Documentation
¶
Overview ¶
Package sra is the library behind the sra command line: the HTTP client, request shaping, and the typed data models for NCBI SRA.
The Client here is the spine every command shares. It sets a real User-Agent, paces requests so a busy session stays polite, and retries the transient failures (429 and 5xx) that any public API throws under load. Search and summary calls follow the standard eUtils two-step: esearch returns a list of numeric UIDs, esummary turns them into records.
Index ¶
- Constants
- type Client
- func (c *Client) FetchRuns(ctx context.Context, ids []string) ([]*Run, error)
- func (c *Client) Get(ctx context.Context, rawURL string) ([]byte, error)
- func (c *Client) GetRun(ctx context.Context, uid string) (*Run, error)
- func (c *Client) Search(ctx context.Context, query string, limit, start int) ([]string, int, error)
- func (c *Client) SearchAndFetch(ctx context.Context, query string, limit, start int) ([]*Run, int, error)
- type Config
- type Domain
- type Run
Constants ¶
const DefaultUserAgent = "sra-cli/dev (+https://github.com/tamnd/sra-cli)"
DefaultUserAgent identifies the client to NCBI.
const Host = "eutils.ncbi.nlm.nih.gov"
Host is the SRA site, used for Locate / URI resolution.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Client ¶
type Client struct {
HTTP *http.Client
// exported shims so domain.go newClient can set them like the scaffold does
UserAgent string
Rate time.Duration
Retries int
// contains filtered or unexported fields
}
Client talks to the NCBI eUtils SRA API over HTTP.
func NewClientWithConfig ¶
NewClientWithConfig returns a Client using the given config.
func (*Client) FetchRuns ¶
FetchRuns fetches esummary for a batch of SRA UIDs and returns Run records.
type Config ¶
type Config struct {
BaseURL string
APIKey string
UserAgent string
Rate time.Duration
Timeout time.Duration
Retries int
}
Config carries the tunable parameters for the SRA client.
func DefaultConfig ¶
func DefaultConfig() Config
DefaultConfig returns a Config with sensible defaults for the free-tier NCBI eUtils API (3 req/s without a key).
type Domain ¶
type Domain struct{}
Domain is the SRA driver. It carries no state; the per-run client is built by the factory Register hands kit.
func (Domain) Classify ¶
Classify turns any accepted input into the canonical (type, id). All-digit strings are SRA UIDs. SRR/ERR/DRR accessions resolve via search. Any other non-empty string is treated as a run reference.
func (Domain) Info ¶
func (Domain) Info() kit.DomainInfo
Info describes the scheme, the hostnames a pasted link is matched against, and the identity reused for the binary's help and version.
type Run ¶
type Run struct {
ID string `json:"id" kit:"id"` // SRA UID (numeric)
Title string `json:"title"`
Accession string `json:"accession,omitempty"` // first run acc (SRR...)
Platform string `json:"platform,omitempty"`
Instrument string `json:"instrument,omitempty"`
TaxID string `json:"tax_id,omitempty"`
TotalSpots string `json:"total_spots,omitempty"`
TotalBases string `json:"total_bases,omitempty"`
Status string `json:"status,omitempty"`
CreateDate string `json:"create_date,omitempty"`
UpdateDate string `json:"update_date,omitempty"`
}
Run is a single SRA experiment/run record.
Source Files