tooluniverse 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

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Files changed (96) hide show
  1. tooluniverse/__init__.py +37 -14
  2. tooluniverse/admetai_tool.py +16 -5
  3. tooluniverse/base_tool.py +36 -0
  4. tooluniverse/biogrid_tool.py +118 -0
  5. tooluniverse/build_optimizer.py +87 -0
  6. tooluniverse/cache/__init__.py +3 -0
  7. tooluniverse/cache/memory_cache.py +99 -0
  8. tooluniverse/cache/result_cache_manager.py +235 -0
  9. tooluniverse/cache/sqlite_backend.py +257 -0
  10. tooluniverse/clinvar_tool.py +90 -0
  11. tooluniverse/compose_scripts/output_summarizer.py +87 -33
  12. tooluniverse/compose_tool.py +2 -2
  13. tooluniverse/custom_tool.py +28 -0
  14. tooluniverse/data/adverse_event_tools.json +97 -98
  15. tooluniverse/data/agentic_tools.json +81 -162
  16. tooluniverse/data/arxiv_tools.json +1 -4
  17. tooluniverse/data/compose_tools.json +0 -54
  18. tooluniverse/data/core_tools.json +1 -4
  19. tooluniverse/data/dataset_tools.json +7 -7
  20. tooluniverse/data/doaj_tools.json +1 -3
  21. tooluniverse/data/drug_discovery_agents.json +282 -0
  22. tooluniverse/data/europe_pmc_tools.json +1 -2
  23. tooluniverse/data/genomics_tools.json +174 -0
  24. tooluniverse/data/geo_tools.json +86 -0
  25. tooluniverse/data/literature_search_tools.json +15 -35
  26. tooluniverse/data/markitdown_tools.json +51 -0
  27. tooluniverse/data/monarch_tools.json +1 -2
  28. tooluniverse/data/openalex_tools.json +1 -5
  29. tooluniverse/data/opentarget_tools.json +8 -16
  30. tooluniverse/data/output_summarization_tools.json +23 -20
  31. tooluniverse/data/packages/bioinformatics_core_tools.json +2 -2
  32. tooluniverse/data/packages/cheminformatics_tools.json +1 -1
  33. tooluniverse/data/packages/genomics_tools.json +1 -1
  34. tooluniverse/data/packages/single_cell_tools.json +1 -1
  35. tooluniverse/data/packages/structural_biology_tools.json +1 -1
  36. tooluniverse/data/pmc_tools.json +1 -4
  37. tooluniverse/data/ppi_tools.json +139 -0
  38. tooluniverse/data/pubmed_tools.json +1 -3
  39. tooluniverse/data/semantic_scholar_tools.json +1 -2
  40. tooluniverse/data/tool_composition_tools.json +2 -4
  41. tooluniverse/data/unified_guideline_tools.json +206 -4
  42. tooluniverse/data/xml_tools.json +15 -15
  43. tooluniverse/data/zenodo_tools.json +1 -2
  44. tooluniverse/dbsnp_tool.py +71 -0
  45. tooluniverse/default_config.py +6 -0
  46. tooluniverse/ensembl_tool.py +61 -0
  47. tooluniverse/execute_function.py +235 -76
  48. tooluniverse/generate_tools.py +303 -20
  49. tooluniverse/genomics_gene_search_tool.py +56 -0
  50. tooluniverse/geo_tool.py +116 -0
  51. tooluniverse/gnomad_tool.py +63 -0
  52. tooluniverse/logging_config.py +64 -2
  53. tooluniverse/markitdown_tool.py +159 -0
  54. tooluniverse/mcp_client_tool.py +10 -5
  55. tooluniverse/molecule_2d_tool.py +9 -3
  56. tooluniverse/molecule_3d_tool.py +9 -3
  57. tooluniverse/output_hook.py +217 -150
  58. tooluniverse/smcp.py +18 -10
  59. tooluniverse/smcp_server.py +89 -199
  60. tooluniverse/string_tool.py +112 -0
  61. tooluniverse/tools/{MultiAgentLiteratureSearch.py → ADMETAnalyzerAgent.py} +18 -18
  62. tooluniverse/tools/ArXiv_search_papers.py +3 -3
  63. tooluniverse/tools/CMA_Guidelines_Search.py +52 -0
  64. tooluniverse/tools/CORE_search_papers.py +3 -3
  65. tooluniverse/tools/ClinVar_search_variants.py +52 -0
  66. tooluniverse/tools/ClinicalTrialDesignAgent.py +63 -0
  67. tooluniverse/tools/CompoundDiscoveryAgent.py +59 -0
  68. tooluniverse/tools/DOAJ_search_articles.py +2 -2
  69. tooluniverse/tools/DiseaseAnalyzerAgent.py +52 -0
  70. tooluniverse/tools/DrugInteractionAnalyzerAgent.py +52 -0
  71. tooluniverse/tools/DrugOptimizationAgent.py +63 -0
  72. tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py +52 -0
  73. tooluniverse/tools/EuropePMC_search_articles.py +1 -1
  74. tooluniverse/tools/GIN_Guidelines_Search.py +52 -0
  75. tooluniverse/tools/GWAS_search_associations_by_gene.py +52 -0
  76. tooluniverse/tools/LiteratureSynthesisAgent.py +59 -0
  77. tooluniverse/tools/PMC_search_papers.py +3 -3
  78. tooluniverse/tools/PubMed_search_articles.py +2 -2
  79. tooluniverse/tools/SemanticScholar_search_papers.py +1 -1
  80. tooluniverse/tools/UCSC_get_genes_by_region.py +67 -0
  81. tooluniverse/tools/Zenodo_search_records.py +1 -1
  82. tooluniverse/tools/__init__.py +33 -3
  83. tooluniverse/tools/convert_to_markdown.py +59 -0
  84. tooluniverse/tools/dbSNP_get_variant_by_rsid.py +46 -0
  85. tooluniverse/tools/gnomAD_query_variant.py +52 -0
  86. tooluniverse/tools/openalex_literature_search.py +4 -4
  87. tooluniverse/ucsc_tool.py +60 -0
  88. tooluniverse/unified_guideline_tools.py +1175 -57
  89. tooluniverse/utils.py +51 -4
  90. tooluniverse/zenodo_tool.py +2 -1
  91. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/METADATA +10 -3
  92. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/RECORD +96 -61
  93. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/entry_points.txt +0 -3
  94. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/WHEEL +0 -0
  95. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/licenses/LICENSE +0 -0
  96. {tooluniverse-1.0.7.dist-info → tooluniverse-1.0.9.dist-info}/top_level.txt +0 -0
tooluniverse/utils.py CHANGED
@@ -4,6 +4,7 @@ import re
4
4
  import hashlib
5
5
  import os
6
6
  import time
7
+ import sys
7
8
  from typing import Dict, Any, Union, List
8
9
  from huggingface_hub import hf_hub_download
9
10
  from pydantic._internal._model_construction import ModelMetaclass
@@ -15,11 +16,22 @@ def download_from_hf(tool_config):
15
16
  relative_local_path = hf_parameters.get("save_to_local_dir")
16
17
 
17
18
  # Compute absolute path to save locally
18
- if not os.path.isabs(relative_local_path):
19
- project_root = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
20
- absolute_local_dir = os.path.join(project_root, relative_local_path)
19
+ project_root = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
20
+
21
+ # If not provided, default to user cache directory under datasets
22
+ is_missing_path = relative_local_path is None
23
+ is_empty_string = (
24
+ isinstance(relative_local_path, str) and relative_local_path.strip() == ""
25
+ )
26
+ if is_missing_path or is_empty_string:
27
+ absolute_local_dir = os.path.join(get_user_cache_dir(), "datasets")
21
28
  else:
22
- absolute_local_dir = relative_local_path
29
+ # Expand '~' and environment variables
30
+ expanded_path = os.path.expanduser(os.path.expandvars(relative_local_path))
31
+ if os.path.isabs(expanded_path):
32
+ absolute_local_dir = expanded_path
33
+ else:
34
+ absolute_local_dir = os.path.join(project_root, expanded_path)
23
35
 
24
36
  # Ensure the directory exists
25
37
  os.makedirs(absolute_local_dir, exist_ok=True)
@@ -62,6 +74,38 @@ def get_md5(input_str):
62
74
  return md5_hash.hexdigest()
63
75
 
64
76
 
77
+ def get_user_cache_dir() -> str:
78
+ """
79
+ Return a cross-platform user cache directory for ToolUniverse.
80
+
81
+ macOS: ~/Library/Caches/ToolUniverse
82
+ Linux: $XDG_CACHE_HOME or ~/.cache/tooluniverse
83
+ Windows: %LOCALAPPDATA%\\ToolUniverse\\Cache
84
+ """
85
+ # Allow explicit override via environment variable
86
+ override_dir = os.getenv("TOOLUNIVERSE_TMPDIR")
87
+ if override_dir and override_dir.strip():
88
+ return os.path.expanduser(os.path.expandvars(override_dir))
89
+
90
+ platform = sys.platform
91
+ home_dir = os.path.expanduser("~")
92
+
93
+ if platform == "darwin":
94
+ return os.path.join(home_dir, "Library", "Caches", "ToolUniverse")
95
+
96
+ if platform.startswith("win"):
97
+ local_app_data = os.getenv("LOCALAPPDATA") or os.path.join(
98
+ home_dir, "AppData", "Local"
99
+ )
100
+ return os.path.join(local_app_data, "ToolUniverse", "Cache")
101
+
102
+ # Default: Linux/Unix
103
+ xdg_cache = os.getenv("XDG_CACHE_HOME")
104
+ if xdg_cache and xdg_cache.strip():
105
+ return os.path.join(xdg_cache, "tooluniverse")
106
+ return os.path.join(home_dir, ".cache", "tooluniverse")
107
+
108
+
65
109
  def yaml_to_dict(yaml_file_path):
66
110
  """
67
111
  Convert a YAML file to a dictionary.
@@ -138,6 +182,9 @@ def evaluate_function_call(tool_definition, function_call):
138
182
  type_mismatches = []
139
183
 
140
184
  for param, value in function_call["arguments"].items():
185
+ # Skip validation for special parameters that are handled internally
186
+ if param == "_tooluniverse_stream":
187
+ continue
141
188
  if param not in valid_params:
142
189
  invalid_params.append(param)
143
190
  else:
@@ -32,7 +32,8 @@ class ZenodoTool(BaseTool):
32
32
  "size": max(1, min(max_results, 200)),
33
33
  "all_versions": 1,
34
34
  }
35
- if community:
35
+ # Only add communities filter if community is provided and not empty
36
+ if community and community.strip():
36
37
  params["communities"] = community
37
38
 
38
39
  try:
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: tooluniverse
3
- Version: 1.0.7
3
+ Version: 1.0.9
4
4
  Summary: A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows.
5
5
  Author-email: Shanghua Gao <shanghuagao@gmail.com>
6
6
  Project-URL: Homepage, https://github.com/mims-harvard/ToolUniverse
@@ -29,21 +29,28 @@ Requires-Dist: sentence-transformers>=5.1.0
29
29
  Requires-Dist: fitz>=0.0.1.dev2
30
30
  Requires-Dist: pandas>=2.2.3
31
31
  Requires-Dist: admet-ai>=1.2.0
32
+ Requires-Dist: setuptools>=70.0.0
32
33
  Requires-Dist: pdfplumber>=0.11.0
33
34
  Requires-Dist: playwright>=1.55.0
34
35
  Requires-Dist: faiss-cpu>=1.12.0
35
36
  Requires-Dist: flask>=2.0.0
36
37
  Requires-Dist: chemprop==1.6.1
37
38
  Requires-Dist: aiohttp
39
+ Requires-Dist: beautifulsoup4>=4.12.0
40
+ Requires-Dist: markitdown[all]>=0.1.0
41
+ Requires-Dist: psutil>=5.9.0
38
42
  Provides-Extra: dev
39
- Requires-Dist: pytest>=6.0; extra == "dev"
40
- Requires-Dist: pytest-cov>=2.0; extra == "dev"
43
+ Requires-Dist: pytest>=7.0; extra == "dev"
44
+ Requires-Dist: pytest-cov>=4.0; extra == "dev"
41
45
  Requires-Dist: pytest-timeout>=2.3.1; extra == "dev"
42
46
  Requires-Dist: pytest-mock>=3.14.0; extra == "dev"
47
+ Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
43
48
  Requires-Dist: requests-mock>=1.12.1; extra == "dev"
44
49
  Requires-Dist: black>=22.0; extra == "dev"
45
50
  Requires-Dist: flake8>=4.0; extra == "dev"
46
51
  Requires-Dist: pre-commit>=2.0; extra == "dev"
52
+ Requires-Dist: pytest-xdist>=3.0; extra == "dev"
53
+ Requires-Dist: pytest-html>=3.0; extra == "dev"
47
54
  Provides-Extra: docs
48
55
  Requires-Dist: sphinx>=4.0; extra == "docs"
49
56
  Requires-Dist: furo>=2024.8.6; extra == "docs"
@@ -1,57 +1,66 @@
1
- tooluniverse/__init__.py,sha256=V8tmwPEEdlQ6H7WItWDVW0aiqD-xG40RpbsBV3VZqPI,16819
2
- tooluniverse/admetai_tool.py,sha256=nEfq7dwvFqjDryKv3nivGoBSRap6LT7_m76iMu72Q6E,3009
1
+ tooluniverse/__init__.py,sha256=PvYhaTdU4pSC8V3DMzbybfkLSad2OkpQWgf74P-lfH8,17507
2
+ tooluniverse/admetai_tool.py,sha256=xeYCpROq7oGjYrzKtDCHSN94sB5jVLuLSu3E_eT5Ko8,3470
3
3
  tooluniverse/agentic_tool.py,sha256=i0TEs6WhF21B4gs5k7DM67qTND4qDMPD2lUzLyEWnnM,25627
4
4
  tooluniverse/alphafold_tool.py,sha256=NkKQttC0MfuetCTTcWTFEG2MdhyKwy3jb5TR4odiqAw,4658
5
5
  tooluniverse/arxiv_tool.py,sha256=60e5moGt3XnwZeKx_nrvRZrwAavE11ok0j78AI5F6Xs,3610
6
- tooluniverse/base_tool.py,sha256=wX2D5JumEhYmpqOQRjjtLW8AzFTkutpvCGo3j1IvECo,11174
6
+ tooluniverse/base_tool.py,sha256=zagthjIceQN0F32pDhKE0uCqm9uqVEDG6OZgSIbNCRo,12479
7
+ tooluniverse/biogrid_tool.py,sha256=tszza6Kf1-PKsoVw5GIqLak20FvhFY_PFSVY9XxDuIQ,4274
7
8
  tooluniverse/biorxiv_tool.py,sha256=uffhxXMOWR6b2jzxka-Qss1LjliQTuX-skIIc7RAaPs,4133
8
9
  tooluniverse/boltz_tool.py,sha256=Kfcymeu6FRRpWLw7dWhEON4PUBTsHuBiTAPJlYH5ZGs,7930
10
+ tooluniverse/build_optimizer.py,sha256=UReMfhTGhGJqcEWdH6d5xfI-y3zJlaNfsei7qXxeCN0,2832
9
11
  tooluniverse/cellosaurus_tool.py,sha256=W_npl3ga45-Hpsdq7YyGsD5_DnR2AmyaQVYNjiZoNOs,47902
10
12
  tooluniverse/chem_tool.py,sha256=tJusjamWNp0x8Ke-cvVgKB7-clvD6LXTaXA0Q0fqQv4,8336
11
- tooluniverse/compose_tool.py,sha256=f_3X_fbdrzogBdKJXoXXpxVvdb1OWt7KMxhpPUtEu24,17109
13
+ tooluniverse/clinvar_tool.py,sha256=2NKPKC3b3eBzuwK0yc65bzPuRF4I-Jv_KjsVnBdiE6M,2945
14
+ tooluniverse/compose_tool.py,sha256=Q0KwVPgbac17VDnkP3pV-st0rNbG__CX0AMux-Os5lg,17117
12
15
  tooluniverse/core_tool.py,sha256=hHD8nVSIy6lK2vF3ygKz73gsDEPYEL-otXZXeR7M2SY,5083
13
16
  tooluniverse/crossref_tool.py,sha256=oba0kkWI9m9dugf_th1nEXPWPF4onJkFUyhp5h5H4pM,5736
14
17
  tooluniverse/ctg_tool.py,sha256=3nR_F-YGpxVmTa6u5xi-mrTmLSH7OBehP4EJo-CQS0Y,46053
15
- tooluniverse/custom_tool.py,sha256=w2LMMRT82byxSNYPBKmuEJ2lbKktDJt_iW0Ew24M5VY,2701
18
+ tooluniverse/custom_tool.py,sha256=cUX16ADw3vBtyqb7cIBpgHo_-CjVnkAPPQhw9H0k6T8,3793
16
19
  tooluniverse/dailymed_tool.py,sha256=sxIs0xYwX0CVlkhHaPwvGV-Oo1OW2tvsWZypAWujt9k,3800
17
20
  tooluniverse/dataset_tool.py,sha256=cmcCz_SFs7V78EZDNLesnQ2Qe9fVz1jOLghrpwe8hM8,11371
18
21
  tooluniverse/dblp_tool.py,sha256=aPyEivx5TYUxws7zOsHswQtkVphblMsVPw0lSpyoIQA,4488
19
- tooluniverse/default_config.py,sha256=81nZu2AiFaXXKCNLeunY_T7GpO0z_SuFHSHQLGIf2_4,9103
22
+ tooluniverse/dbsnp_tool.py,sha256=xOa3t7YdZlnhZ146fDS13Yx6Qo0eiJ7BO6zPQY41WQ8,2188
23
+ tooluniverse/default_config.py,sha256=cI8Z7seXqxDdIYFbIuIU9vXprNRD3ca4rTJTFAH0zsE,9384
20
24
  tooluniverse/doaj_tool.py,sha256=mzpnUwYfXdqvyn-txbV1cdWNS7Ty8g6fbvWgF2JN30I,7032
21
25
  tooluniverse/doctor.py,sha256=QQ6LiV3HPkWljVKh52QptQmV3xFj53_2yo-A_n8NQ5Y,1326
22
26
  tooluniverse/efo_tool.py,sha256=J4tjPFlNa9KhmQTEToBZN-m8jMuF1IKf2yQb1dyTeXI,1394
23
27
  tooluniverse/embedding_database.py,sha256=ua-yIyv3dPq2GHdyZmiwZyaUlkKYyV3nslB4H9asvDo,24682
24
28
  tooluniverse/embedding_sync.py,sha256=Cq3g64MjNXXpiImrzPMNsCTvGZeEI9009OlHOD3EloI,14669
25
29
  tooluniverse/enrichr_tool.py,sha256=YXuHwoG_Hi-kUWK7cY_X21b5pbqoREdG7fJxKq050Jg,9472
30
+ tooluniverse/ensembl_tool.py,sha256=i-kYliN5juitLTJqGiWcm7RXFV8k29XlfNBUC1Y1Z-M,2195
26
31
  tooluniverse/europe_pmc_tool.py,sha256=-3CAq5tDhS5NoeHifevadBgP_MHDZJdwNmM5SvjbAa8,6080
27
32
  tooluniverse/exceptions.py,sha256=3svVCG7H_G_8E1mco74KWi44u1M7V1JojVycSEWdi_o,5386
28
- tooluniverse/execute_function.py,sha256=Lj5v3t23An6FNbfGZxUMdkfqOF9gqzMVrZbzuiCElG0,101216
33
+ tooluniverse/execute_function.py,sha256=hJxcHbewIfXXjPvV7HBZ0PrECMOKTQVhMOFRI5K6fbQ,107533
29
34
  tooluniverse/extended_hooks.py,sha256=1Cg0rETh6_D21YFVqD-FhL7y4inZAGyQ6vMtHyugueg,15376
30
35
  tooluniverse/fatcat_tool.py,sha256=-QEOYbv6KEcrOiOa27Ms1xm0sySB-vW4rWEinsS6EDw,2051
31
36
  tooluniverse/gene_ontology_tool.py,sha256=l89XYdBEBm3eN3dG0lR4oV01H16_9IUB6a2c7W_c7Lg,7180
32
- tooluniverse/generate_tools.py,sha256=9AuQmvW8874Br7gDSSrpyAZ1xjV_4gN78qtGu7VnsWE,5705
37
+ tooluniverse/generate_tools.py,sha256=rx-FMNPBSZ0_lP8yNNsW9BtBtT6WtORGuEK-kJVRKic,15226
38
+ tooluniverse/genomics_gene_search_tool.py,sha256=beK6mJTBBvXb9TKF8piYoq-plpm36DETl05SRMFjDNg,1953
39
+ tooluniverse/geo_tool.py,sha256=t73P_rbeYE_NeDEVkV6_1wYV_PYGgK8gFTINxOwu2e4,4136
40
+ tooluniverse/gnomad_tool.py,sha256=imVgxNiNHfQSdOiDj-Ub1gKIGj1XEVnSoTSL18NY5Yk,1817
33
41
  tooluniverse/graphql_tool.py,sha256=y7ztNyb9hn4OdSGKhLsHev_snkNgbAwJZL8ZGHm0LEk,8980
34
42
  tooluniverse/gwas_tool.py,sha256=hq4VhB93DhczZo0xRGjGS9AtdKWL0O_XQy3eoV_fi8E,12351
35
43
  tooluniverse/hal_tool.py,sha256=HrU27B6TK_gMtk8tjafpVkpD1ABDlCOo1bsLmBNhaQU,2485
36
44
  tooluniverse/hpa_tool.py,sha256=siRA0usQ0Rggloy3VL1b56QlytabndXS8Xzc9H3uWs8,64998
37
45
  tooluniverse/humanbase_tool.py,sha256=xojNboYvFrW_LAzOzKaexp6tvyGSbUazpMfOvX5ETXY,15006
38
46
  tooluniverse/llm_clients.py,sha256=6EAhxUmEpdKYjWMG6S0Q57mdp1JuCPxPehIudofCPzA,30484
39
- tooluniverse/logging_config.py,sha256=SWM8TCrv0RZJZbC8NNwy8h04V9BvqSVyzwJFcW43eFI,7212
40
- tooluniverse/mcp_client_tool.py,sha256=R2WWAbnjzCFEKfeddTvtZTSZqtnvKRayV2ha2xdV9EU,28741
47
+ tooluniverse/logging_config.py,sha256=rMjpGw5jkJGsIN2AakLOCQ-jVEYf8UhET7sJGdrfCNQ,9107
48
+ tooluniverse/markitdown_tool.py,sha256=bnUA0Sw8KjVygqf8F6k3ATY7K23NWFqycnnfs9mm5qQ,5492
49
+ tooluniverse/mcp_client_tool.py,sha256=1AxczGYkW6kMynLwz1WLzH3KoIKM2cDQ9WMUTOsejTo,29053
41
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- tooluniverse/molecule_2d_tool.py,sha256=p08EgesUytxxsbva66aVxctO3BMSsqbteCHnTtgyv4I,10278
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- tooluniverse/molecule_3d_tool.py,sha256=XbruNN2Tg_pgXf199KE7xCmReo6_mHcrT0q2W5vpevg,18437
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+ tooluniverse/molecule_2d_tool.py,sha256=SPXqi_KTN76ksG1DO0QP9ZKzcRbdQpXjfOau11hgC0w,10568
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+ tooluniverse/molecule_3d_tool.py,sha256=uq3Q58q0LlB4y7xRaOUzoyQQp8GLjbWSSFdHin4tOsg,18727
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- tooluniverse/output_hook.py,sha256=2f95WFXA9DC6-HV4uJb8ZJAF-VmlmM2DPVvG2up_4EE,46279
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+ tooluniverse/output_hook.py,sha256=6alRemNqe367xKX1USyXB-FEzDmmPVF9me_DPtopDCc,49433
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  tooluniverse/protein_structure_3d_tool.py,sha256=byvtvW-B6aPUmW_OpcYKHFdbL-g3IWZk1RSN0cNYjcg,12318
@@ -63,23 +72,29 @@ tooluniverse/reactome_tool.py,sha256=ngmJXCcQfsu5d8XcX258ZHW4DIBi45sSjYNwUBk8nxo
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- tooluniverse/smcp.py,sha256=ZfGrruGnPyC_Q11hKNc_NEeOly51PdqV1MD8sPpuwoM,103674
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- tooluniverse/smcp_server.py,sha256=SAItoFvUsVwGktRZBqMvHRZrHAdVGOmgxetgA0IwyAQ,35960
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+ tooluniverse/smcp.py,sha256=8wUqsfU23hokFheTec3arbezLTWhyC-j-AQ4gbTSA0Y,104045
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+ tooluniverse/smcp_server.py,sha256=7_e7Pwd5nMenKz1B9Y0HDkRcPaDbWy-RdFqKbXWKI_0,32428
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+ tooluniverse/string_tool.py,sha256=3rio0Lt97FuU6fbpykq3ETqD9pA4h_gPR0uXKRb7Zu4,3936
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- tooluniverse/unified_guideline_tools.py,sha256=q8XTctQ8fu3aiqpAaQ163aMyOQ2WUsZT6kF1ariZPgU,44819
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+ tooluniverse/ucsc_tool.py,sha256=0ZB2otPTfUYz2VxloC6OZXu2657sWWcj0mb0a3AvcjI,1879
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+ tooluniverse/unified_guideline_tools.py,sha256=Vhnqis4je3JZDJb7KfynAMX2D2yvW9I71_9mIsG1COU,88376
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- tooluniverse/utils.py,sha256=b3JUNmfInFaiDsx9MvXnb3PLu1UNzl4xmFhSrGpGqP4,18955
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+ tooluniverse/utils.py,sha256=9ZjQY_zp1Alfulpyt8bpoJ7n_d0y2IxBaxLmorp7BSw,20697
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- tooluniverse/zenodo_tool.py,sha256=S2S6OAFY-GFrBQmyzz8AahpqV29qiwIqpsTEk1ApCG4,2336
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+ tooluniverse/zenodo_tool.py,sha256=Ea5Za8A9uELJ7sL4pk0CerIke2ulvM590b7XjudwYbo,2435
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+ tooluniverse/cache/__init__.py,sha256=laKHcIpRjv_mJ8SkIO51-vYn0C4_9EZgHXeODeg818w,108
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+ tooluniverse/cache/memory_cache.py,sha256=MxfjdCL8O89q2lzs1M4hgVDStU2-eOlafrmvUS5Wh9Y,2757
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+ tooluniverse/cache/result_cache_manager.py,sha256=NagKpT_f8BX1eX4RGAGHLlAuA6NjG_IOOOFWCFkk4T8,7653
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+ tooluniverse/cache/sqlite_backend.py,sha256=D_BnyTld9oONmOuDKWyiy8pmUMO5VCb4DAAK-ynY_uE,8161
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@@ -87,7 +102,7 @@ tooluniverse/compose_scripts/drug_safety_analyzer.py,sha256=4lmGYY8a4T4WbeHIUG1a
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- tooluniverse/compose_scripts/output_summarizer.py,sha256=dCT9GAcplaaIWuOjF9uJTVer7z-xbclb2V9tqR1BPAY,10331
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+ tooluniverse/compose_scripts/output_summarizer.py,sha256=jcUA-6kIIMjOzS78QvobIWPDiAzl7M70KU9qBAb0ZXo,12225
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@@ -95,27 +110,28 @@ tooluniverse/compose_scripts/tool_graph_generation.py,sha256=rbkvAZFnGu1frsafHt_
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- tooluniverse/data/agentic_tools.json,sha256=GlY5yi7NX16iUfPElPyfLLVJMO4vipkr0Nb8g_On4Wc,95981
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+ tooluniverse/data/adverse_event_tools.json,sha256=gmO2euqIvLqc9lfmf9h9W0_TR33AYpMg_M1tzBNKm7w,12084
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+ tooluniverse/data/agentic_tools.json,sha256=Z5BSUxwC9uTJuP0SK5k_WnFs6qq4ow8Ib7m0mY-NlLo,93696
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+ tooluniverse/data/compose_tools.json,sha256=3CiMpiFdGNkJDw07CH4M-SU0Kl_xVGAQC376IxmlUtg,11721
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+ tooluniverse/data/core_tools.json,sha256=UB8aFpPZ5MVIju0OrfjQcJQedTPwCcVNqYNhPs0FmLU,3461
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+ tooluniverse/data/drug_discovery_agents.json,sha256=MXtIzEGAtx7LXmSXE55nwtF8uyjMK56Yyz5CNuhFwCQ,18392
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- tooluniverse/data/europe_pmc_tools.json,sha256=5mbtfisz_8p1oNgt9nXB7S_MnwUdCKrXMvBfW2mrDe4,3358
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+ tooluniverse/data/genomics_tools.json,sha256=2Ph0Tw3TsqY0UXi9yjL31jhZUE4zqJUmaqow4li2V7g,5962
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+ tooluniverse/data/geo_tools.json,sha256=_ZC_YHqErFCxod-XMU-ko_x2v1eXm_s5N8iG04JkChA,2834
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+ tooluniverse/data/literature_search_tools.json,sha256=nguJ7BTHvkexJUb82lHsDRvPNJVAoBleCyG5CdMe68I,10664
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+ tooluniverse/data/markitdown_tools.json,sha256=RPYWiJnvnYgIzwuZh649F9ky1VxdHvQ3pQHb8cdN4Oc,1483
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+ tooluniverse/data/pmc_tools.json,sha256=01RsH8y6wF8CdX3hQO4qqTgyGDA7uoJ4bD8H4Ss5MIs,3645
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+ tooluniverse/data/ppi_tools.json,sha256=tWpPiPbBkvrPFXpn-W1DEXjtuMQrZIcwXrjER37vO0E,4541
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+ tooluniverse/tools/CMA_Guidelines_Search.py,sha256=glO3Ro-ZzU-PKcrZyZymoknO3G7IuaDiMavRzCsXpA0,1370
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+ tooluniverse/tools/ClinVar_search_variants.py,sha256=ggmnsb8apm0J_wxDI5Vq0P028Q9_wvFYphhy--ra9a4,1314
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+ tooluniverse/tools/DrugInteractionAnalyzerAgent.py,sha256=91Ob6GcGPdo9iPwU5iIjDMzxZfCfO4Ap_0c0-SNOHso,1433
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+ tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py,sha256=49sFDwX8qpfaTq38Faz0xUE0jtk127rU8iFsLcPOqkM,1381
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+ tooluniverse/tools/GIN_Guidelines_Search.py,sha256=2GAwy7eF-Dg_0-NeAJ5IpeoA7iTdDHJBbBNkPcM5gCc,1370
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+ tooluniverse/tools/GWAS_search_associations_by_gene.py,sha256=DSxm7VWGr8yxvF-4738dYVmluYvsnHzKTwnQnr_K_rs,1365
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@@ -424,6 +455,7 @@ tooluniverse/tools/HypothesisGenerator.py,sha256=imtp_vMSHN-Nqz009qTWSl-HCVph2X-
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+ tooluniverse/tools/LiteratureSynthesisAgent.py,sha256=HHes1D2VkKqlXVE5r_oopyz1B6tify2CDiOpnH0QOYM,1509
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@@ -433,7 +465,6 @@ tooluniverse/tools/MedlinePlus_get_genetics_gene_by_name.py,sha256=6o4HPtrHF7cqc
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- tooluniverse/tools/PMC_search_papers.py,sha256=anhm_g4mi57gDkfXziOeMoEKuEkHIBTYExAxIdMxC3Y,1940
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+ tooluniverse/tools/PMC_search_papers.py,sha256=DaJf_7w8EOID9jnsgJFlYkNbwkfbrgGkn9ycDJTT64I,1991
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@@ -510,7 +541,7 @@ tooluniverse/tools/PubChem_get_compound_xrefs_by_CID.py,sha256=LpuLaUpTT-aBIZz0l
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  tooluniverse/tools/PubChem_search_compounds_by_substructure.py,sha256=tjFpoqofRQSCJN81NUbLiiFcxj7tECOQU96ALlwgWuU,1271
512
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  tooluniverse/tools/PubMed_Guidelines_Search.py,sha256=gO5Lxv2W2ATDenpyXpWNXtl24WbY0LaI2sDicfDv-C0,1537
513
- tooluniverse/tools/PubMed_search_articles.py,sha256=dWnkgbUeu3IRmykUkfg8goCeAfGgpLOwJIF5bpeJT5g,1547
544
+ tooluniverse/tools/PubMed_search_articles.py,sha256=LElAzC46YjylnAq_3Bms67W0bgraG4jODjfPGcrXfNM,1579
514
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  tooluniverse/tools/PubTator3_EntityAutocomplete.py,sha256=NN4snaloj6uLUuwlEG48bXf9olyyHPsLKzo2kbWyC5c,1645
515
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  tooluniverse/tools/PubTator3_LiteratureSearch.py,sha256=He9IQXl3etz0bVbmN7WCYFtZtGBy_BT5VSzkbnkHDKM,1525
516
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  tooluniverse/tools/QuestionRephraser.py,sha256=BMGWA5qwTwg_rFk3MS5dd0x49n_I4y5EBArWunQJIRQ,1369
@@ -518,7 +549,7 @@ tooluniverse/tools/Reactome_get_pathway_reactions.py,sha256=Qj0_sDHfAr9QRzojIw7-
518
549
  tooluniverse/tools/ReproducibilityTransparencyReviewer.py,sha256=P8PoYdej_vt7t3_h1OqBxs7kcYWjz_qI-efwXv-YBKY,1213
519
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  tooluniverse/tools/ResultsInterpretationReviewer.py,sha256=oVZPhI9NyA43bG817TW-8npHWQaZekMhltdXj8Jydsw,1325
520
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  tooluniverse/tools/ScientificTextSummarizer.py,sha256=ufld67qjywZs7ZP48l78mLNnKPbDRHdqVa0tZH_2exI,1614
521
- tooluniverse/tools/SemanticScholar_search_papers.py,sha256=ud-6B66ewsXJAmheUjHST71Il3fESJRHBm3kJ6AcBlM,1535
552
+ tooluniverse/tools/SemanticScholar_search_papers.py,sha256=MN7Rk7I2-AOOVmPB2xC2tCeLL2clwaYxSvkPQzFTV2c,1552
522
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  tooluniverse/tools/TRIP_Database_Guidelines_Search.py,sha256=hMPZbDkIRvjTk1b34EwSEdH6nnqSuXt-nRP1KlyxazU,1581
523
554
  tooluniverse/tools/TestCaseGenerator.py,sha256=RofMgoFDe-Xfm6SOg4-olck9Z8I6HQqp0vQKNrj5qsw,1244
524
555
  tooluniverse/tools/ToolCompatibilityAnalyzer.py,sha256=eZ1NirvA1aIoU7KdzeZbMqBBaMHINonQLGwXM9g0NTc,1686
@@ -540,6 +571,7 @@ tooluniverse/tools/Tool_Finder.py,sha256=8FS2PFkLfhXRmxwKovjE5HqRZci8HRLCNU8pe-N
540
571
  tooluniverse/tools/Tool_Finder_Keyword.py,sha256=1ivIsXJNylYFPDJbqC5bo7oWsWOLa9N39CDceGEaDtk,1955
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  tooluniverse/tools/Tool_Finder_LLM.py,sha256=kIqUNPUbRNjsM1jWqDSZ5bBd2z6f25BFVVXVrNInE9s,1973
542
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  tooluniverse/tools/Tool_RAG.py,sha256=BVF7re1cdn-84kCtyWKYpquUaG-JyihxjFCplxx3_WM,1188
574
+ tooluniverse/tools/UCSC_get_genes_by_region.py,sha256=_nAOBnyGUYeLTZPF0Vw76Igsqu8JHFYMfKAMbO7UuTg,1626
543
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  tooluniverse/tools/UniProt_get_alternative_names_by_accession.py,sha256=1YlnKrFkRl4S7aU6NF67AXk1tUclGWY8j7ZWa3WdFlA,1243
544
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  tooluniverse/tools/UniProt_get_disease_variants_by_accession.py,sha256=slx49NQ8Vjb9yMR_3XSSFlbR35SkIBhMw8N7dGG_pN0,1293
545
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  tooluniverse/tools/UniProt_get_entry_by_accession.py,sha256=a9VOFKgjHZoJnTASgjJjRO_ZkbCW2BJkeNJ3rJQTfnw,1189
@@ -555,8 +587,8 @@ tooluniverse/tools/WHO_Guideline_Full_Text.py,sha256=GkM3_FjGc4t-VWYIdhW1t6zd_dR
555
587
  tooluniverse/tools/WHO_Guidelines_Search.py,sha256=skaP8MvndBmB8bg9HM3mQjWpFTJFLIO_cfRI4WVcSL0,1380
556
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  tooluniverse/tools/Wikidata_SPARQL_query.py,sha256=7KoUwdza5R9uVOT6TzyU3oshRzUYDO91qqpwJA8PB_8,1426
557
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  tooluniverse/tools/WritingPresentationReviewer.py,sha256=7OiJnRcSWjZSp1lJsM9wxBupdMAeHXNymYev-AWU-iI,1171
558
- tooluniverse/tools/Zenodo_search_records.py,sha256=hhTOb71icJq2kTN6kK0iglAbAasWWwb97QP0DWdrqCg,1621
559
- tooluniverse/tools/__init__.py,sha256=kVVAOC9gxGC5krx5pEauYwPtAe-0-K59om9OZUzNpN4,77196
590
+ tooluniverse/tools/Zenodo_search_records.py,sha256=PfoUaXvGUCifJqFvlkFei6t8CeiT5BHuiEO7d5WApUE,1638
591
+ tooluniverse/tools/__init__.py,sha256=TjCVrrE0xDFTZGmXR_FL7_6KpXNLdjB9y9aI8cOd0Ng,78576
560
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  tooluniverse/tools/_shared_client.py,sha256=USiz6n6TD5T42TRasjOvYqUvl8GnDIxzubfiv_U5obE,4839
561
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  tooluniverse/tools/alphafold_get_annotations.py,sha256=QqykC55liO1JyPebtS_fnnAGaJ9niTgex6IL14JplIo,1401
562
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  tooluniverse/tools/alphafold_get_prediction.py,sha256=7W9r_U6ZoZAnMKUBWWZwnaY4WVpMORJxkIdnCiXmBTo,1489
@@ -568,6 +600,8 @@ tooluniverse/tools/cellosaurus_get_cell_line_info.py,sha256=qIscXy2aT49n_Fuits5H
568
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  tooluniverse/tools/cellosaurus_query_converter.py,sha256=QaZnONoID32c9-zeLjeAZQUfh_geG2LKg2fx5WLU3d4,1475
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  tooluniverse/tools/cellosaurus_search_cell_lines.py,sha256=KBJ4fisp-DxCR5FBzcaFkn68WFhkjvd3Siy932yoV-0,1478
570
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  tooluniverse/tools/chembl_disease_target_score.py,sha256=Zm9dbl4JVuIKjWhe42EzBNDzAc0cRlszCy7hL_btl18,1415
603
+ tooluniverse/tools/convert_to_markdown.py,sha256=GcCsCoTKLzC_gS6CUiIP-9VdnWsF4A9VWztgQV6jD3g,1534
604
+ tooluniverse/tools/dbSNP_get_variant_by_rsid.py,sha256=O58MhyK2XUSw6C12HTQNRqIa848pC4c7ITfE1ssR6Yc,1174
571
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  tooluniverse/tools/dict_search.py,sha256=Ux7FL7yON8OkS9QHfpwV63NXMOea5gpjpioQ8vUO38I,1849
572
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  tooluniverse/tools/dili_search.py,sha256=s9EsrUB8JV6oj9z82FA6TX0GL5D8CYrmj4PoL4VPxRw,1809
573
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  tooluniverse/tools/diqt_search.py,sha256=T-vZPnXdF6VnzGEnYu9bSBkhOKXlB_POnO_cMkoC3YQ,1841
@@ -820,6 +854,7 @@ tooluniverse/tools/get_xarray_info.py,sha256=FM1FAINtYc6s_A9cW9kG77lph0b_EaJXIxD
820
854
  tooluniverse/tools/get_xesmf_info.py,sha256=qGm7AFt024R71uv6KeXJP06gKzJKtLhn987ceOFKNN8,1029
821
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  tooluniverse/tools/get_xgboost_info.py,sha256=KGEy1aH3wIvV6WVog7zg_JcfJq2bf4Ry6frL8k7nZMg,1037
822
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  tooluniverse/tools/get_zarr_info.py,sha256=e9x-YgEFXbk6S8qtR0tErs51FZQBLiuO4x5ywB9mBnI,1027
857
+ tooluniverse/tools/gnomAD_query_variant.py,sha256=KI031hxoq-KaYyg_LNVYqO4Ucxd9DJyoI2ea2cFKkno,1351
823
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  tooluniverse/tools/gwas_get_association_by_id.py,sha256=peCKnGAww2wwVVSHSuWaUbXWZ6j4NIR4-8ZjG9_hW4c,1188
824
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  tooluniverse/tools/gwas_get_associations_for_snp.py,sha256=Zo1AmKB9Upj7BzPc6TVG8pRmq4sp7_UW9VVNeP0TD8s,1695
825
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  tooluniverse/tools/gwas_get_associations_for_study.py,sha256=AcobAhYhZ9BPKG9uVby7GREyu1V2zgq3-A0F4oNKfEo,1409
@@ -841,15 +876,15 @@ tooluniverse/tools/odphp_itemlist.py,sha256=WG6SfBH_NOoaGknMl4HuHX7RkfOOJliKuQys
841
876
  tooluniverse/tools/odphp_myhealthfinder.py,sha256=63TT6qurOPvhWdhJ382m69-1Ry6reII6_6mr4lOXCOs,1666
842
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  tooluniverse/tools/odphp_outlink_fetch.py,sha256=0XEAlUab5QodcNNKlzN7uTj019crSyM-bkicdBnAQgA,1570
843
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  tooluniverse/tools/odphp_topicsearch.py,sha256=nqgAzxqrU1WE6BFZzsv73vtpJ-Zd57s5HpDe3CmMxbg,1723
844
- tooluniverse/tools/openalex_literature_search.py,sha256=f-tjB0zmbKvw_fjPGjXIWLqWePZyscmgOHwWNQWuvJM,2023
879
+ tooluniverse/tools/openalex_literature_search.py,sha256=U2vc_hfb21FdZnJPkVoaykbH2zLIyQVXA86ApX_vWLg,2089
845
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  tooluniverse/tools/reactome_disease_target_score.py,sha256=pSSPBCJjgyugexkzf8y5s9w44vJ87lKJlHxMftUe1_c,1423
846
881
  tooluniverse/tools/search_clinical_trials.py,sha256=skW3aPZ1gXfjKJz8WkxGpt93XlHpnFc5oLIJbffUWc8,2044
847
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  tooluniverse/tools/visualize_molecule_2d.py,sha256=yaaGErioVPG5qMi8nR6DbZbojJVCUc2mDiO7icBG60U,2462
848
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  tooluniverse/tools/visualize_molecule_3d.py,sha256=0fFkjGz0hrNyRBiXRV_FY8yWXR47jZQXatXLxXwbrXw,2693
849
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  tooluniverse/tools/visualize_protein_structure_3d.py,sha256=ifTkgPvtNtvJ9q8d7zmSqSnd32oFmRcKkoO8p1SdVUU,2358
850
- tooluniverse-1.0.7.dist-info/licenses/LICENSE,sha256=0P0qDClpVzrnQUe3QAu7V-alszSBa-6hVHXyn9Xe60k,11351
851
- tooluniverse-1.0.7.dist-info/METADATA,sha256=F2pqZIsxseBxx_OW2GOblaTR_4aWpmcd0DBOMOKLoOc,20869
852
- tooluniverse-1.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
853
- tooluniverse-1.0.7.dist-info/entry_points.txt,sha256=IL3WSOgt9bAT8IWPMQSUYJmV_mma7a60E77oO0u3Jik,928
854
- tooluniverse-1.0.7.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
855
- tooluniverse-1.0.7.dist-info/RECORD,,
885
+ tooluniverse-1.0.9.dist-info/licenses/LICENSE,sha256=0P0qDClpVzrnQUe3QAu7V-alszSBa-6hVHXyn9Xe60k,11351
886
+ tooluniverse-1.0.9.dist-info/METADATA,sha256=O-jvVL_cYpObdnviT8DoBx4ciJ384Ry31TRPgRhoGA8,21159
887
+ tooluniverse-1.0.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
888
+ tooluniverse-1.0.9.dist-info/entry_points.txt,sha256=SAdqP4tU4mMOtp1YWaOHTwnIHhnoiD1wmfKGlSfNSy0,647
889
+ tooluniverse-1.0.9.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
890
+ tooluniverse-1.0.9.dist-info/RECORD,,
@@ -1,13 +1,10 @@
1
1
  [console_scripts]
2
2
  generate-mcp-tools = tooluniverse.generate_mcp_tools:run_generate
3
- tooluniverse-agent-search = tooluniverse.web_tools.literature_search_ui.agent_search_app:main
4
3
  tooluniverse-doctor = tooluniverse.doctor:main
5
4
  tooluniverse-expert-feedback = tooluniverse.remote.expert_feedback.human_expert_mcp_tools:main
6
5
  tooluniverse-expert-feedback-web = tooluniverse.remote.expert_feedback.start_web_interface:main
7
6
  tooluniverse-mcp = tooluniverse.smcp_server:run_http_server
8
7
  tooluniverse-mcp-claude = tooluniverse.smcp_server:run_stdio_server
9
- tooluniverse-regular-search = tooluniverse.web_tools.literature_search_ui.regular_search_app:main
10
8
  tooluniverse-smcp = tooluniverse.smcp_server:run_smcp_server
11
9
  tooluniverse-smcp-server = tooluniverse.smcp_server:run_http_server
12
10
  tooluniverse-smcp-stdio = tooluniverse.smcp_server:run_stdio_server
13
- tooluniverse-wide-research = tooluniverse.web_tools.literature_search_ui.simple_app:main