sapiopycommons 2024.3.19a157__tar.gz → 2025.1.17a402__tar.gz

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  1. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/.gitignore +2 -0
  2. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/PKG-INFO +5 -4
  3. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/README.md +1 -0
  4. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/pyproject.toml +3 -3
  5. sapiopycommons-2025.1.17a402/src/sapiopycommons/callbacks/callback_util.py +2041 -0
  6. sapiopycommons-2025.1.17a402/src/sapiopycommons/callbacks/field_builder.py +545 -0
  7. sapiopycommons-2025.1.17a402/src/sapiopycommons/chem/IndigoMolecules.py +95 -0
  8. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/chem/Molecules.py +100 -21
  9. sapiopycommons-2025.1.17a402/src/sapiopycommons/customreport/column_builder.py +60 -0
  10. sapiopycommons-2025.1.17a402/src/sapiopycommons/customreport/custom_report_builder.py +137 -0
  11. sapiopycommons-2025.1.17a402/src/sapiopycommons/customreport/term_builder.py +315 -0
  12. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/datatype/attachment_util.py +14 -15
  13. sapiopycommons-2025.1.17a402/src/sapiopycommons/datatype/data_fields.py +61 -0
  14. sapiopycommons-2025.1.17a402/src/sapiopycommons/datatype/pseudo_data_types.py +440 -0
  15. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/eln/experiment_handler.py +355 -91
  16. sapiopycommons-2025.1.17a402/src/sapiopycommons/eln/experiment_report_util.py +649 -0
  17. sapiopycommons-2025.1.17a402/src/sapiopycommons/eln/plate_designer.py +152 -0
  18. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/complex_data_loader.py +31 -0
  19. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/file_bridge.py +215 -0
  20. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/file_bridge_handler.py +555 -0
  21. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/file_data_handler.py +633 -0
  22. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/files/file_util.py +263 -163
  23. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/file_validator.py +569 -0
  24. sapiopycommons-2025.1.17a402/src/sapiopycommons/files/file_writer.py +377 -0
  25. sapiopycommons-2025.1.17a402/src/sapiopycommons/flowcyto/flow_cyto.py +77 -0
  26. sapiopycommons-2025.1.17a402/src/sapiopycommons/flowcyto/flowcyto_data.py +75 -0
  27. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/accession_service.py +375 -0
  28. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/aliases.py +296 -0
  29. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/audit_log.py +185 -0
  30. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/custom_report_util.py +285 -0
  31. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/directive_util.py +86 -0
  32. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/exceptions.py +88 -0
  33. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/general/popup_util.py +59 -7
  34. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/sapio_links.py +50 -0
  35. sapiopycommons-2025.1.17a402/src/sapiopycommons/general/storage_util.py +148 -0
  36. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/general/time_util.py +91 -7
  37. sapiopycommons-2025.1.17a402/src/sapiopycommons/multimodal/multimodal.py +146 -0
  38. sapiopycommons-2025.1.17a402/src/sapiopycommons/multimodal/multimodal_data.py +490 -0
  39. sapiopycommons-2025.1.17a402/src/sapiopycommons/processtracking/custom_workflow_handler.py +406 -0
  40. sapiopycommons-2025.1.17a402/src/sapiopycommons/processtracking/endpoints.py +192 -0
  41. sapiopycommons-2025.1.17a402/src/sapiopycommons/recordmodel/__init__.py +0 -0
  42. sapiopycommons-2025.1.17a402/src/sapiopycommons/recordmodel/record_handler.py +1112 -0
  43. sapiopycommons-2025.1.17a402/src/sapiopycommons/rules/__init__.py +0 -0
  44. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/rules/eln_rule_handler.py +87 -8
  45. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/rules/on_save_rule_handler.py +87 -12
  46. sapiopycommons-2025.1.17a402/src/sapiopycommons/sftpconnect/__init__.py +0 -0
  47. sapiopycommons-2025.1.17a402/src/sapiopycommons/sftpconnect/sftp_builder.py +70 -0
  48. sapiopycommons-2025.1.17a402/src/sapiopycommons/webhook/__init__.py +0 -0
  49. sapiopycommons-2025.1.17a402/src/sapiopycommons/webhook/webhook_context.py +39 -0
  50. sapiopycommons-2025.1.17a402/src/sapiopycommons/webhook/webhook_handlers.py +790 -0
  51. sapiopycommons-2025.1.17a402/src/sapiopycommons/webhook/webservice_handlers.py +317 -0
  52. sapiopycommons-2025.1.17a402/tests/AF-A0A009IHW8-F1-model_v4.cif +3455 -0
  53. sapiopycommons-2025.1.17a402/tests/_do_not_add_init_py_here +0 -0
  54. sapiopycommons-2025.1.17a402/tests/accession_test.py +41 -0
  55. sapiopycommons-2025.1.17a402/tests/bio_reg_test.py +33 -0
  56. sapiopycommons-2025.1.17a402/tests/chem_test.py +229 -0
  57. sapiopycommons-2025.1.17a402/tests/chem_test_curation_queue.py +31 -0
  58. sapiopycommons-2025.1.17a402/tests/curation_queue_test.sdf +168 -0
  59. sapiopycommons-2025.1.17a402/tests/data_type_models.py +58006 -0
  60. sapiopycommons-2025.1.17a402/tests/flowcyto/101_DEN084Y5_15_E01_008_clean.fcs +0 -0
  61. sapiopycommons-2025.1.17a402/tests/flowcyto/101_DEN084Y5_15_E03_009_clean.fcs +0 -0
  62. sapiopycommons-2025.1.17a402/tests/flowcyto/101_DEN084Y5_15_E05_010_clean.fcs +0 -0
  63. sapiopycommons-2025.1.17a402/tests/flowcyto/8_color_ICS.wsp +4833 -0
  64. sapiopycommons-2025.1.17a402/tests/flowcyto/COVID19_W_001_O.fcs +0 -0
  65. sapiopycommons-2025.1.17a402/tests/flowcyto_test.py +71 -0
  66. sapiopycommons-2025.1.17a402/tests/kappa.chains.fasta +45 -0
  67. sapiopycommons-2025.1.17a402/tests/mafft_test.py +66 -0
  68. sapiopycommons-2025.1.17a402/tests/test.gb +124 -0
  69. sapiopycommons-2024.3.19a157/src/sapiopycommons/chem/IndigoMolecules.py +0 -50
  70. sapiopycommons-2024.3.19a157/src/sapiopycommons/files/file_bridge.py +0 -91
  71. sapiopycommons-2024.3.19a157/src/sapiopycommons/general/aliases.py +0 -61
  72. sapiopycommons-2024.3.19a157/src/sapiopycommons/general/custom_report_util.py +0 -65
  73. sapiopycommons-2024.3.19a157/src/sapiopycommons/general/exceptions.py +0 -26
  74. sapiopycommons-2024.3.19a157/src/sapiopycommons/recordmodel/record_handler.py +0 -639
  75. sapiopycommons-2024.3.19a157/src/sapiopycommons/webhook/webhook_handlers.py +0 -247
  76. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/LICENSE +0 -0
  77. {sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/src/sapiopycommons/__init__.py +0 -0
  78. {sapiopycommons-2024.3.19a157/src/sapiopycommons/chem → sapiopycommons-2025.1.17a402/src/sapiopycommons/callbacks}/__init__.py +0 -0
  79. {sapiopycommons-2024.3.19a157/src/sapiopycommons/datatype → sapiopycommons-2025.1.17a402/src/sapiopycommons/chem}/__init__.py +0 -0
  80. {sapiopycommons-2024.3.19a157/src/sapiopycommons/eln → sapiopycommons-2025.1.17a402/src/sapiopycommons/customreport}/__init__.py +0 -0
  81. {sapiopycommons-2024.3.19a157/src/sapiopycommons/files → sapiopycommons-2025.1.17a402/src/sapiopycommons/datatype}/__init__.py +0 -0
  82. {sapiopycommons-2024.3.19a157/src/sapiopycommons/general → sapiopycommons-2025.1.17a402/src/sapiopycommons/eln}/__init__.py +0 -0
  83. {sapiopycommons-2024.3.19a157/src/sapiopycommons/recordmodel → sapiopycommons-2025.1.17a402/src/sapiopycommons/files}/__init__.py +0 -0
  84. {sapiopycommons-2024.3.19a157/src/sapiopycommons/rules → sapiopycommons-2025.1.17a402/src/sapiopycommons/general}/__init__.py +0 -0
  85. {sapiopycommons-2024.3.19a157/src/sapiopycommons/webhook → sapiopycommons-2025.1.17a402/src/sapiopycommons/processtracking}/__init__.py +0 -0
{sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/.gitignore RENAMED
@@ -6,3 +6,5 @@
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  **/*.versionsBackup
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  **/target
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  /sapiopycommons/sapiopycommons.egg-info/
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+ /sapiopycommons/dist**
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+ /.pydevproject
{sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/PKG-INFO RENAMED
@@ -1,11 +1,10 @@
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  Metadata-Version: 2.3
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  Name: sapiopycommons
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- Version: 2024.3.19a157
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+ Version: 2025.1.17a402
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  Summary: Official Sapio Python API Utilities Package
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  Project-URL: Homepage, https://github.com/sapiosciences
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  Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>
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- License-Expression: MPL-2.0
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- License-File: LICENSE
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+ License: MPL-2.0
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  Keywords: eln,lims,rest,sapio
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  Classifier: Development Status :: 5 - Production/Stable
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  Classifier: Intended Audience :: Developers
@@ -17,7 +16,8 @@ Classifier: Programming Language :: Python :: 3.10
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Classifier: Topic :: Software Development :: Libraries :: Python Modules
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  Requires-Python: >=3.10
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- Requires-Dist: sapiopylib>=2023.12.13.174
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+ Requires-Dist: databind>=4.5
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+ Requires-Dist: sapiopylib>=2024.5.24.210
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  Description-Content-Type: text/markdown
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@@ -50,6 +50,7 @@ This license does not provide any rights to use any other copyrighted artifacts
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  ## Dependencies
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  The following dependencies are required for this package:
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  - [sapiopylib - The official Sapio Informatics Platform Python API package.](https://pypi.org/project/sapiopylib/)
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+ - [databind - Databind is a library inspired by jackson-databind to de-/serialize Python dataclasses.](https://pypi.org/project/databind/)
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  ## Getting Help
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  If you have a support contract with Sapio Sciences, please use our [technical support channels](https://sapio-sciences.atlassian.net/servicedesk/customer/portals).
{sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/README.md RENAMED
@@ -28,6 +28,7 @@ This license does not provide any rights to use any other copyrighted artifacts
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  ## Dependencies
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  The following dependencies are required for this package:
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  - [sapiopylib - The official Sapio Informatics Platform Python API package.](https://pypi.org/project/sapiopylib/)
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+ - [databind - Databind is a library inspired by jackson-databind to de-/serialize Python dataclasses.](https://pypi.org/project/databind/)
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  ## Getting Help
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  If you have a support contract with Sapio Sciences, please use our [technical support channels](https://sapio-sciences.atlassian.net/servicedesk/customer/portals).
{sapiopycommons-2024.3.19a157 → sapiopycommons-2025.1.17a402}/pyproject.toml RENAMED
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  [build-system]
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- requires = ["hatchling"]
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+ requires = ["hatchling==1.26.3"]
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  build-backend = "hatchling.build"
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  [project]
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  name = "sapiopycommons"
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- version='2024.03.19a157'
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+ version='2025.01.17a402'
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  authors = [
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  { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
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  { name="Yechen Qiao", email="yqiao@sapiosciences.com" },
@@ -14,7 +14,7 @@ license = "MPL-2.0"
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  readme = "README.md"
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  requires-python = ">=3.10"
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  dependencies = [
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- 'sapiopylib>=2023.12.13.174'
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+ 'sapiopylib>=2024.5.24.210', 'databind>=4.5'
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  ]
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  classifiers = [
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  "Intended Audience :: Developers",