nci-cidc-api-modules 1.2.26__tar.gz → 1.2.27__tar.gz

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Files changed (119) hide show
  1. {nci_cidc_api_modules-1.2.26/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.2.27}/PKG-INFO +1 -1
  2. nci_cidc_api_modules-1.2.27/cidc_api/reference/ctcae.py +34 -0
  3. nci_cidc_api_modules-1.2.27/cidc_api/reference/gvhd.py +6 -0
  4. nci_cidc_api_modules-1.2.27/cidc_api/reference/icd10cm.py +12 -0
  5. nci_cidc_api_modules-1.2.27/cidc_api/reference/icdo3.py +12 -0
  6. nci_cidc_api_modules-1.2.27/cidc_api/reference/uberon.py +5 -0
  7. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27/nci_cidc_api_modules.egg-info}/PKG-INFO +1 -1
  8. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/nci_cidc_api_modules.egg-info/SOURCES.txt +5 -0
  9. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/setup.py +1 -0
  10. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/LICENSE +0 -0
  11. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/MANIFEST.in +0 -0
  12. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/README.md +0 -0
  13. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/config/__init__.py +0 -0
  14. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/config/db.py +0 -0
  15. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/config/logging.py +0 -0
  16. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/config/secrets.py +0 -0
  17. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/config/settings.py +0 -0
  18. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/__init__.py +0 -0
  19. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/data.py +0 -0
  20. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/base_orm.py +0 -0
  21. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/__init__.py +0 -0
  22. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/additional_treatment_orm.py +0 -0
  23. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/administrative_person_orm.py +0 -0
  24. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/administrative_role_assignment_orm.py +0 -0
  25. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/adverse_event_orm.py +0 -0
  26. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/arm_orm.py +0 -0
  27. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/baseline_clinical_assessment_orm.py +0 -0
  28. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/cohort_orm.py +0 -0
  29. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/comorbidity_orm.py +0 -0
  30. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/consent_group_orm.py +0 -0
  31. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/contact_orm.py +0 -0
  32. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/demographic_orm.py +0 -0
  33. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/disease_orm.py +0 -0
  34. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/exposure_orm.py +0 -0
  35. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/file_orm.py +0 -0
  36. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/gvhd_diagnosis_acute_orm.py +0 -0
  37. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/gvhd_diagnosis_chronic_orm.py +0 -0
  38. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/gvhd_organ_acute_orm.py +0 -0
  39. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/gvhd_organ_chronic_orm.py +0 -0
  40. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/institution_orm.py +0 -0
  41. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/medical_history_orm.py +0 -0
  42. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/other_clinical_endpoint_orm.py +0 -0
  43. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/other_malignancy_orm.py +0 -0
  44. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/participant_orm.py +0 -0
  45. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/prior_treatment_orm.py +0 -0
  46. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/publication_orm.py +0 -0
  47. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/radiotherapy_dose_orm.py +0 -0
  48. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/response_by_system_orm.py +0 -0
  49. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/response_orm.py +0 -0
  50. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/shipment_orm.py +0 -0
  51. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/shipment_specimen_orm.py +0 -0
  52. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/specimen_orm.py +0 -0
  53. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/stem_cell_transplant_orm.py +0 -0
  54. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/surgery_orm.py +0 -0
  55. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/therapy_agent_dose_orm.py +0 -0
  56. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/treatment_orm.py +0 -0
  57. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/db/stage2/trial_orm.py +0 -0
  58. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/files/__init__.py +0 -0
  59. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/files/details.py +0 -0
  60. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/files/facets.py +0 -0
  61. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/migrations.py +0 -0
  62. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/models.py +0 -0
  63. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/__init__.py +0 -0
  64. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/additional_treatment.py +0 -0
  65. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/administrative_person.py +0 -0
  66. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/administrative_role_assignment.py +0 -0
  67. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/adverse_event.py +0 -0
  68. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/arm.py +0 -0
  69. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/base.py +0 -0
  70. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/baseline_clinical_assessment.py +0 -0
  71. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/cohort.py +0 -0
  72. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/comorbidity.py +0 -0
  73. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/consent_group.py +0 -0
  74. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/contact.py +0 -0
  75. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/demographic.py +0 -0
  76. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/disease.py +0 -0
  77. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/exposure.py +0 -0
  78. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/file.py +0 -0
  79. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/gvhd_diagnosis_acute.py +0 -0
  80. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/gvhd_diagnosis_chronic.py +0 -0
  81. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/gvhd_organ_acute.py +0 -0
  82. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/gvhd_organ_chronic.py +0 -0
  83. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/institution.py +0 -0
  84. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/medical_history.py +0 -0
  85. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/other_clinical_endpoint.py +0 -0
  86. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/other_malignancy.py +0 -0
  87. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/participant.py +0 -0
  88. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/prior_treatment.py +0 -0
  89. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/publication.py +0 -0
  90. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/radiotherapy_dose.py +0 -0
  91. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/response.py +0 -0
  92. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/response_by_system.py +0 -0
  93. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/shipment.py +0 -0
  94. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/shipment_specimen.py +0 -0
  95. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/specimen.py +0 -0
  96. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/stem_cell_transplant.py +0 -0
  97. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/surgery.py +0 -0
  98. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/therapy_agent_dose.py +0 -0
  99. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/treatment.py +0 -0
  100. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/pydantic/stage2/trial.py +0 -0
  101. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/schemas.py +0 -0
  102. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/models/types.py +0 -0
  103. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/__init__.py +0 -0
  104. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/auth.py +0 -0
  105. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/email_layout.html +0 -0
  106. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/emails.py +0 -0
  107. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/file_handling.py +0 -0
  108. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/gcloud_client.py +0 -0
  109. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/jose.py +0 -0
  110. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/rest_utils.py +0 -0
  111. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/cidc_api/shared/utils.py +0 -0
  112. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/nci_cidc_api_modules.egg-info/dependency_links.txt +0 -0
  113. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/nci_cidc_api_modules.egg-info/not-zip-safe +0 -0
  114. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/nci_cidc_api_modules.egg-info/requires.txt +0 -0
  115. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/nci_cidc_api_modules.egg-info/top_level.txt +0 -0
  116. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/pyproject.toml +0 -0
  117. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/requirements.modules.txt +0 -0
  118. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/setup.cfg +0 -0
  119. {nci_cidc_api_modules-1.2.26 → nci_cidc_api_modules-1.2.27}/tests/test_api.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: nci_cidc_api_modules
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- Version: 1.2.26
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+ Version: 1.2.27
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  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
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  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
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  License: MIT license
@@ -0,0 +1,34 @@
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+ # Stubbed to accept any string
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+ def is_ctcae_event_term(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
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+
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+
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+ # Stubbed to accept any string
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+ def is_ctcae_event_code(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
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+
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+
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+ # Stubbed to accept any string
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+ def is_ctcae_severity_grade(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
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+
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+
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+ # Stubbed to accept any string
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+ def is_ctcae_system_organ_class(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
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+
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+
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+ # Determines if the CTCAE term is one of the "Other, specify" types of terms for which we include
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+ # additional data about the AE.
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+ def is_ctcae_other_term(v):
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+ if isinstance(v, str):
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+ return "Other, specify" in v
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+ return False
@@ -0,0 +1,6 @@
1
+ # Stubbed to accept any string
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+ # Should support MAGIC and Modified Glucksberg
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+ def is_gvhd_organ(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
@@ -0,0 +1,12 @@
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+ # Stubbed to accept any string
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+ def is_ICD10CM_code(v):
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+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
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+ return v
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+
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+
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+ # Stubbed to accept any string
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+ def is_ICD10CM_term(v):
10
+ if not isinstance(v, str):
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+ raise TypeError("Value must be a string")
12
+ return v
@@ -0,0 +1,12 @@
1
+ # Stubbed to accept any string
2
+ def is_ICDO3_code(v):
3
+ if not isinstance(v, str):
4
+ raise TypeError("Value must be a string")
5
+ return v
6
+
7
+
8
+ # Stubbed to accept any string
9
+ def is_ICDO3_term(v):
10
+ if not isinstance(v, str):
11
+ raise TypeError("Value must be a string")
12
+ return v
@@ -0,0 +1,5 @@
1
+ # Stubbed to accept any string
2
+ def is_uberon_term(v):
3
+ if not isinstance(v, str):
4
+ raise TypeError("Value must be a string")
5
+ return v
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: nci_cidc_api_modules
3
- Version: 1.2.26
3
+ Version: 1.2.27
4
4
  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
5
5
  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
6
6
  License: MIT license
@@ -94,6 +94,11 @@ cidc_api/models/pydantic/stage2/surgery.py
94
94
  cidc_api/models/pydantic/stage2/therapy_agent_dose.py
95
95
  cidc_api/models/pydantic/stage2/treatment.py
96
96
  cidc_api/models/pydantic/stage2/trial.py
97
+ cidc_api/reference/ctcae.py
98
+ cidc_api/reference/gvhd.py
99
+ cidc_api/reference/icd10cm.py
100
+ cidc_api/reference/icdo3.py
101
+ cidc_api/reference/uberon.py
97
102
  cidc_api/shared/__init__.py
98
103
  cidc_api/shared/auth.py
99
104
  cidc_api/shared/email_layout.html
@@ -14,6 +14,7 @@ packages = [
14
14
  "cidc_api.config",
15
15
  "cidc_api.models",
16
16
  "cidc_api.shared",
17
+ "cidc_api.reference",
17
18
  ]
18
19
  packages += find_namespace_packages(include=["cidc_api.models.*"])
19
20
  print(packages)