Metadata Export¶

Download dataset metadata from the EGA Private Metadata API and export as TSV, CSV, or JSON.

Auto-download during egafetch download

When downloading a dataset with --cf, metadata is fetched automatically after the data download completes. You only need the standalone metadata command if you want metadata without downloading files, or need to re-fetch metadata separately.

Usage¶

egafetch metadata EGAD... [flags]

Examples¶

# Export as TSV (default)
egafetch metadata EGAD00001001938

# Export as CSV
egafetch metadata EGAD00001001938 --format csv

# Export as JSON to a custom directory
egafetch metadata EGAD00001001938 --format json -o ./my-metadata

# Non-interactive with config file
egafetch metadata EGAD00001001938 --cf credentials.json

Flags¶

Flag	Default	Description
`-f, --format`	`tsv`	Output format: `tsv`, `csv`, or `json`
`-o, --output`	`{datasetID}-metadata`	Output directory
`--cf, --config-file`		JSON config file with credentials

Output Files¶

The command creates a directory with individual mapping files plus a merged file:

EGAD00001001938-metadata/
    study_experiment_run_sample.tsv    # Study/experiment/run/sample mappings
    run_sample.tsv                     # Run-to-sample mappings
    study_analysis_sample.tsv          # Study/analysis/sample mappings
    analysis_sample.tsv                # Analysis-to-sample mappings
    sample_file.tsv                    # Sample-to-file mappings
    EGAD00001001938_merged_metadata.tsv # Merged main file

Merged Metadata File¶

This file merges study_experiment_run_sample with sample_file on the sample_accession_id column. This gives you a single wide table linking studies, experiments, runs, samples, and files.

If a column name exists in both tables, the sample_file column is prefixed with file_ to avoid collisions.

Authentication¶

The metadata API uses a separate Identity Provider from the download API. This means:

With --cf: Credentials are read from the file -- no prompts
Without --cf: You must be logged in (egafetch auth login first), and you will be prompted for your password

The metadata token is short-lived (300 seconds) but the entire metadata fetch completes well within that window.

EGA Mapping Endpoints¶

EGAfetch fetches from these EGA Private Metadata API endpoints:

Mapping	Description
`study_experiment_run_sample`	Links studies to experiments, runs, and samples
`run_sample`	Maps sequencing runs to samples
`study_analysis_sample`	Links studies to analyses and samples
`analysis_sample`	Maps analyses to samples
`sample_file`	Maps samples to their EGA file accessions and filenames