api

Documentation

Index

• Constants
• Variables
• func Do(r Request) (io.ReadCloser, error)
• func LoadAPIData() (map[string]any, error)
• type Endpoint
  • func (ae Endpoint) FindParam(name string) (Param, error)
• type MimeType
  • func (mt MimeType) Extension() string
  • func (mt MimeType) Name() string
  • func (mt MimeType) String() string
• type Param
• type Request
  • func MakeRequest(endpoint *Endpoint, params map[string]any, contentType MimeType) (Request, error)
• type Table
  • func (at Table) FindEndpoint(section, name string) (*Endpoint, error)

Constants

const Server = "https://rest.ensembl.org"

Variables

var FiletypeMap = map[string]MimeType{
	"compgen":  JSON,
	"info":     JSON,
	"lookup":   JSON,
	"mapping":  JSON,
	"sequence": FASTA,
	"ontology": JSON,
	"overlap":  JSON,
	"taxonomy": JSON,
}

var ModuleMap = map[string]map[string]string{
	"compgen": {
		"homology_species_gene_id": "homology_id",
		"homology_symbol":          "homology_symbol",
	},
	"info": {
		"species": "species",
	},
	"lookup": {
		"symbol_post": "symbol",
		"lookup_post": "id",
	},
	"mapping": {
		"assembly_cdna":        "cdna2gen",
		"assembly_cds":         "cds2gen",
		"assembly_translation": "prot2gen",
		"assembly_map":         "asm2asm",
	},
	"ontology": {
		"ontology_id":   "id",
		"ontology_name": "name",
	},
	"overlap": {
		"overlap_id":     "id",
		"overlap_region": "region",
	},
	"taxonomy": {
		"taxonomy_classification": "classification",
		"taxonomy_id":             "term",
	},
	"sequence": {
		"sequence_id_post": "id",
		"sequence_region":  "region",
	},
}

Functions

func Do

func Do(r Request) (io.ReadCloser, error)

func LoadAPIData

func LoadAPIData() (map[string]any, error)

Types

type Endpoint

type Endpoint struct {
	Name, Description, Method, Path string
	ParamsReq                       []Param `json:"params_req"`
	ParamsOpt                       []Param `json:"params_opt"`
}

func (Endpoint) FindParam

func (ae Endpoint) FindParam(name string) (Param, error)

type MimeType

type MimeType int

const (
	FASTA MimeType = iota
	GFF3
	BED
	JSON
	Newick
	SeqXML
	PhyloXML
	XML
	YAML
)

func (MimeType) Extension

func (mt MimeType) Extension() string

func (MimeType) Name

func (mt MimeType) Name() string

func (MimeType) String

func (mt MimeType) String() string

type Param

type Param struct {
	Name, Description, Example string
	ValType                    string `json:"type"`
	Def                        string `json:"default"`
}

type Request

type Request struct {
	Endpoint    *Endpoint
	Params      map[string]any
	ContentType MimeType
}

func MakeRequest

func MakeRequest(
	endpoint *Endpoint,
	params map[string]any,
	contentType MimeType,
) (Request, error)

type Table

type Table map[string][]Endpoint

var Data Table

func (Table) FindEndpoint

func (at Table) FindEndpoint(section, name string) (*Endpoint, error)