alexmandClaude
88379d152c
The six console scripts (paperspec-check, -build, -validate, -load, -stress, -site) become subcommands of a single `paperspec` command: paperspec validate, load, check, build, stress and site. `python -m paperspec COMMAND` runs the same thing. - paperspec/cli/main.py builds the whole parser, apart from the commands, so `paperspec --help` and `paperspec COMMAND --help` work without a checkout or the tools extra; a command's module is imported only when it runs. - `paperspec` with no command prints the overview: what each command does, examples, and which work anywhere (validate, load) and which need a checkout (check, build, stress, site). Each command's help has a description with advice, and worked examples; a misspelled command gets a suggestion (argparse suggest_on_error); `--version` prints the version and the pinned Unicode version. - Each command module exposes run(args) and returns the exit status. Arguments that parse but do not fit together raise UsageError, which prints the command's usage and exits 2: load now also refuses --built-from or --store without --bundle. - The failure messages say what to do: install paperspec[tools], clone the repository, rerun stress with the printed seed, or run paperspec build when the rebuild check differs. check and stress say how many failures they did not list. - check runs the rebuild as `python -m paperspec build`. - pyproject installs one script, `paperspec`; the pixi tasks and the docs use the subcommands. pixi run check passes (run here as `python -m paperspec check` with src/ on the path); the rebuild is byte-identical. pixi.lock still needs `pixi lock`. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
67 lines
3.9 KiB
Markdown
67 lines
3.9 KiB
Markdown
# SQL
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This folder holds the table definitions for the database form of packages, a team's store, and the bundle.
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## What the database form is for
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A package is a folder of canonical JSON files, one document per folder ([chapter 12](../spec/12-package.md)).
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Canonical JSON is JSON with exactly one valid byte sequence, so a file's hash changes only when its content does.
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Handing over a folder is easy.
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Querying across hundreds of documents in folders is hard.
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The database form holds the same data as rows so that a team can ask SQL questions of it, and a package loaded into the tables unloads back to the same bytes.
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About 500 documents come to about a million and a half rows, and SQLite and Dolt hold that comfortably ([chapter 13](../spec/13-database.md#132-tables)).
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## The three files
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| File | Holds | Runs on |
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| --- | --- | --- |
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| `doc.sql` | Documents: works, documents, witnesses, nodes, pages, locations, references, citations, corrections, IDs, receipts, revocations, suspects and package files. | SQLite, Dolt, PostgreSQL |
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| `store.sql` | What a team adds: roster keys, projects, members, reading paths, layers, annotations, datasets, digitizations, views, policies, submissions and grades. Load `doc.sql` first. | SQLite, Dolt, PostgreSQL |
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| `bundle-sqlite.sql` | The bundle's extra tables: metadata, a full-text index (FTS5, SQLite's search extension) and room for embeddings. Load both files above first. | SQLite |
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## Creating a database
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```sh
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sqlite3 lab.db < sql/doc.sql && sqlite3 lab.db < sql/store.sql
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psql -d lab -f sql/doc.sql && psql -d lab -f sql/store.sql
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dolt sql < sql/doc.sql && dolt sql < sql/store.sql
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```
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The PostgreSQL database `lab` and the Dolt repository must already exist.
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The `sqlite3` line runs as shown; the `psql` and `dolt` lines follow the portability rules of [chapter 13](../spec/13-database.md#131-portability) but have not been run on those engines in this repository.
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To load packages into SQLite without pixi, install the package with its `tools` extra on Python 3.14, then run `paperspec load --sqlite lab.db PACKAGE…`.
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The file [docs/examples.md](../docs/examples.md#load-packages-into-sqlite) has queries to try.
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The loader copies files that have no table (assets, dataset files, derived files) by SHA-256 into `lab.db.assets/`.
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## A first query
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The query below finds every sentence that cites a given reference, which is the citation's context.
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It returns sentence IDs, and `nodes.content` holds each sentence's text.
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```sql
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SELECT c.sentence
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FROM citations c
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JOIN refs r ON r.doc_key = c.doc_key AND r.node = c.ref_node
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WHERE c.doc_key = 'hale2026harmonic-damb' AND r.label = '2';
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```
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On `fixtures/packages/hale2026harmonic-damb` it returns one row, `hca6dc5`: the sentence ending "served as the first test case, with a bending band near 1595 cm⁻¹."
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## Conventions
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- Foreign keys: none.
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Validators check references, so the same file runs everywhere.
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- Types: enumerations are `VARCHAR` with a `CHECK`, JSON values are canonical JSON in `TEXT`, and booleans are `INTEGER` 0 or 1.
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- Names: no table, column or index name is reserved in SQLite, PostgreSQL or MySQL (Dolt is MySQL-compatible).
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The formats' `key`, `index`, `at`, `by`, `before` and `after` become `doc_key`, `idx`, `made_at`, `signer`, `before_hash` and `after_hash`.
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- Round trip: each row keeps every property of its record, so unloading restores the same bytes and the same manifest hash.
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Unloading copies the files with no table from the asset store, which must travel with the database. `paperspec check` tests this for every fixture package.
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- Derived tables: `citations`, `receipt_nodes` and `annotation_targets` are built on load for queries and are not part of the package.
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## Status
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The version is 0.1.0.
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In `registry/formats.json`, `scienting-doc/1` is `candidate`, and the bundle and the project, dataset, digitization and view formats are `provisional`. [Chapter 13](../spec/13-database.md) defines the mapping from files to tables.
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