Implement metadata unification process

src/app.py

@@ -38,13 +38,14 @@
 
 def server(input, output, session: Session):
     _adata: reactive.Value[ad.AnnData] = reactive.value(None)
+    _adata_meta: reactive.Value[ad.AnnData] = reactive.value(None)
     _adata_filtered: reactive.Value[ad.AnnData] = reactive.value(None)
     _file_name = reactive.value(None)
     _distributions = reactive.value({})
     _metadata = reactive.value(pd.DataFrame)
 
-    distributions_server("distributions", _adata, _pretty_names, _distributions)
-    slider_server("sliders", _adata, _adata_filtered, _pretty_names, _distributions)
+    distributions_server("distributions", _adata_meta, _pretty_names, _distributions)
+    slider_server("sliders", _adata_meta, _adata_filtered, _pretty_names, _distributions)
     plots_server("plots", _adata_filtered, _pretty_names, _distributions)
     metadata_server("metadata", _adata, _metadata)
 
@@ -60,9 +61,20 @@ def load_adata():
         used_file = file[0]
         _file_name.set(used_file["name"])
         adata = sc.read_h5ad(used_file["datapath"])
-        calculate_qc_metrics(adata)
         _adata.set(adata)
 
+    @reactive.effect
+    def update_adata_meta():
+        adata = _adata.get()
+        metadata = _metadata.get()
+        if adata is None or metadata is None:
+            return
+        adata_meta = adata.copy()
+        adata_meta.obs = metadata.copy()
+        calculate_qc_metrics(adata_meta)
+        print("Updating adata_meta")
+        _adata_meta.set(adata_meta)
+
     @render.download(
         filename = lambda: _file_name.get().replace(".h5ad", "_filtered.h5ad"),
     )

src/metadata.py

@@ -6,10 +6,10 @@
 
 @module.ui
 def metadata_ui():
-    return ui.accordion(
-        ui.accordion_panel("Columns",
+    return ui.navset_tab(
+        ui.nav_panel("Columns",
                            ui.output_ui("column_cards")),
-        ui.accordion_panel("Preview")
+        ui.nav_panel("Preview", ui.output_data_frame("metadata_table"))
     )
 
 @module.server
@@ -44,30 +44,41 @@ def update_columns():
 
     def column_card(column: str):
         select_accession = f"select_type_{column}"
-        type_string = input[select_accession].get() if select_accession in input else None
+        type_string = input[select_accession].get() if select_accession in input else "Constant value"
         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)
+            select_concat_accession = f"select_concat_{column}"
+            included_columns = list(input[select_concat_accession].get()) if select_concat_accession in input else []
+            interface = ui.input_selectize(select_concat_accession, "Columns", _input_columns.get(), selected=included_columns, multiple=True)
         elif type_string == "Map existing":
             mapcol_accession = f"select_mapcol_{column}"
-            colselect = ui.input_select(mapcol_accession, "Column", _input_columns.get())
+            available_columns = _input_columns.get()
+            colselect = ui.input_select(mapcol_accession, "Column", available_columns)
 
-            series = adata.obs[input[mapcol_accession].get()] if mapcol_accession in input else None
+            series = adata.obs[input[mapcol_accession].get() if mapcol_accession in input else available_columns[0]]
+            unique_values = series.unique() if series is not None else []
 
             interface = ui.div(
                     colselect,
                     ui.accordion(
                         ui.accordion_panel("Mapping",
-                            *([ui.input_text(f"mapping_{column}_{col}", col, placeholder="New value") for col in series.unique()] if series is not None else [])
+                            *[ui.input_text(f"mapping_{column}_{value}", 
+                                            value, 
+                                            input[f"mapping_{column}_{value}"].get() if f"mapping_{column}_{value}" in input else "", 
+                                            placeholder="Unknown") for value in unique_values]
                     ))
                 )
+        elif type_string == "Constant value":
+            value_accession = f"select_constant_{column}"
+            existing_value = input[value_accession].get() if value_accession in input else ""
+            interface = ui.input_text(value_accession, "Value", existing_value, placeholder="Unknown")
         else:
-            interface = ui.input_text(f"input_{column}", "Value", placeholder="Unknown")
+            raise ValueError(f"Unknown type {type_string}")
 
 
         return ui.card(
@@ -94,4 +105,30 @@ def column_cards():
             add_card
         )
 
-
+    @reactive.effect
+    def update_metadata():
+        adata = _adata.get()
+        if adata is None:
+            return
+        metadata = pd.DataFrame(index=adata.obs.index)
+        for column in _all_columns.get():
+            select_accession = f"select_type_{column}"
+            type_string = input[select_accession].get() if select_accession in input else None
+            if type_string == "Concat existing columns":
+                included_columns = list(input[f"select_concat_{column}"].get()) if f"select_concat_{column}" in input else []
+                metadata[column] = adata.obs[included_columns].astype(str).apply(lambda x: "_".join(x), axis=1) if included_columns else "Unknown"
+            elif type_string == "Map existing":
+                mapcol_accession = f"select_mapcol_{column}"
+                available_columns = _input_columns.get()
+                series = adata.obs[input[mapcol_accession].get() if mapcol_accession in input else available_columns[0]]
+
+                mapping = {value: input[f"mapping_{column}_{value}"].get() for value in series.unique()}
+                metadata[column] = series.map(mapping)
+            else:
+                constant_accession = f"select_constant_{column}"
+                metadata[column] = input[constant_accession].get() if constant_accession in input else "Unknown"
+        _metadata.set(metadata)
+
+    @render.data_frame
+    def metadata_table():
+        return _metadata.get()

src/sliders.py

@@ -20,11 +20,6 @@ def slider_server(input, output, session,
                    ):
     _adata_sample = reactive.value(None)
     _prev_mads = reactive.value({})
-
-    @output
-    @render.text
-    def out():
-        return f"Click count is {_adata.get()}\n\nPretty names are {_pretty_names.get()}\n\nDistributions are {_distributions.get()}"
 
     @output
     @render.ui
@@ -60,6 +55,7 @@ def slider_filters():
 
         for col, pretty_name in pretty_names.items():
             if distributions[col]['min'] == distributions[col]['max']:
+                print(f"Skipping {col}")
                 continue
             else:
                 mads = ui.input_slider(f"{col}_mads", "MADs", 0.25, 10, 2, step=0.25)