Add conflation taxon report - #697
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Introduces a pattern where dropping a .sql file into input_data/sql/reports/ is sufficient to add a new report to the pipeline -- no Python or Snakemake changes required. - Add run_sql_report() to duckdb_reports.py: registers Edges, Cliques, Nodes, Synonyms views over Parquet, applies an optional YAML sidecar for per-query DuckDB config, runs the SQL, and writes TSV output. - Add glob_wildcards discovery, rule run_sql_report (wildcard per file), and rule all_sql_reports to duckdb.snakefile. - Wire reports/sql/done into rule all in Snakefile. - Add label_distribution.sql (example report) and its YAML sidecar, plus a README documenting available views, sidecar format, and usage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Check for an empty result set. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Fix documentation. Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
- Move `import yaml` to module level - Replace os.path.exists() + open() with try/except FileNotFoundError - Remove redundant ternary (empty dict is handled by setup_duckdb) - Add db.close() after writing output to avoid connection leak - Add missing blank lines before function definition Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds a new report that checks for cross-species conflation in the GeneProtein conflation file by mapping each clique's CURIEs back to their taxa from the Gene and Protein compendia, warning on any clique spanning multiple taxa. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Closes #695.
WIP