Query and trace lineage of projects, samples, and datasets in B-Fabric LIMS.
npx skills add https://github.com/cpanse/skills --skill bfabric-query-cpanse
Please help me install this Agent Skill. Skill: bfabric-query Source: https://github.com/cpanse/skills/tree/main/bfabric-lims/skills/bfabric-query Command: npx skills add https://github.com/cpanse/skills --skill bfabric-query-cpanse
containerid, not projectid). - Lineage Tracing: Trace datasets upstream to source samples, list workunit outputs, and find downstream analyses for a given sample. - Metadata Export: Generate project summaries, sample sheets, and resource listings in Markdown, CSV, TSV, or JSON formats. - Use Case: A bioinformatician needs to find all BAM files in project p31662 and export a sample sheet for order 39391; the skill provides ready-made scripts and query patterns to accomplish both in minutes. ## Quick Start Ask the agent to find all samples and workunits for B-Fabric project 31662 and export a project summary report.High-intent search queries and answers about installing and using this skill.
Use bfabricPy's read method with the sample endpoint and an orderid filter, such as bf.read('sample', {'orderid': 39391}).to_list_dict(). Samples belong to orders, not directly to projects, so query orders first when starting from a project.
Run the trace_lineage.py script with a dataset ID to recursively follow input datasets back through producing workunits. The LineageTracer class reads each dataset's workunitid and the workunit's inputdatasetids to build the upstream chain.
Workunits link to projects via the containerid field, not projectid, so querying with projectid returns nothing. Also verify the ID type and check that your credentials in ~/.bfabricpy.yml are valid for the PRODUCTION environment.
Implement pagination using BFABRIC_QUERY_LIMIT from bfabric.utils.paginator, looping with offset and limit parameters until an empty batch is returned. This avoids timeouts when fetching all workunits or resources in large projects.
Yes, the export_metadata.py script exports project summaries, sample sheets, and workunit resource lists in Markdown, CSV, TSV, or JSON formats. Specify the object ID, format, and optional output file via command-line arguments.
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