aiagents4pharma 1.31.0__py3-none-any.whl → 1.33.0__py3-none-any.whl

{aiagents4pharma-1.31.0.dist-info → aiagents4pharma-1.33.0.dist-info}/RECORD

@@ -75,7 +75,7 @@ aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
 aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=IcXSZ2qQA1m-gS-o0Pj_g1oar8uPdhsbaovloUFka3Q,3058
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
-aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=bag4w3JCSqaojG37MTksy3ZehAPe3qoVzjIN2uh3nrc,229
+aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=KubbjqcaMgSMiJ4085F7O-cul-dYUAF7cWLqaM8Ss-g,277
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
 aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
@@ -112,6 +112,7 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransfo
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py,sha256=N6HRr4lWHXY7bTHe2uXJe4D_EG9WqZPibZne6qLl9_k,1447
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py,sha256=JhY7axvVULLywDJ2ctA-gob5YPeaJYWsaMNjHT6L9CU,3021
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=bk27KElJxOvKJ2RTz4ftleExQPMyWWS755KKmlImzbk,1241
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py,sha256=pal76wi7WgQWUNk56BrzfFV8jKpbDaHHdbwtgx_gXLI,2410
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=C07YqUNYW7ofpKAzKh0lBovXKLvaiXFb3oJU6k1dvu4,411
 aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=zpD4h7EYtyq0QNOqLd6bkxrPlPb2XN64ceI9ncgESrA,171
@@ -128,31 +129,32 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/nim_molmim.py,sha256=XH6JNfmMS38UEU7UGJeeabHfRykharnQpQaqjO86OlQ,1537
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/ollama.py,sha256=8w0sjt3Ex5YJ_XvpKl9UbhdTiiaoMIarbPUxLBU-1Uw,2378
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
-aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=JKGavA-umsGX3ng17_UYAvDBdbg-W-mPn8Q6JfP7J9U,143
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=gkHVwImeTnDBP_q4TWjn_CMJ-BMmt8NJqNkA1IOLvuI,174
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256=qsVlDCGGDkUCv-R5_xFGhrtLS7P0CfagnM2qATwiOFM,1333
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py,sha256=z0Jb3tt8VzRjzqI9oVcUvRlPPg6BUdmslfKDIEFE_h8,3013
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=NOZxTklAH1j1ggu97Ib8Xn9LCKudEWt-8dx8w7yxVD8,180
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=c_0Pk85bt-RfK5RMyALM3MXo3qXVMoYS7BOqM9wuFME,317
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=KdKbnc-5zxktLUkzEZHC3bvn8_iKa8Kk4So90i48cdE,3275
-aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=wrK9CPy5evH56fyOZ2BlkBfY5aEj6tefc4jSDPVzYvs,3041
-aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=xt_bgCTVJ6jOCkhc_rHh8pngq4uS8kuNOevuP3eC-sA,3702
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ua1bjKE2HBKZuLnDn8me5fuV1lSvdZbwAlo3Yp27TT4,4659
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=f11kNqtyZnpBiIf3Fe9gU0WqQ0-ohhngTKl-o0u997Q,4442
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=oCSWPj3TUgTIERmYbBTYipNrU1g956LXJEUx-7-KAQ0,3354
+aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=pYHW3R7VQjRA3PhgWGQYI3ErfdILYQ0FM1WGXii3r1k,2996
+aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=GEXzJMQxIeZ7zLP-AlnTMU-n_KXZ7g22Qd9L3USIc_4,3626
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=oui0CMSyXmBGBJ7LnYq8Ce0V8Qc3BS6GgH5Qx5wI6oM,4565
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=NAmEURIhH-sjXGO-dqAigUA10m-Re9Qe1hY8db4CIP0,4370
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=Y9-4PxsNCMoxyyQgDSbPByJnO9wnyem5SYL3eOZt1HY,189
 aiagents4pharma/talk2scholars/configs/config.yaml,sha256=-8X0_gTmjEuXAeIrnppw3Npy8HICelHZOvTKEScI-rs,596
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=plv5Iw34gvbGZbRyJapvoOiiFXekRQIwjV_yy5AR_SI,104
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=D94LW4cXLmJe4dNl5qoR9QN0JnBqGLbQDgDLqhCNUE0,213
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=GZRqZoUy8eAWXyd9GJDh-A4mYSJOhnkid6TaIJTGBeU,1192
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=EmUAxeQSnH4U5Op5_XOzCbcexDCp-Rpz3z0yVPRtQUg,1315
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=UIYkr060IpoLHMXVPxGAjrkCJSjX7H0DzcFSasyW6sE,1185
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=_sSt2jCgSILwrXkywDAxkXONCZn896owLBaf46iFI0I,1323
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=09nMAlI4CTLlss03trR0ZaEeLdABQfkwUUE6ZCK4WzY,718
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=SOdjRiGUxjW9JeCRDd_U1RjCclItkoPODrj5RpIrxSY,2030
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=tXpOW3R4eAfNoqvoaHfabSG-DcMHmUGSTg_4zH_vlgw,94
 aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
@@ -172,39 +174,37 @@ aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=ifOt
 aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/zotero_write/default.yaml,sha256=gB7y7pznviQUzu49Eu4ONNkjQjT8wPKNSw6S_vfd9kI,1222
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=ReScKLpEvedq4P6ww52NRQS0Xr6SSQV7hqoQ83Mt75U,138
-aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=8ZFfv55tXO3LU-2DzKC5JjH4_ryodgu-H1ieKBmVFvw,2844
+aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=MGB-rWjbOpLN-pK3nY9YKAuskcjeR62rjXbZl1Ppjas,2836
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
 aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=FBRqS06IKJYFOudQEHQr-9oJ4tftkH-gTCowTAqwWSg,3686
-aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=hgKgMXAGGqGJ6EXbjfsdZ5t1IWo2W67tc_F7vK747Qg,6844
-aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=CP4fKFU_JYP_AXvTptnwpjaVar1d5lVKV5vxYgH_1j4,5309
-aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=_bGuoo4b6zD_vwLa7jGziWDT5qRtavsf02Jiaa7JIRU,5817
-aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=TN4Sq5-SCxv-9VfFyq7sOlBlxbekmnWuB7-qh4MrhkA,4656
-aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=te6w1tPvuNSNCTihIwaCT083BzUCowjOQPwuCodXR4k,8723
+aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=IZYSocYVwqPil2lF6L07mKm8PUq7vjopmqNiCm6IJEA,6876
+aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=gKSQp-sw62FplNnGYW0wv2ZIUEefh3o0tFWbRzy9yLs,5068
+aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=3mycLeEgH5XkwxuoXfTpQb8c8xFtIX2HjVnACPrSf60,7141
+aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=scGCTgka2JuoUhzZwzDn0OgIYihOLhXbwb5uGFR02aI,4302
+aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=_zzg4_XVVEuvYDsJ5la0kFLf9dT45P67-UnUZWDUkhY,34874
 aiagents4pharma/talk2scholars/tests/test_routing_logic.py,sha256=g79tG68ZrUOL3-duCCJwvFK6OieR5KedRf3yTUDqIFk,2784
-aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=BhW1wGc-wUPS4fwNBQRtBXJaJ_i7L6t_G9Bq57fK7rI,7784
-aiagents4pharma/talk2scholars/tests/test_s2_display.py,sha256=w1TqgEdl9WpW_A2Ud1slfI5fkRFkKtKadAlkEfSLOZk,2247
+aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=xvlPU4Lz_DdQLTpdtoHW9l_AMvFrzC-FXE5royGbtLM,7806
+aiagents4pharma/talk2scholars/tests/test_s2_display.py,sha256=TfJE74KsocAHLbitMLjVrfUwAwyIYpzEvkdrQMBzM2g,2263
 aiagents4pharma/talk2scholars/tests/test_s2_multi.py,sha256=VCTfexhtX7FgWOBS0YtSm1zghbByZnni1NBLGVTJVGI,11166
-aiagents4pharma/talk2scholars/tests/test_s2_query.py,sha256=hEcBt142nn_bKV9lor__Yk4LusgE1tN5dA-qpT606Bc,2443
+aiagents4pharma/talk2scholars/tests/test_s2_query.py,sha256=_pDVolOmhrjZnh37Ig97-LcDHUe0lm3GvTWjNDKgMkc,2461
 aiagents4pharma/talk2scholars/tests/test_s2_retrieve.py,sha256=YtA2nbPRtoSR7mPqEjqLF5ERGVzTfeULztsNoCI48X8,2003
 aiagents4pharma/talk2scholars/tests/test_s2_search.py,sha256=mCGpoCYVn0SJ9BPcEjTz2MLy_K2XJIxvPngwsMoKijA,9945
 aiagents4pharma/talk2scholars/tests/test_s2_single.py,sha256=KjSh7V2cl1IuO_M9O6dj0vnMHr13H-xKxia_ZgT4qag,10313
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=_iHXvoZnU_eruf8l1sQKBSCIVnxNkH_9VzkVtZZA6bY,384
-aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=fQDQj28uFNC1TyMPzNaNfDJacuw1_DqwGiX6IgliR3Y,6130
+aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=jFEtfQVEwEQ6v3kq7A1_p2MKCu5wbtX47V4bE-fKD6M,6158
 aiagents4pharma/talk2scholars/tests/test_zotero_human_in_the_loop.py,sha256=YelLQu9Y_r1SNQsC1xoLHJoJ3soIZtBt1MFbbNhY-Dg,10744
-aiagents4pharma/talk2scholars/tests/test_zotero_path.py,sha256=i1bS-5uSv25z4UFrc_W5rKZ0bwOg6ZK5cwLHMkjWgt8,18592
-aiagents4pharma/talk2scholars/tests/test_zotero_read.py,sha256=ecu9C-RWaLNgmAFqGN8s7dzCrtODqXOSZDievzjtAfQ,15511
+aiagents4pharma/talk2scholars/tests/test_zotero_path.py,sha256=Ko0HyXCrpm-vs8Bkf-syxp3MfL1IvZwXXgPExyQy_F8,18618
+aiagents4pharma/talk2scholars/tests/test_zotero_read.py,sha256=yQTksJhqW036Scs7pnc_bBC23N210mcjaZ6sJZl8QnM,29492
 aiagents4pharma/talk2scholars/tests/test_zotero_write.py,sha256=qWlO0XoZJ6vxUxgisjYv9Np87CoTEDxiQBEOhdj9foo,6111
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=c8pYHDqR9P0Frz2jWjbvyizfSTBMlMFzGsiQzx2KC9c,189
-aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=0XmPLEqCply536Y1uWksmHYjlgNWcmcMpZx63XvGEFI,413
-aiagents4pharma/talk2scholars/tools/paper_download/abstract_downloader.py,sha256=nwVhRUqkdta3WLgd9roAWpx-bhJm3aAgJLx4RSYSJXQ,1327
-aiagents4pharma/talk2scholars/tools/paper_download/arxiv_downloader.py,sha256=hM9fdbwtOxuW1mpAfmfbILTI7kSVALgrGpjC2vMsvf8,3970
-aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=zndAnNFRBztuBK-tpW9UyYsGL8tB3gFjYhiTq6nzZu4,2203
+aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=tNTLSPNdir4XSKRF0HjXI_tBGBXXXwDhWRI5VnwbZpM,214
+aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=WTWvXbh0C96OoMoPf8Bgu0AgorsdkWslac_WqlHc4bo,3900
 aiagents4pharma/talk2scholars/tools/pdf/__init__.py,sha256=DPpOfON3AySko5EBBAe_3udOoSaAdQWNyGeNvJyV5R8,138
-aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=tNv0frCr0dxA0lfbwf5yudKRyWtbuRGMwqW5mk9u4eE,8797
-aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=u_qh1bpDhVdyTr_S2wVfPwQ_lMz77NQ-ZDWtOP_PWzo,420
-aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=UR0PtEHGDpOhPH0Di5HT8-Fip2RkEMTJgzROsChb1gc,2959
+aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=RfICBn4VorvpTrb_GunFFAi6fnzUlees_k0poQm0VKc,21853
+aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=w_eiw0pG8HNp79F9O_icXs_Yl_4odsmagYNKDTjIsvk,428
+aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py,sha256=YtnCrI0c3Fhi68R6ndPUnVM3E5u7CuBB_myIzLN6nXg,3040
 aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=N6GwG3oCQFEcntpjTQObAELzM5OpZq0u9J9-gUWU2kc,2716
-aiagents4pharma/talk2scholars/tools/s2/query_results.py,sha256=5yXuHqz5UKO9BbovEUnqgjcMvqVG4vp9VJO8Zaz5N1w,2029
+aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=inaWWctaylJAJsXinQA63qPs5n-gn7axJz8ijj66Jmw,2746
 aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=llzMMnEQKeYVamJbF4_DTMx-BgVe79vwDcUIFGLrmUY,2615
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=NGzo1rF5VJJuZJbSLDwy2f220wSh7DWEw6xT1qQA2V0,2452
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=7VivBGHcmaJZN7v7gYwddC-rfrDHaZo74pSNBYlJ2xU,2673
@@ -213,16 +213,16 @@ aiagents4pharma/talk2scholars/tools/s2/utils/multi_helper.py,sha256=rrR0DRNeGHpY
 aiagents4pharma/talk2scholars/tools/s2/utils/search_helper.py,sha256=_eP7q4ZTSWisEF4Stffe-IpR2MD9WrQ0u3jbbeJBRLU,6363
 aiagents4pharma/talk2scholars/tools/s2/utils/single_helper.py,sha256=ahTDT0lp5VRZS5hLL3-hsHx4wB3LUVY2OBTCTEJyR3Y,6983
 aiagents4pharma/talk2scholars/tools/zotero/__init__.py,sha256=wXiQILLq-utV35PkDUpm_F074mG9yRMyGQAFlr9UAOw,197
-aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=B21TOdB1nR--2Ug6Zx7nYjAKfCbndMF4L-cWcHPBWII,2267
+aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=RqFXP2DXmkHLhVLirrTnmSk-E8Jipi4ue_Zw65npbnM,2263
 aiagents4pharma/talk2scholars/tools/zotero/zotero_review.py,sha256=iqwpolg7GWAjXizubLrPaAsgOpsOhKz-tFRyLOiBvC0,6325
 aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py,sha256=KnDcnUBB0lwMcxNpC3hsVnICWkj23MDAePdHlK-Kekk,3024
 aiagents4pharma/talk2scholars/tools/zotero/utils/__init__.py,sha256=uIyKZSFB07-zd3vjS9ABL0r6fdBX9JHw60j8oUfxHQs,209
-aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=6f2yu5admNZp7xw5VW2TFGF4wh_oyVn9aLaQF47FLMc,6038
+aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=lyrfpx8NHYiAN1qQSJWqPka7cML5BASwRXaI66fb-u8,13662
 aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9yrBYaDnRe7sR6PrpwR82OBJbA2P_Tc6RbxAbM,2748
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
-aiagents4pharma-1.31.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.31.0.dist-info/METADATA,sha256=H-RfFD-It0EISgKem1wBcEYtOK-LEfx37I4CWM48IzA,15802
-aiagents4pharma-1.31.0.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-aiagents4pharma-1.31.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.31.0.dist-info/RECORD,,
+aiagents4pharma-1.33.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.33.0.dist-info/METADATA,sha256=cv2sm_J63wHmZipscCFn4rQtFNAJSz-trdl-bAsHwDw,16043
+aiagents4pharma-1.33.0.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+aiagents4pharma-1.33.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.33.0.dist-info/RECORD,,

{aiagents4pharma-1.31.0.dist-info → aiagents4pharma-1.33.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.0.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

aiagents4pharma/talk2scholars/tools/paper_download/abstract_downloader.py

@@ -1,45 +0,0 @@
-"""
-Abstract Base Class for Paper Downloaders.
-
-This module defines the `AbstractPaperDownloader` class, which serves as a
-base class for downloading scholarly papers from different sources
-(e.g., arXiv, PubMed, IEEE Xplore). Any specific downloader should
-inherit from this class and implement its methods.
-"""
-
-from abc import ABC, abstractmethod
-from typing import Any, Dict
-
-
-class AbstractPaperDownloader(ABC):
-    """
-    Abstract base class for scholarly paper downloaders.
-
-    This is designed to be extended for different paper sources
-    like arXiv, PubMed, IEEE Xplore, etc. Each implementation
-    must define methods for fetching metadata and downloading PDFs.
-    """
-
-    @abstractmethod
-    def fetch_metadata(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Fetch metadata for a given paper ID.
-
-        Args:
-            paper_id (str): The unique identifier for the paper.
-
-        Returns:
-            Dict[str, Any]: The metadata dictionary (format depends on the data source).
-        """
-
-    @abstractmethod
-    def download_pdf(self, paper_id: str) -> bytes:
-        """
-        Download the PDF for a given paper ID.
-
-        Args:
-            paper_id (str): The unique identifier for the paper.
-
-        Returns:
-            bytes: The binary content of the downloaded PDF.
-        """

aiagents4pharma/talk2scholars/tools/paper_download/arxiv_downloader.py

@@ -1,115 +0,0 @@
-"""
-Arxiv Paper Downloader
-
-This module provides an implementation of `AbstractPaperDownloader` for arXiv.
-It connects to the arXiv API, retrieves metadata for a research paper, and
-downloads the corresponding PDF.
-
-By using an abstract base class, this implementation is extendable to other
-APIs like PubMed, IEEE Xplore, etc.
-"""
-
-import xml.etree.ElementTree as ET
-from typing import Any, Dict
-import logging
-import hydra
-import requests
-from .abstract_downloader import AbstractPaperDownloader
-
-# Configure logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-
-class ArxivPaperDownloader(AbstractPaperDownloader):
-    """
-    Downloader class for arXiv.
-
-    This class interfaces with the arXiv API to fetch metadata
-    and retrieve PDFs of academic papers based on their arXiv IDs.
-    """
-
-    def __init__(self):
-        """
-        Initializes the arXiv paper downloader.
-
-        Uses Hydra for configuration management to retrieve API details.
-        """
-        with hydra.initialize(version_base=None, config_path="../../configs"):
-            cfg = hydra.compose(
-                config_name="config", overrides=["tools/download_arxiv_paper=default"]
-            )
-            self.api_url = cfg.tools.download_arxiv_paper.api_url
-            self.request_timeout = cfg.tools.download_arxiv_paper.request_timeout
-            self.chunk_size = cfg.tools.download_arxiv_paper.chunk_size
-            self.pdf_base_url = cfg.tools.download_arxiv_paper.pdf_base_url
-
-    def fetch_metadata(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Fetch metadata from arXiv for a given paper ID.
-
-        Args:
-            paper_id (str): The arXiv ID of the paper.
-
-        Returns:
-            Dict[str, Any]: A dictionary containing metadata, including the XML response.
-        """
-        logger.info("Fetching metadata from arXiv for paper ID: %s", paper_id)
-        api_url = f"{self.api_url}?search_query=id:{paper_id}&start=0&max_results=1"
-        response = requests.get(api_url, timeout=self.request_timeout)
-        response.raise_for_status()
-        return {"xml": response.text}
-
-    def download_pdf(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Download the PDF of a paper from arXiv.
-
-        This function first retrieves the paper's metadata to locate the PDF link
-        before downloading the file.
-
-        Args:
-            paper_id (str): The arXiv ID of the paper.
-
-        Returns:
-            Dict[str, Any]: A dictionary containing:
-                - `pdf_object`: The binary content of the downloaded PDF.
-                - `pdf_url`: The URL from which the PDF was fetched.
-                - `arxiv_id`: The arXiv ID of the downloaded paper.
-        """
-        metadata = self.fetch_metadata(paper_id)
-
-        # Parse the XML response to locate the PDF link.
-        root = ET.fromstring(metadata["xml"])
-        ns = {"atom": "http://www.w3.org/2005/Atom"}
-        pdf_url = next(
-            (
-                link.attrib.get("href")
-                for entry in root.findall("atom:entry", ns)
-                for link in entry.findall("atom:link", ns)
-                if link.attrib.get("title") == "pdf"
-            ),
-            None,
-        )
-
-        if not pdf_url:
-            raise RuntimeError(f"Failed to download PDF for arXiv ID {paper_id}.")
-
-        logger.info("Downloading PDF from: %s", pdf_url)
-        pdf_response = requests.get(pdf_url, stream=True, timeout=self.request_timeout)
-        pdf_response.raise_for_status()
-        # print (pdf_response)
-
-        # Combine the PDF data from chunks.
-        pdf_object = b"".join(
-            chunk
-            for chunk in pdf_response.iter_content(chunk_size=self.chunk_size)
-            if chunk
-        )
-        # print (pdf_object)
-        print("PDF_URL", pdf_url)
-
-        return {
-            "pdf_object": pdf_object,
-            "pdf_url": pdf_url,
-            "arxiv_id": paper_id,
-        }

aiagents4pharma/talk2scholars/tools/s2/query_results.py

@@ -1,61 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-This tool is used to display the table of studies.
-"""
-
-import logging
-from typing import Annotated
-import pandas as pd
-from langchain_experimental.agents import create_pandas_dataframe_agent
-from langchain_core.tools import tool
-from langgraph.prebuilt import InjectedState
-
-# Configure logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-
-class NoPapersFoundError(Exception):
-    """Exception raised when no papers are found in the state."""
-
-
-@tool("query_results", parse_docstring=True)
-def query_results(question: str, state: Annotated[dict, InjectedState]) -> str:
-    """
-    Query the last displayed papers from the state. If no papers are found,
-    raises an exception.
-
-    Use this also to get the last displayed papers from the state,
-    and then use the papers to get recommendations for a single paper or
-    multiple papers.
-
-    Args:
-        question (str): The question to ask the agent.
-        state (dict): The state of the agent containing the papers.
-
-    Returns:
-        str: A message with the last displayed papers.
-    """
-    logger.info("Querying last displayed papers with question: %s", question)
-    llm_model = state.get("llm_model")
-    if not state.get("last_displayed_papers"):
-        logger.info("No papers displayed so far, raising NoPapersFoundError")
-        raise NoPapersFoundError(
-            "No papers found. A search needs to be performed first."
-        )
-    context_key = state.get("last_displayed_papers", "pdf_data")
-    dic_papers = state.get(context_key)
-    df_papers = pd.DataFrame.from_dict(dic_papers, orient="index")
-    df_agent = create_pandas_dataframe_agent(
-        llm_model,
-        allow_dangerous_code=True,
-        agent_type="tool-calling",
-        df=df_papers,
-        max_iterations=5,
-        include_df_in_prompt=True,
-        number_of_head_rows=df_papers.shape[0],
-        verbose=True,
-    )
-    llm_result = df_agent.invoke(question, stream_mode=None)
-    return llm_result["output"]