bfabric-query

B-Fabric Query and Exploration

Query, explore, and trace lineage in B-Fabric LIMS. For dataset registration and resource management, use bfabric-tools instead.

Setup

conda activate gi_py3.11.5

Credentials in ~/.bfabricpy.yml:

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

from bfabric import Bfabric
bf = Bfabric.from_config()

Quick Queries

# Projects
project = bf.read('project', {'id': 31662}).to_list_dict()[0]
projects = bf.read('project', {'name': 'UM_Atlas'}).to_list_dict()

# Orders and Samples
orders = bf.read('order', {'projectid': 31662}).to_list_dict()
samples = bf.read('sample', {'orderid': 39391}).to_list_dict()
sample = bf.read('sample', {'id': 393911}).to_list_dict()[0]

# Workunits and Datasets
workunits = bf.read('workunit', {'containerid': 31662}).to_list_dict()
datasets = bf.read('dataset', {'workunitid': 108483}).to_list_dict()
resources = bf.read('resource', {'datasetid': 123456}).to_list_dict()

# Applications
apps = bf.read('application', {'name': 'CellRangerCount'}).to_list_dict()

Relationship Navigation

Key relationships (query field in parentheses):

• Project → Orders (projectid)
• Order → Samples (orderid)
• Project → Workunits (containerid, NOT projectid!)
• Workunit → Datasets (workunitid)
• Dataset → Resources (datasetid)

# Full traversal example
project_id = 31662
orders = bf.read('order', {'projectid': project_id}).to_list_dict()
for order in orders:
    samples = bf.read('sample', {'orderid': order['id']}).to_list_dict()
    print(f"Order {order['name']}: {len(samples)} samples")

See references/lineage-tracing.md for detailed lineage functions.

Path Conversions

# gStore → SUSHI download URL
gstore_path = "/srv/gstore/projects/p31662/data.bam"
sushi_url = gstore_path.replace('/srv/gstore/projects/', 'https://fgcz-sushi.uzh.ch/projects/')

# gStore → exploreSC Shiny URL
seurat_path = "/srv/gstore/projects/p33974/neurons.qs2"
shiny_url = f"https://fgcz-shiny.uzh.ch/app/exploreSC/?data={seurat_path.replace('/srv/gstore/projects/', '')}"

Standard paths:

• gStore (read-only): /srv/gstore/projects/pXXXXX/
• Analysis (read/write): /srv/GT/analysis/pXXXXX/
• References: /srv/GT/reference/

Command-Line Scripts

# Trace dataset lineage
python scripts/trace_lineage.py --dataset 123456

# Trace workunit outputs
python scripts/trace_lineage.py --workunit 108483

# Export project summary
python scripts/export_metadata.py --project 31662 --format markdown -o report.md

# Export sample sheet
python scripts/export_metadata.py --order 39391 --format tsv -o samples.tsv

Helper Functions

from quick_query import find_project, get_order_samples, summarize_project
from trace_lineage import LineageTracer
from export_metadata import MetadataExporter

# Find projects
projects = find_project("UM")

# Get samples
samples = get_order_samples(39391)

# Trace lineage
tracer = LineageTracer()
lineage = tracer.trace_dataset_upstream(dataset_id=123456)

# Export
exporter = MetadataExporter()
markdown = exporter.export_project_summary(31662, format='markdown')

Common Endpoints

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

Status Values

Workunit: pending, processing, available, failed Resource: available, archived, deleted

Detailed Documentation

• references/lineage-tracing.md - Dataset/sample lineage tracing
• references/bulk-operations.md - Multi-project queries, batch operations
• references/troubleshooting.md - Common errors and solutions

For dataset registration and resource management, use the bfabric-tools skill.