add explicit user-confirmation gates to parse-table and schema-match - #60
Open
yzjanee wants to merge 6 commits into
Open
add explicit user-confirmation gates to parse-table and schema-match#60yzjanee wants to merge 6 commits into
yzjanee wants to merge 6 commits into
Conversation
…ch skills Both skills now declare astrodb-build-artifacts/ as the required output directory at the top of their instructions, with an explicit mkdir -p step before any files are written. schema-match also gains concrete output paths mirroring the -parsed-data-table pattern from parse-table. Closes #203 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
commit 73a0348 Author: yzjanee <janeweiowo@gmail.com> Date: Mon Jun 29 15:38:49 2026 -0400 ingest-publications: fix disambiguation to use DOI suffix on shortname When two papers share the same first-author/year shortname, append the last 4 characters of the DOI as a suffix (e.g. Bona20.a51a) rather than omitting the shortname and citing in a comments field. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> commit 6a03a48 Author: yzjanee <janeweiowo@gmail.com> Date: Mon Jun 29 13:35:55 2026 -0400 ingest-publications: enforce 4-letter reference naming convention - Adds prominent Reference naming convention section to SKILL.md with worked examples (Bona20, Smit20, WuXi21) - For disambiguation (two papers same first-author/year): second reference goes in the comments field of the data row (e.g. Sources.comments), never as a variant shortname (no Bona20a, no Bona20.800c) - Updates API reference to be explicit about the comments approach - Fixes example shortname Bonaca2020 → Bona20 throughout - Adds eval assertion that Bona20 is the generated shortname Closes astrodbtoolkit#37 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
commit 83635b7 Author: yzjanee <janeweiowo@gmail.com> Date: Mon Jun 29 13:34:45 2026 -0400 setup: add directions document to initial workflow Adds Step 6 to astrodb-build-setup that creates an artifacts/ directory and prompts the user to write a directions document (artifacts/directions.md) capturing dataset-specific decisions, known issues, and ingestion notes. Includes an example directions document in references/directions_example.md. astrodb-build-parse-table and astrodb-build-schema-match now check for artifacts/directions.md at startup and incorporate its guidance. Closes astrodbtoolkit#36 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…t just the second When two papers share the same base shortname, every paper in the collision gets a DOI suffix — including the first. Clarified that bare letter suffixes are never used; letters appearing inside a DOI suffix are fine. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ames, not just the second" This reverts commit d3cf410.
parse-table: Step 6 now requires explicit user confirmation before the skill is done — user must review the HTML output and approve the column list, descriptions, and types. Also clarifies that schema.yaml is created by schema-generate, not schema-match. schema-match: adds a checkpoint before writing any output files — all Low and Medium confidence matches are presented in a single table for user review. Overrides are applied before the files are written. Directions.md is still honored without re-asking; the gate only fires for undirected ambiguities. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
yzjanee
marked this pull request as draft
July 10, 2026 19:13
yzjanee
marked this pull request as ready for review
July 16, 2026 00:55
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
astrodb-build-parse-table: Step 6 is now an explicit blocking gate — the skill presents a summary (columns found, metadata vs. inferred vs. missing) and waits for user confirmation before it is considered done. Clarifies thatschema.yamlis not produced here or in schema-match.astrodb-build-schema-match: Adds a checkpoint before any output files are written — all Low and Medium confidence matches are compiled into a single table and shown to the user for confirmation or override. Honorsartifacts/directions.mdwithout re-asking; only undirected ambiguities trigger the gate.Motivation
Skills were too eager to proceed without confirming with the user when column mappings were ambiguous. This change makes the ambiguity explicit and gives the user a natural review point between parse and match, and another before the mapping is finalized.
What is NOT changed