From 68d2a10303e39f1ad6e3c6a0c815778e293999bc Mon Sep 17 00:00:00 2001 From: Romain Bazile Date: Thu, 3 Dec 2020 15:15:13 +0100 Subject: [PATCH] flow: add mL to concentrated sample volume and add process_description field to metadata --- flows/main.json | 178 ++++++++++++++++++++++++------------------------ 1 file changed, 90 insertions(+), 88 deletions(-) diff --git a/flows/main.json b/flows/main.json index b55953f..c363715 100644 --- a/flows/main.json +++ b/flows/main.json @@ -741,24 +741,6 @@ "width": 5, "height": 1 }, - { - "id": "226903fb.014ba4", - "type": "ui_spacer", - "name": "spacer", - "group": "3e1ba03d.f01d8", - "order": 9, - "width": 5, - "height": 1 - }, - { - "id": "a393ee49.38373", - "type": "ui_spacer", - "name": "spacer", - "group": "cf5d9f0e.d57e7", - "order": 13, - "width": 4, - "height": 1 - }, { "id": "a7d64879.38298", "type": "ui_group", @@ -875,6 +857,24 @@ "width": 8, "height": 1 }, + { + "id": "692eec9a.2996cc", + "type": "ui_spacer", + "name": "spacer", + "group": "3e1ba03d.f01d8", + "order": 10, + "width": 5, + "height": 1 + }, + { + "id": "9c34106a.4c5998", + "type": "ui_spacer", + "name": "spacer", + "group": "cf5d9f0e.d57e7", + "order": 13, + "width": 4, + "height": 1 + }, { "id": "4e78af2d.90be7", "type": "ui_ui_control", @@ -1837,7 +1837,7 @@ "delay": "1000", "topic": "sample_ship", "x": 670, - "y": 340, + "y": 80, "wires": [ [ "9f501f49.45645" @@ -1893,7 +1893,7 @@ "payload": "", "topic": "sample_sampling_gear", "x": 630, - "y": 460, + "y": 200, "wires": [ [ "9f501f49.45645", @@ -1917,7 +1917,7 @@ "delay": "1000", "topic": "sample_operator", "x": 650, - "y": 420, + "y": 160, "wires": [ [ "9f501f49.45645", @@ -1941,7 +1941,7 @@ "delay": "1000", "topic": "sample_project", "x": 660, - "y": 300, + "y": 40, "wires": [ [ "9f501f49.45645" @@ -1964,7 +1964,7 @@ "delay": "1000", "topic": "sample_id", "x": 670, - "y": 380, + "y": 120, "wires": [ [ "9f501f49.45645" @@ -1982,7 +1982,7 @@ "initialize": "", "finalize": "", "x": 1080, - "y": 460, + "y": 200, "wires": [ [] ] @@ -2061,8 +2061,8 @@ "z": "b771c342.49603", "name": "", "events": "change", - "x": 460, - "y": 1300, + "x": 340, + "y": 880, "wires": [ [] ] @@ -2081,8 +2081,8 @@ "raw": false, "topic": "", "name": "", - "x": 770, - "y": 1420, + "x": 650, + "y": 1000, "wires": [ [] ] @@ -2097,8 +2097,8 @@ "noerr": 0, "initialize": "", "finalize": "", - "x": 470, - "y": 1360, + "x": 350, + "y": 940, "wires": [ [ "726a7822.cd6298", @@ -2126,8 +2126,8 @@ "device": false, "gst": false, "att": false, - "x": 290, - "y": 1420, + "x": 170, + "y": 1000, "wires": [ [] ] @@ -2138,8 +2138,8 @@ "z": "b771c342.49603", "name": "", "events": "change", - "x": 760, - "y": 1340, + "x": 640, + "y": 920, "wires": [ [] ] @@ -2160,7 +2160,7 @@ "delay": "1000", "topic": "object_lat", "x": 620, - "y": 820, + "y": 560, "wires": [ [ "7953b1b2.d53ed8" @@ -2183,7 +2183,7 @@ "delay": "1000", "topic": "object_lon", "x": 610, - "y": 860, + "y": 600, "wires": [ [ "7953b1b2.d53ed8" @@ -2203,7 +2203,7 @@ "passthru": true, "topic": "object_date", "x": 1250, - "y": 820, + "y": 560, "wires": [ [ "29f2b365.4327ec" @@ -2226,7 +2226,7 @@ "delay": 300, "topic": "object_time", "x": 1250, - "y": 860, + "y": 600, "wires": [ [ "1a945afa.d60aad" @@ -2591,8 +2591,8 @@ "payload": "{\"tab\":\"Home\"}", "payloadType": "json", "topic": "", - "x": 300, - "y": 1300, + "x": 180, + "y": 880, "wires": [ [ "222c851d.5d0a3a" @@ -2617,8 +2617,8 @@ "payload": "{\"tab\":\"Home\"}", "payloadType": "json", "topic": "", - "x": 300, - "y": 1360, + "x": 180, + "y": 940, "wires": [ [ "986d960a.c75908" @@ -3522,7 +3522,7 @@ "type": "function", "z": "baa1e3d9.cb29d", "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;", "outputs": 1, "noerr": 0, "initialize": "", @@ -3629,7 +3629,7 @@ "initialize": "", "finalize": "", "x": 330, - "y": 300, + "y": 40, "wires": [ [ "9c882b37.fde668" @@ -3647,7 +3647,7 @@ "initialize": "", "finalize": "", "x": 330, - "y": 340, + "y": 80, "wires": [ [ "4557d689.a4fa88" @@ -3665,7 +3665,7 @@ "initialize": "", "finalize": "", "x": 320, - "y": 380, + "y": 120, "wires": [ [ "94eb4221.9b92c" @@ -3683,7 +3683,7 @@ "initialize": "", "finalize": "", "x": 340, - "y": 420, + "y": 160, "wires": [ [ "82c5fc77.59c97" @@ -3695,11 +3695,13 @@ "type": "function", "z": "b771c342.49603", "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;", "outputs": 1, "noerr": 0, + "initialize": "", + "finalize": "", "x": 360, - "y": 460, + "y": 200, "wires": [ [ "fcfc31ae.af3af" @@ -3834,7 +3836,7 @@ "name": "", "env": [], "x": 90, - "y": 380, + "y": 120, "wires": [ [ "d027a6bf.7049e8", @@ -3851,8 +3853,8 @@ "z": "b771c342.49603", "name": "", "env": [], - "x": 750, - "y": 1380, + "x": 630, + "y": 960, "wires": [ [] ] @@ -3873,7 +3875,7 @@ "delay": "1000", "topic": "object_lat_end", "x": 600, - "y": 940, + "y": 680, "wires": [ [ "7953b1b2.d53ed8" @@ -3896,7 +3898,7 @@ "delay": "1000", "topic": "object_lon_end", "x": 600, - "y": 980, + "y": 720, "wires": [ [ "7953b1b2.d53ed8" @@ -3916,7 +3918,7 @@ "passthru": true, "topic": "object_date_end", "x": 1230, - "y": 940, + "y": 680, "wires": [ [ "29f2b365.4327ec" @@ -3939,7 +3941,7 @@ "delay": 300, "topic": "object_time_end", "x": 1230, - "y": 980, + "y": 720, "wires": [ [ "1a945afa.d60aad" @@ -3957,7 +3959,7 @@ "initialize": "", "finalize": "", "x": 1540, - "y": 860, + "y": 600, "wires": [ [] ] @@ -3973,7 +3975,7 @@ "initialize": "", "finalize": "", "x": 1540, - "y": 820, + "y": 560, "wires": [ [] ] @@ -4202,8 +4204,8 @@ "d": true, "name": "GPS Status", "scope": [], - "x": 310, - "y": 1500, + "x": 190, + "y": 1080, "wires": [ [ "7116e906.9f50f" @@ -4223,8 +4225,8 @@ "label": "GPS Status:", "format": "{{msg.status.text}}", "layout": "row-left", - "x": 810, - "y": 1500, + "x": 690, + "y": 1080, "wires": [] }, { @@ -4356,7 +4358,7 @@ "label": "Object depth Max", "tooltip": "", "group": "3e1ba03d.f01d8", - "order": 7, + "order": 8, "width": 5, "height": 1, "passthru": true, @@ -4364,7 +4366,7 @@ "delay": "1000", "topic": "object_depth_max", "x": 650, - "y": 540, + "y": 280, "wires": [ [ "9f501f49.45645" @@ -4379,7 +4381,7 @@ "label": "Object Depth Min", "tooltip": "", "group": "3e1ba03d.f01d8", - "order": 6, + "order": 7, "width": 5, "height": 1, "passthru": true, @@ -4387,7 +4389,7 @@ "delay": "1000", "topic": "object_depth_min", "x": 650, - "y": 580, + "y": 320, "wires": [ [ "9f501f49.45645" @@ -5108,7 +5110,7 @@ "35eb925e.5f8016" ], "x": 815, - "y": 420, + "y": 160, "wires": [] }, { @@ -5507,7 +5509,7 @@ "repair": false, "outputs": 2, "x": 1090, - "y": 420, + "y": 160, "wires": [ [ "66b362ee.80b5b4" @@ -5544,7 +5546,7 @@ "to": "", "reg": false, "x": 1290, - "y": 400, + "y": 140, "wires": [ [ "cbb123ab.fd3428" @@ -5578,7 +5580,7 @@ "to": "", "reg": false, "x": 1300, - "y": 440, + "y": 180, "wires": [ [ "cbb123ab.fd3428" @@ -5592,7 +5594,7 @@ "name": "", "events": "change", "x": 1500, - "y": 420, + "y": 160, "wires": [ [] ] @@ -5613,7 +5615,7 @@ "delay": "1000", "topic": "object_lat", "x": 620, - "y": 700, + "y": 440, "wires": [ [ "7953b1b2.d53ed8" @@ -5636,7 +5638,7 @@ "delay": "1000", "topic": "object_lon", "x": 610, - "y": 740, + "y": 480, "wires": [ [ "7953b1b2.d53ed8" @@ -5656,7 +5658,7 @@ "passthru": true, "topic": "object_date", "x": 1250, - "y": 700, + "y": 440, "wires": [ [ "29f2b365.4327ec" @@ -5679,7 +5681,7 @@ "delay": 300, "topic": "object_time", "x": 1250, - "y": 740, + "y": 480, "wires": [ [ "1a945afa.d60aad" @@ -5701,7 +5703,7 @@ "resendOnRefresh": true, "templateScope": "local", "x": 590, - "y": 780, + "y": 520, "wires": [ [] ] @@ -5721,7 +5723,7 @@ "resendOnRefresh": true, "templateScope": "local", "x": 590, - "y": 900, + "y": 640, "wires": [ [] ] @@ -5903,10 +5905,10 @@ "type": "ui_text_input", "z": "b771c342.49603", "name": "sample_concentrated_sample_volume", - "label": "Concentrated sample volume", - "tooltip": "Volume extracted from the net", + "label": "Concentrated sample volume (mL)", + "tooltip": "Volume extracted from the net (in mL)", "group": "3e1ba03d.f01d8", - "order": 8, + "order": 9, "width": 5, "height": 1, "passthru": true, @@ -5914,7 +5916,7 @@ "delay": "1000", "topic": "sample_concentrated_sample_volume", "x": 590, - "y": 500, + "y": 240, "wires": [ [ "9f501f49.45645" @@ -5937,7 +5939,7 @@ "delay": "1000", "topic": "sample_gear_net_opening", "x": 620, - "y": 620, + "y": 360, "wires": [ [ "9f501f49.45645" @@ -6117,7 +6119,7 @@ "tooltip": "", "place": "Coordinates type", "group": "3e1ba03d.f01d8", - "order": 5, + "order": 6, "width": 0, "height": 0, "passthru": true, @@ -6137,7 +6139,7 @@ "payload": "", "topic": "coordinates_type", "x": 590, - "y": 1020, + "y": 760, "wires": [ [ "8318ab20.aa34f8" @@ -6155,7 +6157,7 @@ "initialize": "", "finalize": "", "x": 870, - "y": 840, + "y": 580, "wires": [ [ "9f501f49.45645" @@ -6187,7 +6189,7 @@ "topic": "", "name": "", "x": 1070, - "y": 860, + "y": 600, "wires": [ [] ] @@ -6203,7 +6205,7 @@ "initialize": "", "finalize": "", "x": 780, - "y": 1020, + "y": 760, "wires": [ [] ] @@ -6230,7 +6232,7 @@ "payload": "dd", "payloadType": "str", "x": 390, - "y": 1020, + "y": 760, "wires": [ [ "db44a49e.960558"