database

Documentation

Index

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

Types

type BackendType

type BackendType string

BackendType The type of the database backend to use

const (
	//SQLite Use an sqlite database in the backend
	SQLite BackendType = "SQLite"
	//Postgres User a postgres database in the backend
	Postgres BackendType = "Postgres"
	//Mysql Use a myswql database in the backend
	Mysql BackendType = "MySQl"
)

type Handler

type Handler struct {
	DB             *gorm.DB
	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) (*Job, string, error)

CreateJob Creates a new bakta job in init mode

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) GetJobsStatus

func (handler *Handler) GetJobsStatus(jobIDs []string) ([]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, conf 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 `gorm:"primaryKey"`
	Secret      string
	K8sID       string `gorm:"index"`
	Updated     int64  `gorm:"autoUpdateTime"` // Use unix milli seconds as updating time
	Created     int64  `gorm:"autoCreateTime"` // Use unix seconds as creating time
	Status      string `gorm:"index"`
	DataBucket  string
	FastaKey    string
	ProdigalKey string
	RepliconKey string
	ResultKey   string
	Error       string
	ExpiryDate  time.Time
	ConfString  string
	IsDeleted   bool
}

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"
)