david-andrew · January 16, 2025 15:23
diff --git a/gistfile1.txt b/gistfile1.txt
 $ 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?'}

 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? $ 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 understand what gene panel data is and how it can be accessed 
 programmatically to assist the user in obtaining it.
 tool: ask_api
 tool_input: {'query': 'What is gene panel data and how can it be accessed programmatically?'}

 observation: Gene panel data refers to structured information about collections of genes within
 specific panels, often used in molecular profiling contexts. This data can include identifiers 
 for molecular profiles, patients, samples, and studies, as well as flags indicating whether the
 gene panel has been profiled.

 To access gene panel data programmatically, the API provides several endpoints and methods:

 1. **Retrieve Specific Gene Panel Information:**
   - **Endpoint:** `/api/gene-panels/{genePanelId}`
   - **Method:** GET
   - **Description:** This endpoint retrieves information about a specific gene panel 
 identified by `genePanelId`. The response includes details structured according to the 
 `GenePanel` schema.

 2. **Fetch Multiple Gene Panels:**
   - **Endpoint:** `/api/gene-panels/fetch`
   - **Method:** POST
   - **Description:** This endpoint allows retrieval of information about multiple gene panels 
 by providing an array of gene panel IDs in the request body. The response returns a JSON array 
 of gene panels.

 3. **Retrieve Gene Panel Data for Specific Molecular Profiles:**
   - **Endpoint:** `/api/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch`
   - **Method:** POST
   - **Description:** This endpoint fetches gene panel data associated with a specific 
 molecular profile. The request requires a `molecularProfileId` and a JSON payload conforming to
 the `GenePanelDataFilter` schema. The response includes data structured according to the 
 `GenePanelData` schema.

 4. **Fetch Gene Panel Data Across Multiple Molecular Profiles:**
   - **Endpoint:** `/api/gene-panel-data/fetch`
   - **Method:** POST
   - **Description:** This endpoint is used to retrieve gene panel data across multiple 
 molecular profiles. The request body must adhere to the `GenePanelDataMultipleStudyFilter` 
 schema, specifying criteria for selecting the data. The response is an array of objects 
 conforming to the `GenePanelData` schema.

 These endpoints provide flexible options for accessing and analyzing gene panel data, 
 supporting both specific and broad queries across multiple studies and profiles.

 thought: Calling tool 'use_api'
 tool: use_api
 tool_input: {'goal': 'Retrieve information about available gene panels using the API.'}

 observation: import requests

 # Base URL for the API
 base_url = "https://www.cbioportal.org"

 # Function to retrieve a list of gene panels
 def get_all_gene_panels(projection="SUMMARY", page_size=10000000, page_number=0, 
 sort_by="genePanelId", direction="ASC"):
    endpoint = f"{base_url}/api/gene-panels"
    params = {
        "projection": projection,
        "pageSize": page_size,
        "pageNumber": page_number,
        "sortBy": sort_by,
        "direction": direction
    }
    response = requests.get(endpoint, params=params)
    if response.status_code == 200:
        return response.json()
    else:
        response.raise_for_status()

 # Function to retrieve information about a specific gene panel
 def get_gene_panel(gene_panel_id):
    endpoint = f"{base_url}/api/gene-panels/{gene_panel_id}"
    response = requests.get(endpoint)
    if response.status_code == 200:
        return response.json()
    else:
        response.raise_for_status()

 # Function to fetch gene panels using POST request
 def fetch_gene_panels(gene_panel_ids, projection="SUMMARY"):
    endpoint = f"{base_url}/api/gene-panels/fetch"
    headers = {"Content-Type": "application/json"}
    data = {
        "projection": projection,
        "genePanelIds": gene_panel_ids
    }
    response = requests.post(endpoint, json=data, headers=headers)
    if response.status_code == 200:
        return response.json()
    else:
        response.raise_for_status()

 # Example usage
 try:
    # Retrieve all gene panels
    all_gene_panels = get_all_gene_panels()
    print("All Gene Panels:", all_gene_panels)

    # Retrieve a specific gene panel
    specific_gene_panel = get_gene_panel("NSCLC_UNITO_2016_PANEL")
    print("Specific Gene Panel:", specific_gene_panel)

    # Fetch gene panels using POST
    fetched_gene_panels = fetch_gene_panels(["NSCLC_UNITO_2016_PANEL"])
    print("Fetched Gene Panels:", fetched_gene_panels)

 except requests.exceptions.RequestException as e:
    print(f"An error occurred: {e}")

 thought: Calling tool 'run'
 tool: run
 tool_input: {'code': 'import requests\n\n# Base URL for the API\nbase_url = 
 "https://www.cbioportal.org"\n\n# Function to retrieve a list of gene panels\ndef 
 get_all_gene_panels(projection="SUMMARY", page_size=10000000, page_number=0, 
 sort_by="genePanelId", direction="ASC"):\n    endpoint = f"{base_url}/api/gene-panels"\n    
 params = {\n        "projection": projection,\n        "pageSize": page_size,\n        
 "pageNumber": page_number,\n        "sortBy": sort_by,\n        "direction": direction\n    }\n
 response = requests.get(endpoint, params=params)\n    if response.status_code == 200:\n        
 return response.json()\n    else:\n        response.raise_for_status()\n\n# Function to 
 retrieve information about a specific gene panel\ndef get_gene_panel(gene_panel_id):\n    
 endpoint = f"{base_url}/api/gene-panels/{gene_panel_id}"\n    response = 
 requests.get(endpoint)\n    if response.status_code == 200:\n        return response.json()\n  
 else:\n        response.raise_for_status()\n\n# Function to fetch gene panels using POST 
 request\ndef fetch_gene_panels(gene_panel_ids, projection="SUMMARY"):\n    endpoint = 
 f"{base_url}/api/gene-panels/fetch"\n    headers = {"Content-Type": "application/json"}\n    
 data = {\n        "projection": projection,\n        "genePanelIds": gene_panel_ids\n    }\n   
 response = requests.post(endpoint, json=data, headers=headers)\n    if response.status_code == 
 200:\n        return response.json()\n    else:\n        response.raise_for_status()\n\n# 
 Example usage\ntry:\n    # Retrieve all gene panels\n    all_gene_panels = 
 get_all_gene_panels()\n    print("All Gene Panels:", all_gene_panels)\n\n    # Retrieve a 
 specific gene panel\n    specific_gene_panel = get_gene_panel("NSCLC_UNITO_2016_PANEL")\n    
 print("Specific Gene Panel:", specific_gene_panel)\n\n    # Fetch gene panels using POST\n    
 fetched_gene_panels = fetch_gene_panels(["NSCLC_UNITO_2016_PANEL"])\n    print("Fetched Gene 
 Panels:", fetched_gene_panels)\n\nexcept requests.exceptions.RequestException as e:\n    
 print(f"An error occurred: {e}")'}

 observation: All Gene Panels: [{'description': 'Targeted (27 cancer genes) sequencing of 
 adenoid cystic carcinomas on Illumina HiSeq sequencers.', 'genePanelId': 'ACYC_FMI_27'}, 
 {'description': 'Targeted panel of 232 genes.', 'genePanelId': 'Agilent'}, {'description': 
 'Targeted panel of 8 genes.', 'genePanelId': 'AmpliSeq'}, {'description': 'ARCHER-HEME gene 
 panel (199 genes)', 'genePanelId': 'ARCHER-HEME-CV1'}, {'description': 'ARCHER-SOLID Gene Panel
 (62 genes)', 'genePanelId': 'ARCHER-SOLID-CV1'}, {'description': 'Targeted sequencing of 
 various tumor types via bait v3.', 'genePanelId': 'bait_v3'}, {'description': 'Targeted 
 sequencing of various tumor types via bait v4.', 'genePanelId': 'bait_v4'}, {'description': 
 'Targeted sequencing of various tumor types via bait v5.', 'genePanelId': 'bait_v5'}, 
 {'description': 'Targeted panel of 387 cancer-related genes.', 'genePanelId': 
 'bcc_unige_2016_cancer_panel'}, {'description': 'Research (CMO) IMPACT-Heme gene panel version 
 3.', 'genePanelId': 'HemePACT_v3'}, {'description': 'Targeted sequencing of 18 genes via 
 Resolution ctDx Lung assay.', 'genePanelId': 'ctDx_lung_panel'}, {'description': 'Targeted 
 sequencing of 503 cancer-associated genes on Illumina HiSeq sequencers.', 'genePanelId': 
 'DFCI_504'}, {'description': 'FoundationOne Heme gene panel targets the entire coding sequence 
 of 406 genes, selected introns of 31 genes involved in rearrangements and utilizes RNA 
 sequencing to interrogate 265 genes', 'genePanelId': 'FMI-D2'}, {'description': 'FoundationOne 
 Heme gene panel targets the entire coding sequence of 406 genes, selected introns of 31 genes 
 involved in rearrangements and utilizes RNA sequencing to interrogate 265 genes', 
 'genePanelId': 'FMI-R2'}, {'description': 'Foundation Medicine T4b gene panel (214 genes)', 
 'genePanelId': 'FMI-T4b'}, {'description': 'Foundation Medicine T5a gene panel (323 genes)', 
 'genePanelId': 'FMI-T5a'}, {'description': 'Foundation Medicine T7 gene panel (429 genes)', 
 'genePanelId': 'FMI-T7'}, {'description': 'Targeted panel of 600 genes.', 'genePanelId': 
 'gbm_tcga_pub_cancer_panel'}, {'description': 'DFCI-ONCOPANEL-1 (304 genes)', 'genePanelId': 
 'glioma_dfci_2020_DFCI-ONCOPANEL-1'}, {'description': 'DFCI-ONCOPANEL-2 (326 genes)', 
 'genePanelId': 'glioma_dfci_2020_DFCI-ONCOPANEL-2'}, {'description': 'DFCI-ONCOPANEL-3 (447 
 genes)', 'genePanelId': 'glioma_dfci_2020_DFCI-ONCOPANEL-3'}, {'description': 'Foundation 
 Medicine T5 gene panel (326 genes)', 'genePanelId': 'glioma_mskcc_2019_fmi_t5'}, 
 {'description': 'Foundation Medicine T7 gene panel (434 genes)', 'genePanelId': 
 'glioma_mskcc_2019_fmi_t7'}, {'description': 'High-intensity targeted sequencing assay by GRAIL
 covering 508 genes.', 'genePanelId': 'grail_cfdna_508'}, {'description': 'Targeted variant 
 analysis from 73 cancer genes by Next-Generation (NGS)/Massively parallel sequencing (MPS).', 
 'genePanelId': 'GUARDANT_73'}, {'description': 'Targeted (400 cancer genes) sequencing of 
 various tumor types via MSK-IMPACT Heme on Illumina HiSeq sequencers.', 'genePanelId': 
 'IMPACT-HEME-400'}, {'description': 'Targeted (467 cancer genes) sequencing of various tumor 
 types via MSK-IMPACT Heme on Illumina HiSeq sequencers. Originally 468 genes with CDKN2Ap14ARF 
 and CDKN2Ap16INK4A, merged into CDKN2A.', 'genePanelId': 'IMPACT-HEME-468'}, {'description': 
 'Hotspot sequencing panel for MSK-IMPACT Heme on Illumina HiSeq sequencers (204 genes).', 
 'genePanelId': 'IMPACT-HEME-HS'}, {'description': 'Targeted sequencing of urcc tumor via 
 MSK-IMPACT.', 'genePanelId': 'IMPACT230'}, {'description': 'Targeted (279 cancer genes) 
 sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
 'IMPACT279'}, {'description': 'Targeted (300 cancer genes) sequencing of bladder urothelial 
 carcinomas via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT300'}, 
 {'description': 'Targeted (341 cancer genes) sequencing of various tumor types via MSK-IMPACT 
 on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT341'}, {'description': 'Targeted (410 
 cancer genes) sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 
 'genePanelId': 'IMPACT410'}, {'description': 'Targeted (468 cancer genes) sequencing of various
 tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT468'}, 
 {'description': 'Targeted (505 cancer genes) sequencing of various tumor types via MSK-IMPACT 
 on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT505'}, {'description': 'Targeted (152 
 genes) sequencing of MDS samples from the International Working Group (IWG) for the prognosis 
 of MDS', 'genePanelId': 'MDSIWG152'}, {'description': 'Targeted NGS of AML/MDs Samples.', 
 'genePanelId': 'Papaemmanuil_NEJM_2016_MDS_2013_panel'}, {'description': 'Targeted (173 cancer 
 genes) sequencing of breast cancers on Illumina HiSeq sequencers.', 'genePanelId': 
 'METABRIC_173'}, {'description': 'Targeted (129 genes) sequencing of cfDNA via MSK-ACCESS on 
 Illumina HiSeq sequencers.', 'genePanelId': 'ACCESS129'}, {'description': 'Targeted sequencing 
 of 15 oncogenes and tumor suppressor genes, selected for their potential as predictive 
 biomarkers of response to targeted agents by Sanger sequencing.', 'genePanelId': 
 'MSKCC_BLCA_15'}, {'description': 'Targeted (343 cancer genes, IMPACT341 plus MYB and NFIB) 
 sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
 'MYB-IMPACT341'}, {'description': 'Targeted (412 cancer genes, IMPACT410 plus MYB and NFIB) 
 sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
 'MYB-IMPACT410'}, {'description': 'Targeted (470 cancer genes, IMPACT468 plus MYB and NFIB) 
 sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
 'MYB-IMPACT468'}, {'description': 'Targeted NGS of NSCLC Samples.', 'genePanelId': 
 'NSCLC_UNITO_2016_PANEL'}, {'description': 'Targeted panel of 137 genes.', 'genePanelId': 
 'prad_mskcc_sanger'}, {'description': 'Targeted panel of 145 genes. (merge of prad_mskcc_sanger
 and prad_mskcc_sequenom)', 'genePanelId': 'prad_mskcc_sequenom_sanger'}, {'description': 
 'Targeted panel of 21 genes.', 'genePanelId': 'prad_mskcc_sequenom'}, {'description': 'Targeted
 panel for cfDNA sequencing (2 genes)', 'genePanelId': 'rbl_cfdna_msk_2020_panel'}, 
 {'description': 'Targeted sequencing of clinical cases via Thunderbolts NGS Target Enrichment 
 System, RainDance Technologies.', 'genePanelId': 'RDTB49'}, {'description': 'Targeted 
 sequencing of clinical cases via ThunderStorm NGS Target Enrichment System, RainDance 
 Technologies.', 'genePanelId': 'RDTS30'}, {'description': "A panel that's designed to target 
 all exons of 262 genes that are recurrently mutated in de novo MDS/AML (â\x80\x98RMG 
 reagentâ\x80\x99).", 'genePanelId': 'RMG'}, {'description': 'Targeted panel of 226 
 protein-coding genes.', 'genePanelId': 'sarc_mskcc_panel'}, {'description': 'Targeted deep 
 sequencing (TDS) of 1202 genes on Illumina HiSeq2000 sequencers.', 'genePanelId': 'UCLA_1202'},
 {'description': 'DNA sequencing of 622 genes with known or potential relationships to cancer.',
 'genePanelId': 'WUSTL-DFCI_623'}, {'description': 'Targeted massively parallel sequencing of 
 4047 cancer genes.', 'genePanelId': 'NOVARTIS_BROAD_1651'}, {'description': 'Foundation 
 Medicine T7 gene panel (430 cancer genes, FMI-T7 plus TERT)', 'genePanelId': 'TERT-FMI-T7'}, 
 {'description': 'FoundationOne gene panel (317 genes)', 'genePanelId': 'FoundationOne'}, 
 {'description': 'DFCI-ONCOPANEL-3.1, Number of Genes - 447', 'genePanelId': 
 'DFCI-ONCOPANEL-3.1'}, {'description': 'DFCI-ONCOPANEL-3, Number of Genes - 447', 
 'genePanelId': 'DFCI-ONCOPANEL-3'}, {'description': 'DFCI-ONCOPANEL-1, Number of Genes - 304', 
 'genePanelId': 'DFCI-ONCOPANEL-1'}, {'description': 'DFCI-ONCOPANEL-2, Number of Genes - 326', 
 'genePanelId': 'DFCI-ONCOPANEL-2'}, {'description': 'ARCHER-SOLID-CV4 Gene Panel (123 genes)', 
 'genePanelId': 'ARCHER-SOLID-CV4'}, {'description': 'Targeted panel of 262 genes.', 
 'genePanelId': 'MDAnderson_T200'}, {'description': 'Targeted panel of 476 cancer-related 
 genes.', 'genePanelId': 'sarcoma_msk_2022_panel'}]
 Specific Gene Panel: {'description': 'Targeted NGS of NSCLC Samples.', 'genes': 
 [{'entrezGeneId': 25, 'hugoGeneSymbol': 'ABL1'}, {'entrezGeneId': 207, 'hugoGeneSymbol': 
 'AKT1'}, {'entrezGeneId': 324, 'hugoGeneSymbol': 'APC'}, {'entrezGeneId': 472, 
 'hugoGeneSymbol': 'ATM'}, {'entrezGeneId': 673, 'hugoGeneSymbol': 'BRAF'}, {'entrezGeneId': 
 999, 'hugoGeneSymbol': 'CDH1'}, {'entrezGeneId': 1029, 'hugoGeneSymbol': 'CDKN2A'}, 
 {'entrezGeneId': 1956, 'hugoGeneSymbol': 'EGFR'}, {'entrezGeneId': 2064, 'hugoGeneSymbol': 
 'ERBB2'}, {'entrezGeneId': 2066, 'hugoGeneSymbol': 'ERBB4'}, {'entrezGeneId': 2263, 
 'hugoGeneSymbol': 'FGFR2'}, {'entrezGeneId': 2261, 'hugoGeneSymbol': 'FGFR3'}, {'entrezGeneId':
 2322, 'hugoGeneSymbol': 'FLT3'}, {'entrezGeneId': 6927, 'hugoGeneSymbol': 'HNF1A'}, 
 {'entrezGeneId': 3417, 'hugoGeneSymbol': 'IDH1'}, {'entrezGeneId': 3791, 'hugoGeneSymbol': 
 'KDR'}, {'entrezGeneId': 3815, 'hugoGeneSymbol': 'KIT'}, {'entrezGeneId': 3845, 
 'hugoGeneSymbol': 'KRAS'}, {'entrezGeneId': 4233, 'hugoGeneSymbol': 'MET'}, {'entrezGeneId': 
 4851, 'hugoGeneSymbol': 'NOTCH1'}, {'entrezGeneId': 5290, 'hugoGeneSymbol': 'PIK3CA'}, 
 {'entrezGeneId': 5781, 'hugoGeneSymbol': 'PTPN11'}, {'entrezGeneId': 5925, 'hugoGeneSymbol': 
 'RB1'}, {'entrezGeneId': 5979, 'hugoGeneSymbol': 'RET'}, {'entrezGeneId': 4089, 
 'hugoGeneSymbol': 'SMAD4'}, {'entrezGeneId': 6608, 'hugoGeneSymbol': 'SMO'}, {'entrezGeneId': 
 6794, 'hugoGeneSymbol': 'STK11'}, {'entrezGeneId': 7157, 'hugoGeneSymbol': 'TP53'}, 
 {'entrezGeneId': 7428, 'hugoGeneSymbol': 'VHL'}], 'genePanelId': 'NSCLC_UNITO_2016_PANEL'}
 An error occurred: 400 Client Error:  for url: https://www.cbioportal.org/api/gene-panels/fetch


 I successfully retrieved information about available gene panels using the API. Here are some highlights:

 1. **All Gene Panels:**
   - There are numerous gene panels available, each with a unique ID and description. For example, the "ACYC_FMI_27" panel targets 27 cancer genes, and the "IMPACT505" panel targets 505 cancer genes.

 2. **Specific Gene Panel:**
   - I retrieved detailed information about the "NSCLC_UNITO_2016_PANEL" gene panel, which is used for targeted NGS of NSCLC samples. This panel includes genes such as ABL1, AKT1, APC, ATM, BRAF, and many others.

 Unfortunately, there was an error when attempting to fetch gene panels using a POST request, which resulted in a 400 Client Error. This might be due to incorrect parameters or an issue with the API endpoint.

 If you have any specific gene panels or further exploration in mind, feel free to let me know!
 >>>
	$ 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?'}

	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? $ 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 understand what gene panel data is and how it can be accessed
	programmatically to assist the user in obtaining it.
	tool: ask_api
	tool_input: {'query': 'What is gene panel data and how can it be accessed programmatically?'}

	observation: Gene panel data refers to structured information about collections of genes within
	specific panels, often used in molecular profiling contexts. This data can include identifiers
	for molecular profiles, patients, samples, and studies, as well as flags indicating whether the
	gene panel has been profiled.

	To access gene panel data programmatically, the API provides several endpoints and methods:

	1. Retrieve Specific Gene Panel Information:
	- Endpoint: `/api/gene-panels/{genePanelId}`
	- Method: GET
	- Description: This endpoint retrieves information about a specific gene panel
	identified by `genePanelId`. The response includes details structured according to the
	`GenePanel` schema.

	2. Fetch Multiple Gene Panels:
	- Endpoint: `/api/gene-panels/fetch`
	- Method: POST
	- Description: This endpoint allows retrieval of information about multiple gene panels
	by providing an array of gene panel IDs in the request body. The response returns a JSON array
	of gene panels.

	3. Retrieve Gene Panel Data for Specific Molecular Profiles:
	- Endpoint: `/api/molecular-profiles/{molecularProfileId}/gene-panel-data/fetch`
	- Method: POST
	- Description: This endpoint fetches gene panel data associated with a specific
	molecular profile. The request requires a `molecularProfileId` and a JSON payload conforming to
	the `GenePanelDataFilter` schema. The response includes data structured according to the
	`GenePanelData` schema.

	4. Fetch Gene Panel Data Across Multiple Molecular Profiles:
	- Endpoint: `/api/gene-panel-data/fetch`
	- Method: POST
	- Description: This endpoint is used to retrieve gene panel data across multiple
	molecular profiles. The request body must adhere to the `GenePanelDataMultipleStudyFilter`
	schema, specifying criteria for selecting the data. The response is an array of objects
	conforming to the `GenePanelData` schema.

	These endpoints provide flexible options for accessing and analyzing gene panel data,
	supporting both specific and broad queries across multiple studies and profiles.

	thought: Calling tool 'use_api'
	tool: use_api
	tool_input: {'goal': 'Retrieve information about available gene panels using the API.'}

	observation: import requests

	# Base URL for the API
	base_url = "https://www.cbioportal.org"

	# Function to retrieve a list of gene panels
	def get_all_gene_panels(projection="SUMMARY", page_size=10000000, page_number=0,
	sort_by="genePanelId", direction="ASC"):
	endpoint = f"{base_url}/api/gene-panels"
	params = {
	"projection": projection,
	"pageSize": page_size,
	"pageNumber": page_number,
	"sortBy": sort_by,
	"direction": direction
	}
	response = requests.get(endpoint, params=params)
	if response.status_code == 200:
	return response.json()
	else:
	response.raise_for_status()

	# Function to retrieve information about a specific gene panel
	def get_gene_panel(gene_panel_id):
	endpoint = f"{base_url}/api/gene-panels/{gene_panel_id}"
	response = requests.get(endpoint)
	if response.status_code == 200:
	return response.json()
	else:
	response.raise_for_status()

	# Function to fetch gene panels using POST request
	def fetch_gene_panels(gene_panel_ids, projection="SUMMARY"):
	endpoint = f"{base_url}/api/gene-panels/fetch"
	headers = {"Content-Type": "application/json"}
	data = {
	"projection": projection,
	"genePanelIds": gene_panel_ids
	}
	response = requests.post(endpoint, json=data, headers=headers)
	if response.status_code == 200:
	return response.json()
	else:
	response.raise_for_status()

	# Example usage
	try:
	# Retrieve all gene panels
	all_gene_panels = get_all_gene_panels()
	print("All Gene Panels:", all_gene_panels)

	# Retrieve a specific gene panel
	specific_gene_panel = get_gene_panel("NSCLC_UNITO_2016_PANEL")
	print("Specific Gene Panel:", specific_gene_panel)

	# Fetch gene panels using POST
	fetched_gene_panels = fetch_gene_panels(["NSCLC_UNITO_2016_PANEL"])
	print("Fetched Gene Panels:", fetched_gene_panels)

	except requests.exceptions.RequestException as e:
	print(f"An error occurred: {e}")

	thought: Calling tool 'run'
	tool: run
	tool_input: {'code': 'import requests\n\n# Base URL for the API\nbase_url =
	"https://www.cbioportal.org"\n\n# Function to retrieve a list of gene panels\ndef
	get_all_gene_panels(projection="SUMMARY", page_size=10000000, page_number=0,
	sort_by="genePanelId", direction="ASC"):\n endpoint = f"{base_url}/api/gene-panels"\n
	params = {\n "projection": projection,\n "pageSize": page_size,\n
	"pageNumber": page_number,\n "sortBy": sort_by,\n "direction": direction\n }\n
	response = requests.get(endpoint, params=params)\n if response.status_code == 200:\n
	return response.json()\n else:\n response.raise_for_status()\n\n# Function to
	retrieve information about a specific gene panel\ndef get_gene_panel(gene_panel_id):\n
	endpoint = f"{base_url}/api/gene-panels/{gene_panel_id}"\n response =
	requests.get(endpoint)\n if response.status_code == 200:\n return response.json()\n
	else:\n response.raise_for_status()\n\n# Function to fetch gene panels using POST
	request\ndef fetch_gene_panels(gene_panel_ids, projection="SUMMARY"):\n endpoint =
	f"{base_url}/api/gene-panels/fetch"\n headers = {"Content-Type": "application/json"}\n
	data = {\n "projection": projection,\n "genePanelIds": gene_panel_ids\n }\n
	response = requests.post(endpoint, json=data, headers=headers)\n if response.status_code ==
	200:\n return response.json()\n else:\n response.raise_for_status()\n\n#
	Example usage\ntry:\n # Retrieve all gene panels\n all_gene_panels =
	get_all_gene_panels()\n print("All Gene Panels:", all_gene_panels)\n\n # Retrieve a
	specific gene panel\n specific_gene_panel = get_gene_panel("NSCLC_UNITO_2016_PANEL")\n
	print("Specific Gene Panel:", specific_gene_panel)\n\n # Fetch gene panels using POST\n
	fetched_gene_panels = fetch_gene_panels(["NSCLC_UNITO_2016_PANEL"])\n print("Fetched Gene
	Panels:", fetched_gene_panels)\n\nexcept requests.exceptions.RequestException as e:\n
	print(f"An error occurred: {e}")'}

	observation: All Gene Panels: [{'description': 'Targeted (27 cancer genes) sequencing of
	adenoid cystic carcinomas on Illumina HiSeq sequencers.', 'genePanelId': 'ACYC_FMI_27'},
	{'description': 'Targeted panel of 232 genes.', 'genePanelId': 'Agilent'}, {'description':
	'Targeted panel of 8 genes.', 'genePanelId': 'AmpliSeq'}, {'description': 'ARCHER-HEME gene
	panel (199 genes)', 'genePanelId': 'ARCHER-HEME-CV1'}, {'description': 'ARCHER-SOLID Gene Panel
	(62 genes)', 'genePanelId': 'ARCHER-SOLID-CV1'}, {'description': 'Targeted sequencing of
	various tumor types via bait v3.', 'genePanelId': 'bait_v3'}, {'description': 'Targeted
	sequencing of various tumor types via bait v4.', 'genePanelId': 'bait_v4'}, {'description':
	'Targeted sequencing of various tumor types via bait v5.', 'genePanelId': 'bait_v5'},
	{'description': 'Targeted panel of 387 cancer-related genes.', 'genePanelId':
	'bcc_unige_2016_cancer_panel'}, {'description': 'Research (CMO) IMPACT-Heme gene panel version
	3.', 'genePanelId': 'HemePACT_v3'}, {'description': 'Targeted sequencing of 18 genes via
	Resolution ctDx Lung assay.', 'genePanelId': 'ctDx_lung_panel'}, {'description': 'Targeted
	sequencing of 503 cancer-associated genes on Illumina HiSeq sequencers.', 'genePanelId':
	'DFCI_504'}, {'description': 'FoundationOne Heme gene panel targets the entire coding sequence
	of 406 genes, selected introns of 31 genes involved in rearrangements and utilizes RNA
	sequencing to interrogate 265 genes', 'genePanelId': 'FMI-D2'}, {'description': 'FoundationOne
	Heme gene panel targets the entire coding sequence of 406 genes, selected introns of 31 genes
	involved in rearrangements and utilizes RNA sequencing to interrogate 265 genes',
	'genePanelId': 'FMI-R2'}, {'description': 'Foundation Medicine T4b gene panel (214 genes)',
	'genePanelId': 'FMI-T4b'}, {'description': 'Foundation Medicine T5a gene panel (323 genes)',
	'genePanelId': 'FMI-T5a'}, {'description': 'Foundation Medicine T7 gene panel (429 genes)',
	'genePanelId': 'FMI-T7'}, {'description': 'Targeted panel of 600 genes.', 'genePanelId':
	'gbm_tcga_pub_cancer_panel'}, {'description': 'DFCI-ONCOPANEL-1 (304 genes)', 'genePanelId':
	'glioma_dfci_2020_DFCI-ONCOPANEL-1'}, {'description': 'DFCI-ONCOPANEL-2 (326 genes)',
	'genePanelId': 'glioma_dfci_2020_DFCI-ONCOPANEL-2'}, {'description': 'DFCI-ONCOPANEL-3 (447
	genes)', 'genePanelId': 'glioma_dfci_2020_DFCI-ONCOPANEL-3'}, {'description': 'Foundation
	Medicine T5 gene panel (326 genes)', 'genePanelId': 'glioma_mskcc_2019_fmi_t5'},
	{'description': 'Foundation Medicine T7 gene panel (434 genes)', 'genePanelId':
	'glioma_mskcc_2019_fmi_t7'}, {'description': 'High-intensity targeted sequencing assay by GRAIL
	covering 508 genes.', 'genePanelId': 'grail_cfdna_508'}, {'description': 'Targeted variant
	analysis from 73 cancer genes by Next-Generation (NGS)/Massively parallel sequencing (MPS).',
	'genePanelId': 'GUARDANT_73'}, {'description': 'Targeted (400 cancer genes) sequencing of
	various tumor types via MSK-IMPACT Heme on Illumina HiSeq sequencers.', 'genePanelId':
	'IMPACT-HEME-400'}, {'description': 'Targeted (467 cancer genes) sequencing of various tumor
	types via MSK-IMPACT Heme on Illumina HiSeq sequencers. Originally 468 genes with CDKN2Ap14ARF
	and CDKN2Ap16INK4A, merged into CDKN2A.', 'genePanelId': 'IMPACT-HEME-468'}, {'description':
	'Hotspot sequencing panel for MSK-IMPACT Heme on Illumina HiSeq sequencers (204 genes).',
	'genePanelId': 'IMPACT-HEME-HS'}, {'description': 'Targeted sequencing of urcc tumor via
	MSK-IMPACT.', 'genePanelId': 'IMPACT230'}, {'description': 'Targeted (279 cancer genes)
	sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
	'IMPACT279'}, {'description': 'Targeted (300 cancer genes) sequencing of bladder urothelial
	carcinomas via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT300'},
	{'description': 'Targeted (341 cancer genes) sequencing of various tumor types via MSK-IMPACT
	on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT341'}, {'description': 'Targeted (410
	cancer genes) sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.',
	'genePanelId': 'IMPACT410'}, {'description': 'Targeted (468 cancer genes) sequencing of various
	tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT468'},
	{'description': 'Targeted (505 cancer genes) sequencing of various tumor types via MSK-IMPACT
	on Illumina HiSeq sequencers.', 'genePanelId': 'IMPACT505'}, {'description': 'Targeted (152
	genes) sequencing of MDS samples from the International Working Group (IWG) for the prognosis
	of MDS', 'genePanelId': 'MDSIWG152'}, {'description': 'Targeted NGS of AML/MDs Samples.',
	'genePanelId': 'Papaemmanuil_NEJM_2016_MDS_2013_panel'}, {'description': 'Targeted (173 cancer
	genes) sequencing of breast cancers on Illumina HiSeq sequencers.', 'genePanelId':
	'METABRIC_173'}, {'description': 'Targeted (129 genes) sequencing of cfDNA via MSK-ACCESS on
	Illumina HiSeq sequencers.', 'genePanelId': 'ACCESS129'}, {'description': 'Targeted sequencing
	of 15 oncogenes and tumor suppressor genes, selected for their potential as predictive
	biomarkers of response to targeted agents by Sanger sequencing.', 'genePanelId':
	'MSKCC_BLCA_15'}, {'description': 'Targeted (343 cancer genes, IMPACT341 plus MYB and NFIB)
	sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
	'MYB-IMPACT341'}, {'description': 'Targeted (412 cancer genes, IMPACT410 plus MYB and NFIB)
	sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
	'MYB-IMPACT410'}, {'description': 'Targeted (470 cancer genes, IMPACT468 plus MYB and NFIB)
	sequencing of various tumor types via MSK-IMPACT on Illumina HiSeq sequencers.', 'genePanelId':
	'MYB-IMPACT468'}, {'description': 'Targeted NGS of NSCLC Samples.', 'genePanelId':
	'NSCLC_UNITO_2016_PANEL'}, {'description': 'Targeted panel of 137 genes.', 'genePanelId':
	'prad_mskcc_sanger'}, {'description': 'Targeted panel of 145 genes. (merge of prad_mskcc_sanger
	and prad_mskcc_sequenom)', 'genePanelId': 'prad_mskcc_sequenom_sanger'}, {'description':
	'Targeted panel of 21 genes.', 'genePanelId': 'prad_mskcc_sequenom'}, {'description': 'Targeted
	panel for cfDNA sequencing (2 genes)', 'genePanelId': 'rbl_cfdna_msk_2020_panel'},
	{'description': 'Targeted sequencing of clinical cases via Thunderbolts NGS Target Enrichment
	System, RainDance Technologies.', 'genePanelId': 'RDTB49'}, {'description': 'Targeted
	sequencing of clinical cases via ThunderStorm NGS Target Enrichment System, RainDance
	Technologies.', 'genePanelId': 'RDTS30'}, {'description': "A panel that's designed to target
	all exons of 262 genes that are recurrently mutated in de novo MDS/AML (â\x80\x98RMG
	reagentâ\x80\x99).", 'genePanelId': 'RMG'}, {'description': 'Targeted panel of 226
	protein-coding genes.', 'genePanelId': 'sarc_mskcc_panel'}, {'description': 'Targeted deep
	sequencing (TDS) of 1202 genes on Illumina HiSeq2000 sequencers.', 'genePanelId': 'UCLA_1202'},
	{'description': 'DNA sequencing of 622 genes with known or potential relationships to cancer.',
	'genePanelId': 'WUSTL-DFCI_623'}, {'description': 'Targeted massively parallel sequencing of
	4047 cancer genes.', 'genePanelId': 'NOVARTIS_BROAD_1651'}, {'description': 'Foundation
	Medicine T7 gene panel (430 cancer genes, FMI-T7 plus TERT)', 'genePanelId': 'TERT-FMI-T7'},
	{'description': 'FoundationOne gene panel (317 genes)', 'genePanelId': 'FoundationOne'},
	{'description': 'DFCI-ONCOPANEL-3.1, Number of Genes - 447', 'genePanelId':
	'DFCI-ONCOPANEL-3.1'}, {'description': 'DFCI-ONCOPANEL-3, Number of Genes - 447',
	'genePanelId': 'DFCI-ONCOPANEL-3'}, {'description': 'DFCI-ONCOPANEL-1, Number of Genes - 304',
	'genePanelId': 'DFCI-ONCOPANEL-1'}, {'description': 'DFCI-ONCOPANEL-2, Number of Genes - 326',
	'genePanelId': 'DFCI-ONCOPANEL-2'}, {'description': 'ARCHER-SOLID-CV4 Gene Panel (123 genes)',
	'genePanelId': 'ARCHER-SOLID-CV4'}, {'description': 'Targeted panel of 262 genes.',
	'genePanelId': 'MDAnderson_T200'}, {'description': 'Targeted panel of 476 cancer-related
	genes.', 'genePanelId': 'sarcoma_msk_2022_panel'}]
	Specific Gene Panel: {'description': 'Targeted NGS of NSCLC Samples.', 'genes':
	[{'entrezGeneId': 25, 'hugoGeneSymbol': 'ABL1'}, {'entrezGeneId': 207, 'hugoGeneSymbol':
	'AKT1'}, {'entrezGeneId': 324, 'hugoGeneSymbol': 'APC'}, {'entrezGeneId': 472,
	'hugoGeneSymbol': 'ATM'}, {'entrezGeneId': 673, 'hugoGeneSymbol': 'BRAF'}, {'entrezGeneId':
	999, 'hugoGeneSymbol': 'CDH1'}, {'entrezGeneId': 1029, 'hugoGeneSymbol': 'CDKN2A'},
	{'entrezGeneId': 1956, 'hugoGeneSymbol': 'EGFR'}, {'entrezGeneId': 2064, 'hugoGeneSymbol':
	'ERBB2'}, {'entrezGeneId': 2066, 'hugoGeneSymbol': 'ERBB4'}, {'entrezGeneId': 2263,
	'hugoGeneSymbol': 'FGFR2'}, {'entrezGeneId': 2261, 'hugoGeneSymbol': 'FGFR3'}, {'entrezGeneId':
	2322, 'hugoGeneSymbol': 'FLT3'}, {'entrezGeneId': 6927, 'hugoGeneSymbol': 'HNF1A'},
	{'entrezGeneId': 3417, 'hugoGeneSymbol': 'IDH1'}, {'entrezGeneId': 3791, 'hugoGeneSymbol':
	'KDR'}, {'entrezGeneId': 3815, 'hugoGeneSymbol': 'KIT'}, {'entrezGeneId': 3845,
	'hugoGeneSymbol': 'KRAS'}, {'entrezGeneId': 4233, 'hugoGeneSymbol': 'MET'}, {'entrezGeneId':
	4851, 'hugoGeneSymbol': 'NOTCH1'}, {'entrezGeneId': 5290, 'hugoGeneSymbol': 'PIK3CA'},
	{'entrezGeneId': 5781, 'hugoGeneSymbol': 'PTPN11'}, {'entrezGeneId': 5925, 'hugoGeneSymbol':
	'RB1'}, {'entrezGeneId': 5979, 'hugoGeneSymbol': 'RET'}, {'entrezGeneId': 4089,
	'hugoGeneSymbol': 'SMAD4'}, {'entrezGeneId': 6608, 'hugoGeneSymbol': 'SMO'}, {'entrezGeneId':
	6794, 'hugoGeneSymbol': 'STK11'}, {'entrezGeneId': 7157, 'hugoGeneSymbol': 'TP53'},
	{'entrezGeneId': 7428, 'hugoGeneSymbol': 'VHL'}], 'genePanelId': 'NSCLC_UNITO_2016_PANEL'}
	An error occurred: 400 Client Error: for url: https://www.cbioportal.org/api/gene-panels/fetch


	I successfully retrieved information about available gene panels using the API. Here are some highlights:

	1. All Gene Panels:
	- There are numerous gene panels available, each with a unique ID and description. For example, the "ACYC_FMI_27" panel targets 27 cancer genes, and the "IMPACT505" panel targets 505 cancer genes.

	2. Specific Gene Panel:
	- I retrieved detailed information about the "NSCLC_UNITO_2016_PANEL" gene panel, which is used for targeted NGS of NSCLC samples. This panel includes genes such as ABL1, AKT1, APC, ATM, BRAF, and many others.

	Unfortunately, there was an error when attempting to fetch gene panels using a POST request, which resulted in a 400 Client Error. This might be due to incorrect parameters or an issue with the API endpoint.

	If you have any specific gene panels or further exploration in mind, feel free to let me know!
	>>>