vs vanillla adhoc api

gistfile1.txt

>>> can you run code to get gene panel data?
thought: I need more information about the specific gene panel data the user is 
interested in to proceed effectively.
tool: ask_user
tool_input: {'query': 'Could you please provide more details about the gene 
panel data you are interested in? For example, are you looking for specific 
genes, a particular type of analysis, or data from a specific source?'}

Could you please provide more details about the gene panel data you are interested in? For example, are you looking for specific genes, a particular type of analysis, or data from a specific source? $ I'm just doing early exploration, I don't know what I want.
observation: I'm just doing early exploration, I don't know what I want.

thought: I need to check if there are any APIs available that provide gene panel
data or related information.
tool: list_apis
tool_input: {}

observation: {'cbioportal': {'description': "The cBioPortal for Cancer Genomics 
was originally developed at \nMemorial Sloan Kettering Cancer Center (MSK). The 
public cBioPortal \nsite is hosted by the Center for Molecular Oncology at MSK. 
The \ncBioPortal software is now available under an open source license \nvia 
GitHub. The software is now developed and maintained by a \nmulti-institutional 
team, consisting of MSK, the Dana Farber Cancer \nInstitute, Princess Margaret 
Cancer Centre in Toronto, Children's \nHospital of Philadelphia, Caris Life 
Sciences, The Hyve and SE4BIO \nin the Netherlands, and Bilkent University in 
Ankara, Turkey.\n"}}

thought: I want to understand what gene panel data is available through the 
cBioPortal API, as it might be relevant to the user's request.
tool: ask_api
tool_input: {'api': 'cbioportal', 'query': 'What gene panel data is available?'}

INFO {'api': 'cbioportal', 'ASK_API': 'What gene panel data is available?'}
observation: To get information about all available gene panels, you can use the
`/api/gene-panels` endpoint with a GET request. This endpoint will return a list
of all gene panels, including details such as their descriptions and associated 
genes. You can also specify the level of detail you want in the response using 
the `projection` query parameter, which can be set to "ID", "SUMMARY", 
"DETAILED", or "META".

thought: Calling tool 'use_api'
tool: use_api
tool_input: {'api': 'cbioportal', 'goal': 'Retrieve a list of all available gene
panels with detailed information.'}

INFO {'api': 'cbioportal', 'WRITE_CODE': 'Retrieve a list of all available gene panels with detailed information.'}
observation: import requests

base_url = "https://www.cbioportal.org/api"
endpoint = "/api/gene-panels"
params = {
    "projection": "DETAILED"
}

response = requests.get(base_url + endpoint, params=params)

if response.status_code == 200:
    gene_panels = response.json()
    for panel in gene_panels:
        print(panel)
else:
    print("Failed to retrieve gene panels:", response.status_code)

thought: Calling tool 'run'
tool: run
tool_input: {'code': 'import requests\n\nbase_url = 
"https://www.cbioportal.org/api"\nendpoint = "/api/gene-panels"\nparams = {\n   
"projection": "DETAILED"\n}\n\nresponse = requests.get(base_url + endpoint, 
params=params)\n\nif response.status_code == 200:\n    gene_panels = 
response.json()\n    for panel in gene_panels:\n        print(panel)\nelse:\n   
print("Failed to retrieve gene panels:", response.status_code)'}

observation: Failed to retrieve gene panels: 404


Error: 
Error message:
  I attempted to retrieve gene panel data from the cBioPortal API, but encountered a 404 error, indicating that the endpoint may not exist or is incorrect. Without access to the correct API endpoint or further details, I am unable to proceed with retrieving the gene panel data.

Extra details:
  Failed to retrieve gene panels: 404

>>>