annotation

type AnnotationGroupId struct {

	// unique identifier for the annotation
	Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
	// unique identifier of a group
	GroupId string `protobuf:"bytes,2,opt,name=group_id,json=groupId,proto3" json:"group_id,omitempty"`
	// contains filtered or unexported fields
}

type AnnotationId struct {

	// unique identifier for the annotation
	Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
	// contains filtered or unexported fields
}

type AnnotationIdList struct {

	// list of unique identifiers
	Ids []string `protobuf:"bytes,1,rep,name=ids,proto3" json:"ids,omitempty"`
	// contains filtered or unexported fields
}

type AnnotationTag struct {

	// tag identifier
	Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
	// human readable name
	Name string `protobuf:"bytes,2,opt,name=name,proto3" json:"name,omitempty"`
	// ontology to which this tag belong
	Ontology string `protobuf:"bytes,3,opt,name=ontology,proto3" json:"ontology,omitempty"`
	// status for active or retired tag
	IsObsolete bool `protobuf:"varint,4,opt,name=is_obsolete,json=isObsolete,proto3" json:"is_obsolete,omitempty"`
	// contains filtered or unexported fields
}

type DeleteAnnotationRequest struct {

	// unique identifier for the annotation
	Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
	// flag to indicate whether the entry will be wiped or turned obsolete(soft delete)
	Purge bool `protobuf:"varint,2,opt,name=purge,proto3" json:"purge,omitempty"`
	// contains filtered or unexported fields
}

type EntryAnnotationRequest struct {

	// An identifiable tagname for the annotation, primarily
	// a structured tag, generally an ontology term.
	Tag string `protobuf:"bytes,1,opt,name=tag,proto3" json:"tag,omitempty"`
	// unique identifier of a biological entity that is being annotated
	EntryId string `protobuf:"bytes,2,opt,name=entry_id,json=entryId,proto3" json:"entry_id,omitempty"`
	// Name of ontology in which the tag name is taken
	Ontology string `protobuf:"bytes,3,opt,name=ontology,proto3" json:"ontology,omitempty"`
	// Ordering of annotation when an entry has multiple annotations with
	// identical tag from the same ontology. By default, rank 0 is assumed.
	Rank int64 `protobuf:"varint,4,opt,name=rank,proto3" json:"rank,omitempty"`
	// Status for active or retired annotation. Active annotation is chosen by default.
	IsObsolete bool `protobuf:"varint,5,opt,name=is_obsolete,json=isObsolete,proto3" json:"is_obsolete,omitempty"`
	// contains filtered or unexported fields
}

type GroupEntryId struct {

	// unique identifier of a group
	GroupId string `protobuf:"bytes,1,opt,name=group_id,json=groupId,proto3" json:"group_id,omitempty"`
	// contains filtered or unexported fields
}

type ListGroupParameters struct {

	// A unique pointer to the next set of result in the list
	Cursor int64 `protobuf:"varint,1,opt,name=cursor,proto3" json:"cursor,omitempty"`
	// Maximum number of records that can be fetch per request
	Limit int64 `protobuf:"varint,2,opt,name=limit,proto3" json:"limit,omitempty"`
	// The `filter` field restricts the data return by the collection. To use
	// it, supply one or multiple allowed fields to filter followed
	// by a filter expression. It uses the following syntax...
	//
	//	field_name operator expression
	//
	// The following fields of `AnnotationAttributes` definition are allowed to
	// be used for filtering
	//   - entry_id    - The entry that is being annotated (string)
	//   - created_by  - Email id of the user (string)
	//   - tag         - Tag name, a term from an ontology (string).
	//   - ontology    - Ontology that provides the tag names (string).
	//   - rank        - Ordering of annotation (number).
	//
	// operator - Defines the type of filter match to use. It could be any of
	// the following four and all of them should be URL-encoded for http request.
	//
	//	Operators for strings
	//	      =~    Contains substring
	//	      !~   Not contains substring
	//	      ===  Equals
	//	      !==  Not equals
	//
	//	Operators for numbers
	//	      ==  Equals
	//	      !=  Not equals
	//	      >   Greater than
	//	      <   Less than
	//	      =<  Less than equal to
	//	      >=  Greater than equal to
	//
	// expression - The value that will be included or excluded from the
	// result. URL-reserved characters must be URL-encoded for http request.
	//
	//	filter: "created_by==caboose@abc.com"
	//	filter: "entry_id==DDB_G4839483"
	//	filter: "tag==growth"
	//
	// Filter can be combined using OR or AND boolean logic.
	//
	//   - The OR is represented using a comma(,).
	//
	//   - The AND is represented using a semi-colon(;).
	//
	//   - AND and OR operators can be combined and AND takes precedence over OR.
	//
	//     filter: "tag~cytoskeletion;entry_id==DDB_G4839783;ontology==cellular"
	//     filter: "tag~membrane;entry_id==DDB_G4839783;ontology==cellular;rank=0"
	Filter string `protobuf:"bytes,3,opt,name=filter,proto3" json:"filter,omitempty"`
	// contains filtered or unexported fields
}

type ListParameters struct {

	// A unique pointer to the next set of result in the list
	Cursor int64 `protobuf:"varint,1,opt,name=cursor,proto3" json:"cursor,omitempty"`
	// Maximum number of records that can be fetch per request
	Limit int64 `protobuf:"varint,2,opt,name=limit,proto3" json:"limit,omitempty"`
	// The `filter` field restricts the data return by the collection. To use
	// it, supply one or multiple allowed fields to filter followed
	// by a filter expression. It uses the following syntax...
	//
	//	field_name operator expression
	//
	// The following fields of `AnnotationAttributes` definition are allowed to
	// be used for filtering
	//   - entry_id    - The entry that is being annotated (string)
	//   - value       - The annotation in plain text format (string)
	//   - created_by  - Email id of the user (string)
	//   - tag         - Tag name, a term from an ontology (string).
	//   - ontology    - Ontology that provides the tag names (string).
	//   - version     - Version no (number).
	//   - value       - annotation in plain text format (number).
	//
	// operator - Defines the type of filter match to use. It could be any of
	// the following four and all of them should be URL-encoded for http request.
	//
	//	Operators for strings
	//	      =~    Contains substring
	//	      !~   Not contains substring
	//	      ===  Equals
	//	      !==  Not equals
	//
	//	Operators for numbers
	//	      ==  Equals
	//	      !=  Not equals
	//	      >   Greater than
	//	      <   Less than
	//	      =<  Less than equal to
	//	      >=  Greater than equal to
	//
	// expression - The value that will be included or excluded from the
	// result. URL-reserved characters must be URL-encoded for http request.
	//
	//	filter: "created_by==caboose@abc.com"
	//	filter: "entry_id==DDB_G4839483"
	//	filter: "value~actin"
	//
	// Filter can be combined using OR or AND boolean logic.
	//
	//   - The OR is represented using a comma(,).
	//
	//   - The AND is represented using a semi-colon(;).
	//
	//   - AND and OR operators can be combined and AND takes precedence over OR.
	//
	//     filter: "value~cytoskeletion;tag==cell membrane;ontology==cellular"
	Filter string `protobuf:"bytes,3,opt,name=filter,proto3" json:"filter,omitempty"`
	// contains filtered or unexported fields
}

type Meta struct {

	// A unique pointer to the next set of result in the collection. Set the
	// cursor value parameter to the value of next_cursor to retrieve the next
	// set of collection using the same method
	NextCursor int64 `protobuf:"varint,1,opt,name=next_cursor,json=nextCursor,proto3" json:"next_cursor,omitempty"`
	// Maximum number of records that can be fetch per request
	Limit int64 `protobuf:"varint,2,opt,name=limit,proto3" json:"limit,omitempty"`
	// contains filtered or unexported fields
}

type NewTaggedAnnotation struct {
	Data *NewTaggedAnnotation_Data `protobuf:"bytes,1,opt,name=data,proto3" json:"data,omitempty"`
	// contains filtered or unexported fields
}

type NewTaggedAnnotationAttributes struct {

	// annotation in plain text format
	Value string `protobuf:"bytes,1,opt,name=value,proto3" json:"value,omitempty"`
	// serialized text content in a format recognized by frontend rich text
	// editor
	EditableValue string `protobuf:"bytes,2,opt,name=editable_value,json=editableValue,proto3" json:"editable_value,omitempty"`
	// Unique identifier(generally email) of the user who created the annotation
	CreatedBy string `protobuf:"bytes,3,opt,name=created_by,json=createdBy,proto3" json:"created_by,omitempty"`
	// An identifiable tagname for the annotation, primarily
	// a structured tag, generally an ontology term.
	Tag string `protobuf:"bytes,4,opt,name=tag,proto3" json:"tag,omitempty"`
	// unique identifier of a biological entity that is being annotated
	EntryId string `protobuf:"bytes,5,opt,name=entry_id,json=entryId,proto3" json:"entry_id,omitempty"`
	// Name of ontology from which the tag name is taken
	Ontology string `protobuf:"bytes,6,opt,name=ontology,proto3" json:"ontology,omitempty"`
	// Ordering of annotation when an entry has multiple annotations with
	// identical tag from the same ontology. By default, rank 0 is used.
	Rank int64 `protobuf:"varint,7,opt,name=rank,proto3" json:"rank,omitempty"`
	// contains filtered or unexported fields
}

type NewTaggedAnnotation_Data struct {

	// resource name, by default should be annotation
	Type       string                         `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	Attributes *NewTaggedAnnotationAttributes `protobuf:"bytes,2,opt,name=attributes,proto3" json:"attributes,omitempty"`
	// contains filtered or unexported fields
}

type TagRequest struct {

	// human readable name
	Name string `protobuf:"bytes,1,opt,name=name,proto3" json:"name,omitempty"`
	// ontology to which this tag belong
	Ontology string `protobuf:"bytes,2,opt,name=ontology,proto3" json:"ontology,omitempty"`
	// status for active or retired tag
	IsObsolete bool `protobuf:"varint,3,opt,name=is_obsolete,json=isObsolete,proto3" json:"is_obsolete,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotation struct {
	Data *TaggedAnnotation_Data `protobuf:"bytes,1,opt,name=data,proto3" json:"data,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationAttributes struct {

	// annotation in plain text format
	Value string `protobuf:"bytes,1,opt,name=value,proto3" json:"value,omitempty"`
	// serialized text content in a format recognized by frontend rich text
	// editor
	EditableValue string `protobuf:"bytes,2,opt,name=editable_value,json=editableValue,proto3" json:"editable_value,omitempty"`
	// Unique identifier(generally email) of the user who created the annotation
	CreatedBy string `protobuf:"bytes,3,opt,name=created_by,json=createdBy,proto3" json:"created_by,omitempty"`
	// Timestamp for creation
	CreatedAt *timestamppb.Timestamp `protobuf:"bytes,4,opt,name=created_at,json=createdAt,proto3" json:"created_at,omitempty"`
	// An identifiable tagname for the annotation, primarily
	// a structured tag, generally an ontology term.
	Tag string `protobuf:"bytes,5,opt,name=tag,proto3" json:"tag,omitempty"`
	// version refers to the current version no
	Version int64 `protobuf:"varint,6,opt,name=version,proto3" json:"version,omitempty"`
	// unique identifier of a biological entity that is being annotated
	EntryId string `protobuf:"bytes,7,opt,name=entry_id,json=entryId,proto3" json:"entry_id,omitempty"`
	// Name of ontology in which the tag name is taken
	Ontology string `protobuf:"bytes,8,opt,name=ontology,proto3" json:"ontology,omitempty"`
	// Ordering of annotation when an entry has multiple annotations with
	// identical tag from the same ontology.
	Rank int64 `protobuf:"varint,9,opt,name=rank,proto3" json:"rank,omitempty"`
	// Status for active or retired annotation
	IsObsolete bool `protobuf:"varint,10,opt,name=is_obsolete,json=isObsolete,proto3" json:"is_obsolete,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationCollection struct {
	Data []*TaggedAnnotationCollection_Data `protobuf:"bytes,1,rep,name=data,proto3" json:"data,omitempty"`
	Meta *Meta                              `protobuf:"bytes,3,opt,name=meta,proto3" json:"meta,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationCollection_Data struct {

	// resource name, by default should be annotation
	Type string `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	// unique identifier for the annotation
	Id         string                      `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	Attributes *TaggedAnnotationAttributes `protobuf:"bytes,3,opt,name=attributes,proto3" json:"attributes,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationGroup struct {
	Data []*TaggedAnnotationGroup_Data `protobuf:"bytes,1,rep,name=data,proto3" json:"data,omitempty"`
	// unique identifier for the annotation group
	GroupId string `protobuf:"bytes,2,opt,name=group_id,json=groupId,proto3" json:"group_id,omitempty"`
	// Timestamp for creation an update
	CreatedAt *timestamppb.Timestamp `protobuf:"bytes,3,opt,name=created_at,json=createdAt,proto3" json:"created_at,omitempty"`
	UpdatedAt *timestamppb.Timestamp `protobuf:"bytes,4,opt,name=updated_at,json=updatedAt,proto3" json:"updated_at,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationGroupCollection struct {
	Data []*TaggedAnnotationGroupCollection_Data `protobuf:"bytes,1,rep,name=data,proto3" json:"data,omitempty"`
	Meta *Meta                                   `protobuf:"bytes,2,opt,name=meta,proto3" json:"meta,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationGroupCollection_Data struct {

	// resource name, by default it should be annotation group
	Type  string                 `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	Group *TaggedAnnotationGroup `protobuf:"bytes,2,opt,name=group,proto3" json:"group,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationGroup_Data struct {

	// resource name, by default should be annotation
	Type string `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	// unique identifier for the annotation
	Id         string                      `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	Attributes *TaggedAnnotationAttributes `protobuf:"bytes,3,opt,name=attributes,proto3" json:"attributes,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationServiceClient interface {
	// Retrieves the specified tagged annotation
	GetAnnotation(ctx context.Context, in *AnnotationId, opts ...grpc.CallOption) (*TaggedAnnotation, error)
	// Retrieves a single tagged annotation associated with a specific entry
	GetEntryAnnotation(ctx context.Context, in *EntryAnnotationRequest, opts ...grpc.CallOption) (*TaggedAnnotation, error)
	// List tagged annotations using pagination, ten entries are retrieved by default
	ListAnnotations(ctx context.Context, in *ListParameters, opts ...grpc.CallOption) (*TaggedAnnotationCollection, error)
	// Create a tagged annotation
	CreateAnnotation(ctx context.Context, in *NewTaggedAnnotation, opts ...grpc.CallOption) (*TaggedAnnotation, error)
	// Update an existing annotation, in this case a new annotation entry is
	// created with a link to the previous annotation(copy on write).
	UpdateAnnotation(ctx context.Context, in *TaggedAnnotationUpdate, opts ...grpc.CallOption) (*TaggedAnnotation, error)
	// Delete an existing annotation
	DeleteAnnotation(ctx context.Context, in *DeleteAnnotationRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
	// Creates an annotation group from bunch of existing tagged annotations.
	CreateAnnotationGroup(ctx context.Context, in *AnnotationIdList, opts ...grpc.CallOption) (*TaggedAnnotationGroup, error)
	// Retrieves an annotation group
	GetAnnotationGroup(ctx context.Context, in *GroupEntryId, opts ...grpc.CallOption) (*TaggedAnnotationGroup, error)
	// Adds an existing annotation into an existing annotation group
	AddToAnnotationGroup(ctx context.Context, in *AnnotationGroupId, opts ...grpc.CallOption) (*TaggedAnnotationGroup, error)
	// Remove an annotation group
	DeleteAnnotationGroup(ctx context.Context, in *GroupEntryId, opts ...grpc.CallOption) (*emptypb.Empty, error)
	// List tagged annotation groups using pagination, ten entries are retrieved by default
	ListAnnotationGroups(ctx context.Context, in *ListGroupParameters, opts ...grpc.CallOption) (*TaggedAnnotationGroupCollection, error)
	// Retrieves tag information
	GetAnnotationTag(ctx context.Context, in *TagRequest, opts ...grpc.CallOption) (*AnnotationTag, error)
	// Upload obojson formatted file through client side streaming
	OboJSONFileUpload(ctx context.Context, opts ...grpc.CallOption) (TaggedAnnotationService_OboJSONFileUploadClient, error)
}

type TaggedAnnotationServiceServer interface {
	// Retrieves the specified tagged annotation
	GetAnnotation(context.Context, *AnnotationId) (*TaggedAnnotation, error)
	// Retrieves a single tagged annotation associated with a specific entry
	GetEntryAnnotation(context.Context, *EntryAnnotationRequest) (*TaggedAnnotation, error)
	// List tagged annotations using pagination, ten entries are retrieved by default
	ListAnnotations(context.Context, *ListParameters) (*TaggedAnnotationCollection, error)
	// Create a tagged annotation
	CreateAnnotation(context.Context, *NewTaggedAnnotation) (*TaggedAnnotation, error)
	// Update an existing annotation, in this case a new annotation entry is
	// created with a link to the previous annotation(copy on write).
	UpdateAnnotation(context.Context, *TaggedAnnotationUpdate) (*TaggedAnnotation, error)
	// Delete an existing annotation
	DeleteAnnotation(context.Context, *DeleteAnnotationRequest) (*emptypb.Empty, error)
	// Creates an annotation group from bunch of existing tagged annotations.
	CreateAnnotationGroup(context.Context, *AnnotationIdList) (*TaggedAnnotationGroup, error)
	// Retrieves an annotation group
	GetAnnotationGroup(context.Context, *GroupEntryId) (*TaggedAnnotationGroup, error)
	// Adds an existing annotation into an existing annotation group
	AddToAnnotationGroup(context.Context, *AnnotationGroupId) (*TaggedAnnotationGroup, error)
	// Remove an annotation group
	DeleteAnnotationGroup(context.Context, *GroupEntryId) (*emptypb.Empty, error)
	// List tagged annotation groups using pagination, ten entries are retrieved by default
	ListAnnotationGroups(context.Context, *ListGroupParameters) (*TaggedAnnotationGroupCollection, error)
	// Retrieves tag information
	GetAnnotationTag(context.Context, *TagRequest) (*AnnotationTag, error)
	// Upload obojson formatted file through client side streaming
	OboJSONFileUpload(TaggedAnnotationService_OboJSONFileUploadServer) error
	// contains filtered or unexported methods
}

type TaggedAnnotationService_OboJSONFileUploadClient interface {
	Send(*upload.FileUploadRequest) error
	CloseAndRecv() (*upload.FileUploadResponse, error)
	grpc.ClientStream
}

type TaggedAnnotationService_OboJSONFileUploadServer interface {
	SendAndClose(*upload.FileUploadResponse) error
	Recv() (*upload.FileUploadRequest, error)
	grpc.ServerStream
}

type TaggedAnnotationUpdate struct {
	Data *TaggedAnnotationUpdate_Data `protobuf:"bytes,1,opt,name=data,proto3" json:"data,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationUpdateAttributes struct {

	// annotation in plain text format
	Value string `protobuf:"bytes,1,opt,name=value,proto3" json:"value,omitempty"`
	// serialized text content in a format recognized by frontend rich text
	// editor
	EditableValue string `protobuf:"bytes,2,opt,name=editable_value,json=editableValue,proto3" json:"editable_value,omitempty"`
	// Unique identifier(generally email) of the user who created the annotation
	CreatedBy string `protobuf:"bytes,3,opt,name=created_by,json=createdBy,proto3" json:"created_by,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotationUpdate_Data struct {

	// resource name, by default should be annotation
	Type string `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	// unique identifier for the annotation
	Id         string                            `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	Attributes *TaggedAnnotationUpdateAttributes `protobuf:"bytes,3,opt,name=attributes,proto3" json:"attributes,omitempty"`
	// contains filtered or unexported fields
}

type TaggedAnnotation_Data struct {

	// resource name, by default should be annotation
	Type string `protobuf:"bytes,1,opt,name=type,proto3" json:"type,omitempty"`
	// unique identifier for the annotation
	Id         string                      `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	Attributes *TaggedAnnotationAttributes `protobuf:"bytes,3,opt,name=attributes,proto3" json:"attributes,omitempty"`
	// contains filtered or unexported fields
}

type UnimplementedTaggedAnnotationServiceServer struct {
}

type UnsafeTaggedAnnotationServiceServer interface {
	// contains filtered or unexported methods
}