Documentation
¶
Overview ¶
Package encode is the library behind the encode command line: the HTTP client, request shaping, and the typed data models for the ENCODE (Encyclopedia of DNA Elements) Project.
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. Build your endpoint calls and JSON decoding on top of it.
Index ¶
- Constants
- type Client
- func (c *Client) GetExperiment(ctx context.Context, accession string) (*Experiment, error)
- func (c *Client) SearchExperiments(ctx context.Context, assayType, status string, limit int) ([]*Experiment, int, error)
- func (c *Client) SearchFiles(ctx context.Context, fileType string, limit int) ([]*File, int, error)
- type Config
- type Domain
- type Experiment
- type File
Constants ¶
const BaseURL = "https://" + Host
BaseURL is the root every request is built from.
const DefaultUserAgent = "encode-cli/0.1.0 (github.com/tamnd/encode-cli)"
DefaultUserAgent identifies the client to the ENCODE portal.
const Host = "www.encodeproject.org"
Host is the ENCODE portal 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 the ENCODE portal over HTTPS.
func (*Client) GetExperiment ¶
GetExperiment fetches a single ENCODE experiment by its accession (e.g. ENCSR961MEG). The portal auto-redirects /<accession>?format=json to the canonical path.
func (*Client) SearchExperiments ¶
func (c *Client) SearchExperiments(ctx context.Context, assayType, status string, limit int) ([]*Experiment, int, error)
SearchExperiments searches ENCODE for experiment records. assayType filters by assay title (e.g. "Hi-C", "ChIP-seq"); status filters by release status. Returns the matching experiments, the total hit count, and any error.
type Config ¶
type Config struct {
BaseURL string
Rate time.Duration
Retries int
Timeout time.Duration
UserAgent string
}
Config holds the runtime settings for the ENCODE client.
func DefaultConfig ¶
func DefaultConfig() Config
DefaultConfig returns a Config with sensible defaults: 400ms rate limit, 3 retries, and a 30s timeout — staying well within ENCODE's request limits.
type Domain ¶
type Domain struct{}
Domain is the ENCODE 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). Any non-empty string maps to ("experiment", input).
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 Experiment ¶
type Experiment struct {
ID string `json:"id" kit:"id"`
Accession string `json:"accession"`
AssayTitle string `json:"assay_title,omitempty"`
Biosample string `json:"biosample,omitempty"`
Status string `json:"status,omitempty"`
Released string `json:"date_released,omitempty"`
}
Experiment is a single ENCODE experiment record.
type File ¶
type File struct {
ID string `json:"id" kit:"id"`
Accession string `json:"accession"`
FileType string `json:"file_type,omitempty"`
OutputType string `json:"output_type,omitempty"`
FileSize int64 `json:"file_size,omitempty"`
Status string `json:"status,omitempty"`
}
File is a single ENCODE file record.
Source Files