resolver

package
v0.0.0-...-eec5682 Latest Latest
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 Go to latest Published: May 2, 2026 License: BSD-2-Clause Imports: 54 Imported by: 0

Documentation

Overview

Package resolver contains the GraphQL resolvers for the stock service. This includesolvers for strains and plasmids, as well as any related types. The resolvers in this package are responsible for handling GraphQL queries and mutations related to stocks, and they interact with the stock service to perform the necessary operations.

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Slugify 

func Slugify(name string) string

Types

type CollectPublicationResultsParams 

type CollectPublicationResultsParams struct {
	Ctx     context.Context
	PubChan <-chan *models.PublicationWithGene
	ErrChan <-chan error
	Logger  *logrus.Entry
}

CollectPublicationResultsParams defines the parameters for the collectPublicationResults function.

type FetchGeneAnnotationParams 

type FetchGeneAnnotationParams struct {
	Ctx    context.Context
	Client feature.FeatureAnnotationServiceClient
	GeneID string
	Logger *logrus.Entry
}

FetchGeneAnnotationParams defines the parameters for the fetchGeneAnnotation function.

type FetchPublicationDetailsParams 

type FetchPublicationDetailsParams struct {
	Ctx        context.Context
	PubID      string
	GeneID     string // For logging context
	Qrs        *QueryResolver
	FeatClient feature.FeatureAnnotationServiceClient
}

FetchPublicationDetailsParams defines the parameters for the fetchPublicationDetails function.

type LaunchPublicationFetchersParams 

type LaunchPublicationFetchersParams struct {
	Ctx        context.Context
	Gene       string
	PubIDs     []string
	FeatClient feature.FeatureAnnotationServiceClient
	PubChan    chan<- *models.PublicationWithGene
	ErrChan    chan<- error
	Sem        *concurrency.Semaphore
	Wg         *sync.WaitGroup
	CancelFunc context.CancelFunc
	Qrs        *QueryResolver
}

LaunchPublicationFetchersParams defines the parameters for the launchPublicationFetchers method.

type MutationResolver 

type MutationResolver struct {
	registry.Registry
	Logger *logrus.Entry
}

func (*MutationResolver) AddStrainPhenotype 

func (mrs *MutationResolver) AddStrainPhenotype(
	ctx context.Context,
	strainID string,
	input models.AddStrainPhenotypeInput,
) (*models.Strain, error)

func (*MutationResolver) CreateContent 

func (mrs *MutationResolver) CreateContent(
	ctx context.Context,
	input *models.CreateContentInput,
) (*pb.Content, error)

func (*MutationResolver) CreateGeneGeneralInfo 

func (mrs *MutationResolver) CreateGeneGeneralInfo(
	ctx context.Context,
	id string,
	input models.CreateGeneGeneralInfoInput,
) (*models.GeneGeneralInfo, error)

func (*MutationResolver) CreateOrder 

func (mrs *MutationResolver) CreateOrder(
	ctx context.Context,
	input *models.CreateOrderInput,
) (*pb.Order, error)

CreateOrder creates a new stock order.

func (*MutationResolver) CreatePermission 

func (mrs *MutationResolver) CreatePermission(
	ctx context.Context,
	input *models.CreatePermissionInput,
) (*pb.Permission, error)

func (*MutationResolver) CreatePlasmid 

func (mrs *MutationResolver) CreatePlasmid(
	ctx context.Context,
	input *models.CreatePlasmidInput,
) (*models.Plasmid, error)

func (*MutationResolver) CreateRole 

func (mrs *MutationResolver) CreateRole(
	ctx context.Context,
	input *models.CreateRoleInput,
) (*pb.Role, error)

func (*MutationResolver) CreateRolePermissionRelationship 

func (mrs *MutationResolver) CreateRolePermissionRelationship(
	ctx context.Context,
	roleID string,
	permissionID string,
) (*pb.Role, error)

func (*MutationResolver) CreateStrain 

func (mrs *MutationResolver) CreateStrain(
	ctx context.Context,
	input *models.CreateStrainInput,
) (*models.Strain, error)

func (*MutationResolver) CreateUser 

func (mrs *MutationResolver) CreateUser(
	ctx context.Context,
	input *models.CreateUserInput,
) (*pb.User, error)

func (*MutationResolver) CreateUserRoleRelationship 

func (mrs *MutationResolver) CreateUserRoleRelationship(
	ctx context.Context,
	userID string,
	roleID string,
) (*pb.User, error)

func (*MutationResolver) DeleteContent 

func (mrs *MutationResolver) DeleteContent(
	ctx context.Context,
	id string,
) (*models.DeleteContent, error)

func (*MutationResolver) DeletePermission 

func (mrs *MutationResolver) DeletePermission(
	ctx context.Context,
	id string,
) (*models.DeletePermission, error)

func (*MutationResolver) DeleteRole 

func (mrs *MutationResolver) DeleteRole(
	ctx context.Context,
	id string,
) (*models.DeleteRole, error)

func (*MutationResolver) DeleteStock 

func (mrs *MutationResolver) DeleteStock(
	ctx context.Context,
	id string,
) (*models.DeleteStock, error)

func (*MutationResolver) DeleteStrainPhenotype 

func (mrs *MutationResolver) DeleteStrainPhenotype(
	ctx context.Context,
	strainID string,
	input models.DeleteStrainPhenotypeInput,
) (*models.DeleteStrainPhenotype, error)

func (*MutationResolver) DeleteUser 

func (mrs *MutationResolver) DeleteUser(
	ctx context.Context,
	id string,
) (*models.DeleteUser, error)

func (*MutationResolver) Login 

func (mrs *MutationResolver) Login(
	ctx context.Context,
	input *models.LoginInput,
) (*pb.Auth, error)

func (*MutationResolver) Logout 

func (mrs *MutationResolver) Logout(ctx context.Context) (*models.Logout, error)

func (*MutationResolver) UpdateContent 

func (mrs *MutationResolver) UpdateContent(
	ctx context.Context,
	input *models.UpdateContentInput,
) (*pb.Content, error)

func (*MutationResolver) UpdateGeneGeneralInfo 

func (mrs *MutationResolver) UpdateGeneGeneralInfo(
	ctx context.Context,
	id string,
	input models.UpdateGeneGeneralInfoInput,
) (*models.GeneGeneralInfo, error)

func (*MutationResolver) UpdateOrder 

func (mrs *MutationResolver) UpdateOrder(
	ctx context.Context,
	id string,
	input *models.UpdateOrderInput,
) (*pb.Order, error)

UpdateOrder updates an existing stock order.

func (*MutationResolver) UpdatePermission 

func (mrs *MutationResolver) UpdatePermission(
	ctx context.Context,
	id string,
	input *models.UpdatePermissionInput,
) (*pb.Permission, error)

func (*MutationResolver) UpdatePlasmid 

func (mrs *MutationResolver) UpdatePlasmid(
	ctx context.Context,
	id string,
	input *models.UpdatePlasmidInput,
) (*models.Plasmid, error)

func (*MutationResolver) UpdateRole 

func (mrs *MutationResolver) UpdateRole(
	ctx context.Context,
	id string,
	input *models.UpdateRoleInput,
) (*pb.Role, error)

func (*MutationResolver) UpdateStrain 

func (mrs *MutationResolver) UpdateStrain(
	ctx context.Context,
	id string,
	input *models.UpdateStrainInput,
) (*models.Strain, error)

func (*MutationResolver) UpdateStrainPhenotype 

func (mrs *MutationResolver) UpdateStrainPhenotype(
	ctx context.Context,
	strainID string,
	target models.UpdateStrainPhenotypeTargetInput,
	payload models.UpdateStrainPhenotypePayloadInput,
) (*models.Strain, error)

func (*MutationResolver) UpdateUser 

func (mrs *MutationResolver) UpdateUser(
	ctx context.Context,
	id string,
	input *models.UpdateUserInput,
) (*pb.User, error)

func (*MutationResolver) UploadFile 

func (mrs *MutationResolver) UploadFile(
	ctx context.Context,
	file graphql.Upload,
) (*models.ImageFile, error)

type QueryResolver 

type QueryResolver struct {
	registry.Registry
	Dataloaders dataloader.Retriever
	Logger      *logrus.Entry
}

func (*QueryResolver) AllOrthologs 

func (qrs *QueryResolver) AllOrthologs(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

func (*QueryResolver) AllPublications 

func (qrs *QueryResolver) AllPublications(
	ctx context.Context,
	gene string,
	limit *int,
	sortBy *string,
) (*models.NumberOfPublicationsWithGene, error)

AllPublications is the resolver for the allPublications field.

func (*QueryResolver) AllStrains 

func (qrs *QueryResolver) AllStrains(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

func (*QueryResolver) Content 

func (qrs *QueryResolver) Content(
	ctx context.Context,
	id string,
) (*pb.Content, error)

func (*QueryResolver) ContentBySlug 

func (qrs *QueryResolver) ContentBySlug(
	ctx context.Context,
	slug string,
) (*pb.Content, error)

func (*QueryResolver) Gene 

func (qrs *QueryResolver) Gene(
	ctx context.Context,
	geneID string,
) (*models.Gene, error)

func (*QueryResolver) GeneGeneralInformation 

func (qrs *QueryResolver) GeneGeneralInformation(
	ctx context.Context,
	gene string,
) (*models.GeneGeneralInfo, error)

GeneGeneralInformation is the resolver for the geneGeneralInformation field.

func (*QueryResolver) GeneOntologyAnnotation 

func (qrs *QueryResolver) GeneOntologyAnnotation(
	ctx context.Context,
	gene string,
) ([]*models.GOAnnotation, error)

func (*QueryResolver) GeneralInformation 

func (qrs *QueryResolver) GeneralInformation(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

func (*QueryResolver) GetAssociatedSequnces 

func (qrs *QueryResolver) GetAssociatedSequnces(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

GetAssociatedSequnces is the resolver for the getAssociatedSequnces field. 

func (qrs *QueryResolver) GetLinks(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

GetLinks is the resolver for the getLinks field.

func (*QueryResolver) GetProteinInformation 

func (qrs *QueryResolver) GetProteinInformation(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

GetProteinInformation is the resolver for the getProteinInformation field.

func (*QueryResolver) GetRefreshToken 

func (qrs *QueryResolver) GetRefreshToken(
	ctx context.Context,
	token string,
) (*pb.Auth, error)

func (*QueryResolver) ListContentByNamespace 

func (qrs *QueryResolver) ListContentByNamespace(
	ctx context.Context,
	namespace string,
) ([]*pb.Content, error)

func (*QueryResolver) ListGeneProductInfo 

func (qrs *QueryResolver) ListGeneProductInfo(
	ctx context.Context,
	gene string,
) (*models.Gene, error)

ListGeneProductInfo is the resolver for the listGeneProductInfo field.

func (*QueryResolver) ListOrders 

func (qrs *QueryResolver) ListOrders(
	ctx context.Context,
	cursor *int,
	limit *int,
	filter *string,
) (*models.OrderListWithCursor, error)

ListOrders retrieves all orders in the database.

func (*QueryResolver) ListOrganisms 

func (qrs *QueryResolver) ListOrganisms(
	ctx context.Context,
) ([]*models.Organism, error)

func (*QueryResolver) ListPermissions 

func (qrs *QueryResolver) ListPermissions(
	ctx context.Context,
) ([]*pb.Permission, error)

func (*QueryResolver) ListPhenotypeAssays 

func (qrs *QueryResolver) ListPhenotypeAssays(
	ctx context.Context,
	search string,
) ([]string, error)

func (*QueryResolver) ListPhenotypeEnvironments 

func (qrs *QueryResolver) ListPhenotypeEnvironments(
	ctx context.Context,
	search string,
) ([]string, error)

func (*QueryResolver) ListPhenotypes 

func (qrs *QueryResolver) ListPhenotypes(
	ctx context.Context,
	search string,
) ([]string, error)

func (*QueryResolver) ListPlasmids 

func (qrs *QueryResolver) ListPlasmids(
	ctx context.Context,
	cursor *int,
	limit *int,
	filter *models.PlasmidListFilter,
) (*models.PlasmidListWithCursor, error)

func (*QueryResolver) ListPlasmidsWithAnnotation 

func (qrs *QueryResolver) ListPlasmidsWithAnnotation(
	ctx context.Context,
	cursor *int,
	limit *int,
	typeArg string,
	annotation string,
) (*models.PlasmidListWithCursor, error)

func (*QueryResolver) ListPublicationsWithGene 

func (qrs *QueryResolver) ListPublicationsWithGene(
	ctx context.Context,
	gene string,
) ([]*models.PublicationWithGene, error)

ListPublicationsWithGene fetches all publications associated with a gene ID and includes related genes for each publication. Returns an empty list if gene is not found or has no publications. If any error occurs during fetching of publication details (other than not-found errors), the entire operation fails and no results are returned.

func (*QueryResolver) ListRecentGenes 

func (qrs *QueryResolver) ListRecentGenes(
	ctx context.Context,
	limit int,
) ([]*models.Gene, error)

ListRecentGenes is the resolver for the listRecentGenes field.

func (*QueryResolver) ListRecentPlasmids 

func (qrs *QueryResolver) ListRecentPlasmids(
	ctx context.Context,
	limit int,
) ([]*models.Plasmid, error)

ListRecentPlasmids is the resolver for the listRecentPlasmids field.

func (*QueryResolver) ListRecentPublications 

func (qrs *QueryResolver) ListRecentPublications(
	ctx context.Context,
	limit int,
) ([]*models.Publication, error)

ListRecentPublications is the resolver for the listRecentPublications field.

func (*QueryResolver) ListRecentStrains 

func (qrs *QueryResolver) ListRecentStrains(
	ctx context.Context,
	limit int,
) ([]*models.Strain, error)

ListRecentStrains is the resolver for the listRecentStrains field.

func (*QueryResolver) ListRoles 

func (qrs *QueryResolver) ListRoles(ctx context.Context) ([]*pb.Role, error)

func (*QueryResolver) ListStrains 

func (qrs *QueryResolver) ListStrains(
	ctx context.Context,
	cursor *int,
	limit *int,
	filter *models.StrainListFilter,
) (*models.StrainListWithCursor, error)

ListStrains resolves the listStrains GraphQL query. It returns a cursor-paginated list of strains, applying any supplied StrainListFilter.

Deduplication and pagination contract

The resolver deduplicates strain records after retrieving them from the backing store. Consequently, the number of items in a single response page may be strictly less than the requested limit, even when additional pages are available. Callers MUST NOT infer end-of-list from receiving fewer items than requested.

Pagination MUST be driven exclusively by the NextCursor field of the returned StrainListWithCursor value:

  • NextCursor != 0 — a subsequent page exists; supply its value as the cursor argument on the next request.
  • NextCursor == 0 — all pages have been consumed; iteration must stop.

func (*QueryResolver) ListStrainsWithAnnotation 

func (qrs *QueryResolver) ListStrainsWithAnnotation(
	ctx context.Context,
	cursor *int,
	limit *int,
	typeArg string,
	annotation string,
) (*models.StrainListWithCursor, error)

func (*QueryResolver) ListStrainsWithGene 

func (qrs *QueryResolver) ListStrainsWithGene(
	ctx context.Context,
	gene string,
) ([]*models.Strain, error)

ListStrainsWithGene is the resolver for the listStrainsWithGene field.

func (*QueryResolver) ListUsers 

func (qrs *QueryResolver) ListUsers(
	ctx context.Context,
	pagenum string,
	pagesize string,
	filter string,
) (*models.UserList, error)

func (*QueryResolver) Order 

func (qrs *QueryResolver) Order(
	ctx context.Context,
	id string,
) (*pb.Order, error)

Order retrieves an individual order by ID.

func (*QueryResolver) Organism 

func (qrs *QueryResolver) Organism(
	ctx context.Context,
	taxonID string,
) (*models.Organism, error)

func (*QueryResolver) Permission 

func (qrs *QueryResolver) Permission(
	ctx context.Context,
	id string,
) (*pb.Permission, error)

func (*QueryResolver) Plasmid 

func (qrs *QueryResolver) Plasmid(
	ctx context.Context,
	id string,
) (*models.Plasmid, error)

func (*QueryResolver) Publication 

func (qrs *QueryResolver) Publication(
	ctx context.Context,
	id string,
) (*models.Publication, error)

Publication is the resolver for getting an individual publication by ID.

func (*QueryResolver) Role 

func (qrs *QueryResolver) Role(
	ctx context.Context,
	id string,
) (*pb.Role, error)

func (*QueryResolver) Strain 

func (qrs *QueryResolver) Strain(
	ctx context.Context,
	id string,
) (*models.Strain, error)

func (*QueryResolver) User 

func (qrs *QueryResolver) User(
	ctx context.Context,
	id string,
) (*pb.User, error)

func (*QueryResolver) UserByEmail 

func (qrs *QueryResolver) UserByEmail(
	ctx context.Context,
	email string,
) (*pb.User, error)

type Resolver 

type Resolver struct {
	registry.Registry
	Dataloaders dataloader.Retriever
	Logger      *logrus.Entry
}

func NewResolver 

func NewResolver(
	nr registry.Registry,
	dl dataloader.Retriever,
	logger *logrus.Entry,
) *Resolver

func (*Resolver) Auth 

func (rrs *Resolver) Auth() generated.AuthResolver

func (*Resolver) Author 

func (rrs *Resolver) Author() generated.AuthorResolver

func (*Resolver) Content 

func (rrs *Resolver) Content() generated.ContentResolver

func (*Resolver) Mutation 

func (rrs *Resolver) Mutation() generated.MutationResolver

func (*Resolver) Order 

func (rrs *Resolver) Order() generated.OrderResolver

func (*Resolver) Organism 

func (rrs *Resolver) Organism() generated.OrganismResolver

func (*Resolver) Permission 

func (rrs *Resolver) Permission() generated.PermissionResolver

func (*Resolver) Plasmid 

func (rrs *Resolver) Plasmid() generated.PlasmidResolver

func (*Resolver) Query 

func (rrs *Resolver) Query() generated.QueryResolver

func (*Resolver) Role 

func (rrs *Resolver) Role() generated.RoleResolver

func (*Resolver) Strain 

func (rrs *Resolver) Strain() generated.StrainResolver

func (*Resolver) User 

func (rrs *Resolver) User() generated.UserResolver

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