Category: python

  • Setting an environment variable in Jupyter

    Short one. I wanted to setup an API key env variable in such a way that it’s easily available to Jupyter.

    It turns out that the easiest way is by adding it to IPython startup directly.

    You can find the path under, ~/.ipython/profile_default/startup/00-startup.py and if it’s not present, create it.

    The code that you add in this file is Python and can look in the following format:

    import os
    os.environ['MY_VAR'] = 'my_value'

    After you saved the edited file, don’t forget to restart the kernel.

    Cheers

  • Transforming from dict to separate columns

    I queried, some time ago, trace route info for IP’s in a list and took the wrong decision to save it in the following form.

    At first sight it’s not really an issue but if you want to retrieve it and create a dataframe it will look not as expected.

    Here is the actual code to separate the payload column to column defined by keys in dictionary

    import pandas as pd
    
    # Assuming 'df' is your DataFrame and 'payload' is the column containing dictionaries
    df_expanded = pd.json_normalize(trace_rt_df['payload'])
    
    # Rename columns to match original keys (optional)
    df_expanded.columns = df_expanded.columns.map(lambda x: x.split('.')[-1])
    
    # Concatenate the expanded columns with the original DataFrame
    df_final = pd.concat([trace_rt_df, df_expanded], axis=1)
    
    # Drop the original 'payload' column (optional)
    df_final.drop('payload', axis=1, inplace=True)

    After the processing the dataframe will look like

    That’s all.

    Sorin

  • Powerlifting play ground

    It’s true that I switched a little bit from this blog to Medium in hope of a larger audience but I will leave the link also here:

    https://medium.com/@sorin.tudor/powerlifting-play-ground-582c7e4da17d

    Hopefully even more analysis will come.

    Cheers!

  • Plotting unique values in a dataframe column

    Today, I began experimenting with a Kaggle dataframe for the first time. Here is the link to it: https://www.kaggle.com/datasets/open-powerlifting/powerlifting-database

    To make a long story short, if you want to plot the count for each individual column and capture the unique values of a particular column inside that dataframe, you can simply achieve it by using the following command:

    mycategory = powerlifting[powerlifting['Best3DeadliftKg'] == 140.0]
    mycategory.dropna(subset=['Country'], inplace=True)

    This allows you to filter the records that you are interested in, as well as remove the columns that have the value NAN.

    The last step involves the counting of the values for the country column and also creating a barplot:

    country_series =mycategory['Country'].value_counts()
    country_series.head(10).plot(kind='bar')

    We will select the first 10 countries in the series since the actual number of unique countries in the dataset is actually 118.

    And the plot looks like this.

    I wanted to document it because it’s an operation that I have done before, and the actual feedback from the chatbot when asked what is the solution was quite a bit more complex.

    First of all it consisted of the code to filter the values and save the definition of the bar plot to a JSON file, using vega-altair library (subject for exploration at one moment in time – https://altair-viz.github.io/) and parsing the data to create the plot.

    The first part worked without any issues, with the following piece of code:

    import altair as alt
    import pandas as pd
    
    # Assuming df is your DataFrame (from the previous example)
    
    # 1. Filter to column 'Country' and calculate unique value counts
    value_counts = mycategory['Country'].value_counts()
    
    # 2. Convert to DataFrame for plotting
    value_counts_df = pd.DataFrame({'Value': value_counts.index, 'Count': value_counts.values})
    
    # 3. Create bar plot
    chart = alt.Chart(value_counts_df).mark_bar().encode(
        x=alt.X('Value:N', axis=alt.Axis(title='Value')),
        y=alt.Y('Count:Q', axis=alt.Axis(title='Count')),
        tooltip=['Value', 'Count']
    ).properties(
        title='Value Counts for Column Country'
    )
    
    # Save the chart
    chart.save('value_counts_column_a_bar_chart.json')

    But the second part was a little bit tricky since the chatbot didn’t have a read idea of how the structure of the file was formed, suggesting:

    import plotly.graph_objects as go
    import json
    
    # Load JSON data
    with open('value_counts_column_a_bar_chart.json', 'r') as f:
        chart_data = json.load(f)
    
    # Extract data for plotting correctly, handling both nominal and quantitative data
    if 'Column Name' in chart_data['datasets'][0]['data'][0]:
        # Nominal data (e.g., categories like 'A', 'B', 'C')
        x = [d['Column Name'] for d in chart_data['datasets'][0]['data']]
        y = [d['Unique Value Count'] for d in chart_data['datasets'][0]['data']]
    else:
        # Quantitative data (e.g., numeric values)
        x = [d['Value'] for d in chart_data['datasets'][0]['data']]
        y = [d['Count'] for d in chart_data['datasets'][0]['data']]
    
    # Create Plotly bar chart
    fig = go.Figure([go.Bar(x=x, y=y)])
    
    # Customize layout (optional)
    fig.update_layout(
        title='Value Counts for Column A',
        xaxis_title='Value',
        yaxis_title='Count'
    )
    
    # Show the chart
    fig.show()
    

    If you try to compile that it will return a KeyError:0 which is cause by the index of the chart_data[datasets][0] which is not correct.

    Taking a look in the actual JSON structure you quickly find that the right key is data-85d48ef46f547bd16ab0f88b32c209fb, which bring us to the correct version:

    import plotly.graph_objects as go
    import json
    
    # Load JSON data
    with open('value_counts_column_a_bar_chart.json', 'r') as f:
        chart_data = json.load(f)
    
    # Extract data for plotting correctly, handling both nominal and quantitative data
    if 'Column Name' in chart_data['datasets']['data-85d48ef46f547bd16ab0f88b32c209fb']:
        # Nominal data (e.g., categories like 'A', 'B', 'C')
        x = [d['Column Name'] for d in chart_data['datasets']['data-85d48ef46f547bd16ab0f88b32c209fb']]
        y = [d['Unique Value Count'] for d in chart_data['datasets']['data-85d48ef46f547bd16ab0f88b32c209fb']]
    else:
        # Quantitative data (e.g., numeric values)
        x = [d['Value'] for d in chart_data['datasets']['data-85d48ef46f547bd16ab0f88b32c209fb']]
        y = [d['Count'] for d in chart_data['datasets']['data-85d48ef46f547bd16ab0f88b32c209fb']]
    
    # Create Plotly bar chart
    fig = go.Figure([go.Bar(x=x, y=y)])
    
    # Customize layout (optional)
    fig.update_layout(
        title='Value Counts for Country',
        xaxis_title='Value',
        yaxis_title='Count'
    )
    
    # Show the chart
    fig.show()

    Or even a more elegant one suggested by the LLM:

    mport plotly.graph_objects as go
    import json
    
    # Load JSON data
    with open('value_counts_column_a_bar_chart.json', 'r') as f:
        chart_data = json.load(f)
    
    # Find the correct data key within 'datasets'
    data_key = list(chart_data['datasets'].keys())[0]
    
    # Extract data for plotting correctly, handling both nominal and quantitative data
    if 'Column Name' in chart_data['datasets'][data_key][0]:
        # Nominal data (e.g., categories like 'A', 'B', 'C')
        x = [d['Column Name'] for d in chart_data['datasets'][data_key][:10]]
        y = [d['Unique Value Count'] for d in chart_data['datasets'][data_key][:10]]
    else:
        # Quantitative data (e.g., numeric values)
        x = [d['Value'] for d in chart_data['datasets'][data_key][:10]]
        y = [d['Count'] for d in chart_data['datasets'][data_key][:10]]
    
    # Create Plotly bar chart
    fig = go.Figure([go.Bar(x=x, y=y)])
    
    # Customize layout (optional)
    fig.update_layout(
        title='Value Counts for Country',
        xaxis_title='Value',
        yaxis_title='Count'
    )
    
    # Show the chart
    fig.show()

    Somewhere in the code is also a trim of the first 10 values in order to have similar outcomes. But the final plot looks like it should.

    And that my friends is a small “pill” of working with Data Analysis, assisted by a LLM.

    Cheers

  • Getting unique IP from mongoDB and use it for traceroute query

    Hi,

    Some time ago, I tried to write some python code in order to grab each unique IP from my traffic logs and trying to trace it so that We can find similar nodes which were used for the jumps.

    This is also a good exercise in order to improve the basic dataframe information and a good baseline for some explorations.

    I will put here the code so that it is available for me as reference and also maybe for you if you want to take pieces of it.

    I know that it is not optimised, but you can modify it or maybe use a chatbot to improve it.

    import pymongo
    import scapy.all as scapy
    
    myclient = pymongo.MongoClient("mongodb://localhost:27017/")
    db = myclient["mydatabase"]
    read_col = db["unique_ip"]
    write_col = db["unique_ip_trace_tcp"]
    lastid = 0
    index_last_ip = write_col.find().sort([('_id', -1)]).limit(1)
    for doc in index_last_ip:
        doc['source_ip']
        index_id = read_col.find({"payload":doc['source_ip']})
        for elem in index_id:
            lastid=elem['id']
    print(lastid)
    for i in range(lastid, read_col.count_documents({})):
        mydoc = read_col.find({ "id": i })
        for x in mydoc:
            try:  
                for element in x['payload']:
                    response = {}
                    ans, unans = scapy.traceroute(element)    
                    response['source_ip'] = element
                    payload = {}
                    for sdr,rcv in ans:
                        payload[str(sdr.ttl)]= rcv.src
                    response['payload'] = payload    
                    write_col.insert_one(response)
            except Exception as e:
                print(e)
                continue

    That would be all.

    Cheers!

  • Fixing “local issuer certificate” in Python

    I am putting this here more as a reference since this error appeared a couple of time when using urllib library.

    For example there is the classical case of

    from urllib.request import urlopen
    
    from bs4 import BeautifulSoup 
    
    
    html = urlopen('http://en.wikipedia.org/wiki/Kevin_Bacon')
    bs = BeautifulSoup(html, 'html.parser')
    for link in bs.find_all('a'):
        if 'href' in link.attrs:
            print(link.attrs['href'])

    And if you run it for the first time in your Jupyter Kernel, it will return

    URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:997)>

    The easiest way to fix it is by adding two extra lines to the code

    from urllib.request import urlopen
    import ssl
    from bs4 import BeautifulSoup 
    
    ssl._create_default_https_context = ssl._create_unverified_context
    
    html = urlopen('http://en.wikipedia.org/wiki/Kevin_Bacon')
    bs = BeautifulSoup(html, 'html.parser')
    for link in bs.find_all('a'):
        if 'href' in link.attrs:
            print(link.attrs['href'])

    The first one is to import the ssl library and the second one to actually create an unverified context.

    The interesting fact is that once this is loaded to the kernel, it will actually work even if you comment the lines and re-execute it.

    That would be all.

    Cheers!

  • Using Google Gemini to optimise my scraping code

    I wanted for Gemini to take a look on the code that I posted here

    Here is his answer:

    Absolutely! Here’s a breakdown of improvements and considerations for refining the provided web scraping code:

    Enhancements:

    • Robust Error Handling: Incorporate try-except blocks around the scraping logic and network calls. This will prevent the script from crashing due to unexpected issues like elements not being found or the website being temporarily down.
    • Optimized Waits: Replace the fixed time.sleep(2) with more precise WebDriverWait conditions. For instance, wait for specific elements that indicate successful loading. This improves efficiency.
    • Reusable Function: Convert the alcopascrap function to accept additional parameters (like wait times) for greater flexibility in various scraping scenarios.
    • Data Cleaning: Within the loop, sanitize the extracted data, removing unnecessary whitespace or non-standard characters to ensure data consistency.
    • Comments: Add clear comments to explain the purpose of different code sections, which is crucial for understanding and maintenance.

    Optimization Considerations

    • Scrolling Logic: Investigate if the website uses infinite scroll or lazy loading. If it does, adjust the scrolling logic to trigger loading of new content only when necessary.
    • Parallelism (Advanced): Consider parallelizing requests for different brands using threading or multiprocessing, especially if the scraping scope is large.

    from bs4 import BeautifulSoup
    from selenium import webdriver
    from selenium.webdriver.common.by import By
    from selenium.webdriver.support.ui import WebDriverWait
    from selenium.webdriver.support import expected_conditions as EC
    from selenium.common.exceptions import TimeoutException, NoSuchElementException
    import time
    
    def alcopascrap(brand, max_wait_time=10):
        driver = webdriver.Chrome()  
    
        try:
            driver.get(f"https://www.alcopa-auction.fr/ro/cautare?brand={brand}")
            WebDriverWait(driver, max_wait_time).until(
                EC.element_to_be_clickable((By.ID, "CybotCookiebotDialogBodyButtonAccept"))
            ).click()
    
            # Optimized scrolling (Implementation depends on the site's scrolling mechanism)
    
            list_of_cars = []
    
            ratings = soup.find_all('div',{'data-brand':brand})
            for rating in ratings:
                data = {}
                try: 
                    data['title'] = rating.find('li',{'class':'mb-2 list-group-item border-0 p-0'}).get_text().strip()
                    data['price'] = rating['data-prices']
                    data['details'] = [element.get_text().strip() for element in rating.find_all('li', {'class':'list-group-item border-0 p-0'})]
                    data['link'] = rating.find('a', {'class':'no-decoration'}).get('href')
                    list_of_cars.append(data)
                except NoSuchElementException:
                    print(f"Error processing car data in rating block: {rating}")
    
            # ... (rest of your code)
    
        except TimeoutException:
            print(f"Timeout waiting for elements on page for brand: {brand}")
        finally:
            driver.quit()
    
    alcopascrap('nissan') 
    

    It lacks a couple of lines like:

            html_source = driver.page_source
            soup = BeautifulSoup(html_source, 'html.parser')

    And

      for car in list_of_cars:
                print(car, end='\n')

    But otherwise it works like charm and it’s faster than my first implementation

    Use chatbots, they know better most of the times.

    Cheers!

  • Scraping Alcopa auction site using python

    Just for reference a small example of scrapping https://www.alcopa-auction.fr/ for new cars on specific brand.

    It can be improved a lot but just as a reference of the code.

    from bs4 import BeautifulSoup
    from selenium.webdriver.common.by import By
    from selenium.webdriver.support.ui import WebDriverWait
    from selenium.webdriver.support import expected_conditions as EC
    from selenium import webdriver
    import time
    
    # Set up a headless browser
    driver = webdriver.Chrome()  
    
    
    # Load the website with JavaScript
    def alcopascrap(brand):
    
        driver.get(f"https://www.alcopa-auction.fr/ro/cautare?brand={brand}")
    
        # Wait for JavaScript to execute (adjust wait time if needed)
        driver.implicitly_wait(180)  
    
    
        WebDriverWait(driver, 1).until(
        EC.element_to_be_clickable((By.ID, "CybotCookiebotDialogBodyButtonAccept"))
    ).click()
    
    # Get initial scroll height
        last_height = driver.execute_script("return document.body.scrollHeight")
    
        while True:
        # Scroll down
            driver.execute_script("window.scrollTo(0, document.body.scrollHeight);")
    
        # Wait for loading
            time.sleep(2)  # Adjust wait time as needed
    
        # Calculate new scroll height and compare with previous
            new_height = driver.execute_script("return document.body.scrollHeight")
            if new_height == last_height:
                break
            last_height = new_height
    
    # Get the HTML source with JavaScript modifications
        html_source = driver.page_source
    
    
    # Parse the HTML with BeautifulSoup 
        soup = BeautifulSoup(html_source, 'html.parser')
    
    #Create a list to store the data
    
        list_of_cars = []
    # Now you can use BeautifulSoup to extract the data you need
    # ...
        ratings = soup.find_all('div',{'data-brand':brand})
        for rating in ratings:
            data = {}
            data['title'] = rating.find('li',{'class':'mb-2 list-group-item border-0 p-0'}).get_text()
            data['price'] = rating['data-prices']
            data['details'] = [ element.get_text().strip() for element in rating.find_all('li',{'class':'list-group-item border-0 p-0'})]
            data['link'] = rating.find('a', {'class':'no-decoration'}).get('href')
            list_of_cars.append(data)
       
    # Print the data
        for car in list_of_cars:
            print(car, end='\n')
    
    # Close browser
    
        driver.quit()
        
    
    alcopascrap('nissan')

    As for the code description, here is the one from Github Copilot, you judge if it’s good or not.

    This Python script uses Selenium and BeautifulSoup to scrape car data from the Alcopa Auction website. Here’s a step-by-step breakdown:

    1. Import necessary libraries: BeautifulSoup for parsing HTML, Selenium for browser automation, and time for controlling the script’s timing.
    2. Set up a headless browser using Selenium’s webdriver. This script uses Chrome as the browser.
    3. Define a function alcopascrap(brand), which takes a car brand as an argument and scrapes data for that brand from the website.
    4. The function first navigates to the Alcopa Auction website’s search page for the specified brand.
    5. It waits for the page to load, then clicks the accept button on the cookie consent dialog.
    6. It then enters a loop where it continually scrolls to the bottom of the page, waits for more content to load, and repeats until no more new content is loaded. This is done to ensure all the dynamic content loaded by JavaScript is captured.
    7. After all content is loaded, it gets the page’s HTML source.
    8. It then parses the HTML using BeautifulSoup.
    9. It creates an empty list list_of_cars to store the car data.
    10. It finds all div elements with a data-brand attribute matching the specified brand. For each of these elements, it extracts the car title, price, details, and link, and stores them in a dictionary. Each dictionary is then appended to list_of_cars.
    11. It prints out the data for each car.
    12. Finally, it closes the browser.
    13. The function is then called with ‘nissan’ as the argument, so it scrapes data for Nissan cars.

    This script is a good example of how to use Selenium and BeautifulSoup together to scrape data from a website that uses JavaScript to load content.

  • Using line_profiler in Python

    Currently I am reading one of the chapters from Python Data Science Handbook and saw that there are some magic commands that can be used in IPython.

    One of them gives you the possibility to time the execution and it’s called %timeit. Going further it seems that there are other commands like %prun but it is not present in plain old Python, so I asked Gemini, the lovely chatbot, what were the alternatives. Here is his answer:

    Unfortunately, there’s no single command in standard Python that perfectly replicates the functionality of IPython’s %prun magic command. Let me explain why and provide the closest alternatives:

    What %prun Does

    IPython’s %prun offers detailed profiling of a code statement. It shows you:

    • Number of times each function was called.
    • Time spent in each function (cumulative and per-call).
    • Other profiling information

    Python Equivalents

    Here are the most common alternatives:

    1. cProfile Module:
    • Usage:
      Python
      import cProfile
      cProfile.run(‘my_function()’)
    • Provides similar profiling information to %prun.
    • Advantage: More granular control over profiling.
    1. line_profiler Module (External Install):
    • Install: pip install line_profiler
    • Usage: Decorate functions with @profile
    • Provides line-by-line profiling, showing execution time for each code line within a function.
    1. Timeit Module:
    • Best for measuring short code snippets’ execution time.
    • Not a full-fledged profiler, but useful for quick timing comparisons.

    Example: Using cProfile

    Python

    import cProfile

    def my_function():
      # Code you want to profile

    if __name__ == ‘__main__’:
        cProfile.run(‘my_function()’)

    Choosing the Right Tool

    • For general profiling: cProfile is a good starting point.
    • For line-by-line analysis: Consider line_profiler.
    • For simple timing: timeit is sufficient.

    So I tried to install line_profiler with pip, created a test py file with the example from the book

    @profile
    def sum_of_lists(N):
                total = 0
                for i in range(5):
                    L = [j ^ (j >> i) for j in range(N)]
                    total += sum(L)
                return total
    
    sum_of_lists(1000000)

    It seems like in order to grab the statistics you need to use kernprof which I likely found in my anaconda installation.

    I executed it with the following output

    kernprof -l lineprofiler_test.py 
    Wrote profile results to lineprofiler_test.py.lprof
    Inspect results with:
    python -m line_profiler -rmt "lineprofiler_test.py.lprof"
    python -m line_profiler -rmt "lineprofiler_test.py.lprof"
    Timer unit: 1e-06 s
    
    Total time: 0.906589 s
    File: lineprofiler_test.py
    Function: sum_of_lists at line 1
    
    Line #      Hits         Time  Per Hit   % Time  Line Contents
    ==============================================================
         1                                           @profile
         2                                           def sum_of_lists(N):
         3         1         21.0     21.0      0.0      total = 0
         4         6         51.0      8.5      0.0      for i in range(5):
         5         5     862782.0 172556.4     95.2          L = [j ^ (j >> i) for j in range(N)]
         6         5      43735.0   8747.0      4.8          total +=sum(L)
         7         1          0.0      0.0      0.0      return total
    
      0.91 seconds - lineprofiler_test.py:1 - sum_of_lists

    Which is kind of cool taking into consideration that we wrote in the past a lot of scripts without optimising for performance.

    Cheers

  • Merging initial data load with IP info

    Getting back to my traffic statistics project, I managed to play with aggregation of the two main collections that had the information I needed.

    First of all there is the normal code to load data from Mongo and check also the columns that can be used for the join. Which is available below

    import pandas as pd
    from pymongo import MongoClient
    
    # Connect to MongoDB
    client = MongoClient('localhost', 27017)
    db = client['mydatabase']
    traffic_init_load = db['traffic_init_load']
    unique_ip_info = db['unique_ip_info']
    
    # Read the data from MongoDB
    traffic_init_load_data = traffic_init_load.find()
    unique_ip_info_data = unique_ip_info.find()
    
    # Convert the data to a DataFrame
    traffic_init_load_df = pd.DataFrame(list(traffic_init_load_data))
    unique_ip_info_df = pd.DataFrame(list(unique_ip_info_data))
    
    traffic_init_load_columns = list(traffic_init_load_df.columns)
    unique_ip_info_columns = list(unique_ip_info_df.columns)
    
    # Print the columns
    print(traffic_init_load_columns)
    print(unique_ip_info_columns)

    After this, we can safely perform the merge and drop the _id columns

    merged_df = pd.merge(traffic_init_load_df, unique_ip_info_df, left_on='SourceIP', right_on='query')
    merged_df = merged_df.drop(['_id_x', 'query', '_id_y'], axis=1)

    Check it again and we also see that there are also two columns that are not really required: index and message which was returned by whois API. We drop those as well

    merged_df = merged_df.drop(['index', 'message'], axis=1)

    And now we are finally ready to convert it and put it back to the database

    # Convert DataFrame to a list of records
    records = merged_df.to_records(index=False)
    
    # Connect to MongoDB
    client = MongoClient('localhost', 27017)
    db = client['mydatabase']
    base_merged_data = db['base_merged_data']
    
    # Insert records into MongoDB collection
    dicts = []
    for record in records:
        record_dict = {}
        for field_name, value in zip(merged_df.columns, record):
            record_dict[field_name] = value
        dicts.append(record_dict)
    
    base_merged_data.insert_many(dicts)

    What I can tell you is that insert_many method is significantly faster than insert_one. At first I played with insert_one and it took 12 min to do the job, and with insert_many, that time was reduced to 3 min.

    That is all for today,

    Sorin