Claude/add unit tests#82
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Lifts overall coverage from 31% to 42% by adding tests for previously untested modules and edge cases. Reuses the existing redis_mock and postgres_mock fixtures and the generate_messages TRAPI helpers. New test files: - tests/unit/test_shared_utils.py: combine_unique_dicts, merge_kgraph, is_support_edge, recursive support-graph traversal, validate_message, filter_kgraph_orphans, wrap_up_task, handle_task_failure - tests/unit/test_trapi_to_networkx.py: full matrix of trapi_kg_to_nx modes (multigraph/collapsed, directed/undirected, weight derivation and aggregation, transform fallback, input format variants) - tests/unit/test_db.py: encode/decode codecs, sync get/save variants, save_logs/get_logs roundtrip, retry-on-failure for save_message - tests/unit/test_broker.py: consumer group create idempotency, add/get/ack roundtrip, lock acquire/release with token compare - tests/unit/test_logger.py: ReasonerLogEntryFormatter, QueryLogger handler ordering, maxlen, kubernetes vs local config selection - tests/unit/test_filter_analyses_top_n.py: cap behavior, default, empty results - tests/unit/aragorn/test_aragorn_examine_query.py: all examine_query branches (lookup, infer, pathfinder, mixed errors) plus workflow selection on the aragorn entrypoint - tests/unit/aragorn/test_aragorn_lookup_helpers.py: examine_query, get_infer_parameters, get_rule_key, expand_aragorn_query, plus pure-lookup and gandalf branches of aragorn_lookup - tests/unit/test_merge_message_helpers.py: get_edgeset, create_aux_graph, add_knowledge_edge, _normalize_query, queries_equivalent, has_unique_nodes, filter_repeated_nodes, get_promiscuous_qnodes, remove_promiscuous_knode_results, get_answer_node, group_results_by_qnode, merge_messages (lookup/creative/pathfinder) - tests/unit/test_finish_query_edge_cases.py: missing query state, ERROR status propagation, callback retries, logs attachment https://claude.ai/code/session_01Bk7CnUHNrYjz6VeUS2JMwX
Lifts coverage from 42% to 50% with 60 new tests across 6 files. Covers workers that previously had no test coverage at all. Also adds workers/sipr/__init__.py: the directory was missing one, which prevented native package import. Source layout otherwise unchanged. New test files: - tests/unit/test_aragorn_pathfinder.py: shadowfax happy path, three-hop query construction, validation errors (two pinned nodes, single constraint, single intermediate category), gandalf parameter passthrough - tests/unit/test_bte.py: examine_query branches, bte() workflow selection, pathfinder rejection, preexisting-workflow preservation - tests/unit/test_bte_lookup.py: examine_query, get_params (qualifier extraction), match_templates against the real template_groups.json, fill_templates substitution in both subject/object directions, expand_bte_query, AsyncResponse, plus pure-lookup and pathfinder-rejection branches of bte_lookup - tests/unit/test_sipr.py: write_trapi (per-hop categories), distribute_weights (PageRank with/without seed), get_nodes (kgraph filtering, HP curie exclusion), sipr() entrypoint set-input vs not - tests/unit/test_sipr_graph_filterer.py: remove_isolated, add_hub_node, filter_graph_by_weight (above/below cutoff, missing weight, attribute preservation, post-filter orphan removal), apply_to_graph - tests/unit/test_inject_shepherd_arax_provenance.py: source injection on every edge, idempotency, defensive paths for malformed inputs https://claude.ai/code/session_01Bk7CnUHNrYjz6VeUS2JMwX
Lifts coverage from 50% to 56% with 79 new tests across 4 files. Focuses on the postgres-backed db helpers (which had no tests at all), the pure scoring helpers in aragorn_score, and the process_task wrappers across the simple workers. New test files: - tests/unit/test_db_postgres.py: add_query (redis + postgres), add_callback_id / remove_callback_id (with OperationalError retry), get_running_callbacks, cleanup_callbacks, get_callback_query_id, get_query_state, set_query_completed, initialize_db / shutdown_db, check_connection - tests/unit/aragorn/test_aragorn_score_helpers.py: get_base_weight, get_source_weight, get_source_sigmoid (centered, saturated, unknown), get_profile (parametrized over all four profiles + unknown fallback), kirchhoff (unit resistor + 3-node line + invalid index), and get_edge_support_kg (recursion through support graphs, missing aux, missing edges, accumulator threading) - tests/unit/test_process_task_wrappers.py: 22 tests for the process_task happy/cancellation/failure paths across 10 workers (filter_kgraph_orphans, filter_results_top_n, filter_analyses_top_n, sort_results_score, example_ara, example_score, example_lookup, aragorn, aragorn_pathfinder, bte) plus wrap_up_task swallow check - tests/unit/test_misc_branch_coverage.py: targeted branches in merge_kgraph (overlapping edge merge), validate_message, aragorn_omnicorp helpers (create_log_entry, add_node_pmid_counts default 0, add_shared_pmid_counts existing-OMNICORP-aux reuse, generate_curie_pairs setnode pairings), finish_query.process_task (success + failure + ack-failure + cancellation) https://claude.ai/code/session_01Bk7CnUHNrYjz6VeUS2JMwX
Lifts coverage from 56% to 59% with 47 new tests across 2 files. Both targeted modules (aragorn_score and bte_lookup) reach 89% coverage. aragorn_score went from 70% to 89%; bte_lookup went from 69% to 89%. New test files: - tests/unit/aragorn/test_aragorn_score_ranker.py (31 tests): Ranker.__init__ profile selection, probes() (probe node selection from qgraph connectivity), get_omnicorp_node_pubs (cache, alternate attribute names, unparseable values, missing nodes), get_edge_values (publications splitting by pipe/comma/string, evidence_count, p_value extraction with list/string/numeric, affinity, confidence, literature_cooccurrence with omnicorp predicate), get_rgraph (per-analysis graph construction, support graph inclusion, missing edges), graph_laplacian (laplacian shape, zero-row pruning protecting probes), score (jaccard_like transform), rank (sorted output) - tests/unit/test_bte_lookup_branches.py (16 tests): run_async_lookup (200/non-200/exception, callback URL injection), bte_lookup inferred fanout (expand_bte_query call count, failed callback removal, exception logging), polling loop branches (in-progress drain, db error retry, timeout cleanup), default submitter injection, process_task (happy/failure/cancellation/wrap_up_failure paths) https://claude.ai/code/session_01Bk7CnUHNrYjz6VeUS2JMwX
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