fix(protocols/gsdx): add flashing option, fix liquid volume display

data/data/fields.csv

@@ -383,6 +383,7 @@ dna_well_plate_tmod,1
 do_cool_samples,1
 do_deactivate_tc,1
 do_dnase_step,1
+do_flash,1
 do_mm_resusp_pause,1
 do_plate_mm,1
 do_premix,1

protocols/gsdx/bacgene.ot2.apiv2.py

@@ -29,12 +29,19 @@
 
 def run(ctx):
 
+    def flash_lights():
+        initial_status = ctx.rail_lights_on
+        for _ in range(19):
+            ctx.set_rail_lights(not ctx.rail_lights_on)
+            ctx.delay(seconds=0.25)
+        ctx.set_rail_lights(initial_status)
+
     [num_samples_listeria, num_samples_salmonella,
      num_samples_listeria_remaining, num_samples_salmonella_remaining,
-     sample_rack_type, salmonella_meat] = get_values(  # noqa: F821
+     sample_rack_type, salmonella_meat, do_flash] = get_values(  # noqa: F821
         'num_samples_listeria', 'num_samples_salmonella',
         'num_samples_listeria_remaining', 'num_samples_salmonella_remaining',
-        'sample_rack_type', 'salmonella_meat')
+        'sample_rack_type', 'salmonella_meat', 'do_flash')
 
     # modules
     tempdeck = ctx.load_module('temperature module gen2', '10')
@@ -190,11 +197,15 @@ def run(ctx):
         num_cols_offset_samples_listeria*8+num_samples_salmonella]
 
     # load liquids
+    vol_sample = 5.0
+
     try:
         if num_samples_listeria > 0:
-            positive_control_l.load_liquid(positive_control_l_liq, volume=10)
+            positive_control_l.load_liquid(
+                positive_control_l_liq, volume=vol_sample)
         if num_samples_salmonella > 0:
-            positive_control_s.load_liquid(positive_control_s_liq, volume=10)
+            positive_control_s.load_liquid(
+                positive_control_s_liq, volume=vol_sample)
         [well.load_liquid(samples_listeria_liq_sample,
                           volume=30/len(samples_single_listeria))
          for well in samples_single_listeria]
@@ -635,8 +646,6 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0):
         ctx.delay(minutes=10, msg='Incubating for 10 minutes @ 95C.')
         tempdeck.set_temperature(37)
 
-    vol_sample = 5.0
-
     if DO_TRANSFER_SAMPLE_TO_PCR:
         """ transfer samples to PCR plate """
 
@@ -713,3 +722,6 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0):
             drop(m20)
 
     tempdeck.deactivate()
+
+    if do_flash:
+        flash_lights()

protocols/gsdx/fields.json

@@ -1,44 +1,59 @@
 [
-    {
-        "type": "int",
-        "label": "number of listeria wells to run (including +/- controls)",
-        "name": "num_samples_listeria",
-        "default": 48
-    },
-    {
-        "type": "int",
-        "label": "number of salmonella wells to run (including +/- controls)",
-        "name": "num_samples_salmonella",
-        "default": 48
-    },
-    {
-        "type": "int",
-        "label": "number of listeria wells in kit remaining",
-        "name": "num_samples_listeria_remaining",
-        "default": 96
-    },
-    {
-        "type": "int",
-        "label": "number of salmonella wells in kit remaining",
-        "name": "num_samples_salmonella_remaining",
-        "default": 96
-    },
-    {
-        "type": "dropDown",
-        "label": "sample rack format",
-        "name": "sample_rack_type",
-        "options": [
-          {"label": "KingFisher 96 Tube Rack with GoldStandard 1.1 mL", "value": "kingfisher_96_tuberack_1100ul"},
-          {"label": "BIOPlastics BV 96 Aluminum Block 200 µL", "value": "bioplasticsbv_96_aluminumblock_200ul"}
-        ]
-    },
-    {
-        "type": "dropDown",
-        "label": "running salmonella meat",
-        "name": "salmonella_meat",
-        "options": [
-          {"label": "no", "value": false},
-          {"label": "yes", "value": true}
-        ]
-    }
-]
+  {
+    "type": "int",
+    "label": "number of listeria wells to run (including +/- controls)",
+    "name": "num_samples_listeria",
+    "default": 48
+  },
+  {
+    "type": "int",
+    "label": "number of salmonella wells to run (including +/- controls)",
+    "name": "num_samples_salmonella",
+    "default": 48
+  },
+  {
+    "type": "int",
+    "label": "number of listeria wells in kit remaining",
+    "name": "num_samples_listeria_remaining",
+    "default": 96
+  },
+  {
+    "type": "int",
+    "label": "number of salmonella wells in kit remaining",
+    "name": "num_samples_salmonella_remaining",
+    "default": 96
+  },
+  {
+    "type": "dropDown",
+    "label": "sample rack format",
+    "name": "sample_rack_type",
+    "options": [
+      {
+        "label": "KingFisher 96 Tube Rack with GoldStandard 1.1 mL",
+        "value": "kingfisher_96_tuberack_1100ul"
+      },
+      {
+        "label": "BIOPlastics BV 96 Aluminum Block 200 µL",
+        "value": "bioplasticsbv_96_aluminumblock_200ul"
+      }
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "running salmonella meat",
+    "name": "salmonella_meat",
+    "options": [
+      { "label": "no", "value": false },
+      { "label": "yes", "value": true }
+    ]
+  },
+  {
+    "type": "dropDown",
+    "label": "flash on completion",
+    "name": "do_flash",
+    "options": [
+      { "label": "no", "value": false },
+      { "label": "yes", "value": true }
+    ]
+  }
+]