xfetch

name	xfetch
description	Use when retrieving records from a local EDirect archive via the `x*` local-cache stack, not when calling the remote NCBI `efetch` service directly.
disable-model-invocation	true
user-invocable	true

xfetch

Local-archive fetch helper built on xcommon.sh plus rchive. It takes UIDs from -id, -input, stdin, or an ENTREZ_DIRECT message, then fetches matching records from a configured local archive/postings installation rather than from the live NCBI service.

Quick Start

• Command: xfetch -db <database> -id <uid>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xfetch
• Critical environment: EDIRECT_LOCAL_ARCHIVE

When To Use This Tool

• Fetching records from a prepared local PubMed/PMC/etc. archive instead of the live E-utilities endpoint
• Streaming or turbo-fetching locally archived XML by UID
• Consuming UIDs from stdin or an upstream ENTREZ_DIRECT message and retrieving the matching local records
• Working inside a local/offline EDirect archive workflow

Common Patterns

# Fetch one UID from a local archive
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xfetch -db pubmed -id 2539356

# Read UIDs from stdin
printf '2539356\n' | xfetch -db pubmed

# Use stream mode against the local archive
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xfetch -db pubmed -stream -input ids.txt

Recommended Workflow

1. Point EDIRECT_LOCAL_ARCHIVE at a valid local archive root.
2. Supply -db plus a UID source (-id, -input, or stdin).
3. Use plain fetch mode for wrapped XML output or -stream when you want streamed archive content.
4. If the command prints wrapper XML but no records, debug the local archive/postings configuration before blaming UID parsing.

Guardrails

• xfetch is a local-cache tool, not a remote efetch synonym.
• -h/--help are safe and show usage; -version works and prints 24.0, but --version is unrecognized.
• In local testing without a configured archive, xfetch -db pubmed -id 2539356 still printed the PubMed XML wrapper prologue/epilogue and then failed with Insufficient command-line arguments supplied to rchive.
• The script sources xcommon.sh, loads database-specific wrappers from xfetch.ini, and then delegates to rchive -fetch or rchive -stream.
• If EDIRECT_LOCAL_ARCHIVE is missing, the shared helper prints the missing-path error first.