| name | expand-current |
| description | Use when expanding and rebuilding the local EDirect PubMed `Current` archive plus its derived index layers. |
| disable-model-invocation | true |
| user-invocable | true |
expand-current
CLI tool for expanding and indexing current PubMed archive files for local EDirect operations.
Quick Start
- Command:
EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/expand-current
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/expand-current
- Full reference: See references/help.md for complete documentation
When To Use This Tool
- Refresh the local
Current PubMed archive inside an EDirect local archive installation.
- Expand
*.xml.gz current-archive files into indexed XML and rebuild derived merged / indexed / inverted layers.
- Maintain a local offline-style PubMed archive workflow after new archive content arrives.
Common Patterns
EDIRECT_LOCAL_ARCHIVE=/data/edirect-archive \
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
/home/vimalinx/miniforge3/envs/bio/bin/expand-current
export EDIRECT_LOCAL_ARCHIVE=/data/edirect-archive
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH
/home/vimalinx/miniforge3/envs/bio/bin/expand-current
Recommended Workflow
- Confirm
EDIRECT_LOCAL_ARCHIVE resolves to a real local archive tree before running anything.
- Make sure companion commands such as
rchive, pm-collect, and xtract are available.
- Run
expand-current during a maintenance window, because it deletes previous derived index files before rebuilding them.
- Verify that fresh XML files and rebuilt index layers exist before pointing downstream local queries at the archive.
Guardrails
- This is an operational maintenance script, not a safe metadata probe.
- It deletes prior
*.e2x*, *.inv*, and *.mrg* files under the derived archive layers before rebuilding them.
- In the current environment, a missing
EDIRECT_LOCAL_ARCHIVE or missing helpers such as pm-collect can still lead to noisy partial execution and a final EXIT 0, so pre-flight checks matter.
- Sufficient disk space is required because compressed current-archive XML is expanded into plain XML during the rebuild.
