aurelian 0.4.1__tar.gz → 0.4.2__tar.gz

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  1. {aurelian-0.4.1 → aurelian-0.4.2}/PKG-INFO +1 -1
  2. {aurelian-0.4.1 → aurelian-0.4.2}/pyproject.toml +1 -1
  3. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/ubergraph/ubergraph_tools.py +18 -6
  4. {aurelian-0.4.1 → aurelian-0.4.2}/LICENSE +0 -0
  5. {aurelian-0.4.1 → aurelian-0.4.2}/README.md +0 -0
  6. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/__init__.py +0 -0
  7. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/__init__.py +0 -0
  8. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/__init__.py +0 -0
  9. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_agent.py +0 -0
  10. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_config.py +0 -0
  11. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_evals.py +0 -0
  12. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_gradio.py +0 -0
  13. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_mcp.py +0 -0
  14. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/amigo/amigo_tools.py +0 -0
  15. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/__init__.py +0 -0
  16. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/biblio_agent.py +0 -0
  17. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/biblio_config.py +0 -0
  18. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/biblio_gradio.py +0 -0
  19. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/biblio_mcp.py +0 -0
  20. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio/biblio_tools.py +0 -0
  21. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/biblio_agent.py +0 -0
  22. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/__init__.py +0 -0
  23. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/checklist_agent.py +0 -0
  24. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/checklist_config.py +0 -0
  25. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/checklist_gradio.py +0 -0
  26. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/checklist_mcp.py +0 -0
  27. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/checklist_tools.py +0 -0
  28. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/content/checklists.yaml +0 -0
  29. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist/content/streams.csv +0 -0
  30. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/checklist_agent.py +0 -0
  31. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/__init__.py +0 -0
  32. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_agent.py +0 -0
  33. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_config.py +0 -0
  34. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_evals.py +0 -0
  35. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_gradio.py +0 -0
  36. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_mcp.py +0 -0
  37. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/chemistry_tools.py +0 -0
  38. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/chemistry/image_agent.py +0 -0
  39. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/__init__.py +0 -0
  40. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/d4d_agent.py +0 -0
  41. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/d4d_config.py +0 -0
  42. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/d4d_gradio.py +0 -0
  43. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/d4d_mcp.py +0 -0
  44. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d/d4d_tools.py +0 -0
  45. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/d4d_agent.py +0 -0
  46. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/__init__.py +0 -0
  47. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_agent.py +0 -0
  48. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_config.py +0 -0
  49. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_evals.py +0 -0
  50. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_gradio.py +0 -0
  51. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_mcp.py +0 -0
  52. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis/diagnosis_tools.py +0 -0
  53. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/diagnosis_agent.py +0 -0
  54. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/__init__.py +0 -0
  55. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/draw_agent.py +0 -0
  56. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/draw_config.py +0 -0
  57. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/draw_gradio.py +0 -0
  58. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/draw_mcp.py +0 -0
  59. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/draw_tools.py +0 -0
  60. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/draw/judge_agent.py +0 -0
  61. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/__init__.py +0 -0
  62. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/filesystem_config.py +0 -0
  63. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/filesystem_gradio.py +0 -0
  64. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/filesystem_mcp.py +0 -0
  65. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/filesystem_tools.py +0 -0
  66. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/filesystem/py.typed +0 -0
  67. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/__init__.py +0 -0
  68. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_agent.py +0 -0
  69. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_cli.py +0 -0
  70. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_config.py +0 -0
  71. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_gradio.py +0 -0
  72. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_mcp.py +0 -0
  73. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_tools.py +0 -0
  74. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/github/github_tools.py.tmp +0 -0
  75. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/__init__.py +0 -0
  76. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.md +0 -0
  77. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines.pdf +0 -0
  78. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.md +0 -0
  79. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/documents/Transcription_Factors_Annotation_Guidelines_Paper.pdf +0 -0
  80. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_agent.py +0 -0
  81. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_config.py +0 -0
  82. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_evals.py +0 -0
  83. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_gradio.py +0 -0
  84. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_mcp.py +0 -0
  85. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/goann/goann_tools.py +0 -0
  86. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/__init__.py +0 -0
  87. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.docx +0 -0
  88. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/DNA-binding transcription factor activity annotation guidelines.pdf +0 -0
  89. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/DNA-binding_transcription_factor_activity_annotation_guidelines.md +0 -0
  90. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/E3 ubiquitin ligases.docx +0 -0
  91. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/E3 ubiquitin ligases.pdf +0 -0
  92. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/E3_ubiquitin_ligases.md +0 -0
  93. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.docx +0 -0
  94. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM annotation guidelines README.pdf +0 -0
  95. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.docx +0 -0
  96. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM modelling guidelines TO DO.pdf +0 -0
  97. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM_annotation_guidelines_README.md +0 -0
  98. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/GO-CAM_modelling_guidelines_TO_DO.md +0 -0
  99. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.docx +0 -0
  100. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate complexes in GO-CAM.pdf +0 -0
  101. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate molecular adaptors.docx +0 -0
  102. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate molecular adaptors.pdf +0 -0
  103. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate sequestering proteins.docx +0 -0
  104. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How to annotate sequestering proteins.pdf +0 -0
  105. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How_to_annotate_complexes_in_GO-CAM.md +0 -0
  106. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How_to_annotate_molecular_adaptors.md +0 -0
  107. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/How_to_annotate_sequestering_proteins.md +0 -0
  108. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular adaptor activity.docx +0 -0
  109. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular adaptor activity.pdf +0 -0
  110. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular carrier activity.docx +0 -0
  111. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular carrier activity.pdf +0 -0
  112. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular_adaptor_activity.md +0 -0
  113. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Molecular_carrier_activity.md +0 -0
  114. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Protein sequestering activity.docx +0 -0
  115. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Protein sequestering activity.pdf +0 -0
  116. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Protein_sequestering_activity.md +0 -0
  117. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.docx +0 -0
  118. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Signaling receptor activity annotation guidelines.pdf +0 -0
  119. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Signaling_receptor_activity_annotation_guidelines.md +0 -0
  120. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transcription coregulator activity.docx +0 -0
  121. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transcription coregulator activity.pdf +0 -0
  122. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transcription_coregulator_activity.md +0 -0
  123. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.docx +0 -0
  124. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transporter activity annotation annotation guidelines.pdf +0 -0
  125. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/Transporter_activity_annotation_annotation_guidelines.md +0 -0
  126. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/WIP - Regulation and Regulatory Processes in GO-CAM.docx +0 -0
  127. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/WIP - Regulation and Regulatory Processes in GO-CAM.pdf +0 -0
  128. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/WIP_-_Regulation_and_Regulatory_Processes_in_GO-CAM.md +0 -0
  129. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/DNA-binding_transcription_factor_activity_annotation_guidelines.md +0 -0
  130. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/E3_ubiquitin_ligases.md +0 -0
  131. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/GO-CAM_annotation_guidelines_README.md +0 -0
  132. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/GO-CAM_modelling_guidelines_TO_DO.md +0 -0
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  137. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/Molecular_carrier_activity.md +0 -0
  138. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/Protein_sequestering_activity.md +0 -0
  139. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/Signaling_receptor_activity_annotation_guidelines.md +0 -0
  140. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/documents/md/Transcription_coregulator_activity.md +0 -0
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  144. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_agent.py +0 -0
  145. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_config.py +0 -0
  146. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_curator_agent.py +0 -0
  147. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_evals.py +0 -0
  148. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_gradio.py +0 -0
  149. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_mcp.py +0 -0
  150. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/gocam/gocam_tools.py +0 -0
  151. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/linkml/__init__.py +0 -0
  152. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/linkml/linkml_agent.py +0 -0
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  157. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/linkml/linkml_tools.py +0 -0
  158. {aurelian-0.4.1 → aurelian-0.4.2}/src/aurelian/agents/literature/__init__.py +0 -0
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@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: aurelian
3
- Version: 0.4.1
3
+ Version: 0.4.2
4
4
  Summary: aurelian
5
5
  License: MIT
6
6
  Author: Author 1
@@ -3,7 +3,7 @@ name = "aurelian"
3
3
 
4
4
  [tool.poetry]
5
5
  name = "aurelian"
6
- version = "0.4.1"
6
+ version = "0.4.2"
7
7
  description = "aurelian"
8
8
  authors = ["Author 1 <author@org.org>"]
9
9
  license = "MIT"
@@ -4,9 +4,9 @@ Tools for interacting with the UberGraph SPARQL endpoint.
4
4
  import asyncio
5
5
  from typing import Any, Dict, List, Optional
6
6
 
7
+ import requests
7
8
  from pydantic import BaseModel
8
9
  from pydantic_ai import RunContext, ModelRetry
9
- from SPARQLWrapper import JSON, SPARQLWrapper
10
10
 
11
11
  from .ubergraph_config import Dependencies, get_config
12
12
 
@@ -88,13 +88,23 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
88
88
  print("##")
89
89
 
90
90
  try:
91
- # Create SPARQL wrapper
92
- sw = SPARQLWrapper(endpoint)
93
- sw.setQuery(prefixed_query)
94
- sw.setReturnFormat(JSON)
91
+ # Define a function to execute in a thread pool
92
+ def run_query():
93
+ response = requests.post(
94
+ endpoint,
95
+ data={
96
+ 'query': prefixed_query,
97
+ },
98
+ headers={
99
+ 'Accept': 'application/sparql-results+json',
100
+ 'Content-Type': 'application/x-www-form-urlencoded'
101
+ }
102
+ )
103
+ response.raise_for_status() # Raise an exception for HTTP errors
104
+ return response.json()
95
105
 
96
106
  # Execute the query in a thread pool
97
- ret = await asyncio.to_thread(sw.queryAndConvert)
107
+ ret = await asyncio.to_thread(run_query)
98
108
 
99
109
  # Process the results
100
110
  results = simplify_results(ret, prefixes, limit=config.max_results)
@@ -105,6 +115,8 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
105
115
  raise ModelRetry(f"No results found for SPARQL query. Try refining your query.")
106
116
 
107
117
  return QueryResults(results=results)
118
+ except requests.RequestException as e:
119
+ raise ModelRetry(f"Error connecting to SPARQL endpoint: {str(e)}")
108
120
  except Exception as e:
109
121
  if "ModelRetry" in str(type(e)):
110
122
  raise e
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