[app] First implementation of Somatic Seeker analysis_list and `new…

…_analysis` views. Related issues: #40 and #41

app/app.py

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+#!/usr/bin/env python3
+#-*- coding: utf-8 -*-
+
+import dash
+import dash_bootstrap_components as dbc
+
+app = dash.Dash(__name__, suppress_callback_exceptions=True, external_stylesheets=[dbc.themes.BOOTSTRAP])
+server = app.server

app/apps/analysis_list.py

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+#!/usr/bin/env python3
+#-*- coding: utf-8 -*-
+
+from dash import html, dcc, dash_table
+import dash_bootstrap_components as dbc
+from dash.dependencies import Input, Output, State
+from app import app
+import pandas as pd
+from pymongo import MongoClient
+
+# Analysis list data table
+
+def load_analysis_list_df(db_name: str, collection_name: str):
+    """
+    """
+
+    # Empty dataframe
+    df = pd.DataFrame({
+        'analysis_id': [],
+        'analysis_name': [],
+        'creation_date': [],
+        'last_accession_date': [],
+        'last_update_date': [],
+        'curator_name': [],
+        'analysis_progress': [],
+        })
+
+    # Colname mapping
+    column_display_names_mapping = {
+        'analysis_id': 'Analysis ID',
+        'analysis_name': 'Analysis Name',
+        'creation_date': 'Creation Date',
+        'last_accession_date': 'Last Accession',
+        'last_update_date': 'Last Update',
+        'curator_name': 'Curator',
+        'analysis_progress': 'Progress',
+    }
+
+    c = MongoClient()
+    db = c[db_name]
+    collection = db[collection_name]
+    documents = list(collection.find())
+    if len(documents) == 0: # If no DB available or empty DB, return empty dataframe
+        return df
+    else:
+        # Update dataframe data with DB documents
+        df = pd.DataFrame(documents)[df.columns]
+        # Convert datetimes to human-readable format
+        datetime_display_format = "%Y/%m/%d (%H:%M:%S)"
+        df['creation_date'] = pd.DatetimeIndex(df['creation_date']).strftime(datetime_display_format)
+        df['last_accession_date'] = pd.DatetimeIndex(df['last_accession_date']).strftime(datetime_display_format)
+        df['last_update_date'] = pd.DatetimeIndex(df['last_update_date']).strftime(datetime_display_format)
+        # Rename colnames with display names
+        df = df.rename(column_display_names_mapping, axis=1)
+        return df
+
+analysis_list_df = load_analysis_list_df(db_name='somaticseeker', collection_name='analysis_list')
+
+analysis_list_datatable = dash_table.DataTable(
+    id='analysis_list_datatable',
+    columns=[{'name': column, 'id': column, 'deletable': False, 'renamable': False} for column in analysis_list_df.columns],
+    data=analysis_list_df.to_dict('records'),
+    filter_action="native",
+    sort_action="native",
+    sort_mode='single',
+    row_selectable='single',
+    selected_rows=[],
+    page_action='native',
+    page_current= 0,
+    page_size= 10,
+    fill_width=True,
+    export_format=None,
+    export_headers='display',
+    export_columns='visible',
+    style_table={
+        'maxHeight': '50ex',
+        'overflowY': 'scroll',
+        'overflowX': 'scroll',
+        'width': 'auto',
+        'marginLeft': '50px',
+        'marginRight': '50px',
+        'marginTop': '50px',
+        'marginBottom': '50px',
+    },
+    style_cell={'padding': '5px'},
+    style_header={
+        'backgroundColor': 'rgb(30, 30, 30)',
+        'color': 'white',
+        'fontWeight': 'bold',
+    },
+)
+
+# Buttons
+
+button_style = {
+    'marginLeft': '50px',
+    'marginRight': '0px',
+}
+
+new_analysis_button = dbc.Button(
+    "New Analysis",
+    id='new_analysis_button',
+    color="secondary",
+    href="somatic_seeker/new_analysis",
+    style=button_style,
+)
+
+view_analysis_button = dbc.Button(
+    'View Analysis',
+    id='view_analysis_button',
+    color='secondary',
+    href='somatic_seeker/view_analysis',
+    disabled=True,
+    style={'marginLeft': '10px'},
+)
+
+local_storage = dcc.Store(
+    id='local_storage',
+    storage_type='local'
+)
+
+# Callbacks
+
+@app.callback(
+    Output('analysis_list_datatable', component_property='data'),
+    Input('analysis_list_datatable', component_property='data'),
+)
+
+def update_analysis_list_df(data):
+    analysis_list_df = load_analysis_list_df(db_name='somaticseeker', collection_name='analysis_list')
+    if len(data) != len(analysis_list_df):
+        return analysis_list_df.to_dict(orient='records')
+    else:
+        return data
+
+@app.callback(
+    Output('selected_analysis', component_property='children'),
+    [
+        Input('analysis_list_datatable', component_property='data'),
+        Input('analysis_list_datatable', component_property='selected_rows'),
+    ]
+)
+
+def selected_analysis(data, selected_rows):
+    if selected_rows:
+        df = pd.DataFrame(data)
+        selected_analysis_id = df.query(f"index in {selected_rows}").to_dict('records')[0]['Analysis ID']
+        return selected_analysis_id
+
+@app.callback(
+    Output('view_analysis_button', component_property='disabled'),
+    Input('analysis_list_datatable', component_property='selected_rows'),
+)
+
+def view_analysis_button_disabled(selected_rows):
+    if selected_rows:
+        disabled = False
+    else:
+        disabled = True
+    return disabled
+
+# Layout
+
+h_style = {
+    'text-align':'left',
+    'marginLeft': '20px',
+    'marginRight': '20px',
+    'marginTop': '20px',
+    'marginBottom': '20px',
+    'fontWeight': 'bold',
+}
+
+layout = html.Div([
+    html.H1('Somatic Seeker', style=h_style),
+    html.Hr(),
+    html.H2('Analysis List', style=h_style),
+    analysis_list_datatable,
+    new_analysis_button,
+    view_analysis_button,
+    html.Div(id='selected_analysis'),
+])
+