david-andrew

$ python -m graphrag.graphrag
Successfully loaded graph @ /home/david/dev/adhoc-api/graphrag/cbioportal from disk.
>>> 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 certain database or source?'}

david-andrew

>>> for the PDC api, can you ask if there are any fields necessary for various requests that look like they might be drawn from a fixed enumerated set of values? Not things like case IDs which do have a fixed set of values--but are always changing. But rather other parameters used to filter for data that are likely to have a stable set of fixed possible values
thought: I need to list the available APIs to find the PDC API and then ask about the fields 
that might be drawn from a fixed enumerated set of values.
tool: AdhocApi.list_apis
tool_input: None

observation: {'Proteomic Data Commons': {'description': "The Proteomics Data Commons (PDC) is a
comprehensive, open-access resource that stores,\nmanages, and shares large-scale proteomic 
data for cancer and other biomedical research.\nIt is part of the National Cancer Institute's 
broader data ecosystem, enabling researchers\nto access and analyze proteomic datasets, 

david-andrew

>>> From the Proteomic Data Commons, use the api tool to download a metadata file with information about proteome protein assembly data files from primary tumor samples. Exclude any disqualified cases and specimens.
thought: First, I need to list the available APIs to find the Proteomic Data Commons API.
tool: AdhocApi.list_apis
tool_input: None

observation: {'Proteomic Data Commons': {'description': "The Proteomics Data Commons (PDC) is a comprehensive, open-access resource that stores,\nmanages, and shares large-scale proteomic 
data for cancer and other biomedical research.\nIt is part of the National Cancer Institute's broader data ecosystem, enabling researchers\nto access and analyze proteomic datasets, including
mass spectrometry data and related\nmetadata. The PDC supports integrative research by providing standardized data formats\nand analysis tools, facilitating the discovery of protein 
biomarkers and insights into\ncancer biology, which helps in advancing personalized medicine and treatment appr

david-andrew

>>> From the Proteomic Data Commons site, use the api tool to download the biospecimen metadata for specimens with processed mass spectra data from patients with endometrial cancer.
thought: I need to list the available APIs to find the one related to the Proteomic Data Commons.
tool: AdhocApi.list_apis
tool_input: None

observation: {'Proteomic Data Commons': {'description': "The Proteomics Data Commons (PDC) is a comprehensive, open-access resource that stores,\nmanages, and shares large-scale proteomic 
data for cancer and other biomedical research.\nIt is part of the National Cancer Institute's broader data ecosystem, enabling researchers\nto access and analyze proteomic datasets, including
mass spectrometry data and related\nmetadata. The PDC supports integrative research by providing standardized data formats\nand analysis tools, facilitating the discovery of protein 
biomarkers and insights into\ncancer biology, which helps in advancing personalized medicine and treatment approaches.\n"}}

david-andrew

>>> what apis are available?
thought: I will list all the available APIs to provide the user with the information they need.
tool: AdhocApi.list_apis
tool_input: None

observation: {'Proteomic Data Commons': {'description': "The Proteomics Data Commons (PDC) is a comprehensive, open-access resource that stores,\nmanages, and shares large-scale proteomic 
data for cancer and other biomedical research.\nIt is part of the National Cancer Institute's broader data ecosystem, enabling researchers\nto access and analyze proteomic datasets, including
mass spectrometry data and related\nmetadata. The PDC supports integrative research by providing standardized data formats\nand analysis tools, facilitating the discovery of protein 
biomarkers and insights into\ncancer biology, which helps in advancing personalized medicine and treatment approaches.\n"}}

david-andrew

>>> On the Proteomic Data Commons site, find the number of clinical cases with Hepatocellular Carcinoma
thought: I need to find an API related to the Proteomic Data Commons to retrieve information about clinical cases with Hepatocellular Carcinoma.
tool: AdhocApi.list_apis
tool_input: None

observation: {'Proteomic Data Commons': {'description': "The Proteomics Data Commons (PDC) is a comprehensive, open-access resource that stores,\nmanages, and shares large-scale proteomic 
data for cancer and other biomedical research.\nIt is part of the National Cancer Institute's broader data ecosystem, enabling researchers\nto access and analyze proteomic datasets, including
mass spectrometry data and related\nmetadata. The PDC supports integrative research by providing standardized data formats\nand analysis tools, facilitating the discovery of protein 
biomarkers and insights into\ncancer biology, which helps in advancing personalized medicine and treatment approaches.\n"}}

david-andrew

import requests
from bs4 import BeautifulSoup
from collections import defaultdict
# from markdownify import markdownify as md
from weasyprint import HTML
from tqdm import tqdm
from enum import Enum


import pdb

david-andrew

>>> can you help me do a geo power analysis
⠙ thinking...[2024-08-23 11:05:30,632] {_client.py:1026} INFO - HTTP Request: POST https://api.openai.com/v1/chat/completions "HTTP/1.1 200 OK"
thought: I need to gather the necessary parameters for the geo power analysis.
tool: geo_power_api
tool_input: {'data': {}}

observation: {'1_user_inputs': {'application': 'power', 'latitude': None, 'Longitude': None, 'subsurface favorability': 1.0, 'surface favorability': 1.0, 'geothermal gradient': 74.0, 'Surface
Temperature': 25.0, 'Depth to Basement': 4.7, 'Production Temperature': 150.0, 'Derisking Time': 1, 'Production Well Count': 5, 'Discount Rate': 9.0, 'Mass Flow Rate / Well': 50.0, 'Linear 
Temperature Decline': 1.0, 'Sedimentary Drilling Cost Adjuster': 100.0, 'Basement Drilling Cost Multiplier': 1.2, 'Horizontal Well Length': 1000.0, 'Capital Expenditure Subsidy': 0.0, 'Annual
Fixed OPEX as % of Total CAPEX': 2.0, 'Wells and Plant Construction Time': 2, 'Power Plant Efficiency Increase Over Baseline': 0.0, 'Powe

david-andrew

>>> what kind of analysis can you help me with?
⠸ thinking...[2024-08-13 12:20:07,022] {_client.py:1026} INFO - HTTP Request: POST https://api.openai.com/v1/chat/completions "HTTP/1.1 200 OK"
thought: I need to provide the user with information about the types of analysis that can be 
performed using the geo_power_api.
tool: final_answer
tool_input: I can help you with various types of geothermal energy analysis, including but not 
limited to: assessing geothermal potential, evaluating the feasibility of geothermal projects, 
analyzing geothermal resource data, and providing insights into geothermal energy production. 
If you have specific data or a particular question in mind, please provide the details, and I 
can assist you further.

david-andrew

import timeit
import random

# Class definitions
class Class0: pass
class Class1: pass
class Class2: pass
class Class3: pass
class Class4: pass