BDP CLI-Referenz#

Diese Dokumentation wird automatisch aus dem CLI-Quellcode generiert.

Überblick#

BDP (Bioinformatics Dependencies Platform) ist ein Kommandozeilen-Tool zum Verwalten biologischer Datensätze mit Versionskontrolle, Prüfsummen und Audit-Protokollen.

Installation#

Aus dem Quellcode#

Mit Cargo#

Schnellstart#

Befehle#

Command Overview:

• bdp↴
• bdp init↴
• bdp source↴
• bdp source add↴
• bdp source remove↴
• bdp source list↴
• bdp pull↴
• bdp status↴
• bdp audit↴
• bdp audit list↴
• bdp audit verify↴
• bdp audit export↴
• bdp clean↴
• bdp config↴
• bdp config get↴
• bdp config set↴
• bdp config show↴
• bdp uninstall↴
• bdp search↴
• bdp cache↴
• bdp cache set↴
• bdp cache show↴
• bdp cache reset↴
• bdp generate↴
• bdp generate python↴
• bdp generate snakemake↴
• bdp generate nextflow↴
• bdp generate cwl↴
• bdp generate r↴
• bdp completions↴
• bdp auth↴
• bdp auth login↴
• bdp auth logout↴
• bdp auth status↴
• bdp auth api-key↴
• bdp auth api-key create↴
• bdp auth api-key list↴
• bdp auth api-key revoke↴
• bdp query↴

bdp#

BDP - Bioinformatics Dependencies Platform

Usage: bdp [OPTIONS] [COMMAND]

Subcommands:#

• init — Initialize a new BDP project
• source — Manage data sources
• pull — Download and cache sources from manifest
• status — Show status of cached sources
• audit — Audit trail management
• clean — Clean cache
• config — Manage configuration
• uninstall — Uninstall BDP from your system
• search — Search for data sources and tools in the registry
• cache — Manage local data cache directory
• generate — Generate workflow integration files (Python, Snakemake, Nextflow, CWL, R)
• completions — Generate shell completion scripts
• auth — Manage authentication
• query — Advanced SQL-like querying of data sources and metadata

Options:#

• -v, --verbose — Verbose output

• --server-url <SERVER_URL> — Server URL

  Default value: http://localhost:8000

bdp init#

Initialize a new BDP project

Usage: bdp init [OPTIONS] [PATH]

Arguments:#

• <PATH> — Project directory or name (creates directory if it doesn't exist)

  Default value: .

Options:#

• -n, --name <NAME> — Project name (defaults to directory name)

• -V, --version <VERSION> — Project version

  Default value: 0.1.0

• -d, --description <DESCRIPTION> — Project description

• -f, --force — Force overwrite if bdp.yml exists

bdp source#

Manage data sources

Usage: bdp source <COMMAND>

Subcommands:#

• add — Add a source to the manifest
• remove — Remove a source from the manifest
• list — List sources in the manifest

bdp source add#

Add a source to the manifest

Usage: bdp source add <SOURCE>

Arguments:#

• <SOURCE> — Source specification (e.g., "uniprot:P01308-fasta@1.0")

bdp source remove#

Remove a source from the manifest

Usage: bdp source remove <SOURCE>

Arguments:#

• <SOURCE> — Source specification

bdp source list#

List sources in the manifest

Usage: bdp source list

bdp pull#

Download and cache sources from manifest

Usage: bdp pull [OPTIONS]

Options:#

• -f, --force — Force re-download even if cached
• --dry-run — Show what would be downloaded without fetching anything

bdp status#

Show status of cached sources

Usage: bdp status

bdp audit#

Audit trail management

Usage: bdp audit <COMMAND>

Subcommands:#

• list — List audit events
• verify — Verify audit trail integrity
• export — Export audit trail to regulatory format

bdp audit list#

List audit events

Usage: bdp audit list [OPTIONS]

Options:#

• -l, --limit <LIMIT> — Limit number of events to show

  Default value: 20

• -s, --source <SOURCE> — Show events from specific source

bdp audit verify#

Verify audit trail integrity

Usage: bdp audit verify

bdp audit export#

Export audit trail to regulatory format

Usage: bdp audit export [OPTIONS]

Options:#

• -f, --format <FORMAT> — Export format (fda, nih, ema, das, json)

  Default value: fda

• -o, --output <OUTPUT> — Output file path (optional, defaults to audit-{format}.{ext})

• --from <FROM> — Filter events from date (ISO 8601)

• --to <TO> — Filter events to date (ISO 8601)

• -n, --project-name <PROJECT_NAME> — Project name for report

• --project-version <PROJECT_VERSION> — Project version for report

bdp clean#

Clean cache

Usage: bdp clean [OPTIONS]

Options:#

• -a, --all — Clean all cached files
• --search-cache — Clean only search cache
• -y, --yes — Skip confirmation prompt

bdp config#

Manage configuration

Usage: bdp config <COMMAND>

Subcommands:#

• get — Get configuration value
• set — Set configuration value
• show — Show all configuration

bdp config get#

Get configuration value

Usage: bdp config get <KEY>

Arguments:#

• <KEY> — Configuration key

bdp config set#

Set configuration value

Usage: bdp config set <KEY> <VALUE>

Arguments:#

• <KEY> — Configuration key
• <VALUE> — Configuration value

bdp config show#

Show all configuration

Usage: bdp config show

bdp uninstall#

Uninstall BDP from your system

Usage: bdp uninstall [OPTIONS]

Options:#

• -y, --yes — Skip confirmation prompt
• --purge — Also remove cache and configuration files

bdp search#

Search for data sources and tools in the registry

Usage: bdp search [OPTIONS] <QUERY>...

Arguments:#

• <QUERY> — Search query (multiple words will be joined)

Options:#

• -o, --org <ORG> — Filter by organization (e.g., uniprot, ncbi)

• -t, --type <ENTRY_TYPE> — Filter by entry type (can be repeated)

• -s, --source-type <SOURCE_TYPE> — Filter by source type (can be repeated)

• -f, --format <FORMAT> — Output format

  Default value: interactive

• --no-interactive — Force non-interactive mode

• -l, --limit <LIMIT> — Number of results per page (1-100)

  Default value: 10

• -p, --page <PAGE> — Page number (for non-interactive pagination)

  Default value: 1

bdp cache#

Manage local data cache directory

Usage: bdp cache <COMMAND>

Subcommands:#

• set — Set cache directory path
• show — Show current cache directory
• reset — Reset cache path to default (.bdp/data)

bdp cache set#

Set cache directory path

Usage: bdp cache set <PATH>

Arguments:#

• <PATH> — Path to cache directory (relative to project root, or absolute)

bdp cache show#

Show current cache directory

Usage: bdp cache show

bdp cache reset#

Reset cache path to default (.bdp/data)

Usage: bdp cache reset

bdp generate#

Generate workflow integration files (Python, Snakemake, Nextflow, CWL, R)

Usage: bdp generate <COMMAND>

Subcommands:#

• python — Generate Python data paths module (bdp_data.py)
• snakemake — Generate Snakemake config file (config/bdp_data.yaml)
• nextflow — Generate Nextflow config file (conf/bdp_data.config)
• cwl — Generate CWL v1.2 inputs file (cwl/bdp-inputs.yml)
• r — Generate R data config and loader (r/bdp_data.yml + r/bdp_data.R)

bdp generate python#

Generate Python data paths module (bdp_data.py)

Usage: bdp generate python

bdp generate snakemake#

Generate Snakemake config file (config/bdp_data.yaml)

Usage: bdp generate snakemake

bdp generate nextflow#

Generate Nextflow config file (conf/bdp_data.config)

Usage: bdp generate nextflow

bdp generate cwl#

Generate CWL v1.2 inputs file (cwl/bdp-inputs.yml)

Usage: bdp generate cwl

bdp generate r#

Generate R data config and loader (r/bdp_data.yml + r/bdp_data.R)

Usage: bdp generate r

bdp completions#

Generate shell completion scripts

Usage: bdp completions <SHELL>

Arguments:#

• <SHELL> — Shell to generate completions for

  Possible values: bash, elvish, fish, powershell, zsh

bdp auth#

Manage authentication

Usage: bdp auth <COMMAND>

Subcommands:#

• login — Authenticate with the BDP server
• logout — Clear stored credentials
• status — Show current authentication state
• api-key — Manage API keys

bdp auth login#

Authenticate with the BDP server

Usage: bdp auth login [OPTIONS]

Options:#

• --api-key <API_KEY> — Authenticate with an API key instead of email/password

bdp auth logout#

Clear stored credentials

Usage: bdp auth logout

bdp auth status#

Show current authentication state

Usage: bdp auth status

bdp auth api-key#

Manage API keys

Usage: bdp auth api-key <COMMAND>

Subcommands:#

• create — Create a new API key
• list — List your API keys
• revoke — Revoke an API key by ID

bdp auth api-key create#

Create a new API key

Usage: bdp auth api-key create <NAME>

Arguments:#

• <NAME> — Human-readable name for this key

bdp auth api-key list#

List your API keys

Usage: bdp auth api-key list

bdp auth api-key revoke#

Revoke an API key by ID

Usage: bdp auth api-key revoke <ID>

Arguments:#

• <ID> — API key ID to revoke

bdp query#

Advanced SQL-like querying of data sources and metadata

Usage: bdp query [OPTIONS] [ENTITY]

Arguments:#

• <ENTITY> — Entity to query (protein, gene, genome, tools, orgs, etc.) or use --sql for raw SQL

Options:#

• --select <SELECT> — Select specific fields (comma-separated)

• -w, --where <WHERE_CLAUSE> — Filter results (can be repeated, AND combined) Simple: --where organism=human Complex: --where "organism='human' AND downloads>1000"

• --order-by <ORDER_BY> — Sort results by field[:asc|desc]

• -l, --limit <LIMIT> — Limit number of results (default: 1000)

  Default value: 1000

• --offset <OFFSET> — Skip first N results

• --group-by <GROUP_BY> — Group results by field

• --aggregate <AGGREGATE> — Aggregation expression (COUNT(*), SUM(field), etc.)

• --having <HAVING> — Filter grouped results

• --join <JOIN> — Join with another entity/table

• --on <ON> — Join condition

• --sql <SQL> — Execute raw SQL query directly

• -f, --format <FORMAT> — Output format

• -o, --output <OUTPUT> — Write output to file instead of stdout

• --no-header — Omit header row (for CSV/TSV)

• --explain — Show query execution plan

• --dry-run — Show generated SQL without executing

Umgebungsvariablen#

• BDP_SERVER_URL – Backend-Server-URL (Standard: http://localhost:8000)
• RUST_LOG – Log-Level (z. B. debug, info, warn, error)

Konfiguration#

BDP verwendet eine bdp.yml-Manifestdatei im Projektverzeichnis. Diese Datei wird automatisch erstellt, wenn Sie bdp init ausführen.

Beispiel bdp.yml:

Audit-Protokoll#

BDP führt ein kryptografisch verknüpftes Audit-Protokoll aller Operationen in .bdp/audit.db. Dies bietet:

• Manipulationssichere Protokollierung
• Einhaltung gesetzlicher Vorschriften (FDA 21 CFR Part 11, NIH, EMA)
• Vollständige Rückverfolgbarkeit der Datenquellen

Audit-Protokolle für Compliance exportieren:

Beispiele#

Mit mehreren Quellen arbeiten#

Datenintegrität überprüfen#

Support#

• Codeberg Issues: https://codeberg.org/datadir/bdp/issues
• Dokumentation: https://bdp.datadir.io/docs

Diese Dokumentation wird automatisch aus dem CLI-Quellcode generiert. Zum Aktualisieren: cargo xtask docs cli.