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Fix handle names (#55)

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* fix handle names

* improve evacuateAndRefill gas source finding
This commit is contained in:
Junhan Chang
2025-06-29 17:31:44 +08:00
committed by GitHub
parent 68871358c2
commit 64832718be
4 changed files with 180 additions and 80 deletions
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14
test/experiments/comprehensive_protocol/comprehensive_station.json
View File

@@ -680,7 +680,7 @@
"type": "fluid",
"port": {
"multiway_valve_1": "5",
"rotavap_1": "sample_in"
"rotavap_1": "samplein"
}
},
{
@@ -770,7 +770,7 @@
"type": "transport",
"port": {
"multiway_valve_2": "4",
"filter_1": "filter_in"
"filter_1": "filterin"
}
},
{
@@ -800,7 +800,7 @@
"type": "fluid",
"port": {
"multiway_valve_2": "6",
"separator_1": "separator_in"
"separator_1": "separatorin"
}
},
{
@@ -809,7 +809,7 @@
"target": "collection_bottle_3",
"type": "fluid",
"port": {
"separator_1": "bottom_phase_out",
"separator_1": "bottomphaseout",
"collection_bottle_3": "top"
}
},
@@ -859,7 +859,7 @@
"target": "waste_bottle_2",
"type": "fluid",
"port": {
"separator_1": "top_phase_out",
"separator_1": "topphaseout",
"waste_bottle_2": "top"
}
},
@@ -879,7 +879,7 @@
"target": "collection_bottle_1",
"type": "transport",
"port": {
"filter_1": "filtrate_out",
"filter_1": "filtrateout",
"collection_bottle_1": "top"
}
},
@@ -889,7 +889,7 @@
"target": "waste_bottle_1",
"type": "transport",
"port": {
"filter_1": "retentate_out",
"filter_1": "retentateout",
"waste_bottle_1": "top"
}
}

128
unilabos/compile/evacuateandrefill_protocol.py
View File

@@ -5,38 +5,138 @@ from .pump_protocol import generate_pump_protocol_with_rinsing, generate_pump_pr
def find_gas_source(G: nx.DiGraph, gas: str) -> str:
"""根据气体名称查找对应的气源"""
# 按照命名规则查找气源
"""
根据气体名称查找对应的气源，支持多种匹配模式：
1. 容器名称匹配
2. 气体类型匹配（data.gas_type）
3. 默认气源
"""
print(f"EVACUATE_REFILL: 正在查找气体 '{gas}' 的气源...")
# 第一步：通过容器名称匹配
gas_source_patterns = [
f"gas_source_{gas}",
f"gas_{gas}",
f"flask_{gas}",
f"{gas}_source"
f"{gas}_source",
f"source_{gas}",
f"reagent_bottle_{gas}",
f"bottle_{gas}"
]
for pattern in gas_source_patterns:
if pattern in G.nodes():
print(f"EVACUATE_REFILL: 通过名称匹配找到气源: {pattern}")
return pattern
# 模糊匹配
for node in G.nodes():
node_class = G.nodes[node].get('class', '') or ''
if 'gas_source' in node_class and gas.lower() in node.lower():
return node
if node.startswith('flask_') and gas.lower() in node.lower():
return node
# 第二步：通过气体类型匹配 (data.gas_type)
for node_id in G.nodes():
node_data = G.nodes[node_id]
node_class = node_data.get('class', '') or ''
# 检查是否是气源设备
if ('gas_source' in node_class or
'gas' in node_id.lower() or
node_id.startswith('flask_')):
# 检查 data.gas_type
data = node_data.get('data', {})
gas_type = data.get('gas_type', '')
if gas_type.lower() == gas.lower():
print(f"EVACUATE_REFILL: 通过气体类型匹配找到气源: {node_id} (gas_type: {gas_type})")
return node_id
# 检查 config.gas_type
config = node_data.get('config', {})
config_gas_type = config.get('gas_type', '')
if config_gas_type.lower() == gas.lower():
print(f"EVACUATE_REFILL: 通过配置气体类型匹配找到气源: {node_id} (config.gas_type: {config_gas_type})")
return node_id
# 查找所有可用的气源
available_gas_sources = [
# 第三步：查找所有可用的气源设备
available_gas_sources = []
for node_id in G.nodes():
node_data = G.nodes[node_id]
node_class = node_data.get('class', '') or ''
if ('gas_source' in node_class or
'gas' in node_id.lower() or
(node_id.startswith('flask_') and any(g in node_id.lower() for g in ['air', 'nitrogen', 'argon']))):
data = node_data.get('data', {})
gas_type = data.get('gas_type', 'unknown')
available_gas_sources.append(f"{node_id} (gas_type: {gas_type})")
print(f"EVACUATE_REFILL: 可用气源列表: {available_gas_sources}")
# 第四步：如果找不到特定气体，使用默认的第一个气源
default_gas_sources = [
node for node in G.nodes()
if ((G.nodes[node].get('class') or '').startswith('virtual_gas_source')
or ('gas' in node and 'source' in node)
or (node.startswith('flask_') and any(g in node.lower() for g in ['air', 'nitrogen', 'argon', 'vacuum'])))
or 'gas_source' in node)
]
if default_gas_sources:
default_source = default_gas_sources[0]
print(f"EVACUATE_REFILL: ⚠️ 未找到特定气体 '{gas}'，使用默认气源: {default_source}")
return default_source
raise ValueError(f"找不到气体 '{gas}' 对应的气源。可用气源: {available_gas_sources}")
def find_gas_source_by_any_match(G: nx.DiGraph, gas: str) -> str:
"""
增强版气源查找，支持各种匹配方式的别名函数
"""
return find_gas_source(G, gas)
def get_gas_source_type(G: nx.DiGraph, gas_source: str) -> str:
"""获取气源的气体类型"""
if gas_source not in G.nodes():
return "unknown"
node_data = G.nodes[gas_source]
data = node_data.get('data', {})
config = node_data.get('config', {})
# 检查多个可能的字段
gas_type = (data.get('gas_type') or
config.get('gas_type') or
data.get('gas') or
config.get('gas') or
"air") # 默认为空气
return gas_type
def find_vessels_by_gas_type(G: nx.DiGraph, gas: str) -> List[str]:
"""
根据气体类型查找所有匹配的容器/气源
"""
matching_vessels = []
for node_id in G.nodes():
node_data = G.nodes[node_id]
# 检查容器名称匹配
if gas.lower() in node_id.lower():
matching_vessels.append(f"{node_id} (名称匹配)")
continue
# 检查气体类型匹配
data = node_data.get('data', {})
config = node_data.get('config', {})
gas_type = data.get('gas_type', '') or config.get('gas_type', '')
if gas_type.lower() == gas.lower():
matching_vessels.append(f"{node_id} (gas_type: {gas_type})")
return matching_vessels
def find_vacuum_pump(G: nx.DiGraph) -> str:
"""查找真空泵设备"""
vacuum_pumps = [

18
unilabos/registry/devices/virtual_device.yaml
View File

@@ -631,7 +631,7 @@ virtual_filter:
data_source: handle
data_type: transport
description: 需要过滤的样品容器
handler_key: filter_in
handler_key: filterin
io_type: target
label: filter_in
side: NORTH
@@ -639,7 +639,7 @@ virtual_filter:
data_source: handle
data_type: transport
description: 滤液出口
handler_key: filtrate_out
handler_key: filtrateout
io_type: source
label: filtrate_out
side: SOUTH
@@ -647,7 +647,7 @@ virtual_filter:
data_source: handle
data_type: transport
description: 滤渣/固体出口
handler_key: retentate_out
handler_key: retentateout
io_type: source
label: retentate_out
side: EAST
@@ -2433,7 +2433,7 @@ virtual_rotavap:
data_source: handle
data_type: fluid
description: 样品连接口
handler_key: sample_in
handler_key: samplein
io_type: target
label: sample_in
side: NORTH
@@ -2441,7 +2441,7 @@ virtual_rotavap:
data_source: handle
data_type: fluid
description: 浓缩产物出口
handler_key: product_out
handler_key: productout
io_type: source
label: product_out
side: SOUTH
@@ -2449,7 +2449,7 @@ virtual_rotavap:
data_source: handle
data_type: fluid
description: 冷凝溶剂出口
handler_key: solvent_out
handler_key: solventout
io_type: source
label: solvent_out
side: EAST
@@ -2774,7 +2774,7 @@ virtual_separator:
data_source: handle
data_type: fluid
description: 需要分离的混合液体输入口
handler_key: separator_in
handler_key: separatorin
io_type: target
label: separator_in
side: NORTH
@@ -2782,7 +2782,7 @@ virtual_separator:
data_source: executor
data_type: fluid
description: 下相（重相）液体输出口
handler_key: bottom_phase_out
handler_key: bottomphaseout
io_type: source
label: bottom_phase_out
side: SOUTH
@@ -2790,7 +2790,7 @@ virtual_separator:
data_source: executor
data_type: fluid
description: 上相（轻相）液体输出口
handler_key: top_phase_out
handler_key: topphaseout
io_type: source
label: top_phase_out
side: EAST

100
unilabos/registry/devices/work_station.yaml
View File

@@ -271,7 +271,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: reagent
data_source: handle
@@ -282,7 +282,7 @@ workstation:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -373,13 +373,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -460,7 +460,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: solvent
data_source: handle
@@ -471,7 +471,7 @@ workstation:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -580,7 +580,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: solvent
data_source: handle
@@ -591,7 +591,7 @@ workstation:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -675,7 +675,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: solvent
data_source: handle
@@ -686,7 +686,7 @@ workstation:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -766,13 +766,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -875,13 +875,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -992,7 +992,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: vessel
data_source: handle
@@ -1003,7 +1003,7 @@ workstation:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
- data_key: vessel
data_source: executor
@@ -1102,12 +1102,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel
handler_key: FromVessel
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel
handler_key: ToVessel
label: To Vessel
- data_key: solvent
data_source: handle
@@ -1118,12 +1118,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel_out
handler_key: FromVesselOut
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel_out
handler_key: ToVesselOut
label: To Vessel
result: {}
schema:
@@ -1211,13 +1211,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -1288,13 +1288,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -1352,13 +1352,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -1428,12 +1428,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel
handler_key: FromVessel
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel
handler_key: ToVessel
label: To Vessel
- data_key: solvent
data_source: handle
@@ -1444,12 +1444,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel_out
handler_key: FromVesselOut
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel_out
handler_key: ToVesselOut
label: To Vessel
result: {}
schema:
@@ -1569,23 +1569,23 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel
handler_key: FromVessel
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel
handler_key: ToVessel
label: To Vessel
output:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel_out
handler_key: FromVesselOut
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel_out
handler_key: ToVesselOut
label: To Vessel
result: {}
schema:
@@ -1673,12 +1673,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel
handler_key: FromVessel
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel
handler_key: ToVessel
label: To Vessel
- data_key: solvent
data_source: handle
@@ -1689,12 +1689,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel_out
handler_key: FromVesselOut
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel_out
handler_key: ToVesselOut
label: To Vessel
result: {}
schema:
@@ -1823,13 +1823,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -1900,13 +1900,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -1964,13 +1964,13 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
output:
- data_key: vessel
data_source: executor
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel
result: {}
schema:
@@ -2046,12 +2046,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel
handler_key: FromVessel
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel
handler_key: ToVessel
label: To Vessel
- data_key: solvent
data_source: handle
@@ -2062,12 +2062,12 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: from_vessel_out
handler_key: FromVesselOut
label: From Vessel
- data_key: vessel
data_source: executor
data_type: resource
handler_key: to_vessel_out
handler_key: ToVesselOut
label: To Vessel
result: {}
schema:
@@ -2173,7 +2173,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel
handler_key: Vessel
label: Vessel
- data_key: solvent
data_source: handle
@@ -2189,7 +2189,7 @@ workstation:
- data_key: vessel
data_source: handle
data_type: resource
handler_key: vessel_out
handler_key: VesselOut
label: Vessel Out
- data_key: vessel
data_source: executor