test-pubmed-index

name	test-pubmed-index
description	Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.
disable-model-invocation	true
user-invocable	true

test-pubmed-index

EDirect shell smoke test for a local PubMed archive and postings setup. It relies on xcommon.sh to locate archive/postings/data folders, round-trips random PubMed titles through xfetch and xsearch, prints field/term diagnostics with xinfo, performs a local cit2pmid -local lookup, and climbs a MeSH tree using meshconv.xml.

Quick Start

• Command: test-pubmed-index
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/test-pubmed-index
• Critical environment: EDIRECT_LOCAL_ARCHIVE

When To Use This Tool

• Validating a full local PubMed archive/postings/data installation
• Troubleshooting local xfetch, xsearch, xinfo, or cit2pmid -local behavior
• Checking whether the archive, postings, and auxiliary data folders are all discoverable through EDirect local configuration
• Running a deeper local PubMed check than a simple one-command query

Common Patterns

# Run against a configured local archive root
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
test-pubmed-index

# Save diagnostics for later inspection
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
test-pubmed-index > pubmed-index-check.txt

# Time the run externally
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
time test-pubmed-index

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE to the correct local archive root.
2. Run test-pubmed-index with no arguments.
3. Read early errors first: archive/postings/data folder failures usually make the later checks meaningless.
4. Only interpret the title-roundtrip and MeSH-tree sections after the environment-location steps succeed.

Guardrails

• The script has no real help/version parser. -h and --version were treated like a normal run and triggered the full error cascade.
• Without EDIRECT_LOCAL_ARCHIVE, local testing produced repeated path errors, Unable to get folder Postings for database pubmed, Unable to get folder Archive for database pubmed, and cat: /meshconv.xml: No such file or directory.
• Source inspection shows the script depends on sibling helpers from xcommon.sh, especially FindArchiveFolder, FindPostingsFolder, and FindDataFolder.
• This is a broad local-environment smoke test, not a clean pass/fail API checker, so misconfiguration can surface as noisy mixed errors.