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@@ -1,914 +0,0 @@
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# Draft: Resource And Material Sync Guidance For Sirna And Similar Bioyond Systems
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Status: draft for discussion, not an implementation mandate.
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This note triangulates across five source categories with different authority:
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1. `docs/developer_guide/examples/workstation_architecture.md`: desired shape
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and vocabulary. It is a design target, not proof that the current code has
|
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every behavior.
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2. `BioyondWorkstation`, `BioyondResourceSynchronizer`, and shared graphio code:
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the current compatibility anchor. New guidance should mostly preserve this
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lifecycle and extend it deliberately.
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3. Existing non-Sirna Bioyond stations: practical examples of how the shared
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base is used, including shortcuts that should not become policy.
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4. Sirna implementation, plans, findings, and guide notes: stress-test evidence.
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They expose real missing cases, but the current Sirna code is not the
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architecture authority because parts were added without fully aligning to the
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shared base.
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5. UniLabOS resource framework behavior around PLR resources,
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`ResourceTreeSet`, serialize/deserialize, and `update_resource(resources=...)`.
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The short recommendation is:
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Keep the shared Bioyond workstation lifecycle as the center of gravity. Evolve
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the shared synchronizer with small project hooks for classification, ID-based
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resolution, and non-slot material handling, rather than letting Sirna become a
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parallel synchronization model. For Sirna, those hooks should resolve placement
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by Bioyond IDs, distinguish physical slot labware from reagent liquid contents,
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preserve Bioyond IDs in `unilabos_extra`, mutate the local PLR deck, and publish
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the full deck through `update_resource(resources=[deck])`.
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Do not treat every Bioyond stock row as a deck resource.
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## Evidence Weighting
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This task is not a Sirna implementation retrospective. It is a best-practice
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alignment pass across the architecture target, the shared base class, observed
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station behavior, and Sirna's newly exposed edge cases.
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Use the sources this way:
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- Architecture doc: ask "what shape should this system eventually have?"
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- Shared Bioyond base: ask "what behavior must remain compatible today?"
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- Other Bioyond stations: ask "what patterns are already working in practice?"
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- Sirna current code and notes: ask "what did the base model fail to handle, and
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which Sirna fixes conflict with the shared lifecycle?"
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- Live API/schema evidence: ask "what is true for this deployment's material,
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warehouse, and coordinate data?"
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The Sirna AGENT_GUIDE is useful for finding caveats and prior investigations,
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but it should not be cited as an independent source of truth when source code,
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framework behavior, live API evidence, or architecture docs can answer the same
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question.
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## Mental Model
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There are three resource worlds. Confusing them is the main source of bugs.
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| World | Owner | Purpose | Recommended truth |
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| --- | --- | --- | --- |
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| Bioyond/LIMS | Bioyond APIs through `BioyondV1RPC` | External stock, material IDs, warehouse IDs, location IDs, inbound/outbound side effects | External material truth |
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| PLR deck | Workstation driver | Runtime workstation material layout, warehouse occupancy, liquid contents | Local mutation surface |
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| UniLabOS resource tree | `ResourceTreeSet` / ROS node / host resource APIs | Canonical UniLabOS/cloud representation | Framework/cloud truth |
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The architecture guide describes `Deck` as the local material system and
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`ResourceSynchronizer` as the optional external-system bridge
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(`docs/developer_guide/examples/workstation_architecture.md:221`). The broader
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framework serializes PLR objects into `ResourceTreeSet`, whose resource dicts
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carry `id`, `uuid`, `parent_uuid`, `type`, `class`, `pose`, `config`, `data`,
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and `extra` (`unilabos/resources/resource_tracker.py:107`).
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Therefore the correct path is:
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```text
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Bioyond rows
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-> normalized material records
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-> preserve Bioyond materialTypeMode: Sample / Consumables / Reagent
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-> resolve material/location/warehouse IDs
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-> choose UniLabOS handling for that mode
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-> mutate PLR deck
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-> ResourceTreeSet.from_plr_resources([deck])
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-> ROS update_resource(resources=[deck])
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-> host/cloud resource-tree update
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```
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Avoid direct cloud JSON patches and avoid treating Bioyond records as already
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being UniLabOS resource nodes.
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## Target Architecture
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The ideal architecture in `workstation_architecture.md` is still the right
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direction:
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1. `WorkstationBase` owns the local `deck`, workflow state, and hardware
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||||
interface.
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2. `ResourceSynchronizer` owns external material synchronization.
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3. `BioyondResourceSynchronizer` owns the Bioyond-specific use of
|
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`BioyondV1RPC`.
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4. `ROS2WorkstationNode.update_resource(resources)` owns the UniLabOS/cloud
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resource-tree update.
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5. Optional HTTP report handlers may trigger local deck mutation, external sync,
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and cloud publication.
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The documented startup sequence is:
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1. Create workstation.
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2. Initialize PLR deck and warehouses.
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3. Create Bioyond RPC hardware interface.
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4. Create resource synchronizer.
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5. `sync_from_external()`.
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6. Initialize ROS node and children.
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7. `post_init(ros_node)`.
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8. Upload `resources=[deck]`.
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See `docs/developer_guide/examples/workstation_architecture.md:308`,
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`docs/developer_guide/examples/workstation_architecture.md:497`, and
|
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`docs/developer_guide/examples/workstation_architecture.md:737`.
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Important caveat: that document is the hope. It is still valuable because it
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names the desired responsibilities, but current Bioyond stations implement a
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more limited, best-effort side-effect sync. When the doc and current code
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diverge, use the doc to choose direction and the shared base code to choose the
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next compatible step.
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## Current Practical Behavior
|
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The shared `BioyondWorkstation` implementation is the current behavioral
|
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baseline. It does this today:
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|
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1. Requires a deck.
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2. Reconstructs `deck.warehouses` from deck children/config when needed.
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3. Creates `BioyondV1RPC`.
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4. Installs `BioyondResourceSynchronizer`.
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5. Immediately calls `sync_from_external()`.
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6. Later, in `post_init`, publishes the whole deck with
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`ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True,
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resources=[self.deck])`.
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|
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Relevant code:
|
||||
|
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- `BioyondResourceSynchronizer` is defined in
|
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`unilabos/devices/workstation/bioyond_studio/station.py:117`.
|
||||
- `sync_from_external()` fetches stock `typeMode` 0, 1, and 2, then passes all
|
||||
rows to `resource_bioyond_to_plr(...)`
|
||||
(`unilabos/devices/workstation/bioyond_studio/station.py:147`).
|
||||
- `BioyondWorkstation.__init__` installs the synchronizer and syncs immediately
|
||||
(`unilabos/devices/workstation/bioyond_studio/station.py:856`).
|
||||
- `post_init()` uploads the deck (`unilabos/devices/workstation/bioyond_studio/station.py:893`).
|
||||
- `resource_tree_add()` performs Bioyond create/inbound side effects
|
||||
(`unilabos/devices/workstation/bioyond_studio/station.py:958`).
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|
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This practical behavior works for simple physical-resource stock import, but it
|
||||
does not provide full continuous two-way sync, conflict resolution, or reliable
|
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stale-state cleanup. In particular:
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|
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- Re-fetching stock does not clearly clear stale local deck state first.
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- Local-to-external update no-ops unless `unilabos_extra["update_resource_site"]`
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is present.
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- `process_material_change_report()` is mostly TODO-level in the base station.
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- Some station-specific code bypasses the shared synchronizer with direct LIMS
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calls.
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- Some existing stations contain shortcuts that should not be copied, such as
|
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duplicate initialization, stale globals, or hardcoded warehouse/axis cases.
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||||
|
||||
Treat current Bioyond behavior as operationally useful and compatibility
|
||||
important, not as proof that the ideal architecture is already achieved. The
|
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goal is to tighten this base path, not replace it with a Sirna-only path.
|
||||
|
||||
## Recommended Shared Pipeline
|
||||
|
||||
For Sirna and similar Bioyond systems, the base synchronizer should evolve from
|
||||
the current shared path into one shared pipeline with small project hooks:
|
||||
|
||||
```text
|
||||
sync_from_external()
|
||||
fetch stock rows from Bioyond
|
||||
update RPC material cache
|
||||
normalize rows into a common internal shape
|
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preserve materialTypeMode: Sample / Consumables / Reagent
|
||||
resolve warehouse/location by Bioyond IDs when available
|
||||
choose handling for the row's mode
|
||||
apply Sample / Consumables rows as mapped slot labware by default
|
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apply Reagent rows as physical reagent labware or liquid content by evidence
|
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report unknown modes or unmapped handling loudly
|
||||
publish deck if deck changed and ROS node is available
|
||||
```
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|
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Suggested extension points:
|
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|
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```python
|
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class BioyondResourceSynchronizer(ResourceSynchronizer):
|
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def external_material_mode(self, row: dict) -> str:
|
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return row["materialTypeMode"] # Sample | Consumables | Reagent
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|
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def resolve_external_row(self, row: dict) -> dict:
|
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...
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|
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def apply_external_row(self, row: dict, mode: str, resolved: dict) -> None:
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...
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```
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|
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The base class should continue to own:
|
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|
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- stock fetches for `typeMode` 0/1/2;
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- material-cache refresh;
|
||||
- common normalization;
|
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- mode validation for `Sample` / `Consumables` / `Reagent`;
|
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- publication orchestration;
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||||
- error aggregation;
|
||||
- stale-state policy once agreed.
|
||||
|
||||
Project code should own only the parts that are truly deployment-specific:
|
||||
|
||||
- material type/mode to PLR class mapping;
|
||||
- project-local handling inside `Sample` / `Consumables` / `Reagent`;
|
||||
- project-local warehouse ID/name mapping;
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||||
- project-local coordinate conventions;
|
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- special row handling such as Sirna reagent-as-liquid.
|
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|
||||
This keeps existing Bioyond stations close to the same lifecycle while still
|
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absorbing the Sirna lessons that the earlier base did not model. The default
|
||||
hook behavior can remain "Sample/Consumables/Reagent rows become mapped slot
|
||||
labware" for simpler stations; Sirna should override Reagent handling where
|
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evidence requires liquid-content behavior.
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|
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## Sirna Findings To Feed Back Into Shared Design
|
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|
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Treat Sirna as a stress test for the shared base, not as a replacement design.
|
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It raises real questions that earlier stations did not need to answer:
|
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|
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- within the `Reagent` mode, some external rows may be liquid contents rather
|
||||
than slot-occupying reagent labware;
|
||||
- placement should be ID-first where Bioyond supplies material/location IDs;
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- warehouse and axis metadata must survive serialize/deserialize;
|
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project-specific mode handling is available.
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|
||||
For Sirna-like deployments, the old implicit rule "stock row equals PLR
|
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resource" is too coarse. For simpler deployments, it can remain the default
|
||||
mode-handling behavior.
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|
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### IDs Win
|
||||
|
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Placement identity should prefer:
|
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|
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```text
|
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materialId
|
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locationId
|
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materialTypeId
|
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warehouseId / whid
|
||||
```
|
||||
|
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Display/debug fields are not identity:
|
||||
|
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```text
|
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materialName
|
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materialCode
|
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locationCode
|
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locationShowName
|
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warehouseName / whName
|
||||
```
|
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|
||||
`locationCode` such as `1-1` is not globally unique. It can exist in multiple
|
||||
warehouses. Code-only resolution may be kept as a diagnostic fallback, but it
|
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must raise on ambiguity.
|
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|
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The current Sirna ID-first resolver is useful source evidence for this direction
|
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(`unilabos/devices/workstation/bioyond_studio/sirna_station/sirna_station.py:3659`).
|
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The Sirna mega plan captures the same concern, but the implementation and live
|
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Bioyond IDs are the stronger evidence.
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|
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### Bioyond Modes And UniLabOS Handling Are Different
|
||||
|
||||
Bioyond has three primary material modes in this context:
|
||||
|
||||
```text
|
||||
Sample
|
||||
Consumables
|
||||
Reagent
|
||||
```
|
||||
|
||||
Those modes should be preserved as the external taxonomy. UniLabOS still needs a
|
||||
handling decision inside the mode: should the row create/place a physical PLR
|
||||
resource, or update contents on an already-placed parent resource?
|
||||
|
||||
Physical slot resources include things like:
|
||||
|
||||
- tip racks;
|
||||
- plates;
|
||||
- cell culture plates;
|
||||
- empty trough/bottle labware;
|
||||
- other objects that occupy a warehouse slot.
|
||||
|
||||
Reagents are contents of a parent labware when the row describes a liquid rather
|
||||
than a physical holder. For Sirna, Bioyond `stock_material(typeMode=2)` returns
|
||||
`materialTypeMode="Reagent"` rows; those rows still need evidence-based handling
|
||||
as either physical reagent labware or reagent liquid content. The finding in
|
||||
`temp_benyao/sirna/_findings/2026-05-07_reagents_vs_resources.md:6` records the
|
||||
bug: the generic path can fall back to `RegularContainer`, fail registry lookup,
|
||||
and drop reagent rows such as `试剂槽裂解液/Betame`.
|
||||
|
||||
Recommended behavior:
|
||||
|
||||
1. Validate `materialTypeMode` as `Sample`, `Consumables`, or `Reagent`.
|
||||
2. For `Sample` and `Consumables`, default to mapped slot labware: instantiate
|
||||
the mapped PLR class and place it into the resolved warehouse slot.
|
||||
3. For `Reagent`, decide whether the row represents physical reagent labware or
|
||||
reagent liquid content from material type evidence, row shape, and live data.
|
||||
4. For physical reagent labware, place the mapped PLR resource in the resolved
|
||||
slot.
|
||||
5. For reagent liquid content, find the parent trough/bottle and attach liquid
|
||||
metadata to its tracker.
|
||||
6. Preserve Bioyond IDs in `parent.unilabos_extra["reagent_bioyond_ids"]`.
|
||||
7. Make liquid attachment idempotent by Bioyond material ID.
|
||||
8. If the parent labware is missing or the mode/handling cannot be resolved,
|
||||
defer or log with IDs; do not guess.
|
||||
|
||||
The existing Sirna helper `_attach_liquid_to_parent()` already follows the
|
||||
idempotent metadata direction
|
||||
(`unilabos/devices/workstation/bioyond_studio/sirna_station/sirna_station.py:4074`).
|
||||
|
||||
### The `0003` Question Must Stay Evidence-Based
|
||||
|
||||
Do not blindly map `materialTypeCode 0003` to `BioyondSirna_ReagentTrough`.
|
||||
|
||||
If live/schema evidence says a `0003` row is physical trough labware, map it to
|
||||
a PLR resource class. If evidence says it is liquid content, attach it to the
|
||||
parent trough. If evidence is contradictory, mark it unsupported and log the
|
||||
Bioyond IDs.
|
||||
|
||||
Treat this as an open design decision until source/schema/live evidence settles
|
||||
the row shape. The Sirna plan records the question, but it should not decide the
|
||||
mapping by itself.
|
||||
|
||||
### Sirna Warehouse And Axis Rules Are Project-Local
|
||||
|
||||
Sirna warehouse layout and axis conventions must be verified from Sirna source,
|
||||
Sirna schema, current deck behavior, and live/read-only Sirna APIs when
|
||||
available. Do not import Peptide, reaction, dispensing, or cell station layout
|
||||
truth.
|
||||
|
||||
For Sirna specifically, the current integrated deck display should be treated as
|
||||
the good baseline. The prior col-row slot-key fix is already present in the
|
||||
deck/graphio path, and any remaining x/y or y-reverse correction should be
|
||||
handled through shared warehouse metadata and shared graphio/display mapping
|
||||
rather than by reshaping the Sirna station display ad hoc.
|
||||
|
||||
### Display Geometry: Evidence Before Axis Values
|
||||
|
||||
Peptide resource sync should not be treated as a validated model, but its
|
||||
UniLabOS display work is useful and should influence this guidance.
|
||||
|
||||
Confirmed Peptide behavior:
|
||||
|
||||
- Peptide live warehouse evidence found `自动化堆栈` with 170 locations where
|
||||
`code="10-17"` appears at `x=17, y=10`
|
||||
(`../Uni-Lab-OS-Peptide/temp_benyao/peptide/_findings/2026-05-13_1404_peptide_col_row_deck.md:6`).
|
||||
- Peptide's current display convention is Peptide-specific evidence:
|
||||
`bioyond_axis="xy_col_row"` and `bioyond_key_axis="col_row"` in the current
|
||||
Peptide station implementation. Do not copy that pair into Sirna or any other
|
||||
project without live warehouse evidence for that target system. With this
|
||||
Peptide combination, graphio does not apply the legacy x/y swap
|
||||
(`../Uni-Lab-OS-Peptide/unilabos/resources/graphio.py:868`).
|
||||
- Peptide models the main automation stack as 17 visual rows by 10 visual
|
||||
columns while preserving labels such as `10-17`
|
||||
(`../Uni-Lab-OS-Peptide/unilabos/resources/bioyond/decks.py:308`).
|
||||
- Peptide warehouses and deck child positions use `frontend_y_flip=True` /
|
||||
`_frontend_y_flipped_coordinate(...)` so stored PLR coordinates compensate for
|
||||
the frontend y-axis inversion
|
||||
(`../Uni-Lab-OS-Peptide/unilabos/resources/bioyond/decks.py:299`;
|
||||
`temp_benyao/peptide/_findings/2026-05-13_1514_frontend_y_flip_layout.md:6`).
|
||||
- The older Peptide graph-layout note is stale for the Sirna discussion. The
|
||||
current Sirna integrated station/deck display is a good baseline; the reusable
|
||||
Peptide lesson is axis metadata and frontend y-reverse compatibility.
|
||||
- Peptide tests encode the intended behavior: `10-17` lands at row 17 /
|
||||
column 10, and after frontend y-flip the displayed site positions match the
|
||||
expected top-to-bottom layout
|
||||
(`../Uni-Lab-OS-Peptide/temp_benyao/peptide/tests/test_peptide_deck_layout.py:60`).
|
||||
|
||||
Guidance for Sirna and similar systems:
|
||||
|
||||
1. Treat `bioyond_axis` and `bioyond_key_axis` as two separate concepts:
|
||||
- `bioyond_axis` describes how Bioyond numeric `x/y` map to visual axes.
|
||||
- `bioyond_key_axis` describes how slot labels such as `10-17` are generated
|
||||
or preserved.
|
||||
2. Do not infer display orientation from label strings alone. Both `row_col`
|
||||
and `col_row` can preserve the same final label text while producing
|
||||
different visual layouts and graphio swap behavior.
|
||||
3. Use live/read-only `code/x/y` evidence for each project and each warehouse
|
||||
family before choosing axis metadata.
|
||||
4. Keep visual orientation fixes separate from material identity. IDs and slot
|
||||
labels determine registration; display dimensions and frontend y-flip only
|
||||
determine how the deck appears.
|
||||
5. Author intended display coordinates first, then convert stored y coordinates
|
||||
for the active frontend convention:
|
||||
- deck child stored y = `deck_height - display_y - child_height`;
|
||||
- warehouse site stored y = `warehouse_height - display_y - site_height`;
|
||||
- graph-level y values should be transformed only when the active frontend
|
||||
convention requires it.
|
||||
6. Preserve the current Sirna display as the baseline unless concrete frontend
|
||||
evidence shows a y-reverse problem. Do not change station/deck graph
|
||||
semantics just to match stale Peptide layout notes.
|
||||
7. Add layout tests that assert:
|
||||
- warehouse `num_items_x`, `num_items_y`, capacity, first key, and last key;
|
||||
- representative `code/x/y` examples land on the intended site key;
|
||||
- frontend y-flip produces expected displayed positions;
|
||||
- generated deck children do not overlap in displayed coordinates.
|
||||
8. When borrowing from Peptide, borrow the evidence pattern: live discovery,
|
||||
axis/key-axis metadata, y-flip tests, and display fixtures. Do not borrow a
|
||||
literal axis pair or Peptide resource-sync behavior as a validated path.
|
||||
|
||||
Concrete live discovery workflow:
|
||||
|
||||
1. Prefer the reusable read-only probe pattern before reading old findings:
|
||||
|
||||
```bash
|
||||
python3 temp_benyao/sirna/tests/probe_readonly_storage_inventory.py \
|
||||
--base-url <api_host> \
|
||||
--api-key <api_key> \
|
||||
--output temp_benyao/<project>/_logs/<timestamp>_readonly_storage_inventory_probe.json
|
||||
```
|
||||
|
||||
This probe checks swagger candidates, project storage/location endpoints,
|
||||
material type endpoints, `warehouse-info-by-mat-type-id`, and `stock-material`,
|
||||
then writes a redacted evidence file and a merged warehouse summary.
|
||||
|
||||
2. For Sirna quick checks, `temp_benyao/sirna/tests/discover_sirna_warehouses.py`
|
||||
is the narrower historical helper. Treat it as a template unless it has been
|
||||
parameterized for the target config.
|
||||
3. Query `/api/storage/location/locations-by-type?type=0&typeMode=0&materialType=0`
|
||||
first for stack names, warehouse IDs, full slot lists, `code`, `x`, `y`, `z`,
|
||||
and display mode. This endpoint is the topology source when available.
|
||||
4. Cross-reference with `/api/lims/storage/material-types` and
|
||||
`/api/lims/storage/warehouse-info-by-mat-type-id` to learn material-type
|
||||
placement constraints. Use `stock-material` only for occupied-slot evidence;
|
||||
it cannot reveal empty topology.
|
||||
5. Infer `bioyond_key_axis` from how slot labels must be generated or preserved,
|
||||
and infer `bioyond_axis` from how raw Bioyond `x/y` must map to PLR holder
|
||||
indices. A label such as `10-17` alone is ambiguous; compare it to the same
|
||||
record's `x/y`, and use boundary examples from non-square stacks.
|
||||
6. Encode the discovered convention on the warehouse resource, not in a one-off
|
||||
station branch. The metadata must serialize/deserialize with the warehouse
|
||||
because graph load and cloud sync rebuild resources.
|
||||
7. Add or update layout tests before changing Sirna display behavior. For Sirna,
|
||||
test against the current good display first, then only change shared x/y or
|
||||
y-reverse mapping if the fixture demonstrates a real mismatch.
|
||||
|
||||
### Deserialize Must Be Idempotent
|
||||
|
||||
This is confirmed framework behavior, not a possible risk. Resource publication
|
||||
builds `ResourceTreeSet` from live PLR resources by calling
|
||||
`resource.serialize()` and `resource.serialize_all_state()`
|
||||
(`unilabos/resources/resource_tracker.py:547`). Readback/reconstruction goes
|
||||
through `ResourceTreeSet.to_plr_resources()`, finds the PLR subclass, calls
|
||||
`sub_cls.deserialize(...)`, then restores PLR state, UUIDs, and `unilabos_extra`
|
||||
(`unilabos/resources/resource_tracker.py:637`). `ResourceTreeSet.dump()` also
|
||||
serializes resource nodes while excluding `children` from each individual node
|
||||
record (`unilabos/resources/resource_tracker.py:914`), so parent/child
|
||||
relationships and object state must survive the framework tree shape rather than
|
||||
only an in-memory PLR object graph.
|
||||
|
||||
Sirna resource/deck classes therefore must survive:
|
||||
|
||||
1. registry-time construction;
|
||||
2. `Resource.deserialize()` round trips;
|
||||
3. cloud-synced deck state with serialized children.
|
||||
|
||||
If a synced deck already has serialized `children`, default setup must not
|
||||
create duplicate/stale child resources. Sirna noticed this problem, but the
|
||||
reason is framework-level: cloud/resource-tree sync reconstructs PLR objects
|
||||
from serialized state, so constructors and setup logic must be idempotent.
|
||||
|
||||
Existing Sirna deck code already acknowledges the issue: `BIOYOND_Sirna_Deck`
|
||||
turns `setup=False` during deserialize when serialized `children` are present
|
||||
(`unilabos/resources/bioyond/decks.py:153`). Sirna material classes also use
|
||||
registry-visible `@resource(...)` decorators and tolerant constructors with
|
||||
`*args, **kwargs`, defaults, and `ordering` fallbacks
|
||||
(`unilabos/resources/bioyond/sirna_materials.py:14`). Treat those as required
|
||||
patterns for any new synced resource class.
|
||||
|
||||
Guidance:
|
||||
|
||||
- Do not add a deck/resource class until it round-trips through
|
||||
`Resource.serialize()` / `Resource.deserialize()` and
|
||||
`ResourceTreeSet.from_plr_resources(...).to_plr_resources()`.
|
||||
- Preserve `unilabos_uuid`, parentage, `unilabos_extra`, and liquid state across
|
||||
the round trip.
|
||||
- Make default setup conditional: if serialized children exist, do not recreate
|
||||
default warehouses or default child resources on top of them.
|
||||
- Itemized PLR subclasses must provide `ordered_items` or `ordering`; otherwise
|
||||
deserialization can fail or rebuild a different structure.
|
||||
|
||||
## Startup And Resync Recommendation
|
||||
|
||||
The current Sirna code installs `SirnaResourceSynchronizer` after
|
||||
`super().post_init(ros_node)` (`sirna_station.py:363`). That is useful as a
|
||||
phase patch and as evidence that classification hooks are needed, but it should
|
||||
not become the long-term lifecycle. Base initialization may already have run
|
||||
generic stock sync and base post-init may already have published the deck before
|
||||
the Sirna synchronizer is installed.
|
||||
|
||||
Recommended pathway:
|
||||
|
||||
1. Keep the `BioyondWorkstation` lifecycle as the base path.
|
||||
2. Add a synchronizer factory or hook registration point before eager sync, for
|
||||
example `create_resource_synchronizer()`.
|
||||
3. Let Sirna provide classification/resolution hooks through that shared
|
||||
synchronizer shape.
|
||||
4. Make startup sync use the installed hook-aware synchronizer before the first
|
||||
deck publication.
|
||||
5. Make manual resync, reset resync, report-triggered resync, and future
|
||||
periodic sync all call `self.resource_synchronizer.sync_from_external()`.
|
||||
6. Do not instantiate fresh base synchronizers inside Sirna actions, because
|
||||
that bypasses the installed project logic.
|
||||
|
||||
This directly addresses the overlap finding in
|
||||
`temp_benyao/sirna/_findings/2026-05-12_sirna_synchronizer_overlap.md:6`.
|
||||
|
||||
## Material Registration From Create-Order Results
|
||||
|
||||
Create-order allocation registration should remain separate from stock sync, but
|
||||
it should use the same classification and apply logic.
|
||||
|
||||
Recommended create-order pipeline:
|
||||
|
||||
1. Normalize allocation records into:
|
||||
|
||||
```python
|
||||
{
|
||||
"materialId": "...",
|
||||
"materialCode": "...",
|
||||
"materialName": "...",
|
||||
"materialTypeId": "...",
|
||||
"materialTypeCode": "...",
|
||||
"materialTypeMode": "Sample|Consumables|Reagent",
|
||||
"materialTypeName": "...",
|
||||
"locationId": "...",
|
||||
"locationCode": "...",
|
||||
"locationShowName": "...",
|
||||
}
|
||||
```
|
||||
|
||||
2. Resolve warehouse and slot by:
|
||||
|
||||
```text
|
||||
material-info(materialId)
|
||||
-> warehouse-info-by-mat-type-id(materialTypeId) matched by locationId
|
||||
-> code-only diagnostic fallback only if unambiguous
|
||||
```
|
||||
|
||||
3. Classify as `slot_labware`, `liquid_content`, or `unsupported`.
|
||||
4. Apply mutation to the PLR deck.
|
||||
5. Publish the full deck once after the batch.
|
||||
|
||||
The current Sirna `_register_materials_to_tree()` already documents this flow
|
||||
(`sirna_station.py:3659`) and should be the local reference implementation until
|
||||
the shared hook is designed.
|
||||
|
||||
## Cloud / UniLabOS Publication Rules
|
||||
|
||||
Always mutate real tracked PLR resources first. Then publish through the
|
||||
framework.
|
||||
|
||||
Correct call shape:
|
||||
|
||||
```python
|
||||
ROS2DeviceNode.run_async_func(
|
||||
self._ros_node.update_resource,
|
||||
True,
|
||||
**{"resources": [self.deck]},
|
||||
)
|
||||
```
|
||||
|
||||
The real method is:
|
||||
|
||||
```python
|
||||
async def update_resource(self, resources: List["ResourcePLR"])
|
||||
```
|
||||
|
||||
See `unilabos/ros/nodes/base_device_node.py:727`.
|
||||
|
||||
Do not call:
|
||||
|
||||
```python
|
||||
update_resource(resource_name=..., resource_data=...)
|
||||
```
|
||||
|
||||
Do not manually serialize the deck for this path. `update_resource()` creates a
|
||||
`ResourceTreeSet`, sends it to `/c2s_update_resource_tree`, and applies returned
|
||||
UUID mappings. Missing root parent UUIDs are auto-mounted to the current device,
|
||||
so parentage should be preserved on PLR objects before publication.
|
||||
|
||||
## Metadata Contract
|
||||
|
||||
Every Bioyond-originated slot resource should carry enough metadata for unload,
|
||||
audit, and later sync:
|
||||
|
||||
```python
|
||||
plr_resource.unilabos_extra = {
|
||||
"material_bioyond_id": mat["materialId"],
|
||||
"material_bioyond_code": mat["materialCode"],
|
||||
"material_bioyond_name": mat["materialName"],
|
||||
"material_bioyond_type_id": mat["materialTypeId"],
|
||||
"material_bioyond_type_code": mat["materialTypeCode"],
|
||||
"material_bioyond_type_mode": mat["materialTypeMode"],
|
||||
"location_bioyond_id": mat["locationId"],
|
||||
"location_code": resolved["location_code"],
|
||||
"warehouse_bioyond_id": resolved["warehouse_id"],
|
||||
"warehouse_bioyond_name": resolved["warehouse_name"],
|
||||
"location_resolution_source": resolved["source"],
|
||||
}
|
||||
```
|
||||
|
||||
Every Bioyond-originated liquid content should preserve equivalent metadata on
|
||||
the parent labware:
|
||||
|
||||
```python
|
||||
parent.unilabos_extra.setdefault("reagent_bioyond_ids", []).append({
|
||||
"material_bioyond_id": mat["materialId"],
|
||||
"material_bioyond_code": mat["materialCode"],
|
||||
"material_bioyond_name": mat["materialName"],
|
||||
"material_bioyond_type_id": mat["materialTypeId"],
|
||||
"material_bioyond_type_code": mat["materialTypeCode"],
|
||||
"location_bioyond_id": mat["locationId"],
|
||||
"quantity": mat.get("quantity"),
|
||||
"location_resolution_source": resolved["source"],
|
||||
})
|
||||
```
|
||||
|
||||
This metadata is not decorative. It is required for correct unload, audit,
|
||||
duplicate prevention, and future round-trip sync.
|
||||
|
||||
## Stale State And Conflict Policy
|
||||
|
||||
This is confirmed current behavior, not just a theoretical risk.
|
||||
|
||||
Current stock import places resources into empty warehouse slots and skips
|
||||
occupied slots. That prevents overwrites, but it can leave stale local resources
|
||||
after external moves/deletes.
|
||||
|
||||
Evidence:
|
||||
|
||||
- `BioyondResourceSynchronizer.sync_from_external()` fetches Bioyond stock and
|
||||
delegates to `resource_bioyond_to_plr(...)`, but it does not compute a
|
||||
before/after diff or remove local resources absent from the snapshot
|
||||
(`unilabos/devices/workstation/bioyond_studio/station.py:147`).
|
||||
- `resource_bioyond_to_plr(...)` only assigns when the target warehouse position
|
||||
is empty or a placeholder; when a real resource already occupies the slot, it
|
||||
logs "跳过放置" and leaves the existing object in place
|
||||
(`unilabos/resources/graphio.py:936`).
|
||||
- Bioyond outbound/removal logic exists in separate local-to-external hooks such
|
||||
as `resource_tree_remove(...)`, but that is not invoked by stock refresh for
|
||||
Bioyond rows that disappeared externally
|
||||
(`unilabos/devices/workstation/bioyond_studio/station.py:987`).
|
||||
|
||||
Recommended direction:
|
||||
|
||||
1. Define Bioyond as the source of truth for external stock snapshots unless a
|
||||
local operation is in progress.
|
||||
2. Before applying a stock snapshot, compute a diff by Bioyond material ID.
|
||||
3. Remove or mark local resources whose Bioyond IDs disappeared from the
|
||||
snapshot, subject to workflow safety checks.
|
||||
4. Move local resources whose Bioyond location ID changed.
|
||||
5. Attach/detach liquid contents idempotently by Bioyond material ID.
|
||||
6. Publish once after applying the batch.
|
||||
7. In ambiguous or active-operation cases, log and require manual confirmation.
|
||||
|
||||
Until this policy exists, call the current implementation "refresh/import" rather
|
||||
than "authoritative synchronization."
|
||||
|
||||
## External-To-Local And Local-To-External Boundaries
|
||||
|
||||
External-to-local:
|
||||
|
||||
- Bioyond stock and create-order allocation rows mutate the local PLR deck.
|
||||
- Then UniLabOS publication derives resource trees from the PLR deck.
|
||||
|
||||
Local-to-external:
|
||||
|
||||
- `resource_tree_add` / update / remove may call Bioyond add, inbound, outbound,
|
||||
or move APIs.
|
||||
- These paths should require Bioyond IDs or explicit creation parameters.
|
||||
- Movement should use `unilabos_extra["update_resource_site"]` only as an
|
||||
explicit request, not as hidden ambient state.
|
||||
- After successful Bioyond side effects, refresh or update the PLR deck and
|
||||
publish the deck.
|
||||
|
||||
Avoid station-level direct LIMS calls that bypass the synchronizer unless the
|
||||
action explicitly reconciles the deck afterward.
|
||||
|
||||
## Error Handling Rules
|
||||
|
||||
Fail loudly on:
|
||||
|
||||
- unknown material type code/name;
|
||||
- unresolved warehouse ID/name;
|
||||
- location ID not found in `warehouse-info-by-mat-type-id`;
|
||||
- code-only location ambiguity;
|
||||
- missing parent labware for liquid content;
|
||||
- invalid PLR resource class or `Resource.deserialize()` failure;
|
||||
- Bioyond RPC returning empty/fallback values where an ID is required.
|
||||
|
||||
Do not silently create `RegularContainer` to hide mapping failures. The Sirna
|
||||
finding at `temp_benyao/sirna/_findings/2026-05-07_reagents_vs_resources.md:52`
|
||||
calls this out as a reusable trap.
|
||||
|
||||
## Tests And Validation
|
||||
|
||||
Minimum offline tests:
|
||||
|
||||
1. `update_resource` is called only with `resources=[deck]`.
|
||||
2. `ResourceTreeSet.from_plr_resources([deck])` preserves UUIDs, parentage,
|
||||
`data`, and `unilabos_extra`.
|
||||
3. Sirna allocation records resolve by `material-info` first.
|
||||
4. `warehouse-info-by-mat-type-id` resolves by `locationId`.
|
||||
5. Code-only fallback raises on ambiguous slots.
|
||||
6. `Sample` and `Consumables` rows become slot labware.
|
||||
7. Reagent content rows become parent liquid metadata.
|
||||
8. Re-running registration does not duplicate liquid entries.
|
||||
9. Missing parent labware is deferred/logged, not guessed.
|
||||
10. Unknown material type emits Bioyond IDs.
|
||||
11. Deck deserialize does not recreate duplicate default children.
|
||||
12. Warehouse coordinate mapping is tested per warehouse, not globally.
|
||||
13. A synced Sirna deck round-trips through PLR deserialize and
|
||||
`ResourceTreeSet` conversion without duplicate default children.
|
||||
14. Stock refresh with a missing Bioyond material ID proves current add/skip
|
||||
behavior first, then verifies the chosen diff/delete policy once implemented.
|
||||
15. Display geometry tests cover project-local live discovery fixtures,
|
||||
`bioyond_axis`, `bioyond_key_axis`, representative `code/x/y` mappings,
|
||||
frontend y-flip, and no-overlap deck layout.
|
||||
|
||||
Focused Sirna command:
|
||||
|
||||
```bash
|
||||
pytest temp_benyao/sirna/tests/test_sirna_resource_system.py -q
|
||||
```
|
||||
|
||||
Shared conversion command, when changing graphio or Bioyond converters:
|
||||
|
||||
```bash
|
||||
pytest tests/resources/test_converter_bioyond.py -q
|
||||
```
|
||||
|
||||
Live/read-only validation should capture fixtures for:
|
||||
|
||||
- `stock_material(typeMode=0/1/2, includeDetail=true)`;
|
||||
- `material-info(materialId)`;
|
||||
- `warehouse-info-by-mat-type-id(materialTypeId)`;
|
||||
- create-order allocation records;
|
||||
- frontend/cloud resource-tree readback after publication.
|
||||
|
||||
## Discrepancies To Discuss
|
||||
|
||||
### 1. Architecture Is Direction; Base Code Is The Compatibility Anchor
|
||||
|
||||
The architecture guide presents `ResourceSynchronizer` as bidirectional. Current
|
||||
Bioyond code is mostly eager external import plus selected add/remove/update
|
||||
side effects. It has no complete continuous conflict-resolution loop.
|
||||
|
||||
Sirna current code should be read in this context: it exposes missing
|
||||
capabilities, but parts of it conflict with the existing base lifecycle because
|
||||
it was layered on after the base sync behavior already existed.
|
||||
|
||||
Recommendation: keep the bidirectional architecture as the target, preserve
|
||||
`BioyondWorkstation` as the implementation anchor, and introduce shared hooks
|
||||
for the missing Sirna-class problems. Describe the current implementation as
|
||||
best-effort refresh plus Bioyond side effects until a diff/conflict policy
|
||||
exists.
|
||||
|
||||
### 2. The Doc Centers `Deck`; The Framework Centers `ResourceTreeSet`
|
||||
|
||||
The architecture guide uses PLR `Deck` as the material system. UniLabOS resource
|
||||
tracking uses `ResourceTreeSet` as the canonical serialized representation.
|
||||
|
||||
Recommendation: phrase the model as "Deck is the local PLR mutation surface;
|
||||
ResourceTreeSet is the UniLabOS/cloud representation derived from it."
|
||||
|
||||
### 3. Base Bioyond Sync Treats Every Stock Row As PLR Resource
|
||||
|
||||
`BioyondResourceSynchronizer.sync_from_external()` currently feeds typeMode
|
||||
0/1/2 rows into `resource_bioyond_to_plr(...)`.
|
||||
|
||||
Sirna evidence shows this is wrong for reagent/content-like rows.
|
||||
|
||||
Recommendation: add classification hooks before conversion. Rows classified as
|
||||
liquid content must not go through standalone PLR resource conversion.
|
||||
|
||||
### 4. Sirna Fix Exists As A Fork, Not A Shared Hook
|
||||
|
||||
Current `SirnaResourceSynchronizer` captures the important reagent-as-liquid
|
||||
question, but it duplicates or bypasses shared sync mechanics. Startup can run
|
||||
base sync before the Sirna synchronizer is installed, and manual/reset paths
|
||||
have used fresh base synchronizers.
|
||||
|
||||
Recommendation: keep the discovered behavior where evidence supports it, but
|
||||
refactor the shape. A factory/hook in the shared synchronizer is preferable to a
|
||||
long-lived parallel sync class.
|
||||
|
||||
### 5. Sirna Create-Order Registration Is Stronger Than Stock Sync
|
||||
|
||||
Create-order registration now has ID-first resolution and a clearer classifier.
|
||||
That is valuable evidence, not automatically the canonical sync design. The
|
||||
stock sync path still resolves external liquid rows by warehouse name/code and
|
||||
stores weaker metadata.
|
||||
|
||||
Recommendation: extract the stronger resolver/classifier ideas into shared
|
||||
hooks, then converge stock sync and create-order registration on the same
|
||||
functions.
|
||||
|
||||
### 6. Graphio Has Shared Fragility
|
||||
|
||||
`resource_bioyond_to_plr()` contains hardcoded warehouse/coordinate cases and a
|
||||
fallback to `RegularContainer`. Hardening it affects multiple Bioyond projects.
|
||||
|
||||
Recommendation: after Sirna is green, discuss shared graphio hardening in a
|
||||
separate change: no silent `RegularContainer`, explicit unknown-type diagnostics,
|
||||
and project-specific axis metadata instead of hardcoded names.
|
||||
|
||||
### 7. Serialize/Deserialize Is A Gating Contract
|
||||
|
||||
This is not optional documentation neatness. Any new resource/deck class or sync
|
||||
metadata must pass the framework serialize/deserialize path before it can be
|
||||
trusted in cloud-synced operation.
|
||||
|
||||
Recommendation: make round-trip tests part of acceptance for resource-system
|
||||
changes, especially for Sirna deck setup, warehouse metadata, `reagent_bioyond_ids`,
|
||||
liquid tracker state, and itemized labware ordering.
|
||||
|
||||
### 8. Existing Stock Sync Is Add/Skip-Biased, Not Delete-Aware
|
||||
|
||||
Current `sync_from_external()` imports and places observed Bioyond resources,
|
||||
but it does not delete local resources missing from the latest stock snapshot.
|
||||
When a target slot is occupied by a real resource, graphio skips placement rather
|
||||
than replacing it.
|
||||
|
||||
Recommendation: describe the current behavior as "stock refresh/import" until a
|
||||
Bioyond-ID diff policy is implemented. Deletion/removal must be a deliberate
|
||||
phase, with workflow-safety checks and tests, not implied by the current stock
|
||||
sync name.
|
||||
|
||||
### 9. Peptide Display Is Useful; Peptide Sync Is Not Yet Authority
|
||||
|
||||
Peptide's latest display work is useful evidence for Peptide's own warehouse
|
||||
axis/key-axis metadata and for the shared need to account for frontend y-axis
|
||||
inversion. It does not define Sirna's axis values. Its resource sync remains
|
||||
untested/problematic and should not be treated as the model for Sirna sync
|
||||
behavior.
|
||||
|
||||
Recommendation: fold the Peptide display lesson into shared guidance as a
|
||||
discovery-and-test pattern, not as a literal axis pair. Keep Sirna display
|
||||
behavior grounded in Sirna live evidence and the current good deck baseline; keep
|
||||
resource synchronization recommendations grounded in the Sirna ID-first
|
||||
registration path and the shared Bioyond synchronizer refactor.
|
||||
|
||||
### 10. Some Existing Stations Should Be Examples Only, Not Templates
|
||||
|
||||
Non-Sirna stations show useful patterns, but also shortcuts:
|
||||
|
||||
- direct LIMS calls bypassing the synchronizer;
|
||||
- duplicate `super().__init__()` in reaction station;
|
||||
- stale/undefined `WAREHOUSE_MAPPING` references;
|
||||
- RPC methods collapsing failures into empty values;
|
||||
- no robust stale deck cleanup on stock refresh.
|
||||
|
||||
Recommendation: borrow the shared deck publication and Bioyond ID metadata
|
||||
patterns, not the incidental shortcuts.
|
||||
|
||||
## Recommended Discussion Path
|
||||
|
||||
For the next implementation discussion, decide these in order:
|
||||
|
||||
1. What is the smallest shared-base extension that lets project hooks exist
|
||||
before eager sync without breaking existing Bioyond stations?
|
||||
2. Should `BioyondWorkstation` gain a synchronizer factory, a hook registry, or
|
||||
a delayed eager-sync point?
|
||||
3. Is `materialTypeCode 0003` in current Sirna live data physical labware,
|
||||
liquid content, or both depending on row shape?
|
||||
4. Where should Sirna warehouse Bioyond IDs live: station config, deck metadata,
|
||||
or both?
|
||||
5. Should stock refresh clear/diff deck state now, or remain append/skip until
|
||||
after create-order registration is stable?
|
||||
6. Should `update_resource` remain async/non-blocking for material registration,
|
||||
or should selected user-facing actions fail if publication fails?
|
||||
7. Which parts of the Sirna reagent-as-liquid rule are project-local, and which
|
||||
should become shared Bioyond behavior after Peptide/cell validation?
|
||||
8. Should graphio fallback hardening land before or after Sirna stock sync is
|
||||
fully validated?
|
||||
9. Should any remaining Sirna x/y or y-reverse issue be fixed in shared
|
||||
graphio/display mapping after a live fixture proves it, or should the current
|
||||
Sirna deck remain untouched?
|
||||
|
||||
## Recommended Pathway
|
||||
|
||||
The pragmatic path is:
|
||||
|
||||
1. Preserve and test the current `BioyondWorkstation` lifecycle as the shared
|
||||
compatibility baseline.
|
||||
2. Treat Sirna create-order registration as a local proof of the missing
|
||||
classification/ID-resolution behavior, not as the architecture shape to copy.
|
||||
3. Validate live/read-only Sirna fixtures for `0003`, warehouse IDs, and stock
|
||||
reagent rows.
|
||||
4. Refactor the shared Bioyond synchronizer to expose classification,
|
||||
resolution, and non-slot row hooks with default behavior matching existing
|
||||
stations.
|
||||
5. Make Sirna install hooks before the first external sync and first deck
|
||||
publication through the shared lifecycle.
|
||||
6. Route startup, manual resync, reset resync, and report-triggered resync
|
||||
through the installed synchronizer.
|
||||
7. Converge stock sync and create-order registration on one
|
||||
resolver/classifier/apply implementation.
|
||||
8. Add stale-state diffing only after the basic ID-first path is stable.
|
||||
9. Harden graphio fallback as a shared follow-up.
|
||||
|
||||
This gives Sirna the necessary behavior without locking in a second Bioyond sync
|
||||
system that future projects will have to debug around.
|
||||
576
plan/2026-05-20_add_two_node.md
Normal file
576
plan/2026-05-20_add_two_node.md
Normal file
@@ -0,0 +1,576 @@
|
||||
# Peptide Station 新增三个节点：等待订单完成 + 下料确认 + take-out 同步
|
||||
|
||||
> 日期: 2026-05-20
|
||||
> 目标文件: [peptide_station.py](../unilabos/devices/workstation/bioyond_studio/peptide_station/peptide_station.py)
|
||||
> 参考实现:
|
||||
> - [bioyond_cell_workstation.py](/Users/dp/python/yxz/unilabos/devices/workstation/bioyond_studio/bioyond_cell/bioyond_cell_workstation.py)（`wait_for_order_finish`、`get_material_info`）
|
||||
> - [bioyond_rpc.py L782-824](../unilabos/devices/workstation/bioyond_studio/bioyond_rpc.py)（`take_out`）
|
||||
> - [workstation_architecture.md](../docs/developer_guide/examples/workstation_architecture.md)（HTTP 报送进入 workstation，运行态记录保存在 workstation 内存）
|
||||
> 状态: 仅需求草稿，不写代码
|
||||
|
||||
---
|
||||
|
||||
## 一、需求背景
|
||||
|
||||
`BioyondPeptideStation` 当前实验流程在 `start_experiment`（manual_confirm 启动调度器）之后即结束，缺少：
|
||||
|
||||
1. **等待奔耀回报实验完成**：调度器跑完后，奔耀通过 LIMS 推送 `POST /report/order_finish` 回调；目前 peptide_station 没有把这条推送封装成 action 节点，下游无法在工作流图上等待结果，也拿不到 `usedMaterials` 等下游所需信息。
|
||||
2. **下料引导**：实验完成后操作员需要把样品/产物从仓位里取出，下料前需要看到每个物料对应的 **仓库 / 位置 / 物料名称 / 数量**；下料完成后还需要回写奔耀（调用 `take-out` 接口），让奔耀清空相应库位状态。
|
||||
|
||||
本轮新增三个 action 节点，串在 `start_experiment` 之后：
|
||||
|
||||
```text
|
||||
submit_experiment_dayN
|
||||
-> start_experiment(manual_confirm 上料)
|
||||
-> wait_for_order_finish (等回调 + 生成 unloadTable)
|
||||
-> confirm_unload_materials (manual_confirm 下料确认)
|
||||
-> take_out_materials (调用 take-out 同步奔耀)
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 二、关键设计决策
|
||||
|
||||
### D1. 本轮只支持单订单，`order_ids` 只做占位
|
||||
|
||||
当前不实现多订单等待、乱序回调缓存、并发 wait 隔离。节点输入以 `order_id` 为主，`order_code` 可作为调试兜底。
|
||||
|
||||
`order_ids` 可在 handle/返回值中保留为占位字段，但实现只处理第一笔或直接忽略多订单列表。多订单、乱序回调、跨节点重跑复用缓存放到后续迭代。
|
||||
|
||||
### D2. `start_experiment` 需要显式透传订单字段
|
||||
|
||||
当前 `start_experiment` 只有输入 handles，缺少输出 handles；如果下游 wait 节点要接在 `start_experiment` 之后，必须让 `start_experiment` 透传：
|
||||
|
||||
- `order_id`
|
||||
- `order_ids`（占位）
|
||||
- `order_code`
|
||||
- `resultTable`
|
||||
|
||||
实现时给 `start_experiment` 增加对应 `ActionOutputHandle`，并在返回值里保留这些字段。`submit_experiment_dayN` 的 `start_experiment` 嵌套字典也应包含 `order_code`，便于工作流编辑器连线。
|
||||
|
||||
### D3. `unloadTable` 必须与 `resultTable` 字段一致
|
||||
|
||||
`unloadTable` 不新增 `posX/posY/posZ/unit` 列，直接复用现有 `RESULT_TABLE_COLUMNS` 的四列：
|
||||
|
||||
```python
|
||||
RESULT_TABLE_COLUMNS = [
|
||||
{"name": "设备", "key": "whName"},
|
||||
{"name": "位置", "key": "locationCode"},
|
||||
{"name": "物料名称", "key": "materialName"},
|
||||
{"name": "数量", "key": "quantity"},
|
||||
]
|
||||
```
|
||||
|
||||
`submit_experiment_dayN` 现有上料确认表 `resultTable` 形状如下；`unloadTable` 也必须保持同一 shape，只改 `tableName` 和行数据来源：
|
||||
|
||||
```json
|
||||
{
|
||||
"data": [
|
||||
{
|
||||
"whName": "自动化堆栈",
|
||||
"locationCode": "A1",
|
||||
"materialName": "96孔板",
|
||||
"quantity": "1"
|
||||
}
|
||||
],
|
||||
"columns": [
|
||||
{"name": "设备", "key": "whName"},
|
||||
{"name": "位置", "key": "locationCode"},
|
||||
{"name": "物料名称", "key": "materialName"},
|
||||
{"name": "数量", "key": "quantity"}
|
||||
],
|
||||
"tableName": "resultTable"
|
||||
}
|
||||
```
|
||||
|
||||
`material-info` 官方 schema 中位置坐标字段是 `locations[].x/y/z`，不是 `posX/posY/posZ`。本轮下料表不展示坐标。
|
||||
|
||||
### D4. manual_confirm 只做人确认，take-out 放到普通 action
|
||||
|
||||
`confirm_unload_materials` 只负责展示下料表、等待操作员确认并透传数据；真正的 `take-out` 调用放到后续普通 action `take_out_materials`。
|
||||
|
||||
这样更接近 UniLab manual_confirm 的推荐模式：manual_confirm 是人机确认检查点，副作用由独立普通 action 执行。
|
||||
|
||||
### D5. 本轮不做 unload context 缓存
|
||||
|
||||
虽然 workstation architecture 文档支持在 workstation 内存保存 HTTP 报送记录，但本轮暂不实现 `unload_context_cache` 或 order report 缓存。
|
||||
|
||||
因此本轮限制如下：
|
||||
|
||||
- `wait_for_order_finish` 只等待本次进入节点之后到达的 `/report/order_finish`。
|
||||
- 如果 push 早于 wait 节点到达，本轮不自动补救。
|
||||
- 如果用户在 `confirm_unload_materials` approve 时忘记勾选，节点失败；当前架构不支持原地重新弹出同一个 manual_confirm，也不在本轮实现失败节点重跑。
|
||||
- 后续若要支持重跑复用，应在 `BioyondPeptideStation` 实例上新增 station runtime 的 `unload_context_cache`，按 `orderCode` 缓存 `unloadTable/material_ids/order_id` 等上下文。
|
||||
|
||||
---
|
||||
|
||||
## 三、节点 1：`wait_for_order_finish`（等推送 + 生成 unloadTable）
|
||||
|
||||
### 行为
|
||||
|
||||
1. 解析单订单目标：
|
||||
- 首选 `order_id`。
|
||||
- 如果没有 `order_code`，通过 `self.hardware_interface.order_report(order_id)` 取返回数据中的 `code` 作为 `orderCode`。
|
||||
- `order_ids` 仅占位，本轮不实现多订单循环。
|
||||
2. 设置 `self.last_order_code = order_code`、`self.last_order_report = None`，并 `self.order_finish_event.clear()`。
|
||||
3. 阻塞在 `self.order_finish_event.wait(timeout=timeout_seconds)` 等 LIMS 推送。
|
||||
4. peptide_station override `process_order_finish_report(report_request, used_materials)`：
|
||||
- 先调用 `super().process_order_finish_report(...)` 保留父类行为（状态发布、物料同步等）。
|
||||
- 当 `report_request.data.orderCode == self.last_order_code` 时，把 `report_request.data` 存入 `self.last_order_report`，并 `set()` event。
|
||||
- 非当前订单推送只记录日志，本轮不缓存。
|
||||
5. 解除阻塞后解析 `status`：
|
||||
- `"30"` -> `success`
|
||||
- `"-11"` -> `abnormal_stop`
|
||||
- `"-12"` -> `manual_stop`
|
||||
- 其它 -> `unknown_<status>`
|
||||
- 超时 -> `timeout`
|
||||
6. 对 `report.usedMaterials[].materialId` 调用 `self.hardware_interface.material_info(material_id)`，带本地函数级 `material_info_cache` 避免重复请求。
|
||||
7. 组装 `unloadTable`、`material_ids`、`preintake_ids`、`unload_summary` 并作为输出 handles 暴露。
|
||||
|
||||
### 入参（goal_default）
|
||||
|
||||
| 参数 | 类型 | 说明 |
|
||||
|------|------|------|
|
||||
| `order_id` | `str` | 来自 `start_experiment` 透传输出，必填优先 |
|
||||
| `order_code` | `str` | 调试兜底；若已知 orderCode 可跳过 `order_report` 反查 |
|
||||
| `order_ids` | `List[str]` | 占位字段；本轮不实现多订单 |
|
||||
| `timeout_seconds` | `int` | 默认 `36000`（10h） |
|
||||
| `poll_mode` | `bool` | 默认 `False`；如需要可沿用 bioyond_cell 的轮询等待风格 |
|
||||
|
||||
### 输出 handles
|
||||
|
||||
| key | data_type | 说明 |
|
||||
|-----|-----------|------|
|
||||
| `order_finish_status` | `str` | `success` / `abnormal_stop` / `manual_stop` / `timeout` / `unknown_*` |
|
||||
| `order_finish_report` | `json` | 完整 `report_request.data` |
|
||||
| `used_materials` | `json` | JSON 化后的 `usedMaterials` 列表 |
|
||||
| `material_ids` | `json` | 从 `used_materials` 抽出的 `materialId` 列表，可为空 |
|
||||
| `preintake_ids` | `json` | 本轮默认 `[]`，保留扩展点 |
|
||||
| `unloadTable` | `table` | 下料表，字段与 `resultTable` 一致 |
|
||||
| `unload_summary` | `json` | `{ "order_code": ..., "total_items": N, "missing_material_info": [...] }` |
|
||||
| `order_id` | `str` | 透传给后续节点 |
|
||||
| `order_code` | `str` | 透传给后续节点 |
|
||||
| `order_ids` | `json` | 占位透传 |
|
||||
|
||||
### `unloadTable` 组装规则
|
||||
|
||||
返回结构：
|
||||
|
||||
```json
|
||||
{
|
||||
"data": [
|
||||
{
|
||||
"whName": "自动化堆栈",
|
||||
"locationCode": "A1",
|
||||
"materialName": "多肽产物",
|
||||
"quantity": "10 mg"
|
||||
}
|
||||
],
|
||||
"columns": [
|
||||
{"name": "设备", "key": "whName"},
|
||||
{"name": "位置", "key": "locationCode"},
|
||||
{"name": "物料名称", "key": "materialName"},
|
||||
{"name": "数量", "key": "quantity"}
|
||||
],
|
||||
"tableName": "unloadTable"
|
||||
}
|
||||
```
|
||||
|
||||
每行字段：
|
||||
|
||||
| key | 数据来源 |
|
||||
|-----|----------|
|
||||
| `whName` | `material_info.locations` 中匹配 `usedMaterials.locationId` 的 location 的 `whName`；匹配不到取第一条 location 的 `whName`；失败为空串 |
|
||||
| `locationCode` | 匹配 location 的 `code`；匹配不到取第一条 location 的 `code`；再兜底 `usedMaterials.locationId` |
|
||||
| `materialName` | `material_info.name`；失败为空串 |
|
||||
| `quantity` | `usedMaterials.usedQuantity`，若 `material_info.unit` 存在则拼成字符串（如 `"10 mg"`） |
|
||||
|
||||
`material-info` 失败时不抛异常，对应行尽量保留 `locationCode` / `quantity`，`whName` 和 `materialName` 用空串，并把 `materialId` 放入 `unload_summary.missing_material_info`。
|
||||
|
||||
### 接口依赖
|
||||
|
||||
| 接口 | 调用方式 | 用途 |
|
||||
|------|----------|------|
|
||||
| `process_order_finish_report` 钩子 | 基类 HTTP 服务已注册 | 接 LIMS push |
|
||||
| `POST /api/lims/order/order-report` | `self.hardware_interface.order_report(order_id)` | 从 `order_id` 反查 `orderCode` |
|
||||
| `POST /api/lims/storage/material-info` | `self.hardware_interface.material_info(material_id)` | 查 `whName/locationCode/materialName/unit` |
|
||||
|
||||
#### `order_report(order_id)` API 形式
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": "<orderId UUID>"
|
||||
}
|
||||
```
|
||||
|
||||
响应中本节点只依赖 `data.code`：
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": {
|
||||
"id": "<orderId UUID>",
|
||||
"name": "实验260520-103000",
|
||||
"code": "EXP260520-103000",
|
||||
"status": 30,
|
||||
"statusName": "完成"
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.order_report(order_id)` 已经返回响应中的 `data`，所以实现中应读取 `raw.get("code")`，不是 `raw["data"]["code"]`。
|
||||
|
||||
#### `material_info(material_id)` API 形式
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": "<materialId UUID>"
|
||||
}
|
||||
```
|
||||
|
||||
响应中本节点依赖：
|
||||
|
||||
```json
|
||||
{
|
||||
"id": "<materialId UUID>",
|
||||
"name": "多肽产物",
|
||||
"unit": "mg",
|
||||
"locations": [
|
||||
{
|
||||
"id": "<locationId UUID>",
|
||||
"whid": "<warehouse UUID>",
|
||||
"whName": "自动化堆栈",
|
||||
"code": "A1",
|
||||
"x": 1,
|
||||
"y": 1,
|
||||
"z": 1,
|
||||
"quantity": 10
|
||||
}
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.material_info(material_id)` 已经返回响应中的 `data`。字段映射：
|
||||
|
||||
| unloadTable key | 来源 |
|
||||
|-----------------|------|
|
||||
| `whName` | 匹配 `locationId` 的 `locations[].whName` |
|
||||
| `locationCode` | 匹配 `locationId` 的 `locations[].code` |
|
||||
| `materialName` | `name` |
|
||||
| `quantity` | `usedMaterials[].usedQuantity` + `unit` |
|
||||
|
||||
### 实现要点
|
||||
|
||||
- `BioyondPeptideStation.__init__` 末尾追加 `self.order_finish_event = threading.Event()`、`self.last_order_code = None`、`self.last_order_report = None`。
|
||||
- 新增 `process_order_finish_report` override，先 `super()`，再做单订单匹配。
|
||||
- `used_materials` 参数是 `MaterialUsage` dataclass 列表；输出前必须转成 JSON dict。
|
||||
- `unloadTable` 复用 `RESULT_TABLE_COLUMNS`，不新增 `UNLOAD_TABLE_COLUMNS`。
|
||||
|
||||
---
|
||||
|
||||
## 四、节点 2：`confirm_unload_materials`（人工下料确认）
|
||||
|
||||
### 行为
|
||||
|
||||
1. 接收节点 1 输出的 `order_id` / `order_code` / `material_ids` / `preintake_ids` / `unloadTable`。
|
||||
2. 进入 `NodeType.MANUAL_CONFIRM` 阻塞，操作员根据 `unloadTable` 物理下料。
|
||||
3. 操作员勾选 `materials_unloaded=True` 并 approve 后，节点函数体继续。
|
||||
4. 校验 `materials_unloaded == True`：
|
||||
- 为 True：返回确认结果，并透传 `order_id/material_ids/preintake_ids/unloadTable` 给节点 3。
|
||||
- 为 False：抛 `RuntimeError("下料未确认，拒绝继续 take-out")`。
|
||||
|
||||
### 入参（goal_default）
|
||||
|
||||
| 参数 | 类型 | 说明 |
|
||||
|------|------|------|
|
||||
| `order_id` | `str` | 来自节点 1，必填 |
|
||||
| `order_code` | `str` | 来自节点 1，日志/排错用 |
|
||||
| `material_ids` | `List[str]` | 来自节点 1，可为空 |
|
||||
| `preintake_ids` | `List[str]` | 来自节点 1，默认 `[]` |
|
||||
| `unloadTable` | `table` | 来自节点 1，供人工确认展示 |
|
||||
| `materials_unloaded` | `bool` | manual_confirm 勾选字段，默认 `False` |
|
||||
| `timeout_seconds` | `int` | 默认 `3600` |
|
||||
| `assignee_user_ids` | `List[str]` | `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}` |
|
||||
|
||||
### 输出 handles
|
||||
|
||||
| key | data_type | 说明 |
|
||||
|-----|-----------|------|
|
||||
| `unload_confirmed` | `bool` | 是否已人工确认下料 |
|
||||
| `order_id` | `str` | 透传 |
|
||||
| `order_code` | `str` | 透传 |
|
||||
| `material_ids` | `json` | 透传 |
|
||||
| `preintake_ids` | `json` | 透传 |
|
||||
| `unloadTable` | `table` | 透传 |
|
||||
|
||||
### 实现要点
|
||||
|
||||
- 装饰器使用 `node_type=NodeType.MANUAL_CONFIRM`。
|
||||
- `always_free=True`、`placeholder_keys`、`feedback_interval=300` 与现有 `start_experiment` 保持一致。
|
||||
- 本节点不调用 `take_out`，只做确认与透传。
|
||||
- 忘记勾选后不会自动重新显示下料指引；本轮不实现缓存或失败节点原地重跑。
|
||||
|
||||
---
|
||||
|
||||
## 五、节点 3：`take_out_materials`（调用 take-out 同步奔耀）
|
||||
|
||||
### 行为
|
||||
|
||||
1. 接收节点 2 透传的 `order_id` / `material_ids` / `preintake_ids`。
|
||||
2. 校验 `order_id` 非空。
|
||||
3. 调用 `self.hardware_interface.take_out(order_id, preintake_ids=preintake_ids, material_ids=material_ids)`。
|
||||
4. 返回 `take_out_result`、`unloaded_count`、`success`。
|
||||
|
||||
### 入参
|
||||
|
||||
| 参数 | 类型 | 说明 |
|
||||
|------|------|------|
|
||||
| `order_id` | `str` | 必填 |
|
||||
| `material_ids` | `List[str]` | 可为空；为空时由奔耀按 `orderId` 处理的能力以后现场确认 |
|
||||
| `preintake_ids` | `List[str]` | 可为空，默认 `[]` |
|
||||
| `order_code` | `str` | 日志/排错用 |
|
||||
|
||||
### 输出 handles
|
||||
|
||||
| key | data_type | 说明 |
|
||||
|-----|-----------|------|
|
||||
| `take_out_result` | `json` | `take-out` 原始响应 `{code, message, timestamp, data}` |
|
||||
| `unloaded_count` | `int` | `len(material_ids)` |
|
||||
| `success` | `bool` | `take_out_result.code == 1` 且 `data` 不为 False |
|
||||
|
||||
### 接口依赖
|
||||
|
||||
| 接口 | 调用方式 | 用途 |
|
||||
|------|----------|------|
|
||||
| `POST /api/lims/order/take-out` | `self.hardware_interface.take_out(order_id, preintake_ids, material_ids)` | 通知奔耀同步取出 |
|
||||
|
||||
请求体 schema（helper script 已核对）：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": {
|
||||
"orderId": "<UUID>",
|
||||
"preintakeIds": [],
|
||||
"materialIds": ["<UUID-1>", "<UUID-2>"]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
响应 schema：
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": true
|
||||
}
|
||||
```
|
||||
|
||||
`BioyondV1RPC.take_out(...)` 返回完整响应包，因此 `take_out_materials` 应保留原始包到 `take_out_result`。
|
||||
|
||||
### 实现要点
|
||||
|
||||
- 本轮不修改 `sample_waste_removal`，保持 backward compatibility。
|
||||
- 新节点只调用现有完整能力的 `take_out(...)`。
|
||||
- `preintake_ids` / `material_ids` 都按可选列表处理，默认 `[]`。
|
||||
- `take-out` 返回 `code != 1` 时返回 `success=False` 并记录 warning；是否抛异常留作开放问题。
|
||||
|
||||
---
|
||||
|
||||
## 六、端到端工作流连线
|
||||
|
||||
```mermaid
|
||||
flowchart LR
|
||||
submit["submit_experiment_dayN"] --> start["start_experiment<br/>manual_confirm: 上料"]
|
||||
start -->|order_id, order_code| wait["wait_for_order_finish<br/>等 order_finish + 生成 unloadTable"]
|
||||
wait -->|order_id, material_ids,<br/>preintake_ids, unloadTable| confirm["confirm_unload_materials<br/>manual_confirm: 操作员下料确认"]
|
||||
confirm -->|order_id, material_ids,<br/>preintake_ids| takeout["take_out_materials<br/>调用 take-out 同步奔耀"]
|
||||
bioyond["奔耀 LIMS"] -.HTTP POST /report/order_finish.-> wait
|
||||
wait -.material-info.-> bioyond
|
||||
takeout -.take-out.-> bioyond
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 七、影响面与兼容性
|
||||
|
||||
- **`peptide_station.py`**
|
||||
- 修改 `start_experiment`：增加 `order_id/order_code/order_ids/resultTable` 输出 handles，并在返回值透传。
|
||||
- 增加 `wait_for_order_finish`、`confirm_unload_materials`、`take_out_materials` 三个 action。
|
||||
- 增加 `process_order_finish_report` override。
|
||||
- 增加 `_build_unload_table(...)` 等私有辅助方法。
|
||||
- **`bioyond_rpc.py` 不动**
|
||||
- `take_out` 已有完整 schema 能力。
|
||||
- `sample_waste_removal` 本轮不改，保持兼容。
|
||||
- **基类 `station.py` 不动**
|
||||
- override 中保留 `super().process_order_finish_report(...)` 调用。
|
||||
- **HTTP 服务不动**
|
||||
- `WorkstationHTTPService` 已支持 `/report/order_finish`。
|
||||
- **本轮不做缓存**
|
||||
- 不新增 `unload_context_cache`。
|
||||
- 不支持 push 早于 wait 的自动补救。
|
||||
- 不支持失败 manual_confirm 原地重跑。
|
||||
- **测试**：补在现有路径 `unilabos/devices/workstation/bioyond_studio/peptide_station/tests/test_peptide_station_contracts.py`
|
||||
1. `start_experiment` 输出 handles/返回值透传 `order_id/order_code/order_ids/resultTable`。
|
||||
2. `process_order_finish_report` orderCode 匹配 / 不匹配时 event 是否触发。
|
||||
3. `wait_for_order_finish` 单订单成功、超时、状态映射、`used_materials` JSON 化。
|
||||
4. `_build_unload_table` 列顺序严格等于 `RESULT_TABLE_COLUMNS`，且无 `posX/posY/posZ/unit` 列。
|
||||
5. `material-info` 失败时不抛异常，`missing_material_info` 正确记录。
|
||||
6. `confirm_unload_materials` 未勾选时报错，勾选后透传下游字段且不调用 `take_out`。
|
||||
7. `take_out_materials` 调用 `hardware_interface.take_out(order_id, preintake_ids, material_ids)`，不调用 `sample_waste_removal`。
|
||||
|
||||
---
|
||||
|
||||
## 八、待人类确认的开放问题
|
||||
|
||||
1. **过滤产物 vs 全量**：`usedMaterials` 同时包含试剂、耗材、样品（`typeMode` 区分），下料表是否需要默认排除试剂/耗材？当前默认全量列出。
|
||||
2. **take-out 失败是否阻塞工作流**：本计划暂定返回 `success=False` 并 warning，不抛异常；如果希望奔耀仓位状态必须一致，可改为抛 `RuntimeError`。
|
||||
3. **后续缓存/重跑能力**：如果要支持 push 早到、忘勾选后重跑复用 `unloadTable`，后续应在 `BioyondPeptideStation` station runtime 上实现 `unload_context_cache`，但本轮不做。
|
||||
4. **多订单**：本轮只保留 `order_ids` 占位，不实现多订单等待、乱序回调或并发 wait。
|
||||
|
||||
---
|
||||
|
||||
## 附录 A：API schema 核对摘要
|
||||
|
||||
使用 `temp_benyao/scripts/api_helper.py --root temp_benyao/peptide` 核对：
|
||||
|
||||
### A.1 `POST /api/lims/storage/material-info`
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": "<materialId UUID>"
|
||||
}
|
||||
```
|
||||
|
||||
响应关键字段：
|
||||
|
||||
```json
|
||||
{
|
||||
"id": "<materialId UUID>",
|
||||
"typeName": "样品",
|
||||
"code": "MAT-001",
|
||||
"barCode": "BC-001",
|
||||
"name": "多肽产物",
|
||||
"quantity": 10,
|
||||
"lockQuantity": 0,
|
||||
"unit": "mg",
|
||||
"status": 1,
|
||||
"isUse": true,
|
||||
"locations": [
|
||||
{
|
||||
"id": "<locationId UUID>",
|
||||
"whid": "<warehouse UUID>",
|
||||
"whName": "自动化堆栈",
|
||||
"code": "A1",
|
||||
"x": 1,
|
||||
"y": 1,
|
||||
"z": 1,
|
||||
"quantity": 10
|
||||
}
|
||||
],
|
||||
"detail": []
|
||||
}
|
||||
```
|
||||
|
||||
注意：schema 没有 `posX/posY/posZ`，本轮也不展示坐标。
|
||||
|
||||
### A.2 `POST /api/lims/order/take-out`
|
||||
|
||||
请求：
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-20T10:50:00.123Z",
|
||||
"data": {
|
||||
"orderId": "<orderId UUID>",
|
||||
"preintakeIds": [],
|
||||
"materialIds": ["<materialId UUID>"]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
响应：
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": null,
|
||||
"timestamp": 1779255000000,
|
||||
"data": true
|
||||
}
|
||||
```
|
||||
|
||||
源码中已有 `BioyondV1RPC.take_out(order_id, preintake_ids=None, material_ids=None)`，本轮复用它。
|
||||
|
||||
### A.3 `/report/order_finish`
|
||||
|
||||
`/report/order_finish` 不在 Peptide JSON OpenAPI specs 中；schema 依据：
|
||||
|
||||
- `unilabos/devices/workstation/workstation_http_service.py`
|
||||
- `temp_benyao/peptide/docs/reference/api_manual.md`
|
||||
|
||||
关键字段：
|
||||
|
||||
```json
|
||||
{
|
||||
"token": "token-from-lims",
|
||||
"request_time": "2026-05-20 10:50:00.123",
|
||||
"data": {
|
||||
"orderCode": "EXP260520-103000",
|
||||
"orderName": "实验260520-103000",
|
||||
"startTime": "2026-05-20 09:00:00",
|
||||
"endTime": "2026-05-20 10:50:00",
|
||||
"status": "30",
|
||||
"usedMaterials": [
|
||||
{
|
||||
"materialId": "<materialId UUID>",
|
||||
"locationId": "<locationId UUID>",
|
||||
"typeMode": "1",
|
||||
"usedQuantity": 10
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
```
|
||||
|
||||
`WorkstationHTTPService` 会把 `usedMaterials[]` 转成 `MaterialUsage` dataclass 列表传给 `process_order_finish_report(report_request, used_materials)`；peptide 输出 `used_materials` handle 前需要转回 JSON dict：
|
||||
|
||||
```json
|
||||
[
|
||||
{
|
||||
"materialId": "<materialId UUID>",
|
||||
"locationId": "<locationId UUID>",
|
||||
"typeMode": "1",
|
||||
"usedQuantity": 10
|
||||
}
|
||||
]
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 附录 B：本轮不实现的内容
|
||||
|
||||
- 不做 station runtime 的 `unload_context_cache`。
|
||||
- 不做多订单。
|
||||
- 不做 push 早到后的补救。
|
||||
- 不做 failed manual_confirm 原地重跑。
|
||||
- 不改前端。
|
||||
- 不改 `sample_waste_removal`。
|
||||
461
plan/2026-05-21_01_peptide_reset_four_checkbox_plan.md
Normal file
461
plan/2026-05-21_01_peptide_reset_four_checkbox_plan.md
Normal file
@@ -0,0 +1,461 @@
|
||||
# Peptide Four-Checkbox Reset Plan
|
||||
|
||||
Date: 2026-05-21 16:30
|
||||
Status: Proposal only / not executed
|
||||
|
||||
## Scope
|
||||
|
||||
This plan replaces `2026-05-21_1556_peptide_reset_sirna_reference_plan.md` for Peptide reset work.
|
||||
|
||||
User direction captured here:
|
||||
|
||||
- `take_out` is unnecessary for Peptide reset.
|
||||
- Do not add a material-cache refresh checkbox.
|
||||
- Change reset to four checkbox-controlled operations:
|
||||
- 调度器复位
|
||||
- 订单状态复位
|
||||
- 库位复位
|
||||
- 仪器复位
|
||||
- The first three checkboxes default to checked.
|
||||
- The fourth checkbox, 仪器复位 / `reset_devices`, defaults to unchecked.
|
||||
- Replace the current public `reset` action with:
|
||||
- `reset_auto`: normal ILab action node. This is the renamed/replaced version of the current reset implementation.
|
||||
- `reset_manual`: manual-confirm action node with a physical cleanup confirmation message.
|
||||
|
||||
## Evidence Summary
|
||||
|
||||
Current Peptide source:
|
||||
|
||||
- Reset action code is currently in `unilabos/devices/workstation/bioyond_studio/peptide_station/peptide_station.py`.
|
||||
- Current Peptide reset selects `scheduler_reset`, `reset_order_status`, and `reset_location`, and passes ids to order/location resets.
|
||||
- `BioyondV1RPC.reset_devices()` already calls `/api/lims/device/reset-devices` with only `apiKey` and `requestTime`.
|
||||
- `BioyondV1RPC.scheduler_reset()` already calls `/api/lims/scheduler/reset` with only `apiKey` and `requestTime`.
|
||||
- `BioyondV1RPC.reset_order_status(order_id)` and `reset_location(location_id)` currently send `data`, but live probes showed that omitted `data` succeeds.
|
||||
|
||||
Live Peptide no-data reset probes using `temp_benyao/peptide/peptide_station_config.example.json`:
|
||||
|
||||
- `POST /api/lims/order/reset-order-status` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `POST /api/lims/scheduler/reset` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `POST /api/lims/storage/reset-location` with request keys `["apiKey", "requestTime"]` returned HTTP 200 and `code=1`.
|
||||
- `reset-devices` was not live-probed in this session, but the current RPC wrapper already sends no `data`.
|
||||
|
||||
Raw findings:
|
||||
|
||||
- `temp_benyao/peptide/_findings/2026-05-21_1613_reset_order_status_no_data_live.md`
|
||||
- `temp_benyao/peptide/_findings/2026-05-21_1615_remaining_resets_no_data_live.md`
|
||||
|
||||
## Proposed Public Actions
|
||||
|
||||
### `reset_auto`
|
||||
|
||||
Normal action node. This is the auto/no-manual-confirm path. It replaces the current public `reset` action; do not leave a second public `reset` action unless a later compatibility request explicitly asks for an alias.
|
||||
|
||||
Checkbox schema rule:
|
||||
|
||||
- Use plain `bool` annotations in the action signature.
|
||||
- Do not use `Annotated[bool, Field(...)]` for these checkbox params in this implementation plan.
|
||||
- The current AST registry schema path does not unwrap `Annotated[...]`; plain `bool` is required so generated JSON Schema marks the fields as boolean and the renderer can show checkboxes.
|
||||
- Put human-facing labels/descriptions in the method docstring or action description. If field-level `Field(description=...)` metadata is required later, add registry `Annotated` support and a schema test as a separate change.
|
||||
|
||||
Decorator shape:
|
||||
|
||||
```python
|
||||
@action(
|
||||
always_free=True,
|
||||
goal_default={
|
||||
"reset_scheduler": True,
|
||||
"reset_order_status": True,
|
||||
"reset_location": True,
|
||||
"reset_devices": False,
|
||||
},
|
||||
description="自动复位调度器/订单状态/库位，可选仪器复位",
|
||||
)
|
||||
def reset_auto(
|
||||
self,
|
||||
reset_scheduler: bool = True,
|
||||
reset_order_status: bool = True,
|
||||
reset_location: bool = True,
|
||||
reset_devices: bool = False,
|
||||
**kwargs: Any,
|
||||
) -> Dict[str, Any]:
|
||||
"""自动复位调度器/订单状态/库位，可选仪器复位。
|
||||
|
||||
Args:
|
||||
reset_scheduler[调度器复位]: 调用 /api/lims/scheduler/reset，默认勾选。
|
||||
reset_order_status[订单状态复位]: 调用 /api/lims/order/reset-order-status，默认勾选。
|
||||
reset_location[库位复位]: 调用 /api/lims/storage/reset-location，默认勾选。
|
||||
reset_devices[仪器复位]: 调用 /api/lims/device/reset-devices，默认不勾选。
|
||||
"""
|
||||
...
|
||||
```
|
||||
|
||||
Implementation notes:
|
||||
|
||||
- Use real plain-`bool` parameters, not hidden `**kwargs` and not `Annotated`, so the action renderer can expose four checkboxes.
|
||||
- Rename/replace the existing `reset` action as `reset_auto`; the implementation should not keep the old id-shaped `reset` action as another public path by default.
|
||||
- Keep the three routine reset defaults checked.
|
||||
- Keep `reset_devices` unchecked because it can be broader and more disruptive.
|
||||
- Do not require or resolve order ids or location ids.
|
||||
- Do not call `take_out`.
|
||||
- Do not call `refresh_material_cache`.
|
||||
|
||||
### `reset_manual`
|
||||
|
||||
Manual-confirm node. It should show the operator a physical cleanup warning, then execute the same reset helper as `reset_auto` after the operator confirms.
|
||||
|
||||
Actual manual-confirm decorator pattern in this repo:
|
||||
|
||||
- Use `@action(node_type=NodeType.MANUAL_CONFIRM)`.
|
||||
- Set `always_free=True`.
|
||||
- Add `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}`.
|
||||
- Include `timeout_seconds: int` and `assignee_user_ids: list[str]`.
|
||||
- Add `goal_default` for `timeout_seconds` and `assignee_user_ids`.
|
||||
- Manual-confirm actions are normally side-effect-light, but existing Peptide `start_experiment` is already a `MANUAL_CONFIRM` action that performs scheduler start after the operator gate, so a reset-after-confirm pattern is compatible with current Peptide style.
|
||||
|
||||
Proposed confirmation text:
|
||||
|
||||
```text
|
||||
请确认G3、CEM、Tecan、撕膜机、封膜机、打标机、旋转堆栈上下料位、3个转台等位置的物料已清理完毕；
|
||||
请开门检查冰箱、IDOT、酶标仪、离心机、LCMS内部没有遗留物料。
|
||||
```
|
||||
|
||||
Decorator/function shape:
|
||||
|
||||
```python
|
||||
RESET_MANUAL_CONFIRM_MESSAGE = (
|
||||
"请确认G3、CEM、Tecan、撕膜机、封膜机、打标机、旋转堆栈上下料位、3个转台等位置的物料已清理完毕；\n"
|
||||
"请开门检查冰箱、IDOT、酶标仪、离心机、LCMS内部没有遗留物料。"
|
||||
)
|
||||
|
||||
@action(
|
||||
always_free=True,
|
||||
node_type=NodeType.MANUAL_CONFIRM,
|
||||
placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"},
|
||||
goal_default={
|
||||
"reset_scheduler": True,
|
||||
"reset_order_status": True,
|
||||
"reset_location": True,
|
||||
"reset_devices": False,
|
||||
"physical_cleanup_confirmed": False,
|
||||
"timeout_seconds": 3600,
|
||||
"assignee_user_ids": [],
|
||||
},
|
||||
feedback_interval=300,
|
||||
description=RESET_MANUAL_CONFIRM_MESSAGE,
|
||||
)
|
||||
def reset_manual(
|
||||
self,
|
||||
reset_scheduler: bool = True,
|
||||
reset_order_status: bool = True,
|
||||
reset_location: bool = True,
|
||||
reset_devices: bool = False,
|
||||
physical_cleanup_confirmed: bool = False,
|
||||
timeout_seconds: int = 3600,
|
||||
assignee_user_ids: Optional[List[str]] = None,
|
||||
**kwargs: Any,
|
||||
) -> Dict[str, Any]:
|
||||
"""人工确认物理清理后执行复位。
|
||||
|
||||
Args:
|
||||
reset_scheduler[调度器复位]: 调用 /api/lims/scheduler/reset，默认勾选。
|
||||
reset_order_status[订单状态复位]: 调用 /api/lims/order/reset-order-status，默认勾选。
|
||||
reset_location[库位复位]: 调用 /api/lims/storage/reset-location，默认勾选。
|
||||
reset_devices[仪器复位]: 调用 /api/lims/device/reset-devices，默认不勾选。
|
||||
physical_cleanup_confirmed[物理清理确认]: 确认清理提示中的物料检查已经完成，默认不勾选。
|
||||
"""
|
||||
...
|
||||
```
|
||||
|
||||
Execution rule:
|
||||
|
||||
- If `physical_cleanup_confirmed` is false, return a blocked result and do not call any reset API.
|
||||
- If it is true, call the same internal helper as `reset_auto`.
|
||||
- Return `confirmation_message` in the result payload so call logs preserve the exact operator instruction text.
|
||||
|
||||
Renderer caveat:
|
||||
|
||||
- `description` should carry the warning in generated action metadata.
|
||||
- `physical_cleanup_confirmed` must remain a plain `bool` so it renders as a checkbox.
|
||||
- The cleanup warning should be carried by the action `description` and the docstring param description. Do not rely on `Field(description=...)` unless registry `Annotated` support has been implemented and tested.
|
||||
- If the current frontend does not show action descriptions or docstring field descriptions reliably, add a read-only string parameter such as `confirmation_message: str = RESET_MANUAL_CONFIRM_MESSAGE` with `goal_default`, or use a handle-based display only after renderer behavior is verified.
|
||||
|
||||
## Shared Internal Helper
|
||||
|
||||
Both public actions should delegate to one helper, for example:
|
||||
|
||||
```python
|
||||
def _execute_reset_operations(
|
||||
self,
|
||||
*,
|
||||
reset_scheduler: bool,
|
||||
reset_order_status: bool,
|
||||
reset_location: bool,
|
||||
reset_devices: bool,
|
||||
) -> Dict[str, Any]:
|
||||
...
|
||||
```
|
||||
|
||||
Call order:
|
||||
|
||||
1. `scheduler_reset`
|
||||
2. `reset_order_status`
|
||||
3. `reset_location`
|
||||
4. `reset_devices`
|
||||
|
||||
Result shape:
|
||||
|
||||
```python
|
||||
{
|
||||
"selected_operations": [
|
||||
{"key": "reset_scheduler", "label": "调度器复位", "selected": True},
|
||||
{"key": "reset_order_status", "label": "订单状态复位", "selected": True},
|
||||
{"key": "reset_location", "label": "库位复位", "selected": True},
|
||||
{"key": "reset_devices", "label": "仪器复位", "selected": False},
|
||||
],
|
||||
"executed_calls": [
|
||||
{"operation": "scheduler_reset", "endpoint": "/api/lims/scheduler/reset", "result": {"code": 1}},
|
||||
],
|
||||
"skipped_operations": [
|
||||
{"operation": "reset_devices", "reason": "checkbox_disabled"},
|
||||
],
|
||||
"warnings": [],
|
||||
}
|
||||
```
|
||||
|
||||
Failure handling:
|
||||
|
||||
- Execute selected operations sequentially and record each result.
|
||||
- If an operation returns non-`1` code, add a warning and continue unless the caller later requests fail-fast.
|
||||
- If an RPC method raises, catch it, record an error entry, and continue to the next selected operation unless fail-fast is introduced.
|
||||
|
||||
## RPC Wrapper Adjustment
|
||||
|
||||
Adjust the two id-shaped wrappers to no-data calls:
|
||||
|
||||
- `BioyondV1RPC.reset_order_status()` should no longer require `order_id`.
|
||||
- `BioyondV1RPC.reset_location()` should no longer require `location_id`.
|
||||
|
||||
Current no-data wrappers already exist:
|
||||
|
||||
- `scheduler_reset()`
|
||||
- `reset_devices()`
|
||||
|
||||
Suggested RPC signatures:
|
||||
|
||||
```python
|
||||
def scheduler_reset(self) -> int: ...
|
||||
def reset_order_status(self) -> int: ...
|
||||
def reset_location(self) -> int: ...
|
||||
def reset_devices(self) -> int: ...
|
||||
```
|
||||
|
||||
Compatibility option:
|
||||
|
||||
```python
|
||||
def reset_order_status(self, order_id: Optional[str] = None) -> int:
|
||||
del order_id
|
||||
...
|
||||
|
||||
def reset_location(self, location_id: Optional[str] = None) -> int:
|
||||
del location_id
|
||||
...
|
||||
```
|
||||
|
||||
This keeps older code from crashing while making the actual wire request no-data.
|
||||
|
||||
## Adjusted Runtime API Schemas
|
||||
|
||||
These are the schemas Peptide reset code should target at runtime after the live no-data probes. They intentionally omit `data`, even though OpenAPI models nullable `data` for these endpoints.
|
||||
|
||||
All four requests use:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "string",
|
||||
"requestTime": "date-time"
|
||||
}
|
||||
```
|
||||
|
||||
No `data` field should be sent by default.
|
||||
|
||||
All four responses use:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 0
|
||||
}
|
||||
```
|
||||
|
||||
### 调度器复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/scheduler/reset
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:15:16.494Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351316072
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable int32.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
|
||||
### 订单状态复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/order/reset-order-status
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:13:34.750Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351214422
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
- Do not model this as order-id scoped unless Bioyond confirms backend behavior.
|
||||
|
||||
### 库位复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/storage/reset-location
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "2026-05-21T08:15:18.924Z"
|
||||
}
|
||||
```
|
||||
|
||||
Live response:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 1779351318565
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Live Peptide accepted omitted `data`.
|
||||
- Do not model this as location-id scoped unless Bioyond confirms backend behavior.
|
||||
|
||||
### 仪器复位
|
||||
|
||||
Endpoint:
|
||||
|
||||
```text
|
||||
POST /api/lims/device/reset-devices
|
||||
```
|
||||
|
||||
Adjusted request:
|
||||
|
||||
```json
|
||||
{
|
||||
"apiKey": "B10B5995",
|
||||
"requestTime": "date-time"
|
||||
}
|
||||
```
|
||||
|
||||
Expected response shape:
|
||||
|
||||
```json
|
||||
{
|
||||
"code": 1,
|
||||
"message": "",
|
||||
"timestamp": 0
|
||||
}
|
||||
```
|
||||
|
||||
Notes:
|
||||
|
||||
- OpenAPI says `data` is nullable string.
|
||||
- Current `BioyondV1RPC.reset_devices()` already sends no `data`.
|
||||
- This endpoint was not live-probed in the no-data reset session.
|
||||
- Keep checkbox default unchecked.
|
||||
|
||||
## Tests To Add Before Implementation
|
||||
|
||||
1. `reset_auto` is not `NodeType.MANUAL_CONFIRM`.
|
||||
2. `reset_manual` has `node_type=NodeType.MANUAL_CONFIRM`.
|
||||
3. `reset_manual` metadata includes:
|
||||
- `always_free=True`
|
||||
- `placeholder_keys={"assignee_user_ids": "unilabos_manual_confirm"}`
|
||||
- `timeout_seconds=3600`
|
||||
- `assignee_user_ids=[]`
|
||||
- `physical_cleanup_confirmed=False`
|
||||
4. Both reset actions expose four real boolean params:
|
||||
- `reset_scheduler`
|
||||
- `reset_order_status`
|
||||
- `reset_location`
|
||||
- `reset_devices`
|
||||
5. The generated registry schema marks those reset params as JSON Schema `type: boolean`, not `object` or `string`, so the frontend can render checkboxes.
|
||||
6. `reset_auto` replaces the current public `reset` action. Unless a later compatibility request adds an alias, no old id-shaped public `reset` action remains.
|
||||
7. Goal defaults are:
|
||||
- first three reset checkboxes `True`
|
||||
- `reset_devices=False`
|
||||
8. `reset_manual(..., physical_cleanup_confirmed=False)` does not call any RPC reset method.
|
||||
9. `reset_auto()` with defaults calls:
|
||||
- `scheduler_reset()`
|
||||
- `reset_order_status()`
|
||||
- `reset_location()`
|
||||
- not `reset_devices()`
|
||||
10. `reset_auto(reset_devices=True)` also calls `reset_devices()`.
|
||||
11. `reset_order_status()` and `reset_location()` RPC wrappers send no `data` key.
|
||||
12. No reset path calls `take_out`.
|
||||
13. No reset path calls `refresh_material_cache`.
|
||||
|
||||
## Non-Goals
|
||||
|
||||
- Do not implement `take_out` in reset.
|
||||
- Do not refresh `material_cache` from reset.
|
||||
- Do not resolve order ids or location ids for reset.
|
||||
- Do not add Project/cache/browser cleanup routes.
|
||||
- Do not make `reset_devices` default-on.
|
||||
- Do not execute this plan during planning.
|
||||
@@ -779,6 +779,49 @@ class BioyondV1RPC(BaseRequest):
|
||||
|
||||
return response.get("data", {})
|
||||
|
||||
def take_out(
|
||||
self,
|
||||
order_id: str,
|
||||
preintake_ids: list[str] | None = None,
|
||||
material_ids: list[str] | None = None,
|
||||
) -> dict:
|
||||
"""取出订单关联通量/物料
|
||||
|
||||
参数:
|
||||
order_id: 订单ID
|
||||
preintake_ids: 通量ID列表，可为空
|
||||
material_ids: 物料ID列表，可为空
|
||||
|
||||
返回值:
|
||||
dict: 服务端响应包，失败返回空字典
|
||||
"""
|
||||
if not order_id:
|
||||
self._logger.error("取出订单关联通量/物料错误: 缺少订单ID")
|
||||
return {}
|
||||
|
||||
params = {
|
||||
"orderId": order_id,
|
||||
"preintakeIds": list(preintake_ids or []),
|
||||
"materialIds": list(material_ids or []),
|
||||
}
|
||||
|
||||
response = self.post(
|
||||
url=f'{self.host}/api/lims/order/take-out',
|
||||
params={
|
||||
"apiKey": self.api_key,
|
||||
"requestTime": self.get_current_time_iso8601(),
|
||||
"data": params,
|
||||
})
|
||||
|
||||
if not response:
|
||||
return {}
|
||||
|
||||
if response['code'] != 1:
|
||||
self._logger.error(f"取出订单关联通量/物料错误: {response.get('message', '')}")
|
||||
return response
|
||||
|
||||
return response
|
||||
|
||||
def cancel_order(self, json_str: str) -> bool:
|
||||
"""取消指定任务
|
||||
|
||||
|
||||
@@ -8,7 +8,7 @@ returned. Outside of an active session the wrapped method delegates to the
|
||||
original (unwrapped) implementation, leaving non-debug behavior intact.
|
||||
|
||||
The session writes a Markdown file under ``out_dir`` mirroring the format of
|
||||
``temp_benyao/peptide/_logs/2026-04-30_160316_day3_samplefile_only_raw_calls.md``
|
||||
``bioyond_debug_records/2026-04-30_160316_day3_samplefile_only_raw_calls.md``
|
||||
minus the "Raw Payload Argument" section.
|
||||
|
||||
This module has no dependency on ``BioyondV1RPC`` itself; the only contract is
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
from .peptide_station import BioyondPeptideStation, fetch_workflow_list, load_peptide_config
|
||||
|
||||
__all__ = ["BioyondPeptideStation", "fetch_workflow_list", "load_peptide_config"]
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,681 @@
|
||||
"""多肽站 AST/参数/结果表 离线契约测试。"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import importlib
|
||||
import inspect
|
||||
import json
|
||||
import sys
|
||||
from pathlib import Path
|
||||
from typing import Any, Dict, List
|
||||
from unittest.mock import MagicMock
|
||||
|
||||
import pytest
|
||||
|
||||
REPO_ROOT = Path(__file__).resolve().parents[6]
|
||||
if str(REPO_ROOT) not in sys.path:
|
||||
sys.path.insert(0, str(REPO_ROOT))
|
||||
|
||||
MODULE_PATH = "unilabos.devices.workstation.bioyond_studio.peptide_station.peptide_station"
|
||||
CLASS_NAME = "BioyondPeptideStation"
|
||||
|
||||
ORDER_GUID = "3a20eabe-bad5-ef95-49bd-7ffbd5df189d"
|
||||
CREATE_ALLOCATION = {
|
||||
ORDER_GUID: [
|
||||
{
|
||||
"materialId": "mat-tip",
|
||||
"materialName": "200μL枪头盒",
|
||||
"materialCode": "0008-00105",
|
||||
"quantity": "1个",
|
||||
"materialTypeMode": "Consumables",
|
||||
"locationCode": "1-01",
|
||||
"locationShowName": "1-01",
|
||||
},
|
||||
{
|
||||
"materialId": "mat-plate",
|
||||
"materialName": "96孔板",
|
||||
"materialCode": "PLATE-96",
|
||||
"quantity": "1",
|
||||
"materialTypeMode": "Sample",
|
||||
"locationCode": "A1",
|
||||
"locationShowName": "A1-show",
|
||||
},
|
||||
{
|
||||
"materialId": "mat-extra",
|
||||
"materialName": "未知耗材",
|
||||
"materialCode": "X-1",
|
||||
"quantity": "2",
|
||||
"materialTypeMode": "Future",
|
||||
"locationCode": "Z9",
|
||||
"locationShowName": "",
|
||||
},
|
||||
]
|
||||
}
|
||||
|
||||
FLATTENED_LIVE = [
|
||||
{"step": "39c78d4b-b5d3-f721-2001-9d52000084c3", "step_name": "S1", "Key": "SampleFile", "m": 0, "n": 0, "Value": "", "DisplayValue": "", "TaskDisplayable": 1},
|
||||
{"step": "39c78d4b-b5d3-f721-2001-9d52000084c3", "step_name": "S1", "Key": "Example", "m": 0, "n": 0, "Value": "x", "DisplayValue": "x", "TaskDisplayable": 1},
|
||||
{"step": "39c78d4b-b5d3-f721-2001-9d52000084c4", "step_name": "S2", "Key": "protocol", "m": 14, "n": 28, "Value": "", "DisplayValue": "", "TaskDisplayable": 1},
|
||||
{"step": "39c78d4b-b5d3-f721-2001-9d52000084c5", "step_name": "S3", "Key": "CEMMethodFileName", "m": 0, "n": 0, "Value": "", "DisplayValue": "", "TaskDisplayable": 1},
|
||||
]
|
||||
|
||||
|
||||
def _import_module() -> Any:
|
||||
return importlib.import_module(MODULE_PATH)
|
||||
|
||||
|
||||
def _make_station() -> Any:
|
||||
module = _import_module()
|
||||
cls = getattr(module, CLASS_NAME)
|
||||
station = object.__new__(cls)
|
||||
station.bioyond_config = {"api_host": "http://test", "api_key": "k", "warehouse_mapping": {}}
|
||||
rpc = MagicMock()
|
||||
rpc.host = "http://test"
|
||||
rpc.api_key = "k"
|
||||
rpc.material_info.return_value = {"locations": [{"whName": "自动化堆栈", "code": "1-01"}]}
|
||||
station.hardware_interface = rpc
|
||||
return station
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 1. AST/导入面
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_required_actions_exposed() -> None:
|
||||
cls = getattr(_import_module(), CLASS_NAME)
|
||||
required = {
|
||||
"upload_sample_excel",
|
||||
"list_sample_excels",
|
||||
"get_step_parameters",
|
||||
"submit_experiment",
|
||||
"submit_experiment_day1",
|
||||
"submit_experiment_day2",
|
||||
"submit_experiment_day3",
|
||||
"submit_experiment_day4",
|
||||
"submit_experiment_day4_LCMS",
|
||||
"start_experiment",
|
||||
"reset",
|
||||
"scheduler_start",
|
||||
"scheduler_stop",
|
||||
"scheduler_pause",
|
||||
"scheduler_continue",
|
||||
"get_order_list",
|
||||
"get_order_report",
|
||||
"get_aggregated_order_report",
|
||||
}
|
||||
have = {name for name, _ in inspect.getmembers(cls, inspect.isfunction)}
|
||||
missing = sorted(required - have)
|
||||
assert not missing, f"缺少动作: {missing}"
|
||||
|
||||
|
||||
def test_manual_confirm_node_types() -> None:
|
||||
module = _import_module()
|
||||
cls = getattr(module, CLASS_NAME)
|
||||
manual = {"submit_experiment_day1", "start_experiment"}
|
||||
normal = {
|
||||
"submit_experiment",
|
||||
"submit_experiment_day2",
|
||||
"submit_experiment_day3",
|
||||
"submit_experiment_day4",
|
||||
"submit_experiment_day4_LCMS",
|
||||
"reset",
|
||||
"scheduler_start",
|
||||
"list_sample_excels",
|
||||
"get_step_parameters",
|
||||
"get_order_list",
|
||||
"get_order_report",
|
||||
}
|
||||
for name in manual:
|
||||
meta = getattr(getattr(cls, name), "_action_registry_meta", {})
|
||||
assert meta.get("node_type") == module.NodeType.MANUAL_CONFIRM, name
|
||||
for name in normal:
|
||||
meta = getattr(getattr(cls, name), "_action_registry_meta", {})
|
||||
assert meta.get("node_type") != module.NodeType.MANUAL_CONFIRM, name
|
||||
|
||||
|
||||
def test_submit_and_reset_signatures_exclude_legacy_manual_confirm() -> None:
|
||||
cls = getattr(_import_module(), CLASS_NAME)
|
||||
for name in (
|
||||
"submit_experiment",
|
||||
"submit_experiment_day2",
|
||||
"submit_experiment_day3",
|
||||
"submit_experiment_day4",
|
||||
"submit_experiment_day4_LCMS",
|
||||
"reset",
|
||||
):
|
||||
params = inspect.signature(getattr(cls, name)).parameters
|
||||
assert "timeout_seconds" not in params, name
|
||||
assert "assignee_user_ids" not in params, name
|
||||
|
||||
|
||||
def test_day1_submit_accepts_manual_confirm_kwargs() -> None:
|
||||
"""plan: Day1 是 MANUAL_CONFIRM；框架会注入 timeout_seconds/assignee_user_ids，函数必须能接收。"""
|
||||
cls = getattr(_import_module(), CLASS_NAME)
|
||||
sig = inspect.signature(cls.submit_experiment_day1)
|
||||
has_kwargs = any(p.kind == inspect.Parameter.VAR_KEYWORD for p in sig.parameters.values())
|
||||
assert has_kwargs, "submit_experiment_day1 必须有 **kwargs 以容纳人工确认框架字段"
|
||||
|
||||
|
||||
def test_typed_dicts_present() -> None:
|
||||
module = _import_module()
|
||||
for cls_name in (
|
||||
"PeptideGenericSubmitRequiredParams",
|
||||
"PeptideGenericSubmitOptionalParams",
|
||||
"PeptideDay1RequiredParams",
|
||||
"PeptideDay1OptionalParams",
|
||||
"PeptideDay2RequiredParams",
|
||||
"PeptideDay2OptionalParams",
|
||||
"PeptideDay3RequiredParams",
|
||||
"PeptideDay3OptionalParams",
|
||||
"PeptideDay4RequiredParams",
|
||||
"PeptideDay4OptionalParams",
|
||||
"PeptideDay4LCMSRequiredParams",
|
||||
"PeptideDay4LCMSOptionalParams",
|
||||
):
|
||||
assert hasattr(module, cls_name), cls_name
|
||||
|
||||
|
||||
def test_workflow_constants_split() -> None:
|
||||
module = _import_module()
|
||||
assert module.DAY4_PEPTIDE_WORKFLOW_NAME == "Day4环肽酰化-酶标"
|
||||
assert module.DAY4_LCMS_PEPTIDE_WORKFLOW_NAME == "Day4环肽酰化-酶标+LCMS"
|
||||
assert module.DAY_WORKFLOW_BINDINGS["day4_lcms"]["sub_name"] == "Day4环肽酰化-酶标LCMS"
|
||||
assert module.DAY1_CEM_METHOD_DEFAULT == "5microdouble-20250911.MPM"
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 2. Sample Excel
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_list_sample_excels_modes() -> None:
|
||||
station = _make_station()
|
||||
records = [
|
||||
{"fileName": "DPR019-a.xlsx", "relativePath": "upload\\sample\\DPR019-a.xlsx"},
|
||||
{"fileName": "DPR019-b.xlsx", "relativePath": "upload\\sample\\DPR019-b.xlsx"},
|
||||
]
|
||||
station._list_sample_excels = MagicMock(return_value=records) # type: ignore[method-assign]
|
||||
|
||||
info = station.list_sample_excels(sample_excel_pattern="DPR019-a", deterministic_resolve=False)
|
||||
assert "sample_excel_data" in info
|
||||
assert "sample_excel_relative_path" not in info
|
||||
|
||||
resolved = station.list_sample_excels(sample_excel_pattern="DPR019-a", deterministic_resolve=True)
|
||||
assert resolved["sample_excel_relative_path"] == "upload\\sample\\DPR019-a.xlsx"
|
||||
|
||||
with pytest.raises(Exception):
|
||||
station.list_sample_excels(sample_excel_pattern="DPR019", deterministic_resolve=True)
|
||||
|
||||
|
||||
def test_resolve_submit_sample_file_direct_path() -> None:
|
||||
station = _make_station()
|
||||
relative, selected = station._resolve_submit_sample_file({}, {}, "upload/sample/x.xlsx")
|
||||
assert relative == "upload\\sample\\x.xlsx"
|
||||
assert selected["fileName"] == "x.xlsx"
|
||||
|
||||
|
||||
def test_filename_matches_pattern_substring_and_glob() -> None:
|
||||
station = _make_station()
|
||||
assert station._filename_matches_pattern("DPR019-20260421-thrombin-5.xlsx", "DPR019")
|
||||
assert station._filename_matches_pattern("a.xlsx", "*.xlsx")
|
||||
assert not station._filename_matches_pattern("a.xlsx", "*.docx")
|
||||
assert station._filename_matches_pattern("a.xlsx", "")
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 3. Step parameter helper
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_filter_step_parameters_preserves_zero_and_skips_unknown() -> None:
|
||||
station = _make_station()
|
||||
records = [
|
||||
{"TaskDisplayable": 1, "Value": 0, "DisplayValue": ""},
|
||||
{"TaskDisplayable": 1, "Value": "", "DisplayValue": ""},
|
||||
{"TaskDisplayable": 0, "Value": "", "DisplayValue": ""},
|
||||
{"TaskDisplayable": None, "Value": "", "DisplayValue": ""},
|
||||
]
|
||||
filtered = station._filter_step_parameter_records(records, True, True, True)
|
||||
assert {(r.get("Value"), r.get("TaskDisplayable")) for r in filtered} == {(0, 1), ("", 1), ("", 0)}
|
||||
|
||||
|
||||
def test_get_step_parameters_zero_match_returns_status() -> None:
|
||||
station = _make_station()
|
||||
station._query_workflow_records = MagicMock(return_value=[]) # type: ignore[method-assign]
|
||||
out = station.get_step_parameters(workflow_name_filter="不存在")
|
||||
status = out["step_parameters_raw_json"]
|
||||
assert status.get("code") == -1
|
||||
assert out["filtered_subworkflows"] == []
|
||||
|
||||
|
||||
def test_get_step_parameters_multi_match_returns_status() -> None:
|
||||
station = _make_station()
|
||||
station._query_workflow_records = MagicMock(return_value=[ # type: ignore[method-assign]
|
||||
{"workflowId": "w1", "workflowName": "A", "subworkflowId": "s1", "subworkflowName": "A1"},
|
||||
{"workflowId": "w1", "workflowName": "A", "subworkflowId": "s2", "subworkflowName": "A2"},
|
||||
])
|
||||
out = station.get_step_parameters(workflow_name_filter="A")
|
||||
assert out["step_parameters_raw_json"].get("code") == 0
|
||||
assert len(out["filtered_subworkflows"]) == 2
|
||||
|
||||
|
||||
def test_get_step_parameters_direct_sub_workflow_id() -> None:
|
||||
station = _make_station()
|
||||
station._query_step_parameters = MagicMock(return_value={ # type: ignore[method-assign]
|
||||
"39c78d4b-b5d3-f721-2001-9d52000084c3": [
|
||||
{"name": "S1", "m": 0, "n": 0, "parameterList": [
|
||||
{"Key": "SampleFile", "TaskDisplayable": 1, "Value": "", "DisplayValue": ""},
|
||||
]},
|
||||
]
|
||||
})
|
||||
out = station.get_step_parameters(sub_workflow_id="39c78d4b-b5d3-f721-2001-9d52000084c3")
|
||||
augmented = out["step_parameters_raw_json"]
|
||||
assert augmented["code"] == 1
|
||||
assert any(p["Key"] == "SampleFile" for p in augmented["data"]["filteredParameters"])
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 4. Partial parameter entries + live resolution
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_partial_entries_inject_samplefile_and_overrides() -> None:
|
||||
station = _make_station()
|
||||
entries, warnings = station._build_partial_parameter_entries(
|
||||
sample_excel_relative_path="upload\\sample\\f.xlsx",
|
||||
day_key="day2",
|
||||
parameter_overrides=[{"Key": "Example", "Value": 0}],
|
||||
)
|
||||
assert entries[0] == {"Key": "SampleFile", "Value": "upload\\sample\\f.xlsx"}
|
||||
assert any(e["Key"] == "Example" and e["Value"] == 0 for e in entries)
|
||||
assert warnings == []
|
||||
|
||||
|
||||
def test_day1_partial_entries_inject_cem_default() -> None:
|
||||
station = _make_station()
|
||||
entries, _ = station._build_partial_parameter_entries(
|
||||
sample_excel_relative_path="upload\\sample\\f.xlsx",
|
||||
day_key="day1",
|
||||
extra_autofill=[{"Key": "CEMMethodFileName", "Value": "5microdouble-20250911.MPM"}],
|
||||
)
|
||||
assert any(e["Key"] == "CEMMethodFileName" and e["Value"] == "5microdouble-20250911.MPM" for e in entries)
|
||||
|
||||
|
||||
def test_overrides_duplicate_last_write_wins_warning() -> None:
|
||||
station = _make_station()
|
||||
entries, warnings = station._build_partial_parameter_entries(
|
||||
sample_excel_relative_path="x",
|
||||
day_key="day2",
|
||||
parameter_overrides=[
|
||||
{"Key": "Example", "m": 0, "n": 0, "Value": "first"},
|
||||
{"Key": "Example", "m": 0, "n": 0, "Value": "second"},
|
||||
],
|
||||
)
|
||||
example_entries = [e for e in entries if e["Key"] == "Example"]
|
||||
assert len(example_entries) == 1
|
||||
assert example_entries[0]["Value"] == "second"
|
||||
assert any("重复" in w for w in warnings)
|
||||
|
||||
|
||||
def test_resolve_against_live_unique_match_and_failure() -> None:
|
||||
station = _make_station()
|
||||
resolved = station._resolve_parameter_entries_against_live_steps(
|
||||
[{"Key": "SampleFile", "Value": "upload\\sample\\f.xlsx"}], FLATTENED_LIVE
|
||||
)
|
||||
assert resolved[0]["step"] == "39c78d4b-b5d3-f721-2001-9d52000084c3"
|
||||
assert resolved[0]["m"] == 0 and resolved[0]["n"] == 0
|
||||
# 没有 protocol 在 m/n=0/0 处 → 0 匹配
|
||||
with pytest.raises(Exception) as exc:
|
||||
station._resolve_parameter_entries_against_live_steps(
|
||||
[{"Key": "protocol", "m": 0, "n": 0, "Value": "v"}], FLATTENED_LIVE
|
||||
)
|
||||
assert "0 条" in str(exc.value)
|
||||
|
||||
|
||||
def test_group_resolved_entries_uses_lowercase_keys() -> None:
|
||||
station = _make_station()
|
||||
grouped = station._group_resolved_entries_to_param_values([
|
||||
{"step": "39c78d4b-b5d3-f721-2001-9d52000084c3", "Key": "SampleFile", "m": 0, "n": 0, "Value": "x"},
|
||||
])
|
||||
step_entries = grouped["39c78d4b-b5d3-f721-2001-9d52000084c3"]
|
||||
assert step_entries[0] == {"key": "SampleFile", "value": "x", "m": 0, "n": 0}
|
||||
|
||||
|
||||
def test_create_order_payload_shape() -> None:
|
||||
station = _make_station()
|
||||
payload = station._create_order_payload(
|
||||
order_code="EXP260518-103000",
|
||||
order_name="实验260518-103000",
|
||||
sub_workflow_id="3a1d35f9-63ce-67d6-1784-9f6abcca4eda",
|
||||
param_values={"39c78d4b-b5d3-f721-2001-9d52000084c3": [{"key": "SampleFile", "value": "x", "m": 0, "n": 0}]},
|
||||
border_number=1,
|
||||
extend_properties=None,
|
||||
)
|
||||
assert isinstance(payload, list) and len(payload) == 1
|
||||
item = payload[0]
|
||||
assert item["workFlowId"] == "3a1d35f9-63ce-67d6-1784-9f6abcca4eda"
|
||||
assert item["paramValues"]
|
||||
assert item["extendProperties"] == ""
|
||||
assert item["borderNumber"] == 1
|
||||
|
||||
|
||||
def test_order_identity_format() -> None:
|
||||
station = _make_station()
|
||||
code, name = station._build_order_identity("day2")
|
||||
assert code.startswith("EXP") and len(code) == 16 # EXP + YYMMDD-HHmmss
|
||||
assert name.startswith("实验")
|
||||
code2, name2 = station._build_order_identity("day2", "自定义")
|
||||
assert name2 == "自定义"
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 5. Generic submit / day wrappers (含会抦住 BUG 1 的用例)
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def _wire_submit_pipeline(station: Any) -> None:
|
||||
station._resolve_workflow_binding_from_names = MagicMock(return_value={ # type: ignore[method-assign]
|
||||
"workflow_name": "DAY2多肽定量",
|
||||
"root_workflow_id": "3a1d35f0-9436-895b-2eda-039a5465275e",
|
||||
"sub_workflow_id": "3a1d35f0-9f7e-c2c1-0bc0-8d94b81d90ca",
|
||||
"sub_workflow_name": "DAY2多肽定量",
|
||||
"raw": {},
|
||||
})
|
||||
station._resolve_workflow_binding = MagicMock(side_effect=lambda day_key: station._resolve_workflow_binding_from_names("DAY2多肽定量")) # type: ignore[method-assign]
|
||||
station._query_step_parameters = MagicMock(return_value={}) # type: ignore[method-assign]
|
||||
station._flatten_step_parameters = MagicMock(return_value=FLATTENED_LIVE) # type: ignore[method-assign]
|
||||
station._create_order = MagicMock(return_value=json.dumps(CREATE_ALLOCATION)) # type: ignore[method-assign]
|
||||
|
||||
|
||||
def test_submit_experiment_generic_succeeds() -> None:
|
||||
"""plan §「Generic And Day 1 Submit」line 919-924；这条同时抦住 BUG 1（binding= 关键字）。"""
|
||||
station = _make_station()
|
||||
_wire_submit_pipeline(station)
|
||||
result = station.submit_experiment(
|
||||
{"workflow_name": "DAY2多肽定量", "sample_excel_pattern": ""},
|
||||
{"parameter_overrides": []},
|
||||
sample_excel_relative_path="upload/sample/f.xlsx",
|
||||
)
|
||||
assert result["success"] is True
|
||||
assert result["order_id"] == ORDER_GUID
|
||||
assert result["resultTable"]["tableName"] == "resultTable"
|
||||
|
||||
|
||||
def test_submit_experiment_rejects_day1_alias() -> None:
|
||||
station = _make_station()
|
||||
with pytest.raises(Exception):
|
||||
station.submit_experiment(
|
||||
{"workflow_name": "Day1线肽合成", "sample_excel_pattern": "x"},
|
||||
{},
|
||||
sample_excel_relative_path="upload/sample/f.xlsx",
|
||||
)
|
||||
|
||||
|
||||
def test_submit_experiment_day2_calls_pipeline() -> None:
|
||||
station = _make_station()
|
||||
_wire_submit_pipeline(station)
|
||||
result = station.submit_experiment_day2(
|
||||
{"sample_excel_pattern": ""},
|
||||
{"parameter_overrides": []},
|
||||
sample_excel_relative_path="upload/sample/f.xlsx",
|
||||
)
|
||||
assert result["success"] is True
|
||||
assert result["order_ids"] == [ORDER_GUID]
|
||||
assert result["auto_register_materials"] is True
|
||||
assert result["material_registration"]["status"] == "not_implemented"
|
||||
|
||||
|
||||
def test_day1_placeholder_does_not_call_create_order() -> None:
|
||||
station = _make_station()
|
||||
station._resolve_workflow_binding = MagicMock(return_value={ # type: ignore[method-assign]
|
||||
"workflow_name": "Day1线肽合成",
|
||||
"root_workflow_id": "rid",
|
||||
"sub_workflow_id": "sid",
|
||||
"sub_workflow_name": "Day1线肽合成",
|
||||
"raw": {},
|
||||
})
|
||||
station._create_order = MagicMock(side_effect=AssertionError("Day1 不应触达 create_order")) # type: ignore[method-assign]
|
||||
out = station.submit_experiment_day1(
|
||||
{"sample_excel_pattern": "", "cem_method_file_name": ""},
|
||||
{},
|
||||
sample_excel_relative_path="upload/sample/f.xlsx",
|
||||
# 模拟人工确认框架注入的字段（这条会抦住 BUG 3）
|
||||
timeout_seconds=3600,
|
||||
assignee_user_ids=[],
|
||||
materials_loaded=False,
|
||||
)
|
||||
assert out["status"] == "manual_confirm_placeholder"
|
||||
assert out["cem_method_file_name"] == "5microdouble-20250911.MPM"
|
||||
assert isinstance(out["partial_parameter_entries"], list)
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 6. Allocation map parsing + resultTable
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_parse_allocation_map_extracts_order_id_and_groups() -> None:
|
||||
station = _make_station()
|
||||
parsed = station._parse_create_order_allocation_map(json.dumps(CREATE_ALLOCATION))
|
||||
assert parsed["order_ids"] == [ORDER_GUID]
|
||||
assert len(parsed["allocation_rows"]) == 3
|
||||
assert set(parsed["materials_by_type"].keys()) == {"Consumables", "Sample", "Future"}
|
||||
|
||||
|
||||
def test_parse_allocation_map_handles_python_str_repr() -> None:
|
||||
"""RPC.create_order 返回的是 str(dict)，含单引号。"""
|
||||
station = _make_station()
|
||||
parsed = station._parse_create_order_allocation_map(str(CREATE_ALLOCATION))
|
||||
assert parsed["order_ids"] == [ORDER_GUID]
|
||||
|
||||
|
||||
def test_parse_allocation_map_empty() -> None:
|
||||
station = _make_station()
|
||||
parsed = station._parse_create_order_allocation_map("{}")
|
||||
assert parsed["allocation_rows"] == []
|
||||
assert parsed["order_ids"] == []
|
||||
|
||||
|
||||
def test_build_result_table_order_and_columns() -> None:
|
||||
station = _make_station()
|
||||
parsed = station._parse_create_order_allocation_map(json.dumps(CREATE_ALLOCATION))
|
||||
table = station._build_result_table(parsed["materials_by_type"])
|
||||
assert table["tableName"] == "resultTable"
|
||||
assert [c["key"] for c in table["columns"]] == ["whName", "locationCode", "materialName", "quantity"]
|
||||
# 顺序：Sample → Consumables → Future（未知 mode 保留在末尾）
|
||||
names = [row["materialName"] for row in table["data"]]
|
||||
assert names == ["96孔板", "200μL枪头盒", "未知耗材"]
|
||||
# locationShowName 优先 locationCode
|
||||
assert table["data"][0]["locationCode"] == "A1-show"
|
||||
assert table["data"][1]["locationCode"] == "1-01"
|
||||
|
||||
|
||||
def test_build_result_table_empty_returns_empty_data() -> None:
|
||||
station = _make_station()
|
||||
table = station._build_result_table({})
|
||||
assert table["data"] == []
|
||||
assert [c["key"] for c in table["columns"]] == ["whName", "locationCode", "materialName", "quantity"]
|
||||
|
||||
|
||||
def test_resolve_wh_name_handles_material_info_failure() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.material_info.side_effect = RuntimeError("HTTP 500")
|
||||
cache: Dict[str, Dict[str, Any]] = {}
|
||||
assert station._resolve_wh_name_by_material_id("mat-1", cache) == ""
|
||||
|
||||
|
||||
def test_submit_returns_warning_when_allocation_empty() -> None:
|
||||
station = _make_station()
|
||||
_wire_submit_pipeline(station)
|
||||
station._create_order = MagicMock(return_value="{}") # type: ignore[method-assign]
|
||||
result = station.submit_experiment_day2(
|
||||
{"sample_excel_pattern": ""},
|
||||
{},
|
||||
sample_excel_relative_path="upload/sample/f.xlsx",
|
||||
)
|
||||
assert "create_order_allocation_unavailable_for_result_table" in result["warnings"]
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 7. Reports + workflow records
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_get_order_list_passes_json_string() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.order_query.return_value = {"items": [], "totalCount": 0}
|
||||
station.get_order_list(filter_text="abc", page_count=10)
|
||||
args, kwargs = station.hardware_interface.order_query.call_args
|
||||
payload = json.loads(args[0])
|
||||
assert payload["filter"] == "abc"
|
||||
assert payload["pageCount"] == 10
|
||||
|
||||
|
||||
def test_get_order_report_calls_typed_rpc() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.order_report.return_value = {"id": ORDER_GUID, "name": "x", "preIntakes": [], "resultList": []}
|
||||
out = station.get_order_report(ORDER_GUID)
|
||||
station.hardware_interface.order_report.assert_called_once_with(ORDER_GUID)
|
||||
assert out["success"] is True
|
||||
assert out["summary"]["id"] == ORDER_GUID
|
||||
|
||||
|
||||
def test_get_aggregated_order_report_is_todo_placeholder() -> None:
|
||||
station = _make_station()
|
||||
out = station.get_aggregated_order_report(ORDER_GUID)
|
||||
assert out["status"] == "not_implemented"
|
||||
|
||||
|
||||
def test_query_workflow_records_filters_unsaved_subworkflows() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.query_workflow.return_value = {
|
||||
"items": [
|
||||
{
|
||||
"id": "rid",
|
||||
"name": "Day3线肽环化",
|
||||
"subWorkflows": [
|
||||
{"id": "saved-id", "name": "Day3线肽环化", "isSaved": True},
|
||||
{"id": "draft-id", "name": "Day3线肽环化-草稿", "isSaved": False},
|
||||
],
|
||||
}
|
||||
]
|
||||
}
|
||||
records = station._query_workflow_records("Day3线肽环化")
|
||||
assert [r["subworkflowId"] for r in records] == ["saved-id"]
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 8. Debug / fetch_workflow_list 守护
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_module_fetch_workflow_list_is_debug_guarded() -> None:
|
||||
module = _import_module()
|
||||
assert module.DEBUG_CLI_ENABLED is False
|
||||
with pytest.raises(AssertionError):
|
||||
module.fetch_workflow_list(config={"api_host": "http://x", "api_key": "k"})
|
||||
|
||||
|
||||
def test_station_fetch_workflow_list_uses_rpc() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.query_workflow.return_value = {"items": [], "totalCount": 0}
|
||||
station.fetch_workflow_list(filter_text="Day2")
|
||||
args, _ = station.hardware_interface.query_workflow.call_args
|
||||
payload = json.loads(args[0])
|
||||
assert payload["filter"] == "Day2"
|
||||
assert payload["includeDetail"] is True
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 9. start_experiment 装载闸门
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_start_experiment_blocks_when_materials_not_loaded() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.scheduler_start.return_value = 1
|
||||
with pytest.raises(RuntimeError):
|
||||
station.start_experiment(
|
||||
order_id=ORDER_GUID,
|
||||
resultTable={"data": [{"materialName": "x"}]},
|
||||
materials_loaded=False,
|
||||
)
|
||||
|
||||
|
||||
def test_start_experiment_starts_when_table_empty() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.scheduler_start.return_value = 1
|
||||
result = station.start_experiment(order_id=ORDER_GUID, resultTable={"data": []})
|
||||
assert result["success"] is True
|
||||
assert result["order_ids"] == [ORDER_GUID]
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# 10. Reset
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
def test_reset_signature_drops_legacy_params_and_uses_literal() -> None:
|
||||
"""plan 调整：删除 dry_run/order_id/location_id；reset_operations 用 Literal 注解。"""
|
||||
cls = getattr(_import_module(), CLASS_NAME)
|
||||
sig = inspect.signature(cls.reset)
|
||||
params = sig.parameters
|
||||
for legacy in ("dry_run", "order_id", "location_id"):
|
||||
assert legacy not in params, f"reset 不应再有 {legacy} 入参"
|
||||
assert "reset_operations" in params
|
||||
assert any(p.kind == inspect.Parameter.VAR_KEYWORD for p in params.values()), \
|
||||
"reset 必须保留 **kwargs 以兜底 reset_order_id/reset_location_id"
|
||||
|
||||
annotation = params["reset_operations"].annotation
|
||||
rendered = annotation if isinstance(annotation, str) else repr(annotation)
|
||||
for op in ("scheduler_reset", "reset_order_status", "reset_location"):
|
||||
assert op in rendered, f"reset_operations 的 Literal 必须包含 {op}"
|
||||
|
||||
|
||||
def test_reset_goal_default_contains_all_operations() -> None:
|
||||
"""像 sirna 一样，goal_default 默认勾选全部三个 reset 操作。"""
|
||||
cls = getattr(_import_module(), CLASS_NAME)
|
||||
meta = getattr(cls.reset, "_action_registry_meta", {})
|
||||
goal_default = meta.get("goal_default") or {}
|
||||
assert goal_default.get("reset_operations") == [
|
||||
"scheduler_reset",
|
||||
"reset_order_status",
|
||||
"reset_location",
|
||||
]
|
||||
|
||||
|
||||
def test_reset_executes_typed_rpc_calls() -> None:
|
||||
station = _make_station()
|
||||
station.hardware_interface.scheduler_reset.return_value = 1
|
||||
station.hardware_interface.reset_order_status.return_value = 1
|
||||
station.hardware_interface.reset_location.return_value = 1
|
||||
out = station.reset(
|
||||
reset_operations=["scheduler_reset", "reset_order_status", "reset_location"],
|
||||
reset_order_id=ORDER_GUID,
|
||||
reset_location_id="loc-1",
|
||||
)
|
||||
station.hardware_interface.scheduler_reset.assert_called_once_with()
|
||||
station.hardware_interface.reset_order_status.assert_called_once_with(ORDER_GUID)
|
||||
station.hardware_interface.reset_location.assert_called_once_with("loc-1")
|
||||
assert out["selected_operations"] == [
|
||||
"scheduler_reset",
|
||||
"reset_order_status",
|
||||
"reset_location",
|
||||
]
|
||||
assert len(out["executed_calls"]) == 3
|
||||
assert out["skipped_operations"] == []
|
||||
|
||||
|
||||
def test_reset_skips_when_ids_missing() -> None:
|
||||
"""没有 order_id / location_id 时应该 skip 而不是抛错。"""
|
||||
station = _make_station()
|
||||
station.hardware_interface.scheduler_reset.return_value = 1
|
||||
out = station.reset(
|
||||
reset_operations=["scheduler_reset", "reset_order_status", "reset_location"],
|
||||
)
|
||||
station.hardware_interface.scheduler_reset.assert_called_once_with()
|
||||
station.hardware_interface.reset_order_status.assert_not_called()
|
||||
station.hardware_interface.reset_location.assert_not_called()
|
||||
skipped_ops = {item["operation"] for item in out["skipped_operations"]}
|
||||
assert skipped_ops == {"reset_order_status", "reset_location"}
|
||||
@@ -1,3 +0,0 @@
|
||||
from .sirna_station import BioyondSirnaStation, fetch_workflow_list, load_sirna_config
|
||||
|
||||
__all__ = ["BioyondSirnaStation", "fetch_workflow_list", "load_sirna_config"]
|
||||
File diff suppressed because it is too large
Load Diff
@@ -56,13 +56,17 @@ class ConnectionMonitor:
|
||||
def _monitor_loop(self):
|
||||
while self._running:
|
||||
try:
|
||||
# 使用 lightweight API 检查连接
|
||||
# query_matial_type_list 是比较快的查询
|
||||
start_time = time.time()
|
||||
result = self.workstation.hardware_interface.material_type_list()
|
||||
# 使用轻量级调度状态接口检查连接，避免启动时打印完整物料类型列表。
|
||||
result = self.workstation.hardware_interface.scheduler_status()
|
||||
|
||||
status = "online" if result else "offline"
|
||||
msg = "Connection established" if status == "online" else "Failed to get material type list"
|
||||
if status == "online":
|
||||
msg = (
|
||||
f"Scheduler status={result.get('status')}, "
|
||||
f"hasTask={result.get('hasTask')}"
|
||||
)
|
||||
else:
|
||||
msg = "Failed to get scheduler status"
|
||||
|
||||
if status != self._last_status:
|
||||
logger.info(f"Bioyond连接状态变更: {self._last_status} -> {status}")
|
||||
@@ -730,7 +734,7 @@ class BioyondWorkstation(WorkstationBase):
|
||||
"""解析 ``debug_log_dir`` 为绝对路径。"""
|
||||
configured = (getattr(self, "bioyond_config", {}) or {}).get("debug_log_dir")
|
||||
default_dir = getattr(self, "_DEBUG_LOG_DEFAULT_DIR", None)
|
||||
candidate = configured or default_dir or "temp_benyao/_logs/bioyond_debug"
|
||||
candidate = configured or default_dir or "bioyond_debug_records"
|
||||
path = Path(candidate)
|
||||
if not path.is_absolute():
|
||||
repo_root = Path(__file__).resolve().parents[4]
|
||||
|
||||
@@ -1 +1,9 @@
|
||||
from . import sirna_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize
|
||||
try:
|
||||
from . import peptide_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize
|
||||
except Exception: # pragma: no cover - 允许轻量环境导入非资源辅助函数
|
||||
peptide_materials = None # type: ignore[assignment]
|
||||
|
||||
try:
|
||||
from . import sirna_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize
|
||||
except Exception: # pragma: no cover - 允许轻量环境导入非资源辅助函数
|
||||
sirna_materials = None # type: ignore[assignment]
|
||||
|
||||
@@ -258,13 +258,13 @@ class BIOYOND_PeptideStation_Deck(Deck):
|
||||
],
|
||||
"xy_col_row",
|
||||
)
|
||||
WAREHOUSE_BIOYOND_KEY_AXIS = dict.fromkeys(WAREHOUSE_BIOYOND_AXIS, "row_col")
|
||||
WAREHOUSE_BIOYOND_KEY_AXIS = dict.fromkeys(WAREHOUSE_BIOYOND_AXIS, "col_row")
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
name: str = "PeptideStation_Deck",
|
||||
size_x: float = 3500.0,
|
||||
size_y: float = 1800.0,
|
||||
size_x: float = 2700.0,
|
||||
size_y: float = 2000.0,
|
||||
size_z: float = 1500.0,
|
||||
category: str = "deck",
|
||||
setup: bool = False
|
||||
@@ -276,6 +276,8 @@ class BIOYOND_PeptideStation_Deck(Deck):
|
||||
@classmethod
|
||||
def deserialize(cls, data: dict, allow_marshal: bool = False):
|
||||
if data.get("children") and data.get("setup") is True:
|
||||
data = data.copy()
|
||||
data["setup"] = False
|
||||
# 已有序列化子资源，跳过 setup 避免重复创建
|
||||
result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
|
||||
else:
|
||||
@@ -293,81 +295,140 @@ class BIOYOND_PeptideStation_Deck(Deck):
|
||||
if key_axis and not hasattr(child, "bioyond_key_axis"):
|
||||
child.bioyond_key_axis = key_axis
|
||||
|
||||
def _frontend_y_flipped_coordinate(self, display_x: float, display_y: float, child) -> Coordinate:
|
||||
"""把期望显示坐标转换为兼容前端 y 轴翻转的存储坐标。"""
|
||||
return Coordinate(display_x, self.get_size_y() - display_y - child.get_size_y(), 0.0)
|
||||
|
||||
def setup(self) -> None:
|
||||
# 多肽工作站仓库配置
|
||||
# 基于 2026-05-09 live API probe 发现的实际仓库拓扑 (12个仓库)
|
||||
# 数据来源: temp_benyao/peptide/_logs/warehouse_discovery_raw_live_2026-05-09.json
|
||||
# 数据来源: Bioyond 现场仓库发现结果。
|
||||
self.warehouses = {
|
||||
# 主自动化堆栈 - live API: code 10-17 -> x=17, y=10，显示为 10 行×17 列
|
||||
# 主自动化堆栈 - live API: code 10-17 -> x=17, y=10，显示为 17 行×10 列
|
||||
"自动化堆栈": bioyond_warehouse_numeric_stack(
|
||||
"自动化堆栈", rows=10, columns=17, bioyond_axis="xy_col_row", bioyond_key_axis="row_col"
|
||||
"自动化堆栈",
|
||||
rows=17,
|
||||
columns=10,
|
||||
bioyond_axis="xy_col_row",
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 低温存储
|
||||
"低温冰箱仓库": bioyond_warehouse_live_grid(
|
||||
"低温冰箱仓库", rows=2, columns=3, slot_keys=["1", "2", "3", "4", "5", "6"]
|
||||
"低温冰箱仓库",
|
||||
rows=3,
|
||||
columns=2,
|
||||
slot_keys=["1", "2", "3", "4", "5", "6"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 移液站库位
|
||||
"Tecan移液站库": bioyond_warehouse_live_grid(
|
||||
"Tecan移液站库", rows=1, columns=18, slot_keys=[str(index) for index in range(1, 19)]
|
||||
"Tecan移液站库",
|
||||
rows=18,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 19)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"G3移液站库": bioyond_warehouse_live_grid(
|
||||
"G3移液站库",
|
||||
rows=1,
|
||||
columns=18,
|
||||
rows=18,
|
||||
columns=1,
|
||||
slot_keys=["1", "2", "3", "4", "垃圾桶", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"IDOT移液站库": bioyond_warehouse_live_grid(
|
||||
"IDOT移液站库",
|
||||
rows=1,
|
||||
columns=12,
|
||||
rows=12,
|
||||
columns=1,
|
||||
slot_keys=[f"0009-{index:04d}" for index in range(1, 13)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 缓冲库位
|
||||
"G3缓冲库": bioyond_warehouse_live_grid(
|
||||
"G3缓冲库", rows=1, columns=5, slot_keys=[str(index) for index in range(1, 6)]
|
||||
"G3缓冲库",
|
||||
rows=5,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 6)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"盖板缓冲库": bioyond_warehouse_live_grid(
|
||||
"盖板缓冲库", rows=1, columns=7, slot_keys=[str(index) for index in range(1, 8)]
|
||||
"盖板缓冲库",
|
||||
rows=7,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 8)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"配平板缓冲库": bioyond_warehouse_live_grid(
|
||||
"配平板缓冲库", rows=1, columns=3, slot_keys=[str(index) for index in range(1, 4)]
|
||||
"配平板缓冲库",
|
||||
rows=3,
|
||||
columns=1,
|
||||
slot_keys=[str(index) for index in range(1, 4)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"IDOT缓冲库": bioyond_warehouse_live_grid(
|
||||
"IDOT缓冲库", rows=1, columns=2, slot_keys=["1", "1"]
|
||||
"IDOT缓冲库",
|
||||
rows=2,
|
||||
columns=1,
|
||||
slot_keys=["1", "1"],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"固相合成板底座缓冲位": bioyond_warehouse_live_grid(
|
||||
"固相合成板底座缓冲位",
|
||||
rows=1,
|
||||
columns=4,
|
||||
rows=4,
|
||||
columns=1,
|
||||
slot_keys=[f"0015-{index:04d}" for index in range(1, 5)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
|
||||
# 设备库位
|
||||
"离心机库位": bioyond_warehouse_live_grid(
|
||||
"离心机库位", rows=1, columns=4, slot_keys=[f"0017-{index:04d}" for index in range(1, 5)]
|
||||
"离心机库位",
|
||||
rows=4,
|
||||
columns=1,
|
||||
slot_keys=[f"0017-{index:04d}" for index in range(1, 5)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
"热封膜机位": bioyond_warehouse_live_grid(
|
||||
"热封膜机位", rows=1, columns=2, slot_keys=[f"0016-{index:04d}" for index in range(1, 3)]
|
||||
"热封膜机位",
|
||||
rows=2,
|
||||
columns=1,
|
||||
slot_keys=[f"0016-{index:04d}" for index in range(1, 3)],
|
||||
bioyond_key_axis="col_row",
|
||||
frontend_y_flip=True,
|
||||
),
|
||||
}
|
||||
|
||||
# 仓库位置布局 (需根据实际硬件布局调整)
|
||||
# 仓库显示布局：紧凑排列；存储 y 坐标按前端兼容翻转预先反向。
|
||||
display_layout = {
|
||||
"自动化堆栈": (0.0, 0.0),
|
||||
"Tecan移液站库": (1520.0, 0.0),
|
||||
"G3移液站库": (1710.0, 0.0),
|
||||
"IDOT移液站库": (1900.0, 0.0),
|
||||
"G3缓冲库": (2090.0, 0.0),
|
||||
"盖板缓冲库": (2090.0, 580.0),
|
||||
"低温冰箱仓库": (2280.0, 0.0),
|
||||
"配平板缓冲库": (2280.0, 370.0),
|
||||
"IDOT缓冲库": (2470.0, 370.0),
|
||||
"固相合成板底座缓冲位": (2280.0, 740.0),
|
||||
"离心机库位": (2470.0, 740.0),
|
||||
"热封膜机位": (2280.0, 1210.0),
|
||||
}
|
||||
self.warehouse_locations = {
|
||||
"自动化堆栈": Coordinate(0.0, 0.0, 0.0),
|
||||
"Tecan移液站库": Coordinate(0.0, 1150.0, 0.0),
|
||||
"G3移液站库": Coordinate(0.0, 1300.0, 0.0),
|
||||
"IDOT移液站库": Coordinate(0.0, 1450.0, 0.0),
|
||||
"G3缓冲库": Coordinate(0.0, 1600.0, 0.0),
|
||||
"盖板缓冲库": Coordinate(850.0, 1600.0, 0.0),
|
||||
"低温冰箱仓库": Coordinate(2700.0, 0.0, 0.0),
|
||||
"配平板缓冲库": Coordinate(2700.0, 300.0, 0.0),
|
||||
"IDOT缓冲库": Coordinate(2700.0, 450.0, 0.0),
|
||||
"固相合成板底座缓冲位": Coordinate(2700.0, 600.0, 0.0),
|
||||
"离心机库位": Coordinate(2700.0, 750.0, 0.0),
|
||||
"热封膜机位": Coordinate(2700.0, 900.0, 0.0),
|
||||
name: self._frontend_y_flipped_coordinate(x, y, self.warehouses[name])
|
||||
for name, (x, y) in display_layout.items()
|
||||
}
|
||||
|
||||
for warehouse_name, warehouse in self.warehouses.items():
|
||||
|
||||
247
unilabos/resources/bioyond/peptide_materials.py
Normal file
247
unilabos/resources/bioyond/peptide_materials.py
Normal file
@@ -0,0 +1,247 @@
|
||||
"""Peptide Station Material Resource Definitions."""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
from collections import OrderedDict
|
||||
|
||||
try:
|
||||
from pylabrobot.resources import Container, Plate, TipRack
|
||||
except Exception: # pragma: no cover - 允许无 pylabrobot 的轻量动作测试导入
|
||||
class _FallbackResource:
|
||||
def __init__(self, *args, **kwargs):
|
||||
self.args = args
|
||||
self.kwargs = kwargs
|
||||
|
||||
class Container(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
class Plate(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
class TipRack(_FallbackResource): # type: ignore[no-redef]
|
||||
pass
|
||||
|
||||
try:
|
||||
from unilabos.registry.decorators import resource
|
||||
except Exception: # pragma: no cover - 允许无完整 registry 依赖时导入常量
|
||||
def resource(*args, **kwargs):
|
||||
def decorator(cls):
|
||||
return cls
|
||||
|
||||
return decorator
|
||||
|
||||
|
||||
def _ensure_itemized_ordering(kwargs: dict) -> None:
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
|
||||
|
||||
class _PeptideTipRack(TipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 64.0)
|
||||
kwargs.setdefault("with_tips", True)
|
||||
_ensure_itemized_ordering(kwargs)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
class _PeptidePlate(Plate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 14.35)
|
||||
kwargs.setdefault("plate_type", "skirted")
|
||||
_ensure_itemized_ordering(kwargs)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_1000ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="1000uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_1000ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_1000ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_200ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="200uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_200ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_200ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_50ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="50uL tip rack for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_50ul_TipRack(_PeptideTipRack):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_50ul_tip_rack")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_deep_well_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well deep well plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellDeepWellPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_deep_well_plate")
|
||||
kwargs.setdefault("size_z", 44.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_synthesis_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well solid-phase synthesis plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellSynthesisPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_synthesis_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_synthesis_plate_base",
|
||||
category=["labware", "adapter"],
|
||||
description="96 well solid-phase synthesis plate base for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellSynthesisPlateBase(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_synthesis_plate_base")
|
||||
kwargs.setdefault("size_z", 20.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_96_well_balance_plate",
|
||||
category=["labware", "plate"],
|
||||
description="96 well balance plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_96WellBalancePlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_96_well_balance_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_well_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384WellPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_well_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_lcms_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well LCMS plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384LCMSPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_lcms_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_384_balance_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384 well balance plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_384BalancePlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_384_balance_plate")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_cover_plate",
|
||||
category=["labware", "cover"],
|
||||
description="Cover plate for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_CoverPlate(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_cover_plate")
|
||||
kwargs.setdefault("size_z", 8.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_sealing_base",
|
||||
category=["labware", "adapter"],
|
||||
description="Sealing base for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_SealingBase(_PeptidePlate):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("model", "bioyond_peptide_sealing_base")
|
||||
kwargs.setdefault("size_z", 20.0)
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_peptide_reagent_trough",
|
||||
category=["labware", "trough"],
|
||||
description="Reagent trough for Bioyond peptide station",
|
||||
)
|
||||
class BioyondPeptide_ReagentTrough(Container):
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 44.0)
|
||||
kwargs.setdefault("max_volume", 300000.0)
|
||||
kwargs.setdefault("model", "bioyond_peptide_reagent_trough")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
DEFAULT_PEPTIDE_MATERIAL_TYPE_MAPPINGS = {
|
||||
"bioyond_peptide_1000ul_tip_rack": ["1000μL枪头盒", "3a1890bb-736e-cfdd-3213-eb314e8a60f9"],
|
||||
"bioyond_peptide_200ul_tip_rack": ["200μL枪头盒", "3a1890bb-36d1-964a-18bd-0bf0f2877a7b"],
|
||||
"bioyond_peptide_50ul_tip_rack": ["50μL枪头盒", "3a1890bc-5fae-361c-cc09-e6f2f6dcd71d"],
|
||||
"bioyond_peptide_96_well_deep_well_plate": ["96孔深孔板", "3a1890bc-1fa8-fe39-9faa-12279ed4569b"],
|
||||
"bioyond_peptide_96_well_synthesis_plate": ["96孔固相合成板", "3a1871cb-99f3-f01d-23e2-08dbbd0045b5"],
|
||||
"bioyond_peptide_96_well_synthesis_plate_base": ["96孔固相合成板底座", "3a1b997e-241b-64f0-80d1-47bca08799d1"],
|
||||
"bioyond_peptide_96_well_balance_plate": ["96孔配平板", "3a187661-2378-1e20-fa5c-a27d49fdc15d"],
|
||||
"bioyond_peptide_384_well_plate": ["384孔酶标板", "3a1890bf-2148-ed20-92bd-d85869947d9a"],
|
||||
"bioyond_peptide_384_lcms_plate": ["384孔LCMS板", "3a1e6a8b-cb61-74da-a089-8e6f197f80f0"],
|
||||
"bioyond_peptide_384_balance_plate": ["384孔配平板", "3a18be7e-47cc-888c-fc68-055753286826"],
|
||||
"bioyond_peptide_cover_plate": ["防挥发盖板", "3a19d5a6-b0e2-b486-e5eb-bcabc632f4de"],
|
||||
"bioyond_peptide_sealing_base": ["封膜底座", "3a1d1d7b-e33b-6975-165d-c56cba5ed345"],
|
||||
"bioyond_peptide_reagent_trough": ["12道试剂槽", "3a18b431-ac58-ca2e-9680-2a4f5880ea45"],
|
||||
}
|
||||
|
||||
|
||||
MATERIAL_TYPE_CODE_TO_CLASS = {
|
||||
"0001": BioyondPeptide_96WellSynthesisPlate,
|
||||
"0002": BioyondPeptide_96WellBalancePlate,
|
||||
"0008": BioyondPeptide_200ul_TipRack,
|
||||
"0009": BioyondPeptide_1000ul_TipRack,
|
||||
"0011": BioyondPeptide_96WellDeepWellPlate,
|
||||
"0012": BioyondPeptide_50ul_TipRack,
|
||||
"0016": BioyondPeptide_384WellPlate,
|
||||
"0018": BioyondPeptide_384WellPlate,
|
||||
"0024": BioyondPeptide_ReagentTrough,
|
||||
"0026": BioyondPeptide_384BalancePlate,
|
||||
"0035": BioyondPeptide_CoverPlate,
|
||||
"0039": BioyondPeptide_96WellSynthesisPlateBase,
|
||||
"0041": BioyondPeptide_SealingBase,
|
||||
"0049": BioyondPeptide_384LCMSPlate,
|
||||
}
|
||||
|
||||
|
||||
def get_material_class_by_type_code(type_code: str):
|
||||
"""Return a peptide material class by Bioyond material type code."""
|
||||
return MATERIAL_TYPE_CODE_TO_CLASS.get(type_code)
|
||||
@@ -1,126 +0,0 @@
|
||||
"""Sirna Station Material Resource Definitions
|
||||
|
||||
Defines PyLabRobot resource classes for Bioyond Sirna station materials.
|
||||
Each class is decorated with @resource for AST-based registry discovery.
|
||||
"""
|
||||
|
||||
from collections import OrderedDict
|
||||
|
||||
from pylabrobot.resources import Plate, TipRack, Container
|
||||
|
||||
from unilabos.registry.decorators import resource
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_sirna_g3_200ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="G3-200ul枪头盒 for Sirna station",
|
||||
)
|
||||
class BioyondSirna_G3_200ul_TipRack(TipRack):
|
||||
"""G3-200ul tip rack for Sirna liquid handling."""
|
||||
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 64.0)
|
||||
kwargs.setdefault("model", "bioyond_sirna_g3_200ul_tip_rack")
|
||||
kwargs.setdefault("with_tips", True)
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_sirna_g3_50ul_tip_rack",
|
||||
category=["labware", "tip_rack"],
|
||||
description="G3-50ul枪头盒 for Sirna station",
|
||||
)
|
||||
class BioyondSirna_G3_50ul_TipRack(TipRack):
|
||||
"""G3-50ul tip rack for Sirna liquid handling."""
|
||||
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 64.0)
|
||||
kwargs.setdefault("model", "bioyond_sirna_g3_50ul_tip_rack")
|
||||
kwargs.setdefault("with_tips", True)
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_sirna_384_well_plate",
|
||||
category=["labware", "plate"],
|
||||
description="384孔板 for Sirna assays",
|
||||
)
|
||||
class BioyondSirna_384WellPlate(Plate):
|
||||
"""384-well plate for Sirna reporter gene detection."""
|
||||
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 14.35)
|
||||
kwargs.setdefault("model", "bioyond_sirna_384_well_plate")
|
||||
kwargs.setdefault("plate_type", "skirted")
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_sirna_cell_culture_plate",
|
||||
category=["labware", "plate"],
|
||||
description="细胞培养板 for Sirna cell culture",
|
||||
)
|
||||
class BioyondSirna_CellCulturePlate(Plate):
|
||||
"""Cell culture plate for Sirna experiments."""
|
||||
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 14.35)
|
||||
kwargs.setdefault("model", "bioyond_sirna_cell_culture_plate")
|
||||
kwargs.setdefault("plate_type", "skirted")
|
||||
if kwargs.get("ordering") is None and kwargs.get("ordered_items") is None:
|
||||
kwargs["ordering"] = OrderedDict()
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
@resource(
|
||||
id="bioyond_sirna_reagent_trough",
|
||||
category=["labware", "trough"],
|
||||
description="试剂槽 for Sirna reagents",
|
||||
)
|
||||
class BioyondSirna_ReagentTrough(Container):
|
||||
"""Reagent trough for Sirna station reagents (RiboGreen, etc.)."""
|
||||
|
||||
def __init__(self, *args, **kwargs):
|
||||
kwargs.setdefault("size_x", 127.76)
|
||||
kwargs.setdefault("size_y", 85.48)
|
||||
kwargs.setdefault("size_z", 44.0)
|
||||
kwargs.setdefault("max_volume", 300000.0)
|
||||
kwargs.setdefault("model", "bioyond_sirna_reagent_trough")
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
|
||||
# Material type code mapping for dynamic instantiation
|
||||
MATERIAL_TYPE_CODE_TO_CLASS = {
|
||||
"0016": BioyondSirna_G3_200ul_TipRack,
|
||||
"0017": BioyondSirna_G3_50ul_TipRack,
|
||||
"0015": BioyondSirna_384WellPlate,
|
||||
"0001": BioyondSirna_CellCulturePlate,
|
||||
"0006": BioyondSirna_ReagentTrough,
|
||||
}
|
||||
|
||||
|
||||
def get_material_class_by_type_code(type_code: str):
|
||||
"""Get resource class by Bioyond material type code.
|
||||
|
||||
Args:
|
||||
type_code: Bioyond materialTypeCode (e.g., "0016", "0017")
|
||||
|
||||
Returns:
|
||||
Resource class or None if not found
|
||||
"""
|
||||
return MATERIAL_TYPE_CODE_TO_CLASS.get(type_code)
|
||||
@@ -25,6 +25,7 @@ def bioyond_warehouse_numeric_stack(
|
||||
columns: int = 17,
|
||||
bioyond_axis: str = "xy_row_col",
|
||||
bioyond_key_axis: str = "row_col",
|
||||
frontend_y_flip: bool = False,
|
||||
) -> WareHouse:
|
||||
"""创建 Bioyond 数字库位堆栈，库位名使用服务端返回的 行-列 格式。
|
||||
|
||||
@@ -46,17 +47,22 @@ def bioyond_warehouse_numeric_stack(
|
||||
item_dx = 147.0
|
||||
item_dy = 106.0
|
||||
item_dz = 130.0
|
||||
locations = [
|
||||
Coordinate(dx + col * item_dx, dy + row * item_dy, dz)
|
||||
for row in range(num_items_y)
|
||||
for col in range(num_items_x)
|
||||
]
|
||||
resource_size_x = 127.0
|
||||
resource_size_y = 86.0
|
||||
resource_size_z = 25.0
|
||||
size_y = dy + item_dy * num_items_y
|
||||
locations = []
|
||||
for row in range(num_items_y):
|
||||
display_y = dy + row * item_dy
|
||||
y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
|
||||
for col in range(num_items_x):
|
||||
locations.append(Coordinate(dx + col * item_dx, y, dz))
|
||||
holders = create_homogeneous_resources(
|
||||
klass=ResourceHolder,
|
||||
locations=locations,
|
||||
resource_size_x=127.0,
|
||||
resource_size_y=86.0,
|
||||
resource_size_z=25.0,
|
||||
resource_size_x=resource_size_x,
|
||||
resource_size_y=resource_size_y,
|
||||
resource_size_z=resource_size_z,
|
||||
name_prefix=name,
|
||||
)
|
||||
if bioyond_key_axis == "row_col":
|
||||
@@ -76,7 +82,7 @@ def bioyond_warehouse_numeric_stack(
|
||||
warehouse = BioyondWareHouse(
|
||||
name=name,
|
||||
size_x=dx + item_dx * num_items_x,
|
||||
size_y=dy + item_dy * num_items_y,
|
||||
size_y=size_y,
|
||||
size_z=dz + item_dz * num_items_z,
|
||||
num_items_x=num_items_x,
|
||||
num_items_y=num_items_y,
|
||||
@@ -97,6 +103,7 @@ def bioyond_warehouse_live_grid(
|
||||
slot_keys: list[str] | None = None,
|
||||
bioyond_axis: str = "xy_col_row",
|
||||
bioyond_key_axis: str = "row_col",
|
||||
frontend_y_flip: bool = False,
|
||||
) -> WareHouse:
|
||||
"""创建 Bioyond 实测库位网格，按服务端 code 保存位点标签。
|
||||
|
||||
@@ -112,17 +119,22 @@ def bioyond_warehouse_live_grid(
|
||||
item_dx = 147.0
|
||||
item_dy = 106.0
|
||||
item_dz = 130.0
|
||||
locations = [
|
||||
Coordinate(dx + col * item_dx, dy + row * item_dy, dz)
|
||||
for row in range(num_items_y)
|
||||
for col in range(num_items_x)
|
||||
]
|
||||
resource_size_x = 127.0
|
||||
resource_size_y = 86.0
|
||||
resource_size_z = 25.0
|
||||
size_y = dy + item_dy * num_items_y
|
||||
locations = []
|
||||
for row in range(num_items_y):
|
||||
display_y = dy + row * item_dy
|
||||
y = size_y - display_y - resource_size_y if frontend_y_flip else display_y
|
||||
for col in range(num_items_x):
|
||||
locations.append(Coordinate(dx + col * item_dx, y, dz))
|
||||
holders = create_homogeneous_resources(
|
||||
klass=ResourceHolder,
|
||||
locations=locations,
|
||||
resource_size_x=127.0,
|
||||
resource_size_y=86.0,
|
||||
resource_size_z=25.0,
|
||||
resource_size_x=resource_size_x,
|
||||
resource_size_y=resource_size_y,
|
||||
resource_size_z=resource_size_z,
|
||||
name_prefix=name,
|
||||
)
|
||||
keys = slot_keys or [str(index + 1) for index in range(num_items_x * num_items_y)]
|
||||
@@ -139,7 +151,7 @@ def bioyond_warehouse_live_grid(
|
||||
return BioyondWareHouse(
|
||||
name=name,
|
||||
size_x=dx + item_dx * num_items_x,
|
||||
size_y=dy + item_dy * num_items_y,
|
||||
size_y=size_y,
|
||||
size_z=dz + item_dz * num_items_z,
|
||||
num_items_x=num_items_x,
|
||||
num_items_y=num_items_y,
|
||||
|
||||
@@ -18,3 +18,7 @@ def register():
|
||||
from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
|
||||
from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
|
||||
|
||||
# noinspection PyUnresolvedReferences
|
||||
from unilabos.resources.bioyond.decks import BIOYOND_SirnaStation_Deck
|
||||
# noinspection PyUnresolvedReferences
|
||||
from unilabos.resources.bioyond.decks import BIOYOND_PeptideStation_Deck
|
||||
|
||||
Reference in New Issue
Block a user