opencloning 0.3.8__py3-none-any.whl → 0.4.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. opencloning/app_settings.py +1 -0
  2. opencloning/batch_cloning/EBIC/example.py +1 -3
  3. opencloning/batch_cloning/pombe/pombe_clone.py +29 -37
  4. opencloning/batch_cloning/pombe/pombe_summary.py +11 -7
  5. opencloning/batch_cloning/ziqiang_et_al2024/__init__.py +28 -56
  6. opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json +47 -56
  7. opencloning/bug_fixing/README.md +5 -2
  8. opencloning/bug_fixing/backend_v0_3.py +12 -15
  9. opencloning/dna_functions.py +5 -6
  10. opencloning/dna_utils.py +26 -21
  11. opencloning/endpoints/assembly.py +27 -23
  12. opencloning/endpoints/no_assembly.py +8 -5
  13. opencloning/endpoints/no_input.py +11 -4
  14. opencloning/pydantic_models.py +57 -24
  15. opencloning/request_examples.py +4 -4
  16. {opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/METADATA +6 -5
  17. {opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/RECORD +19 -21
  18. opencloning/assembly2.py +0 -1467
  19. opencloning/batch_cloning/pombe/pombe_all.sh +0 -9
  20. {opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/LICENSE +0 -0
  21. {opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/WHEEL +0 -0
{opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: opencloning
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- Version: 0.3.8
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+ Version: 0.4.2
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  Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
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  License: MIT
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  Author: Manuel Lera-Ramirez
@@ -12,19 +12,20 @@ Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: 3.13
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  Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
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- Requires-Dist: biopython (==1.84)
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+ Requires-Dist: biopython (>=1.85,<2.0)
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  Requires-Dist: fastapi
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  Requires-Dist: httpx (>=0.28.1,<0.29.0)
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- Requires-Dist: opencloning-linkml (==0.3.0a0)
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+ Requires-Dist: opencloning-linkml (==0.4.3)
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  Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
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  Requires-Dist: packaging (>=25.0,<26.0)
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+ Requires-Dist: pairwise-alignments-to-msa (>=0.1.1,<0.2.0)
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  Requires-Dist: pandas (>=2.2.3,<3.0.0)
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  Requires-Dist: primer3-py (==2.2.0)
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  Requires-Dist: pydantic (>=2.7.1,<3.0.0)
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- Requires-Dist: pydna (==5.5.0)
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+ Requires-Dist: pydna (==5.5.2)
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  Requires-Dist: python-multipart
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  Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
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- Requires-Dist: regex (>=2023.10.3,<2024.0.0)
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+ Requires-Dist: regex (>=2024.11.6,<2025.0.0)
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  Requires-Dist: uvicorn
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  Project-URL: Repository, https://github.com/manulera/OpenCloning_backend
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  Description-Content-Type: text/markdown
{opencloning-0.3.8.dist-info → opencloning-0.4.2.dist-info}/RECORD RENAMED
@@ -1,39 +1,37 @@
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  opencloning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  opencloning/_version.py,sha256=6QbWXLSZypjtWL_CwJFHH4dzMRK3AUH4B0YudzvGz9s,200
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  opencloning/api_config_utils.py,sha256=inAXPGYNDz-DuEoSqitImj0Vv5TpQSbMZH9D3dQb5P0,4319
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- opencloning/app_settings.py,sha256=1GFD0_DcKTlhwAcbXRXGWY6d_7LrKbtbHd5NPVasKb8,2874
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- opencloning/assembly2.py,sha256=M-Als7mrEdHc8Ee3Zr_pgQ5WiN7Uqd37BMxr9Q-1myw,61743
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+ opencloning/app_settings.py,sha256=FJFayBMLtE9gRC1e0ns5sVQRUb9DVXJ8o-ix4bTlPmI,2911
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  opencloning/batch_cloning/EBIC/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  opencloning/batch_cloning/EBIC/barcode.gb,sha256=G6kP6MuY23S-n3xg16LQaTasFtYFqik5eEgcooZ9ATM,815
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  opencloning/batch_cloning/EBIC/common_plasmid.gb,sha256=At1HJjqJ2MsLMEx6W3MihJy7tgdtDu3fhwF4YGuw8Dk,13068
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- opencloning/batch_cloning/EBIC/example.py,sha256=FWjROXWsgM-gz2oYnKiywUVKa9uoEe964FlFRle_hYI,6870
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+ opencloning/batch_cloning/EBIC/example.py,sha256=1OENMoPVn5lhTall_DvD7qx7t021a2HMV11kpStVs88,6851
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  opencloning/batch_cloning/EBIC/primer_design_settings.py,sha256=MVML1r1ciJYMFUJoqZVcGLoPM-f28oBN1wSDzlD0y64,1896
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  opencloning/batch_cloning/__init__.py,sha256=uDxAa45g30_S6dJScNMlIxubQXlLRUsWoLX4S4y-l88,244
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  opencloning/batch_cloning/index.html,sha256=HDqPHrJxrrKfGmy_dwYHhOsdUgZHHIch7Z0ey8qyvZI,1332
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  opencloning/batch_cloning/pombe/__init__.py,sha256=Fq7SroO0Fer5CtFBRWdduIvzp1_dTUZwBb8IjBtRQO0,3332
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  opencloning/batch_cloning/pombe/index.html,sha256=3YchoKGpcKDfvTOW1Rdih4PkbZIkMjKIQ0PaVXfV3e8,8348
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- opencloning/batch_cloning/pombe/pombe_all.sh,sha256=0yvDdBaIdt2RsIrvnjgn5L3KtYBToq3Rl8-X8RFHibE,364
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- opencloning/batch_cloning/pombe/pombe_clone.py,sha256=OY6yOlBK-9OAmHu3HUhP50mIXvyR0HJg1_2OjBFifV8,8123
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+ opencloning/batch_cloning/pombe/pombe_clone.py,sha256=3Z51NA0rhU-e4SxuLnlV5iDWeQrqECJTfe8IfiDoiow,7996
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  opencloning/batch_cloning/pombe/pombe_gather.py,sha256=qI-biMZGLxVDV-vOf3sT6bS1BawtTihZNcSYNlnnEi8,2432
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  opencloning/batch_cloning/pombe/pombe_get_primers.py,sha256=nrn6V4_l8FWWfqS4WU3qPt95KwzvCXxETh8E-zWbRhM,3968
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- opencloning/batch_cloning/pombe/pombe_summary.py,sha256=W9DLpnCuwK7w2DhHLu60N7L6jquuYubD3ZRFwdhNPVw,4033
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- opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=zZUbj3uMzd9rKMXi5s9LQ1yUg7sccdS0f_4kpw7SQlk,7584
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+ opencloning/batch_cloning/pombe/pombe_summary.py,sha256=DBpoSEV1xPFm8TFDhrxS4tjqxJVrfH-ttM_0ELjQqok,4350
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+ opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=9-aG8JfZx8Y91qUAchTqRL2Rq5lSrZ34O_VkD8WNyiY,7083
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  opencloning/batch_cloning/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
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- opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=d-7oXbxoKhMKLz4FJ2OGDdedWTisoaRqLAh1NZnScBg,157189
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- opencloning/bug_fixing/README.md,sha256=fGf_4HPTZ2TjGfIOZzw8IAD78-N-RnBrX8mz14wjXEQ,4237
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+ opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=JAOe35VPeG3QF1CnDzZxOzqpBTSpeCCtAo2W1mVOFEo,157159
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+ opencloning/bug_fixing/README.md,sha256=eak5x1NTyTxsklaZ1BzB3RYH26MC_2gNuH-gHvuNpKY,4441
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  opencloning/bug_fixing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- opencloning/bug_fixing/backend_v0_3.py,sha256=BTnqCXYIcOShut0WfwH6tDjJ1fecAHFHVSDTOKJgUZw,4119
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+ opencloning/bug_fixing/backend_v0_3.py,sha256=GfuDRvlmcSBv9emXZSWqW-SktOeI1xH-tl2UET-BSoY,4145
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  opencloning/cre_lox.py,sha256=x_OVYzfaLJH5eVyp05_I9YNycT606UL683AswhQ-gjU,4294
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- opencloning/dna_functions.py,sha256=WvEiKuZEzy3mXjIkOMv4Ymej6xQ3gm4mymM8JCgvE_o,16611
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- opencloning/dna_utils.py,sha256=LmkIScIlogpWxprQfsIdjqtLDpqDmTZp45pcZwWFpZM,6683
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+ opencloning/dna_functions.py,sha256=O5H5DilNUOIzH8gVFiOuG8SVlrenrbwyo9lKwfxIHnY,16663
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+ opencloning/dna_utils.py,sha256=NSS_b5q8u8XNzVqCwzCQaxj4I2xHf_Inmw7iBWS9gc8,6746
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  opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  opencloning/ebic/primer_design.py,sha256=gPZTF9w5SV7WGgnefp_HBM831y0z73M1Kb0QUPnbfIM,2270
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  opencloning/ebic/primer_design_settings.py,sha256=OnFsuh0QCvplUEPXLZouzRo9R7rm4nLbcd2LkDCiIDM,1896
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  opencloning/endpoints/annotation.py,sha256=3rlIXeNQzoqPD9lJUEBGLGxvlhUCTcfkqno814A8P0U,2283
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- opencloning/endpoints/assembly.py,sha256=XBv2Vg0MrBl4WjKlclyJ4QTgydqda9P3LRl_25y3TOo,21307
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+ opencloning/endpoints/assembly.py,sha256=KdVi63Bjmb7qwCQrwMUkRK6lAhlAJvBcHLqj1VJtuAQ,21584
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  opencloning/endpoints/external_import.py,sha256=Z9zd94kzmnbLG_yEAjI-1HK7sIAMcLz3FSZZR66BV-U,18386
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- opencloning/endpoints/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
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- opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
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+ opencloning/endpoints/no_assembly.py,sha256=F6mRZFGUAASZ0v7EhPyBgmn_O-YLySMR1a_0aUH2U70,4806
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+ opencloning/endpoints/no_input.py,sha256=0wc5sTD6nL0SrsXmT__x0g-m6m45ID5hq-D8KDKy98Y,4170
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  opencloning/endpoints/other.py,sha256=7YBXU5UrVCjEjOjdYWw-0sASXn3MhWVZYwDYSZD4C9E,3452
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  opencloning/endpoints/primer_design.py,sha256=3eiQ7MwgeLoAuXFUMNF-DzjzwH_eJGCjd4s32CjxIic,12717
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  opencloning/gateway.py,sha256=pFB3gsCQL715kOFOP1NQOOsQqrkWuQe5qXk4IunF5SA,8486
@@ -42,10 +40,10 @@ opencloning/http_client.py,sha256=coVesi_qJWea-VHBOd-V-Th6e4P9rzl-8ZILPGq2ne0,12
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  opencloning/main.py,sha256=l9PrPBMtGMEWxAPiPWR15Qv2oDNnRoNd8H8E3bZW6Do,3750
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  opencloning/ncbi_requests.py,sha256=b8ow9TDpXbyYk_0HeK-7RXWwwZGrhH-MylSNc3_tH0I,5557
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  opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,9175
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- opencloning/pydantic_models.py,sha256=lMO78M4MwDgzTEGz9qzsaADwAFXagWK4qGsF1K1hLZw,18865
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- opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
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+ opencloning/pydantic_models.py,sha256=N18tl8r6owDxTBRtrvB7DU3kmp59sBc8gYxujT9q6jE,19900
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+ opencloning/request_examples.py,sha256=_VvY4lNpgqhLTM6O_OUs1TujhL7RUbRFZ9ptyssbxLk,2934
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  opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
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- opencloning-0.3.8.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
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- opencloning-0.3.8.dist-info/METADATA,sha256=PUYYRDa7KjQKMswUYWykI9uj15NM-yt7qZ_ik-Hvt4w,9076
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- opencloning-0.3.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- opencloning-0.3.8.dist-info/RECORD,,
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+ opencloning-0.4.2.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
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+ opencloning-0.4.2.dist-info/METADATA,sha256=jdAjLsb539U782FhTf2O7jV3UdQ-07mlCvu4LnFyd-c,9138
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+ opencloning-0.4.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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+ opencloning-0.4.2.dist-info/RECORD,,