How do I install the Test Pubmed Index skill?

Run npx skillmds add vimalinx/test-pubmed-index in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Test Pubmed Index safe to use?

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Which AI agents work with Test Pubmed Index?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Test Pubmed Index free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Test Pubmed Index?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Test Pubmed Index by vimalinx — Agent Skill

Name: Test Pubmed Index
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

Set EDIRECT_LOCAL_ARCHIVE to the correct local archive root.
Run test-pubmed-index with no arguments.
Read early errors first: archive/postings/data folder failures usually make the later checks meaningless.
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.

---name: test-pubmed-indexdescription: Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.--- # 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 ```bash # Run against a configured local archive root export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive test-pubmed-index ``` ```bash # Save diagnostics for later inspection export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive test-pubmed-index > pubmed-index-check.txt ``` ```bash # 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.

Frequently asked questions