Add reproducibility (#177)

* Reproducing Screening and Correlation

* Reproducing Hit Validation

* Remove checkbox changning

* Change gitignore

* Add alerts

* Resolve

.gitignore

@@ -2,7 +2,7 @@ tmp/
 **/out/
 
 # Data
-data
+./data
 data/raw/*
 !data/raw/.gitkeep
 notebooks/data

dashboard/data/json_reader.py

@@ -0,0 +1,21 @@
+import base64
+import io
+import json
+
+
+def load_data_from_json(content: str | None, name: str | None) -> dict | None:
+    if content is None:
+        return None
+    file = None
+
+    _, extension = name.split(".")
+    if extension == "json":
+        _, content_string = content.split(",")
+        decoded = base64.b64decode(content_string)
+        file = io.StringIO(decoded.decode("utf-8"))
+
+    loaded_data = None
+    if file:
+        loaded_data = json.load(file)
+
+    return loaded_data

dashboard/pages/components.py

@@ -26,6 +26,9 @@
         dcc.Store(id="report-data-hit-validation-input", storage_type="local"),
         dcc.Store(id="report-data-hit-validation-hit-browser", storage_type="local"),
         dcc.Store(id="activation-inhibition-screening-options", storage_type="local"),
+        dcc.Store(id="loaded-setings-screening", storage_type="local"),
+        dcc.Store(id="loaded-setings-correlation", storage_type="local"),
+        dcc.Store(id="loaded-setings-hit-validation", storage_type="local"),
     ],
 )
 

dashboard/pages/correlation/callbacks.py

@@ -10,8 +10,10 @@
 from dash import Input, Output, State, callback, html, no_update
 from plotly import express as px
 from plotly import graph_objects as go
+import dash_bootstrap_components as dbc
 
 from dashboard.data import validation
+from dashboard.data.json_reader import load_data_from_json
 from dashboard.data.preprocess import calculate_concentration
 from dashboard.storage import FileStorage
 from dashboard.visualization.plots import (
@@ -111,6 +113,28 @@ def on_both_files_uploaded(
     return ICON_OK, False
 
 
+def upload_settings_data(content: str | None, name: str | None) -> dict:
+    """
+    Callback for file upload. It saves the in local storage for other components.
+
+    :param content: base64 encoded file content
+    :param name: filename
+    :return: dict with loaded data
+    """
+    if not content:
+        return no_update
+    loaded_data = load_data_from_json(content, name)
+    color = "success"
+    text = "Settings uploaded successfully"
+    settings_keys = ["concentration_value", "volume_value"]
+    if loaded_data == None or not set(settings_keys).issubset(loaded_data.keys()):
+        color = "danger"
+        text = (
+            f"Invalid settings uploaded: the file should contain {settings_keys} keys."
+        )
+    return loaded_data, True, html.Span(text), color, no_update
+
+
 # === STAGE 2 ===
 
 
@@ -167,6 +191,35 @@ def on_visualization_stage_entry(
     return feature_fig, concentration_fig, report_data_correlation_plots, False
 
 
+def on_visualization_stage_entry_load_settings(
+    current_stage: int,
+    concentration: float,
+    volume: float,
+    saved_data: dict,
+) -> tuple[float, float]:
+    """
+    Callback for visualization stage entry.
+    Loads the data from local storage and update sliders value
+
+    :param current_stage: current stage index of the process
+    :param concentration: concentration slider value
+    :param volume: volume slider value
+    :return: value for concentration slider
+    :return: value for volume slider
+    """
+
+    if current_stage != 1:
+        return no_update
+
+    concentration_value = concentration
+    volume_value = volume
+    if saved_data != None:
+        concentration_value = saved_data["concentration_value"]
+        volume_value = saved_data["volume_value"]
+
+    return concentration_value, volume_value
+
+
 # === STAGE 3 ===
 
 
@@ -177,7 +230,11 @@ def on_json_generate_button_click(
     filename = (
         f"correlation_analysis_settings_{datetime.now().strftime('%Y-%m-%d')}.json"
     )
-    json_object = json.dumps(correlation_plots_report, indent=4)
+    data_to_save = {
+        "concentration_value": correlation_plots_report["concentration_value"],
+        "volume_value": correlation_plots_report["volume_value"],
+    }
+    json_object = json.dumps(data_to_save, indent=4)
     return dict(content=json_object, filename=filename)
 
 
@@ -229,6 +286,17 @@ def register_callbacks(elements, file_storage: FileStorage):
         State("user-uuid", "data"),
     )(functools.partial(on_both_files_uploaded, file_storage=file_storage))
 
+    callback(
+        Output("loaded-setings-correlation", "data"),
+        Output("alert-upload-settings-correlation", "is_open"),
+        Output("alert-upload-settings-correlation-text", "children"),
+        Output("alert-upload-settings-correlation", "color"),
+        Output("dummy-upload-settings-correlation", "children"),
+        Input("upload-settings-correlation", "contents"),
+        Input("upload-settings-correlation", "filename"),
+        prevent_initial_call=True,
+    )(functools.partial(upload_settings_data))
+
     callback(
         Output("inhibition-graph", "figure"),
         Output("concentration-graph", "figure"),
@@ -239,6 +307,16 @@ def register_callbacks(elements, file_storage: FileStorage):
         Input("volume-slider", "value"),
         State("user-uuid", "data"),
     )(functools.partial(on_visualization_stage_entry, file_storage=file_storage))
+
+    callback(
+        Output("concentration-slider", "value"),
+        Output("volume-slider", "value"),
+        Input(elements["STAGES_STORE"], "data"),
+        State("concentration-slider", "value"),
+        State("volume-slider", "value"),
+        State("loaded-setings-correlation", "data"),
+    )(functools.partial(on_visualization_stage_entry_load_settings))
+
     callback(
         Output("download-json-settings-correlation", "data"),
         Input("generate-json-button", "n_clicks"),

dashboard/pages/correlation/stages/s1_correlation_files_input.py

@@ -2,6 +2,8 @@
 
 from dashboard.pages.components import annotate_with_tooltip
 
+import dash_bootstrap_components as dbc
+
 DESC = [
     html.Span(
         """
@@ -73,6 +75,42 @@
                 ),
             ],
         ),
+        html.Div(
+            className="flex-grow-1",
+            children=[
+                html.H5("Settings File"),
+                dcc.Loading(
+                    children=[
+                        dcc.Upload(
+                            id="upload-settings-correlation",
+                            accept=".json",
+                            children=html.Div(
+                                [
+                                    "Drag and Drop or ",
+                                    html.A("Select", className="select-file"),
+                                    " Settings for correlation analysis",
+                                ]
+                            ),
+                            multiple=False,
+                            className="text-center upload-box",
+                        ),
+                        html.Div(
+                            id="dummy-upload-settings-correlation",
+                            className="p-1",
+                        ),
+                    ],
+                    type="circle",
+                ),
+                dbc.Alert(
+                    html.Div(id="alert-upload-settings-correlation-text"),
+                    id="alert-upload-settings-correlation",
+                    dismissable=True,
+                    is_open=False,
+                    duration=4000,
+                    className="m-1",
+                ),
+            ],
+        ),
     ],
 )
 

dashboard/pages/hit_validation/callbacks.py

@@ -32,6 +32,8 @@
 from dashboard.storage import FileStorage
 from dashboard.visualization.plots import plot_ic50, plot_smiles
 
+from dashboard.data.json_reader import load_data_from_json
+
 SCREENING_FILENAME = "{0}_screening_df.pq"
 HIT_FILENAME = "{0}_hit_df.pq"
 
@@ -177,6 +179,68 @@ def on_file_upload(
 )
 
 
+def upload_settings_data(
+    content: str | None,
+    name: str | None,
+    concentration_lower_bound: float,
+    concentration_upper_bound: float,
+    top_lower_bound: float,
+    top_upper_bound: float,
+) -> tuple[float, float, float, float]:
+    """
+    Callback for file upload. It update concentration lower bound,
+    concentration upper bound, top lower bound, top upper bound
+
+    :param content: base64 encoded file content
+    :param name: filename
+    :param concentration_lower_bound: concentration lower bound
+    :param concentration_upper_bound: concentration upper bound
+    :param top_lower_bound: top lower bound
+    :param top_upper_bound: top upper bound
+    :return: concentration lower bound
+    :return: concentration upper bound
+    :return: top lower bound
+    :return: top_upper_bound
+    """
+    if not content:
+        return no_update
+    loaded_data = load_data_from_json(content, name)
+    settings_keys = [
+        "concentration_lower_bound",
+        "concentration_upper_bound",
+        "top_lower_bound",
+        "top_upper_bound",
+    ]
+    if loaded_data == None or not set(settings_keys).issubset(loaded_data.keys()):
+        concentration_lower_bound_value = concentration_lower_bound
+        concentration_upper_bound_value = concentration_upper_bound
+        top_lower_bound_value = top_lower_bound
+        top_upper_bound_value = top_upper_bound
+        color = "danger"
+        text = (
+            f"Invalid settings uploaded: the file should contain {settings_keys} keys."
+        )
+
+    else:
+        concentration_lower_bound_value = loaded_data["concentration_lower_bound"]
+        concentration_upper_bound_value = loaded_data["concentration_upper_bound"]
+        top_lower_bound_value = loaded_data["top_lower_bound"]
+        top_upper_bound_value = loaded_data["top_upper_bound"]
+        color = "success"
+        text = "Settings uploaded successfully"
+
+    return (
+        concentration_lower_bound_value,
+        concentration_upper_bound_value,
+        top_lower_bound_value,
+        top_upper_bound_value,
+        True,
+        html.Span(text),
+        color,
+        no_update,
+    )
+
+
 def on_bounds_change(
     lower_bound: float, upper_bound: float
 ) -> tuple[float, float, html.Div]:
@@ -451,6 +515,24 @@ def register_callbacks(elements, file_storage: FileStorage):
         prevent_initial_call="initial_duplicate",
     )(functools.partial(on_file_upload, file_storage=file_storage))
 
+    callback(
+        Output("concentration-lower-bound-input", "value"),
+        Output("concentration-upper-bound-input", "value"),
+        Output("top-lower-bound-input", "value"),
+        Output("top-upper-bound-input", "value"),
+        Output("alert-upload-settings-hit-validation", "is_open"),
+        Output("alert-upload-settings-hit-validation-text", "children"),
+        Output("alert-upload-settings-hit-validation", "color"),
+        Output("dummy-upload-settings-hit-validation", "children"),
+        Input("upload-settings-hit-validation", "contents"),
+        Input("upload-settings-hit-validation", "filename"),
+        State("concentration-lower-bound-input", "value"),
+        State("concentration-upper-bound-input", "value"),
+        State("top-lower-bound-input", "value"),
+        State("top-upper-bound-input", "value"),
+        prevent_initial_call=True,
+    )(functools.partial(upload_settings_data))
+
     callback(
         Output("concentration-lower-bound-store", "data"),
         Output("concentration-upper-bound-store", "data"),