repository

type AnnoGroupListNotFoundError struct{}

type AnnoListNotFoundError struct{}

type AnnoNotFoundError struct {
	ID string
}

type AnnoTagNotFoundError struct {
	Tag string
}

type AutocompleteQuery struct {
	// Query is the partial search text. The caller sends it untrimmed;
	// the repository trims it, lowercases it, and strips combining marks.
	Query string
	// Limit is the maximum number of suggestions. A value at or below 0
	// becomes 5. A value above 50 becomes 50.
	Limit int
}

type FeatureAnnotationRepository interface {
	// GetFeatureAnnotation retrieves a feature annotation by ID
	GetFeatureAnnotation(id string) (*model.FeatureAnnotationDoc, error)
	// GetFeatureAnnotationByName retrieves a feature annotation by name
	GetFeatureAnnotationByName(name string) (*model.FeatureAnnotationDoc, error)
	// AddFeatureAnnotation creates a new feature annotation
	AddFeatureAnnotation(
		doc *feature.NewFeatureAnnotation,
	) (*model.FeatureAnnotationDoc, error)
	// EditFeatureAnnotation updates an existing feature annotation
	EditFeatureAnnotation(
		doc *feature.FeatureAnnotationUpdate,
	) (*model.FeatureAnnotationDoc, error)
	// RemoveFeatureAnnotation deletes a feature annotation
	RemoveFeatureAnnotation(id string, purge bool) error
	// ClearFeatureAnnotations removes all feature annotations
	ClearFeatureAnnotations() error
	// Dbh returns the underlying database handler
	Dbh() *manager.Database
	// Tag management methods
	// AddTag adds a single tag to an existing feature annotation
	AddTag(req *feature.AddTagRequest) (*model.FeatureAnnotationDoc, error)
	// AddTags adds multiple tags to an existing feature annotation
	AddTags(req *feature.AddTagsRequest) (*model.FeatureAnnotationDoc, error)
	// SetTags replaces all tags for a feature annotation with the provided set
	SetTags(req *feature.SetTagsRequest) (*model.FeatureAnnotationDoc, error)
	// RemoveTags removes tags from a feature annotation by tag and value
	RemoveTags(req *feature.RemoveTagsRequest) (*model.FeatureAnnotationDoc, error)

	// Publication-based queries
	// ListByPublicationID retrieves all feature annotations associated with the given publication ID and source
	ListByPublicationID(id string, source string) ([]*model.FeatureAnnotationDoc, error)
}

type FeatureNameNotFoundError struct {
	Name string
}

type FullSearchQuery struct {
	// Query is the search text. The caller sends it untrimmed;
	// the repository trims it, lowercases it, and strips combining marks.
	Query string
	// Limit is the maximum number of results. A value at or below 0
	// becomes 50. A value above 50 becomes 50.
	Limit int
}

type FullSearchResult struct {
	// EntryID is the strain identifier of the matched annotation, for
	// example DBS0236126.
	EntryID string
	// Field is the canonical field label that matched (for example,
	// "synonym", "genotype", "phenotype", or "public_note").
	Field string
	// DisplayText is the stored annotation value or cvterm label shown
	// in the user interface.
	DisplayText string
	// Score ranks the match across the four bands (prefix >= 1000,
	// phrase >= 500, token >= 250, fuzzy >= 0).
	Score float64
}

type GroupNotFoundError struct {
	ID string
}

type ListAnnotationsParams struct {
	Cursor int64
	Limit  int64  `validate:"required"`
	Filter string `validate:"required"`
}

type ListNotFoundError struct{}

type OrganismNotFoundError struct {
	ID string
}

type OrganismRepository interface {
	// GetOrganism retrieves an organism by ID
	GetOrganism(id string) (*model.OrganismDoc, error)
	// GetOrganismByName retrieves an organism by scientific name (genus + species)
	GetOrganismByName(genus, species string) (*model.OrganismDoc, error)
	// AddOrganism creates a new organism
	AddOrganism(doc *organism.NewOrganism) (*model.OrganismDoc, error)
	// EditOrganism updates an existing organism
	EditOrganism(doc *organism.OrganismUpdate) (*model.OrganismDoc, error)
	// RemoveOrganism deletes an organism
	RemoveOrganism(id string) error
	// ListOrganisms provides a paginated list of organisms along with optional filtering
	ListOrganisms() ([]*model.OrganismDoc, error)
	// ClearOrganisms removes all organisms
	ClearOrganisms() error
	// Dbh returns the underlying database handler
	Dbh() *manager.Database
}

type PublicationAnnotationNotFoundError struct {
	ID     string
	Source string
}

type Suggestion struct {
	// EntryID is the strain identifier of the matched annotation, for
	// example DBS0236126.
	EntryID string
	// Field is the tag label that matched: "synonym" or "genotype".
	Field string
	// DisplayText is the stored annotation value shown in the user interface.
	DisplayText string
	// Score ranks the match. A prefix match scores above a fuzzy match.
	Score float64
}

type TaggedAnnotationRepository interface {
	// GetAnnotationById retrieves an annotation
	GetAnnotationByID(id string) (*model.AnnoDoc, error)
	GetAnnotationByEntry(
		req *annotation.EntryAnnotationRequest,
	) (*model.AnnoDoc, error)
	AddAnnotation(na *annotation.NewTaggedAnnotation) (*model.AnnoDoc, error)
	EditAnnotation(
		ua *annotation.TaggedAnnotationUpdate,
	) (*model.AnnoDoc, error)
	RemoveAnnotation(id string, purge bool) error
	// ListAnnotationGroup provides a paginated list of annotation along
	// with optional filtering
	ListAnnotations(ctx context.Context, params *ListAnnotationsParams) ([]*model.AnnoDoc, error)
	ClearAnnotations() error
	Clear() error
	// AddAnnotationGroup creates a new annotation group
	AddAnnotationGroup(idslice ...string) (*model.AnnoGroup, error)
	// GetAnnotationGroup retrieves an annotation group
	GetAnnotationGroup(groupID string) (*model.AnnoGroup, error)
	// AppendToAnnotationGroup adds new annotations to an existing group
	AppendToAnnotationGroup(
		groupID string,
		idslice ...string,
	) (*model.AnnoGroup, error)
	// DeleteAnnotationGroup deletes an annotation group
	RemoveAnnotationGroup(groupID string) error
	// RemoveFromAnnotationGroup remove annotations from an existing group
	RemoveFromAnnotationGroup(
		groupID string,
		idslice ...string,
	) (*model.AnnoGroup, error)
	// ListAnnotationGroup provides a paginated list of annotation groups along
	// with optional filtering
	ListAnnotationGroup(
		ctx context.Context,
		cursor, limit int64,
		filter string,
	) ([]*model.AnnoGroup, error)
	// GetAnnotationTag retrieves tag information
	GetAnnotationTag(name, ontology string) (*model.AnnoTag, error)
	// AutocompleteAnnotation returns at most Limit short suggestions for
	// the normalized query of params as a lazy IOEither pipeline.
	AutocompleteAnnotation(
		ctx context.Context,
		params *AutocompleteQuery,
	) IOE.IOEither[error, []*Suggestion]
	// SearchAnnotation returns at most Limit ranked results for the
	// normalized query of params as a lazy IOEither pipeline.
	SearchAnnotation(
		ctx context.Context,
		params *FullSearchQuery,
	) IOE.IOEither[error, []*FullSearchResult]
	Dbh() *manager.Database
	LoadOboJSON(r io.Reader) (*storage.UploadInformation, error)
}