improved cache handling & user feedback

bihealth · Oct 29, 2019 · 4137afd · 4137afd
1 parent 0befa91
commit 4137afd
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Showing 17 changed files with 304 additions and 138 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,13 @@
 History
 =======
 
+------
+v0.7.1
+------
+
+- improved cache handling
+- improved user feedback for filtering & differential expression
+
 ------
 v0.7.0
 ------

diff --git a/README.rst b/README.rst
@@ -25,7 +25,7 @@ SCelVis: Easy Single-Cell Visualization
 
 |
 
-.. image:: scelvis/assets/movie.gif
+.. image:: tutorial/scelvis_movie.gif
     :height: 400px
     :align: center
 
@@ -216,6 +216,7 @@ You can use the following environment variables to configure the server.
 - ``SCELVIS_CACHE_DIR`` -- directory to use for the cache (default is to create a temporary directory)
 - ``SCELVIS_CACHE_REDIS_URL`` -- enable caching with REDIS and provide connection URL
 - ``SCELVIS_CACHE_DEFAULT_TIMEOUT`` -- cache lifetime coverage
+- ``SCELVIS_CACHE_PRELOAD_DATA`` -- will preload all data at startup
 - ``SCELVIS_UPLOAD_DIR`` -- the directory to store uploaded data sets in (default is to create a temporary directory)
 - ``SCELVIS_UPLOAD_DISABLED`` -- set to "0" to disable upload feature
 - ``SCELVIS_CONVERSION_DISABLED`` -- set to "0" to disable the conversion feature

diff --git a/scelvis/app.py b/scelvis/app.py
@@ -51,15 +51,21 @@
 # Setup the cache.
 cache.setup_cache(app)
 
+# preload data if required
+if settings.CACHE_PRELOAD_DATA:
+    from . import store
+
+    logger.info("preloading data ...")
+    store.load_all_metadata()
+    logger.info("preloading done.")
+
 # Set app title
 app.title = "SCelVis v%s" % __version__
 
 # Serve assets locally
 app.css.config.serve_locally = True
 app.scripts.config.serve_locally = True
 
-# TODO: Better use the approach from this URL:
-# - https://community.plot.ly/t/dynamic-controls-and-dynamic-output-components/5519
 app.config.suppress_callback_exceptions = True
 
 # Setup the application's main layout.
@@ -75,13 +81,12 @@
 callbacks.register_select_cell_plot_type(app)
 callbacks.register_update_cell_scatter_plot_params(app)
 callbacks.register_toggle_select_cells_controls(app)
-callbacks.register_update_select_cells_choices(app)
+callbacks.register_update_select_cells_selected(app)
 callbacks.register_activate_select_cells_buttons(app)
 callbacks.register_update_cell_violin_plot_params(app)
 callbacks.register_update_cell_bar_chart_params(app)
 callbacks.register_toggle_filter_cells_controls(app, "meta")
-callbacks.register_update_filter_cells_controls(app, "meta")
-
+callbacks.register_update_filter_cells_controls(app)
 
 # Cellbacks for the "genes" tab pane.
 callbacks.register_select_gene_plot_type(app)
@@ -90,7 +95,6 @@
 callbacks.register_select_gene_violin_plot(app)
 callbacks.register_select_gene_dot_plot(app)
 callbacks.register_toggle_filter_cells_controls(app, "expression")
-callbacks.register_update_filter_cells_controls(app, "expression")
 
 # callbacks for the filter cells div (on "cells" tab pane, but required for both)
 callbacks.register_update_filter_cells_filters(app)
@@ -116,9 +120,6 @@ def find(name, path):
             if name in files:
                 return os.path.join(root, name)
 
-    # TODO: error handling, error handling, error handling
-    # TODO: prettify the form
-    # TODO: protect against "zip bomb"
     if request.method == "POST":
         if "file" not in request.files or not request.files["file"].filename:
             flash("No file uploaded!")
@@ -185,7 +186,6 @@ def find(name, path):
                     out_file, mimetype="application/binary", as_attachment=True
                 )
     else:
-        # TODO: prettify HTML form
         return """
             <!doctype html>
             <title>Convert File</title>

diff --git a/scelvis/assets/cells.png b/scelvis/assets/cells.png
diff --git a/scelvis/assets/genes.png b/scelvis/assets/genes.png
diff --git a/scelvis/assets/movie.gif b/scelvis/assets/movie.gif
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,6 +2,13 @@ @@
     History
     =======
+    ------
+    v0.7.1
+    ------
+    - improved cache handling
+    - improved user feedback for filtering & differential expression
     ------
     v0.7.0
     ------
@@ Expand Down @@