mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2026-02-05 05:45:10 +00:00
Dev backward (#228)
* Workbench example, adjust log level, and ci check (#220)
* TestLatency Return Value Example & gitignore update
* Adjust log level & Add workbench virtual example & Add not action decorator & Add check_mode &
* Add CI Check
* CI Check Fix 1
* CI Check Fix 2
* CI Check Fix 3
* CI Check Fix 4
* CI Check Fix 5
* Upgrade to py 3.11.14; ros 0.7; unilabos 0.10.16
* Update to ROS2 Humble 0.7
* Fix Build 1
* Fix Build 2
* Fix Build 3
* Fix Build 4
* Fix Build 5
* Fix Build 6
* Fix Build 7
* ci(deps): bump actions/configure-pages from 4 to 5 (#222)
Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5.
- [Release notes](https://github.com/actions/configure-pages/releases)
- [Commits](https://github.com/actions/configure-pages/compare/v4...v5)
---
updated-dependencies:
- dependency-name: actions/configure-pages
dependency-version: '5'
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* ci(deps): bump actions/upload-artifact from 4 to 6 (#224)
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 6.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v4...v6)
---
updated-dependencies:
- dependency-name: actions/upload-artifact
dependency-version: '6'
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* ci(deps): bump actions/upload-pages-artifact from 3 to 4 (#225)
Bumps [actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/upload-pages-artifact/releases)
- [Commits](https://github.com/actions/upload-pages-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/upload-pages-artifact
dependency-version: '4'
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* ci(deps): bump actions/checkout from 4 to 6 (#223)
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v6)
---
updated-dependencies:
- dependency-name: actions/checkout
dependency-version: '6'
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix Build 8
* Fix Build 9
* Fix Build 10
* Fix Build 11
* Fix Build 12
* Fix Build 13
* v0.10.17
(cherry picked from commit 176de521b4)
* CI Check use production mode
* Fix OT2 & ReAdd Virtual Devices
* add msg goal
* transfer liquid handles
* gather query
* add unilabos_class
* Support root node change pos
* save class name when deserialize & protocol execute test
* fix upload workflow json
* workflow upload & set liquid fix & add set liquid with plate
* speed up registry load
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: hanhua@dp.tech <2509856570@qq.com>
This commit is contained in:
Xuwznln
GitHub
@@ -1,3 +1,89 @@
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"""
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工作流转换模块 - JSON 到 WorkflowGraph 的转换流程
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==================== 输入格式 (JSON) ====================
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{
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"workflow": [
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{"action": "transfer_liquid", "action_args": {"sources": "cell_lines", "targets": "Liquid_1", "asp_vol": 100.0, "dis_vol": 74.75, ...}},
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...
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],
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"reagent": {
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"cell_lines": {"slot": 4, "well": ["A1", "A3", "A5"], "labware": "DRUG + YOYO-MEDIA"},
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"Liquid_1": {"slot": 1, "well": ["A4", "A7", "A10"], "labware": "rep 1"},
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...
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}
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}
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==================== 转换步骤 ====================
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第一步: 按 slot 去重创建 create_resource 节点（创建板子）
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--------------------------------------------------------------------------------
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- 遍历所有 reagent，按 slot 去重，为每个唯一的 slot 创建一个板子
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- 生成参数:
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res_id: plate_slot_{slot}
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device_id: /PRCXI
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class_name: PRCXI_BioER_96_wellplate
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parent: /PRCXI/PRCXI_Deck/T{slot}
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slot_on_deck: "{slot}"
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- 输出端口: labware（用于连接 set_liquid_from_plate）
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- 控制流: create_resource 之间通过 ready 端口串联
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示例: slot=1, slot=4 -> 创建 2 个 create_resource 节点
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第二步: 为每个 reagent 创建 set_liquid_from_plate 节点（设置液体）
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--------------------------------------------------------------------------------
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- 遍历所有 reagent，为每个试剂创建 set_liquid_from_plate 节点
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- 生成参数:
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plate: []（通过连接传递，来自 create_resource 的 labware）
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well_names: ["A1", "A3", "A5"]（来自 reagent 的 well 数组）
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liquid_names: ["cell_lines", "cell_lines", "cell_lines"]（与 well 数量一致）
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volumes: [1e5, 1e5, 1e5]（与 well 数量一致，默认体积）
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- 输入连接: create_resource (labware) -> set_liquid_from_plate (input_plate)
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- 输出端口: output_wells（用于连接 transfer_liquid）
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- 控制流: set_liquid_from_plate 连接在所有 create_resource 之后，通过 ready 端口串联
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第三步: 解析 workflow，创建 transfer_liquid 等动作节点
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--------------------------------------------------------------------------------
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- 遍历 workflow 数组，为每个动作创建步骤节点
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- 参数重命名: asp_vol -> asp_vols, dis_vol -> dis_vols, asp_flow_rate -> asp_flow_rates, dis_flow_rate -> dis_flow_rates
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- 参数扩展: 根据 targets 的 wells 数量，将单值扩展为数组
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例: asp_vol=100.0, targets 有 3 个 wells -> asp_vols=[100.0, 100.0, 100.0]
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- 连接处理: 如果 sources/targets 已通过 set_liquid_from_plate 连接，参数值改为 []
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- 输入连接: set_liquid_from_plate (output_wells) -> transfer_liquid (sources_identifier / targets_identifier)
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- 输出端口: sources_out, targets_out（用于连接下一个 transfer_liquid）
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==================== 连接关系图 ====================
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控制流 (ready 端口串联):
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create_resource_1 -> create_resource_2 -> ... -> set_liquid_1 -> set_liquid_2 -> ... -> transfer_liquid_1 -> transfer_liquid_2 -> ...
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物料流:
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[create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid]
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(slot=1) (cell_lines) (input_plate) (sources_identifier) (sources_identifier)
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(slot=4) (Liquid_1) (targets_identifier) (targets_identifier)
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==================== 端口映射 ====================
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create_resource:
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输出: labware
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set_liquid_from_plate:
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输入: input_plate
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输出: output_plate, output_wells
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transfer_liquid:
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输入: sources -> sources_identifier, targets -> targets_identifier
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输出: sources -> sources_out, targets -> targets_out
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==================== 校验规则 ====================
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- 检查 sources/targets 是否在 reagent 中定义
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- 检查 sources 和 targets 的 wells 数量是否匹配
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- 检查参数数组长度是否与 wells 数量一致
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- 如有问题，在 footer 中添加 [WARN: ...] 标记
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"""
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import re
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import uuid
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@@ -8,6 +94,28 @@ from typing import Dict, List, Any, Tuple, Optional
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Json = Dict[str, Any]
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# ==================== 默认配置 ====================
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# create_resource 节点默认参数
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CREATE_RESOURCE_DEFAULTS = {
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"device_id": "/PRCXI",
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"parent_template": "/PRCXI/PRCXI_Deck/T{slot}", # {slot} 会被替换为实际的 slot 值
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"class_name": "PRCXI_BioER_96_wellplate",
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}
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# 默认液体体积 (uL)
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DEFAULT_LIQUID_VOLUME = 1e5
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# 参数重命名映射：单数 -> 复数（用于 transfer_liquid 等动作）
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PARAM_RENAME_MAPPING = {
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"asp_vol": "asp_vols",
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"dis_vol": "dis_vols",
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"asp_flow_rate": "asp_flow_rates",
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"dis_flow_rate": "dis_flow_rates",
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}
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# ---------------- Graph ----------------
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@@ -228,7 +336,7 @@ def refactor_data(
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def build_protocol_graph(
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labware_info: List[Dict[str, Any]],
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labware_info: Dict[str, Dict[str, Any]],
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protocol_steps: List[Dict[str, Any]],
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workstation_name: str,
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action_resource_mapping: Optional[Dict[str, str]] = None,
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@@ -236,112 +344,227 @@ def build_protocol_graph(
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"""统一的协议图构建函数，根据设备类型自动选择构建逻辑
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Args:
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labware_info: labware 信息字典
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labware_info: labware 信息字典，格式为 {name: {slot, well, labware, ...}, ...}
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protocol_steps: 协议步骤列表
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workstation_name: 工作站名称
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action_resource_mapping: action 到 resource_name 的映射字典，可选
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"""
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G = WorkflowGraph()
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resource_last_writer = {}
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resource_last_writer = {} # reagent_name -> "node_id:port"
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slot_to_create_resource = {} # slot -> create_resource node_id
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protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
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# 有机化学&移液站协议图构建
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WORKSTATION_ID = workstation_name
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# 为所有labware创建资源节点
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res_index = 0
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# ==================== 第一步：按 slot 去重创建 create_resource 节点 ====================
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# 收集所有唯一的 slot
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slots_info = {} # slot -> {labware, res_id}
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for labware_id, item in labware_info.items():
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# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
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node_id = str(uuid.uuid4())
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slot = str(item.get("slot", ""))
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if slot and slot not in slots_info:
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res_id = f"plate_slot_{slot}"
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slots_info[slot] = {
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"labware": item.get("labware", ""),
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"res_id": res_id,
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}
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# 判断节点类型
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if "Rack" in str(labware_id) or "Tip" in str(labware_id):
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lab_node_type = "Labware"
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description = f"Prepare Labware: {labware_id}"
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liquid_type = []
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liquid_volume = []
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elif item.get("type") == "hardware" or "reactor" in str(labware_id).lower():
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if "reactor" not in str(labware_id).lower():
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continue
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lab_node_type = "Sample"
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description = f"Prepare Reactor: {labware_id}"
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liquid_type = []
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liquid_volume = []
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else:
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lab_node_type = "Reagent"
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description = f"Add Reagent to Flask: {labware_id}"
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liquid_type = [labware_id]
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liquid_volume = [1e5]
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# 为每个唯一的 slot 创建 create_resource 节点
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res_index = 0
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last_create_resource_id = None
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for slot, info in slots_info.items():
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node_id = str(uuid.uuid4())
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res_id = info["res_id"]
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res_index += 1
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G.add_node(
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node_id,
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template_name="create_resource",
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resource_name="host_node",
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name=f"Res {res_index}",
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description=description,
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lab_node_type=lab_node_type,
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name=f"Plate {res_index}",
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description=f"Create plate on slot {slot}",
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lab_node_type="Labware",
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footer="create_resource-host_node",
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param={
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"res_id": labware_id,
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"device_id": WORKSTATION_ID,
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"class_name": "container",
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"parent": WORKSTATION_ID,
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"res_id": res_id,
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"device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
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"class_name": CREATE_RESOURCE_DEFAULTS["class_name"],
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"parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
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"bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
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"liquid_input_slot": [-1],
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"liquid_type": liquid_type,
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"liquid_volume": liquid_volume,
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"slot_on_deck": "",
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"slot_on_deck": slot,
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},
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)
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resource_last_writer[labware_id] = f"{node_id}:labware"
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slot_to_create_resource[slot] = node_id
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last_control_node_id = None
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# create_resource 之间通过 ready 串联
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if last_create_resource_id is not None:
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G.add_edge(last_create_resource_id, node_id, source_port="ready", target_port="ready")
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last_create_resource_id = node_id
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# ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ====================
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set_liquid_index = 0
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last_set_liquid_id = last_create_resource_id # set_liquid_from_plate 连接在 create_resource 之后
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for labware_id, item in labware_info.items():
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# 跳过 Tip/Rack 类型
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if "Rack" in str(labware_id) or "Tip" in str(labware_id):
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continue
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if item.get("type") == "hardware":
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continue
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slot = str(item.get("slot", ""))
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wells = item.get("well", [])
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if not wells or not slot:
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continue
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# res_id 不能有空格
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res_id = str(labware_id).replace(" ", "_")
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well_count = len(wells)
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node_id = str(uuid.uuid4())
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set_liquid_index += 1
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G.add_node(
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node_id,
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template_name="set_liquid_from_plate",
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resource_name="liquid_handler.prcxi",
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name=f"SetLiquid {set_liquid_index}",
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description=f"Set liquid: {labware_id}",
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lab_node_type="Reagent",
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footer="set_liquid_from_plate-liquid_handler.prcxi",
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param={
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"plate": [], # 通过连接传递
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"well_names": wells, # 孔位名数组，如 ["A1", "A3", "A5"]
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"liquid_names": [res_id] * well_count,
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"volumes": [DEFAULT_LIQUID_VOLUME] * well_count,
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},
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)
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# ready 连接：上一个节点 -> set_liquid_from_plate
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if last_set_liquid_id is not None:
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G.add_edge(last_set_liquid_id, node_id, source_port="ready", target_port="ready")
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last_set_liquid_id = node_id
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# 物料流：create_resource 的 labware -> set_liquid_from_plate 的 input_plate
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create_res_node_id = slot_to_create_resource.get(slot)
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if create_res_node_id:
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G.add_edge(create_res_node_id, node_id, source_port="labware", target_port="input_plate")
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# set_liquid_from_plate 的输出 output_wells 用于连接 transfer_liquid
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resource_last_writer[labware_id] = f"{node_id}:output_wells"
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last_control_node_id = last_set_liquid_id
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# 端口名称映射：JSON 字段名 -> 实际 handle key
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INPUT_PORT_MAPPING = {
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"sources": "sources_identifier",
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"targets": "targets_identifier",
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"vessel": "vessel",
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"to_vessel": "to_vessel",
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"from_vessel": "from_vessel",
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"reagent": "reagent",
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"solvent": "solvent",
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"compound": "compound",
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}
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OUTPUT_PORT_MAPPING = {
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"sources": "sources_out", # 输出端口是 xxx_out
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"targets": "targets_out", # 输出端口是 xxx_out
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"vessel": "vessel_out",
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"to_vessel": "to_vessel_out",
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"from_vessel": "from_vessel_out",
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"filtrate_vessel": "filtrate_out",
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"reagent": "reagent",
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"solvent": "solvent",
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"compound": "compound",
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}
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# 需要根据 wells 数量扩展的参数列表（复数形式）
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EXPAND_BY_WELLS_PARAMS = ["asp_vols", "dis_vols", "asp_flow_rates", "dis_flow_rates"]
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# 处理协议步骤
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for step in protocol_steps:
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node_id = str(uuid.uuid4())
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G.add_node(node_id, **step)
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params = step.get("param", {}).copy() # 复制一份，避免修改原数据
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connected_params = set() # 记录被连接的参数
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warnings = [] # 收集警告信息
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# 参数重命名：单数 -> 复数
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for old_name, new_name in PARAM_RENAME_MAPPING.items():
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if old_name in params:
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params[new_name] = params.pop(old_name)
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# 处理输入连接
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for param_key, target_port in INPUT_PORT_MAPPING.items():
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resource_name = params.get(param_key)
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if resource_name and resource_name in resource_last_writer:
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source_node, source_port = resource_last_writer[resource_name].split(":")
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G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
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connected_params.add(param_key)
|
||||
elif resource_name and resource_name not in resource_last_writer:
|
||||
# 资源名在 labware_info 中不存在
|
||||
warnings.append(f"{param_key}={resource_name} 未找到")
|
||||
|
||||
# 获取 targets 对应的 wells 数量，用于扩展参数
|
||||
targets_name = params.get("targets")
|
||||
sources_name = params.get("sources")
|
||||
targets_wells_count = 1
|
||||
sources_wells_count = 1
|
||||
|
||||
if targets_name and targets_name in labware_info:
|
||||
target_wells = labware_info[targets_name].get("well", [])
|
||||
targets_wells_count = len(target_wells) if target_wells else 1
|
||||
elif targets_name:
|
||||
warnings.append(f"targets={targets_name} 未在 reagent 中定义")
|
||||
|
||||
if sources_name and sources_name in labware_info:
|
||||
source_wells = labware_info[sources_name].get("well", [])
|
||||
sources_wells_count = len(source_wells) if source_wells else 1
|
||||
elif sources_name:
|
||||
warnings.append(f"sources={sources_name} 未在 reagent 中定义")
|
||||
|
||||
# 检查 sources 和 targets 的 wells 数量是否匹配
|
||||
if targets_wells_count != sources_wells_count and targets_name and sources_name:
|
||||
warnings.append(f"wells 数量不匹配: sources={sources_wells_count}, targets={targets_wells_count}")
|
||||
|
||||
# 使用 targets 的 wells 数量来扩展参数
|
||||
wells_count = targets_wells_count
|
||||
|
||||
# 扩展单值参数为数组（根据 targets 的 wells 数量）
|
||||
for expand_param in EXPAND_BY_WELLS_PARAMS:
|
||||
if expand_param in params:
|
||||
value = params[expand_param]
|
||||
# 如果是单个值，扩展为数组
|
||||
if not isinstance(value, list):
|
||||
params[expand_param] = [value] * wells_count
|
||||
# 如果已经是数组但长度不对，记录警告
|
||||
elif len(value) != wells_count:
|
||||
warnings.append(f"{expand_param} 数量({len(value)})与 wells({wells_count})不匹配")
|
||||
|
||||
# 如果 sources/targets 已通过连接传递，将参数值改为空数组
|
||||
for param_key in connected_params:
|
||||
if param_key in params:
|
||||
params[param_key] = []
|
||||
|
||||
# 更新 step 的 param 和 footer
|
||||
step_copy = step.copy()
|
||||
step_copy["param"] = params
|
||||
|
||||
# 如果有警告，修改 footer 添加警告标记（警告放前面）
|
||||
if warnings:
|
||||
original_footer = step.get("footer", "")
|
||||
step_copy["footer"] = f"[WARN: {'; '.join(warnings)}] {original_footer}"
|
||||
|
||||
G.add_node(node_id, **step_copy)
|
||||
|
||||
# 控制流
|
||||
if last_control_node_id is not None:
|
||||
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||
last_control_node_id = node_id
|
||||
|
||||
# 物料流
|
||||
params = step.get("param", {})
|
||||
input_resources_possible_names = [
|
||||
"vessel",
|
||||
"to_vessel",
|
||||
"from_vessel",
|
||||
"reagent",
|
||||
"solvent",
|
||||
"compound",
|
||||
"sources",
|
||||
"targets",
|
||||
]
|
||||
|
||||
for target_port in input_resources_possible_names:
|
||||
resource_name = params.get(target_port)
|
||||
if resource_name and resource_name in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||
|
||||
output_resources = {
|
||||
"vessel_out": params.get("vessel"),
|
||||
"from_vessel_out": params.get("from_vessel"),
|
||||
"to_vessel_out": params.get("to_vessel"),
|
||||
"filtrate_out": params.get("filtrate_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources_out": params.get("sources"),
|
||||
"targets_out": params.get("targets"),
|
||||
}
|
||||
|
||||
for source_port, resource_name in output_resources.items():
|
||||
# 处理输出：更新 resource_last_writer
|
||||
for param_key, output_port in OUTPUT_PORT_MAPPING.items():
|
||||
resource_name = step.get("param", {}).get(param_key) # 使用原始参数值
|
||||
if resource_name:
|
||||
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||
resource_last_writer[resource_name] = f"{node_id}:{output_port}"
|
||||
|
||||
return G
|
||||
|
||||
|
||||
Reference in New Issue
Block a user