jdp

Documentation

Index

• func NewDatabase(orcid string) (databases.Database, error)
• type Database
  • func (db *Database) Endpoint() (endpoints.Endpoint, error)
  • func (db *Database) LocalUser(orcid string) (string, error)
  • func (db *Database) Resources(fileIds []string) ([]frictionless.DataResource, error)
  • func (db *Database) Search(params databases.SearchParameters) (databases.SearchResults, error)
  • func (db Database) SpecificSearchParameters() map[string]interface{}
  • func (db *Database) StageFiles(fileIds []string) (uuid.UUID, error)
  • func (db *Database) StagingStatus(id uuid.UUID) (databases.StagingStatus, error)
• type File
• type FileIdNotFoundError
  • func (e FileIdNotFoundError) Error() string
• type Metadata
• type PermissionDeniedError
  • func (e PermissionDeniedError) Error() string

Functions

func NewDatabase

func NewDatabase(orcid string) (databases.Database, error)

Types

type Database

type Database struct {
	// database identifier
	Id string
	// ORCID identifier for database proxy
	Orcid string
	// HTTP client that caches queries
	Client http.Client
	// shared secret used for authentication
	Secret string
	// SSO token used for interim JDP access
	SsoToken string
	// mapping from staging UUIDs to JDP restoration request ID
	StagingIds map[uuid.UUID]int
}

file database appropriate for handling JDP searches and transfers (implements the databases.Database interface)

func (*Database) Endpoint

func (db *Database) Endpoint() (endpoints.Endpoint, error)

func (*Database) LocalUser

func (db *Database) LocalUser(orcid string) (string, error)

func (*Database) Resources

func (db *Database) Resources(fileIds []string) ([]frictionless.DataResource, error)

func (*Database) Search

func (db *Database) Search(params databases.SearchParameters) (databases.SearchResults, error)

func (Database) SpecificSearchParameters

func (db Database) SpecificSearchParameters() map[string]interface{}

func (*Database) StageFiles

func (db *Database) StageFiles(fileIds []string) (uuid.UUID, error)

func (*Database) StagingStatus

func (db *Database) StagingStatus(id uuid.UUID) (databases.StagingStatus, error)

type File

type File struct {
	// unique ID used by the DTS to manipulate the file
	Id string `json:"_id"`
	// name of the file (excluding Path)
	Name string `json:"file_name"`
	// directory in which the file sits
	Path string `json:"file_path"`
	// file size (bytes)
	Size int `json:"file_size"`
	// file metadata
	Metadata Metadata `json:"metadata"`
	// name of the user that owns the file
	Owner string `json:"file_owner"`
	// date that the file was added
	AddedDate string `json:"added_date"`
	// date of last modification to the file
	ModifiedDate string `json:"modified_date"`
	// date file will be purged
	PurgeDate string `json:"dt_to_purge"`
	// file origination date
	Date string `json:"file_date"`
	// string describing the status of the file
	Status string `json:"file_status"`
	// type (or list of types) corresponding to this file
	Type json.RawMessage `json:"file_type"`
	// MD5 checksum
	MD5Sum string `json:"md5sum"`
	// user with access to the file
	User string `json:"user"`
	// name of UNIX group with access to the file
	Group string `json:"file_group"`
	// UNIX file permissions (a string containing the octal representation)
	Permissions string `json:"file_permissions"`
	// name of the group that produced the file's data
	DataGroup string `json:"data_group"`
}

This type represents a single file entry in a JDP ElasticSearch result.

type FileIdNotFoundError

type FileIdNotFoundError struct {
	// contains filtered or unexported fields
}

this error type is returned when a file is requested and is not found

func (FileIdNotFoundError) Error

func (e FileIdNotFoundError) Error() string

type Metadata

type Metadata struct {
	// proposal info
	Proposal struct {
		// DOI of the awarded proposal
		AwardDOI string `json:"award_doi"`
		// info about the Principal Investigator
		PI struct {
			// PI's last name
			LastName string `json:"last_name"`
			// PI's first name
			FirstName string `json:"first_name"`
			// PI's middle name (if any)
			MiddleName string `json:"middle_name"`
			// PI's email address
			EmailAddress string `json:"email_address"`
			// name of academic or industrial institution
			Institution string `json:"institution"`
			// country of institution/PI
			Country string `json:"country"`
		} `json:"pi"`
		// date of proposal approval
		DateApproved string `json:"date_approved"`
		// proposal DOI
		DOI string `json:"doi"`
	} `json:"proposal"`
	// GOLD-related metadata
	GoldData struct {
		// stamp ID
		StampId string `json:"gold_stamp_id"`
		// project URL
		ProjectURL string `json:"gold_project_url"`
		// display name
		DisplayName string `json:"display_name"`
	} `json:"gold_data"`
	IMG struct {
		TaxonOID int `json:"taxon_oid"`
	} `json:"img,omitempty"`
	// sequencing project metadata
	SequencingProject struct {
		// name of scientific program to which project belongs
		ScientificProgramName string `json:"scientific_program_name"`
	} `json:"sequencing_project"`
	// sequencing project ID, sometimes used as ITS project ID. This type can be a
	// list or a number, so we have to unmarshal it into a RawMessage
	SequencingProjectId json.RawMessage `json:"sequencing_project_id"`
	// NCBI taxon metadata
	NCBITaxon struct {
		Order   string `json:"ncbi_taxon_order"`
		Family  string `json:"ncbi_taxon_family"`
		Genus   string `json:"ncbi_taxon_genus"`
		Species string `json:"ncbi_taxon_species"`
	} `json:"ncbi_taxon"`
	// NCBI taxon identifier
	NCBITaxonId int `json:"ncbi_taxon_id"`
	// portal metadata
	Portal struct {
		DisplayLocation []string `json:"display_location"`
	} `json:"portal"`
	// final project delivery metadata
	FinalDeliveryProject struct {
		ProductSearchCategory string `json:"product_search_category"`
	} `json:"final_deliv_project"`
	// analysis project ID, sometimes used as ITS project ID. This type can be a
	// list or a number, so we have to unmarshal it into a RawMessage
	AnalysisProjectId json.RawMessage `json:"analysis_project_id"`
}

this type represents metadata associated with a jdpFile

type PermissionDeniedError

type PermissionDeniedError struct {
	// contains filtered or unexported fields
}

this error type is returned when a file is requested for which the requester does not have permission

func (PermissionDeniedError) Error

func (e PermissionDeniedError) Error() string