Documentation
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Overview ¶
Package ols is the library behind the ols command line: the HTTP client, request shaping, and the typed data models for the EMBL-EBI Ontology Lookup Service (OLS4).
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) Get(ctx context.Context, rawURL string) ([]byte, error)
- func (c *Client) GetOntologies(ctx context.Context, limit int) ([]Ontology, int, error)
- func (c *Client) GetTerm(ctx context.Context, oboID, ontology string) (*Term, error)
- func (c *Client) SearchTerms(ctx context.Context, query, ontology string, limit, offset int) ([]Term, int, error)
- type Domain
- type Ontology
- type Term
Constants ¶
const BaseURL = "https://www.ebi.ac.uk/ols4/api"
BaseURL is the root every request is built from.
const DefaultUserAgent = "ols-cli/0.1.0 (+https://github.com/tamnd/ols-cli)"
DefaultUserAgent identifies the client to OLS4.
const Host = "www.ebi.ac.uk"
Host is the OLS4 site this client talks to.
const HostShort = "ols4"
HostShort is a short display name for the service.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Client ¶
type Client struct {
HTTP *http.Client
UserAgent string
// Rate is the minimum gap between requests. Zero means no pacing.
Rate time.Duration
Retries int
// contains filtered or unexported fields
}
Client talks to OLS4 over HTTP.
func NewClient ¶
func NewClient() *Client
NewClient returns a Client with sensible defaults: a 30s timeout, a 300ms minimum gap between requests, and three retries on transient errors.
func (*Client) Get ¶
Get fetches rawURL and returns the response body. It paces and retries according to the client's settings. The body is read fully and closed here.
func (*Client) GetOntologies ¶
GetOntologies lists ontologies from OLS4. It returns up to limit results.
func (*Client) GetTerm ¶
GetTerm fetches a single ontology term by its OBO ID (e.g. "GO:0051301"). It uses the search endpoint to resolve the ID to a canonical term record. The ontology parameter is used to narrow the search when provided.
func (*Client) SearchTerms ¶
func (c *Client) SearchTerms(ctx context.Context, query, ontology string, limit, offset int) ([]Term, int, error)
SearchTerms queries the OLS4 search API and returns matching Term records along with the total count. If ontology is non-empty, results are filtered to that ontology only.
type Domain ¶
type Domain struct{}
Domain is the OLS4 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 — a bare OBO ID, ontology short name, or full OLS4 URL — into the canonical (type, id).
Rule: if input contains ":" it is a term; otherwise it is an ontology.
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 Ontology ¶
type Ontology struct {
ID string `json:"id" kit:"id"` // ontologyId
Title string `json:"title"`
Description string `json:"description"`
Prefix string `json:"prefix"`
Version string `json:"version"`
}
Ontology is a single OLS4 ontology record.
type Term ¶
type Term struct {
ID string `json:"id" kit:"id"` // obo_id
Label string `json:"label"`
Description string `json:"description"`
Ontology string `json:"ontology"`
Prefix string `json:"prefix"`
Synonyms []string `json:"synonyms"`
IsObsolete bool `json:"is_obsolete"`
}
Term is a single OLS4 ontology term record.
Source Files