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service

package
v0.2.1 Latest Latest
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 Go to latest Published: Oct 20, 2026 License: BSD-2-Clause Imports: 46 Imported by: 0

Documentation

Overview

Package service implements the gRPC service handlers for the annotation service.

Index

Constants

This section is empty.

Variables

View Source 
var LIMIT int64 = 10

LIMIT is the default number of results returned by list operations.

Functions

This section is empty.

Types

type AnnotationService 

type AnnotationService struct {
	*aphgrpc.Service

	annotation.UnimplementedTaggedAnnotationServiceServer
	// contains filtered or unexported fields
}

AnnotationService is the container for managing annotation service definition.

func NewAnnotationService 

func NewAnnotationService(srvP *Params) (*AnnotationService, error)

NewAnnotationService is the constructor for creating a new instance of AnnotationService. The whole construction is one Either pipeline forced once, at the boundary.

func (*AnnotationService) AddToAnnotationGroup 

func (srv *AnnotationService) AddToAnnotationGroup(
	ctx context.Context, rta *annotation.AnnotationGroupId,
) (*annotation.TaggedAnnotationGroup, error)

AddToAnnotationGroup appends an annotation to an existing annotation group.

func (*AnnotationService) AutocompleteAnnotation added in v0.2.0 

func (srv *AnnotationService) AutocompleteAnnotation(
	ctx context.Context,
	r *annotation.AnnotationAutocompleteParameters,
) (*annotation.AnnotationSuggestionCollection, error)

AutocompleteAnnotation returns annotation suggestions for a partial strain synonym or genotype value. Guards are pure Either, the repository call is the only effect, and the whole program is forced once at the boundary.

func (*AnnotationService) CreateAnnotation 

func (srv *AnnotationService) CreateAnnotation(
	ctx context.Context,
	rta *annotation.NewTaggedAnnotation,
) (*annotation.TaggedAnnotation, error)

CreateAnnotation creates a new tagged annotation.

func (*AnnotationService) CreateAnnotationGroup 

func (srv *AnnotationService) CreateAnnotationGroup(
	ctx context.Context, rta *annotation.AnnotationIdList,
) (*annotation.TaggedAnnotationGroup, error)

CreateAnnotationGroup creates a new annotation group from a list of annotation IDs.

func (*AnnotationService) DeleteAnnotation 

func (srv *AnnotationService) DeleteAnnotation(ctx context.Context, r *annotation.DeleteAnnotationRequest) (*empty.Empty, error)

DeleteAnnotation removes a tagged annotation by its ID.

func (*AnnotationService) DeleteAnnotationGroup 

func (srv *AnnotationService) DeleteAnnotationGroup(ctx context.Context, r *annotation.GroupEntryId) (*empty.Empty, error)

DeleteAnnotationGroup removes an annotation group identified by its group ID.

func (*AnnotationService) GetAnnotation 

func (srv *AnnotationService) GetAnnotation(
	ctx context.Context,
	req *annotation.AnnotationId,
) (*annotation.TaggedAnnotation, error)

GetAnnotation retrieves a tagged annotation by its ID.

func (*AnnotationService) GetAnnotationGroup 

func (srv *AnnotationService) GetAnnotationGroup(
	ctx context.Context, rid *annotation.GroupEntryId,
) (*annotation.TaggedAnnotationGroup, error)

GetAnnotationGroup retrieves a tagged annotation group by its group ID.

func (*AnnotationService) GetAnnotationTag 

func (srv *AnnotationService) GetAnnotationTag(
	ctx context.Context, rta *annotation.TagRequest,
) (*annotation.AnnotationTag, error)

GetAnnotationTag retrieves an annotation tag by name and ontology.

func (*AnnotationService) GetEntryAnnotation 

func (srv *AnnotationService) GetEntryAnnotation(
	ctx context.Context, rea *annotation.EntryAnnotationRequest,
) (*annotation.TaggedAnnotation, error)

GetEntryAnnotation retrieves a tagged annotation by entry annotation request parameters.

func (*AnnotationService) GetGroupResourceName 

func (srv *AnnotationService) GetGroupResourceName() string

GetGroupResourceName returns the resource name used for annotation groups.

func (*AnnotationService) ListAnnotationGroups 

func (srv *AnnotationService) ListAnnotationGroups(
	ctx context.Context, rgp *annotation.ListGroupParameters,
) (*annotation.TaggedAnnotationGroupCollection, error)

ListAnnotationGroups returns a paginated collection of tagged annotation groups.

func (*AnnotationService) ListAnnotations 

func (srv *AnnotationService) ListAnnotations(
	ctx context.Context, ral *annotation.ListParameters,
) (*annotation.TaggedAnnotationCollection, error)

ListAnnotations returns a paginated collection of tagged annotations.

func (*AnnotationService) OboJSONFileUpload 

func (srv *AnnotationService) OboJSONFileUpload(
	stream annotation.TaggedAnnotationService_OboJSONFileUploadServer,
) error

OboJSONFileUpload uploads a obojson formatted file to the server.

func (*AnnotationService) SearchAnnotation added in v0.2.0 

func (srv *AnnotationService) SearchAnnotation(
	ctx context.Context,
	r *annotation.AnnotationSearchParameters,
) (*annotation.AnnotationSearchResultCollection, error)

SearchAnnotation returns at most 50 ranked strain annotation matches for a search query of at least 2 normalized characters.

func (*AnnotationService) UpdateAnnotation 

func (srv *AnnotationService) UpdateAnnotation(
	ctx context.Context,
	rta *annotation.TaggedAnnotationUpdate,
) (*annotation.TaggedAnnotation, error)

UpdateAnnotation updates an existing tagged annotation.

type FeatureAnnotationService 

type FeatureAnnotationService struct {
	*aphgrpc.Service

	feature.UnimplementedFeatureAnnotationServiceServer
	// contains filtered or unexported fields
}

FeatureAnnotationService implements the gRPC FeatureAnnotationService server.

func NewFeatureAnnotationService 

func NewFeatureAnnotationService(
	params *FeatureParams,
) (*FeatureAnnotationService, error)

NewFeatureAnnotationService creates a new FeatureAnnotationService from the given parameters.

func (*FeatureAnnotationService) AddTag 

func (srv *FeatureAnnotationService) AddTag(
	ctx context.Context,
	req *feature.AddTagRequest,
) (*feature.FeatureAnnotation, error)

AddTag adds a single tag to the specified feature annotation.

func (*FeatureAnnotationService) AddTags 

func (srv *FeatureAnnotationService) AddTags(
	ctx context.Context,
	req *feature.AddTagsRequest,
) (*feature.FeatureAnnotation, error)

AddTags adds multiple tags to the specified feature annotation.

func (*FeatureAnnotationService) CreateFeatureAnnotation 

func (srv *FeatureAnnotationService) CreateFeatureAnnotation(
	ctx context.Context,
	req *feature.NewFeatureAnnotation,
) (*feature.FeatureAnnotation, error)

CreateFeatureAnnotation creates a new feature annotation from the provided request.

func (*FeatureAnnotationService) DeleteFeatureAnnotation 

func (srv *FeatureAnnotationService) DeleteFeatureAnnotation(
	ctx context.Context,
	req *feature.DeleteFeatureAnnotationRequest,
) (*emptypb.Empty, error)

DeleteFeatureAnnotation removes a feature annotation by its ID.

func (*FeatureAnnotationService) GetFeatureAnnotation 

func (srv *FeatureAnnotationService) GetFeatureAnnotation(
	ctx context.Context,
	req *feature.FeatureAnnotationId,
) (*feature.FeatureAnnotation, error)

GetFeatureAnnotation retrieves a feature annotation by its ID.

func (*FeatureAnnotationService) GetFeatureAnnotationByName 

func (srv *FeatureAnnotationService) GetFeatureAnnotationByName(
	ctx context.Context,
	req *feature.FeatureName,
) (*feature.FeatureAnnotation, error)

GetFeatureAnnotationByName retrieves a feature annotation by its name.

func (*FeatureAnnotationService) ListFeatureAnnotationsByDOI 

func (srv *FeatureAnnotationService) ListFeatureAnnotationsByDOI(
	ctx context.Context,
	req *feature.DOI,
) (*feature.FeatureAnnotationCollection, error)

ListFeatureAnnotationsByDOI lists all feature annotations associated with a DOI.

func (*FeatureAnnotationService) ListFeatureAnnotationsByPubmedId 

func (srv *FeatureAnnotationService) ListFeatureAnnotationsByPubmedId(
	ctx context.Context,
	req *feature.PubmedId,
) (*feature.FeatureAnnotationCollection, error)

ListFeatureAnnotationsByPubmedId lists all feature annotations associated with a PubMed ID.

func (*FeatureAnnotationService) RemoveTags 

func (srv *FeatureAnnotationService) RemoveTags(
	ctx context.Context,
	req *feature.RemoveTagsRequest,
) (*feature.FeatureAnnotation, error)

RemoveTags removes specified tags from a feature annotation.

func (*FeatureAnnotationService) SetTags 

func (srv *FeatureAnnotationService) SetTags(
	ctx context.Context,
	req *feature.SetTagsRequest,
) (*feature.FeatureAnnotation, error)

SetTags replaces all tags on the specified feature annotation.

func (*FeatureAnnotationService) UpdateFeatureAnnotation 

func (srv *FeatureAnnotationService) UpdateFeatureAnnotation(
	ctx context.Context,
	req *feature.FeatureAnnotationUpdate,
) (*feature.FeatureAnnotation, error)

UpdateFeatureAnnotation updates an existing feature annotation.

type FeatureParams 

type FeatureParams struct {
	Repository repository.FeatureAnnotationRepository `validate:"required"`
	Publisher  message.FeatureAnnotationPublisher     `validate:"required"`
	Options    []aphgrpc.Option
}

FeatureParams holds the required parameters for creating a FeatureAnnotationService.

type MockMessage 

type MockMessage struct{}

MockMessage is a no-op message publisher used in tests.

func (*MockMessage) Close 

func (msn *MockMessage) Close() error

Close implements the Publisher interface as a no-op.

func (*MockMessage) Publish 

func (msn *MockMessage) Publish(
	_ string,
	_ *feature.FeatureAnnotation,
) error

Publish implements the Publisher interface as a no-op.

type Params 

type Params struct {
	Repository repository.TaggedAnnotationRepository `validate:"required"`
	Publisher  message.Publisher                     `validate:"required"`
	Options    []aphgrpc.Option                      `validate:"required"`
	Group      string                                `validate:"required"`
}

Params are the attributes that are required for creating a new AnnotationService.

Source Files

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