BIA Study Statistics

A command-line tool for analyzing and visualizing BioImage Archive (BIA) study statistics.

Installation

Clone this repository and install dependencies:

git clone https://github.com/bioimage-archive/bia-study-stats.git
cd bia-study-stats
pip install -e .

Commands

View Study Information

• print_accessions: Display a table of accession IDs and their sizes

  bia-study-stats print_accessions stats.json

• summarize: Show summary statistics including total accessions and storage usage

  bia-study-stats summarize stats.json

Update Size Information

• merge_df_sizes: Merge size information from a df command output file

  bia-study-stats merge_df_sizes stats.json df_output.txt

• merge_s3_cache: Update sizes using an S3 cache file

  bia-study-stats merge_s3_cache stats.json s3_cache.json

• update_from_fire: Fetch sizes directly from S3/FIRE storage for studies with zero size

  bia-study-stats update_from_fire stats.json --failed-log errors.log

Analysis and Visualization

• data_added_after: Calculate total data volume added after a specific date

  bia-study-stats data_added_after stats.json 2023-01-01

• plot_cumulative_size: Generate a bar chart showing cumulative data size by quarter

  bia-study-stats plot_cumulative_size stats.json

• plot_cumulative_entries: Create a bar chart of cumulative study count by quarter

  bia-study-stats plot_cumulative_entries stats.json

• print_ebi_stats: Output monthly cumulative size statistics in EBI format

  bia-study-stats print_ebi_stats stats.json

Configuration

For commands that interact with S3/FIRE storage, create a .env file with:

S3_BUCKET=your-bucket-name
S3_ENDPOINT=https://your-endpoint.com  # Optional
AWS_PROFILE=your-profile  # Optional

Output Files

• quarterly_cumulative_size.png: Generated by plot_cumulative_size
• quarterly_cumulative_entries.png: Generated by plot_cumulative_entries