HTTP & Network

HTTP Methods

http_get(url, opts?) -> response
http_post(url, body, opts?) -> response

All return a response map:

# Fetch gene info from NCBI
# esummary.fcgi needs db, id and retmode; without them it answers with an
# error page, and json_parse then fails on the first character.
let resp = http_get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=672&retmode=json", {
  headers: {"Accept": "application/json"}
})
let data = json_parse(resp.body)

# POST to REST API
resp = http_post("https://api.example.com/submit", "{\"sample\": \"S001\", \"pipeline\": \"rnaseq\"}")

download / upload

Download a file from a URL or upload to an endpoint. Downloads support resume and progress.

download(url, path?) -> string    # returns local path
upload(path, url, opts?) -> response

# Download reference genome
download(
  "https://ftp.ensembl.org/pub/release-111/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
  "reference/GRCh38.fa.gz"
)

# Download (auto-infer filename from URL)
download("https://example.com/data.bam")

ref_genome

Download a reference genome by name from built-in sources registry. Handles URL resolution, checksum verification, and caching.

ref_genome(name, opts?) -> string

let ref = ref_genome("GRCh38")              # downloads if not cached
let ref37 = ref_genome("GRCh37")
let t2t = ref_genome("t2t")
let dbsnp = ref_genome("dbSNP")              # also works for databases

# With specific output location
ref_genome("GRCh38", {outdir: "references/"})

bio_fetch

Fetch a record from a biological database by ID. Supports NCBI, UniProt, Ensembl, and more.

bio_fetch(database, id) -> map

# bio_fetch downloads reference datasets — genomes, annotations, variant
# sets — and its sources are named accordingly. It is not a record lookup:
# there is no "ncbi_gene" or "uniprot" source.
bio_sources() |> take(3) |> println()

# For a single database record, call the API client directly.
let protein = uniprot_entry("P38398")
println("Name:", protein.name)           # "Breast cancer type 1 susceptibility protein"
println("Organism:", protein.organism)   # "Homo sapiens"
println("Function:", protein.function)