flowapy 0.2.0__tar.gz → 0.2.2__tar.gz

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Files changed (320) hide show
  1. {flowapy-0.2.0 → flowapy-0.2.2}/PKG-INFO +1 -1
  2. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/aggregation.json +1207 -1146
  3. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1002%2Fhumu.23878.json +84 -0
  4. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1016%2Fj.ymgmr.2024.101163.json +12 -4
  5. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1038%2Fs41598-022-25914-8.json +105 -0
  6. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs12881-019-0878-8.json +69 -0
  7. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13023-021-01817-1.json +44 -44
  8. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13023-021-02146-z.json +40 -0
  9. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13023-023-02848-6.json +117 -0
  10. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13052-019-0692-0.json +45 -0
  11. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffcvm.2022.1061384.json +37 -0
  12. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffcvm.2023.1261172.json +45 -0
  13. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffimmu.2024.1336599.json +53 -0
  14. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffped.2021.729824.json +53 -0
  15. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffphar.2022.903488.json +77 -0
  16. flowapy-0.2.2/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3390%2Fijns11010016.json +29 -0
  17. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3390%2Fijns6020031.json +3 -3
  18. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo-gateway/uv.lock +36 -36
  19. {flowapy-0.2.0 → flowapy-0.2.2}/packages/react-viewer/package.json +1 -1
  20. {flowapy-0.2.0 → flowapy-0.2.2}/packages/react-viewer/src/pdf-viewer/PdfHighlightViewer.test.tsx +21 -1
  21. {flowapy-0.2.0 → flowapy-0.2.2}/packages/react-viewer/src/pdf-viewer/PdfHighlightViewer.tsx +31 -7
  22. {flowapy-0.2.0 → flowapy-0.2.2}/packages/react-viewer/src/pdf-viewer/types.ts +7 -0
  23. {flowapy-0.2.0 → flowapy-0.2.2}/packages/react-viewer/src/triage/EvidenceViewerShell.tsx +34 -2
  24. {flowapy-0.2.0 → flowapy-0.2.2}/prompts/generic/extraction_prompt.txt +1 -7
  25. {flowapy-0.2.0 → flowapy-0.2.2}/pyproject.toml +1 -1
  26. {flowapy-0.2.0 → flowapy-0.2.2}/src/flowa/aggregate.py +55 -37
  27. flowapy-0.2.2/src/flowa/content_validation.py +153 -0
  28. flowapy-0.2.2/tests/test_content_validation.py +164 -0
  29. {flowapy-0.2.0 → flowapy-0.2.2}/uv.lock +1 -1
  30. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1002%2Fhumu.23878.json +0 -77
  31. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1038%2Fs41598-022-25914-8.json +0 -109
  32. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs12881-019-0878-8.json +0 -61
  33. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13023-021-02146-z.json +0 -37
  34. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13023-023-02848-6.json +0 -133
  35. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.1186%2Fs13052-019-0692-0.json +0 -85
  36. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffcvm.2022.1061384.json +0 -37
  37. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffcvm.2023.1261172.json +0 -69
  38. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffimmu.2024.1336599.json +0 -96
  39. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffped.2021.729824.json +0 -37
  40. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3389%2Ffphar.2022.903488.json +0 -61
  41. flowapy-0.2.0/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/extractions/10.3390%2Fijns11010016.json +0 -37
  42. {flowapy-0.2.0 → flowapy-0.2.2}/.env.example +0 -0
  43. {flowapy-0.2.0 → flowapy-0.2.2}/.github/dependabot.yml +0 -0
  44. {flowapy-0.2.0 → flowapy-0.2.2}/.github/workflows/dependabot-auto-merge.yml +0 -0
  45. {flowapy-0.2.0 → flowapy-0.2.2}/.github/workflows/lint.yaml +0 -0
  46. {flowapy-0.2.0 → flowapy-0.2.2}/.github/workflows/release-chat-service.yaml +0 -0
  47. {flowapy-0.2.0 → flowapy-0.2.2}/.github/workflows/release-flowapy.yaml +0 -0
  48. {flowapy-0.2.0 → flowapy-0.2.2}/.github/workflows/release-react-viewer.yaml +0 -0
  49. {flowapy-0.2.0 → flowapy-0.2.2}/.gitignore +0 -0
  50. {flowapy-0.2.0 → flowapy-0.2.2}/.markdownlint.json +0 -0
  51. {flowapy-0.2.0 → flowapy-0.2.2}/.nvmrc +0 -0
  52. {flowapy-0.2.0 → flowapy-0.2.2}/.pre-commit-config.yaml +0 -0
  53. {flowapy-0.2.0 → flowapy-0.2.2}/.prettierignore +0 -0
  54. {flowapy-0.2.0 → flowapy-0.2.2}/Dockerfile +0 -0
  55. {flowapy-0.2.0 → flowapy-0.2.2}/LICENSE +0 -0
  56. {flowapy-0.2.0 → flowapy-0.2.2}/README.md +0 -0
  57. {flowapy-0.2.0 → flowapy-0.2.2}/docs/images/viewer.png +0 -0
  58. {flowapy-0.2.0 → flowapy-0.2.2}/examples/.gitkeep +0 -0
  59. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/.env.example +0 -0
  60. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/.gitignore +0 -0
  61. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/README.md +0 -0
  62. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/LICENSES.md +0 -0
  63. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/query.json +0 -0
  64. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/runs/cfc0186a7b7e46eb802a516b86ec207f/progress.jsonl +0 -0
  65. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/assessments/NM_000152_5-c_1935C_A/variant_details.json +0 -0
  66. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1002%2Fajmg.a.61481/metadata.json +0 -0
  67. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1002%2Fhumu.23878/markdown.md +0 -0
  68. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1002%2Fhumu.23878/metadata.json +0 -0
  69. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1002%2Fhumu.23878/pdf_index.pkl.zst +0 -0
  70. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1002%2Fhumu.23878/source.pdf +0 -0
  71. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.ejmg.2020.103997/metadata.json +0 -0
  72. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.nmd.2022.02.002/metadata.json +0 -0
  73. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.tjog.2022.07.008/metadata.json +0 -0
  74. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.ymgmr.2024.101163/markdown.md +0 -0
  75. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.ymgmr.2024.101163/metadata.json +0 -0
  76. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.ymgmr.2024.101163/pdf_index.pkl.zst +0 -0
  77. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1016%2Fj.ymgmr.2024.101163/source.pdf +0 -0
  78. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1038%2Fs41598-022-25914-8/markdown.md +0 -0
  79. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1038%2Fs41598-022-25914-8/metadata.json +0 -0
  80. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1038%2Fs41598-022-25914-8/pdf_index.pkl.zst +0 -0
  81. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1038%2Fs41598-022-25914-8/source.pdf +0 -0
  82. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1093%2Fhmg%2Fddz218/metadata.json +0 -0
  83. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1136%2Fjmg-2022-108675/metadata.json +0 -0
  84. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs12881-019-0878-8/markdown.md +0 -0
  85. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs12881-019-0878-8/metadata.json +0 -0
  86. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs12881-019-0878-8/pdf_index.pkl.zst +0 -0
  87. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs12881-019-0878-8/source.pdf +0 -0
  88. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-01817-1/markdown.md +0 -0
  89. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-01817-1/metadata.json +0 -0
  90. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-01817-1/pdf_index.pkl.zst +0 -0
  91. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-01817-1/source.pdf +0 -0
  92. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-02146-z/markdown.md +0 -0
  93. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-02146-z/metadata.json +0 -0
  94. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-02146-z/pdf_index.pkl.zst +0 -0
  95. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-021-02146-z/source.pdf +0 -0
  96. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-023-02848-6/markdown.md +0 -0
  97. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-023-02848-6/metadata.json +0 -0
  98. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-023-02848-6/pdf_index.pkl.zst +0 -0
  99. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13023-023-02848-6/source.pdf +0 -0
  100. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13052-019-0692-0/markdown.md +0 -0
  101. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13052-019-0692-0/metadata.json +0 -0
  102. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13052-019-0692-0/pdf_index.pkl.zst +0 -0
  103. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.1186%2Fs13052-019-0692-0/source.pdf +0 -0
  104. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2022.1061384/markdown.md +0 -0
  105. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2022.1061384/metadata.json +0 -0
  106. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2022.1061384/pdf_index.pkl.zst +0 -0
  107. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2022.1061384/source.pdf +0 -0
  108. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2023.1261172/markdown.md +0 -0
  109. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2023.1261172/metadata.json +0 -0
  110. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2023.1261172/pdf_index.pkl.zst +0 -0
  111. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffcvm.2023.1261172/source.pdf +0 -0
  112. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffimmu.2024.1336599/markdown.md +0 -0
  113. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffimmu.2024.1336599/metadata.json +0 -0
  114. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffimmu.2024.1336599/pdf_index.pkl.zst +0 -0
  115. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffimmu.2024.1336599/source.pdf +0 -0
  116. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffped.2021.729824/markdown.md +0 -0
  117. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffped.2021.729824/metadata.json +0 -0
  118. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffped.2021.729824/pdf_index.pkl.zst +0 -0
  119. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffped.2021.729824/source.pdf +0 -0
  120. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffphar.2022.903488/markdown.md +0 -0
  121. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffphar.2022.903488/metadata.json +0 -0
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  123. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3389%2Ffphar.2022.903488/source.pdf +0 -0
  124. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/fixtures/papers/10.3390%2Fijns11010016/markdown.md +0 -0
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  132. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/next-env.d.ts +0 -0
  133. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/next.config.mjs +0 -0
  134. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/package.json +0 -0
  135. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/postcss.config.cjs +0 -0
  136. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/public/favicon.svg +0 -0
  137. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/scripts/chat-service.ts +0 -0
  138. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/scripts/copy-pdfjs-assets.ts +0 -0
  139. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/scripts/exercise-llm.ts +0 -0
  140. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/scripts/start.ts +0 -0
  141. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/components/literature/LiteratureView.tsx +0 -0
  142. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/components/literature/PaperStatusGroup.tsx +0 -0
  143. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/components/literature/ProgressLog.tsx +0 -0
  144. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/components/literature/matchFilename.ts +0 -0
  145. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/db/migrate.ts +0 -0
  146. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/db/schema.sql +0 -0
  147. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/lib/aggregate.ts +0 -0
  148. {flowapy-0.2.0 → flowapy-0.2.2}/examples/demo/src/lib/chatSessionClient.ts +0 -0
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  Metadata-Version: 2.4
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  Name: flowapy
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  Summary: Variant literature assessment pipeline with AI extraction
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  Project-URL: Homepage, https://github.com/populationgenomics/flowa
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  Project-URL: Source, https://github.com/populationgenomics/flowa