plan: add resource system guidance

fix: change reset and submit_experiment* from manual confirm to normal node
Fix: update sirna_station to support new flexible resultTable
2026-05-23 04:50:01 +00:00 · 2026-05-20 19:17:48 +08:00 · 2026-05-15 15:25:54 +08:00 · 2026-05-15 14:01:34 +08:00 · 2026-05-12 19:35:39 +08:00 · 2026-05-12 19:35:39 +08:00
10 changed files with 6537 additions and 17 deletions
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+# Draft: Resource And Material Sync Guidance For Sirna And Similar Bioyond Systems
+
+Status: draft for discussion, not an implementation mandate.
+
+This note triangulates across five source categories with different authority:
+
+1. `docs/developer_guide/examples/workstation_architecture.md`: desired shape
+   and vocabulary. It is a design target, not proof that the current code has
+   every behavior.
+2. `BioyondWorkstation`, `BioyondResourceSynchronizer`, and shared graphio code:
+   the current compatibility anchor. New guidance should mostly preserve this
+   lifecycle and extend it deliberately.
+3. Existing non-Sirna Bioyond stations: practical examples of how the shared
+   base is used, including shortcuts that should not become policy.
+4. Sirna implementation, plans, findings, and guide notes: stress-test evidence.
+   They expose real missing cases, but the current Sirna code is not the
+   architecture authority because parts were added without fully aligning to the
+   shared base.
+5. UniLabOS resource framework behavior around PLR resources,
+   `ResourceTreeSet`, serialize/deserialize, and `update_resource(resources=...)`.
+
+The short recommendation is:
+
+Keep the shared Bioyond workstation lifecycle as the center of gravity. Evolve
+the shared synchronizer with small project hooks for classification, ID-based
+resolution, and non-slot material handling, rather than letting Sirna become a
+parallel synchronization model. For Sirna, those hooks should resolve placement
+by Bioyond IDs, distinguish physical slot labware from reagent liquid contents,
+preserve Bioyond IDs in `unilabos_extra`, mutate the local PLR deck, and publish
+the full deck through `update_resource(resources=[deck])`.
+
+Do not treat every Bioyond stock row as a deck resource.
+
+## Evidence Weighting
+
+This task is not a Sirna implementation retrospective. It is a best-practice
+alignment pass across the architecture target, the shared base class, observed
+station behavior, and Sirna's newly exposed edge cases.
+
+Use the sources this way:
+
+- Architecture doc: ask "what shape should this system eventually have?"
+- Shared Bioyond base: ask "what behavior must remain compatible today?"
+- Other Bioyond stations: ask "what patterns are already working in practice?"
+- Sirna current code and notes: ask "what did the base model fail to handle, and
+  which Sirna fixes conflict with the shared lifecycle?"
+- Live API/schema evidence: ask "what is true for this deployment's material,
+  warehouse, and coordinate data?"
+
+The Sirna AGENT_GUIDE is useful for finding caveats and prior investigations,
+but it should not be cited as an independent source of truth when source code,
+framework behavior, live API evidence, or architecture docs can answer the same
+question.
+
+## Mental Model
+
+There are three resource worlds. Confusing them is the main source of bugs.
+
+| World | Owner | Purpose | Recommended truth |
+| --- | --- | --- | --- |
+| Bioyond/LIMS | Bioyond APIs through `BioyondV1RPC` | External stock, material IDs, warehouse IDs, location IDs, inbound/outbound side effects | External material truth |
+| PLR deck | Workstation driver | Runtime workstation material layout, warehouse occupancy, liquid contents | Local mutation surface |
+| UniLabOS resource tree | `ResourceTreeSet` / ROS node / host resource APIs | Canonical UniLabOS/cloud representation | Framework/cloud truth |
+
+The architecture guide describes `Deck` as the local material system and
+`ResourceSynchronizer` as the optional external-system bridge
+(`docs/developer_guide/examples/workstation_architecture.md:221`). The broader
+framework serializes PLR objects into `ResourceTreeSet`, whose resource dicts
+carry `id`, `uuid`, `parent_uuid`, `type`, `class`, `pose`, `config`, `data`,
+and `extra` (`unilabos/resources/resource_tracker.py:107`).
+
+Therefore the correct path is:
+
+```text
+Bioyond rows
+  -> normalized material records
+  -> preserve Bioyond materialTypeMode: Sample / Consumables / Reagent
+  -> resolve material/location/warehouse IDs
+  -> choose UniLabOS handling for that mode
+  -> mutate PLR deck
+  -> ResourceTreeSet.from_plr_resources([deck])
+  -> ROS update_resource(resources=[deck])
+  -> host/cloud resource-tree update
+```
+
+Avoid direct cloud JSON patches and avoid treating Bioyond records as already
+being UniLabOS resource nodes.
+
+## Target Architecture
+
+The ideal architecture in `workstation_architecture.md` is still the right
+direction:
+
+1. `WorkstationBase` owns the local `deck`, workflow state, and hardware
+   interface.
+2. `ResourceSynchronizer` owns external material synchronization.
+3. `BioyondResourceSynchronizer` owns the Bioyond-specific use of
+   `BioyondV1RPC`.
+4. `ROS2WorkstationNode.update_resource(resources)` owns the UniLabOS/cloud
+   resource-tree update.
+5. Optional HTTP report handlers may trigger local deck mutation, external sync,
+   and cloud publication.
+
+The documented startup sequence is:
+
+1. Create workstation.
+2. Initialize PLR deck and warehouses.
+3. Create Bioyond RPC hardware interface.
+4. Create resource synchronizer.
+5. `sync_from_external()`.
+6. Initialize ROS node and children.
+7. `post_init(ros_node)`.
+8. Upload `resources=[deck]`.
+
+See `docs/developer_guide/examples/workstation_architecture.md:308`,
+`docs/developer_guide/examples/workstation_architecture.md:497`, and
+`docs/developer_guide/examples/workstation_architecture.md:737`.
+
+Important caveat: that document is the hope. It is still valuable because it
+names the desired responsibilities, but current Bioyond stations implement a
+more limited, best-effort side-effect sync. When the doc and current code
+diverge, use the doc to choose direction and the shared base code to choose the
+next compatible step.
+
+## Current Practical Behavior
+
+The shared `BioyondWorkstation` implementation is the current behavioral
+baseline. It does this today:
+
+1. Requires a deck.
+2. Reconstructs `deck.warehouses` from deck children/config when needed.
+3. Creates `BioyondV1RPC`.
+4. Installs `BioyondResourceSynchronizer`.
+5. Immediately calls `sync_from_external()`.
+6. Later, in `post_init`, publishes the whole deck with
+   `ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True,
+   resources=[self.deck])`.
+
+Relevant code:
+
+- `BioyondResourceSynchronizer` is defined in
+  `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`).
+
+This practical behavior works for simple physical-resource stock import, but it
+does not provide full continuous two-way sync, conflict resolution, or reliable
+stale-state cleanup. In particular:
+
+- Re-fetching stock does not clearly clear stale local deck state first.
+- Local-to-external update no-ops unless `unilabos_extra["update_resource_site"]`
+  is present.
+- `process_material_change_report()` is mostly TODO-level in the base station.
+- Some station-specific code bypasses the shared synchronizer with direct LIMS
+  calls.
+- Some existing stations contain shortcuts that should not be copied, such as
+  duplicate initialization, stale globals, or hardcoded warehouse/axis cases.
+
+Treat current Bioyond behavior as operationally useful and compatibility
+important, not as proof that the ideal architecture is already achieved. The
+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
+  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
+  apply Reagent rows as physical reagent labware or liquid content by evidence
+  report unknown modes or unmapped handling loudly
+  publish deck if deck changed and ROS node is available
+```
+
+Suggested extension points:
+
+```python
+class BioyondResourceSynchronizer(ResourceSynchronizer):
+    def external_material_mode(self, row: dict) -> str:
+        return row["materialTypeMode"]  # Sample | Consumables | Reagent
+
+    def resolve_external_row(self, row: dict) -> dict:
+        ...
+
+    def apply_external_row(self, row: dict, mode: str, resolved: dict) -> None:
+        ...
+```
+
+The base class should continue to own:
+
+- stock fetches for `typeMode` 0/1/2;
+- material-cache refresh;
+- common normalization;
+- mode validation for `Sample` / `Consumables` / `Reagent`;
+- publication orchestration;
+- 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;
+- project-local coordinate conventions;
+- special row handling such as Sirna reagent-as-liquid.
+
+This keeps existing Bioyond stations close to the same lifecycle while still
+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
+evidence requires liquid-content behavior.
+
+## Sirna Findings To Feed Back Into Shared Design
+
+Treat Sirna as a stress test for the shared base, not as a replacement design.
+It raises real questions that earlier stations did not need to answer:
+
+- 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;
+- warehouse and axis metadata must survive serialize/deserialize;
+  project-specific mode handling is available.
+
+For Sirna-like deployments, the old implicit rule "stock row equals PLR
+resource" is too coarse. For simpler deployments, it can remain the default
+mode-handling behavior.
+
+### IDs Win
+
+Placement identity should prefer:
+
+```text
+materialId
+locationId
+materialTypeId
+warehouseId / whid
+```
+
+Display/debug fields are not identity:
+
+```text
+materialName
+materialCode
+locationCode
+locationShowName
+warehouseName / whName
+```
+
+`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
+must raise on ambiguity.
+
+The current Sirna ID-first resolver is useful source evidence for this direction
+(`unilabos/devices/workstation/bioyond_studio/sirna_station/sirna_station.py:3659`).
+The Sirna mega plan captures the same concern, but the implementation and live
+Bioyond IDs are the stronger evidence.
+
+### 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.
--- a/unilabos/devices/workstation/bioyond_studio/debug_call_log.py
+++ b/unilabos/devices/workstation/bioyond_studio/debug_call_log.py
@@ -0,0 +1,459 @@
+"""Per-action raw call/response log for Bioyond stations.
+
+When a debug session is active, ``wrap_rpc_http`` replaces a ``BioyondV1RPC``
+instance's ``post`` / ``get`` methods with closures that perform the HTTP
+transport themselves, capture the request/response details, and append a record
+to the active session before returning exactly what ``BaseRequest`` would have
+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``
+minus the "Raw Payload Argument" section.
+
+This module has no dependency on ``BioyondV1RPC`` itself; the only contract is
+that the wrapped instance descends from ``BaseRequest`` (i.e. has a logger
+returned by ``self.get_logger()``).
+"""
+
+from __future__ import annotations
+
+import contextvars
+import copy
+import inspect
+import json
+import re
+from contextlib import contextmanager
+from dataclasses import dataclass, field
+from datetime import datetime
+from pathlib import Path
+from typing import Any, Iterator, List, Optional
+
+import requests
+
+__all__ = [
+    "CallRecord",
+    "CallLogContext",
+    "session",
+    "wrap_rpc_http",
+    "active_session",
+]
+
+
+_DEFAULT_TIMEOUT_GET = 30
+_DEFAULT_TIMEOUT_POST = 120
+
+
+@dataclass
+class CallRecord:
+    """One captured HTTP call inside a debug session."""
+
+    index: int
+    method: str
+    url: str
+    path: str
+    source: str
+    transport: str
+    http_status: Optional[int]
+    request_body: Any
+    response_body: Any
+    error: Optional[str] = None
+
+
+@dataclass
+class CallLogContext:
+    """State for a single ``session()`` block.
+
+    A session lazily creates its file on the first appended record. Actions
+    that abort before any RPC produce no file.
+    """
+
+    action: str
+    out_dir: Path
+    started_at: datetime
+    calls: List[CallRecord] = field(default_factory=list)
+    file_path: Optional[Path] = None
+
+    def append(self, record: CallRecord) -> None:
+        record.index = len(self.calls) + 1
+        self.calls.append(record)
+        self._write_file()
+
+    # -- file I/O -------------------------------------------------------------
+
+    def _resolve_file_path(self) -> Path:
+        if self.file_path is not None:
+            return self.file_path
+        timestamp = self.started_at.strftime("%Y-%m-%d_%H%M%S")
+        slug = _slugify_action(self.action)
+        candidate = self.out_dir / f"{timestamp}_{slug}_raw_calls.md"
+        suffix = 2
+        while candidate.exists():
+            candidate = (
+                self.out_dir
+                / f"{timestamp}_{slug}_raw_calls_{suffix:02d}.md"
+            )
+            suffix += 1
+        self.file_path = candidate
+        return self.file_path
+
+    def _write_file(self) -> None:
+        path = self._resolve_file_path()
+        path.parent.mkdir(parents=True, exist_ok=True)
+        path.write_text(_render_markdown(self), encoding="utf-8")
+
+
+_active_session: contextvars.ContextVar[Optional[CallLogContext]] = (
+    contextvars.ContextVar("_active_session", default=None)
+)
+
+
+def active_session() -> Optional[CallLogContext]:
+    """Return the currently active :class:`CallLogContext`, if any."""
+    return _active_session.get()
+
+
+@contextmanager
+def session(action: str, out_dir: Path) -> Iterator[CallLogContext]:
+    """Open a per-action debug session.
+
+    On entry, sets the module-level ``_active_session`` ContextVar so any
+    ``wrap_rpc_http``'d clients on the same thread/task record their calls.
+    On exit, the previous active session (if any) is restored.
+    """
+    ctx = CallLogContext(
+        action=str(action),
+        out_dir=Path(out_dir),
+        started_at=datetime.now(),
+    )
+    token = _active_session.set(ctx)
+    try:
+        yield ctx
+    finally:
+        _active_session.reset(token)
+
+
+def wrap_rpc_http(rpc: Any) -> None:
+    """Idempotently wrap ``rpc.post`` / ``rpc.get``.
+
+    When a session is active (``_active_session.get() is not None``), the
+    wrapped methods perform the HTTP call themselves with ``requests`` and
+    record the call before returning the same value ``BaseRequest`` would have
+    returned. When no session is active, the wrapped methods delegate to the
+    original implementation, preserving stock ``BaseRequest`` behavior.
+
+    Calling this twice on the same instance is a no-op. The wrapper does not
+    alter ``rpc.form_post`` (no Sirna action calls it as of plan 3).
+    """
+    if rpc is None:
+        return
+    if getattr(rpc, "_debug_call_log_wrapped", False):
+        return
+
+    rpc._orig_post = rpc.post
+    rpc._orig_get = rpc.get
+
+    def _wrapped_post(
+        url: str,
+        params: Any = None,
+        files: Any = None,
+        headers: Optional[dict] = None,
+    ) -> Any:
+        ctx = _active_session.get()
+        if ctx is None:
+            kwargs = {}
+            if params is not None:
+                kwargs["params"] = params
+            if files is not None:
+                kwargs["files"] = files
+            if headers is not None:
+                kwargs["headers"] = headers
+            return rpc._orig_post(url, **kwargs)
+        effective_params = params if params is not None else {}
+        effective_headers = (
+            headers
+            if headers is not None
+            else {"Content-Type": "application/json"}
+        )
+        source = _detect_source(rpc)
+        request_body = _redact(effective_params)
+        record = CallRecord(
+            index=0,
+            method="POST",
+            url=str(url),
+            path=_url_path(url),
+            source=source,
+            transport=_pick_transport(effective_params),
+            http_status=None,
+            request_body=request_body,
+            response_body=None,
+            error=None,
+        )
+        return_value: Any = None
+        try:
+            response = requests.post(
+                url,
+                data=json.dumps(effective_params) if effective_params else None,
+                headers=effective_headers,
+                timeout=_DEFAULT_TIMEOUT_POST,
+                files=files,
+            )
+        except Exception as exc:  # pragma: no cover - delegated to logger
+            record.error = f"transport error: {exc}"
+            try:
+                rpc.get_logger().error(f"Request ERROR: {exc}")
+            except Exception:
+                pass
+            ctx.append(record)
+            return None
+
+        record.http_status = response.status_code
+        record.response_body, parse_error = _decode_response_body(response)
+        try:
+            rpc.get_logger().debug(
+                f"Request >>> : {response.request.body} "
+                f"{response.status_code} {response.text}"
+            )
+        except Exception:
+            pass
+
+        if response.status_code == 200:
+            if parse_error is not None:
+                record.error = f"json parse error: {parse_error}"
+                return_value = None
+            else:
+                return_value = record.response_body
+        else:
+            record.error = f"HTTP {response.status_code}: {response.text}"
+            try:
+                rpc.get_logger().error(
+                    f"Request ERROR: ('Request ERROR:', {response.text!r})"
+                )
+            except Exception:
+                pass
+            return_value = None
+
+        ctx.append(record)
+        return return_value
+
+    def _wrapped_get(
+        url: str,
+        params: Any = None,
+        headers: Optional[dict] = None,
+    ) -> Any:
+        ctx = _active_session.get()
+        if ctx is None:
+            kwargs = {}
+            if params is not None:
+                kwargs["params"] = params
+            if headers is not None:
+                kwargs["headers"] = headers
+            return rpc._orig_get(url, **kwargs)
+        effective_params = params if params is not None else {}
+        effective_headers = (
+            headers
+            if headers is not None
+            else {"Content-Type": "application/json"}
+        )
+        source = _detect_source(rpc)
+        request_body = _redact(effective_params)
+        record = CallRecord(
+            index=0,
+            method="GET",
+            url=str(url),
+            path=_url_path(url),
+            source=source,
+            transport="params",
+            http_status=None,
+            request_body=request_body,
+            response_body=None,
+            error=None,
+        )
+        return_value: Any = None
+        try:
+            response = requests.get(
+                url,
+                params=effective_params,
+                headers=effective_headers,
+                timeout=_DEFAULT_TIMEOUT_GET,
+            )
+        except Exception as exc:  # pragma: no cover - delegated to logger
+            record.error = f"transport error: {exc}"
+            try:
+                rpc.get_logger().error(f"Request ERROR: {exc}")
+            except Exception:
+                pass
+            ctx.append(record)
+            return None
+
+        record.http_status = response.status_code
+        record.response_body, parse_error = _decode_response_body(response)
+        try:
+            rpc.get_logger().debug(
+                f"Request >>> : {effective_params} "
+                f"{response.status_code} {response.text}"
+            )
+        except Exception:
+            pass
+
+        if response.status_code == 200:
+            if parse_error is not None:
+                record.error = f"json parse error: {parse_error}"
+                return_value = None
+            else:
+                return_value = record.response_body
+
+        ctx.append(record)
+        return return_value
+
+    rpc.post = _wrapped_post
+    rpc.get = _wrapped_get
+    rpc._debug_call_log_wrapped = True
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+
+_URL_PATH_RE = re.compile(r"https?://[^/]+(/.*)?$")
+_SLUG_RE = re.compile(r"[^A-Za-z0-9._-]+")
+
+
+def _slugify_action(action: str) -> str:
+    slug = _SLUG_RE.sub("_", str(action)).strip("_")
+    return slug or "action"
+
+
+def _url_path(url: Any) -> str:
+    text = str(url or "")
+    match = _URL_PATH_RE.match(text)
+    if match and match.group(1):
+        return match.group(1)
+    if text.startswith("/"):
+        return text
+    return text
+
+
+def _pick_transport(params: Any) -> str:
+    if isinstance(params, dict) and "data" in params:
+        return "data"
+    return "params"
+
+
+def _detect_source(rpc: Any) -> str:
+    """Walk the call stack to find the outermost frame whose ``self`` is rpc."""
+    try:
+        stack = inspect.stack()
+    except Exception:
+        return ""
+    candidate = ""
+    try:
+        for frame_info in stack:
+            frame = frame_info.frame
+            if frame.f_locals.get("self", None) is rpc:
+                candidate = frame_info.function
+        return candidate
+    finally:
+        del stack
+
+
+def _redact(params: Any) -> Any:
+    """Return a copy of ``params`` with ``apiKey`` redacted."""
+    try:
+        cloned = copy.deepcopy(params)
+    except Exception:
+        return params
+    _redact_in_place(cloned)
+    return cloned
+
+
+def _redact_in_place(value: Any) -> None:
+    if isinstance(value, dict):
+        for key in list(value.keys()):
+            if isinstance(key, str) and key.lower() == "apikey":
+                value[key] = "<redacted>"
+            else:
+                _redact_in_place(value[key])
+    elif isinstance(value, list):
+        for item in value:
+            _redact_in_place(item)
+
+
+def _decode_response_body(response: Any) -> tuple[Any, Optional[str]]:
+    """Best-effort response decoding used for both record + return value."""
+    text = getattr(response, "text", "")
+    try:
+        return response.json(), None
+    except Exception as exc:
+        if text:
+            return {"raw_text": text}, str(exc)
+        return None, str(exc)
+
+
+# ---------------------------------------------------------------------------
+# Markdown rendering
+# ---------------------------------------------------------------------------
+
+
+def _render_markdown(ctx: CallLogContext) -> str:
+    title = f"# {ctx.action} Raw Call/Response Log"
+    parts: List[str] = [title, ""]
+    parts.append("## LIMS Calls")
+    parts.append("")
+    parts.append("| # | Method | Path | Source | HTTP |")
+    parts.append("|---|---|---|---|---|")
+    for record in ctx.calls:
+        anchor = _row_anchor(record)
+        http = (
+            f"`{record.http_status}`"
+            if record.http_status is not None
+            else "`-`"
+        )
+        parts.append(
+            f"| [{record.index}](#{anchor}) | `{record.method}` | "
+            f"`{record.path}` | `{record.source}` | {http} |"
+        )
+    parts.append("")
+
+    for record in ctx.calls:
+        parts.append(f"## {record.index} {record.method} {record.path}")
+        parts.append("")
+        parts.append(f"- Source: `{record.source}`")
+        parts.append(f"- Transport: `{record.transport}`")
+        if record.http_status is not None:
+            parts.append(f"- HTTP status: `{record.http_status}`")
+        else:
+            parts.append("- HTTP status: `-`")
+        if record.error:
+            parts.append(f"- Error: {record.error}")
+        parts.append("")
+        parts.append("### Request Body")
+        parts.append("")
+        parts.append("```json")
+        parts.append(_to_json_block(record.request_body))
+        parts.append("```")
+        parts.append("")
+        parts.append("### Response Body")
+        parts.append("")
+        parts.append("```json")
+        parts.append(_to_json_block(record.response_body))
+        parts.append("```")
+        parts.append("")
+
+    return "\n".join(parts).rstrip() + "\n"
+
+
+def _row_anchor(record: CallRecord) -> str:
+    """Build a GitHub-style anchor matching ``## N METHOD /path``."""
+    raw = f"{record.index}-{record.method}-{record.path}"
+    raw = raw.lower()
+    raw = re.sub(r"[^a-z0-9]+", "-", raw)
+    return raw.strip("-")
+
+
+def _to_json_block(value: Any) -> str:
+    try:
+        return json.dumps(value, ensure_ascii=False, indent=2, sort_keys=True)
+    except TypeError:
+        return json.dumps(str(value), ensure_ascii=False, indent=2)
--- a/unilabos/devices/workstation/bioyond_studio/sirna_station/init.py
+++ b/unilabos/devices/workstation/bioyond_studio/sirna_station/init.py
@@ -0,0 +1,3 @@
+from .sirna_station import BioyondSirnaStation, fetch_workflow_list, load_sirna_config
+
+__all__ = ["BioyondSirnaStation", "fetch_workflow_list", "load_sirna_config"]
--- a/unilabos/devices/workstation/bioyond_studio/sirna_station/sirna_station.py
+++ b/unilabos/devices/workstation/bioyond_studio/sirna_station/sirna_station.py
--- a/unilabos/devices/workstation/bioyond_studio/station.py
+++ b/unilabos/devices/workstation/bioyond_studio/station.py
@@ -7,6 +7,7 @@ Bioyond Workstation Implementation
 import time
 import traceback
 import threading
+from contextlib import contextmanager
 from datetime import datetime
 from typing import Dict, Any, List, Optional, Union
 import json
@@ -14,6 +15,7 @@ from pathlib import Path

 from unilabos.devices.workstation.workstation_base import WorkstationBase, ResourceSynchronizer
 from unilabos.devices.workstation.bioyond_studio.bioyond_rpc import BioyondV1RPC
+from unilabos.devices.workstation.bioyond_studio import debug_call_log
 from unilabos.registry.placeholder_type import ResourceSlot, DeviceSlot
 from unilabos.resources.warehouse import WareHouse
 from unilabos.utils.log import logger
@@ -174,6 +176,8 @@ class BioyondResourceSynchronizer(ResourceSynchronizer):
                logger.warning("从Bioyond获取的物料数据为空")
                return False

+            self._update_material_cache_from_stock(all_bioyond_data)
+
            # 转换为UniLab格式
            unilab_resources = resource_bioyond_to_plr(
                all_bioyond_data,
@@ -187,6 +191,29 @@ class BioyondResourceSynchronizer(ResourceSynchronizer):
            logger.error(f"从Bioyond同步物料数据失败: {e}")
            return False

+    def _update_material_cache_from_stock(self, materials: List[Dict[str, Any]]) -> None:
+        """用本次库存查询结果同步 RPC 的 name -> material id 缓存。"""
+        material_cache = getattr(self.bioyond_api_client, "material_cache", None)
+        if not isinstance(material_cache, dict):
+            return
+
+        before_count = len(material_cache)
+        for material in materials:
+            material_name = material.get("name")
+            material_id = material.get("id")
+            if material_name and material_id:
+                material_cache[material_name] = material_id
+
+            for detail_material in material.get("detail", []) or []:
+                detail_name = detail_material.get("name")
+                detail_id = detail_material.get("detailMaterialId") or detail_material.get("id")
+                if detail_name and detail_id:
+                    material_cache[detail_name] = detail_id
+
+        logger.debug(
+            f"已用Bioyond库存同步物料缓存: {before_count} -> {len(material_cache)}"
+        )
+
    def sync_to_external(self, resource: Any) -> bool:
        """将本地物料数据变更同步到Bioyond系统"""
        try:
@@ -678,6 +705,70 @@ class BioyondWorkstation(WorkstationBase):
    集成Bioyond物料管理的工作站实现
    """

+    # 子类（如 sirna / peptide）覆写以指定默认 raw-call 日志目录。
+    # 路径相对仓库根；为 None 时若 debug_log=True 仍会写入临时位置。
+    _DEBUG_LOG_DEFAULT_DIR: Optional[str] = None
+
+    def _create_bioyond_rpc(self, config: Dict[str, Any]) -> BioyondV1RPC:
+        """创建 Bioyond RPC 客户端并应用调试包装。
+
+        所有创建 ``BioyondV1RPC`` 的路径（饿汉初始化、Sirna 延迟初始化、
+        以及未来的前端重新配置路径）都应通过该 helper，
+        以确保 debug_log 包装与命名/日志策略保持一致。
+        """
+        rpc = BioyondV1RPC(config)
+        debug_call_log.wrap_rpc_http(rpc)
+        return rpc
+
+    def _set_hardware_interface(self, rpc: BioyondV1RPC) -> BioyondV1RPC:
+        """将已构造的 RPC 客户端设置到 ``self.hardware_interface``，并应用调试包装。"""
+        debug_call_log.wrap_rpc_http(rpc)
+        self.hardware_interface = rpc
+        return rpc
+
+    def _debug_log_resolved_dir(self) -> Path:
+        """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"
+        path = Path(candidate)
+        if not path.is_absolute():
+            repo_root = Path(__file__).resolve().parents[4]
+            path = repo_root / path
+        return path
+
+    def _ensure_debug_log_state(self) -> None:
+        """从 ``self.bioyond_config`` 派生 ``_debug_log_enabled`` / ``_debug_log_dir``。
+
+        每次进入 ``_debug_call_session`` 时都重新解析，以兼容前端在运行时
+        修改 ``bioyond_config['debug_log']`` 或目录的场景；同时也容忍
+        子类（如 Sirna 延迟初始化）在 ``__init__`` 早期未触发本方法。
+        """
+        cfg = getattr(self, "bioyond_config", {}) or {}
+        self._debug_log_enabled = bool(cfg.get("debug_log"))
+        self._debug_log_dir = self._debug_log_resolved_dir()
+
+    @contextmanager
+    def _debug_call_session(self, action_name: str):
+        """在 action 体外加一层 debug 会话上下文。
+
+        - ``debug_log`` 关闭时是空上下文，开销为 0。
+        - ``debug_log`` 开启时进入 :func:`debug_call_log.session`，所有
+          已被 ``wrap_rpc_http`` 包装过的 RPC 客户端都会捕获本次 action
+          产生的 HTTP 调用并写入 Markdown 文件。
+
+        子类（如 ``end_experiment``、``manual_unload`` 等）可以直接在
+        action 体里以 ``with self._debug_call_session("action_name"):`` 包裹。
+        """
+        cfg = getattr(self, "bioyond_config", {}) or {}
+        enabled = bool(cfg.get("debug_log"))
+        if not enabled:
+            yield None
+            return
+        out_dir = BioyondWorkstation._debug_log_resolved_dir(self)
+        with debug_call_log.session(action_name, out_dir) as ctx:
+            yield ctx
+
    def _publish_task_status(
        self,
        task_id: str,
@@ -862,7 +953,7 @@ class BioyondWorkstation(WorkstationBase):
            self.bioyond_config = {}
            print("警告: 未提供 bioyond_config，请确保在 JSON 配置文件中提供完整配置")

-        self.hardware_interface = BioyondV1RPC(self.bioyond_config)
+        self.hardware_interface = self._create_bioyond_rpc(self.bioyond_config)

    def resource_tree_add(self, resources: List[ResourcePLR]) -> None:
        """添加资源到资源树并更新ROS节点
@@ -1338,11 +1429,7 @@ class BioyondWorkstation(WorkstationBase):
            if self.hardware_interface:
                self.hardware_interface.scheduler_reset()

-            # 刷新物料缓存
-            if self.hardware_interface:
-                self.hardware_interface.refresh_material_cache()
-
-            # 重新同步资源
+            # 重新同步资源，并用同一次库存查询结果更新物料缓存
            if self.resource_synchronizer:
                self.resource_synchronizer.sync_from_external()

--- a/unilabos/resources/bioyond/init.py
+++ b/unilabos/resources/bioyond/init.py
@@ -0,0 +1 @@
+from . import sirna_materials  # noqa: F401  ensure @resource classes are importable for PLR deserialize
--- a/unilabos/resources/bioyond/decks.py
+++ b/unilabos/resources/bioyond/decks.py
@@ -1,6 +1,8 @@
 from os import name
+
 from pylabrobot.resources import Deck, Coordinate, Rotation

+from unilabos.registry.decorators import resource
 from unilabos.resources.bioyond.YB_warehouses import (
    bioyond_warehouse_1x4x4,
    bioyond_warehouse_1x4x4_right,  # 新增：右侧仓库 (A05～D08)
@@ -23,6 +25,11 @@ from unilabos.resources.bioyond.YB_warehouses import (
 from unilabos.resources.bioyond.warehouses import (
    bioyond_warehouse_tipbox_storage_left,   # 新增：Tip盒堆栈(左)
    bioyond_warehouse_tipbox_storage_right,  # 新增：Tip盒堆栈(右)
+    bioyond_warehouse_sirna_automation_stack,
+    bioyond_warehouse_sirna_centrifuge_balance_plate_stack,
+    bioyond_warehouse_sirna_g3_liquid_handler,
+    bioyond_warehouse_numeric_stack,  # 新增：数字编码堆栈 (用于多肽站)
+    bioyond_warehouse_live_grid,
 )


@@ -101,6 +108,83 @@ class BIOYOND_PolymerPreparationStation_Deck(Deck):
        for warehouse_name, warehouse in self.warehouses.items():
            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])

+@resource(
+    id="BIOYOND_SirnaStation_Deck",
+    category=["deck"],
+    description="BIOYOND 小核酸工作站 Deck",
+    icon="配液站.webp",
+)
+class BIOYOND_SirnaStation_Deck(Deck):
+    WAREHOUSE_BIOYOND_AXIS = {
+        "G3移液站": "xy_col_row",
+        "自动化堆栈": "xy_col_row",
+        "离心机配平板堆栈": "xy_col_row",
+    }
+    WAREHOUSE_BIOYOND_KEY_AXIS = {
+        "G3移液站": "col_row",
+        "自动化堆栈": "col_row",
+        "离心机配平板堆栈": "col_row",
+    }
+    # Bioyond warehouse UUID -> 本地仓库名称 映射。
+    # 留空时由配置（station config 的 ``warehouse_bioyond_ids``）注入。
+    # graph 节点也可在 deck.config.warehouse_bioyond_ids 覆盖。
+    WAREHOUSE_BIOYOND_IDS: dict = {}
+
+    def __init__(
+        self,
+        name: str = "SirnaStation_Deck",
+        size_x: float = 2700.0,
+        size_y: float = 1080.0,
+        size_z: float = 1500.0,
+        category: str = "deck",
+        setup: bool = False,
+        warehouse_bioyond_ids: dict | None = None,
+        **kwargs,
+    ) -> None:
+        super().__init__(name=name, size_x=size_x, size_y=size_y, size_z=size_z)
+        # 按需写入实例级覆盖；保留默认空 mapping，避免改动模型常量。
+        self.warehouse_bioyond_ids: dict = dict(self.WAREHOUSE_BIOYOND_IDS)
+        if warehouse_bioyond_ids:
+            self.warehouse_bioyond_ids.update(warehouse_bioyond_ids)
+        if setup:
+            self.setup()
+
+    @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
+        result = super().deserialize(data, allow_marshal=allow_marshal)
+        result._ensure_sirna_warehouse_metadata()
+        return result
+
+    def _ensure_sirna_warehouse_metadata(self) -> None:
+        for child in getattr(self, "children", []):
+            name = getattr(child, "name", "")
+            axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
+            if axis and not hasattr(child, "bioyond_axis"):
+                child.bioyond_axis = axis
+            key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
+            if key_axis and not hasattr(child, "bioyond_key_axis"):
+                child.bioyond_key_axis = key_axis
+
+    def setup(self) -> None:
+        # Sirna 读接口 /api/storage/location/locations-by-type 返回完整固定堆栈清单。
+        # LIMS 在库物料接口仍使用相同的 自动化堆栈 名称和数字库位编码。
+        self.warehouses = {
+            "G3移液站": bioyond_warehouse_sirna_g3_liquid_handler(),
+            "自动化堆栈": bioyond_warehouse_sirna_automation_stack(),
+            "离心机配平板堆栈": bioyond_warehouse_sirna_centrifuge_balance_plate_stack(),
+        }
+        self.warehouse_locations = {
+            "G3移液站": Coordinate(0.0, 0.0, 0.0),
+            "自动化堆栈": Coordinate(220.0, 0.0, 0.0),
+            "离心机配平板堆栈": Coordinate(1740.0, 0.0, 0.0),
+        }
+
+        for warehouse_name, warehouse in self.warehouses.items():
+            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
+
 class BIOYOND_YB_Deck(Deck):
    def __init__(
        self,
@@ -150,12 +234,146 @@ class BIOYOND_YB_Deck(Deck):
        for warehouse_name, warehouse in self.warehouses.items():
            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])

+@resource(
+    id="BIOYOND_PeptideStation_Deck",
+    category=["deck"],
+    description="BIOYOND 多肽工作站 Deck",
+    icon="preparation_station.webp",
+)
+class BIOYOND_PeptideStation_Deck(Deck):
+    WAREHOUSE_BIOYOND_AXIS = dict.fromkeys(
+        [
+            "自动化堆栈",
+            "低温冰箱仓库",
+            "Tecan移液站库",
+            "G3移液站库",
+            "IDOT移液站库",
+            "G3缓冲库",
+            "盖板缓冲库",
+            "配平板缓冲库",
+            "IDOT缓冲库",
+            "固相合成板底座缓冲位",
+            "离心机库位",
+            "热封膜机位",
+        ],
+        "xy_col_row",
+    )
+    WAREHOUSE_BIOYOND_KEY_AXIS = dict.fromkeys(WAREHOUSE_BIOYOND_AXIS, "row_col")
+
+    def __init__(
+        self,
+        name: str = "PeptideStation_Deck",
+        size_x: float = 3500.0,
+        size_y: float = 1800.0,
+        size_z: float = 1500.0,
+        category: str = "deck",
+        setup: bool = False
+    ) -> None:
+        super().__init__(name=name, size_x=size_x, size_y=size_y, size_z=size_z)
+        if setup:
+            self.setup()
+
+    @classmethod
+    def deserialize(cls, data: dict, allow_marshal: bool = False):
+        if data.get("children") and data.get("setup") is True:
+            # 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:
+            result = super(BIOYOND_PeptideStation_Deck, cls).deserialize(data, allow_marshal=allow_marshal)
+        result._ensure_peptide_warehouse_metadata()
+        return result
+
+    def _ensure_peptide_warehouse_metadata(self) -> None:
+        for child in getattr(self, "children", []):
+            name = getattr(child, "name", "")
+            axis = self.WAREHOUSE_BIOYOND_AXIS.get(name)
+            if axis and not hasattr(child, "bioyond_axis"):
+                child.bioyond_axis = axis
+            key_axis = self.WAREHOUSE_BIOYOND_KEY_AXIS.get(name)
+            if key_axis and not hasattr(child, "bioyond_key_axis"):
+                child.bioyond_key_axis = key_axis
+
+    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
+        self.warehouses = {
+            # 主自动化堆栈 - live API: code 10-17 -> x=17, y=10，显示为 10 行×17 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"
+            ),
+
+            # 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"]
+            ),
+
+            # 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)]
+            ),
+            "G3移液站库": bioyond_warehouse_live_grid(
+                "G3移液站库",
+                rows=1,
+                columns=18,
+                slot_keys=["1", "2", "3", "4", "垃圾桶", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18"],
+            ),
+            "IDOT移液站库": bioyond_warehouse_live_grid(
+                "IDOT移液站库",
+                rows=1,
+                columns=12,
+                slot_keys=[f"0009-{index:04d}" for index in range(1, 13)],
+            ),
+
+            # 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)]
+            ),
+            "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)]
+            ),
+            "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)]
+            ),
+            "IDOT缓冲库": bioyond_warehouse_live_grid(
+                "IDOT缓冲库", rows=1, columns=2, slot_keys=["1", "1"]
+            ),
+            "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,
+                slot_keys=[f"0015-{index:04d}" for index in range(1, 5)],
+            ),
+
+            # 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)]
+            ),
+            "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)]
+            ),
+        }
+
+        # 仓库位置布局 (需根据实际硬件布局调整)
+        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),
+        }
+
+        for warehouse_name, warehouse in self.warehouses.items():
+            self.assign_child_resource(warehouse, location=self.warehouse_locations[warehouse_name])
+
 def YB_Deck(name: str) -> Deck:
    by=BIOYOND_YB_Deck(name=name)
    by.setup()
    return by
-
-
-
-
-
--- a/unilabos/resources/bioyond/sirna_materials.py
+++ b/unilabos/resources/bioyond/sirna_materials.py
@@ -0,0 +1,126 @@
+"""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)
--- a/unilabos/resources/bioyond/warehouses.py
+++ b/unilabos/resources/bioyond/warehouses.py
@@ -1,5 +1,180 @@
+from pylabrobot.resources import Coordinate
+from pylabrobot.resources.carrier import ResourceHolder, create_homogeneous_resources
+
 from unilabos.resources.warehouse import WareHouse, warehouse_factory

+
+class BioyondWareHouse(WareHouse):
+    """Bioyond 仓库，额外保存服务端 x/y 坐标和库位标签语义。"""
+
+    def __init__(self, *args, bioyond_axis: str = "xy_row_col", bioyond_key_axis: str = "row_col", **kwargs):
+        super().__init__(*args, **kwargs)
+        self.bioyond_axis = bioyond_axis
+        self.bioyond_key_axis = bioyond_key_axis
+
+    def serialize(self) -> dict:
+        data = super().serialize()
+        data["bioyond_axis"] = self.bioyond_axis
+        data["bioyond_key_axis"] = self.bioyond_key_axis
+        return data
+
+
+def bioyond_warehouse_numeric_stack(
+    name: str,
+    rows: int = 10,
+    columns: int = 17,
+    bioyond_axis: str = "xy_row_col",
+    bioyond_key_axis: str = "row_col",
+) -> 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。
+
+    bioyond_axis: 仓库级别的 Bioyond 坐标轴约定，供 graphio 的坐标映射使用。
+        - "xy_row_col" (default): Bioyond x→row, y→col (reaction/peptide 历史约定).
+        - "xy_col_row": Bioyond x→col, y→row (Sirna live API 实测约定).
+    bioyond_key_axis: 库位标签生成约定。
+        - "row_col" (default): 视觉行列和标签行列一致，例如 10 行 x 17 列 → 1-1..10-17。
+        - "col_row": 视觉行列转置，但标签仍保持 Bioyond row-col，例如
+          17 行 x 10 列 → 1-1..10-17。
+    未设置时 graphio 回退到默认 "xy_row_col"，其他调用方保持原行为。
+    """
+    num_items_x = columns
+    num_items_y = rows
+    num_items_z = 1
+    dx = 10.0
+    dy = 10.0
+    dz = 10.0
+    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)
+    ]
+    holders = create_homogeneous_resources(
+        klass=ResourceHolder,
+        locations=locations,
+        resource_size_x=127.0,
+        resource_size_y=86.0,
+        resource_size_z=25.0,
+        name_prefix=name,
+    )
+    if bioyond_key_axis == "row_col":
+        keys = [
+            f"{row + 1}-{col + 1}"
+            for row in range(num_items_y)
+            for col in range(num_items_x)
+        ]
+    elif bioyond_key_axis == "col_row":
+        keys = [
+            f"{col + 1}-{row + 1}"
+            for row in range(num_items_y)
+            for col in range(num_items_x)
+        ]
+    else:
+        raise ValueError(f"未知 Bioyond 库位标签约定: {bioyond_key_axis!r}")
+    warehouse = BioyondWareHouse(
+        name=name,
+        size_x=dx + item_dx * num_items_x,
+        size_y=dy + item_dy * num_items_y,
+        size_z=dz + item_dz * num_items_z,
+        num_items_x=num_items_x,
+        num_items_y=num_items_y,
+        num_items_z=num_items_z,
+        ordering_layout="row-major",
+        sites={key: holder for key, holder in zip(keys, holders.values())},
+        category="warehouse",
+        bioyond_axis=bioyond_axis,
+        bioyond_key_axis=bioyond_key_axis,
+    )
+    return warehouse
+
+
+def bioyond_warehouse_live_grid(
+    name: str,
+    rows: int,
+    columns: int,
+    slot_keys: list[str] | None = None,
+    bioyond_axis: str = "xy_col_row",
+    bioyond_key_axis: str = "row_col",
+) -> WareHouse:
+    """创建 Bioyond 实测库位网格，按服务端 code 保存位点标签。
+
+    默认用于 Peptide live API 返回的坐标：x 是视觉列，y 是视觉行。
+    当服务端 code 重复时，为保持 PLR ordering 唯一性，会给后续重复项追加 ``#N``。
+    """
+    num_items_x = columns
+    num_items_y = rows
+    num_items_z = 1
+    dx = 10.0
+    dy = 10.0
+    dz = 10.0
+    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)
+    ]
+    holders = create_homogeneous_resources(
+        klass=ResourceHolder,
+        locations=locations,
+        resource_size_x=127.0,
+        resource_size_y=86.0,
+        resource_size_z=25.0,
+        name_prefix=name,
+    )
+    keys = slot_keys or [str(index + 1) for index in range(num_items_x * num_items_y)]
+    if len(keys) != len(holders):
+        raise ValueError(f"{name} 库位数量不匹配: keys={len(keys)}, holders={len(holders)}")
+
+    seen: dict[str, int] = {}
+    unique_keys: list[str] = []
+    for key in keys:
+        count = seen.get(key, 0) + 1
+        seen[key] = count
+        unique_keys.append(key if count == 1 else f"{key}#{count}")
+
+    return BioyondWareHouse(
+        name=name,
+        size_x=dx + item_dx * num_items_x,
+        size_y=dy + item_dy * num_items_y,
+        size_z=dz + item_dz * num_items_z,
+        num_items_x=num_items_x,
+        num_items_y=num_items_y,
+        num_items_z=num_items_z,
+        ordering_layout="row-major",
+        sites={key: holder for key, holder in zip(unique_keys, holders.values())},
+        category="warehouse",
+        bioyond_axis=bioyond_axis,
+        bioyond_key_axis=bioyond_key_axis,
+    )
+
+
+# ================ 小核酸工作站相关堆栈 ================
+
+def bioyond_warehouse_sirna_g3_liquid_handler(name: str = "G3移液站") -> WareHouse:
+    """创建小核酸 G3 移液站库位堆栈：显示为 14 行 x 1 列，标签保持 1-1..1-14。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=14, columns=1, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )
+
+
+def bioyond_warehouse_sirna_automation_stack(name: str = "自动化堆栈") -> WareHouse:
+    """创建小核酸自动化堆栈：显示为 17 行 x 10 列，标签保持 1-1..10-17。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=17, columns=10, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )
+
+
+def bioyond_warehouse_sirna_centrifuge_balance_plate_stack(name: str = "离心机配平板堆栈") -> WareHouse:
+    """创建小核酸离心机配平板堆栈：显示为 1 行 x 2 列，标签保持 1-1、2-1。"""
+    return bioyond_warehouse_numeric_stack(
+        name, rows=1, columns=2, bioyond_axis="xy_col_row", bioyond_key_axis="col_row"
+    )
+
+
 # ================ 反应站相关堆栈 ================

 def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
--- a/unilabos/resources/graphio.py
+++ b/unilabos/resources/graphio.py
@@ -736,7 +736,7 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
            logger.warning(f"物料 {unique_name} 不是有效的 ResourcePLR 实例，类型: {type(plr_material)}")
            continue

-        plr_material.code = material.get("code", "") and material.get("barCode", "") or ""
+        plr_material.code = material.get("barCode") or material.get("code") or ""
        plr_material.unilabos_uuid = str(uuid.uuid4())

        # ⭐ 保存 Bioyond 原始信息到 unilabos_extra（用于出库时查询）
@@ -864,11 +864,22 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
                    warehouse = deck.warehouses[wh_name]
                    logger.debug(f"[Warehouse匹配] 找到warehouse: {wh_name} (容量: {warehouse.capacity}, 行×列: {warehouse.num_items_x}×{warehouse.num_items_y})")

-                    # Bioyond坐标映射 (重要！): x→行(1=A,2=B...), y→列(1=01,2=02...), z→层(通常=1)
-                    x = loc.get("x", 1)  # 行号 (1-based: 1=A, 2=B, 3=C, 4=D)
-                    y = loc.get("y", 1)  # 列号 (1-based: 1=01, 2=02, 3=03...)
+                    # Bioyond坐标映射:
+                    # - 历史 row_col 仓库中 x/y 直接按行/列参与索引。
+                    # - Sirna 的库位标签为 col-row，stock-material 返回 x=标签第二段、y=标签第一段。
+                    #   因此 x=13,y=4 应落到 key=4-13，而不是交换后落到 3-5。
+                    x = loc.get("x", 1)
+                    y = loc.get("y", 1)
                    z = loc.get("z", 1)  # 层号 (1-based, 通常为1)

+                    # 仓库级别的轴约定覆盖。
+                    # 对旧的 row-col 视觉标签，bioyond_axis="xy_col_row" 需要交换 x/y。
+                    # 对 Sirna 的 col-row 库位标签，原始 x/y 已能直接索引到 code 对应位置，不再交换。
+                    bioyond_axis = getattr(warehouse, "bioyond_axis", "xy_row_col")
+                    bioyond_key_axis = getattr(warehouse, "bioyond_key_axis", "row_col")
+                    if bioyond_axis == "xy_col_row" and bioyond_key_axis != "col_row":
+                        x, y = y, x
+
                    # 如果是右侧堆栈，需要调整列号 (5→1, 6→2, 7→3, 8→4)
                    if wh_name == "堆栈1右":
                        y = y - 4  # 将5-8映射到1-4
@@ -912,10 +923,43 @@ def resource_bioyond_to_plr(bioyond_materials: list[dict], type_mapping: Dict[st
                            logger.debug(f"列优先warehouse {wh_name}: x={x}(行),y={y}(列) → row={row_idx},col={col_idx} → idx={idx}")

                    if 0 <= idx < warehouse.capacity:
-                        if warehouse[idx] is None or isinstance(warehouse[idx], ResourceHolder):
+                        slot_key = None
+                        ordering = getattr(warehouse, "_ordering", {})
+                        sites = getattr(warehouse, "sites", [])
+                        if isinstance(ordering, dict) and idx < len(sites):
+                            site_at_idx = sites[idx]
+                            slot_key = next(
+                                (key for key, site in ordering.items() if site is site_at_idx),
+                                None,
+                            )
+
+                        current_resource = warehouse[idx]
+                        if current_resource is None or isinstance(current_resource, (ResourceHolder, str)):
+                            if isinstance(current_resource, str):
+                                logger.warning(
+                                    f"⚠️ 物料 {unique_name} 覆盖 {wh_name}[{idx}]"
+                                    f"{f'({slot_key})' if slot_key else ''} 的旧占位 occupied_by={current_resource!r}"
+                                )
                            # 物料尺寸已在放入warehouse前根据需要进行了交换
                            warehouse[idx] = plr_material
-                            logger.debug(f"✅ 物料 {unique_name} 放置到 {wh_name}[{idx}] (Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})")
+                            logger.debug(
+                                f"✅ 物料 {unique_name} 放置到 {wh_name}[{idx}]"
+                                f"{f'({slot_key})' if slot_key else ''} "
+                                f"(Bioyond坐标: x={loc.get('x')}, y={loc.get('y')})"
+                            )
+                        else:
+                            parent = getattr(current_resource, "parent", None)
+                            current_repr = repr(current_resource)
+                            current_len = len(current_resource) if isinstance(current_resource, str) else None
+                            logger.warning(
+                                f"⚠️ 物料 {unique_name} 跳过放置到 {wh_name}[{idx}]"
+                                f"{f'({slot_key})' if slot_key else ''}：目标库位已有 "
+                                f"{type(current_resource).__name__}"
+                                f"(value={current_repr}, len={current_len})"
+                                f"(name={getattr(current_resource, 'name', None)}, "
+                                f"parent={getattr(parent, 'name', None)}, "
+                                f"uuid={getattr(current_resource, 'unilabos_uuid', None)})"
+                            )
                    else:
                        logger.warning(f"❌ 物料 {unique_name} 的索引 {idx} 超出仓库 {wh_name} 容量 {warehouse.capacity}")
                else:
Author	SHA1	Message	Date
yxz321	45b9fd5262	plan: add resource system guidance	2026-05-20 19:17:48 +08:00
yxz321	a1c0b83490	fix: change reset and submit_experiment* from manual confirm to normal node	2026-05-15 15:25:54 +08:00
yxz321	570d6763c0	Fix: update sirna_station to support new flexible resultTable	2026-05-15 14:01:34 +08:00
yxz321	633c8b3d2c	feat: RNA add Sirna experiment controls and workflow bindings - Add bound Sirna workflow names for experiment 1 and experiment 2 submissions. - Route named workflow submission through a shared create-order core with minimal param payloads. - Add direct scheduler controls and cancel/take-out manual confirmation handling.	2026-05-12 19:35:39 +08:00
yxz321	e6ee6fc964	fix: sync Bioyond materials over stale slot placeholders	2026-05-12 19:35:39 +08:00
yxz321	765342c4ff	feat: RNA aggregate Bioyond LIMS reports - Add get_order_report and frontend-like get_aggregated_order_report actions for Sirna LIMS debugging. - Preserve raw checked-section LIMS responses, including collapsed error envelopes, while allowing partial aggregate success. - Add order-id matching safeguards, aggregate report tests, and scaffold assertions for the new manual-confirm actions. - Keep Sirna graph debug logging enabled for report/live-probe troubleshooting.	2026-05-12 19:35:39 +08:00
yxz321	3fc94c6720	feat: RNA refine Sirna material sync and placement - Publish resource tree updates after shared Bioyond external material sync succeeds. - Keep start_experiment scheduler startup non-blocking while reporting unchecked manual load gates. - Prefer Bioyond barCode as PLR material code and add safer occupied-slot diagnostics for warehouse placement.	2026-05-12 19:35:39 +08:00
yxz321	d5f0bca643	fix: RNA use preexisting sync_from_external() from base class. Leave _register_materials_to_tree() commented	2026-05-12 19:35:39 +08:00
yxz321	de51b19e88	fix: RNA restrore manual-confirm table	2026-05-12 19:35:39 +08:00
yxz321	6b94bdd2da	fix: align Bioyond deck warehouse axes - Preserve Sirna col-row labels while flipping visual stack dimensions. - Rebuild Peptide deck warehouses from live API slot geometry and avoid initial graph overlap. - Add Peptide deck layout tests and keep Sirna resource tests passing.	2026-05-12 19:35:39 +08:00
yxz321	d009863c8c	feat: RNA add guided manual unload end_experiment action - Add end_experiment manual_confirm action mirroring start_experiment, with three boolean operator gates and twelve EXECUTOR sibling-array output handles for unloaded material manifests. - Add helpers _build_unload_materials_by_type, _classify_labware_mode, _iter_reagent_liquids, and _clear_unloaded_materials. - Clear unloaded slots and zero reagent liquid contents on confirmation while preserving trough labware; publish single resource tree update after mutations. - Wrap action body in _debug_call_session("end_experiment") for opt-in raw call capture.	2026-05-12 19:35:39 +08:00
yxz321	cae828ce74	feat: RNA add per-action raw HTTP call log for Bioyond station - Add debug_call_log module: contextvar-scoped session(), idempotent wrap_rpc_http, lazy markdown writer with apiKey redaction, source attribution via stack walk, raw_text fallback. - Centralize Bioyond RPC creation in BioyondWorkstation via _create_bioyond_rpc / _set_hardware_interface / _debug_call_session helpers and _DEBUG_LOG_DEFAULT_DIR. - Wrap reset, submit_experiment_1, start_experiment, get_order_list action bodies in _debug_call_session for opt-in per-action capture. - ConnectionMonitor polling stays outside debug sessions and is not logged.	2026-05-12 19:35:39 +08:00
yxz321	5b9f77e81f	feat: RNA simplify station action signatures and add order query - Add explicit reset_operations default; keep hidden plumbing kwargs-only. - Add read-only get_order_list manual_confirm action that calls order_query with latest_only and exposes order_id/order_ids handles. - Collapse start_experiment visible signature to (order_id, materials_loaded, timeout_seconds, assignee_user_ids); legacy params consumed from kwargs to preserve runtime contract. - Reduce submit_experiment_1 graph handles to order_id, resource, coin_cell_code, mount_resource; result dict gains order_id while keeping existing keys.	2026-05-12 19:35:39 +08:00
yxz321	7c83e1bd51	feat: RNA land resource-system mega plan Phases 1-4 plus Phase 5 stack orientation - Phase 1: fix _publish_resource_tree_update to call update_resource via run_async_func with deck resource list. - Phase 2: add ID-first material placement resolver chain with material_info and warehouse_inventory caches. - Phase 3: classify stock-material rows as slot_labware vs liquid_content; idempotent reagent attachment by Bioyond materialId. - Phase 4: introduce SirnaResourceSynchronizer over BioyondResourceSynchronizer; install once in post_init without double-sync. - Phase 5: numeric stack orientation and bioyond_axis support in bioyond warehouses/__init__/decks (carries forward prior in-progress edits). - _resolve_location_to_warehouse now raises on ambiguity; deck constructor accepts warehouse_bioyond_ids kwarg.	2026-05-12 19:35:39 +08:00
yxz321	1f93740580	fix: add assert for convenient API call only when DEBUG_CLI_ENABLED	2026-05-12 19:35:39 +08:00
yxz321	98c27cde40	feat: RNA add guided siRNA manual load gate - Expose siRNA order and material handles for manual-confirm load workflows. - Gate scheduler start on explicit material-load confirmation before calling Bioyond RPC. - Improve lazy API config diagnostics and Sirna warehouse/material resource handling.	2026-05-12 19:35:39 +08:00
yxz321	18c3263e92	feat: RNA refine Bioyond siRNA Experiment 1 submission	2026-05-12 19:35:39 +08:00
yxz321	1519a7d985	feat: RNA add Bioyond siRNA station resources and Experiment 1 submission - Add siRNA station runtime, decorator metadata, and lazy init - Implement Experiment 1 submit, start, and reset flows - Add siRNA deck and numeric warehouse stack resources - Move siRNA example config to temp_benyao	2026-05-12 19:35:39 +08:00
yxz321	96c3f5a3e5	feat: RNA. Initial sirna workstation implementation.	2026-05-12 19:35:39 +08:00
				`@@ -0,0 +1 @@`
				`from . import sirna_materials # noqa: F401 ensure @resource classes are importable for PLR deserialize`