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Sql base tables pytest
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Commits on Feb 24, 2026
local postgres boilerplate
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Update dbsetup_local to use TEST_DATABASE variable and enhance local_test_database.sql with local settings
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Commits on Mar 9, 2026
reverting back to pre-commit being added although not used as this time
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Add .factory mission infrastructure for deep-upsert mission
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Add SchemaGraph class for FK dependency introspection
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Fix scrutiny gates: exclude test_api.py (AWS), add typecheck/lint commands, run formatters
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Update worker skill: correct test command, per-feature imports, add pre-commit step
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Fix test coverage gaps: validate fk_map against reflected schema, check composite FK ordering
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Add deep upsert primitives: get_or_create, resolve_fk_value, deep_upsert
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Fix deep_upsert trigger ordering: auto-create obj_desc_quant/obj_desc_cat
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Fix _ensure_obj_desc_inst to match specific (object, desc_inst) pair
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Add Ingest class with row/batch/get/session API, error handling, and lookup table protection
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Fix scrutiny issues: lookup table guard, write-based session tests, stronger error assertions
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Add is_lookup guard to Ingest.batch() with regression tests
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Add integration validation tests: E2E, no external URLs, idempotency, batch 100+, cross-table consistency
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Update worker skill: scope external-URL grep to mission test files only
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Fix integration test gaps: strict rg exit code check and batch PK/SQL verification
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Update README.org with ingestion layer docs, usage example, and setup instructions
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Commits on Mar 25, 2026
Revert README.org to original; add docs/deep-upsert-upgrade.md for ingestion layer summary
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Add snapshot extraction module and f006 gold-standard fixture files
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Add snapshot comparison utilities with structured diff results
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Record gold-standard-snapshots scrutiny failures
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Fix snapshot scrutiny issues: full-row equality tests, shared rebuild_database, missing file detection, row count mismatch
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Fix rebuild_database dependency in test fixtures
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Add mission infrastructure: worker skill, services, library, validation artifacts
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Add entity metadata extraction (extract_v2) with 37 tests
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Add fascicle/fiber CSV extraction and JPX file extraction (extract_v2)
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Apply blue formatter to extract_v2.py and test_extract_v2.py
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Add macOS path length constraint to environment docs
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Add NCBITaxon_9606 species alias to _translate_species()
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Override extraction-layer scrutiny: CSV issues are platform constraints, not code defects
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Record extraction-layer user-testing validation: all 4 assertions passed
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Add dump-based ingest v2 pipeline: extract, delete, re-insert f006 data
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Add TestComparisonProof: exact count assertions, breakdown verification, spot-checks, and idempotency test
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Record deep-upsert-ingest scrutiny findings
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Fix VAL-ING-013 spot-check: compare re-ingested values against pre-delete baseline
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Record deep-upsert-ingest milestone validation: all 17 assertions passed
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Add AWS schema setup/teardown scripts, test_aws.py with --run-aws flag
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Commits on Mar 26, 2026
AWS E2E: add ingest tests, fix TRIGGER USER for RDS, fix teardown hang, handle cross-dataset equiv_inst
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Fix AWS E2E: DISABLE TRIGGER USER, teardown performance, SQL alias do->do2
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Remove .factory/ and AI-generated docs from git tracking
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Add .factory mission infrastructure for MicroCT dataset ingestion
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Add MicroCT schema lookup data: units mm/mm2, sd agg type, nerve/fascicle/summary descriptors, edge descriptors_cat, boolean controlled_terms
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Add MicroCT extraction module with all parsing functions and 57 unit tests
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Fix pixel conversion, SQL idempotency, and descriptor units for MicroCT
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Add MicroCT ingestion pipeline and 22 integration tests
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Commits on May 4, 2026
tutorial
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