Sample type labeling m8

index.py

@@ -32,7 +32,6 @@
     EMPTY_BORDER_PX,
     make_tab,
     get_tab_id,
-    SAMPLE_TYPE_OPTIONS
 )
 
 pd.set_option('future.no_silent_downcasting', True)
@@ -530,6 +529,8 @@ def plate_mapper(plate_ids, objects):
                         if str(well.well_position_id) in selected_well_ids:
                             well.get_sample(app_state).sample_type = sample_type
 
+
+
             warnings = collect_missing_sample_warnings(app_state)
             show_warning = bool(warnings)
             warning_msg = build_warning_msg(warnings)
@@ -748,9 +749,9 @@ def sync_plate_style(cell_evt, row_data, virtual_row_data, fig):
         fills.append(fill_color)
         customdata.append([w, st])
 
-        if w in error_wells:
+        if w in error_wells and st in ("Library", "Positive Control"):
             line_colors.append(ERROR_BORDER); line_widths.append(3)
-        elif w in warn_wells:
+        elif w in warn_wells and st in ("Library", "Positive Control"):
             line_colors.append(WARN_BORDER);  line_widths.append(3)
         else:
             line_colors.append(DEFAULT_BORDER); line_widths.append(BORDER_PX)
@@ -796,8 +797,6 @@ def update_rows_callback(_, app_data_state_json, table_id):
 
     df = plate.dataset(app_state, tidy=False).replace(['None', 'none', 'NaN', 'nan', ''], np.nan).infer_objects(copy=False)
 
-    print("Plate dataset: ", df.head(3))
-
     # Keep columns tidy, but do not drop keys AG Grid needs (e.g., well_position_id if you use getRowId)
     if is_qpcr:
         df = df.dropna(axis=1, how="all")
@@ -1047,7 +1046,6 @@ def toggle_delete_plate_modal(n_open, n_cancel, n_confirm):
         return False
     return no_update
 
-
 # Here we run the app on the specified host and port.
 if __name__ == "__main__":
     app.run(debug=bfabric_web_apps.DEBUG, port=bfabric_web_apps.PORT, host=bfabric_web_apps.HOST)

utils/api_call_utils.py

@@ -21,14 +21,14 @@ def format_tube_id(val):
             return "/".join(parts)
     return val
 
-def initialize_sample_attributes(plate: Plate, app_state):
+def populate_samples_by_identifier_lookup(plate: Plate, app_state):
 
     B = bfabric_interface.get_wrapper()
     formatted_tube_ids = []
 
     for well in plate.plate_wells:
         tube_id = str(getattr(well, "file_sample_identifier", "")).strip()
-        print("tube_id", tube_id)
+
         if tube_id:
             formatted = format_tube_id(tube_id)
             formatted_tube_ids.append(formatted)

utils/plate_render_utils.py

@@ -10,15 +10,6 @@
 
 pd.set_option('future.no_silent_downcasting', True)
 
-# Mapping of sample types to their display options
-SAMPLE_TYPE_OPTIONS = [
-    {"label": "Negative Control", "value": "Negative Control"},
-    {"label": "Positive Control", "value": "Positive Control"},
-    {"label": "Standard", "value": "Standard"},
-    {"label": "PhiX", "value": "PhiX"},
-    {"label": "Library", "value": "Library"},
-]
-
 SAMPLE_TYPE_COLORS = {
     "Negative Control": "#ef5350",  # red
     "Positive Control": "#2979ff",  # blue
@@ -174,6 +165,23 @@ def build_tab_body(plate, app_state):
     import dash_bootstrap_components as dbc
     import dash_ag_grid as dag
 
+    # Dynamic options for the sample_type dropdown:
+    if plate.plate_type == "qPCR":
+        SAMPLE_TYPE_OPTIONS = [
+            {"label": "Negative Control", "value": "Negative Control"},
+            {"label": "Positive Control", "value": "Positive Control"},
+            {"label": "Standard", "value": "Standard"},
+            {"label": "PhiX", "value": "PhiX"},
+            {"label": "Library", "value": "Library"},
+        ]
+    else:
+        SAMPLE_TYPE_OPTIONS = [
+            {"label": "Negative Control", "value": "Negative Control"},
+            {"label": "Positive Control", "value": "Positive Control"},
+            {"label": "PhiX", "value": "PhiX"},
+            {"label": "Library", "value": "Library"},
+        ]
+
     pid = str(plate.plate_id)                      # normalize once; reuse everywhere
     is_qpcr = (plate.plate_type == "qPCR")
 
@@ -199,8 +207,22 @@ def build_tab_body(plate, app_state):
 
     getRowStyle = {
         "styleConditions": [
-            {"condition": "params.data.__error__ === true", "style": {"backgroundColor": "#ffcccc"}},
-            {"condition": "params.data.__warning__ === true", "style": {"backgroundColor": "#f9f490"}},
+            {
+                "condition": (
+                    "params.data.__error__ === true && " +
+                    "params.data.sample_type !== 'Negative Control' && " +
+                    "params.data.sample_type !== 'PhiX'"
+                ),
+                "style": {"backgroundColor": "#ffcccc"},
+            },
+            {
+                "condition": (
+                    "params.data.__warning__ === true && " +
+                    "params.data.sample_type !== 'Negative Control' && " +
+                    "params.data.sample_type !== 'PhiX'"
+                ),
+                "style": {"backgroundColor": "#f9f490"},
+            },
         ]
     }
 
@@ -238,17 +260,29 @@ def _is_num(s):
                 "cellEditorParams": {"values": [opt["value"] for opt in SAMPLE_TYPE_OPTIONS]},
                 "singleClickEdit": True,
                 "cellStyle": {
-                    "function": """(params) => {
-                        const colors = {
-                            'Negative Control': '#ef5350',
-                            'Positive Control': '#2979ff',
-                            'Standard': '#153677',
-                            'PhiX': '#ffd600',
-                            'Library': '#43a047'
-                        };
-                        const c = colors[params.value] || '';
-                        return { backgroundColor: c, color: (params.value==='PhiX'?'black':'white') };
-                    }"""
+                    "styleConditions": [
+                        {
+                            "condition": "params.value === 'Negative Control'",
+                            "style": {"backgroundColor": "rgb(247,169,168)", "color": "black", "borderRadius": "10px"},
+                        },
+                        {
+                            "condition": "params.value === 'Positive Control'",
+                            "style": {"backgroundColor": "rgb(148,188,255)", "color": "black", "borderRadius": "10px"},
+                        },
+                        {
+                            "condition": "params.value === 'Standard'",
+                            "style": {"backgroundColor": "rgb(138,154,187)", "color": "black", "borderRadius": "10px"},
+                        },
+                        {
+                            "condition": "params.value === 'PhiX'",
+                            "style": {"backgroundColor": "rgb(255,235,127)", "color": "black", "borderRadius": "10px"},
+                        },
+                        {
+                            "condition": "params.value === 'Library'",
+                            "style": {"backgroundColor": "rgb(161,207,163)", "color": "black", "borderRadius": "10px"},
+                        },
+                    ],
+                    "defaultStyle": {"backgroundColor": "white", "color": "black"},
                 },
                 "cellRenderer": {
                     "function": {"code": """
@@ -269,7 +303,9 @@ def _is_num(s):
         # ensure sample_id is editable and right after sample_type
         col_sample_id = {
             "field": "sample_id",
-            "editable": True,
+            "editable": {
+                    "function": "params.data.sample_type === 'Library' || params.data.sample_type === 'Positive Control'"
+                },
             "filter": "agTextColumnFilter",
             "valueFormatter": {"function": "params.value == null ? '' : params.value"},
         }
@@ -422,6 +458,24 @@ def _is_num(s):
         )
     ])
 
+
+    delete_plate_modal = html.Div([
+        dbc.Modal(
+            [
+                dbc.ModalHeader(dbc.ModalTitle("Delete Plate")),
+                dbc.ModalBody(
+                    "Are you sure you want to delete this plate? This will remove all associated wells and their data. This action cannot be undone."
+                ),
+                dbc.ModalFooter([
+                    dbc.Button("Delete", id={"type": "confirm-delete-plate", "index": pid}, color="danger"),
+                    dbc.Button("Cancel", id={"type": "cancel-delete-plate", "index": pid}, className="ms-auto"),
+                ]),
+            ],
+            id={"type": "modal-delete-plate", "index": pid},
+            is_open=False, backdrop="static",
+        )
+    ])
+
     dummy = html.Div(id={"type": "dummy-div", "index": pid}, style={"display": "none"})
 
     return [table_wrap, plate_wrap, buttons_row, delete_plate_modal, flagging_modal, delete_rows_modal, dummy]

utils/plates_callback_utils.py

@@ -5,7 +5,7 @@
 from dash import html
 from models import Plate, PlateWell, Measurement, AppSpecificFile, Sample
 from app_state import AppState
-from .api_call_utils import initialize_sample_attributes, safe_str
+from .api_call_utils import populate_samples_by_identifier_lookup, safe_str
 from bfabric_web_apps.objects.BfabricInterface import bfabric_interface
 
 def find_and_populate_samples_by_sample_id(
@@ -45,12 +45,14 @@ def find_and_populate_samples_by_sample_id(
             sample_name = safe_str(bfabric_sample.get("name"))
             container_id = safe_str(bfabric_sample.get("container", {}).get("id"))
             well.well_note = "Sample found"
+            sample_type = well.get_sample(app_state).sample_type
 
             new_sample = Sample(
                 sample_id=sample_id,
                 sample_name=sample_name,
                 container=container_id,
-                file_sample_identifier=tube_id
+                file_sample_identifier=tube_id,
+                sample_type=sample_type
             )
             app_state.sample_registry.append(new_sample)
             well.file_sample_identifier = tube_id
@@ -71,11 +73,14 @@ def handle_plate_upload(contents, filenames, app_state):
         uploaded_file = AppSpecificFile.create_from_raw_data(name=name, raw_data=decoded_str)
         app_state, plate = Plate.from_file(input_file=uploaded_file, app_state=app_state)
 
+        # here we make the new functon to automatically populate sample_type
+        app_state, plate = populate_sample_types(app_state, plate)
+
         if plate.plate_type in ("D1000", "D5000", "HSD1000"):
-            plate = initialize_sample_attributes(plate, app_state)
+            plate = populate_samples_by_identifier_lookup(plate, app_state)
 
+        #print("intial app state sample_registry:", app_state.sample_registry)
         # print("intial app state plate_registry:", app_state.plate_registry)
-
         # print("Added plate:", plate.plate_id)
 
 
@@ -142,14 +147,59 @@ def update_app_state_from_ui(app_state, all_ui_tables):
                 if sample: 
                     if sample.sample_type != sample_type:
                         sample.sample_type = sample_type
-                        # print(f"Updated well {well_pos} with sample_type: {sample_type}")
+
                         break
                     if sample_id: 
-                        if sample.sample_id != sample_id:
+                        if sample.sample_id != sample_id and sample.sample_type in ("Library", "Positive Control"):
                             find_and_populate_samples_by_sample_id(app_state, sample_id, well=pw)
                             break
 
-                    # print(f"Updated well {well_pos} with sample_id: {sample_id}, sample_type: {sample_type}")
+def populate_sample_types(app_state, plate):
+    if plate.plate_type.lower() == "qpcr":
+        for well in plate.plate_wells:
+            position = well.well_position_id
+            row = position[0]
+            col = int(position[1:])
+
+            # Only consider columns 1, 4, 7, 10
+            if col not in (1, 4, 7, 10):
+                continue
+
+            # Assign sample types based on postion
+            if "A" <= row <= "F" and 1 <= col <= 3:
+                sample_type = "Standard"
+            elif row in ("G", "H") and 1 <= col <= 3:
+                sample_type = "Negative Control"
+            else:
+                sample_type = "Library"
+
+            sample = well.get_sample(app_state)
+            sample.sample_type = sample_type
+
+        return app_state, plate
+
+
+    else:
+        for well in plate.plate_wells:
+            desc = well.sample_identifier
+            desc_lower = desc.lower()
+
+            if (
+                "negative control" in desc_lower
+                or "neg" in desc_lower
+            ):
+                sample_type = "Negative Control"
+            elif "2220" in desc_lower:
+                sample_type = "Positive Control"
+            elif "phi" in desc_lower:
+                sample_type = "PhiX"
+            else:
+                sample_type = "Library"
+
+            sample = well.get_sample(app_state)
+            sample.sample_type = sample_type
+
+        return app_state, plate
 
 
 

utils/warning_utils.py

@@ -12,7 +12,17 @@ def collect_missing_sample_warnings(app_state):
         # Tab label, just like in UI
         tab_name = f"Tapestation-{tapestation_index} ({plate.plate_id})"
         tapestation_index += 1
-        missing = [w for w in plate.plate_wells if getattr(w, "well_note", None) in ("No sample found", "Multiple samples found")]
+
+        missing = []
+        for w in plate.plate_wells:
+            sample = w.get_sample(app_state)
+            sample_type = getattr(sample, "sample_type", None)
+            if (
+                getattr(w, "well_note", None) in ("No sample found", "Multiple samples found")
+                and sample_type in ("Library", "Positive Control")
+            ):
+                missing.append(w)
+
         if missing:
             for note in set(w.well_note for w in missing):
                 wells = [w.well_position_id for w in missing if w.well_note == note]