APICall Case Study - Notebook

VueGen is a tool that automates the creation of reports from bioinformatics outputs, allowing researchers with minimal coding experience to communicate their results effectively. An overview of the VueGen workflow is shown below:

This case study focuses on the APICall component, which enables interaction with external APIs by using HTTP methods such as GET and POST. The retrieved data is displayed in the report, allowing users to integrate external data sources into their anlyses. This component is restricted to Streamlit reports.

For general VueGen usage examples, see the predefined directory and earth microbiome case study notebooks.

Notebook structure

First, we will set up the work environment by installing the necessary packages and importing the required libraries. Next, we will create APICall components with different HTTP methods. Finally, we will create a Streamlit report with sections for the APICall components with the different HTTP methods.

0. Work environment setup

1. APICall component

2. Streamlit report generation

Credits and Contributors

• This notebook was created by Sebastián Ayala-Ruano under the supervision of Henry Webel and Alberto Santos, head of the Multiomics Network Analytics Group (MoNA) at the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain).

• You can find more details about the project in this GitHub repository.

• Part of the code from the APICall section was adapated from this blog post.

0. Work environment setup

0.1. Installing libraries and creating global variables for platform and working directory

To run this notebook locally, you should create a virtual environment with the required libraries. If you are running this notebook on Google Colab, everything should be set.

# Vuegen library
%pip install vuegen

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Note: you may need to restart the kernel to use updated packages.

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import os

IN_COLAB = "COLAB_GPU" in os.environ

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# Optional library to launch a streamlit app from colab
if IN_COLAB:
    !npm install localtunnel

0.2. Importing libraries

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# Imports
import yaml
from vuegen import report_generator

if IN_COLAB:
    import urllib

0.3. Helper functions

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def save_yaml_config(config, path):
    def multiline_str_handler(dumper, data):
        if "\n" in data:
            return dumper.represent_scalar(
                "tag:yaml.org,2002:str", data.strip() + "\n", style="|"
            )
        return dumper.represent_scalar("tag:yaml.org,2002:str", data)

    yaml.add_representer(str, multiline_str_handler)

    with open(path, "w") as f:
        yaml.dump(config, f, sort_keys=False, default_flow_style=False)

1. APICall component

To test the different HTTP methods of the APICall component, we will use the JSONPlaceholder API as a mock API. This API provides fake data for testing and prototyping.

First, we create a basic config file for the report with general information like the title and description. Then, we create an APICall component for each HTTP method: GET, POST, PUT, and DELETE. Each component will interact with the JSONPlaceholder API and display the results in the report.

# Let's create a dictionary with a minimal config
config = {
    "report": {
        "title": "VueGen APICall Case Study",
        "description": "This report demonstrates how to use the apicall component in VueGen",
    },
    "sections": [
        {
            "title": "API Examples",
            "subsections": [{"title": "Basic HTTP Methods", "components": []}],
        }
    ],
}

1.1. GET Request

The GET method retrieves data from an API endpoint. Below, we configure a simple GET request to fetch a todo item from JSONPlaceholder API.

get_component = {
    "title": "GET request",
    "component_type": "apicall",
    "api_url": "https://jsonplaceholder.typicode.com/todos/1",
    "method": "GET",
}

config["sections"][0]["subsections"][0]["components"].append(get_component)
print("✅ GET request added.")

✅ GET request added.

1.2. POST Request

The POST method sends new data to an API. Here we simulate adding a new todo item.

post_component = {
    "title": "POST request",
    "component_type": "apicall",
    "api_url": "https://jsonplaceholder.typicode.com/todos",
    "method": "POST",
    "request_body": """{
  "userId": 1,
  "title": "Go running",
  "completed": false
}""",
}

config["sections"][0]["subsections"][0]["components"].append(post_component)
print("✅ POST request added.")

✅ POST request added.

1.3. PUT Request

The PUT method replaces an existing resource with new data. Here we update a todo item completely.

put_component = {
    "title": "PUT request",
    "component_type": "apicall",
    "api_url": "https://jsonplaceholder.typicode.com/todos/10",
    "method": "PUT",
    "request_body": """
{
  "userId": 1,
  "title": "Play the guitar",
  "completed": true
}
""",
}

config["sections"][0]["subsections"][0]["components"].append(put_component)
save_yaml_config(config, "apicall_config.yaml")
print("✅ PUT request added.")

✅ PUT request added.

1.4. PATCH Request

The PATCH method updates part of an existing resource. Below, we only update the title of a todo item.

patch_component = {
    "title": "PATCH request",
    "component_type": "apicall",
    "api_url": "https://jsonplaceholder.typicode.com/todos/10",
    "method": "PATCH",
    "request_body": """
{
  "title": "Go for a hike"
}
""",
}

config["sections"][0]["subsections"][0]["components"].append(patch_component)
print("✅ PATCH request added.")

✅ PATCH request added.

1.5. DELETE Request

The DELETE method removes a resource. Here’s how to delete a todo item.

delete_component = {
    "title": "DELETE request",
    "component_type": "apicall",
    "api_url": "https://jsonplaceholder.typicode.com/todos/10",
    "method": "DELETE",
}

config["sections"][0]["subsections"][0]["components"].append(delete_component)
print("✅ DELETE request added.")

✅ DELETE request added.

1.6. Save the report config file

# Save the report config file
config_path = "apicall_config.yaml"
save_yaml_config(config, config_path)

2. Streamlit report generation

You now have a complete configuration file with all 5 basic HTTP methods. You can run VueGen with this config to see it in action.

Note: To launch the Streamlit web application from Colab, open the generated URL and copy the localtunnel entry point IP into the corresponding field on the opened page. Once submited, you will be redirected to your Streamlit web application.

# Generate the report
report_type = "streamlit"
_ = report_generator.get_report(
    config_path=config_path, report_type=report_type, logger=None
)

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[2026-02-10 13:04:44,188] vuegen: INFO - Path to log file: logs/2026-02-10_13-04-44_report.log
[2026-02-10 13:04:44,195] vuegen: INFO - Report 'VueGen APICall Case Study' initialized with 1 sections.
[2026-02-10 13:04:44,196] vuegen: INFO - running in a normal Python process
[2026-02-10 13:04:44,197] vuegen: DEBUG - Generating 'streamlit' report in directory: 'streamlit_report/sections'
[2026-02-10 13:04:44,198] vuegen: INFO - Created output directory: 'streamlit_report/sections'
[2026-02-10 13:04:44,201] vuegen: INFO - Created output directory for static content: 'streamlit_report/static'
[2026-02-10 13:04:44,201] vuegen: DEBUG - Processing app navigation code.
[2026-02-10 13:04:44,202] vuegen: DEBUG - Processing home section.
[2026-02-10 13:04:44,205] vuegen: DEBUG - Created home directory: streamlit_report/sections/Home
[2026-02-10 13:04:44,205] vuegen: INFO - Home page content written to 'streamlit_report/sections/Home/Homepage.py'.
[2026-02-10 13:04:44,206] vuegen: INFO - Home page added to the report manager content.
[2026-02-10 13:04:44,208] vuegen: DEBUG - Created section directory: streamlit_report/sections/API_Examples
[2026-02-10 13:04:44,210] vuegen: INFO - Created app navigation script: report_manager.py
[2026-02-10 13:04:44,211] vuegen: INFO - Starting to generate sections for the report.
[2026-02-10 13:04:44,212] vuegen: DEBUG - Processing section '1': 'API Examples' - 1 subsection(s)
[2026-02-10 13:04:44,213] vuegen: DEBUG - Processing subsection '1': 'Basic HTTP Methods' - 5 component(s)
[2026-02-10 13:04:44,214] vuegen: INFO - Making GET request to API: https://jsonplaceholder.typicode.com/todos/1
[2026-02-10 13:04:44,216] vuegen: DEBUG - Headers: {}
[2026-02-10 13:04:44,217] vuegen: DEBUG - Params: {}
[2026-02-10 13:04:44,285] vuegen: INFO - Request successful with status code 200.
[2026-02-10 13:04:44,289] vuegen: INFO - Successfully generated content for APICall 'GET request' using method 'GET'
[2026-02-10 13:04:44,291] vuegen: INFO - Making POST request to API: https://jsonplaceholder.typicode.com/todos
[2026-02-10 13:04:44,292] vuegen: DEBUG - Headers: {}
[2026-02-10 13:04:44,292] vuegen: DEBUG - Params: {}
[2026-02-10 13:04:44,374] vuegen: INFO - Request successful with status code 201.
[2026-02-10 13:04:44,377] vuegen: INFO - Successfully generated content for APICall 'POST request' using method 'POST'
[2026-02-10 13:04:44,378] vuegen: INFO - Making PUT request to API: https://jsonplaceholder.typicode.com/todos/10
[2026-02-10 13:04:44,380] vuegen: DEBUG - Headers: {}
[2026-02-10 13:04:44,381] vuegen: DEBUG - Params: {}
[2026-02-10 13:04:44,512] vuegen: INFO - Request successful with status code 200.
[2026-02-10 13:04:44,515] vuegen: INFO - Successfully generated content for APICall 'PUT request' using method 'PUT'
[2026-02-10 13:04:44,517] vuegen: INFO - Making PATCH request to API: https://jsonplaceholder.typicode.com/todos/10
[2026-02-10 13:04:44,518] vuegen: DEBUG - Headers: {}
[2026-02-10 13:04:44,519] vuegen: DEBUG - Params: {}
[2026-02-10 13:04:44,597] vuegen: INFO - Request successful with status code 200.
[2026-02-10 13:04:44,600] vuegen: INFO - Successfully generated content for APICall 'PATCH request' using method 'PATCH'
[2026-02-10 13:04:44,602] vuegen: INFO - Making DELETE request to API: https://jsonplaceholder.typicode.com/todos/10
[2026-02-10 13:04:44,604] vuegen: DEBUG - Headers: {}
[2026-02-10 13:04:44,604] vuegen: DEBUG - Params: {}
[2026-02-10 13:04:44,683] vuegen: INFO - Request successful with status code 200.
[2026-02-10 13:04:44,686] vuegen: INFO - Successfully generated content for APICall 'DELETE request' using method 'DELETE'
[2026-02-10 13:04:44,688] vuegen: INFO - Generated content and imports for subsection: 'Basic HTTP Methods'
[2026-02-10 13:04:44,689] vuegen: INFO - Subsection file created: 'streamlit_report/sections/API_Examples/Basic_HTTP_Methods.py'
[2026-02-10 13:04:44,691] vuegen: INFO - All the scripts to build the Streamlit app are available at streamlit_report/sections
[2026-02-10 13:04:44,693] vuegen: INFO - To run the Streamlit app, use the following command:
[2026-02-10 13:04:44,694] vuegen: INFO - streamlit run streamlit_report/sections/report_manager.py

All the scripts to build the Streamlit app are available at: streamlit_report/sections

To run the Streamlit app, use the following command:

	streamlit run streamlit_report/sections/report_manager.py

run_streamlit = False
# run_streamlit = True  # uncomment line to run the streamlit report
# Launch the Streamlit report depneding on the platform
if not IN_COLAB and run_streamlit:
    !streamlit run streamlit_report/sections/report_manager.py
elif run_streamlit:
    # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399
    print(
        "Password/Enpoint IP for localtunnel is:",
        urllib.request.urlopen("https://ipv4.icanhazip.com")
        .read()
        .decode("utf8")
        .strip("\n"),
    )
    # Run the Streamlit app in the background
    !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &
    # Expose the Streamlit app on port 8501
    !npx localtunnel --port 8501 --subdomain vuegen-demo
else:
    print("Streamlit report not executed, set run_streamlit to True to run the report")

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Streamlit report not executed, set run_streamlit to True to run the report