Implement basic column mapping functionalities

src/app.py

@@ -31,8 +31,8 @@
     ui.nav_panel("4. Download",
                  ui.download_button("download", "Download filtered data")
                  ),
-    title="Quality control for SIMBA🦁",
-    window_title="SIMBA🦁: QC"
+    title="Preprocessing for SIMBA🦁",
+    window_title="SIMBA🦁: Preprocessing"
 )
 
 

src/metadata.py

@@ -1,23 +1,34 @@
-from shiny import App, module, reactive, render, ui
+from shiny import module, reactive, render, ui
 import anndata as ad
 import pandas as pd
 
 mandatory_columns = ["batch", "cell_type", "condition", "sex", "patient", "tissue"]
 
 @module.ui
 def metadata_ui():
-    return ui.div(
-        ui.output_ui("column_cards")
+    return ui.accordion(
+        ui.accordion_panel("Columns",
+                           ui.output_ui("column_cards")),
+        ui.accordion_panel("Preview")
     )
 
 @module.server
 def metadata_server(input, output, session,
                    _adata: reactive.Value[ad.AnnData],
                    _metadata: reactive.Value[pd.DataFrame]
                    ):
+    _input_columns = reactive.value([])
     _additional_columns = reactive.value([])
     _all_columns = reactive.value(mandatory_columns)
 
+    @reactive.effect
+    def update_input_columns():
+        adata = _adata.get()
+        if adata is None:
+            return
+        categorical_columns = adata.obs.select_dtypes(include=["category"]).columns.tolist()
+        _input_columns.set(categorical_columns)
+
     @reactive.effect
     @reactive.event((input["add_column"]))
     def add_column():
@@ -30,19 +41,52 @@ def add_column():
     def update_columns():
         _all_columns.set(mandatory_columns + _additional_columns.get())
 
+
+    def column_card(column: str):
+        select_accession = f"select_type_{column}"
+        type_string = input[select_accession].get() if select_accession in input else None
+        adata = _adata.get()
+
+        if adata is None:
+            print("No adata")
+            return None
+
+        if type_string == "Concat existing columns":
+            interface = ui.input_selectize(f"select_{column}", "Columns", _input_columns.get(), multiple=True)
+        elif type_string == "Map existing":
+            mapcol_accession = f"select_mapcol_{column}"
+            series = adata.obs[input[mapcol_accession].get()] if mapcol_accession in input else None
+
+            interface = ui.div(
+                    ui.input_select(mapcol_accession, "Column", _input_columns.get()),
+                    *([ui.input_text(f"mapping_{column}_{col}", col, placeholder="New value") for col in series.unique()] if series is not None else [])
+                )
+        else:
+            interface = ui.input_text(f"input_{column}", "Value", placeholder="Unknown")
+
+
+        return ui.card(
+                    ui.card_header(column),
+                    ui.input_select(select_accession, "Type", ["Constant value", "Concat existing columns", "Map existing"], selected=type_string),
+                    interface,
+                    ui.card_footer(
+                        ui.input_action_button("remove_column", "Remove")
+                    )
+                )
+
     @render.ui
     def column_cards():
         add_card = ui.card(
             ui.card_header("Add column"),
             ui.input_text("column_name", "", placeholder="Column name"),
-            ui.input_action_button("add_column", "Add column")
+            ui.card_footer(
+                ui.input_action_button("add_column", "Add")
+            )
         )
 
         return ui.layout_columns(
-            *[ui.card(
-                    ui.card_header(column),
-                    ui.p("This is a column")
-                )
-            for column in _all_columns.get()],
+            *[column_card(column) for column in _all_columns.get()],
             add_card
         )
+
+