Making evaluate_gemini.py script take a file path as an argument for better development; fixing error in utility.py that leads to entities not being extracted (check Piazza)

cachegpt/joblib/kg_rag/utility/get_Gemini_response/003cd7b92cf6ea167343bced92140d7c/metadata.json

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+{"duration": 0.35046935081481934, "input_args": {"instruction": "\"Context: Disease Takayasu's arteritis associates Gene HLA-B. Variant HLA-B*5201 associates Disease Takayasu's arteritisDisease psoriatic arthritis associates Gene HLA-B\\nQuestion: Out of the given list, which Gene is associated with Takayasu's arteritis and psoriatic arthritis. Given list is:  RELN, HLA-B,  HLA-B,  SNTB1, SCN1A\"", "system_prompt": "'You are an expert biomedical researcher. For answering the Question at the end, you need to first read the Context provided.\\nBased on that Context, provide your answer in the following JSON format for the Question asked.\\n{{\\n  \"answer\": <correct answer>\\n}}\\n'", "temperature": "0"}, "time": 1761789208.6641073}

cachegpt/joblib/kg_rag/utility/get_Gemini_response/0076f841094b496009de3bd8de7eeb2f/metadata.json

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+{"duration": 0.809091329574585, "input_args": {"instruction": "'Context: {\\n  \"diseases\": [\\n    {\\n      \"lung small cell carcinoma\": [\\n        {\\n          \"statement\": \"Variant rs876660821 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs876658468 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057520001 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057520005 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057520003 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057520006 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs864622237 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519985 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519989 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs876660754 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs483352697 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519747 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913295 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs587782329 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519990 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519879 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519927 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs985033810 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519877 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs55853698 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR29B1 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913274 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR34B associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs116427960 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR29B2 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913275 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1057519991 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913343 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913297 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR34C associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121909229 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs121913273 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs886039484 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3813565 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR34A associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR125B2 associates Disease lung small cell carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs587782082 associates Disease lung small cell carcinoma.\"\\n        }\\n      ]\\n    },\\n    {\\n      \"cervix carcinoma\": [\\n        {\\n          \"statement\": \"Gene MIR590 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR106B associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Disease cervix carcinoma associates Gene ADGRV1.\"\\n        },\\n        {\\n          \"statement\": \"Disease cervix carcinoma associates Gene EXOC1.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs59661306 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs139337062 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR27B associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Disease cervix carcinoma associates Gene LTA.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR155 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR135B associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR34A associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3132461 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR139 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs57079996 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR26B associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR4262 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR361 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Disease cervix carcinoma associates Gene HLA-G.\"\\n        },\\n        {\\n          \"statement\": \"Disease cervix carcinoma associates Gene TUBB.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR381 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR25 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR491 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs57746686 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs138446575 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR519D associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9257927 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR503 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3131631 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR494 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs138885312 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR346 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR429 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR362 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR107 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR497 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR31 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs145023077 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR145 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR502 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9277952 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs142979264 associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR146A associates Disease cervix carcinoma.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3130218 associates Disease cervix carcinoma.\"\\n        }\\n      ]\\n    }\\n  ]\\n}\\nQuestion: Out of the given list, which Gene is associated with lung small cell carcinoma and cervix carcinoma. Given list is: TERT, ADGRV1,  PHGDH,  CACNA1D,  TFAP2B'", "system_prompt": "'You are an expert biomedical researcher. For answering the Question at the end, you need to first read the Context provided.\\nBased on that Context, provide your answer in the following JSON format for the Question asked.\\n{{\\n  \"answer\": <correct answer>\\n}}\\n'", "temperature": "0"}, "time": 1761772466.0517707}

cachegpt/joblib/kg_rag/utility/get_Gemini_response/00e800c2132e66eb161178bb54885aa6/metadata.json

@@ -0,0 +1 @@
+{"duration": 0.4534342288970947, "input_args": {"instruction": "'Context: Disease central nervous system cancer associates Gene BRCA2. Disease central nervous system cancer associates Gene TERTDisease lung adenocarcinoma associates Gene TERT\\nQuestion: Out of the given list, which Gene is associated with central nervous system cancer and lung adenocarcinoma. Given list is:  ADGRG6,  CDKAL1, TERT,  HLA-DPA1, BRCA2'", "system_prompt": "'You are an expert biomedical researcher. For answering the Question at the end, you need to first read the Context provided.\\nBased on that Context, provide your answer in the following JSON format for the Question asked.\\n{{\\n  \"answer\": <correct answer>\\n}}\\n'", "temperature": "0"}, "time": 1761789886.366661}

cachegpt/joblib/kg_rag/utility/get_Gemini_response/00f2d497fb434fcda69b79aee76f3c74/metadata.json

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+{"duration": 0.6181433200836182, "input_args": {"instruction": "'Context: {\\n  \"retrieval_mode\": \"entity\",\\n  \"entities\": [\\n    \"membranous glomerulonephritis\",\\n    \"cutaneous lupus erythematosus\"\\n  ],\\n  \"nodes\": [\\n    {\\n      \"node_name\": \"membranous glomerulonephritis\",\\n      \"context\": [\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene HLA-DQA1.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3132580 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene TCF19.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3134945 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene FOXP3.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9267522 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1265159 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9405192 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9271573 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs1480380 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs7750641 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3134792 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9272729 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3130618 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs230540 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene BTNL2.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3130544 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3115663 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs3129939 associates Disease membranous glomerulonephritis.\"\\n        },\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene RNF5.\"\\n        },\\n        {\\n          \"statement\": \"Disease membranous glomerulonephritis associates Gene EGFL8.\"\\n        }\\n      ]\\n    },\\n    {\\n      \"node_name\": \"cutaneous lupus erythematosus\",\\n      \"context\": [\\n        {\\n          \"statement\": \"Disease cutaneous lupus erythematosus associates Gene HLA-DQA1.\"\\n        },\\n        {\\n          \"statement\": \"Gene MIR485 associates Disease cutaneous lupus erythematosus.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs9267531 associates Disease cutaneous lupus erythematosus.\"\\n        },\\n        {\\n          \"statement\": \"Variant rs2187668 associates Disease cutaneous lupus erythematosus.\"\\n        },\\n        {\\n          \"statement\": \"Disease cutaneous lupus erythematosus associates Gene CSNK2B.\"\\n        }\\n      ]\\n    }\\n  ]\\n}\\nQuestion: Out of the given list, which Gene is associated with membranous glomerulonephritis and cutaneous lupus erythematosus. Given list is:  ZFHX3,  HLA-DQA1, EPDR1,  CRTC1, HLA-DQA1'", "system_prompt": "'You are an expert biomedical researcher. For answering the Question at the end, you need to first read the Context provided.\\nBased on that Context, provide your answer in the following JSON format for the Question asked.\\n{{\\n  \"answer\": <correct answer>\\n}}\\n'", "temperature": "0"}, "time": 1761769757.0007198}