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Register specimens and containers through one module (slice 1: bulk combined import) - #90

Draft

m-murphy wants to merge 27 commits into

chore/agent-guardrailsfrom

refactor/specimen-registration

Draft

Register specimens and containers through one module (slice 1: bulk combined import)#90
m-murphy wants to merge 27 commits into
chore/agent-guardrailsfrom
refactor/specimen-registration

Commits on Oct 6, 2026
- refactor(api): register specimens and containers through one module.
  
  m-murphy
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  claude
  committed
  c2b2256
- fix(db): give each request its own transaction on the shared connection.
  
  m-murphy
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  claude
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  4ebfa8c
- docs(db): document withRolledBackTransaction and the transaction lock.
  
  m-murphy
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  1b73036
- fix(imports): keep every error on a bulk combined 409.
  
  m-murphy
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  claude
  committed
  dd73488
- fix(api): reply 409 when a container write hits a constraint.
  
  m-murphy
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  committed
  753fcd4
- fix(registration): blame a collection insert conflict on the row that asked for it.
  
  m-murphy
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  40f483f
- fix(registration): name the identifier that found a plate with another name.
  
  m-murphy
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  committed
  e2c8ef8
Commits on Oct 7, 2026
- fix(registration): reject a location that contradicts the collection's own.
  
  m-murphy
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  committed
  244e1a1
- refactor(api): validate and register /specimens/bulk through Specimen registration.
  
  m-murphy
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  committed
  b6320fd
- refactor(registration): drop collectionsToCreate from the check result.
  
  m-murphy
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  bb9bbe5
- refactor(registration): remove the duplicated container type, error class, and lookups.
  
  m-murphy
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  4b33093
- refactor(registration): map container types to collections and tables in one place.
  
  m-murphy
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  402ebf5
- refactor(registration): replace string claim keys, -1 sentinels, and message matching.
  
  m-murphy
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  claude
  committed
  87aa5c5
- refactor(registration): rename only() to insertedRow().
  
  m-murphy
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  941bc0b
- refactor(registration): word errors for any caller and let the CSV import say "your file".
  
  m-murphy
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  e772047
- test(imports): check validate against per_subject imports and document the difference.
  
  m-murphy
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  claude
  committed
  74b0df2
- Merge branch 'chore/agent-guardrails' into refactor/specimen-registration
  m-murphy
  committed
  74f775a
Commits on Oct 30, 2026
- fix(imports): validate per_subject imports one subject at a time.
  
  m-murphy
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  committed
  c6b04b3
- docs(adr): say that ADR 0010 amends ADR 0006.
  
  m-murphy
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  9404f22
- docs(adr): state that collection identifiers must now agree.
  
  m-murphy
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  c3e03b8
- test(api): add factories for allowed container types and units, and use them.
  
  m-murphy
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  committed
  eaede3b
- refactor(registration): check a required position in one place and reuse the collection type unions.
  
  m-murphy
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  committed
  c67fc14
- refactor(registration): plan a new Specimen with its Source and name the entry-to-specimen map.
  
  m-murphy
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  claude
  committed
  b07abf8
- refactor(registration): leave the paper barcode check to the schema.
  
  m-murphy
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  claude
  committed
  d5aae40
- Merge branch 'chore/agent-guardrails' into refactor/specimen-registration
  m-murphy
  committed
  adc06ca
- Merge branch 'chore/agent-guardrails' into refactor/specimen-registration
  m-murphy
  committed
  eff66d6
- Merge branch 'chore/agent-guardrails' into refactor/specimen-registration
  m-murphy
  committed
  353e95d

Commits

Commits on Oct 6, 2026

Commits on Oct 7, 2026

Commits on Oct 30, 2026