database

Documentation

Index

• Constants
• type BackendType
• type Handler
  • func InitDatabaseHandler() (*Handler, error)
  • func (handler *Handler) CheckSecret(id string, secretKey string) error
  • func (handler *Handler) CreateJob(repliconTypeAPI api.RepliconTableType, jobname string) (*Job, string, error)
  • func (handler *Handler) DeleteJob(id string) error
  • func (handler *Handler) GetJob(id string) (*Job, error)
  • func (handler *Handler) GetJobStatus(jobID string) (*Job, error)
  • func (handler *Handler) GetJobs(jobIDs []*api.JobAuth) ([]Job, error)
  • func (handler *Handler) GetRunningJobs() ([]*Job, error)
  • func (handler *Handler) UpdateK8s(id string, k8s string) error
  • func (handler *Handler) UpdateStatus(id string, status api.JobStatusEnum, errorMsg string, isDeleted bool) error
• type Job
• type UploadFileType

Constants

const COLLECTIONNAME = "jobs"

const RESULTFILENAME = "results.tar.gz"

Types

type BackendType

type BackendType string

BackendType The type of the database backend to use

type Handler

type Handler struct {
	DB             *mongo.Client
	Collection     *mongo.Collection
	BaseKey        string
	UserDataBucket string
	DBBucket       string
	ExpiryTime     int64
}

Handler Wraps the database with convinence methods

func InitDatabaseHandler

func InitDatabaseHandler() (*Handler, error)

InitDatabaseHandler Initializes the database to store the Job

func (*Handler) CheckSecret

func (handler *Handler) CheckSecret(id string, secretKey string) error

CheckSecret Compares the provided secret/JobID with a job in the database

func (*Handler) CreateJob

func (handler *Handler) CreateJob(repliconTypeAPI api.RepliconTableType, jobname string) (*Job, string, error)

CreateJob Creates a new bakta job in init mode

func (*Handler) DeleteJob

func (handler *Handler) DeleteJob(id string) error

func (*Handler) GetJob

func (handler *Handler) GetJob(id string) (*Job, error)

GetJob Returns the stored config of a job

func (*Handler) GetJobStatus

func (handler *Handler) GetJobStatus(jobID string) (*Job, error)

GetJobStatus Returns the status of an individual job

func (*Handler) GetJobs

func (handler *Handler) GetJobs(jobIDs []*api.JobAuth) ([]Job, error)

GetJobsStatus Returns the status of a list of jobs

func (*Handler) GetRunningJobs

func (handler *Handler) GetRunningJobs() ([]*Job, error)

func (*Handler) UpdateK8s

func (handler *Handler) UpdateK8s(id string, k8s string) error

UpdateK8s Updates a job with its k8s id

func (*Handler) UpdateStatus

func (handler *Handler) UpdateStatus(id string, status api.JobStatusEnum, errorMsg string, isDeleted bool) error

UpdateStatus Updates the status of a job

type 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
}

Job The database model for a bakta job

type UploadFileType

type UploadFileType string

UploadFileType type of file to upload

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"
)