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flow: add mL to concentrated sample volume and add process_description field to metadata

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This commit is contained in:
Romain Bazile 2020-12-03 15:15:13 +01:00
parent 981dd12646
commit 68d2a10303
1 changed files with 90 additions and 88 deletions
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178
flows/main.json
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@ -741,24 +741,6 @@
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@ -1837,7 +1837,7 @@
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@ -2591,8 +2591,8 @@
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@ -2617,8 +2617,8 @@
"payload": "{\"tab\":\"Home\"}", "payload": "{\"tab\":\"Home\"}",
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@ -3522,7 +3522,7 @@
"type": "function", "type": "function",
"z": "baa1e3d9.cb29d", "z": "baa1e3d9.cb29d",
"name": "Encapsulate config", "name": "Encapsulate config",
"func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera_name\": global.get(\"acq_camera_name\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object_lat\"),\n\t\t\"object_lon\": global.get(\"object_lon\"),\n\t\t\"object_depth_min\": global.get(\"object_depth_min\"),\n\t\t\"object_depth_max\": global.get(\"object_depth_max\"),\n\n\t\t\"process_pixel\": global.get(\"process_pixel\"),\n\t\t\"process_id\": global.get(\"process_id\")\n\t}\n};\n\nif (msg.payload.config.sample_sampling_gear == \"net\") {\n\tmsg.payload.config = { ...msg.payload.config ,\n\t\t\t\"sample_gear_net_opening\": global.get(\"sample_gear_net_opening\"),\n\t\t\t\"object_date_end\": global.get(\"object_date_end\"),\n\t\t\t\"object_time_end\": global.get(\"object_time_end\"),\n\t\t\t\"object_lat_end\": global.get(\"object_lat_end\"),\n\t\t\t\"object_lon_end\": global.get(\"object_lon_end\")\n\t};\n}\nreturn msg;", "func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n \t\"description\": {\n \t\t\"sample_project\": \"Project's name\",\n \t\t\"sample_id\": \"Sample ID\",\n \t\t\"sample_uuid\": \"Sample UUID (Autogenerated)\",\n \t\t\"sample_ship\": \"Ship's name\",\n \t\t\"sample_operator\": \"Operator's name\",\n \t\t\"sample_sampling_gear\": \"Sampling gear used\",\n \t\t\"sample_concentrated_sample_volume\": \"Volume of concentrated sample, in mL\",\n \t\t\"acq_id\": \"Acquisition ID\",\n \t\t\"acq_uuid\": \"Acquisition UUID (Autogenerated)\",\n \t\t\"acq_instrument\": \"Instrument type\",\n \t\t\"acq_instrument_id\": \"Instrument ID\",\n \t\t\"acq_celltype\": \"Flow cell dimension thickness, in µm\",\n \t\t\"acq_minimum_mesh\": \"Minimum filtration mesh size, in µm\",\n \t\t\"acq_maximum_mesh\": \"Maximum filtration mesh size, in µm\",\n \t\t\"acq_min_esd\": \"\",\n \t\t\"acq_max_esd\": \"\",\n \t\t\"acq_volume\": \"Imaged volume, in mL\",\n \t\t\"acq_magnification\": \"Optical magnification\",\n \t\t\"acq_fnumber_objective\": \"Focal length of the objective, in mm\",\n \t\t\"acq_camera_name\": \"Name of the camera used\",\n \t\t\"acq_nb_frame\": \"Number of picture taken\",\n \"acq_local_datetime\": \"Instrument local datetime\",\n \"acq_camera_resolution\": \"Resolution of the images\",\n \"acq_camera_iso\": \"ISO Number of the images\",\n \"acq_camera_shutter_speed\": \"Shutter speed of the images, in µs\",\n \t\t\"object_date\": \"Sample collection date (or beginning if using a net)\",\n \t\t\"object_time\": \"Sample collection time (or beginning if using a net)\",\n \t\t\"object_lat\": \"Sample collection latitude (or beginning if using a net)\",\n \t\t\"object_lon\": \"Sample collection longitude (or beginning if using a net)\",\n \t\t\"object_depth_min\": \"Sample collection minimal depth, in m\",\n \t\t\"object_depth_max\": \"Sample collection maximum depth, in m\",\n \t\t\"process_pixel\": \"Pixel imaging resolution, in µm/pixel\",\n \t\t\"process_id\": \"Segmentation ID\",\n \t\t\"process_uuid\": \"Segmentation UUID (Autogenerated)\",\n \t\t\"sample_gear_net_opening\": \"Sample mouth opening dimension, in mm\",\n \t\t\"object_date_end\": \"Sample end collection date when using a net\",\n \t\t\"object_time_end\": \"Sample end collection time when using a net\",\n \t\t\"object_lat_end\": \"Sample end collection latitude when using a net\",\n \t\t\"object_lon_end\": \"Sample end collection longitude when using a net\",\n \t},\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera_name\": global.get(\"acq_camera_name\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object_lat\"),\n\t\t\"object_lon\": global.get(\"object_lon\"),\n\t\t\"object_depth_min\": global.get(\"object_depth_min\"),\n\t\t\"object_depth_max\": global.get(\"object_depth_max\"),\n\n\t\t\"process_pixel\": global.get(\"process_pixel\"),\n\t\t\"process_id\": global.get(\"process_id\")\n\t}\n};\n\nif (msg.payload.config.sample_sampling_gear == \"net\") {\n\tmsg.payload.config = { ...msg.payload.config ,\n\t\t\t\"sample_gear_net_opening\": global.get(\"sample_gear_net_opening\"),\n\t\t\t\"object_date_end\": global.get(\"object_date_end\"),\n\t\t\t\"object_time_end\": global.get(\"object_time_end\"),\n\t\t\t\"object_lat_end\": global.get(\"object_lat_end\"),\n\t\t\t\"object_lon_end\": global.get(\"object_lon_end\")\n\t};\n}\nreturn msg;",
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@ -3629,7 +3629,7 @@
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@ -3695,11 +3695,13 @@
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"z": "b771c342.49603", "z": "b771c342.49603",
"name": "get sample_sampling_gear", "name": "get sample_sampling_gear",
"func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", "func": "if (msg.payload.sample_sampling_gear === null){\n msg.payload = \"net\";\n}\nelse\n{\n msg.payload = msg.payload.sample_sampling_gear;\n}\nreturn msg;",
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@ -3873,7 +3875,7 @@
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@ -3896,7 +3898,7 @@
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@ -3916,7 +3918,7 @@
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@ -3939,7 +3941,7 @@
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@ -3973,7 +3975,7 @@
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@ -4202,8 +4204,8 @@
"d": true, "d": true,
"name": "GPS Status", "name": "GPS Status",
"scope": [], "scope": [],
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@ -4223,8 +4225,8 @@
"label": "GPS Status:", "label": "GPS Status:",
"format": "{{msg.status.text}}", "format": "{{msg.status.text}}",
"layout": "row-left", "layout": "row-left",
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"wires": [] "wires": []
}, },
{ {
@ -4356,7 +4358,7 @@
"label": "Object depth Max", "label": "Object depth Max",
"tooltip": "", "tooltip": "",
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"order": 7, "order": 8,
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"passthru": true, "passthru": true,
@ -4364,7 +4366,7 @@
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@ -4379,7 +4381,7 @@
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"tooltip": "", "tooltip": "",
"group": "3e1ba03d.f01d8", "group": "3e1ba03d.f01d8",
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@ -4387,7 +4389,7 @@
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"y": 740, "y": 480,
"wires": [ "wires": [
[ [
"7953b1b2.d53ed8" "7953b1b2.d53ed8"
@ -5656,7 +5658,7 @@
"passthru": true, "passthru": true,
"topic": "object_date", "topic": "object_date",
"x": 1250, "x": 1250,
"y": 700, "y": 440,
"wires": [ "wires": [
[ [
"29f2b365.4327ec" "29f2b365.4327ec"
@ -5679,7 +5681,7 @@
"delay": 300, "delay": 300,
"topic": "object_time", "topic": "object_time",
"x": 1250, "x": 1250,
"y": 740, "y": 480,
"wires": [ "wires": [
[ [
"1a945afa.d60aad" "1a945afa.d60aad"
@ -5701,7 +5703,7 @@
"resendOnRefresh": true, "resendOnRefresh": true,
"templateScope": "local", "templateScope": "local",
"x": 590, "x": 590,
"y": 780, "y": 520,
"wires": [ "wires": [
[] []
] ]
@ -5721,7 +5723,7 @@
"resendOnRefresh": true, "resendOnRefresh": true,
"templateScope": "local", "templateScope": "local",
"x": 590, "x": 590,
"y": 900, "y": 640,
"wires": [ "wires": [
[] []
] ]
@ -5903,10 +5905,10 @@
"type": "ui_text_input", "type": "ui_text_input",
"z": "b771c342.49603", "z": "b771c342.49603",
"name": "sample_concentrated_sample_volume", "name": "sample_concentrated_sample_volume",
"label": "Concentrated sample volume", "label": "Concentrated sample volume (mL)",
"tooltip": "Volume extracted from the net", "tooltip": "Volume extracted from the net (in mL)",
"group": "3e1ba03d.f01d8", "group": "3e1ba03d.f01d8",
"order": 8, "order": 9,
"width": 5, "width": 5,
"height": 1, "height": 1,
"passthru": true, "passthru": true,
@ -5914,7 +5916,7 @@
"delay": "1000", "delay": "1000",
"topic": "sample_concentrated_sample_volume", "topic": "sample_concentrated_sample_volume",
"x": 590, "x": 590,
"y": 500, "y": 240,
"wires": [ "wires": [
[ [
"9f501f49.45645" "9f501f49.45645"
@ -5937,7 +5939,7 @@
"delay": "1000", "delay": "1000",
"topic": "sample_gear_net_opening", "topic": "sample_gear_net_opening",
"x": 620, "x": 620,
"y": 620, "y": 360,
"wires": [ "wires": [
[ [
"9f501f49.45645" "9f501f49.45645"
@ -6117,7 +6119,7 @@
"tooltip": "", "tooltip": "",
"place": "Coordinates type", "place": "Coordinates type",
"group": "3e1ba03d.f01d8", "group": "3e1ba03d.f01d8",
"order": 5, "order": 6,
"width": 0, "width": 0,
"height": 0, "height": 0,
"passthru": true, "passthru": true,
@ -6137,7 +6139,7 @@
"payload": "", "payload": "",
"topic": "coordinates_type", "topic": "coordinates_type",
"x": 590, "x": 590,
"y": 1020, "y": 760,
"wires": [ "wires": [
[ [
"8318ab20.aa34f8" "8318ab20.aa34f8"
@ -6155,7 +6157,7 @@
"initialize": "", "initialize": "",
"finalize": "", "finalize": "",
"x": 870, "x": 870,
"y": 840, "y": 580,
"wires": [ "wires": [
[ [
"9f501f49.45645" "9f501f49.45645"
@ -6187,7 +6189,7 @@
"topic": "", "topic": "",
"name": "", "name": "",
"x": 1070, "x": 1070,
"y": 860, "y": 600,
"wires": [ "wires": [
[] []
] ]
@ -6203,7 +6205,7 @@
"initialize": "", "initialize": "",
"finalize": "", "finalize": "",
"x": 780, "x": 780,
"y": 1020, "y": 760,
"wires": [ "wires": [
[] []
] ]
@ -6230,7 +6232,7 @@
"payload": "dd", "payload": "dd",
"payloadType": "str", "payloadType": "str",
"x": 390, "x": 390,
"y": 1020, "y": 760,
"wires": [ "wires": [
[ [
"db44a49e.960558" "db44a49e.960558"