bfabric-tools

B-Fabric Tools (btools)

CLI toolkit and Python library for B-Fabric operations: dataset registration, resource management, and metadata queries.

When to Use

• Register datasets from SUSHI/gStore into B-Fabric
• Query project metadata, order information, or sample details
• Retrieve user comments and annotations
• Track dataset lineage and provenance
• Manage resources (create, update status, delete)

Setup

conda activate gi_py3.11.5
# Check: python -c "from bfabric import Bfabric; print('OK')"

Credentials at ~/.bfabricpy.yml:

PRODUCTION:
  login: your_username
  password: your_password
  base_url: http://fgcz-bfabric.uzh.ch/bfabric

Core Commands

Register SUSHI Dataset

register_sushi_dataset_into_bfabric PROJECT_ID DATASET_TSV WORKUNIT_NAME [ORDER_ID] [PARENT_DS]

# Example
register_sushi_dataset_into_bfabric p31662 results.tsv RNAseqCount_Analysis o39391 -i RNAseqCount --verbose

Options:

• -a/--application <id>: Application ID (138=gStore import, 206=Analysis import)
• -i/--sushi-app <name>: SUSHI application name
• --verbose: Enable verbose output

Check Dataset

check_dataset_bfabric -id 12345
# Returns: True or False

Update Resource Status

update_resource_status 98765 available -v
update_resource_status -k relativepath "p1234/file.txt" archived

Statuses: available, pending, archived, deleted

Delete Workunit

delete_workunit_by_dataset_id -id 12345 -f

Get Project from Order

get_project_id_from_order 56789

Python Quick Start

from bfabric import Bfabric

bf = Bfabric.from_config()

# Get project
project = bf.read('project', {'id': 31662}).to_list_dict()[0]

# Get orders in project
orders = bf.read('order', {'projectid': 31662}).to_list_dict()

# Get samples
samples = bf.read('sample', {'containerid': 31662}).to_list_dict()

# Get workunits
workunits = bf.read('workunit', {'containerid': 31662}).to_list_dict()

# Get comments on project
annotations = bf.read('annotation', {'objectid': 31662, 'classname': 'Project'}).to_list_dict()

Common Endpoints

Endpoint	Query Keys	Description
project	id, name	Project metadata
order	id, projectid	Order details
sample	id, containerid, orderid	Sample metadata
workunit	id, containerid, applicationid	Analysis workunits
dataset	id, workunitid	Dataset information
resource	id, workunitid, relativepath	File resources
annotation	objectid + classname	Comments/notes

Detailed Documentation

• references/python-queries.md - Advanced Python use cases:

  • Complete project information
  • User comments and annotations
  • Dataset lineage tracking
  • Application-based searches
  • Resource status audits
  • Sample custom attributes

• references/tsv-format.md - TSV specification for dataset registration

• references/troubleshooting.md - Common issues and workflows

Quick Reference

# Register dataset
register_sushi_dataset_into_bfabric p1234 data.tsv WorkunitName -i SUSHIApp --verbose

# Check dataset
check_dataset_bfabric -id 12345

# Update resource
update_resource_status 98765 available -v

# Get project from order
get_project_id_from_order 56789

Resources

• btools repo: ~/git/btools
• B-Fabric web: http://fgcz-bfabric.uzh.ch
• B-Fabric test: https://fgcz-bfabric-test.uzh.ch