stockcenter

type AnnotationContext struct {
	Client    pb.TaggedAnnotationServiceClient
	PlasmidID string
	Tag       string
	Value     string
}

type DBBuildContext struct {
	Reader            io.ReadCloser
	GoldenBraidReader io.ReadCloser
	Context           context.Context
	Builder           *filesql.DBBuilder
}

type Deps struct {
	StockClient      stock.StockServiceClient
	AnnotationClient pb.TaggedAnnotationServiceClient
	Logger           *slog.Logger
}

type GoldenBraidProcessingResult struct {
	CreatedCount int      // New plasmids created
	SkippedCount int      // Existing plasmids skipped (already exist)
	Successes    []string // All plasmid IDs (created + skipped)
	Errors       []error
	ErrorCount   int
}

type GoldenBraidResult struct {
	PlasmidID string
	Created   bool // true=created, false=skipped
	Error     error
}

type InventoryLoaderConfig struct {
	DB                *sql.DB
	Reader            io.ReadCloser
	GoldenBraidReader io.ReadCloser
	Logger            *slog.Logger
	Cmd               *cli.Context
}

type InventoryLoaderIOE = IOE.IOEither[error, InventoryLoaderConfig]

type InventoryProcessingSummary struct {
	SuccessCount  int
	ErrorCount    int
	ExpectedCount int
	Errors        []string
}

type LoaderConfig struct {
	LoaderContext
	Cmd     *cli.Context
	Reader  *csv.Reader
	Closer  io.Closer
	Slogger *slog.Logger
}

type LoaderContext struct{}

type LookupContext struct{}

type LookupTuple struct {
	Annotator  source.StockAnnotatorLookup
	PubLookup  source.StockPubLookup
	GeneLookup source.StockGeneLookup
}

type OntologyUpdateStats struct {
	ProcessedCount int       `json:"processed_count"` // Total plasmids examined
	UpdatedCount   int       `json:"updated_count"`   // Successfully updated
	ErrorCount     int       `json:"error_count"`     // Failed updates
	Errors         []error   `json:"-"`               // Error samples (first 5)
	StartTime      time.Time `json:"start_time"`
	EndTime        time.Time `json:"end_time"`
}

type PipelineContext struct {
	Deps             Deps
	PlasmidName      string
	Location         string
	PlasmidID        string
	Inventory        *pb.TaggedAnnotationGroupCollection
	InventoryDeleted bool
	AnnotationIDs    []string
	GroupCreated     bool
}

type PlasmidEnv struct {
	Logger    *logrus.Entry
	APIClient pb.StockServiceClient
}

type ProcessContext struct {
	Client  stockpb.StockServiceClient
	Term    string
	Plasmid *stockpb.PlasmidCollection_Data
}

type Processing[A any] = RE.ReaderIOEither[Deps, error, A]

type ProcessingResult struct {
	Successes  []string // Successfully processed plasmid IDs
	Errors     error    // All validation/processing errors
	ErrorCount int      // Number of errors (for accurate statistics)
}

type Status int

type UpdateContext struct {
	Client  stockpb.StockServiceClient
	Term    string
	Plasmid *stockpb.Plasmid
}

type WithAnnotator struct {
	LookupContext
	Annotator source.StockAnnotatorLookup
}

type WithGeneLookup struct {
	WithPubLookup
	GeneLookup source.StockGeneLookup
}

type WithPubLookup struct {
	WithAnnotator
	PubLookup source.StockPubLookup
}