stockcenter

var GenoCmd = &cobra.Command{
	Use:   "genotype",
	Short: "load stockcenter genotype data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadGeno,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(viper.GetString("genotype-input"), regsc.GenoReader); err != nil {
			return err
		}
		return nil
	},
}

var GwdiCmd = &cobra.Command{
	Use:   "gwdi",
	Short: "load gwdi strains",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadGwdi,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetStockAPIClient(); err != nil {
			return err
		}
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(viper.GetString("gwdi-input"), regsc.GwdiReader); err != nil {
			return err
		}
		return nil
	},
}

var OrderCmd = &cobra.Command{
	Use:     "order",
	Short:   "load stockcenter order data",
	Args:    cobra.NoArgs,
	RunE:    loader.LoadOrder,
	PreRunE: setOrderPreRun,
}

var PhenoCmd = &cobra.Command{
	Use:   "phenotype",
	Short: "load stockcenter phenotype data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadPheno,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(viper.GetString("phenotype-input"), regsc.PhenoReader); err != nil {
			return err
		}
		return nil
	},
}

var PlasmidCmd = &cobra.Command{
	Use:     "plasmid",
	Short:   "load stockcenter plasmid data",
	Args:    cobra.NoArgs,
	RunE:    loader.LoadPlasmid,
	PreRunE: setPlasmidPreRun,
}

var PlasmidInvCmd = &cobra.Command{
	Use:   "plasmid-inventory",
	Short: "load plasmid inventory data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadPlasmidInv,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(
			viper.GetString("plasmid-inventory-input"),
			regsc.InvReader,
		); err != nil {
			return err
		}
		return nil
	},
}

var ReadFileCmd = &cobra.Command{
	Use:     "readfile",
	Short:   "read data from any file",
	Args:    cobra.NoArgs,
	RunE:    LoadReadFile,
	PreRunE: setReadFilePreRun,
}

var StockCenterCmd = &cobra.Command{
	Use:   "stockcenter",
	Short: "subcommand for stockcenter data loading",
}

var StrainCharCmd = &cobra.Command{
	Use:   "strainchar",
	Short: "load stockcenter strain characteristics data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadStrainChar,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(
			viper.GetString("strainchar-input"),
			regsc.StraincharReader,
		); err != nil {
			return err
		}
		return nil
	},
}

var StrainCmd = &cobra.Command{
	Use:     "strain",
	Short:   "load stockcenter strain data",
	Args:    cobra.NoArgs,
	RunE:    loader.LoadStrain,
	PreRunE: setStrainPreRun,
}

var StrainInvCmd = &cobra.Command{
	Use:   "strain-inventory",
	Short: "load strain inventory data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadStrainInv,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(
			viper.GetString("strain-inventory-input"),
			regsc.InvReader,
		); err != nil {
			return err
		}
		return nil
	},
}

var StrainPropCmd = &cobra.Command{
	Use:   "strainprop",
	Short: "load stockcenter strain properties data",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadStrainProp,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(
			viper.GetString("strainprop-input"),
			regsc.StrainpropReader,
		); err != nil {
			return err
		}
		return nil
	},
}

var StrainSynCmd = &cobra.Command{
	Use:   "strainsyn",
	Short: "load stockcenter strain synonyms",
	Args:  cobra.NoArgs,
	RunE:  loader.LoadStrainSynProp,
	PreRunE: func(_ *cobra.Command, _ []string) error {
		if err := SetAnnoAPIClient(); err != nil {
			return err
		}
		if err := setReader(viper.GetString("strainsyn-input"), regsc.StrainSynReader); err != nil {
			return err
		}
		return nil
	},
}