CLI Examples

Practical command-line examples for the current PMCGrab CLI.

PMC IDs

uv run python -m pmcgrab --pmcids 7181753 --output-dir ./papers
uv run python -m pmcgrab --pmcids PMC7181753 PMC3539614 --workers 4

PubMed IDs and DOIs

uv run python -m pmcgrab --pmids 33087749 --output-dir ./papers
uv run python -m pmcgrab --dois 10.1038/s41586-020-2832-5 --output-dir ./papers

Text File

Create pmcids.txt:

# Comments and blank lines are ignored.
PMC7181753
3539614
10.1038/s41586-020-2832-5

Process the list:

uv run python -m pmcgrab --from-id-file pmcids.txt --output-dir ./papers

Bare numeric values in --from-id-file are treated as PMC IDs. Use --pmids for PubMed IDs.

Local XML

# Directory of JATS XML files.
uv run python -m pmcgrab --from-dir ./pmc_bulk_xml --output-dir ./papers

# Specific XML files.
uv run python -m pmcgrab --from-file article1.xml article2.xml --output-dir ./papers

JSONL Output

uv run python -m pmcgrab \
    --pmcids 7181753 3539614 \
    --output-dir ./papers \
    --format jsonl

This writes output.jsonl plus summary.json.

The JSON and JSONL output is strict JSON. Missing values from pandas/numpy tables and author metadata are emitted as null.

Common Parameters

Parameter	Description	Example
--output-dir, --out	Output directory for JSON files	--output-dir ./papers
--workers, --batch-size	Number of worker threads	--workers 4
--format	json or jsonl	--format jsonl
--verbose	Enable debug logging	--verbose
--quiet	Suppress progress bars	--quiet
--version	Print installed version	--version