Category: prophet-api

Hi Team,

We’ll enhance our last post on Covid-19 prediction & try to capture them in a real-time dashboard, where the values in the visual display points will be affected as soon as the source data changes. In short, this is genuinely a real-time visual dashboard displaying all the graphs, trends depending upon the third-party API source data change.

However, I would like to share the run before we dig deep into this.

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Architecture:

Let us understand the architecture for this solution –

From the above diagram, one can see that we’re maintaining a similar approach compared to our last initiative. However, we’ve used a different framework to display the data live.

To achieve this, we’ve used a compelling python-based framework called Dash. Other than that, we’ve used Ably, Plotly & Prophet API.

If you need to know more about our last post, please visit this link.

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Package Installation:

Let us understand the sample packages that require for this task.

Step – 1:

Step – 2:

Step – 3:

Step – 4:

And, here is the command to install those packages –

pip install pandas
pip install plotly
pip install prophet
pip install dash
pip install pandas
pip install ably

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Code:

Since this is an extension to our previous post, we’re not going to discuss other scripts, which we’ve already discussed over there. Instead, we will talk about the enhanced scripts & the new scripts that require for this use case.

1. clsConfig.py ( This native Python script contains the configuration entries. )

A few of the new entries, which are essential to this task are -> ABLY_ID & FinData.

2. clsPublishStream.py ( This script will publish the data transformed for Covid-19 predictions from the third-party sources. )

We’ve already discussed this script. The only new line that appears here is –

json_data = [{'Year_Mon': '201911', 'Brazil': 0.0, 'Canada': 0.0, 'Germany': 0.0, 'India': 0.0, 'Indonesia': 0.0, 'UnitedKingdom': 0.0, 'UnitedStates': 0.0, 'Status': flg},
            {'Year_Mon': '201912', 'Brazil': 0.0, 'Canada': 0.0, 'Germany': 0.0, 'India': 0.0, 'Indonesia': 0.0, 'UnitedKingdom': 0.0, 'UnitedStates': 0.0, 'Status': flg}]

This statement is more like a dummy feed, which creates the basic structure of your graph.

3. clsStreamConsume.py ( This script will consume the stream from Ably Queue configuration entries. )

We’ve already discussed this script in one of my earlier posts, which you will get here.

So, I’m not going to discuss all the steps in detail.

The only added part was to introduce some temporary local caching mechanism.

if df_conv.empty:
    df_conv = p.read_csv(fileName, index = True)
else:
    l.logr(fileName, debug_ind, df_conv, 'log')

4. callPredictCovidAnalysisRealtime.py ( Main calling script to fetch the COVID-19 data from the third-party source & then publish it to the Ably message queue after transforming the data & adding the prediction using Facebook’s prophet API. )

Let us understand the enhancement part of this script –

We’ve taken out the plotly part as we will use a separate dashboard script to visualize the data trend.

However, we need to understand the initial consumed data from API & how we transform the data, which will be helpful for visualization.

The initial captured data should look like this after extracting only the relevant elements from the API response.

As you can see that based on the country & reported date, our application is consuming attributes like Total-Reported-Death, Total-Recovered, New-death, New-Confirmed & so on.

From this list, we’ve taken two attributes for our use cases & they are New-Death & New-Confirmed. Also, we’re predicting the Future-New-Death & Future-New-Confirmed based on the historical data using Facebook’s prophet API.

And, we would be transposing them & extract the countries & put them as columns for better representations.

Hence, here is the code that we should be exploring –

def toPivot(inDF, colName):
    try:
        iDF = inDF

        iDF_Piv = iDF.pivot_table(colName, ['ReportedDate'], 'Country')
        iDF_Piv.reset_index( drop=False, inplace=True )

        list1 = ['ReportedDate']

        iDF_Arr = iDF['Country'].unique()
        list2 = iDF_Arr.tolist()

        listV = list1 + list2

        iDF_Piv.reindex([listV], axis=1)

        return iDF_Piv
    except Exception as e:
        x = str(e)
        print(x)

        df = p.DataFrame()

        return df

Now, using the pivot_table function, we’re transposing the row values into the columns. And, later we’ve realigned the column heading as per our desired format.

However, we still have the data as per individual daily dates in this case. We want to eliminate that by removing the daypart & then aggregate them by month as shown below –

And, here is the code for that –

def toAgg(inDF, var, debugInd, flg):
    try:
        iDF = inDF
        colName = "ReportedDate"

        list1 = list(iDF.columns.values)
        list1.remove(colName)

        list1 = ["Brazil", "Canada", "Germany", "India", "Indonesia", "UnitedKingdom", "UnitedStates"]

        iDF['Year_Mon'] = iDF[colName].apply(lambda x:x.strftime('%Y%m'))
        iDF.drop(columns=[colName], axis=1, inplace=True)

        ColNameGrp = "Year_Mon"
        print('List1 Aggregate:: ', str(list1))
        print('ColNameGrp :: ', str(ColNameGrp))

        iDF_T = iDF[["Year_Mon", "Brazil", "Canada", "Germany", "India", "Indonesia", "UnitedKingdom", "UnitedStates"]]
        iDF_T.fillna(0, inplace = True)
        print('iDF_T:: ')
        print(iDF_T)

        iDF_1_max_group = iDF_T.groupby(ColNameGrp, as_index=False)[list1].sum()
        iDF_1_max_group['Status'] = flg

        return iDF_1_max_group
    except Exception as e:
        x = str(e)
        print(x)

        df = p.DataFrame()

        return df

From the above snippet we can conclude that the application is taking out the daypart & then aggregate it based on the Year_Mon attribute.

The following snippet will push the final transformed data to Ably queue –

x1 = cps.clsPublishStream()

# Pushing both the Historical Confirmed Cases
retVal_1 = x1.pushEvents(iDF1_Agg, debugInd, var, NC)

if retVal_1 == 0:
    print('Successfully historical event pushed!')
else:
    print('Failed to push historical events!')

5. dashboard_realtime.py ( Main calling script to consume the data from Ably queue & then visualize the trend. )

Let us explore the critical snippet as this is a brand new script –

external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']

app = dash.Dash(__name__, external_stylesheets=external_stylesheets)

app.layout = html.Div(
    html.Div([
        html.H1("Covid-19 Trend Dashboard",
                        className='text-center text-primary mb-4'),
        html.H5(children='''
            Dash: Covid-19 Trend - (Present Vs Future)
        '''),
        html.P("Covid-19: New Confirmed Cases:",
               style={"textDecoration": "underline"}),
        dcc.Graph(id='live-update-graph-1'),
        html.P("Covid-19: New Death Cases:",
               style={"textDecoration": "underline"}),
        dcc.Graph(id='live-update-graph-2'),
        dcc.Interval(
            id='interval-component',
            interval=5*1000, # in milliseconds
            n_intervals=0
        )
    ], className="row", style={'marginBottom': 10, 'marginTop': 10})
)

You need to understand the basics of HTML as this framework works seamlessly with it. To know more about the supported HTML, one needs to visit the following link.

def to_OptimizeString(row):
    try:
        x_str = str(row['Year_Mon'])

        dt_format = '%Y%m%d'
        finStr = x_str + '01'

        strReportDate = datetime.datetime.strptime(finStr, dt_format)

        return strReportDate

    except Exception as e:
        x = str(e)
        print(x)

        dt_format = '%Y%m%d'
        var = '20990101'

        strReportDate = datetime.strptime(var, dt_format)

        return strReportDate

The application is converting Year-Month combinations from string to date for better projection.

Also, we’ve implemented a dashboard that will refresh every five milliseconds.

def fetchEvent(var1, DInd):
    try:
        # Let's pass this to our map section
        iDF_M = x1.conStream(var1, DInd)

        # Converting Year_Mon to dates
        iDF_M['Year_Mon_Mod']= iDF_M.apply(lambda row: to_OptimizeString(row), axis=1)

        # Dropping old columns
        iDF_M.drop(columns=['Year_Mon'], axis=1, inplace=True)

        #Renaming new column to old column
        iDF_M.rename(columns={'Year_Mon_Mod':'Year_Mon'}, inplace=True)

        return iDF_M

    except Exception as e:
        x = str(e)
        print(x)

        iDF_M = p.DataFrame()

        return iDF_M

The application will consume all the events from the Ably Queue using the above snippet.

@app.callback(Output('live-update-graph-1', 'figure'),
              Input('interval-component', 'n_intervals'))
def update_graph_live(n):

We’ve implemented the callback mechanism to get the latest data from the Queue & then update the graph accordingly & finally share the updated chart & return that to our method, which is calling it.

# Routing data to dedicated DataFrame
retDFNC = retDF.loc[(retDF['Status'] == 'NewConfirmed')]

Based on the flag, we’re pushing the data into our target dataframe, from where the application will consume the data into the charts.

fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.Brazil,'type':'scatter','name':'Brazil'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.Canada,'type':'scatter','name':'Canada'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.Germany,'type':'scatter','name':'Germany'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.India,'type':'scatter','name':'India'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.Indonesia,'type':'scatter','name':'Indonesia'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.UnitedKingdom,'type':'scatter','name':'United Kingdom'},1,1)
fig.append_trace({'x':retDFNC.Year_Mon,'y':retDFNC.UnitedStates,'type':'scatter','name':'United States'},1,1)

Different country’s KPI elements are fetched & mapped into their corresponding axis to project the graph with visual details.

Same approach goes for the other graph as well.

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Run:

Let us run the application –

Dashboard:

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So, we’ve done it.

You will get the complete codebase in the following Github link.

I’ll bring some more exciting topic in the coming days from the Python verse.

Till then, Happy Avenging! 😀

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Note: All the data & scenario posted here are representational data & scenarios & available over the internet & for educational purpose only.

One more thing you need to understand is that this prediction based on limited data points. The actual event may happen differently. Ideally, countries are taking a cue from this kind of analysis & are initiating appropriate measures to avoid the high-curve. And, that is one of the main objective of time series analysis.

There is always a room for improvement of this kind of models & the solution associated with it. I’ve shown the basic ways to achieve the same for the education purpose only.