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Update docs
This commit is contained in:
Xuwznln
@@ -1,186 +0,0 @@
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{
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"workflow": [
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_1",
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"targets": "Liquid_2",
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"asp_vol": 66.0,
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"dis_vol": 66.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_2",
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"targets": "Liquid_3",
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"asp_vol": 58.0,
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"dis_vol": 96.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_4",
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"targets": "Liquid_2",
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"asp_vol": 85.0,
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"dis_vol": 170.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_4",
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"targets": "Liquid_2",
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"asp_vol": 63.333333333333336,
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"dis_vol": 170.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_2",
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"targets": "Liquid_3",
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"asp_vol": 72.0,
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"dis_vol": 150.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_4",
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"targets": "Liquid_2",
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"asp_vol": 85.0,
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"dis_vol": 170.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_4",
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"targets": "Liquid_2",
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"asp_vol": 63.333333333333336,
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"dis_vol": 170.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_2",
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"targets": "Liquid_3",
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"asp_vol": 72.0,
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"dis_vol": 150.0,
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"asp_flow_rate": 94.0,
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"dis_flow_rate": 94.0
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_2",
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"targets": "Liquid_3",
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"asp_vol": 20.0,
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"dis_vol": 20.0,
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"asp_flow_rate": 7.6,
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"dis_flow_rate": 7.6
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_5",
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"targets": "Liquid_2",
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"asp_vol": 6.0,
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"dis_vol": 12.0,
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"asp_flow_rate": 7.6,
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"dis_flow_rate": 7.6
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_5",
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"targets": "Liquid_2",
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"asp_vol": 10.666666666666666,
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"dis_vol": 12.0,
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"asp_flow_rate": 7.599999999999999,
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"dis_flow_rate": 7.6
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}
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},
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{
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"action": "transfer_liquid",
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"action_args": {
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"sources": "Liquid_2",
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"targets": "Liquid_6",
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"asp_vol": 12.0,
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"dis_vol": 10.0,
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"asp_flow_rate": 7.6,
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"dis_flow_rate": 7.6
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}
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}
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],
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"reagent": {
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"Liquid_6": {
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"slot": 1,
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"well": [
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"A2"
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],
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"labware": "elution plate"
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},
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"Liquid_1": {
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"slot": 2,
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"well": [
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"A1",
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"A2",
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"A4"
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],
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"labware": "reagent reservoir"
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},
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"Liquid_4": {
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"slot": 2,
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"well": [
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"A1",
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"A2",
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"A4"
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],
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"labware": "reagent reservoir"
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},
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"Liquid_5": {
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"slot": 2,
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"well": [
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"A1",
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"A2",
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"A4"
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],
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"labware": "reagent reservoir"
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},
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"Liquid_2": {
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"slot": 4,
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"well": [
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"A2"
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],
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"labware": "TAG1 plate on Magnetic Module GEN2"
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},
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"Liquid_3": {
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"slot": 12,
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"well": [
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"A1"
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],
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"labware": "Opentrons Fixed Trash"
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}
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}
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}
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@@ -1,63 +0,0 @@
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{
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"steps_info": [
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{
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"step_number": 1,
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"action": "transfer_liquid",
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"parameters": {
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"source": "sample supernatant",
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"target": "antibody-coated well",
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"volume": 100
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}
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},
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{
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"step_number": 2,
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"action": "transfer_liquid",
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"parameters": {
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"source": "washing buffer",
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"target": "antibody-coated well",
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"volume": 200
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}
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},
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{
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"step_number": 3,
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"action": "transfer_liquid",
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"parameters": {
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"source": "washing buffer",
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"target": "antibody-coated well",
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"volume": 200
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}
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},
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{
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"step_number": 4,
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"action": "transfer_liquid",
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"parameters": {
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"source": "washing buffer",
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"target": "antibody-coated well",
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"volume": 200
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}
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},
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{
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"step_number": 5,
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"action": "transfer_liquid",
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"parameters": {
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"source": "TMB substrate",
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"target": "antibody-coated well",
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"volume": 100
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}
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}
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],
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"labware_info": [
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{"reagent_name": "sample supernatant", "material_name": "96深孔板", "positions": 1},
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{"reagent_name": "washing buffer", "material_name": "储液槽", "positions": 2},
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{"reagent_name": "TMB substrate", "material_name": "储液槽", "positions": 3},
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{"reagent_name": "antibody-coated well", "material_name": "96 细胞培养皿", "positions": 4},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 5},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 6},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 7},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 8},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 9},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 10},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 11},
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{"reagent_name": "", "material_name": "300μL Tip头", "positions": 13}
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]
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}
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@@ -1,94 +0,0 @@
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import json
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import sys
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from datetime import datetime
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from pathlib import Path
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ROOT_DIR = Path(__file__).resolve().parents[2]
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if str(ROOT_DIR) not in sys.path:
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sys.path.insert(0, str(ROOT_DIR))
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import pytest
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from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
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ROOT_DIR = Path(__file__).resolve().parents[2]
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if str(ROOT_DIR) not in sys.path:
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sys.path.insert(0, str(ROOT_DIR))
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def _normalize_steps(data):
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normalized = []
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for step in data:
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action = step.get("action") or step.get("operation")
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if not action:
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continue
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raw_params = step.get("parameters") or step.get("action_args") or {}
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params = dict(raw_params)
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if "source" in raw_params and "sources" not in raw_params:
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params["sources"] = raw_params["source"]
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if "target" in raw_params and "targets" not in raw_params:
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params["targets"] = raw_params["target"]
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description = step.get("description") or step.get("purpose")
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step_dict = {"action": action, "parameters": params}
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if description:
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step_dict["description"] = description
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normalized.append(step_dict)
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return normalized
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def _normalize_labware(data):
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labware = {}
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for item in data:
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reagent_name = item.get("reagent_name")
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key = reagent_name or item.get("material_name") or item.get("name")
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if not key:
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continue
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key = str(key)
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idx = 1
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original_key = key
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while key in labware:
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idx += 1
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key = f"{original_key}_{idx}"
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labware[key] = {
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"slot": item.get("positions") or item.get("slot"),
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"labware": item.get("material_name") or item.get("labware"),
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"well": item.get("well", []),
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"type": item.get("type", "reagent"),
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"role": item.get("role", ""),
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"name": key,
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}
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return labware
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@pytest.mark.parametrize("protocol_name", [
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"example_bio",
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# "bioyond_materials_liquidhandling_1",
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"example_prcxi",
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])
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def test_build_protocol_graph(protocol_name):
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data_path = Path(__file__).with_name(f"{protocol_name}.json")
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with data_path.open("r", encoding="utf-8") as fp:
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d = json.load(fp)
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if "workflow" in d and "reagent" in d:
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protocol_steps = d["workflow"]
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labware_info = d["reagent"]
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elif "steps_info" in d and "labware_info" in d:
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protocol_steps = _normalize_steps(d["steps_info"])
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labware_info = _normalize_labware(d["labware_info"])
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else:
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raise ValueError("Unsupported protocol format")
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graph = build_protocol_graph(
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labware_info=labware_info,
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protocol_steps=protocol_steps,
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workstation_name="PRCXi",
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)
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timestamp = datetime.now().strftime("%Y%m%d_%H%M")
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output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
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draw_protocol_graph_with_ports(graph, str(output_path))
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print(graph)
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