import json
import pathlib
from AFL.automation.APIServer.Driver import Driver
# Limited set of labware options for quick loading via the dashboard.
LABWARE_OPTIONS = {
"opentrons/opentrons_96_tiprack_10ul": "Opentrons 96 Tiprack 10uL",
"opentrons/opentrons_96_tiprack_300ul": "Opentrons 96 Tiprack 300uL",
"opentrons/opentrons_96_tiprack_1000ul": "Opentrons 96 Tiprack 1000uL",
"opentrons/corning_96_wellplate_360ul_flat": "Corning 96 Well Plate",
"opentrons/nest_96_wellplate_2ml_deep": "NEST 2mL 96 Deep Well Plate",
"custom_beta/nest_96_wellplate_1p6ml_deep_afl": "NEST 1.6mL 96 Deep Well Plate (AFL Definition)",
"custom_beta/nist_pneumatic_loader": "NIST Pneumatic Loader (slot 10 only)",
"custom_beta/nist_6_20ml_vials": "NIST 6 x 20mL vial carrier",
"custom_beta/nist_2_100ml_bottles": "NIST 2 x 100mL bottle carrier",
"heaterShakerModuleV1": "HeaterShaker Module (still needs labware atop it!)",
"abgenestorage_96_wellplate_1200ul": "Abgenestorage 96 Wellplate 1200 ul",
"aps1296wellon300ulrack_96_wellplate_300ul": "12IDB Sample Collection Plate (in tiprack!!!)",
}
[docs]
class OT2DeckWebAppMixin:
@staticmethod
def _generate_ot2_well_svg(labware_data, available_tips=None, size=90, labware_uuid=None, compact=False):
if not labware_data:
return ""
definition = labware_data.get('definition', {})
wells = definition.get('wells', {})
if not wells:
return ""
labware_type = definition.get('metadata', {}).get('displayCategory', 'default')
is_tiprack = labware_type == 'tipRack' or 'tiprack' in definition.get('parameters', {}).get('loadName', '').lower()
available_tips_for_labware = set()
if is_tiprack and labware_uuid and available_tips:
for mount_tips in available_tips.values():
for tip_labware_uuid, well_name in mount_tips:
if tip_labware_uuid == labware_uuid:
available_tips_for_labware.add(well_name)
well_count = len(wells)
if compact:
if well_count <= 8:
cols = well_count
rows = 1
elif well_count <= 24:
cols = 6
rows = (well_count + 5) // 6
elif well_count <= 96:
cols = 12
rows = 8
else:
cols = 12
rows = (well_count + 11) // 12
cell_width = size / max(cols, 6)
cell_height = size / max(rows, 4)
colors = {
'tipRack_available': '#4caf50',
'tipRack_used': '#f44336',
'tipRack': '#ffa726',
'wellPlate': '#42a5f5',
'reservoir': '#66bb6a',
'default': '#90a4ae',
}
svg_elements = []
well_names = list(wells.keys())
for i, well_name in enumerate(well_names[:min(well_count, rows * cols)]):
row = i % rows
col = i // rows
x = col * cell_width + cell_width / 4
y = row * cell_height + cell_height / 4
if is_tiprack and labware_uuid:
if well_name in available_tips_for_labware:
color = colors['tipRack_available']
status = "Available"
else:
color = colors['tipRack_used']
status = "Used"
tooltip = f"{well_name} - {status}"
else:
color = colors.get(labware_type, '#90a4ae')
tooltip = well_name
svg_elements.append(
f'<circle cx="{x:.1f}" cy="{y:.1f}" r="{min(cell_width, cell_height)/3:.1f}" '
f'fill="{color}" stroke="#333" stroke-width="0.3">'
f'<title>{tooltip}</title></circle>'
)
return (
f'<svg width="{size}" height="{size}" '
f'style="border: 1px solid #ddd; border-radius: 3px;">{"".join(svg_elements)}</svg>'
)
labware_width = definition.get('dimensions', {}).get('xDimension', 127.76)
labware_height = definition.get('dimensions', {}).get('yDimension', 85.48)
scale_x = size / labware_width
scale_y = (size * 0.75) / labware_height
svg_elements = []
well_colors = {
'tipRack_available': '#4caf50',
'tipRack_used': '#f44336',
'tipRack_default': '#ffa726',
'wellPlate': '#42a5f5',
'reservoir': '#66bb6a',
'default': '#90a4ae',
}
for well_name, well_info in wells.items():
x = well_info.get('x', 0) * scale_x
y = (labware_height - well_info.get('y', 0)) * scale_y
shape = well_info.get('shape', 'circular')
if is_tiprack and labware_uuid:
if well_name in available_tips_for_labware:
well_color = well_colors['tipRack_available']
tip_status = "Available"
else:
well_color = well_colors['tipRack_used']
tip_status = "Used"
tooltip = f"{well_name} - {tip_status}"
else:
well_color = well_colors.get(labware_type, well_colors['default'])
tooltip = well_name
if shape == 'circular':
diameter = well_info.get('diameter', 5) * min(scale_x, scale_y)
radius = diameter / 2
svg_elements.append(
f'<circle cx="{x:.1f}" cy="{y:.1f}" r="{radius:.1f}" '
f'fill="{well_color}" stroke="#333" stroke-width="0.5" opacity="0.8">'
f'<title>{tooltip}</title></circle>'
)
elif shape == 'rectangular':
well_width = well_info.get('xDimension', 8) * scale_x
well_height = well_info.get('yDimension', 8) * scale_y
rect_x = x - well_width / 2
rect_y = y - well_height / 2
svg_elements.append(
f'<rect x="{rect_x:.1f}" y="{rect_y:.1f}" '
f'width="{well_width:.1f}" height="{well_height:.1f}" '
f'fill="{well_color}" stroke="#333" stroke-width="0.5" opacity="0.8">'
f'<title>{tooltip}</title></rect>'
)
if svg_elements:
return f'<svg width="{size}" height="{int(size*0.75)}" style="margin: 5px 0;">{"".join(svg_elements)}</svg>'
return ""
def _get_ot2_slot_info(self, slot_num, compact):
if slot_num == "Trash":
return {"name": "Trash", "type": "trash", "color": "#ffcdd2", "svg": ""}
slot_str = str(slot_num)
info = {"name": "Empty", "type": "empty", "color": "#f5f5f5", "svg": ""}
has_labware = slot_str in self.config["loaded_labware"]
has_module = slot_str in self.config["loaded_modules"]
if has_labware:
labware_id, labware_type, labware_data = self.config["loaded_labware"][slot_str]
definition = labware_data.get('definition', {})
display_name = definition.get('metadata', {}).get('displayName', labware_type)
is_tiprack = (
'tiprack' in labware_type.lower() or
definition.get('metadata', {}).get('displayCategory') == 'tipRack'
)
wells = list(definition.get('wells', {}).keys())
def _well_key(w):
import re
m = re.match(r"([A-Za-z]+)(\d+)", w)
if m:
row = m.group(1)
col = int(m.group(2))
return (row, col)
return (w, 0)
wells = sorted(wells, key=_well_key)
mounts = []
if is_tiprack:
for m, d in self.config['loaded_instruments'].items():
if labware_id in d.get('tip_racks', []):
mounts.append(m)
info.update({
"name": display_name[:20] + ("..." if len(display_name) > 20 else ""),
"type": "labware",
"color": "#bbdefb",
"svg": self._generate_ot2_well_svg(
labware_data,
available_tips=self.config.get("available_tips", {}),
size=50 if compact else 90,
labware_uuid=labware_id,
compact=compact,
)
})
if is_tiprack:
info['tiprack'] = True
info['mounts'] = mounts
info['color'] = '#fff3e0'
info['target_count'] = len(wells)
info['targets'] = ','.join([f"{slot_str}{w}" for w in wells])
if has_module:
_, module_type = self.config["loaded_modules"][slot_str]
module_name = module_type.replace('ModuleV1', '').replace('Module', ' Mod')
if has_labware:
info["name"] = f"{module_name}<br><small>{info['name']}</small>"
info["color"] = "#c8e6c9"
else:
info.update({
"name": module_name,
"type": "module_only",
"color": "#e1bee7",
})
return info
[docs]
@Driver.unqueued(render_hint='html')
def visualize_deck(self, mode='full', **kwargs):
slot_layout = [
[10, 11, "Trash"],
[7, 8, 9],
[4, 5, 6],
[1, 2, 3],
]
slot_infos = {}
for row in slot_layout:
for slot in row:
info = self._get_ot2_slot_info(slot, compact=(mode == 'simple'))
slot_label = "T" if slot == "Trash" else str(slot)
info["slot_label"] = slot_label
info["click_attr"] = ""
if info["type"] in ["empty", "module_only"]:
info["click_attr"] = f"onclick=\"showLabwareOptions('{slot}')\" style=\"cursor:pointer;\""
info["buttons"] = ''.join([
f"<button style='margin-top:4px;font-size:10px;' onclick=\"resetTipracks('{m}')\">Reset</button>"
for m in info.get('mounts', [])
])
if info.get('target_count', 0) > 10:
target_str = info.get('targets', '')
slot_id = str(slot)
info["buttons"] += (
f"<button style='margin-top:4px;font-size:10px;' "
f"onclick=\"openPrepTargetDialog('{slot_id}','{target_str}')\">"
"Manage Targets</button>"
)
slot_infos[str(slot)] = info
base = pathlib.Path(__file__).parent.parent / "apps" / "ot2_deck"
html_template = (base / "ot2_deck.html").read_text()
css = (base / "css" / "style.css").read_text()
js = (base / "js" / "main.js").read_text()
from jinja2 import Template
template = Template(html_template)
return template.render(
slot_layout=slot_layout,
slot_infos=slot_infos,
loaded_instruments=self.config.get('loaded_instruments', {}),
mode=mode,
deck_data_json=json.dumps({"labwareChoices": LABWARE_OPTIONS}),
inline_css=css,
inline_js=js,
)
