Documentation
¶
Overview ¶
Package geo is the library behind the geo command line: the HTTP client, request shaping, and the typed data models for NCBI GEO.
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.
Index ¶
- Constants
- type Client
- func (c *Client) FetchDatasets(ctx context.Context, ids []string) ([]*Dataset, error)
- func (c *Client) GetDataset(ctx context.Context, uid string) (*Dataset, 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) ([]*Dataset, int, error)
- type Config
- type Dataset
- type Domain
Constants ¶
const Host = "eutils.ncbi.nlm.nih.gov"
Host is the eUtils hostname this client talks to, and the host the URI driver in domain.go claims.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Client ¶
type Client struct {
// contains filtered or unexported fields
}
Client talks to NCBI eUtils for GEO DataSets records.
func (*Client) FetchDatasets ¶
FetchDatasets fetches dataset details for the given IDs (up to ~500 per call; callers should batch if needed).
func (*Client) GetDataset ¶
GetDataset fetches a single dataset by its GEO numeric UID.
type Config ¶
type Config struct {
BaseURL string
Rate time.Duration
Retries int
Timeout time.Duration
UserAgent string
}
Config holds the runtime settings for the GEO client.
func DefaultConfig ¶
func DefaultConfig() Config
DefaultConfig returns a Config with sensible defaults: 400ms rate limit, 3 retries, and a 30s timeout.
type Dataset ¶
type Dataset struct {
ID string `json:"id" kit:"id"`
Accession string `json:"accession"`
Title string `json:"title"`
Summary string `json:"summary,omitempty"`
Type string `json:"type,omitempty"`
Platform string `json:"platform,omitempty"`
PlatformTitle string `json:"platform_title,omitempty"`
Organism string `json:"organism,omitempty"`
SampleCount string `json:"sample_count,omitempty"`
PubMedIDs []string `json:"pubmed_ids,omitempty"`
EntryType string `json:"entry_type,omitempty"`
Date string `json:"date,omitempty"`
FTPLink string `json:"ftp_link,omitempty"`
}
Dataset is a single GEO DataSets record.
type Domain ¶
type Domain struct{}
Domain is the GEO 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 GEO numeric UIDs; GSE/GDS/GPL/GSM-prefixed strings are GEO accessions — both map to the "dataset" type.
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.
Source Files