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Choose Containers for export and statistics through Container selection (ADR 0011) - #101

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m-murphy wants to merge 94 commits into

docs/adr-coding-standardsfrom

feat/container-selection

Open

Choose Containers for export and statistics through Container selection (ADR 0011)#101
m-murphy wants to merge 94 commits into
docs/adr-coding-standardsfrom
feat/container-selection

Commits on Oct 6, 2026
- refactor(activity): resolve sources with resolveSpecimenSources (ADR 0007).
  
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- test(db): close the snapshot test's database and note why it skips the entry point.
  
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- docs: cite ADRs as "ADR 0006" in the files this PR touches.
  
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- docs: write the coding standards as second-person imperatives.
  
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- docs: allow read-only tools that must not migrate to skip openOperationalDatabase.
  
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- refactor(api): find derivation paper parents through the placement module (ADR 0006).
  
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- docs: say when the hand-rolled session helpers are acceptable.
  
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- docs: put the reason for withWriteTransaction back next to the rule.
  
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- docs: restore the test rules the README rewrite dropped.
  
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- docs: keep the whole-*Api override rule in CODING_STANDARDS.md only.
  
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- docs: describe the pre-commit hook and ci:verify in README.md only.
  
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- docs: name the five triage labels in AGENTS.md.
  
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- docs: rename the AGENTS.md "Checks" heading so it isn't confused with the Checks workflow.
  
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- docs: say what CODING_STANDARDS.md holds in the AGENTS.md pointer.
  
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- docs: give AGENTS.md an H1 heading, as CODING_STANDARDS.md has.
  
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- test(db): compare the snapshot's indexes, foreign keys, NOT NULL and types with the migrated schema.
  
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- docs: make the root README the one place for coverage targets.
  
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- docs: restore the CURRENT_SCHEMA_VERSION bullet in the db README.
  
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- test(api): add collection and container subtype factories, and use them.
  
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- refactor(api): bundle a derivation row's child collection name and paper parent type.
  
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  ad24525
- test(api): pin the derivation source-type warning when row 1 has no parent.
  
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  1b26092
- docs: scope the ADR rules to new code and match each ADR.
  
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  0f2c605
- docs: describe formula neutralization in CONTEXT.md's CSV download entry.
  
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  3382d49
- chore(api): lint any transaction callback that returns a Promise, in tests too.
  
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  14eb9fd
- fix(web): say "control batches" in the wizard's fallback error.
  
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- refactor(api): move chunkArray and dateToUpperBound to lib/sql-helpers.
  
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- refactor(controls): share the control definition name check.
  
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- fix(db): give each request its own transaction on the shared connection.
  
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- docs(db): document withRolledBackTransaction and the transaction lock.
  
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- refactor(api): take an insert's returned row through one insertedRow helper.
  
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- refactor(export): replace the 'all' subject-date sentinel with a SubjectDateSelection union.
  
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- refactor(export): keep the "no date means all dates" rule in the contract.
  
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- fix(imports): keep every error on a bulk combined 409.
  
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- refactor(auth): name the bcrypt cost once as BCRYPT_COST.
  
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- docs(api): put the dashboard statistics doc comment on its function.
  
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- refactor(api): branch on every collection type explicitly when deleting a collection.
  
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- refactor(api): use one named chunk size, SQL_IN_CHUNK_SIZE, for IN lists.
  
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- fix(api): reply 409 when a container write hits a constraint.
  
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- refactor(web): list the command dependencies once and rebuild commands only when one changes.
  
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- fix(registration): blame a collection insert conflict on the row that asked for it.
  
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- refactor(web): load the user once per UserProvider with a ref, not module state.
  
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- fix(registration): name the identifier that found a plate with another name.
  
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- refactor(web): fall back to one shared empty list instead of memoizing `data ?? []` per page.
  
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- fix(web): sign out on a 401 from /auth user and session admin requests.
  
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Commits on Oct 7, 2026
- refactor(web): share the box and bag sheet list and expand state in useCollectionSheets.
  
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  34f1167
- fix(web): apply /specimens filters with Apply, so Back undoes one change.
  
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- fix(registration): reject a location that contradicts the collection's own.
  
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- fix(web): rerun the batch-definition and allowed-container-type effects only on their original triggers.
  
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- fix(web): set up box and bag sheet expansion on load or collection change, not every refetch.
  
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- fix(api): drop the remaining study-sized IN lists from stats and export.
  
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- fix(api): require a parent name for ambiguous source sheets in moves.
  
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- refactor(api): validate and register /specimens/bulk through Specimen registration.
  
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- fix(web): read chart colors for the theme being rendered and drop the exhaustive-deps disables.
  
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- refactor(registration): drop collectionsToCreate from the check result.
  
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- fix(api): check sheet name conflicts inside the sheet move transaction.
  
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- refactor(web): let the ContainerTypeUnitsManager effect call its loader directly.
  
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- fix(db): name the qPCR well result UNIQUE constraint as the schema does.
  
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- test(web): stub scrollIntoView in the web test setup instead of guarding it in Locations.
  
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- style(web): drop trailing whitespace the lint fixes left behind.
  
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- fix(web): say "Control definition not found" when the batch wizard's definition 404s.
  
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- test(web): wait for Apply to be enabled in the /specimens URL tests.
  
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- refactor(registration): remove the duplicated container type, error class, and lookups.
  
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- refactor(activity): drop null checks on the non-null container specimenId.
  
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  1db5aff
- refactor(registration): map container types to collections and tables in one place.
  
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  402ebf5
- refactor(registration): replace string claim keys, -1 sentinels, and message matching.
  
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  87aa5c5
- Merge branch 'fix/audit-medium' into chore/agent-guardrails
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- refactor(registration): rename only() to insertedRow().
  
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- Merge branch 'docs/agents-md-restructure' into docs/adr-coding-standards
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- refactor(registration): word errors for any caller and let the CSV import say "your file".
  
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- test(imports): check validate against per_subject imports and document the difference.
  
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- Merge branch 'chore/agent-guardrails' into refactor/specimen-registration
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- Merge branch 'refactor/specimen-registration' into docs/agents-md-restructure
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- Merge branch 'docs/agents-md-restructure' into docs/adr-coding-standards
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- docs: list the registration paths still migrating after slice 1.
  
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Commits on Oct 22, 2026
- docs: record Container selection in ADR 0011 and the glossary.
  
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- feat(api): add the Container selection module from ADR 0011.
  
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- feat(api): match every selected Tag in GET /containers.
  
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- feat(export): select single-study GET export through Container selection.
  
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  de3dc56
- feat(web): label the dashboard's created filter Specimen created.
  
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  4ce22ee
- fix(export): return the rows from JSON POST container exports.
  
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- feat(export): select single-study POST export through Container selection.
  
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  1bf0076
- refactor(statistics): select dashboard statistics through Container selection.
  
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- refactor(export): select multi-study and barcode exports through Container selection.
  
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- Merge branch 'feat/container-selection' into feat/container-selection-96
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- Merge branch 'feat/container-selection' into feat/container-selection-98
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- Merge branch 'feat/container-selection-96' into feat/container-selection
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- Merge branch 'feat/container-selection' into feat/container-selection-97
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Commits on Oct 23, 2026
- refactor(export): take export study fields from the Source and delete the old selection code.
  
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- docs: point export and statistics code at Container selection.
  
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  edbf023
- refactor(api): let Container selection own its filter rules.
  
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  46deaf8
- fix(export): select available types through Container selection.
  
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- test(api): seed Container selection tests through factories.
  
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- fix(api): bound the parameters of each subject-list query.
  
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- test(api): cover Container selection filters across selection kinds.
  
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  3e79a11

Commits

Commits on Oct 6, 2026

Commits on Oct 7, 2026

Commits on Oct 22, 2026

Commits on Oct 23, 2026