Serafina/execution reduction

src/app.py

@@ -1,92 +1,90 @@
-from shiny import App, reactive, ui, render, Session
-import scanpy as sc
-import os
-import tempfile
-import anndata as ad
-import pandas as pd
-
-from sliders import slider_ui, slider_server
-from distributions import distributions_server
-from plots import plots_server, plots_ui
-from metadata import metadata_server, metadata_ui
-from helpers import calculate_qc_metrics
-
-
-_pretty_names = reactive.value({
-    'total_counts': 'Total counts',
-    'n_genes_by_counts': 'Number of genes with counts',
-    'pct_counts_mt': 'Percentage of counts from mitochondrial genes',
-})
-
-
-app_ui = ui.page_navbar(
-    ui.nav_panel("1. Upload", ui.input_file("file_input", label="Upload your file", accept=".h5ad")),
-    ui.nav_panel("2. Metadata", metadata_ui("metadata")),
-    ui.nav_panel("3. Quality control",
-        ui.layout_sidebar(
-            ui.sidebar(
-                slider_ui("sliders")
-                ),
-            plots_ui("plots")
-        )
-    ),
-    ui.nav_panel("4. Download",
-                 ui.download_button("download", "Download filtered data")
-                 ),
-    title="Preprocessing for SIMBA🦁",
-    window_title="SIMBA🦁: Preprocessing"
-)
-
-
-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(None)
-
-    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)
-
-    @reactive.effect
-    def load_adata():
-        file = input["file_input"].get()
-        if file is None:
-            return
-        if len(file) > 1:
-            print("Only one file at a time")
-            return
-
-        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)
-        _adata_meta.set(adata_meta)
-
-    @render.download(
-        filename = lambda: _file_name.get().replace(".h5ad", "_filtered.h5ad"),
-    )
-    def download():
-        adata_filtered = _adata_filtered.get()
-        if adata_filtered is None:
-            return
-
-        with tempfile.NamedTemporaryFile(suffix=".h5ad", delete=False) as temp:
-            adata_filtered.write(temp.name)
-            return temp.name
-
-app = App(app_ui, server, static_assets=os.path.join(os.path.dirname(__file__), "media"))
+from shiny import App, reactive, ui, render, Session
+import scanpy as sc
+import os
+import tempfile
+import anndata as ad
+import pandas as pd
+
+from sliders import slider_ui, slider_server
+from distributions import distributions_server
+from plots import plots_server, plots_ui
+from metadata import metadata_server, metadata_ui
+from helpers import calculate_qc_metrics
+
+
+_pretty_names = reactive.value({
+    'total_counts': 'Total counts',
+    'n_genes_by_counts': 'Number of genes with counts',
+    'pct_counts_mt': 'Percentage of counts from mitochondrial genes',
+})
+
+
+app_ui = ui.page_navbar(
+    ui.nav_panel("1. Upload", ui.input_file("file_input", label="Upload your file", accept=".h5ad")),
+    ui.nav_panel("2. Metadata", metadata_ui("metadata")),
+    ui.nav_panel("3. Quality control",
+        ui.layout_sidebar(
+            ui.sidebar(
+                slider_ui("sliders")
+                ),
+            plots_ui("plots")
+        )
+    ),
+    ui.nav_panel("4. Download",
+                 ui.download_button("download", "Download filtered data")
+                 ),
+    title="Preprocessing for SIMBA🦁",
+    window_title="SIMBA🦁: Preprocessing"
+)
+
+
+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(None)
+    _calculate_metrics_bool = reactive.value(False)
+
+    distributions_server("distributions", _adata_meta, _pretty_names, _distributions)
+    slider_server("sliders", _adata, _metadata, _adata_meta, _adata_filtered, _pretty_names, _distributions, _calculate_metrics_bool)
+    plots_server("plots", _adata_filtered, _pretty_names, _distributions)
+    metadata_server("metadata", _adata, _metadata)
+
+    @reactive.effect
+    def load_adata():
+        file = input["file_input"].get()
+        if file is None:
+            return
+        if len(file) > 1:
+            print("Only one file at a time")
+            return
+
+        used_file = file[0]
+        _file_name.set(used_file["name"])
+        adata = sc.read_h5ad(used_file["datapath"])
+        _adata.set(adata)
+        _calculate_metrics_bool.set(True)
+
+    @reactive.effect
+    def update_adata_meta():
+        adata = _adata.get()
+        metadata = _metadata.get()
+        if adata is None or metadata is None:
+            return
+        _calculate_metrics_bool.set(True)
+
+    @render.download(
+        filename = lambda: _file_name.get().replace(".h5ad", "_filtered.h5ad"),
+    )
+    def download():
+        adata_filtered = _adata_filtered.get()
+        if adata_filtered is None:
+            return
+
+        with tempfile.NamedTemporaryFile(suffix=".h5ad", delete=False) as temp:
+            adata_filtered.write(temp.name)
+            return temp.name
+
+app = App(app_ui, server, static_assets=os.path.join(os.path.dirname(__file__), "media"))