrpcServer Initializes a new GRPC server that handles bakta-web-api endpoints -func initGrpcUpdateServer(baktaUpdateEndpoints *BaktaUpdateAPI) *grpc.Server { - grpcServer := grpc.NewServer() - api.RegisterBaktaStatusUpdateServer(grpcServer, baktaUpdateEndpoints) - - return grpcServer -} - -// unaryInterceptor calls authenticateClient with current context -func (authHandler *AuthHandler) unaryInterceptor(ctx context.Context, req interface{}, info *grpc.UnaryServerInfo, handler grpc.UnaryHandler) (interface{}, error) { - if md, ok := metadata.FromIncomingContext(ctx); ok { - if token, ok := md["authorization"]; ok { - if len(token) == 1 && token[0] == authHandler.token { - return handler(ctx, req) - } - err := fmt.Errorf("API key does not match") - log.Println(err.Error()) - return "", err - } - } - - err := fmt.Errorf("error authenticating credentials") - log.Println(err.Error()) - return "", err -} diff --git a/endpoints/server_integration_test.go b/endpoints/server_integration_test.go deleted file mode 100644 index 93807a4..0000000 --- a/endpoints/server_integration_test.go +++ /dev/null @@ -1,13 +0,0 @@ -// +build integration - -package endpoints - -import "testing" - -func TestInitAuthHandler(t *testing.T) { - -} - -func TestRunGrpcJobServer(t *testing.T) { - -} diff --git a/endpoints/update.go b/endpoints/update.go deleted file mode 100644 index 9f3852c..0000000 --- a/endpoints/update.go +++ /dev/null @@ -1,87 +0,0 @@ -package endpoints - -import ( - "context" - "log" - "time" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/database" - "github.com/ag-computational-bio/bakta-web-backend/monitor" - "github.com/ag-computational-bio/bakta-web-backend/scheduler" -) - -//BaktaUpdateAPI implements the endpoints of the bakta-web-api -type BaktaUpdateAPI struct { - api.UnimplementedBaktaStatusUpdateServer - dbHandler *database.Handler - scheduler *scheduler.SimpleScheduler - updateMonitor *monitor.SimpleMonitor -} - -//UpdateStatus Updates the status of a running job -func (apiHandler *BaktaUpdateAPI) UpdateStatus(ctx context.Context, request *api.UpdateStatusRequest) (*api.Empty, error) { - go func() { - log.Println("Received job update") - - job, err := apiHandler.dbHandler.GetJob(request.GetJobID()) - if err != nil { - log.Println(err.Error()) - return - } - - if job.IsDeleted { - return - } - - status, err := apiHandler.updateMonitor.GetJobStatus(job.JobID) - if err != nil { - log.Println(err.Error()) - return - } - - isDeleted := false - - repeats := 0 - - for { - repeats = repeats + 1 - status, err = apiHandler.updateMonitor.GetJobStatus(job.JobID) - if err != nil { - log.Println(err.Error()) - return - } - - if status.Status != api.JobStatusEnum_RUNNING { - break - } - - if repeats > 15 { - break - } - - time.Sleep(500 * time.Millisecond) - } - - if status.Status == api.JobStatusEnum_SUCCESSFULL || status.Status == api.JobStatusEnum_ERROR { - if !job.IsDeleted { - err = apiHandler.scheduler.DeleteJob(job.JobID) - if err != nil { - log.Println(err.Error()) - return - } - - isDeleted = true - } - } - - err = apiHandler.dbHandler.UpdateStatus(request.GetJobID(), status.Status, status.ErrorMsg, isDeleted) - if err != nil { - log.Println(err.Error()) - return - } - - }() - - return &api.Empty{}, nil -} diff --git a/endpoints/update_integration_test.go b/endpoints/update_integration_test.go deleted file mode 100644 index 9fff369..0000000 --- a/endpoints/update_integration_test.go +++ /dev/null @@ -1,9 +0,0 @@ -// +build integration - -package endpoints - -import "testing" - -func TestBaktaUpdateAPI_UpdateStatus(t *testing.T) { - -} diff --git a/go.mod b/go.mod deleted file mode 100644 index 30f0368..0000000 --- a/go.mod +++ /dev/null @@ -1,38 +0,0 @@ -module github.com/ag-computational-bio/bakta-web-backend - -go 1.16 - -require ( - github.com/ag-computational-bio/bakta-web-api-go v0.0.0-20210921135611-ac8ba76748b4 - github.com/aws/aws-sdk-go v1.38.66 // indirect - github.com/aws/aws-sdk-go-v2 v1.6.0 - github.com/aws/aws-sdk-go-v2/config v1.3.0 - github.com/aws/aws-sdk-go-v2/service/s3 v1.10.0 - github.com/evanphx/json-patch v4.11.0+incompatible // indirect - github.com/google/gofuzz v1.2.0 // indirect - github.com/google/uuid v1.2.0 - github.com/googleapis/gnostic v0.5.5 // indirect - github.com/grpc-ecosystem/grpc-gateway/v2 v2.5.0 // indirect - github.com/imdario/mergo v0.3.12 // indirect - github.com/jessevdk/go-flags v1.5.0 - github.com/klauspost/compress v1.13.1 // indirect - github.com/spf13/viper v1.8.0 - github.com/youmark/pkcs8 v0.0.0-20201027041543-1326539a0a0a // indirect - go.mongodb.org/mongo-driver v1.5.3 - golang.org/x/crypto v0.0.0-20210616213533-5ff15b29337e // indirect - golang.org/x/net v0.0.0-20210614182718-04defd469f4e // indirect - golang.org/x/oauth2 v0.0.0-20210622215436-a8dc77f794b6 // indirect - golang.org/x/sync v0.0.0-20210220032951-036812b2e83c - golang.org/x/sys v0.0.0-20210616094352-59db8d763f22 // indirect - golang.org/x/term v0.0.0-20210615171337-6886f2dfbf5b // indirect - golang.org/x/time v0.0.0-20210611083556-38a9dc6acbc6 // indirect - google.golang.org/grpc v1.38.0 - google.golang.org/protobuf v1.26.0 - k8s.io/api v0.21.2 - k8s.io/apimachinery v0.21.2 - k8s.io/client-go v0.21.2 - k8s.io/klog/v2 v2.9.0 // indirect - k8s.io/kube-openapi v0.0.0-20210527164424-3c818078ee3d // indirect - k8s.io/utils v0.0.0-20210527160623-6fdb442a123b // indirect - sigs.k8s.io/structured-merge-diff/v4 v4.1.1 // indirect -) diff --git a/go.sum b/go.sum deleted file mode 100644 index 265a939..0000000 --- a/go.sum +++ /dev/null @@ -1,961 +0,0 @@ -cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= -cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= -cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= -cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU= -cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= -cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc= -cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0= -cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To= -cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4= -cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M= -cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc= -cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk= -cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs= -cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc= -cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY= -cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI= -cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk= -cloud.google.com/go v0.78.0/go.mod h1:QjdrLG0uq+YwhjoVOLsS1t7TW8fs36kLs4XO5R5ECHg= -cloud.google.com/go v0.79.0/go.mod h1:3bzgcEeQlzbuEAYu4mrWhKqWjmpprinYgKJLgKHnbb8= -cloud.google.com/go v0.81.0/go.mod h1:mk/AM35KwGk/Nm2YSeZbxXdrNK3KZOYHmLkOqC2V6E0= -cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o= 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h1:bJZC9H9iH24zzfZ/41RGcq60oK1F7G282QMXDPYydCw= -sigs.k8s.io/structured-merge-diff/v4 v4.1.1 h1:nYqY2A6oy37sKLYuSBXuQhbj4JVclzJK13BOIvJG5XU= -sigs.k8s.io/structured-merge-diff/v4 v4.1.1/go.mod h1:bJZC9H9iH24zzfZ/41RGcq60oK1F7G282QMXDPYydCw= -sigs.k8s.io/yaml v1.2.0 h1:kr/MCeFWJWTwyaHoR9c8EjH9OumOmoF9YGiZd7lFm/Q= -sigs.k8s.io/yaml v1.2.0/go.mod h1:yfXDCHCao9+ENCvLSE62v9VSji2MKu5jeNfTrofGhJc= diff --git a/kube/dev-deployment.yaml b/kube/dev-deployment.yaml deleted file mode 100644 index d1c5998..0000000 --- a/kube/dev-deployment.yaml +++ /dev/null @@ -1,113 +0,0 @@ -apiVersion: apps/v1 -kind: Deployment -metadata: - name: bakta-backend - labels: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 -spec: - replicas: 1 - selector: - matchLabels: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 - template: - metadata: - labels: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 - spec: - containers: - - env: - - name: ApiToken - value: foo - - name: MongoPassword - valueFrom: - secretKeyRef: - key: mongodb-password - name: mongo-mongodb - - name: AWS_ACCESS_KEY_ID - valueFrom: - secretKeyRef: - key: AccessKey - name: s3 - - name: AWS_SECRET_ACCESS_KEY - valueFrom: - secretKeyRef: - key: SecretKey - name: s3 - image: harbor.computational.bio.uni-giessen.de/bakta/bakta-web-backend:0.2.9-beta.45 - resources: - limits: - cpu: 2000m - memory: 2000Mi - requests: - cpu: 2000m - memory: 2000Mi - imagePullPolicy: Always - name: baktabackend - ports: - - containerPort: 8080 - name: 8080tcp2 - protocol: TCP - - containerPort: 8081 - name: 8081tcp2 - protocol: TCP - volumeMounts: - - mountPath: /tmp - name: tmp-volume - - mountPath: /config - name: config - readOnly: true - volumes: - - emptyDir: {} - name: tmp-volume - - configMap: - defaultMode: 420 - name: baktabackendconf - name: config ---- -apiVersion: v1 -kind: Service -metadata: - name: bakta - labels: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 -spec: - selector: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 - ports: - - protocol: TCP - port: 9000 - targetPort: 8080 ---- -apiVersion: v1 -kind: Service -metadata: - name: bakta - labels: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 -spec: - selector: - app.kubernetes.io/name: backend - app.kubernetes.io/part-of: bakta-web - app.kubernetes.io/version: v0.1.0 - ports: - - protocol: TCP - name: jobport - port: 9000 - targetPort: 8080 - - protocol: TCP - name: updateport - port: 8081 - targetPort: 8081 - diff --git a/main.go b/main.go deleted file mode 100644 index 5cba0fe..0000000 --- a/main.go +++ /dev/null @@ -1,37 +0,0 @@ -package main - -import ( - "log" - - "github.com/ag-computational-bio/bakta-web-backend/endpoints" - "github.com/jessevdk/go-flags" - "github.com/spf13/viper" -) - -var opts struct { - ConfigFile string `short:"c" long:"configfile" description:"File of the config file" default:"./config/config.yaml"` -} - -//Version Version tag -var Version string - -func main() { - // Enable line numbers in logging - log.SetFlags(log.LstdFlags | log.Lshortfile) - - _, err := flags.Parse(&opts) - if err != nil { - log.Fatalln(err.Error()) - } - - viper.SetConfigFile(opts.ConfigFile) - err = viper.ReadInConfig() - if err != nil { - log.Fatalln(err.Error()) - } - - err = endpoints.RunGrpcJobServer() - if err != nil { - log.Fatalln(err.Error()) - } -} diff --git a/monitor/simple_monitor.go b/monitor/simple_monitor.go deleted file mode 100644 index b0e4d93..0000000 --- a/monitor/simple_monitor.go +++ /dev/null @@ -1,174 +0,0 @@ -package monitor - -import ( - "context" - "fmt" - "log" - "math/rand" - "time" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/database" - "github.com/spf13/viper" - "golang.org/x/sync/errgroup" - k8serrors "k8s.io/apimachinery/pkg/api/errors" - metav1 "k8s.io/apimachinery/pkg/apis/meta/v1" - v1 "k8s.io/apimachinery/pkg/apis/meta/v1" - "k8s.io/client-go/kubernetes" -) - -type SimpleMonitor struct { - k8sClient kubernetes.Interface - databaseHandler *database.Handler - namespace string -} - -type JobStatus struct { - Status api.JobStatusEnum - ErrorMsg string -} - -func New(k8sClient kubernetes.Interface, namespace string, db *database.Handler) SimpleMonitor { - return SimpleMonitor{ - k8sClient: k8sClient, - namespace: namespace, - databaseHandler: db, - } -} - -func (monitor *SimpleMonitor) GetJobStatus(jobID string) (JobStatus, error) { - - k8sJobName := fmt.Sprintf("bakta-job-%s", jobID) - - time.Sleep(2 * time.Second) - - job, err := monitor.k8sClient.BatchV1().Jobs(monitor.namespace).Get(context.TODO(), k8sJobName, v1.GetOptions{}) - if err != nil { - log.Println(err.Error()) - return JobStatus{}, err - } - - jobStatus := JobStatus{ - Status: api.JobStatusEnum_INIT, - } - - if job.Status.Active >= 1 { - jobStatus.Status = api.JobStatusEnum_RUNNING - } else if job.Status.Succeeded >= 1 && job.Status.Active == 0 { - jobStatus.Status = api.JobStatusEnum_SUCCESSFULL - } else if job.Status.Failed >= 1 && job.Status.Active == 0 { - jobStatus.Status = api.JobStatusEnum_ERROR - } else { - jobStatus.Status = api.JobStatusEnum_INIT - errMsg, err := monitor.getJobPodError(jobID) - if err != nil { - log.Println(err.Error()) - } - jobStatus.ErrorMsg = errMsg - } - - return jobStatus, nil -} - -func (monitor *SimpleMonitor) getJobPodError(jobID string) (string, error) { - labelSelector := fmt.Sprintf("job-name=%s%s", "bakta-job-", jobID) - - listOptions := metav1.ListOptions{ - LabelSelector: labelSelector, - } - - pods, err := monitor.k8sClient.CoreV1().Pods(monitor.namespace).List(context.TODO(), listOptions) - if err != nil { - log.Println(err.Error()) - return "", err - } - - if len(pods.Items) == 0 { - err := fmt.Errorf("Could not find pods for job %v", jobID) - log.Println(err.Error()) - return "", err - } - - pod := pods.Items[len(pods.Items)-1] - - return pod.Status.Message, nil -} - -func (monitor *SimpleMonitor) RunFindStragglersLoop() { - go func() { - stragglerWaitTime := viper.GetInt("StragglerWaitTime") - - initialOffset := rand.Intn(stragglerWaitTime) - time.Sleep(time.Duration(initialOffset) * time.Minute) - - for { - log.Println("starting cleanup cycle") - monitor.findRunningStragglers() - log.Println("finished cleanup cycle") - time.Sleep(time.Duration(stragglerWaitTime) * time.Minute) - } - }() -} - -// findRunningStragglers Checks all jobs in the database with running status if they have an correponding -// job running in the Kubernetes cluster -func (monitor *SimpleMonitor) findRunningStragglers() error { - jobs, err := monitor.databaseHandler.GetRunningJobs() - if err != nil { - log.Println(err.Error()) - return err - } - - running_checker_errgp := errgroup.Group{} - jobs_channel := make(chan *database.Job, 500) - - for i := 1; i <= 100; i++ { - running_checker_errgp.Go(func() error { - return monitor.checkAndHandleRunningStraggler(jobs_channel) - }) - } - - go func() { - defer close(jobs_channel) - for _, job := range jobs { - jobs_channel <- job - } - }() - - err = running_checker_errgp.Wait() - if err != nil { - log.Println(err.Error()) - return err - } - - return nil -} - -func (monitor *SimpleMonitor) checkAndHandleRunningStraggler(jobs chan *database.Job) error { - for job := range jobs { - _, err := monitor.GetJobStatus(job.JobID) - if !k8serrors.IsNotFound(err) { - if err != nil { - log.Println(err.Error()) - } - return err - } - - // Check again if job is still running in database to avoid consistency problems with jobs that finish between the initial query and the k8s check - updatedJob, err := monitor.databaseHandler.GetJob(job.JobID) - if err != nil { - log.Println(err.Error()) - } - - if updatedJob.Status == api.JobStatusEnum_RUNNING.String() && !updatedJob.IsDeleted { - err := monitor.databaseHandler.UpdateStatus(job.JobID, api.JobStatusEnum_ERROR, "job was in running state but no running k8s job could be found", true) - if err != nil { - log.Println(err.Error()) - return err - } - } - - } - - return nil -} diff --git a/monitor/simple_monitor_test.go b/monitor/simple_monitor_test.go deleted file mode 100644 index d443cee..0000000 --- a/monitor/simple_monitor_test.go +++ /dev/null @@ -1 +0,0 @@ -package monitor diff --git a/objectStorage/s3_object_storage_handler.go b/objectStorage/s3_object_storage_handler.go deleted file mode 100644 index 63e9dd0..0000000 --- a/objectStorage/s3_object_storage_handler.go +++ /dev/null @@ -1,108 +0,0 @@ -package objectStorage - -import ( - "context" - "log" - "path" - "reflect" - "strings" - - "github.com/aws/aws-sdk-go-v2/aws" - "github.com/aws/aws-sdk-go-v2/config" - "github.com/aws/aws-sdk-go-v2/service/s3" -) - -type S3ObjectStorageHandler struct { - S3Client *s3.Client - PresignClient *s3.PresignClient - S3Endpoint string -} - -type UploadLinks struct { - TSV string `bakta:"tsv"` - GFF3 string `bakta:"gff3"` - GBFF string `bakta:"gbff"` - FNA string `bakta:"fna"` - FAA string `bakta:"faa"` - JSON string `bakta:"json"` - EMBL string `bakta:"embl"` - TSVHypothetical string `bakta:"hypotheticals.tsv"` - FAAHypothetical string `bakta:"hypotheticals.faa"` - FFN string `bakta:"ffn"` -} - -func InitS3ObjectStorageHandler(bucket string) (*S3ObjectStorageHandler, error) { - endpoint := "https://s3.computational.bio.uni-giessen.de" - - cfg, err := config.LoadDefaultConfig( - context.Background(), - config.WithRegion("RegionOne"), - config.WithEndpointResolver(aws.EndpointResolverFunc( - func(service, region string) (aws.Endpoint, error) { - return aws.Endpoint{ - URL: endpoint, - }, nil - })), - ) - - if err != nil { - log.Println(err.Error()) - return nil, err - } - - client := s3.NewFromConfig(cfg) - - presignClient := s3.NewPresignClient(client) - - handler := S3ObjectStorageHandler{ - S3Client: client, - PresignClient: presignClient, - S3Endpoint: endpoint, - } - - return &handler, nil -} - -func (handler *S3ObjectStorageHandler) CreateUploadLink(bucket string, key string) (string, error) { - - presignedRequestURL, err := handler.PresignClient.PresignPutObject(context.Background(), &s3.PutObjectInput{ - Bucket: aws.String(bucket), - Key: aws.String(key), - }) - - if err != nil { - log.Println(err.Error()) - return "", err - } - - return presignedRequestURL.URL, nil -} - -func (handler *S3ObjectStorageHandler) CreateDownloadLinks(bucket string, key string, prefix string) (*UploadLinks, error) { - uploadLinks := UploadLinks{} - - uploadStructType := reflect.TypeOf(UploadLinks{}) - uploadStructValue := reflect.ValueOf(&uploadLinks) - - for i := 0; i < uploadStructType.NumField(); i++ { - fieldFileSuffix := uploadStructType.Field(i).Tag.Get("bakta") - fullFilename := strings.Join([]string{"result", ".", fieldFileSuffix}, "") - - keyWithFilename := path.Join(key, fullFilename) - - presignedRequestURL, err := handler.PresignClient.PresignGetObject(context.Background(), &s3.GetObjectInput{ - Bucket: aws.String(bucket), - Key: aws.String(keyWithFilename), - }) - - if err != nil { - log.Println(err.Error()) - return nil, err - } - - uploadStructValueElem := uploadStructValue.Elem() - uploadStructValueElem.Field(i).SetString(presignedRequestURL.URL) - } - - return &uploadLinks, nil -} diff --git a/objectStorage/s3_object_storage_handler_test.go b/objectStorage/s3_object_storage_handler_test.go deleted file mode 100644 index a6dc694..0000000 --- a/objectStorage/s3_object_storage_handler_test.go +++ /dev/null @@ -1,8 +0,0 @@ -package objectStorage - -import ( - "testing" -) - -func TestInitS3ObjectStorageHandler(t *testing.T) { -} diff --git a/scheduler/job_configurator.go b/scheduler/job_configurator.go deleted file mode 100644 index 7c0f4d1..0000000 --- a/scheduler/job_configurator.go +++ /dev/null @@ -1,146 +0,0 @@ -package scheduler - -import ( - "encoding/json" - "fmt" - "path" - "reflect" - "strings" - - "github.com/spf13/viper" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/database" - "github.com/ag-computational-bio/bakta-web-backend/objectStorage" -) - -//createDownloadConf Creates the configuration string for the download part of a bakta job -//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", bucketString, keyString) - - return confString, nil -} - -//createBaktaConf Creates a bakta config string based on the configuration and job settings provided -func createBaktaConf(job *database.Job, conf *api.JobConfig) ([]byte, error) { - var confStringElements []string - - confStringElements = append(confStringElements, "bakta") - - confStringElements = append(confStringElements, "--tmp-dir", "/cache") - confStringElements = append(confStringElements, "--threads", "12") - confStringElements = append(confStringElements, "--prefix", "result") - confStringElements = append(confStringElements, "-o", "/output") - - if conf.HasProdigal { - confStringElements = append(confStringElements, "--prodigal-tf", "/data/prodigaltraining.tf") - } - - if conf.HasReplicons { - if strings.HasSuffix(job.ProdigalKey, "csv") { - confStringElements = append(confStringElements, "--replicons", "/data/replicons.csv") - } else if strings.HasSuffix(job.ProdigalKey, "csv") { - confStringElements = append(confStringElements, "--replicons", "/data/replicons.tsv") - } - } - - if viper.IsSet("Testing") || viper.IsSet("Debug") { - confStringElements = append(confStringElements, "--db", "/db/db-mock") - } else { - confStringElements = append(confStringElements, "--db", "/db/db") - } - - if conf.CompleteGenome { - confStringElements = append(confStringElements, "--complete") - } - - if conf.Locus != "" { - confStringElements = append(confStringElements, "--locus", fmt.Sprintf("%v", conf.Locus)) - } - - if conf.LocusTag != "" { - confStringElements = append(confStringElements, "--locus-tag", fmt.Sprintf("%v", conf.LocusTag)) - } - - if conf.KeepContigHeaders { - confStringElements = append(confStringElements, "--keep-contig-headers") - } - - if conf.Genus != "" { - confStringElements = append(confStringElements, "--genus", fmt.Sprintf("%v", conf.Genus)) - } - - if conf.Species != "" { - confStringElements = append(confStringElements, "--species", fmt.Sprintf("%v", conf.Species)) - } - - if conf.Strain != "" { - confStringElements = append(confStringElements, "--strain", fmt.Sprintf("%v", conf.Strain)) - } - - if conf.Plasmid != "" { - confStringElements = append(confStringElements, "--plasmid", fmt.Sprintf("%v", conf.Plasmid)) - } - - if conf.Compliant { - confStringElements = append(confStringElements, fmt.Sprintf("--compliant")) - } - - if conf.TranslationalTable == 4 || conf.TranslationalTable == 11 { - confStringElements = append(confStringElements, "--translation-table", fmt.Sprintf("%v", conf.TranslationalTable)) - } - - dermtype := "?" - - switch conf.DermType { - case api.DermType_UNKNOWN: - dermtype = "?" - case api.DermType_MONODERM: - dermtype = "+" - case api.DermType_DIDERM: - dermtype = "-" - } - - confStringElements = append(confStringElements, "--gram", fmt.Sprintf("%s", dermtype)) - - //confString := strings.Join(confStringElements, " ") - - _, fastaFileName := path.Split(job.FastaKey) - //confString = fmt.Sprintf(confString+" /data/%v", fastaFileName) - - confStringElements = append(confStringElements, fmt.Sprintf("/data/%v", fastaFileName)) - - return json.Marshal(confStringElements) -} - -//createUploadConf Creates the configuration string for a bakta job -func createUploadConf(job *database.Job) (string, error) { - uploadStructType := reflect.TypeOf(objectStorage.UploadLinks{}) - - var fields []string - - for i := 0; i < uploadStructType.NumField(); i++ { - fieldFileSuffix := uploadStructType.Field(i).Tag.Get("bakta") - fullFilename := strings.Join([]string{"/output/result", ".", fieldFileSuffix}, "") - fields = append(fields, fullFilename) - - } - - allFiles := strings.Join(fields, ",") - - confString := fmt.Sprintf("upload -e s3.computational.bio.uni-giessen.de -k %v -b %v -f %v", job.ResultKey, job.DataBucket, allFiles) - - return confString, nil -} diff --git a/scheduler/job_configurator_test.go b/scheduler/job_configurator_test.go deleted file mode 100644 index 6990da0..0000000 --- a/scheduler/job_configurator_test.go +++ /dev/null @@ -1 +0,0 @@ -package scheduler diff --git a/scheduler/simple_scheduler.go b/scheduler/simple_scheduler.go deleted file mode 100644 index ddb96ff..0000000 --- a/scheduler/simple_scheduler.go +++ /dev/null @@ -1,159 +0,0 @@ -package scheduler - -import ( - "context" - "flag" - "fmt" - "log" - "path/filepath" - - "github.com/spf13/viper" - - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "github.com/ag-computational-bio/bakta-web-backend/database" - - batchv1 "k8s.io/api/batch/v1" - "k8s.io/apimachinery/pkg/api/errors" - metav1 "k8s.io/apimachinery/pkg/apis/meta/v1" - "k8s.io/client-go/kubernetes" - restclient "k8s.io/client-go/rest" - "k8s.io/client-go/tools/clientcmd" - "k8s.io/client-go/util/homedir" -) - -//SimpleScheduler A simple scheduler to run bakta jobs on a Kubernetes cluster -//The config will be picked up from the -type SimpleScheduler struct { - k8sClient kubernetes.Interface - databaseHandler *database.Handler - namespace string -} - -// InitSimpleScheduler Initiates a scheduler to run bakta jobs -// Can run inside a cluster or outside and will pick up the required Kubernetes configuration -// automatically -func InitSimpleScheduler(dbHandler *database.Handler, clientset kubernetes.Interface) (*SimpleScheduler, error) { - - namespace := viper.GetString("K8sNamespace") - - scheduler := SimpleScheduler{ - k8sClient: clientset, - databaseHandler: dbHandler, - namespace: namespace, - } - - return &scheduler, nil -} - -func CreateClientSet() (*kubernetes.Clientset, error) { - var config *restclient.Config - var err error - - if viper.GetBool("InCluster") { - config, err = restclient.InClusterConfig() - } else { - config, err = createOutOfClusterConfig() - } - if err != nil { - log.Println(err.Error()) - return nil, err - } - - clientset, err := kubernetes.NewForConfig(config) - return clientset, err -} - -//StartJob Starts a pre-configurated bakta job on Kubernetes and returns the started job configuration -func (scheduler *SimpleScheduler) StartJob(jobID string, jobConfig *api.JobConfig) (*batchv1.Job, error) { - job, err := scheduler.databaseHandler.GetJob(jobID) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - downloadConf, err := createDownloadConf(job, jobConfig.HasProdigal, jobConfig.HasReplicons) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - baktaConf, err := createBaktaConf(job, jobConfig) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - uploadConf, err := createUploadConf(job) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - apiJob, err := createBaseJobConf(jobID, scheduler.namespace, downloadConf, string(baktaConf), uploadConf, job.Secret) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - scheduledJob, err := scheduler.k8sClient.BatchV1().Jobs(scheduler.namespace).Create(context.TODO(), apiJob, metav1.CreateOptions{}) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - err = scheduler.databaseHandler.UpdateK8s(jobID, string(scheduledJob.UID)) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - return scheduledJob, nil -} - -// Deletes a given bakta job -func (scheduler *SimpleScheduler) DeleteJob(jobName string) error { - k8sJobName := fmt.Sprintf("%s%s", "bakta-job-", jobName) - - delProp := metav1.DeletePropagationForeground - - err := scheduler.k8sClient.BatchV1().Jobs(scheduler.namespace).Delete(context.TODO(), k8sJobName, metav1.DeleteOptions{ - PropagationPolicy: &delProp, - }) - if err != nil && !errors.IsNotFound(err) { - log.Println(err.Error()) - return err - } - - if errors.IsNotFound(err) { - log.Println(err.Error()) - } - - return nil -} - -//createOutOfClusterConfig tries to create the required k8s configuration from well known config paths -func createOutOfClusterConfig() (*restclient.Config, error) { - var kubeconfig *string - if home := homedir.HomeDir(); home != "" { - kubeconfig = flag.String("kubeconfig", filepath.Join(home, ".kube", "config"), "(optional) absolute path to the kubeconfig file") - } else { - kubeconfig = flag.String("kubeconfig", "", "absolute path to the kubeconfig file") - } - flag.Parse() - - // use the current context in kubeconfig - config, err := clientcmd.BuildConfigFromFlags("", *kubeconfig) - if err != nil { - panic(err.Error()) - } - - return config, err -} - -func (scheduler *SimpleScheduler) GetK8sClient() kubernetes.Interface { - return scheduler.k8sClient -} - -func (scheduler *SimpleScheduler) GetNamespace() string { - return scheduler.namespace -} diff --git a/scheduler/simple_scheduler_test.go b/scheduler/simple_scheduler_test.go deleted file mode 100644 index f08d423..0000000 --- a/scheduler/simple_scheduler_test.go +++ /dev/null @@ -1,46 +0,0 @@ -package scheduler - -import ( - api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" - "k8s.io/client-go/kubernetes/fake" - "testing" -) - -func TestSimpleScheduler_StartJob(t *testing.T) { - simpleScheduler, err := InitSimpleScheduler(nil, fake.NewSimpleClientset()) - if err != nil || simpleScheduler == nil { - t.Fatal("error in simple scheduler init") - } - - _, err = simpleScheduler.StartJob("test", &api.JobConfig{ - HasProdigal: false, - HasReplicons: false, - TranslationalTable: 0, - CompleteGenome: false, - KeepContigHeaders: false, - MinContigLength: 0, - DermType: 0, - Genus: "", - Species: "", - Strain: "", - Plasmid: "", - Locus: "", - LocusTag: "", - }) - if err != nil { - return - } - -} - -func TestSimpleScheduler_GetNamespace(t *testing.T) { - -} - -func TestSimpleScheduler_DeleteJob(t *testing.T) { - -} - -func TestSimpleScheduler_GetK8sClient(t *testing.T) { - -} diff --git a/scheduler/start_job.go b/scheduler/start_job.go deleted file mode 100644 index 49e456e..0000000 --- a/scheduler/start_job.go +++ /dev/null @@ -1,206 +0,0 @@ -package scheduler - -import ( - "fmt" - "log" - - "github.com/spf13/viper" - "k8s.io/apimachinery/pkg/api/resource" - - batchv1 "k8s.io/api/batch/v1" - v1 "k8s.io/api/core/v1" - metav1 "k8s.io/apimachinery/pkg/apis/meta/v1" -) - -// createBaseJobConf -// Create the configured bakta kubernetes job from the configration -func createBaseJobConf( - id string, - namespace string, - downloaderConf string, - baktaConf string, - uploaderConf string, - secret string) (*batchv1.Job, error) { - - updateServiceName := viper.GetString("UpdateService.Name") - if updateServiceName == "" { - err := fmt.Errorf("could not find service under config UpdateService.Name") - log.Println(err) - return nil, err - } - - updateServicePort := viper.GetString("UpdateService.Port") - if updateServicePort == "" { - err := fmt.Errorf("could not find service under config UpdateService.Port") - log.Println(err) - return nil, err - } - - cpuQuantityStringLimit := viper.GetString("Job.CPU.Limit") - if cpuQuantityStringLimit == "" { - cpuQuantityStringLimit = "4" - } - - memoryQuantityStringLimit := viper.GetString("Job.Memory.Limit") - if memoryQuantityStringLimit == "" { - memoryQuantityStringLimit = "4000Mi" - } - - cpuQuantityStringRequest := viper.GetString("Job.CPU.Request") - if cpuQuantityStringRequest == "" { - cpuQuantityStringRequest = "4" - } - - memoryQuantityStringRequest := viper.GetString("Job.Memory.Request") - if memoryQuantityStringRequest == "" { - memoryQuantityStringRequest = "4000Mi" - } - - cpuQuantityLimit, err := resource.ParseQuantity(cpuQuantityStringLimit) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - memoryQuantityLimit, err := resource.ParseQuantity(memoryQuantityStringLimit) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - cpuQuantityRequest, err := resource.ParseQuantity(cpuQuantityStringRequest) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - memoryQuantityRequest, err := resource.ParseQuantity(memoryQuantityStringRequest) - if err != nil { - log.Println(err.Error()) - return nil, err - } - - claimName := viper.GetString("BaktaDatabasePVCName") - if claimName == "" { - log.Println("could not find pvc name for the bakta database") - return nil, fmt.Errorf("could not find pvc name for the bakta database") - } - - resourceRequests := make(map[v1.ResourceName]resource.Quantity) - resourceRequests[v1.ResourceCPU] = cpuQuantityRequest - resourceRequests[v1.ResourceMemory] = memoryQuantityRequest - - resourceLimit := make(map[v1.ResourceName]resource.Quantity) - resourceLimit[v1.ResourceCPU] = cpuQuantityLimit - resourceLimit[v1.ResourceMemory] = memoryQuantityLimit - - //Required to convert const to int32 ref - job_image := viper.GetString("JobContainer") - - job := &batchv1.Job{ - ObjectMeta: metav1.ObjectMeta{ - Name: fmt.Sprintf("bakta-job-%v", id), - Namespace: namespace, - }, - Spec: batchv1.JobSpec{ - Template: v1.PodTemplateSpec{ - Spec: v1.PodSpec{ - RestartPolicy: "Never", - Containers: []v1.Container{ - { - Name: "bakta-job", - Image: job_image, - Resources: v1.ResourceRequirements{ - Limits: resourceLimit, - Requests: resourceRequests, - }, - VolumeMounts: []v1.VolumeMount{ - { - Name: "database", - MountPath: "/db", - }, - { - Name: "cache-volume", - MountPath: "/cache", - }, - }, - Env: []v1.EnvVar{ - { - Name: "DownloaderEnvConfig", - Value: downloaderConf, - }, - { - Name: "BaktaEnvConfig", - Value: baktaConf, - }, - { - Name: "UploaderEnvConfig", - Value: uploaderConf, - }, - { - Name: "JobID", - Value: id, - }, - { - Name: "GRPCUpdaterEndpoint", - Value: updateServiceName, - }, - { - Name: "GRPCUpdaterPort", - Value: updateServicePort, - }, - { - Name: "AWS_ACCESS_KEY_ID", - ValueFrom: &v1.EnvVarSource{ - SecretKeyRef: &v1.SecretKeySelector{ - Key: "AccessKey", - LocalObjectReference: v1.LocalObjectReference{ - Name: "s3", - }, - }, - }, - }, - { - Name: "AWS_SECRET_ACCESS_KEY", - ValueFrom: &v1.EnvVarSource{ - SecretKeyRef: &v1.SecretKeySelector{ - Key: "SecretKey", - LocalObjectReference: v1.LocalObjectReference{ - Name: "s3", - }, - }, - }, - }, - }, - }, - }, - - Volumes: []v1.Volume{ - { - Name: "cache-volume", - VolumeSource: v1.VolumeSource{ - EmptyDir: &v1.EmptyDirVolumeSource{}, - }, - }, - { - Name: "database", - VolumeSource: v1.VolumeSource{ - PersistentVolumeClaim: &v1.PersistentVolumeClaimVolumeSource{ - ClaimName: claimName, - }, - }, - }, - }, - }, - }, - BackoffLimit: int32Link(1), - }, - } - - return job, nil -} - -func int32Link(value int) *int32 { - int32Value := int32(value) - return &int32Value -} diff --git a/src/main.rs b/src/main.rs new file mode 100644 index 0000000..c57c535 --- /dev/null +++ b/src/main.rs @@ -0,0 +1,6 @@ + + + +pub fn main() { + println!("Hello, world!"); +} \ No newline at end of file diff --git a/tests/docker-compose.test.yml b/tests/docker-compose.test.yml deleted file mode 100644 index c60831b..0000000 --- a/tests/docker-compose.test.yml +++ /dev/null @@ -1,45 +0,0 @@ -version: '3.9' -services: - test: - environment: - AWS_ACCESS_KEY_ID: minioadmin - AWS_SECRET_ACCESS_KEY: minioadmin - build: - context: . - dockerfile: tests/Dockerfile - entrypoint: > - /bin/sh -c " - /bin/mc config host add myminio http://minio:9000 minioadmin minioadmin; - /bin/mc mb myminio/test-bucket; - go test --tags=integration - " - depends_on: - - minioConf - - mongo - minio: - image: minio/minio - command: server /data - ports: - - "9000:9000" - healthcheck: - test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"] - interval: 30s - timeout: 20s - retries: 3 - minioConf: - image: minio/mc - depends_on: - - minio - entrypoint: > - /bin/sh -c " - /usr/bin/mc config host add myminio http://minio:9000 minioadmin minioadmin; - /usr/bin/mc rm -r --force myminio/test-bucket; - /usr/bin/mc mb myminio/test-bucket; - exit 0; - " - mongo: - image: mongo - restart: always - environment: - MONGO_INITDB_ROOT_USERNAME: root - MONGO_INITDB_ROOT_PASSWORD: test123 \ No newline at end of file From 2c962e39ae479128c5e1d8350a520b567d2b366f Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Thu, 18 Jul 2024 18:52:17 +0200 Subject: [PATCH 02/10] feat: Move to rust backend, simplified logic --- .env | 11 + Cargo.lock | 2671 ++++++++++++++++++++++++++++++++++++++++++ Cargo.toml | 13 + src/api_paths.rs | 82 ++ src/api_structs.rs | 192 +++ src/argo/client.rs | 100 ++ src/argo/mod.rs | 3 + src/argo/structs.rs | 141 +++ src/argo/urls.rs | 49 + src/bakta_handler.rs | 34 + src/main.rs | 53 +- src/s3_handler.rs | 175 +++ 12 files changed, 3521 insertions(+), 3 deletions(-) create mode 100644 .env create mode 100644 src/api_paths.rs 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"thiserror", +] diff --git a/Cargo.toml b/Cargo.toml index 30cd22c..6c8a78a 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -4,3 +4,16 @@ version = "0.2.0" edition = "2021" [dependencies] +anyhow = "1.0.86" +axum = "0.7.5" +chrono = { version = "0.4.38", features = ["serde"] } +dotenvy = "0.15.7" +reqsign = "0.16.0" +reqwest = { version = "0.12.5", features = ["json"] } +serde = { version = "1.0.204", features = ["derive"] } +serde_json = "1.0.120" +tokio = { version = "1.38.1", features = ["full"] } +url = "2.5.2" +utoipa = { version = "4.2.3", features = ["uuid", "chrono"]} +utoipa-swagger-ui = { version = "7.1.0", features = ["axum"] } +uuid = { version = "1.10.0", features = ["v4", "serde"] } diff --git a/src/api_paths.rs b/src/api_paths.rs new file mode 100644 index 0000000..6c7f513 --- /dev/null +++ b/src/api_paths.rs @@ -0,0 +1,82 @@ +use axum::{extract::Query, response::IntoResponse, Json}; + +use crate::api_structs::{InitRequest, Job, ListRequest, StartRequest}; + +/// Delete an existing Job +#[utoipa::path( + delete, + path = "/api/v1/delete", + params( + Job, + ), + responses( + (status = 200, body = ()) + ) +)] +pub async fn delete_job(query: Query) -> impl IntoResponse { + format!("Job {} deleted", query.id) +} + +/// Create a new BaktaJob +#[utoipa::path( + post, + path = "/api/v1/job/init", + request_body = InitRequest, + responses( + (status = 200, body = InitResponse) + ) +)] +pub async fn init_job(Json(InitRequest): Json) -> impl IntoResponse { + format!("") +} + +/// List status of jobs +#[utoipa::path( + post, + path = "/api/v1/job/list", + request_body = ListRequest, + responses( + (status = 200, body = ListResponse) + ) +)] +pub async fn list_jobs(Json(ListRequest): Json) -> impl IntoResponse { + format!("") +} + +/// Query the result of a job +#[utoipa::path( + post, + path = "/api/v1/job/result", + request_body = Job, + responses( + (status = 200, body = ResultResponse) + ) +)] +pub async fn query_result(Json(job): Json) -> impl IntoResponse { + format!("") +} + +/// Start a job +#[utoipa::path( + post, + path = "/api/v1/job/start", + request_body = StartRequest, + responses( + (status = 200, body = ()) + ) +)] +pub async fn start_job(Json(StartRequest): Json) -> impl IntoResponse { + format!("") +} + +/// Get the current version +#[utoipa::path( + get, + path = "/api/v1/version", + responses( + (status = 200, body = VersionResponse) + ) +)] +pub async fn version() -> impl IntoResponse { + format!("") +} diff --git a/src/api_structs.rs b/src/api_structs.rs new file mode 100644 index 0000000..3e8bff3 --- /dev/null +++ b/src/api_structs.rs @@ -0,0 +1,192 @@ +use crate::api_paths::*; +use chrono::NaiveDateTime; +use serde::{Deserialize, Serialize}; +use utoipa::{IntoParams, OpenApi, ToSchema}; +use uuid::Uuid; + +#[derive(OpenApi)] +#[openapi( + paths(delete_job, init_job, list_jobs, query_result, start_job, version), + components(schemas( + Job, + InitRequest, + InitResponse, + RepliconTableType, + ListRequest, + ListResponse, + JobStatusEnum, + JobStatus, + FailedJobStatus, + FailedJobStatusEnum, + ResultFiles, + ResultResponse, + StartRequest, + JobConfig, + DermType, + VersionResponse, + )) +)] +pub struct BaktaApi; + +#[derive(ToSchema, Serialize, Deserialize, IntoParams)] +pub struct Job { + pub secret: String, + #[serde(rename = "jobID")] + pub id: Uuid, +} + +#[derive(ToSchema, Serialize, Deserialize, Default)] +pub enum RepliconTableType { + #[default] + CSV, + TSV, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct InitRequest { + pub name: String, + #[serde(rename = "repliconTableType")] + pub replicon_type: RepliconTableType, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct InitResponse { + #[serde(rename = "uploadLinkFasta")] + pub fasta_url: String, + #[serde(rename = "uploadLinkProdigal")] + pub prodigal_url: String, + #[serde(rename = "uploadLinkReplicons")] + pub replicon_url: String, + pub job: Job, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct ListRequest { + pub jobs: Vec, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub enum JobStatusEnum { + INIT, + RUNNING, + SUCCESSFULL, + ERROR, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub enum FailedJobStatusEnum { + #[serde(rename = "NOT_FOUND")] + NotFound, + #[serde(rename = "UNAUTHORIZED")] + Unauthorized, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct JobStatus { + #[serde(rename = "jobID")] + pub id: Uuid, + #[serde(rename = "jobStatus")] + pub status: JobStatusEnum, + pub started: NaiveDateTime, + pub updated: NaiveDateTime, + pub name: String, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct FailedJobStatus { + #[serde(rename = "jobID")] + pub id: Uuid, + #[serde(rename = "jobStatus")] + pub status: FailedJobStatusEnum, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct ListResponse { + pub jobs: Vec, + #[serde(rename = "failedJobs")] + pub failed: Vec, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct ResultFiles { + #[serde(rename = "EMBL")] + pub embl: String, + #[serde(rename = "FAA")] + pub faa: String, + #[serde(rename = "FAAHypothetical")] + pub faa_hypothetical: String, + #[serde(rename = "FFN")] + pub ffn: String, + #[serde(rename = "FNA")] + pub fna: String, + #[serde(rename = "GBFF")] + pub gbff: String, + #[serde(rename = "GFF3")] + pub gff3: String, + #[serde(rename = "JSON")] + pub json: String, + #[serde(rename = "TSV")] + pub tsv: String, + #[serde(rename = "TSVHypothetical")] + pub tsv_hypothetical: String, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct ResultResponse { + #[serde(rename = "jobID")] + pub id: Uuid, + pub started: NaiveDateTime, + pub updated: NaiveDateTime, + pub name: String, + #[serde(rename = "ResultFiles")] + pub files: ResultFiles, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub enum DermType { + UNKNOWN, + MONODERM, + DIDERM, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct JobConfig { + #[serde(rename = "hasProdigal")] + pub prodigal: Option, + #[serde(rename = "hasReplicons")] + pub replicons: Option, + #[serde(rename = "translationTable")] + pub table: Option, + #[serde(rename = "completeGenome")] + pub complete: Option, + #[serde(rename = "keepContigHeaders")] + pub headers: Option, + #[serde(rename = "minContigLength")] + pub min_length: Option, + #[serde(rename = "dermType")] + pub derm: Option, + pub genus: Option, + pub species: Option, + pub strain: Option, + pub plasmid: Option, + pub locus: Option, + #[serde(rename = "locusTag")] + pub locus_tag: Option, + pub compliant: Option, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct StartRequest { + pub job: Job, + pub config: JobConfig, +} + +#[derive(ToSchema, Serialize, Deserialize)] +pub struct VersionResponse { + #[serde(rename = "toolVersion")] + pub tool: String, + #[serde(rename = "dbVersion")] + pub db: String, + #[serde(rename = "backendVersion")] + pub backend: String, +} diff --git a/src/argo/client.rs b/src/argo/client.rs new file mode 100644 index 0000000..ef64cdd --- /dev/null +++ b/src/argo/client.rs @@ -0,0 +1,100 @@ +use std::collections::HashMap; + +use reqwest::{Client, Response}; + +use anyhow::Result; + +use super::{ + structs::{SimpleStatusList, SubmitOptions, SubmitWorkflowTemplate}, + urls::{get_status_url, get_status_url_phunter, get_submit_url}, +}; + +pub struct ArgoClient { + token: String, + url: String, + namespace: String, + client: Client, +} + +impl ArgoClient { + pub fn new(token: String, url: String, namespace: String) -> ArgoClient { + ArgoClient { + token, + url, + namespace, + client: reqwest::Client::new(), + } + } +} + +impl ArgoClient { + pub async fn get_workflow_status(&self) -> Result { + let response = self + .client + .get(get_status_url(&self.url, &self.namespace)) + .header("Authorization", &self.token) + .send() + .await? + .json::() + .await?; + Ok(response) + } + + pub async fn get_workflow_status_small(&self) -> Result { + let response = self + .client + .get(get_status_url_phunter(&self.url, &self.namespace)) + .header("Authorization", &self.token) + .send() + .await? + .json::() + .await?; + Ok(response) + } + + pub async fn submit_from_template( + &self, + templatename: String, + name: String, + labels: Option>, + parameters: Option>, + priority: Option, + service_account: Option, + ) -> Result { + let labels = labels.map(|some| { + some.iter() + .map(|(k, v)| format!("{k}={v}")) + .collect::>() + .join(",") + }); + + let parameters = parameters.map(|some| { + some.iter() + .map(|(k, v)| format!("{k}={v}")) + .collect::>() + }); + + let submit_template = SubmitWorkflowTemplate { + namespace: self.namespace.to_string(), + resource_kind: "WorkflowTemplate".to_string(), + resource_name: templatename.to_string(), + submit_options: SubmitOptions { + generate_name: None, + labels, + name: Some(name), + parameters, + priority, + service_account, + }, + }; + + let response = self + .client + .post(get_submit_url(&self.url, &self.namespace)) + .header("Authorization", &self.token) + .json(&submit_template) + .send() + .await?; + Ok(response) + } +} diff --git a/src/argo/mod.rs b/src/argo/mod.rs new file mode 100644 index 0000000..2cb251b --- /dev/null +++ b/src/argo/mod.rs @@ -0,0 +1,3 @@ +pub mod client; +mod structs; +mod urls; diff --git a/src/argo/structs.rs b/src/argo/structs.rs new file mode 100644 index 0000000..87e3a25 --- /dev/null +++ b/src/argo/structs.rs @@ -0,0 +1,141 @@ +use serde::Deserialize; +use serde::Serialize; +use std::collections::HashMap; + +/// SUBMITWORKFLOW +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct SubmitWorkflowTemplate { + pub namespace: String, + pub resource_kind: String, + pub resource_name: String, + pub submit_options: SubmitOptions, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct SubmitOptions { + pub generate_name: Option, + pub labels: Option, + pub name: Option, + pub parameters: Option>, + pub priority: Option, + pub service_account: Option, +} + +/// GET WORKFLOWS REQUEST +#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct GetWorkflowResponse { + pub metadata: Metadata, + pub items: Vec, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Metadata { + pub resource_version: String, +} + +#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Item { + pub metadata: WorkflowMetadata, + pub spec: Spec, + pub status: Status, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct WorkflowMetadata { + pub name: String, + pub generate_name: String, + pub namespace: String, + pub uid: String, + pub resource_version: String, + pub generation: i64, + pub creation_timestamp: String, + pub labels: HashMap, + pub annotations: HashMap, +} + +#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Spec { + pub arguments: Arguments, + pub workflow_template_ref: WorkflowTemplateRef, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Arguments { + pub parameters: Vec, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Parameter { + pub name: String, + pub value: String, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct WorkflowTemplateRef { + pub name: String, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Status { + pub phase: String, + pub started_at: String, + pub finished_at: String, + pub estimated_duration: i64, + pub progress: String, + pub conditions: Vec, + pub resources_duration: ResourcesDuration, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct Condition { + #[serde(rename = "type")] + pub type_field: String, + pub status: String, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct ResourcesDuration { + pub cpu: i64, + pub memory: i64, +} + +#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +#[serde(rename = "items")] +pub struct SimpleStatusList { + pub items: Option>, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +pub struct SimpleStatus { + pub metadata: Name, + pub status: SimplePhase, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +#[serde(rename = "metadata")] +pub struct Name { + pub name: String, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "camelCase")] +#[serde(rename = "Status")] +pub struct SimplePhase { + pub phase: String, +} diff --git a/src/argo/urls.rs b/src/argo/urls.rs new file mode 100644 index 0000000..14b6629 --- /dev/null +++ b/src/argo/urls.rs @@ -0,0 +1,49 @@ +use std::fmt::Display; + +pub fn get_status_url(url: T, namespace: U) -> String +where + T: Display, + U: Display, +{ + format!( + "{url}/api/v1/workflows/{namespace}?fields=\ + -items.metadata.managedFields,\ + items.status.nodes,\ + items.status.storedTemplates,\ + items.status.storedWorkflowTemplateSpec,\ + items.status.artifactRepositoryRef" + ) +} + +pub fn get_status_url_phunter(url: T, namespace: U) -> String +where + T: Display, + U: Display, +{ + format!( + "{url}/api/v1/workflows/{namespace}?fields=\ + items.metadata.name,\ + items.status.phase\ + &listOptions.labelSelector=accession" + ) +} + +pub fn get_submit_url(url: T, namespace: U) -> String +where + T: Display, + U: Display, +{ + format!("{url}/api/v1/workflows/{namespace}/submit") +} + +pub fn get_logs_url(url: T, namespace: U, workflowname: V, podname: W) -> String +where + T: Display, + U: Display, + V: Display, + W: Display, +{ + format!( + "{url}/api/v1/workflows/{namespace}/{workflowname}/log?logOptions.container=main&podName={podname}" + ) +} diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs new file mode 100644 index 0000000..871cce6 --- /dev/null +++ b/src/bakta_handler.rs @@ -0,0 +1,34 @@ +use crate::{api_structs::VersionResponse, argo::client::ArgoClient, s3_handler::S3Handler}; + +pub struct BaktaHandler { + pub argo_client: ArgoClient, + pub s3_handler: S3Handler, + pub version: VersionResponse, +} + +impl BaktaHandler { + pub fn new( + argo_token: String, + argo_url: String, + argo_namespace: String, + s3_access_key: String, + s3_secret_key: String, + bucket: String, + endpoint: String, + bakta_version: String, + database_version: String, + backend_version: String, + ) -> Self { + let argo_client = ArgoClient::new(argo_token, argo_url, argo_namespace); + let s3_handler = S3Handler::new(s3_access_key, s3_secret_key, bucket, endpoint); + BaktaHandler { + argo_client, + s3_handler, + version: VersionResponse { + tool: bakta_version, + db: database_version, + backend: backend_version, + }, + } + } +} diff --git a/src/main.rs b/src/main.rs index c57c535..3f0c505 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,6 +1,53 @@ +use axum::{ + response::Redirect, + routing::{delete, get, post}, + Router, +}; +use bakta_handler::BaktaHandler; +use std::{net::SocketAddr, sync::Arc}; +use utoipa::OpenApi; +use utoipa_swagger_ui::SwaggerUi; +mod api_paths; +mod api_structs; +mod argo; +mod bakta_handler; +mod s3_handler; +#[tokio::main] +async fn main() -> Result<(), Box> { + dotenvy::from_filename(".env")?; -pub fn main() { - println!("Hello, world!"); -} \ No newline at end of file + let socket_address: SocketAddr = dotenvy::var("SOCKET_ADDR") + .unwrap_or("127.0.0.1:8080".to_string()) + .parse()?; + let listener = tokio::net::TcpListener::bind(socket_address).await.unwrap(); + let swagger = SwaggerUi::new("/swagger-ui") + .url("/api-docs/openapi.json", api_structs::BaktaApi::openapi()); + + let bakta_handler = Arc::new(BaktaHandler::new( + dotenvy::var("ARGO_TOKEN")?, + dotenvy::var("ARGO_URL")?, + dotenvy::var("ARGO_NAMESPACE")?, + dotenvy::var("S3_ACCESS_KEY")?, + dotenvy::var("S3_SECRET_KEY")?, + dotenvy::var("S3_BUCKET")?, + dotenvy::var("S3_ENDPOINT")?, + dotenvy::var("BAKTA_VERSION")?, + dotenvy::var("DATABASE_VERSION")?, + dotenvy::var("BACKEND_VERSION")?, + )); + + let app = Router::new() + .merge(swagger) + .route("/", get(|| async { Redirect::permanent("/swagger-ui") })) + .route("/api/v1/delete", delete(api_paths::delete_job)) + .route("/api/v1/job/init", post(api_paths::init_job)) + .route("/api/v1/job/list", post(api_paths::list_jobs)) + .route("/api/v1/job/result", post(api_paths::query_result)) + .route("/api/v1/job/start", post(api_paths::start_job)) + .route("/api/v1/version", get(api_paths::version)) + .with_state(bakta_handler); + axum::serve(listener, app.into_make_service()).await?; + Ok(()) +} diff --git a/src/s3_handler.rs b/src/s3_handler.rs new file mode 100644 index 0000000..1989e74 --- /dev/null +++ b/src/s3_handler.rs @@ -0,0 +1,175 @@ +use anyhow::{anyhow, Result}; +use chrono::format; +use reqsign::{AwsCredential, AwsV4Signer}; +use reqwest::Method; +use url::Url; + +use crate::api_structs::ResultFiles; + +pub struct S3Handler { + access_key: String, + secret_key: String, + bucket: String, + endpoint: String, + is_ssl: bool, +} + +pub enum InputType { + Fasta, + Prodigal, + RepliconsTSV, +} + +impl InputType { + pub fn to_str(&self) -> &str { + match self { + InputType::Fasta => "fastadata.fasta", + InputType::Prodigal => "prodigal.tf", + InputType::RepliconsTSV => "replicons.tsv", + } + } +} + +impl S3Handler { + pub fn new(access_key: String, secret_key: String, bucket: String, endpoint: String) -> Self { + let ssl = if endpoint.starts_with("http://") { + true + } else { + false + }; + S3Handler { + access_key, + secret_key, + bucket, + endpoint, + is_ssl: ssl, + } + } + + pub fn sign_upload_url(&self, job_id: &str, input_type: InputType) -> Result { + let key = format!("jobs/{job_id}/inputs/{}", input_type.to_str()); + sign_url( + Method::PUT, + &self.access_key, + &self.secret_key, + self.is_ssl, + false, + 0, + None, + &self.bucket, + &key, + &self.endpoint, + 10000, // 10000 seconds = 2.77 hours should be enough for uploads + ) + } + pub fn sign_download_urls(&self, job_id: &str) -> Result { + let get_download_url = |output_format: &str| -> Result { + let key = format!("jobs/{job_id}/results/result.{output_format}").to_string(); + sign_url( + Method::GET, + &self.access_key, + &self.secret_key, + self.is_ssl, + false, + 0, + None, + &self.bucket, + &key, + &self.endpoint, + 60 * 86400, // 60 days + ) + }; + Ok(ResultFiles { + embl: get_download_url("embl")?, + faa: get_download_url("faa")?, + faa_hypothetical: get_download_url("hypotheticals.faa")?, + ffn: get_download_url("ffn")?, + fna: get_download_url("fna")?, + gbff: get_download_url("gbff")?, + gff3: get_download_url("gff")?, + json: get_download_url("json")?, + tsv: get_download_url("tsv")?, + tsv_hypothetical: get_download_url("hypotheticals.tsv")?, + }) + } +} + +/// Creates a fully customized presigned S3 url. +/// +/// ## Arguments: +/// +/// * `method: http::Method` - Http method the request is valid for +/// * `access_key: &String` - Secret key id +/// * `secret_key: &String` - Secret key for access +/// * `ssl: bool` - Flag if the endpoint is accessible via ssl +/// * `multipart: bool` - Flag if the request is for a specific multipart part upload +/// * `part_number: i32` - Specific part number if multipart: true +/// * `upload_id: &String` - Multipart upload id if multipart: true +/// * `bucket: &String` - Bucket name +/// * `key: &String` - Full path of object in bucket +/// * `endpoint: &String` - Full path of object in bucket +/// * `duration: i64` - Full path of object in bucket +/// * +/// +/// ## Returns: +/// +/// * `` - +/// +#[allow(clippy::too_many_arguments)] +fn sign_url( + method: Method, + access_key: &str, + secret_key: &str, + ssl: bool, + multipart: bool, + part_number: i32, + upload_id: Option, + bucket: &str, + key: &str, + endpoint: &str, + duration: i64, +) -> Result { + let signer = AwsV4Signer::new("s3", "RegionOne"); + + // Set protocol depending if ssl + let protocol = if ssl { "https://" } else { "http://" }; + + // Remove http:// or https:// from beginning of endpoint url if present + let endpoint_sanitized = if let Some(stripped) = endpoint.strip_prefix("https://") { + stripped.to_string() + } else if let Some(stripped) = endpoint.strip_prefix("http://") { + stripped.to_string() + } else { + endpoint.to_string() + }; + + // Construct request + let url = if multipart { + let upload_id = upload_id + .ok_or_else(|| anyhow!("No upload id provided for multipart presigned url"))?; + Url::parse(&format!( + "{}{}.{}/{}?partNumber={}&uploadId={}", + protocol, bucket, endpoint_sanitized, key, part_number, upload_id + ))? + } else { + Url::parse(&format!( + "{}{}.{}/{}", + protocol, bucket, endpoint_sanitized, key + ))? + }; + + let mut req = reqwest::Request::new(method, url); + + // Signing request with Signer + signer.sign_query( + &mut req, + std::time::Duration::new(duration as u64, 0), // Sec, nano + &AwsCredential { + access_key_id: access_key.to_string(), + secret_access_key: secret_key.to_string(), + session_token: None, + expires_in: None, + }, + )?; + Ok(req.url().to_string()) +} From 3f1705d990e35ebc00185b4a33e10c2d99c62288 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 01:11:22 +0200 Subject: [PATCH 03/10] chore: Implemented main logic --- Cargo.lock | 3 + Cargo.toml | 3 + src/api_paths.rs | 81 +++++++++++++++++-- src/api_structs.rs | 31 ++++++-- src/argo/client.rs | 30 ++++--- src/argo/mod.rs | 2 +- src/argo/structs.rs | 22 +++--- src/argo/urls.rs | 37 ++++----- src/bakta_handler.rs | 184 ++++++++++++++++++++++++++++++++++++++++++- src/main.rs | 27 ++++--- 10 files changed, 346 insertions(+), 74 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 1914b22..42b9807 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -168,6 +168,9 @@ dependencies = [ "axum", "chrono", "dotenvy", + "lazy_static", + "rand", + "regex", "reqsign", "reqwest", "serde", diff --git a/Cargo.toml b/Cargo.toml index 6c8a78a..565317c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -8,6 +8,9 @@ anyhow = "1.0.86" axum = "0.7.5" chrono = { version = "0.4.38", features = ["serde"] } dotenvy = "0.15.7" +lazy_static = "1.5.0" +rand = "0.8.5" +regex = "1.10.5" reqsign = "0.16.0" reqwest = { version = "0.12.5", features = ["json"] } serde = { version = "1.0.204", features = ["derive"] } diff --git a/src/api_paths.rs b/src/api_paths.rs index 6c7f513..758daae 100644 --- a/src/api_paths.rs +++ b/src/api_paths.rs @@ -1,6 +1,16 @@ -use axum::{extract::Query, response::IntoResponse, Json}; +use std::sync::Arc; -use crate::api_structs::{InitRequest, Job, ListRequest, StartRequest}; +use axum::{ + extract::{Query, State}, + response::IntoResponse, + Json, +}; +use reqwest::StatusCode; + +use crate::{ + api_structs::{InitRequest, InitResponse, Job, ListRequest, StartRequest}, + bakta_handler::BaktaHandler, +}; /// Delete an existing Job #[utoipa::path( @@ -10,11 +20,19 @@ use crate::api_structs::{InitRequest, Job, ListRequest, StartRequest}; Job, ), responses( - (status = 200, body = ()) + (status = 200, body = ()), + (status = 400, body = String) ) )] -pub async fn delete_job(query: Query) -> impl IntoResponse { - format!("Job {} deleted", query.id) +pub async fn delete_job( + State(state): State>, + Query(job): Query, +) -> impl IntoResponse { + state + .state_handler + .delete_job((job.id, job.secret)) + .await + .map_err(|e| (StatusCode::BAD_REQUEST, e.to_string())) } /// Create a new BaktaJob @@ -23,11 +41,58 @@ pub async fn delete_job(query: Query) -> impl IntoResponse { path = "/api/v1/job/init", request_body = InitRequest, responses( - (status = 200, body = InitResponse) + (status = 200, body = InitResponse), + (status = 400, body = String) ) )] -pub async fn init_job(Json(InitRequest): Json) -> impl IntoResponse { - format!("") +pub async fn init_job( + State(state): State>, + Json(init_request): Json, +) -> impl IntoResponse { + let (id, secret) = state.state_handler.init_job(init_request.name).await; + + let Ok(fasta_url) = state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Fasta) + else { + return ( + StatusCode::BAD_REQUEST, + Json("Failed to sign URL".to_string()), + ) + .into_response(); + }; + + let Ok(prodigal_url) = state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Prodigal) + else { + return ( + StatusCode::BAD_REQUEST, + Json("Failed to sign URL".to_string()), + ) + .into_response(); + }; + let Ok(replicon_url) = state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::RepliconsTSV) + else { + return ( + StatusCode::BAD_REQUEST, + Json("Failed to sign URL".to_string()), + ) + .into_response(); + }; + + ( + StatusCode::OK, + Json(InitResponse { + job: Job { id, secret }, + fasta_url, + prodigal_url, + replicon_url, + }), + ) + .into_response() } /// List status of jobs diff --git a/src/api_structs.rs b/src/api_structs.rs index 3e8bff3..8fda993 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -1,5 +1,8 @@ use crate::api_paths::*; -use chrono::NaiveDateTime; +use anyhow::anyhow; +use anyhow::Result; +use chrono::DateTime; +use chrono::Utc; use serde::{Deserialize, Serialize}; use utoipa::{IntoParams, OpenApi, ToSchema}; use uuid::Uuid; @@ -65,7 +68,7 @@ pub struct ListRequest { pub jobs: Vec, } -#[derive(ToSchema, Serialize, Deserialize)] +#[derive(ToSchema, Serialize, Deserialize, Clone)] pub enum JobStatusEnum { INIT, RUNNING, @@ -73,6 +76,20 @@ pub enum JobStatusEnum { ERROR, } +impl TryFrom for JobStatusEnum { + type Error = anyhow::Error; + + fn try_from(value: String) -> Result { + match value.as_str() { + "Init" | "Pending" => Ok(JobStatusEnum::INIT), + "Running" => Ok(JobStatusEnum::RUNNING), + "Succeeded" => Ok(JobStatusEnum::SUCCESSFULL), + "Failed" | "Error" => Ok(JobStatusEnum::ERROR), + _ => Err(anyhow!("Invalid JobStatus")), + } + } +} + #[derive(ToSchema, Serialize, Deserialize)] pub enum FailedJobStatusEnum { #[serde(rename = "NOT_FOUND")] @@ -81,14 +98,14 @@ pub enum FailedJobStatusEnum { Unauthorized, } -#[derive(ToSchema, Serialize, Deserialize)] +#[derive(ToSchema, Serialize, Deserialize, Clone)] pub struct JobStatus { #[serde(rename = "jobID")] pub id: Uuid, #[serde(rename = "jobStatus")] pub status: JobStatusEnum, - pub started: NaiveDateTime, - pub updated: NaiveDateTime, + pub started: DateTime, + pub updated: DateTime, pub name: String, } @@ -135,8 +152,8 @@ pub struct ResultFiles { pub struct ResultResponse { #[serde(rename = "jobID")] pub id: Uuid, - pub started: NaiveDateTime, - pub updated: NaiveDateTime, + pub started: DateTime, + pub updated: DateTime, pub name: String, #[serde(rename = "ResultFiles")] pub files: ResultFiles, diff --git a/src/argo/client.rs b/src/argo/client.rs index ef64cdd..895afe9 100644 --- a/src/argo/client.rs +++ b/src/argo/client.rs @@ -6,7 +6,7 @@ use anyhow::Result; use super::{ structs::{SimpleStatusList, SubmitOptions, SubmitWorkflowTemplate}, - urls::{get_status_url, get_status_url_phunter, get_submit_url}, + urls::{get_delete_url, get_status_url_bakta, get_submit_url}, }; pub struct ArgoClient { @@ -28,10 +28,10 @@ impl ArgoClient { } impl ArgoClient { - pub async fn get_workflow_status(&self) -> Result { + pub async fn get_workflow_status(&self, recent: bool) -> Result { let response = self .client - .get(get_status_url(&self.url, &self.namespace)) + .get(get_status_url_bakta(&self.url, &self.namespace, recent)) .header("Authorization", &self.token) .send() .await? @@ -40,16 +40,15 @@ impl ArgoClient { Ok(response) } - pub async fn get_workflow_status_small(&self) -> Result { - let response = self - .client - .get(get_status_url_phunter(&self.url, &self.namespace)) + pub async fn delete_workflow(&self, workflow_name: String) -> Result<()> { + self.client + .delete(get_delete_url(&self.url, &self.namespace, workflow_name)) .header("Authorization", &self.token) .send() .await? - .json::() + .bytes() .await?; - Ok(response) + Ok(()) } pub async fn submit_from_template( @@ -98,3 +97,16 @@ impl ArgoClient { Ok(response) } } + +#[cfg(test)] + +mod tests { + use super::*; + + #[tokio::test] + async fn test_get_workflow_status() { + let client = ArgoClient::new("foo".to_string(), "bar".to_string(), "bakta".to_string()); + let response = client.get_workflow_status(true).await.unwrap(); + dbg!(response); + } +} diff --git a/src/argo/mod.rs b/src/argo/mod.rs index 2cb251b..de20941 100644 --- a/src/argo/mod.rs +++ b/src/argo/mod.rs @@ -1,3 +1,3 @@ pub mod client; -mod structs; +pub mod structs; mod urls; diff --git a/src/argo/structs.rs b/src/argo/structs.rs index 87e3a25..ecf47db 100644 --- a/src/argo/structs.rs +++ b/src/argo/structs.rs @@ -1,3 +1,4 @@ +use chrono::Utc; use serde::Deserialize; use serde::Serialize; use std::collections::HashMap; @@ -113,29 +114,28 @@ pub struct ResourcesDuration { } #[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)] -#[serde(rename_all = "camelCase")] #[serde(rename = "items")] pub struct SimpleStatusList { - pub items: Option>, + pub items: Vec, } #[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] -#[serde(rename_all = "camelCase")] pub struct SimpleStatus { - pub metadata: Name, - pub status: SimplePhase, + pub metadata: StatusMetadata, + pub status: SimpleStatusStatus, } #[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] -#[serde(rename_all = "camelCase")] -#[serde(rename = "metadata")] -pub struct Name { +pub struct StatusMetadata { pub name: String, + pub labels: HashMap, } #[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] -#[serde(rename_all = "camelCase")] -#[serde(rename = "Status")] -pub struct SimplePhase { +pub struct SimpleStatusStatus { pub phase: String, + #[serde(rename = "startedAt")] + pub started_at: chrono::DateTime, + #[serde(rename = "finishedAt")] + pub finished_at: Option>, } diff --git a/src/argo/urls.rs b/src/argo/urls.rs index 14b6629..6f365cf 100644 --- a/src/argo/urls.rs +++ b/src/argo/urls.rs @@ -1,31 +1,15 @@ use std::fmt::Display; -pub fn get_status_url(url: T, namespace: U) -> String +pub fn get_status_url_bakta(url: T, namespace: U, recent: bool) -> String where T: Display, U: Display, { - format!( - "{url}/api/v1/workflows/{namespace}?fields=\ - -items.metadata.managedFields,\ - items.status.nodes,\ - items.status.storedTemplates,\ - items.status.storedWorkflowTemplateSpec,\ - items.status.artifactRepositoryRef" - ) -} - -pub fn get_status_url_phunter(url: T, namespace: U) -> String -where - T: Display, - U: Display, -{ - format!( - "{url}/api/v1/workflows/{namespace}?fields=\ - items.metadata.name,\ - items.status.phase\ - &listOptions.labelSelector=accession" - ) + if recent { + format!("{url}/api/v1/workflows/{namespace}?fields=items.status.finishedAt,items.status.startedAt,items.metadata.name,items.status.phase,items.metadata.labels&listOptions.labelSelector=workflows.argoproj.io/workflow-archiving-status!=Archived") + } else { + format!("{url}/api/v1/workflows/{namespace}?fields=items.status.finishedAt,items.status.startedAt,items.metadata.name,items.status.phase,items.metadata.labels") + } } pub fn get_submit_url(url: T, namespace: U) -> String @@ -47,3 +31,12 @@ where "{url}/api/v1/workflows/{namespace}/{workflowname}/log?logOptions.container=main&podName={podname}" ) } + +pub fn get_delete_url(url: T, namespace: U, workflowname: V) -> String +where + T: Display, + U: Display, + V: Display, +{ + format!("{url}/api/v1/workflows/{namespace}/{workflowname}") +} diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs index 871cce6..f60320c 100644 --- a/src/bakta_handler.rs +++ b/src/bakta_handler.rs @@ -1,13 +1,43 @@ -use crate::{api_structs::VersionResponse, argo::client::ArgoClient, s3_handler::S3Handler}; +use crate::api_structs::FailedJobStatus; +use crate::api_structs::FailedJobStatusEnum; +use crate::api_structs::ListResponse; +use crate::argo::structs::SimpleStatus; +use crate::{ + api_structs::{JobStatus, JobStatusEnum, VersionResponse}, + argo::client::ArgoClient, + s3_handler::S3Handler, +}; +use anyhow::anyhow; +use anyhow::Result; +use chrono::Utc; +use rand::distributions::Alphanumeric; +use rand::distributions::DistString; +use regex::Regex; +use std::{collections::HashMap, str::FromStr, sync::Arc}; +use tokio::sync::RwLock; +use uuid::Uuid; + +pub struct StateHandler { + pub job_state: RwLock>, + pub argo_client: Arc, +} + +pub struct FullJobState { + pub api_status: Option, + pub workflowname: Option, + pub secret: String, + pub name: String, +} pub struct BaktaHandler { - pub argo_client: ArgoClient, + pub argo_client: Arc, pub s3_handler: S3Handler, pub version: VersionResponse, + pub state_handler: Arc, } impl BaktaHandler { - pub fn new( + pub async fn new( argo_token: String, argo_url: String, argo_namespace: String, @@ -19,8 +49,17 @@ impl BaktaHandler { database_version: String, backend_version: String, ) -> Self { - let argo_client = ArgoClient::new(argo_token, argo_url, argo_namespace); + let argo_client = Arc::new(ArgoClient::new(argo_token, argo_url, argo_namespace)); let s3_handler = S3Handler::new(s3_access_key, s3_secret_key, bucket, endpoint); + + let state_handler = Arc::new(StateHandler { + job_state: RwLock::new(HashMap::new()), + argo_client: argo_client.clone(), + }); + + let state_handler_clone = state_handler.clone(); + state_handler_clone.run().await; + BaktaHandler { argo_client, s3_handler, @@ -29,6 +68,143 @@ impl BaktaHandler { db: database_version, backend: backend_version, }, + state_handler, + } + } +} + +lazy_static::lazy_static! { + /// This is an example for using doc comment attributes + static ref REGEX: Regex = Regex::new(r"[^0-9a-zA-Z_.]+").unwrap(); +} + +impl StateHandler { + async fn run(self: Arc) { + let argo_client = self.argo_client.clone(); + tokio::spawn(async move { + let into_state = |simple_status: SimpleStatus| -> Result<(Uuid, FullJobState)> { + let job_id = Uuid::from_str( + &simple_status + .metadata + .labels + .get("jobid") + .ok_or_else(|| anyhow!("Missing JobID"))?, + )?; + let workflowname = simple_status.metadata.name; + + let api_status = JobStatus { + id: job_id.clone(), + status: JobStatusEnum::try_from(simple_status.status.phase)?, + started: simple_status.status.started_at, + updated: simple_status.status.finished_at.unwrap_or(Utc::now()), + name: simple_status + .metadata + .labels + .get("name") + .cloned() + .unwrap_or_else(|| "Unknown name".to_string()), + }; + + let name = api_status.name.clone(); + + Ok(( + api_status.id.clone(), + FullJobState { + api_status: Some(api_status), + workflowname: Some(workflowname), + secret: simple_status + .metadata + .labels + .get("secret") + .cloned() + .unwrap_or_else(|| "Unknown".to_string()), + name, + }, + )) + }; + + let initial = argo_client.get_workflow_status(false).await?; + let mut write_lock = self.job_state.write().await; + for item in initial.items { + let (id, state) = into_state(item)?; + write_lock.insert(id, state); + } + drop(write_lock); + loop { + let initial = argo_client.get_workflow_status(true).await?; + for item in initial.items { + let (id, state) = into_state(item)?; + self.job_state.write().await.insert(id, state); + } + tokio::time::sleep(tokio::time::Duration::from_secs(15)).await; + } + #[allow(unreachable_code)] + Ok::<(), anyhow::Error>(()) + }); + } + + pub async fn get_job_states(&self, job_ids: Vec<(Uuid, String)>) -> ListResponse { + let read_lock = self.job_state.read().await; + let mut jobs = vec![]; + let mut failed = vec![]; + + for (id, secret) in job_ids { + if let Some(state) = read_lock.get(&id) { + if state.secret != secret { + failed.push(FailedJobStatus { + id, + status: FailedJobStatusEnum::Unauthorized, + }); + continue; + } + if let Some(api_status) = &state.api_status { + jobs.push(api_status.clone()); + } + } else { + failed.push(FailedJobStatus { + id, + status: FailedJobStatusEnum::NotFound, + }); + } + } + + ListResponse { jobs, failed } + } + + pub async fn delete_job(&self, (job_id, secret): (Uuid, String)) -> Result<()> { + let mut write_lock = self.job_state.write().await; + if let Some(state) = write_lock.get(&job_id) { + if state.secret != secret { + return Err(anyhow!("Unauthorized")); + } + if let Some(workflowname) = &state.workflowname { + self.argo_client + .delete_workflow(workflowname.clone()) + .await?; + } } + write_lock.remove(&job_id); + Ok(()) + } + + pub async fn init_job(&self, name: String) -> (Uuid, String) { + let mut result = REGEX.replace_all(&name, "_").to_string(); + result.truncate(63); + let stripped = result + .trim_end_matches(|c: char| !c.is_alphanumeric()) + .to_string(); + + let job_id = Uuid::new_v4(); + let secret = Alphanumeric.sample_string(&mut rand::thread_rng(), 32); + self.job_state.write().await.insert( + job_id, + FullJobState { + api_status: None, + workflowname: None, + secret: secret.clone(), + name: stripped, + }, + ); + (job_id, secret) } } diff --git a/src/main.rs b/src/main.rs index 3f0c505..4659c03 100644 --- a/src/main.rs +++ b/src/main.rs @@ -25,18 +25,21 @@ async fn main() -> Result<(), Box> { let swagger = SwaggerUi::new("/swagger-ui") .url("/api-docs/openapi.json", api_structs::BaktaApi::openapi()); - let bakta_handler = Arc::new(BaktaHandler::new( - dotenvy::var("ARGO_TOKEN")?, - dotenvy::var("ARGO_URL")?, - dotenvy::var("ARGO_NAMESPACE")?, - dotenvy::var("S3_ACCESS_KEY")?, - dotenvy::var("S3_SECRET_KEY")?, - dotenvy::var("S3_BUCKET")?, - dotenvy::var("S3_ENDPOINT")?, - dotenvy::var("BAKTA_VERSION")?, - dotenvy::var("DATABASE_VERSION")?, - dotenvy::var("BACKEND_VERSION")?, - )); + let bakta_handler = Arc::new( + BaktaHandler::new( + dotenvy::var("ARGO_TOKEN")?, + dotenvy::var("ARGO_URL")?, + dotenvy::var("ARGO_NAMESPACE")?, + dotenvy::var("S3_ACCESS_KEY")?, + dotenvy::var("S3_SECRET_KEY")?, + dotenvy::var("S3_BUCKET")?, + dotenvy::var("S3_ENDPOINT")?, + dotenvy::var("BAKTA_VERSION")?, + dotenvy::var("DATABASE_VERSION")?, + dotenvy::var("BACKEND_VERSION")?, + ) + .await, + ); let app = Router::new() .merge(swagger) From 4312b7bcd07b501a64578c7bac593370f9e29449 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 09:24:14 +0200 Subject: [PATCH 04/10] feat: Reimplemented logic in Rust --- Dockerfile | 32 +++++++------ README.md | 18 ++++++- src/api_paths.rs | 85 ++++++++++++++++++-------------- src/api_structs.rs | 112 +++++++++++++++++++++++++++++++++++++++---- src/argo/client.rs | 22 ++++----- src/argo/structs.rs | 15 ++++-- src/argo/urls.rs | 2 +- src/bakta_handler.rs | 71 +++++++++++++++++++++++++-- src/s3_handler.rs | 1 - 9 files changed, 273 insertions(+), 85 deletions(-) diff --git a/Dockerfile b/Dockerfile index e9c4c19..c67414f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,17 +1,19 @@ -FROM alpine:latest as certs -RUN apk --update add ca-certificates - -FROM golang:latest as builder - -RUN mkdir /BAKTA-Web-Backend -WORKDIR /BAKTA-Web-Backend +# Build Stage +FROM rust:1-alpine3.20 AS builder +WORKDIR /build +RUN apk update +RUN apk upgrade +ENV RUSTFLAGS="-C target-feature=-crt-static" +ENV CARGO_NET_GIT_FETCH_WITH_CLI=true +RUN apk add llvm cmake gcc ca-certificates libc-dev pkgconfig musl-dev git COPY . . -RUN CGO_ENABLED=0 GOOS=linux go build -a -ldflags '-extldflags "-static"' -o BaktaBackend . - -FROM scratch -ARG GITHUB_SHA -ENV GITHUB_SHA=$GITHUB_SHA -COPY --from=certs /etc/ssl/certs/ca-certificates.crt /etc/ssl/certs/ -COPY --from=builder /BAKTA-Web-Backend/BaktaBackend . +RUN cargo build --release -ENTRYPOINT [ "/BaktaBackend" ] \ No newline at end of file +FROM alpine:3.20 +WORKDIR /run +RUN apk update +RUN apk upgrade +RUN apk add libgcc gcompat ca-certificates +COPY --from=builder /build/target/release/bakta_web_backend . +COPY --from=builder /build/.env . +CMD [ "/run/bakta_web_backend" ] \ No newline at end of file diff --git a/README.md b/README.md index 0e0dce7..8f74084 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@

  license

# Concept -The Bakta-Web backend implements a simple job scheduling system for the Bakta-Web UI. It requires an S3 compatible object storage, a MongoDB and a Kubernetes cluster to run the jobs. Jobs can be submitted via an API. The API is defined using [gRPC](https://grpc.io/) and pregenerated builds are available for Golang. In addition the API can be queried using a JSON-over-REST API that is generated from the gRPC definitions using [grpc-gateway](https://github.com/grpc-ecosystem/grpc-gateway). The corresponding repositories can be found here: +The Bakta-Web backend implements a simple job scheduling system for the Bakta-Web UI. It requires an S3 compatible object storage, a Kubernetes cluster with ArgoWorkflows to run the jobs. Jobs can be submitted via an API. The API is a simple [REST API](https://api.bakta.computational.bio/). The corresponding repositories can be found here: - [Bakta](https://github.com/oschwengers/bakta) - [UI](https://github.com/ag-computational-bio/bakta-web-ui) @@ -13,4 +13,18 @@ The Bakta-Web backend implements a simple job scheduling system for the Bakta-We ## Requirements - S3-compatible object storage - Kubernetes-Cluster -- Argo Workflows +- Argo Workflows with a pre-configured WorkflowTemplate named `bakta-job-{BAKTA_VERSTION}` + +The Container accepts the following settings via env-vars (or .env file): + +- `SOCKET_ADDR=127.0.0.1:8080` +- `ARGO_TOKEN=token` +- `ARGO_URL=https://argo.example.com` +- `ARGO_NAMESPACE=argo` +- `S3_ACCESS_KEY=access_key` +- `S3_SECRET_KEY=secret_key` +- `S3_BUCKET=bucket` +- `S3_ENDPOINT=https://s3.example.com` +- `BAKTA_VERSION=0.1.0` +- `DATABASE_VERSION=0.1.0` +- `BACKEND_VERSION=0.2.0` diff --git a/src/api_paths.rs b/src/api_paths.rs index 758daae..2f6b7bd 100644 --- a/src/api_paths.rs +++ b/src/api_paths.rs @@ -51,9 +51,20 @@ pub async fn init_job( ) -> impl IntoResponse { let (id, secret) = state.state_handler.init_job(init_request.name).await; - let Ok(fasta_url) = state - .s3_handler - .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Fasta) + let Ok((fasta_url, prodigal_url, replicon_url)) = + || -> anyhow::Result<(String, String, String)> { + Ok(( + state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Fasta)?, + state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Prodigal)?, + state + .s3_handler + .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::RepliconsTSV)?, + )) + }() else { return ( StatusCode::BAD_REQUEST, @@ -61,28 +72,6 @@ pub async fn init_job( ) .into_response(); }; - - let Ok(prodigal_url) = state - .s3_handler - .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::Prodigal) - else { - return ( - StatusCode::BAD_REQUEST, - Json("Failed to sign URL".to_string()), - ) - .into_response(); - }; - let Ok(replicon_url) = state - .s3_handler - .sign_upload_url(&id.to_string(), crate::s3_handler::InputType::RepliconsTSV) - else { - return ( - StatusCode::BAD_REQUEST, - Json("Failed to sign URL".to_string()), - ) - .into_response(); - }; - ( StatusCode::OK, Json(InitResponse { @@ -104,8 +93,11 @@ pub async fn init_job( (status = 200, body = ListResponse) ) )] -pub async fn list_jobs(Json(ListRequest): Json) -> impl IntoResponse { - format!("") +pub async fn list_jobs( + State(state): State>, + Json(list_request): Json, +) -> impl IntoResponse { + Json(state.state_handler.get_job_states(list_request.jobs).await) } /// Query the result of a job @@ -114,11 +106,22 @@ pub async fn list_jobs(Json(ListRequest): Json) -> impl IntoRespons path = "/api/v1/job/result", request_body = Job, responses( - (status = 200, body = ResultResponse) + (status = 200, body = ResultResponse), + (status = 400, body = String) ) )] -pub async fn query_result(Json(job): Json) -> impl IntoResponse { - format!("") +pub async fn query_result( + State(state): State>, + Json(job): Json, +) -> impl IntoResponse { + match state + .state_handler + .get_results(job, &state.s3_handler) + .await + { + Ok(result) => (StatusCode::OK, Json(result)).into_response(), + Err(e) => (StatusCode::BAD_REQUEST, Json(e.to_string())).into_response(), + } } /// Start a job @@ -127,11 +130,23 @@ pub async fn query_result(Json(job): Json) -> impl IntoResponse { path = "/api/v1/job/start", request_body = StartRequest, responses( - (status = 200, body = ()) + (status = 200, body = ()), + (status = 400, body = String) ) )] -pub async fn start_job(Json(StartRequest): Json) -> impl IntoResponse { - format!("") +pub async fn start_job( + State(state): State>, + Json(start_request): Json, +) -> impl IntoResponse { + let tool_version = state.version.tool.clone(); + match state + .state_handler + .start_job(start_request, tool_version) + .await + { + Ok(_) => (StatusCode::OK, Json(())).into_response(), + Err(e) => (StatusCode::BAD_REQUEST, Json(e.to_string())).into_response(), + } } /// Get the current version @@ -142,6 +157,6 @@ pub async fn start_job(Json(StartRequest): Json) -> impl IntoRespo (status = 200, body = VersionResponse) ) )] -pub async fn version() -> impl IntoResponse { - format!("") +pub async fn version(State(state): State>) -> impl IntoResponse { + Json(state.version.clone()) } diff --git a/src/api_structs.rs b/src/api_structs.rs index 8fda993..a60652d 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -68,7 +68,7 @@ pub struct ListRequest { pub jobs: Vec, } -#[derive(ToSchema, Serialize, Deserialize, Clone)] +#[derive(ToSchema, Serialize, Deserialize, Clone, PartialEq, Eq, PartialOrd, Ord)] pub enum JobStatusEnum { INIT, RUNNING, @@ -166,18 +166,18 @@ pub enum DermType { DIDERM, } -#[derive(ToSchema, Serialize, Deserialize)] +#[derive(ToSchema, Serialize, Deserialize, Default)] pub struct JobConfig { #[serde(rename = "hasProdigal")] - pub prodigal: Option, + pub prodigal: bool, #[serde(rename = "hasReplicons")] - pub replicons: Option, + pub replicons: bool, #[serde(rename = "translationTable")] - pub table: Option, + pub table: u8, #[serde(rename = "completeGenome")] - pub complete: Option, + pub complete: bool, #[serde(rename = "keepContigHeaders")] - pub headers: Option, + pub headers: bool, #[serde(rename = "minContigLength")] pub min_length: Option, #[serde(rename = "dermType")] @@ -189,7 +189,69 @@ pub struct JobConfig { pub locus: Option, #[serde(rename = "locusTag")] pub locus_tag: Option, - pub compliant: Option, + pub compliant: bool, +} + +impl JobConfig { + pub fn into_parameters(self) -> String { + let mut parameters = Vec::new(); + + if self.prodigal { + parameters.push("--prodigal /data/prodigal.tf".to_string()); + } + + if self.replicons { + parameters.push("--replicons /data/replicons.tsv".to_string()); + } + + if self.complete { + parameters.push("--complete".to_string()); + } + + if let Some(locus) = self.locus { + parameters.push(format!("--locus {}", locus)); + } + + if let Some(locus_tag) = self.locus_tag { + parameters.push(format!("--locus-tag {}", locus_tag)); + } + + if self.headers { + parameters.push("--keep-contig-headers".to_string()); + } + + if let Some(genus) = self.genus { + parameters.push(format!("--genus {}", genus)); + } + + if let Some(species) = self.species { + parameters.push(format!("--species {}", species)); + } + + if let Some(strain) = self.strain { + parameters.push(format!("--strain {}", strain)); + } + + if let Some(plasmid) = self.plasmid { + parameters.push(format!("--plasmid {}", plasmid)); + } + + if self.compliant { + parameters.push("--compliant".to_string()); + } + + if let 4 = self.table { + parameters.push("--translation-table 4".to_string()); + } + + match self.derm { + Some(DermType::MONODERM) => parameters.push("--gram +".to_string()), + Some(DermType::DIDERM) => parameters.push("--gram -".to_string()), + _ => parameters.push("--derm ?".to_string()), + } + + parameters.join(" ") + } } #[derive(ToSchema, Serialize, Deserialize)] @@ -198,7 +260,7 @@ pub struct StartRequest { pub config: JobConfig, } -#[derive(ToSchema, Serialize, Deserialize)] +#[derive(ToSchema, Serialize, Deserialize, Clone)] pub struct VersionResponse { #[serde(rename = "toolVersion")] pub tool: String, @@ -207,3 +269,35 @@ pub struct VersionResponse { #[serde(rename = "backendVersion")] pub backend: String, } + +#[cfg(test)] +mod test { + use super::*; + + #[test] + fn test_into_parameters() { + let params = JobConfig { + prodigal: true, + replicons: true, + table: 4, + complete: true, + headers: true, + min_length: None, + derm: Some(DermType::MONODERM), + genus: Some("Bacillus".to_string()), + species: Some("subtilis".to_string()), + strain: Some("168".to_string()), + plasmid: Some("pBS32".to_string()), + locus: Some("BSU_00010".to_string()), + locus_tag: Some("BSU00010".to_string()), + compliant: true, + }; + + assert_eq!( + params.into_parameters(), + "--prodigal /data/prodigal.tf --replicons /data/replicons.tsv --complete --locus BSU_00010 --locus-tag BSU00010 --keep-contig-headers --genus Bacillus --species subtilis --strain 168 --plasmid pBS32 --compliant --translation-table 4 --gram +" + ); + + assert_eq!(JobConfig::default().into_parameters(), "--derm ?"); + } +} diff --git a/src/argo/client.rs b/src/argo/client.rs index 895afe9..9842182 100644 --- a/src/argo/client.rs +++ b/src/argo/client.rs @@ -1,11 +1,9 @@ -use std::collections::HashMap; - -use reqwest::{Client, Response}; - use anyhow::Result; +use reqwest::Client; +use std::collections::HashMap; use super::{ - structs::{SimpleStatusList, SubmitOptions, SubmitWorkflowTemplate}, + structs::{SimpleStatusList, SubmitOptions, SubmitResult, SubmitWorkflowTemplate}, urls::{get_delete_url, get_status_url_bakta, get_submit_url}, }; @@ -54,12 +52,10 @@ impl ArgoClient { pub async fn submit_from_template( &self, templatename: String, - name: String, labels: Option>, parameters: Option>, - priority: Option, service_account: Option, - ) -> Result { + ) -> Result { let labels = labels.map(|some| { some.iter() .map(|(k, v)| format!("{k}={v}")) @@ -78,23 +74,21 @@ impl ArgoClient { resource_kind: "WorkflowTemplate".to_string(), resource_name: templatename.to_string(), submit_options: SubmitOptions { - generate_name: None, labels, - name: Some(name), parameters, - priority, service_account, }, }; - let response = self + Ok(self .client .post(get_submit_url(&self.url, &self.namespace)) .header("Authorization", &self.token) .json(&submit_template) .send() - .await?; - Ok(response) + .await? + .json() + .await?) } } diff --git a/src/argo/structs.rs b/src/argo/structs.rs index ecf47db..29bd235 100644 --- a/src/argo/structs.rs +++ b/src/argo/structs.rs @@ -1,3 +1,4 @@ +use chrono::DateTime; use chrono::Utc; use serde::Deserialize; use serde::Serialize; @@ -16,11 +17,8 @@ pub struct SubmitWorkflowTemplate { #[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] #[serde(rename_all = "camelCase")] pub struct SubmitOptions { - pub generate_name: Option, pub labels: Option, - pub name: Option, pub parameters: Option>, - pub priority: Option, pub service_account: Option, } @@ -139,3 +137,14 @@ pub struct SimpleStatusStatus { #[serde(rename = "finishedAt")] pub finished_at: Option>, } + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +pub struct SubmitResult { + pub metadata: SubmitResultMetadata, +} + +#[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] +pub struct SubmitResultMetadata { + pub name: String, + pub creation_timestamp: DateTime, +} diff --git a/src/argo/urls.rs b/src/argo/urls.rs index 6f365cf..3c548e2 100644 --- a/src/argo/urls.rs +++ b/src/argo/urls.rs @@ -20,7 +20,7 @@ where format!("{url}/api/v1/workflows/{namespace}/submit") } -pub fn get_logs_url(url: T, namespace: U, workflowname: V, podname: W) -> String +pub fn _get_logs_url(url: T, namespace: U, workflowname: V, podname: W) -> String where T: Display, U: Display, diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs index f60320c..e021a5d 100644 --- a/src/bakta_handler.rs +++ b/src/bakta_handler.rs @@ -1,6 +1,9 @@ use crate::api_structs::FailedJobStatus; use crate::api_structs::FailedJobStatusEnum; +use crate::api_structs::Job; use crate::api_structs::ListResponse; +use crate::api_structs::ResultFiles; +use crate::api_structs::StartRequest; use crate::argo::structs::SimpleStatus; use crate::{ api_structs::{JobStatus, JobStatusEnum, VersionResponse}, @@ -30,7 +33,6 @@ pub struct FullJobState { } pub struct BaktaHandler { - pub argo_client: Arc, pub s3_handler: S3Handler, pub version: VersionResponse, pub state_handler: Arc, @@ -54,14 +56,13 @@ impl BaktaHandler { let state_handler = Arc::new(StateHandler { job_state: RwLock::new(HashMap::new()), - argo_client: argo_client.clone(), + argo_client: argo_client, }); let state_handler_clone = state_handler.clone(); state_handler_clone.run().await; BaktaHandler { - argo_client, s3_handler, version: VersionResponse { tool: bakta_version, @@ -143,12 +144,12 @@ impl StateHandler { }); } - pub async fn get_job_states(&self, job_ids: Vec<(Uuid, String)>) -> ListResponse { + pub async fn get_job_states(&self, request_jobs: Vec) -> ListResponse { let read_lock = self.job_state.read().await; let mut jobs = vec![]; let mut failed = vec![]; - for (id, secret) in job_ids { + for Job { id, secret } in request_jobs { if let Some(state) = read_lock.get(&id) { if state.secret != secret { failed.push(FailedJobStatus { @@ -207,4 +208,64 @@ impl StateHandler { ); (job_id, secret) } + + pub async fn start_job( + &self, + start_settings: StartRequest, + bakta_version: String, + ) -> Result<()> { + let Job { id, secret } = &start_settings.job; + + let parameters = start_settings.config.into_parameters(); + + let mut write_lock = self.job_state.write().await; + if let Some(state) = write_lock.get_mut(&id) { + if state.secret != *secret { + return Err(anyhow!("Unauthorized")); + } + + let result = self + .argo_client + .submit_from_template( + format!("bakta-job-{}", bakta_version), + Some(HashMap::from([ + ("jobid".to_string(), id.to_string()), + ("name".to_string(), state.name.clone()), + ("secret".to_string(), state.secret.clone()), + ])), + Some(HashMap::from([("parameters".to_string(), parameters)])), + None, + ) + .await?; + + state.workflowname = Some(result.metadata.name); + state.api_status = Some(JobStatus { + id: id.clone(), + status: JobStatusEnum::INIT, + started: result.metadata.creation_timestamp, + updated: Utc::now(), + name: state.name.clone(), + }); + } + Ok(()) + } + + pub async fn get_results( + &self, + Job { id, secret }: Job, + s3_handler: &S3Handler, + ) -> Result { + if let Some(state) = self.job_state.read().await.get(&id) { + if state.secret != secret { + return Err(anyhow!("Unauthorized")); + } + + if let Some(state) = &state.api_status { + if state.status != JobStatusEnum::SUCCESSFULL { + return Err(anyhow!("Job not finished")); + } + } + } + s3_handler.sign_download_urls(id.to_string().as_str()) + } } diff --git a/src/s3_handler.rs b/src/s3_handler.rs index 1989e74..611e482 100644 --- a/src/s3_handler.rs +++ b/src/s3_handler.rs @@ -1,5 +1,4 @@ use anyhow::{anyhow, Result}; -use chrono::format; use reqsign::{AwsCredential, AwsV4Signer}; use reqwest::Method; use url::Url; From 96e1d456789d40df5852ff9e1e88ce5977d31c34 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 09:38:29 +0200 Subject: [PATCH 05/10] feat: Update build --- .github/workflows/docker-publish.yml | 20 +------------------- Dockerfile | 8 ++++---- 2 files changed, 5 insertions(+), 23 deletions(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 0f66e1e..233b147 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -12,31 +12,13 @@ on: env: # TODO: Change variable to your image's name. - IMAGE_NAME: bakta-web-gateway + IMAGE_NAME: bakta-web-backend jobs: - # Run tests. - # See also https://docs.docker.com/docker-hub/builds/automated-testing/ - test: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - - name: Run tests - run: | - if [ -f docker-compose.test.yml ]; then - docker-compose --file docker-compose.test.yml build - docker-compose --file docker-compose.test.yml run sut - else - docker build . --file Dockerfile - fi # Push image to GitHub Packages. # See also https://docs.docker.com/docker-hub/builds/ push: - # Ensure test job passes before pushing image. - needs: test runs-on: ubuntu-latest if: github.event_name == 'push' diff --git a/Dockerfile b/Dockerfile index c67414f..4a66472 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,7 +5,7 @@ RUN apk update RUN apk upgrade ENV RUSTFLAGS="-C target-feature=-crt-static" ENV CARGO_NET_GIT_FETCH_WITH_CLI=true -RUN apk add llvm cmake gcc ca-certificates libc-dev pkgconfig musl-dev git +RUN apk add llvm cmake gcc ca-certificates libc-dev pkgconfig musl-dev git openssl-dev curl COPY . . RUN cargo build --release @@ -13,7 +13,7 @@ FROM alpine:3.20 WORKDIR /run RUN apk update RUN apk upgrade -RUN apk add libgcc gcompat ca-certificates -COPY --from=builder /build/target/release/bakta_web_backend . +RUN apk add libgcc gcompat ca-certificates openssl-dev +COPY --from=builder /build/target/release/bakta-web-backend . COPY --from=builder /build/.env . -CMD [ "/run/bakta_web_backend" ] \ No newline at end of file +CMD [ "/run/bakta-web-backend" ] \ No newline at end of file From 592a0b317aef01755944e1b85f3049c5a2cff5bb Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 14:18:50 +0200 Subject: [PATCH 06/10] feat: Added logging / debugging --- Cargo.lock | 145 +++++++++++++++++++++++++++++++++++++++++-- Cargo.toml | 5 +- src/bakta_handler.rs | 24 +++++-- src/main.rs | 26 +++++++- 4 files changed, 189 insertions(+), 11 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 42b9807..3014d63 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -162,7 +162,7 @@ dependencies = [ [[package]] name = "bakta-web-backend" -version = "0.2.0" +version = "0.6.0" dependencies = [ "anyhow", "axum", @@ -176,6 +176,9 @@ dependencies = [ "serde", "serde_json", "tokio", + "tower-http", + "tracing", + "tracing-subscriber", "url", "utoipa", "utoipa-swagger-ui", @@ -904,6 +907,15 @@ version = "0.4.22" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24" +[[package]] +name = "matchers" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8263075bb86c5a1b1427b5ae862e8889656f126e9f77c484496e8b47cf5c5558" +dependencies = [ + "regex-automata 0.1.10", +] + [[package]] name = "matchit" version = "0.7.3" @@ -969,6 +981,16 @@ dependencies = [ "tempfile", ] +[[package]] +name = "nu-ansi-term" +version = "0.46.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "77a8165726e8236064dbb45459242600304b42a5ea24ee2948e18e023bf7ba84" +dependencies = [ + "overload", + "winapi", +] + [[package]] name = "num-bigint" version = "0.4.6" @@ -1132,6 +1154,12 @@ dependencies = [ "hashbrown", ] +[[package]] +name = "overload" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39" + [[package]] name = "parking_lot" version = "0.12.3" @@ -1433,8 +1461,17 @@ checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f" dependencies = [ "aho-corasick", "memchr", - "regex-automata", - "regex-syntax", + "regex-automata 0.4.7", + "regex-syntax 0.8.4", +] + +[[package]] +name = "regex-automata" +version = "0.1.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132" +dependencies = [ + "regex-syntax 0.6.29", ] [[package]] @@ -1445,9 +1482,15 @@ checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df" dependencies = [ "aho-corasick", "memchr", - "regex-syntax", + "regex-syntax 0.8.4", ] +[[package]] +name = "regex-syntax" +version = "0.6.29" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" + [[package]] name = "regex-syntax" version = "0.8.4" @@ -1845,6 +1888,15 @@ dependencies = [ "digest", ] +[[package]] +name = "sharded-slab" +version = "0.1.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6" +dependencies = [ + "lazy_static", +] + [[package]] name = "signal-hook-registry" version = "1.4.2" @@ -2009,6 +2061,16 @@ dependencies = [ "syn 2.0.71", ] +[[package]] +name = "thread_local" +version = "1.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8b9ef9bad013ada3808854ceac7b46812a6465ba368859a37e2100283d2d719c" +dependencies = [ + "cfg-if", + "once_cell", +] + [[package]] name = "time" version = "0.3.36" @@ -2189,6 +2251,23 @@ dependencies = [ "tracing", ] +[[package]] +name = "tower-http" +version = "0.5.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1e9cd434a998747dd2c4276bc96ee2e0c7a2eadf3cae88e52be55a05fa9053f5" +dependencies = [ + "bitflags 2.6.0", + "bytes", + "http", + "http-body", + "http-body-util", + "pin-project-lite", + "tower-layer", + "tower-service", + "tracing", +] + [[package]] name = "tower-layer" version = "0.3.2" @@ -2231,6 +2310,36 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c06d3da6113f116aaee68e4d601191614c9053067f9ab7f6edbcb161237daa54" dependencies = [ "once_cell", + "valuable", +] + +[[package]] +name = "tracing-log" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ee855f1f400bd0e5c02d150ae5de3840039a3f54b025156404e34c23c03f47c3" +dependencies = [ + "log", + "once_cell", + "tracing-core", +] + +[[package]] +name = "tracing-subscriber" +version = "0.3.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ad0f048c97dbd9faa9b7df56362b8ebcaa52adb06b498c050d2f4e32f90a7a8b" +dependencies = [ + "matchers", + "nu-ansi-term", + "once_cell", + "regex", + "sharded-slab", + "smallvec", + "thread_local", + "tracing", + "tracing-core", + "tracing-log", ] [[package]] @@ -2351,6 +2460,12 @@ dependencies = [ "serde", ] +[[package]] +name = "valuable" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d" + [[package]] name = "vcpkg" version = "0.2.15" @@ -2473,6 +2588,22 @@ dependencies = [ "rustls-pki-types", ] +[[package]] +name = "winapi" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419" +dependencies = [ + "winapi-i686-pc-windows-gnu", + "winapi-x86_64-pc-windows-gnu", +] + +[[package]] +name = "winapi-i686-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" + [[package]] name = "winapi-util" version = "0.1.8" @@ -2482,6 +2613,12 @@ dependencies = [ "windows-sys 0.52.0", ] +[[package]] +name = "winapi-x86_64-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" + [[package]] name = "windows-core" version = "0.52.0" diff --git a/Cargo.toml b/Cargo.toml index 565317c..3cce4cd 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "bakta-web-backend" -version = "0.2.0" +version = "0.6.0" edition = "2021" [dependencies] @@ -16,6 +16,9 @@ reqwest = { version = "0.12.5", features = ["json"] } serde = { version = "1.0.204", features = ["derive"] } serde_json = "1.0.120" tokio = { version = "1.38.1", features = ["full"] } +tower-http = { version = "0.5.2", features = ["cors", "trace"]} +tracing = "0.1.40" +tracing-subscriber = { version = "0.3.18", features = ["env-filter", "fmt"]} url = "2.5.2" utoipa = { version = "4.2.3", features = ["uuid", "chrono"]} utoipa-swagger-ui = { version = "7.1.0", features = ["axum"] } diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs index e021a5d..7a78b63 100644 --- a/src/bakta_handler.rs +++ b/src/bakta_handler.rs @@ -124,17 +124,31 @@ impl StateHandler { )) }; - let initial = argo_client.get_workflow_status(false).await?; + let initial = argo_client.get_workflow_status(false).await.map_err(|e| { + tracing::error!(?e, "Failed to get initial workflow status"); + e + })?; let mut write_lock = self.job_state.write().await; for item in initial.items { - let (id, state) = into_state(item)?; + let (id, state) = into_state(item).map_err(|e| { + tracing::error!(?e, "Failed to parse state"); + e + })?; write_lock.insert(id, state); } drop(write_lock); - loop { - let initial = argo_client.get_workflow_status(true).await?; + 'outer: loop { + let Ok(initial) = argo_client.get_workflow_status(true).await.map_err(|e| { + tracing::error!(?e, "Failed to query workflow_status"); + })else{ + continue; + }; for item in initial.items { - let (id, state) = into_state(item)?; + let Ok((id, state)) = into_state(item).map_err(|e| { + tracing::error!(?e, "Failed to parse_state"); + })else{ + continue 'outer; + }; self.job_state.write().await.insert(id, state); } tokio::time::sleep(tokio::time::Duration::from_secs(15)).await; diff --git a/src/main.rs b/src/main.rs index 4659c03..01a49b0 100644 --- a/src/main.rs +++ b/src/main.rs @@ -5,6 +5,9 @@ use axum::{ }; use bakta_handler::BaktaHandler; use std::{net::SocketAddr, sync::Arc}; +use tower_http::cors::CorsLayer; +use tower_http::trace::TraceLayer; +use tracing_subscriber::EnvFilter; use utoipa::OpenApi; use utoipa_swagger_ui::SwaggerUi; @@ -41,6 +44,20 @@ async fn main() -> Result<(), Box> { .await, ); + + let filter = EnvFilter::try_from_default_env() + .unwrap_or("none".into()) + .add_directive("tower_http=debug".parse()?) + .add_directive("bakta_web_backend=trace".parse()?); + + tracing_subscriber::fmt() + .with_env_filter( + filter + ) + .init(); + + tracing::info!(?socket_address, "Starting bakta web backend"); + let app = Router::new() .merge(swagger) .route("/", get(|| async { Redirect::permanent("/swagger-ui") })) @@ -50,7 +67,14 @@ async fn main() -> Result<(), Box> { .route("/api/v1/job/result", post(api_paths::query_result)) .route("/api/v1/job/start", post(api_paths::start_job)) .route("/api/v1/version", get(api_paths::version)) - .with_state(bakta_handler); + .with_state(bakta_handler) + .layer(CorsLayer::very_permissive()) + .layer( + TraceLayer::new_for_http() + .on_response(()) + .on_body_chunk(()) + .on_eos(()), + ); axum::serve(listener, app.into_make_service()).await?; Ok(()) } From 142438f54248db1de266c7a7f024d69744f285ea Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 14:59:05 +0200 Subject: [PATCH 07/10] fix: S3 url parsing, min-contig length --- src/api_structs.rs | 8 ++++++-- src/s3_handler.rs | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/src/api_structs.rs b/src/api_structs.rs index a60652d..e896eeb 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -179,7 +179,7 @@ pub struct JobConfig { #[serde(rename = "keepContigHeaders")] pub headers: bool, #[serde(rename = "minContigLength")] - pub min_length: Option, + pub min_length: u64, #[serde(rename = "dermType")] pub derm: Option, pub genus: Option, @@ -196,6 +196,10 @@ impl JobConfig { pub fn into_parameters(self) -> String { let mut parameters = Vec::new(); + if self.min_length > 1 { + parameters.push(format!("--min-contig-length {}", self.min_length)); + } + if self.prodigal { parameters.push("--prodigal /data/prodigal.tf".to_string()); } @@ -282,7 +286,7 @@ mod test { table: 4, complete: true, headers: true, - min_length: None, + min_length: 1, derm: Some(DermType::MONODERM), genus: Some("Bacillus".to_string()), species: Some("subtilis".to_string()), diff --git a/src/s3_handler.rs b/src/s3_handler.rs index 611e482..1aac6af 100644 --- a/src/s3_handler.rs +++ b/src/s3_handler.rs @@ -31,7 +31,7 @@ impl InputType { impl S3Handler { pub fn new(access_key: String, secret_key: String, bucket: String, endpoint: String) -> Self { - let ssl = if endpoint.starts_with("http://") { + let ssl = if endpoint.starts_with("https://") { true } else { false From f177d0c467b88b3afd7bc4b91c06dc879a250af4 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 16:28:39 +0200 Subject: [PATCH 08/10] chore: Added print to start_job request, fix parameter naming --- src/api_structs.rs | 14 +++++++++----- src/argo/client.rs | 10 ++++++---- src/bakta_handler.rs | 2 +- 3 files changed, 16 insertions(+), 10 deletions(-) diff --git a/src/api_structs.rs b/src/api_structs.rs index e896eeb..e2f11ab 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -166,11 +166,15 @@ pub enum DermType { DIDERM, } +fn default_replicons() -> bool { + true +} + #[derive(ToSchema, Serialize, Deserialize, Default)] pub struct JobConfig { - #[serde(rename = "hasProdigal")] - pub prodigal: bool, - #[serde(rename = "hasReplicons")] + #[serde(rename = "prodigalTrainingFile")] + pub prodigal: Option, + #[serde(rename = "hasReplicons", default = "default_replicons")] pub replicons: bool, #[serde(rename = "translationTable")] pub table: u8, @@ -200,7 +204,7 @@ impl JobConfig { parameters.push(format!("--min-contig-length {}", self.min_length)); } - if self.prodigal { + if self.prodigal.is_some() { parameters.push("--prodigal /data/prodigal.tf".to_string()); } @@ -281,7 +285,7 @@ mod test { #[test] fn test_into_parameters() { let params = JobConfig { - prodigal: true, + prodigal: Some("foo".to_string()), replicons: true, table: 4, complete: true, diff --git a/src/argo/client.rs b/src/argo/client.rs index 9842182..510dea5 100644 --- a/src/argo/client.rs +++ b/src/argo/client.rs @@ -80,15 +80,17 @@ impl ArgoClient { }, }; - Ok(self + + let response = self .client .post(get_submit_url(&self.url, &self.namespace)) .header("Authorization", &self.token) .json(&submit_template) .send() - .await? - .json() - .await?) + .await?.bytes().await?; + + tracing::trace!("Response: {response:?}"); + Ok(serde_json::from_slice(&response)?) } } diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs index 7a78b63..8a63187 100644 --- a/src/bakta_handler.rs +++ b/src/bakta_handler.rs @@ -247,7 +247,7 @@ impl StateHandler { ("name".to_string(), state.name.clone()), ("secret".to_string(), state.secret.clone()), ])), - Some(HashMap::from([("parameters".to_string(), parameters)])), + Some(HashMap::from([("parameter".to_string(), parameters)])), None, ) .await?; From b1bde26d2cfbc40d7edea37ed78e0ff00ad8b230 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Fri, 19 Jul 2024 17:56:45 +0200 Subject: [PATCH 09/10] fix: Fix small parsing issues, fix query result response --- src/api_structs.rs | 26 +++++++++++++++++++------- src/argo/client.rs | 13 ++++++++----- src/argo/structs.rs | 2 ++ src/argo/urls.rs | 8 ++------ src/bakta_handler.rs | 30 ++++++++++++++++++++++-------- src/main.rs | 7 +------ src/s3_handler.rs | 2 +- 7 files changed, 55 insertions(+), 33 deletions(-) diff --git a/src/api_structs.rs b/src/api_structs.rs index e2f11ab..eb110c8 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -217,11 +217,15 @@ impl JobConfig { } if let Some(locus) = self.locus { - parameters.push(format!("--locus {}", locus)); + if !locus.is_empty() { + parameters.push(format!("--locus {}", locus)); + } } if let Some(locus_tag) = self.locus_tag { - parameters.push(format!("--locus-tag {}", locus_tag)); + if !locus_tag.is_empty() { + parameters.push(format!("--locus-tag {}", locus_tag)); + } } if self.headers { @@ -229,19 +233,27 @@ impl JobConfig { } if let Some(genus) = self.genus { - parameters.push(format!("--genus {}", genus)); + if !genus.is_empty() { + parameters.push(format!("--genus {}", genus)); + } } if let Some(species) = self.species { - parameters.push(format!("--species {}", species)); + if !species.is_empty() { + parameters.push(format!("--species {}", species)); + } } if let Some(strain) = self.strain { - parameters.push(format!("--strain {}", strain)); + if !strain.is_empty() { + parameters.push(format!("--strain {}", strain)); + } } if let Some(plasmid) = self.plasmid { - parameters.push(format!("--plasmid {}", plasmid)); + if !plasmid.is_empty() { + parameters.push(format!("--plasmid {}", plasmid)); + } } if self.compliant { @@ -255,7 +267,7 @@ impl JobConfig { match self.derm { Some(DermType::MONODERM) => parameters.push("--gram +".to_string()), Some(DermType::DIDERM) => parameters.push("--gram -".to_string()), - _ => parameters.push("--derm ?".to_string()), + _ => parameters.push("--gram ?".to_string()), } parameters.join(" ") diff --git a/src/argo/client.rs b/src/argo/client.rs index 510dea5..8d02e4e 100644 --- a/src/argo/client.rs +++ b/src/argo/client.rs @@ -26,10 +26,10 @@ impl ArgoClient { } impl ArgoClient { - pub async fn get_workflow_status(&self, recent: bool) -> Result { + pub async fn get_workflow_status(&self) -> Result { let response = self .client - .get(get_status_url_bakta(&self.url, &self.namespace, recent)) + .get(get_status_url_bakta(&self.url, &self.namespace)) .header("Authorization", &self.token) .send() .await? @@ -55,6 +55,7 @@ impl ArgoClient { labels: Option>, parameters: Option>, service_account: Option, + generate_name: Option, ) -> Result { let labels = labels.map(|some| { some.iter() @@ -77,17 +78,19 @@ impl ArgoClient { labels, parameters, service_account, + generate_name, }, }; - let response = self .client .post(get_submit_url(&self.url, &self.namespace)) .header("Authorization", &self.token) .json(&submit_template) .send() - .await?.bytes().await?; + .await? + .bytes() + .await?; tracing::trace!("Response: {response:?}"); Ok(serde_json::from_slice(&response)?) @@ -102,7 +105,7 @@ mod tests { #[tokio::test] async fn test_get_workflow_status() { let client = ArgoClient::new("foo".to_string(), "bar".to_string(), "bakta".to_string()); - let response = client.get_workflow_status(true).await.unwrap(); + let response = client.get_workflow_status().await.unwrap(); dbg!(response); } } diff --git a/src/argo/structs.rs b/src/argo/structs.rs index 29bd235..08cb668 100644 --- a/src/argo/structs.rs +++ b/src/argo/structs.rs @@ -20,6 +20,7 @@ pub struct SubmitOptions { pub labels: Option, pub parameters: Option>, pub service_account: Option, + pub generate_name: Option, } /// GET WORKFLOWS REQUEST @@ -146,5 +147,6 @@ pub struct SubmitResult { #[derive(Default, Debug, Clone, PartialEq, Eq, Serialize, Deserialize)] pub struct SubmitResultMetadata { pub name: String, + #[serde(rename = "creationTimestamp")] pub creation_timestamp: DateTime, } diff --git a/src/argo/urls.rs b/src/argo/urls.rs index 3c548e2..93401fc 100644 --- a/src/argo/urls.rs +++ b/src/argo/urls.rs @@ -1,15 +1,11 @@ use std::fmt::Display; -pub fn get_status_url_bakta(url: T, namespace: U, recent: bool) -> String +pub fn get_status_url_bakta(url: T, namespace: U) -> String where T: Display, U: Display, { - if recent { - format!("{url}/api/v1/workflows/{namespace}?fields=items.status.finishedAt,items.status.startedAt,items.metadata.name,items.status.phase,items.metadata.labels&listOptions.labelSelector=workflows.argoproj.io/workflow-archiving-status!=Archived") - } else { - format!("{url}/api/v1/workflows/{namespace}?fields=items.status.finishedAt,items.status.startedAt,items.metadata.name,items.status.phase,items.metadata.labels") - } + format!("{url}/api/v1/workflows/{namespace}?fields=items.status.finishedAt,items.status.startedAt,items.metadata.name,items.status.phase,items.metadata.labels") } pub fn get_submit_url(url: T, namespace: U) -> String diff --git a/src/bakta_handler.rs b/src/bakta_handler.rs index 8a63187..3fd1ef1 100644 --- a/src/bakta_handler.rs +++ b/src/bakta_handler.rs @@ -2,7 +2,7 @@ use crate::api_structs::FailedJobStatus; use crate::api_structs::FailedJobStatusEnum; use crate::api_structs::Job; use crate::api_structs::ListResponse; -use crate::api_structs::ResultFiles; +use crate::api_structs::ResultResponse; use crate::api_structs::StartRequest; use crate::argo::structs::SimpleStatus; use crate::{ @@ -124,7 +124,7 @@ impl StateHandler { )) }; - let initial = argo_client.get_workflow_status(false).await.map_err(|e| { + let initial = argo_client.get_workflow_status().await.map_err(|e| { tracing::error!(?e, "Failed to get initial workflow status"); e })?; @@ -138,15 +138,15 @@ impl StateHandler { } drop(write_lock); 'outer: loop { - let Ok(initial) = argo_client.get_workflow_status(true).await.map_err(|e| { + let Ok(initial) = argo_client.get_workflow_status().await.map_err(|e| { tracing::error!(?e, "Failed to query workflow_status"); - })else{ + }) else { continue; }; for item in initial.items { let Ok((id, state)) = into_state(item).map_err(|e| { tracing::error!(?e, "Failed to parse_state"); - })else{ + }) else { continue 'outer; }; self.job_state.write().await.insert(id, state); @@ -247,8 +247,12 @@ impl StateHandler { ("name".to_string(), state.name.clone()), ("secret".to_string(), state.secret.clone()), ])), - Some(HashMap::from([("parameter".to_string(), parameters)])), + Some(HashMap::from([ + ("parameter".to_string(), parameters), + ("jobid".to_string(), id.to_string()), + ])), None, + Some(format!("bakta-job-{}-", id.to_string())), ) .await?; @@ -268,7 +272,7 @@ impl StateHandler { &self, Job { id, secret }: Job, s3_handler: &S3Handler, - ) -> Result { + ) -> Result { if let Some(state) = self.job_state.read().await.get(&id) { if state.secret != secret { return Err(anyhow!("Unauthorized")); @@ -279,7 +283,17 @@ impl StateHandler { return Err(anyhow!("Job not finished")); } } + + if let Some(state) = &state.api_status { + return Ok(ResultResponse { + id, + started: state.started, + updated: state.updated, + name: state.name.clone(), + files: s3_handler.sign_download_urls(id.to_string().as_str())?, + }); + } } - s3_handler.sign_download_urls(id.to_string().as_str()) + Err(anyhow!("Job not found")) } } diff --git a/src/main.rs b/src/main.rs index 01a49b0..0ab92fb 100644 --- a/src/main.rs +++ b/src/main.rs @@ -44,17 +44,12 @@ async fn main() -> Result<(), Box> { .await, ); - let filter = EnvFilter::try_from_default_env() .unwrap_or("none".into()) .add_directive("tower_http=debug".parse()?) .add_directive("bakta_web_backend=trace".parse()?); - tracing_subscriber::fmt() - .with_env_filter( - filter - ) - .init(); + tracing_subscriber::fmt().with_env_filter(filter).init(); tracing::info!(?socket_address, "Starting bakta web backend"); diff --git a/src/s3_handler.rs b/src/s3_handler.rs index 1aac6af..7ff6c30 100644 --- a/src/s3_handler.rs +++ b/src/s3_handler.rs @@ -75,7 +75,7 @@ impl S3Handler { &self.bucket, &key, &self.endpoint, - 60 * 86400, // 60 days + 6 * 86400, // 6 days ) }; Ok(ResultFiles { From b77202b5219412fc16d5721c1d9a6aad647d1680 Mon Sep 17 00:00:00 2001 From: Sebastian Beyvers Date: Mon, 25 Nov 2024 15:53:35 +0100 Subject: [PATCH 10/10] feat: Update bakta web to newest version --- Cargo.lock | 1161 +++++++++++++++++++++++--------------------- Cargo.toml | 30 +- src/api_paths.rs | 5 +- src/api_structs.rs | 1 + 4 files changed, 635 insertions(+), 562 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 3014d63..c01e14b 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -4,18 +4,18 @@ version = 3 [[package]] name = "addr2line" -version = "0.22.0" +version = "0.24.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678" +checksum = "dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1" dependencies = [ "gimli", ] [[package]] -name = "adler" -version = "1.0.2" +name = "adler2" +version = "2.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" +checksum = "512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627" [[package]] name = "aes" @@ -54,28 +54,28 @@ dependencies = [ [[package]] name = "anyhow" -version = "1.0.86" +version = "1.0.93" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da" +checksum = "4c95c10ba0b00a02636238b814946408b1322d5ac4760326e6fb8ec956d85775" [[package]] name = "arbitrary" -version = "1.3.2" +version = "1.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7d5a26814d8dcb93b0e5a0ff3c6d80a8843bafb21b39e8e18a6f05471870e110" +checksum = "dde20b3d026af13f561bdd0f15edf01fc734f0dafcedbaf42bba506a9517f223" dependencies = [ "derive_arbitrary", ] [[package]] name = "async-trait" -version = "0.1.81" +version = "0.1.83" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6e0c28dcc82d7c8ead5cb13beb15405b57b8546e93215673ff8ca0349a028107" +checksum = "721cae7de5c34fbb2acd27e21e6d2cf7b886dce0c27388d46c4e6c47ea4318dd" dependencies = [ "proc-macro2", "quote", - "syn 2.0.71", + "syn", ] [[package]] @@ -86,15 +86,15 @@ checksum = "1505bd5d3d116872e7271a6d4e16d81d0c8570876c8de68093a09ac269d8aac0" [[package]] name = "autocfg" -version = "1.3.0" +version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0" +checksum = "ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26" [[package]] name = "axum" -version = "0.7.5" +version = "0.7.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3a6c9af12842a67734c9a2e355436e5d03b22383ed60cf13cd0c18fbfe3dcbcf" +checksum = "edca88bc138befd0323b20752846e6587272d3b03b0343c8ea28a6f819e6e71f" dependencies = [ "async-trait", "axum-core", @@ -116,7 +116,7 @@ dependencies = [ "serde_json", "serde_path_to_error", "serde_urlencoded", - "sync_wrapper 1.0.1", + "sync_wrapper 1.0.2", "tokio", "tower", "tower-layer", @@ -126,9 +126,9 @@ dependencies = [ [[package]] name = "axum-core" -version = "0.4.3" +version = "0.4.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a15c63fd72d41492dc4f497196f5da1fb04fb7529e631d73630d1b491e47a2e3" +checksum = "09f2bd6146b97ae3359fa0cc6d6b376d9539582c7b4220f041a33ec24c226199" dependencies = [ "async-trait", "bytes", @@ -139,7 +139,7 @@ dependencies = [ "mime", "pin-project-lite", "rustversion", - "sync_wrapper 0.1.2", + "sync_wrapper 1.0.2", "tower-layer", "tower-service", "tracing", @@ -147,22 +147,22 @@ dependencies = [ [[package]] name = "backtrace" -version = "0.3.73" +version = "0.3.74" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a" +checksum = "8d82cb332cdfaed17ae235a638438ac4d4839913cc2af585c3c6746e8f8bee1a" dependencies = [ "addr2line", - "cc", "cfg-if", "libc", "miniz_oxide", "object", "rustc-demangle", + "windows-targets", ] [[package]] name = "bakta-web-backend" -version = "0.6.0" +version = "0.6.1" dependencies = [ "anyhow", "axum", @@ -203,12 +203,6 @@ version = "1.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8c3c1a368f70d6cf7302d78f8f7093da241fb8e8807c05cc9e51a125895a6d5b" -[[package]] -name = "bitflags" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" - [[package]] name = "bitflags" version = "2.6.0" @@ -247,9 +241,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b" [[package]] name = "bytes" -version = "1.6.1" +version = "1.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a12916984aab3fa6e39d655a33e09c0071eb36d6ab3aea5c2d78551f1df6d952" +checksum = "9ac0150caa2ae65ca5bd83f25c7de183dea78d4d366469f148435e2acfbad0da" [[package]] name = "cbc" @@ -262,9 +256,12 @@ dependencies = [ [[package]] name = "cc" -version = "1.1.5" +version = "1.2.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "324c74f2155653c90b04f25b2a47a8a631360cb908f92a772695f430c7e31052" +checksum = "fd9de9f2205d5ef3fd67e685b0df337994ddd4495e2a28d185500d0e1edfea47" +dependencies = [ + "shlex", +] [[package]] name = "cfg-if" @@ -284,7 +281,7 @@ dependencies = [ "num-traits", "serde", "wasm-bindgen", - "windows-targets 0.52.6", + "windows-targets", ] [[package]] @@ -335,15 +332,15 @@ dependencies = [ [[package]] name = "core-foundation-sys" -version = "0.8.6" +version = "0.8.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f" +checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b" [[package]] name = "cpufeatures" -version = "0.2.12" +version = "0.2.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "53fe5e26ff1b7aef8bca9c6080520cfb8d9333c7568e1829cef191a9723e5504" +checksum = "16b80225097f2e5ae4e7179dd2266824648f3e2f49d9134d584b76389d31c4c3" dependencies = [ "libc", ] @@ -401,13 +398,13 @@ dependencies = [ [[package]] name = "derive_arbitrary" -version = "1.3.2" +version = "1.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611" +checksum = "30542c1ad912e0e3d22a1935c290e12e8a29d704a420177a31faad4a601a0800" dependencies = [ "proc-macro2", "quote", - "syn 2.0.71", + "syn", ] [[package]] @@ -430,7 +427,7 @@ checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0" dependencies = [ "proc-macro2", "quote", - "syn 2.0.71", + "syn", ] [[package]] @@ -450,9 +447,9 @@ checksum = "1aaf95b3e5c8f23aa320147307562d361db0ae0d51242340f558153b4eb2439b" [[package]] name = "encoding_rs" -version = "0.8.34" +version = "0.8.35" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b45de904aa0b010bce2ab45264d0631681847fa7b6f2eaa7dab7619943bc4f59" +checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3" dependencies = [ "cfg-if", ] @@ -475,15 +472,15 @@ dependencies = [ [[package]] name = "fastrand" -version = "2.1.0" +version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a" +checksum = "486f806e73c5707928240ddc295403b1b93c96a02038563881c4a2fd84b81ac4" [[package]] name = "flate2" -version = "1.0.30" +version = "1.0.35" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae" +checksum = "c936bfdafb507ebbf50b8074c54fa31c5be9a1e7e5f467dd659697041407d07c" dependencies = [ "crc32fast", "miniz_oxide", @@ -521,52 +518,41 @@ dependencies = [ [[package]] name = "futures-channel" -version = "0.3.30" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "eac8f7d7865dcb88bd4373ab671c8cf4508703796caa2b1985a9ca867b3fcb78" +checksum = "2dff15bf788c671c1934e366d07e30c1814a8ef514e1af724a602e8a2fbe1b10" dependencies = [ "futures-core", - "futures-sink", ] [[package]] name = "futures-core" -version = "0.3.30" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dfc6580bb841c5a68e9ef15c77ccc837b40a7504914d52e47b8b0e9bbda25a1d" - -[[package]] -name = "futures-io" -version = "0.3.30" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a44623e20b9681a318efdd71c299b6b222ed6f231972bfe2f224ebad6311f0c1" +checksum = "05f29059c0c2090612e8d742178b0580d2dc940c837851ad723096f87af6663e" [[package]] name = "futures-sink" -version = "0.3.30" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9fb8e00e87438d937621c1c6269e53f536c14d3fbd6a042bb24879e57d474fb5" +checksum = "e575fab7d1e0dcb8d0c7bcf9a63ee213816ab51902e6d244a95819acacf1d4f7" [[package]] name = "futures-task" -version = "0.3.30" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "38d84fa142264698cdce1a9f9172cf383a0c82de1bddcf3092901442c4097004" +checksum = "f90f7dce0722e95104fcb095585910c0977252f286e354b5e3bd38902cd99988" [[package]] name = "futures-util" -version = "0.3.30" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3d6401deb83407ab3da39eba7e33987a73c3df0c82b4bb5813ee871c19c41d48" +checksum = "9fa08315bb612088cc391249efdc3bc77536f16c91f6cf495e6fbe85b20a4a81" dependencies = [ "futures-core", - "futures-io", - "futures-sink", "futures-task", - "memchr", "pin-project-lite", "pin-utils", - "slab", ] [[package]] @@ -594,15 +580,15 @@ dependencies = [ [[package]] name = "gimli" -version = "0.29.0" +version = "0.31.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd" +checksum = "07e28edb80900c19c28f1072f2e8aeca7fa06b23cd4169cefe1af5aa3260783f" [[package]] name = "h2" -version = "0.4.5" +version = "0.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fa82e28a107a8cc405f0839610bdc9b15f1e25ec7d696aa5cf173edbcb1486ab" +checksum = "ccae279728d634d083c00f6099cb58f01cc99c145b84b8be2f6c74618d79922e" dependencies = [ "atomic-waker", "bytes", @@ -623,6 +609,12 @@ version = "0.14.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1" +[[package]] +name = "hashbrown" +version = "0.15.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289" + [[package]] name = "hermit-abi" version = "0.3.9" @@ -689,9 +681,9 @@ dependencies = [ [[package]] name = "httparse" -version = "1.9.4" +version = "1.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0fcc0b4a115bf80b728eb8ea024ad5bd707b615bfed49e0665b6e0f86fd082d9" +checksum = "7d71d3574edd2771538b901e6549113b4006ece66150fb69c0fb6d9a2adae946" [[package]] name = "httpdate" @@ -701,9 +693,9 @@ checksum = "df3b46402a9d5adb4c86a0cf463f42e19994e3ee891101b1841f30a545cb49a9" [[package]] name = "hyper" -version = "1.4.1" +version = "1.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "50dfd22e0e76d0f662d429a5f80fcaf3855009297eab6a0a9f8543834744ba05" +checksum = "97818827ef4f364230e16705d4706e2897df2bb60617d6ca15d598025a3c481f" dependencies = [ "bytes", "futures-channel", @@ 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[[package]] @@ -1493,15 +1497,15 @@ checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" [[package]] name = "regex-syntax" -version = "0.8.4" +version = "0.8.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b" +checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c" [[package]] name = "reqsign" -version = "0.16.0" +version = "0.16.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "03dd4ba7c3901dd43e6b8c7446a760d45bc1ea4301002e1a6fa48f97c3a796fa" +checksum = "eb0075a66c8bfbf4cc8b70dca166e722e1f55a3ea9250ecbb85f4d92a5f64149" dependencies = [ "anyhow", "async-trait", @@ -1531,14 +1535,13 @@ dependencies = [ [[package]] name = "reqwest" -version = "0.12.5" +version = "0.12.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c7d6d2a27d57148378eb5e111173f4276ad26340ecc5c49a4a2152167a2d6a37" 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[[package]] name = "rustls" -version = "0.23.11" +version = "0.23.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4828ea528154ae444e5a642dbb7d5623354030dc9822b83fd9bb79683c7399d0" +checksum = "9c9cc1d47e243d655ace55ed38201c19ae02c148ae56412ab8750e8f0166ab7f" dependencies = [ "once_cell", - "ring", "rustls-pki-types", "rustls-webpki", "subtle", @@ -1700,25 +1691,24 @@ dependencies = [ [[package]] name = "rustls-pemfile" -version = "2.1.2" +version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "29993a25686778eb88d4189742cd713c9bce943bc54251a33509dc63cbacf73d" +checksum = "dce314e5fee3f39953d46bb63bb8a46d40c2f8fb7cc5a3b6cab2bde9721d6e50" dependencies = [ - "base64 0.22.1", "rustls-pki-types", ] [[package]] name = "rustls-pki-types" -version = "1.7.0" +version = "1.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "976295e77ce332211c0d24d92c0e83e50f5c5f046d11082cea19f3df13a3562d" +checksum = "16f1201b3c9a7ee8039bcadc17b7e605e2945b27eee7631788c1bd2b0643674b" [[package]] name = "rustls-webpki" -version = "0.102.5" +version = "0.102.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f9a6fccd794a42c2c105b513a2f62bc3fd8f3ba57a4593677ceb0bd035164d78" +checksum = "64ca1bc8749bd4cf37b5ce386cc146580777b4e8572c7b97baf22c83f444bee9" dependencies = [ "ring", "rustls-pki-types", @@ -1727,9 +1717,9 @@ dependencies = [ [[package]] name = "rustversion" -version = "1.0.17" +version = "1.0.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6" +checksum = "0e819f2bc632f285be6d7cd36e25940d45b2391dd6d9b939e79de557f7014248" [[package]] name = "ryu" @@ -1757,11 +1747,11 @@ dependencies = [ [[package]] name = "schannel" -version = "0.1.23" +version = "0.1.27" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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-1847,9 +1838,9 @@ dependencies = [ [[package]] name = "serde_spanned" -version = "0.6.6" +version = "0.6.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "79e674e01f999af37c49f70a6ede167a8a60b2503e56c5599532a65baa5969a0" +checksum = "87607cb1398ed59d48732e575a4c28a7a8ebf2454b964fe3f224f2afc07909e1" dependencies = [ "serde", ] @@ -1897,6 +1888,12 @@ dependencies = [ "lazy_static", ] +[[package]] +name = "shlex" +version = "1.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64" + [[package]] name = "signal-hook-registry" version = "1.4.2" @@ -1916,6 +1913,12 @@ dependencies = [ "rand_core", ] +[[package]] +name = "simd-adler32" +version = "0.3.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d66dc143e6b11c1eddc06d5c423cfc97062865baf299914ab64caa38182078fe" + [[package]] name = "simple_asn1" version = "0.6.2" @@ -1924,7 +1927,7 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+reqsign = "0.16.1" +reqwest = { version = "0.12.9", features = ["json"] } +serde = { version = "1.0.214", features = ["derive"] } +serde_json = "1.0.133" +tokio = { version = "1.41.1", features = ["full"] } +tower-http = { version = "0.6.2", features = ["cors", "trace"] } tracing = "0.1.40" -tracing-subscriber = { version = "0.3.18", features = ["env-filter", "fmt"]} -url = "2.5.2" -utoipa = { version = "4.2.3", features = ["uuid", "chrono"]} -utoipa-swagger-ui = { version = "7.1.0", features = ["axum"] } -uuid = { version = "1.10.0", features = ["v4", "serde"] } +tracing-subscriber = { version = "0.3.18", features = ["env-filter", "fmt"] } +url = "2.5.4" +utoipa = { version = "5.2.0", features = ["uuid", "chrono"] } +utoipa-swagger-ui = { version = "8.0.3", features = ["axum"] } +uuid = { version = "1.11.0", features = ["v4", "serde"] } diff --git a/src/api_paths.rs b/src/api_paths.rs index 2f6b7bd..8ce1835 100644 --- a/src/api_paths.rs +++ b/src/api_paths.rs @@ -8,7 +8,10 @@ use axum::{ use reqwest::StatusCode; use crate::{ - api_structs::{InitRequest, InitResponse, Job, ListRequest, StartRequest}, + api_structs::{ + InitRequest, InitResponse, Job, ListRequest, ListResponse, ResultResponse, StartRequest, + VersionResponse, + }, bakta_handler::BaktaHandler, }; diff --git a/src/api_structs.rs b/src/api_structs.rs index eb110c8..a6fd159 100644 --- a/src/api_structs.rs +++ b/src/api_structs.rs @@ -9,6 +9,7 @@ use uuid::Uuid; #[derive(OpenApi)] #[openapi( + info(title = "Bakta Web API"), paths(delete_job, init_job, list_jobs, query_result, start_job, version), components(schemas( Job,