Nquire

nquire

Low-level EDirect transport wrapper for HTTP and FTP requests. It can issue GET or POST requests, expose EUtils and PubChem shortcuts, list or download FTP content, and optionally use Aspera when configured.

Quick Start

• Command: nquire
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/nquire
• Observed version: 24.0

When To Use This Tool

• Send raw requests to NCBI E-utilities, PubChem PUG/PUG View, or NCBI Datasets endpoints.
• Fetch XML, JSON, or plain-text payloads before parsing them with xtract or transmute.
• Use the low-level EDirect HTTP / FTP layer instead of a higher-level wrapper such as ecollect.
• List or download remote files when an EDirect workflow needs FTP-style access.

Common Patterns

# 1) Check the installed nquire version
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
nquire -version

# 2) Fetch NCBI database metadata with a direct GET request
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi |
sed -n '1,20p'

# 3) Use the built-in EUtils shortcut instead of spelling out the base URL
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
nquire -eutils esearch.fcgi -db pubmed -term 'tn3 transposition immunity'

Recommended Workflow

1. Decide whether the endpoint expects POST (-url) or GET (-get) before constructing the request.
2. Prefer built-in shortcuts such as -eutils, -pubchem, -pugrest, or -datasets when they match your target service.
3. Smoke-test one request and inspect the raw payload before building a larger parser or downloader around it.
4. Pipe successful responses into xtract, transmute, or downstream shell filters only after the transport layer is behaving predictably.

Guardrails

• -h and --help both print the same built-in usage text; -version returns the plain string 24.0.
• This wrapper appends its own bin directory to PATH, so sibling EDirect helpers remain discoverable even when you invoke it by absolute path.
• -url means HTTP POST, while -get means HTTP GET. Mixing them up is an easy way to get confusing server responses.
• FTP-style listing is not always reliable in the current environment. A live -lst ftp://ftp.ncbi.nlm.nih.gov/... smoke test failed here with curl: (56) response reading failed.
• Optional Aspera downloads (-asp) depend on a working client install and can be disabled with EDIRECT_NO_ASPERA=true.
• Hidden environment knobs such as NQUIRE_HELPER, NQUIRE_TIMEOUT, and NQUIRE_IPV4 can change transport behavior, so record them in reproducible workflows if you use them.