nmdc-runtime 2.9.0__py3-none-any.whl → 2.11.0__py3-none-any.whl

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Files changed (131) hide show
  1. nmdc_runtime/Dockerfile +167 -0
  2. nmdc_runtime/api/analytics.py +90 -0
  3. nmdc_runtime/api/boot/capabilities.py +9 -0
  4. nmdc_runtime/api/boot/object_types.py +126 -0
  5. nmdc_runtime/api/boot/triggers.py +84 -0
  6. nmdc_runtime/api/boot/workflows.py +116 -0
  7. nmdc_runtime/api/core/auth.py +208 -0
  8. nmdc_runtime/api/core/idgen.py +200 -0
  9. nmdc_runtime/api/core/metadata.py +788 -0
  10. nmdc_runtime/api/core/util.py +109 -0
  11. nmdc_runtime/api/db/mongo.py +435 -0
  12. nmdc_runtime/api/db/s3.py +37 -0
  13. nmdc_runtime/api/endpoints/capabilities.py +25 -0
  14. nmdc_runtime/api/endpoints/find.py +634 -0
  15. nmdc_runtime/api/endpoints/jobs.py +143 -0
  16. nmdc_runtime/api/endpoints/lib/helpers.py +274 -0
  17. nmdc_runtime/api/endpoints/lib/linked_instances.py +180 -0
  18. nmdc_runtime/api/endpoints/lib/path_segments.py +165 -0
  19. nmdc_runtime/api/endpoints/metadata.py +260 -0
  20. nmdc_runtime/api/endpoints/nmdcschema.py +502 -0
  21. nmdc_runtime/api/endpoints/object_types.py +38 -0
  22. nmdc_runtime/api/endpoints/objects.py +270 -0
  23. nmdc_runtime/api/endpoints/operations.py +78 -0
  24. nmdc_runtime/api/endpoints/queries.py +701 -0
  25. nmdc_runtime/api/endpoints/runs.py +98 -0
  26. nmdc_runtime/api/endpoints/search.py +38 -0
  27. nmdc_runtime/api/endpoints/sites.py +205 -0
  28. nmdc_runtime/api/endpoints/triggers.py +25 -0
  29. nmdc_runtime/api/endpoints/users.py +214 -0
  30. nmdc_runtime/api/endpoints/util.py +796 -0
  31. nmdc_runtime/api/endpoints/workflows.py +353 -0
  32. nmdc_runtime/api/entrypoint.sh +7 -0
  33. nmdc_runtime/api/main.py +425 -0
  34. nmdc_runtime/api/middleware.py +43 -0
  35. nmdc_runtime/api/models/capability.py +14 -0
  36. nmdc_runtime/api/models/id.py +92 -0
  37. nmdc_runtime/api/models/job.py +37 -0
  38. nmdc_runtime/api/models/lib/helpers.py +78 -0
  39. nmdc_runtime/api/models/metadata.py +11 -0
  40. nmdc_runtime/api/models/nmdc_schema.py +146 -0
  41. nmdc_runtime/api/models/object.py +180 -0
  42. nmdc_runtime/api/models/object_type.py +20 -0
  43. nmdc_runtime/api/models/operation.py +66 -0
  44. nmdc_runtime/api/models/query.py +246 -0
  45. nmdc_runtime/api/models/query_continuation.py +111 -0
  46. nmdc_runtime/api/models/run.py +161 -0
  47. nmdc_runtime/api/models/site.py +87 -0
  48. nmdc_runtime/api/models/trigger.py +13 -0
  49. nmdc_runtime/api/models/user.py +140 -0
  50. nmdc_runtime/api/models/util.py +260 -0
  51. nmdc_runtime/api/models/workflow.py +15 -0
  52. nmdc_runtime/api/openapi.py +178 -0
  53. nmdc_runtime/api/swagger_ui/assets/custom-elements.js +522 -0
  54. nmdc_runtime/api/swagger_ui/assets/script.js +247 -0
  55. nmdc_runtime/api/swagger_ui/assets/style.css +155 -0
  56. nmdc_runtime/api/swagger_ui/swagger_ui.py +34 -0
  57. nmdc_runtime/config.py +7 -8
  58. nmdc_runtime/minter/adapters/repository.py +22 -2
  59. nmdc_runtime/minter/config.py +2 -0
  60. nmdc_runtime/minter/domain/model.py +55 -1
  61. nmdc_runtime/minter/entrypoints/fastapi_app.py +1 -1
  62. nmdc_runtime/mongo_util.py +1 -2
  63. nmdc_runtime/site/backup/nmdcdb_mongodump.py +1 -1
  64. nmdc_runtime/site/backup/nmdcdb_mongoexport.py +1 -3
  65. nmdc_runtime/site/changesheets/data/OmicsProcessing-to-catted-Biosamples.tsv +1561 -0
  66. nmdc_runtime/site/changesheets/scripts/missing_neon_soils_ecosystem_data.py +311 -0
  67. nmdc_runtime/site/changesheets/scripts/neon_soils_add_ncbi_ids.py +210 -0
  68. nmdc_runtime/site/dagster.yaml +53 -0
  69. nmdc_runtime/site/entrypoint-daemon.sh +26 -0
  70. nmdc_runtime/site/entrypoint-dagit-readonly.sh +26 -0
  71. nmdc_runtime/site/entrypoint-dagit.sh +26 -0
  72. nmdc_runtime/site/export/ncbi_xml.py +633 -13
  73. nmdc_runtime/site/export/ncbi_xml_utils.py +115 -1
  74. nmdc_runtime/site/graphs.py +8 -22
  75. nmdc_runtime/site/ops.py +147 -181
  76. nmdc_runtime/site/repository.py +2 -112
  77. nmdc_runtime/site/resources.py +16 -3
  78. nmdc_runtime/site/translation/gold_translator.py +4 -12
  79. nmdc_runtime/site/translation/neon_benthic_translator.py +0 -1
  80. nmdc_runtime/site/translation/neon_soil_translator.py +4 -5
  81. nmdc_runtime/site/translation/neon_surface_water_translator.py +0 -2
  82. nmdc_runtime/site/translation/submission_portal_translator.py +84 -68
  83. nmdc_runtime/site/translation/translator.py +63 -1
  84. nmdc_runtime/site/util.py +8 -3
  85. nmdc_runtime/site/validation/util.py +10 -5
  86. nmdc_runtime/site/workspace.yaml +13 -0
  87. nmdc_runtime/static/NMDC_logo.svg +1073 -0
  88. nmdc_runtime/static/ORCID-iD_icon_vector.svg +4 -0
  89. nmdc_runtime/static/README.md +5 -0
  90. nmdc_runtime/static/favicon.ico +0 -0
  91. nmdc_runtime/util.py +90 -48
  92. nmdc_runtime-2.11.0.dist-info/METADATA +46 -0
  93. nmdc_runtime-2.11.0.dist-info/RECORD +128 -0
  94. {nmdc_runtime-2.9.0.dist-info → nmdc_runtime-2.11.0.dist-info}/WHEEL +1 -2
  95. nmdc_runtime/containers.py +0 -14
  96. nmdc_runtime/core/db/Database.py +0 -15
  97. nmdc_runtime/core/exceptions/__init__.py +0 -23
  98. nmdc_runtime/core/exceptions/base.py +0 -47
  99. nmdc_runtime/core/exceptions/token.py +0 -13
  100. nmdc_runtime/domain/users/queriesInterface.py +0 -18
  101. nmdc_runtime/domain/users/userSchema.py +0 -37
  102. nmdc_runtime/domain/users/userService.py +0 -14
  103. nmdc_runtime/infrastructure/database/db.py +0 -3
  104. nmdc_runtime/infrastructure/database/models/user.py +0 -10
  105. nmdc_runtime/lib/__init__.py +0 -1
  106. nmdc_runtime/lib/extract_nmdc_data.py +0 -41
  107. nmdc_runtime/lib/load_nmdc_data.py +0 -121
  108. nmdc_runtime/lib/nmdc_dataframes.py +0 -829
  109. nmdc_runtime/lib/nmdc_etl_class.py +0 -402
  110. nmdc_runtime/lib/transform_nmdc_data.py +0 -1117
  111. nmdc_runtime/site/drsobjects/ingest.py +0 -93
  112. nmdc_runtime/site/drsobjects/registration.py +0 -131
  113. nmdc_runtime/site/translation/emsl.py +0 -43
  114. nmdc_runtime/site/translation/gold.py +0 -53
  115. nmdc_runtime/site/translation/jgi.py +0 -32
  116. nmdc_runtime/site/translation/util.py +0 -132
  117. nmdc_runtime/site/validation/jgi.py +0 -43
  118. nmdc_runtime-2.9.0.dist-info/METADATA +0 -214
  119. nmdc_runtime-2.9.0.dist-info/RECORD +0 -84
  120. nmdc_runtime-2.9.0.dist-info/top_level.txt +0 -1
  121. /nmdc_runtime/{client → api}/__init__.py +0 -0
  122. /nmdc_runtime/{core → api/boot}/__init__.py +0 -0
  123. /nmdc_runtime/{core/db → api/core}/__init__.py +0 -0
  124. /nmdc_runtime/{domain → api/db}/__init__.py +0 -0
  125. /nmdc_runtime/{domain/users → api/endpoints}/__init__.py +0 -0
  126. /nmdc_runtime/{infrastructure → api/endpoints/lib}/__init__.py +0 -0
  127. /nmdc_runtime/{infrastructure/database → api/models}/__init__.py +0 -0
  128. /nmdc_runtime/{infrastructure/database/models → api/models/lib}/__init__.py +0 -0
  129. /nmdc_runtime/{site/drsobjects/__init__.py → api/models/minter.py} +0 -0
  130. {nmdc_runtime-2.9.0.dist-info → nmdc_runtime-2.11.0.dist-info}/entry_points.txt +0 -0
  131. {nmdc_runtime-2.9.0.dist-info → nmdc_runtime-2.11.0.dist-info}/licenses/LICENSE +0 -0
nmdc_runtime/site/workspace.yaml ADDED
@@ -0,0 +1,13 @@
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+ load_from:
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+ - python_package:
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+ package_name: nmdc_runtime.site.repository
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+ attribute: repo
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+ - python_package:
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+ package_name: nmdc_runtime.site.repository
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+ attribute: biosample_submission_ingest
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+ - python_package:
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+ package_name: nmdc_runtime.site.repository
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+ attribute: biosample_export
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+ - python_package:
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+ package_name: nmdc_runtime.site.repository
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+ attribute: database_records_stitching