nmdc-runtime 1.3.1__py3-none-any.whl → 2.12.0__py3-none-any.whl

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Files changed (143) hide show
  1. nmdc_runtime/Dockerfile +177 -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 +212 -0
  8. nmdc_runtime/api/core/idgen.py +200 -0
  9. nmdc_runtime/api/core/metadata.py +777 -0
  10. nmdc_runtime/api/core/util.py +114 -0
  11. nmdc_runtime/api/db/mongo.py +436 -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 +206 -0
  16. nmdc_runtime/api/endpoints/lib/helpers.py +274 -0
  17. nmdc_runtime/api/endpoints/lib/linked_instances.py +193 -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 +515 -0
  21. nmdc_runtime/api/endpoints/object_types.py +38 -0
  22. nmdc_runtime/api/endpoints/objects.py +277 -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 +817 -0
  31. nmdc_runtime/api/endpoints/wf_file_staging.py +307 -0
  32. nmdc_runtime/api/endpoints/workflows.py +353 -0
  33. nmdc_runtime/api/entrypoint.sh +7 -0
  34. nmdc_runtime/api/main.py +495 -0
  35. nmdc_runtime/api/middleware.py +43 -0
  36. nmdc_runtime/api/models/capability.py +14 -0
  37. nmdc_runtime/api/models/id.py +92 -0
  38. nmdc_runtime/api/models/job.py +57 -0
  39. nmdc_runtime/api/models/lib/helpers.py +78 -0
  40. nmdc_runtime/api/models/metadata.py +11 -0
  41. nmdc_runtime/api/models/nmdc_schema.py +146 -0
  42. nmdc_runtime/api/models/object.py +180 -0
  43. nmdc_runtime/api/models/object_type.py +20 -0
  44. nmdc_runtime/api/models/operation.py +66 -0
  45. nmdc_runtime/api/models/query.py +246 -0
  46. nmdc_runtime/api/models/query_continuation.py +111 -0
  47. nmdc_runtime/api/models/run.py +161 -0
  48. nmdc_runtime/api/models/site.py +87 -0
  49. nmdc_runtime/api/models/trigger.py +13 -0
  50. nmdc_runtime/api/models/user.py +207 -0
  51. nmdc_runtime/api/models/util.py +260 -0
  52. nmdc_runtime/api/models/wfe_file_stages.py +122 -0
  53. nmdc_runtime/api/models/workflow.py +15 -0
  54. nmdc_runtime/api/openapi.py +178 -0
  55. nmdc_runtime/api/swagger_ui/assets/EllipsesButton.js +146 -0
  56. nmdc_runtime/api/swagger_ui/assets/EndpointSearchWidget.js +369 -0
  57. nmdc_runtime/api/swagger_ui/assets/script.js +252 -0
  58. nmdc_runtime/api/swagger_ui/assets/style.css +155 -0
  59. nmdc_runtime/api/swagger_ui/swagger_ui.py +34 -0
  60. nmdc_runtime/config.py +56 -0
  61. nmdc_runtime/minter/adapters/repository.py +22 -2
  62. nmdc_runtime/minter/config.py +30 -4
  63. nmdc_runtime/minter/domain/model.py +55 -1
  64. nmdc_runtime/minter/entrypoints/fastapi_app.py +1 -1
  65. nmdc_runtime/mongo_util.py +89 -0
  66. nmdc_runtime/site/backup/nmdcdb_mongodump.py +1 -1
  67. nmdc_runtime/site/backup/nmdcdb_mongoexport.py +1 -3
  68. nmdc_runtime/site/changesheets/data/OmicsProcessing-to-catted-Biosamples.tsv +1561 -0
  69. nmdc_runtime/site/changesheets/scripts/missing_neon_soils_ecosystem_data.py +311 -0
  70. nmdc_runtime/site/changesheets/scripts/neon_soils_add_ncbi_ids.py +210 -0
  71. nmdc_runtime/site/dagster.yaml +53 -0
  72. nmdc_runtime/site/entrypoint-daemon.sh +29 -0
  73. nmdc_runtime/site/entrypoint-dagit-readonly.sh +26 -0
  74. nmdc_runtime/site/entrypoint-dagit.sh +29 -0
  75. nmdc_runtime/site/export/ncbi_xml.py +1331 -0
  76. nmdc_runtime/site/export/ncbi_xml_utils.py +405 -0
  77. nmdc_runtime/site/export/study_metadata.py +27 -4
  78. nmdc_runtime/site/graphs.py +294 -45
  79. nmdc_runtime/site/ops.py +1008 -230
  80. nmdc_runtime/site/repair/database_updater.py +451 -0
  81. nmdc_runtime/site/repository.py +368 -133
  82. nmdc_runtime/site/resources.py +154 -80
  83. nmdc_runtime/site/translation/gold_translator.py +235 -83
  84. nmdc_runtime/site/translation/neon_benthic_translator.py +212 -188
  85. nmdc_runtime/site/translation/neon_soil_translator.py +82 -58
  86. nmdc_runtime/site/translation/neon_surface_water_translator.py +698 -0
  87. nmdc_runtime/site/translation/neon_utils.py +24 -7
  88. nmdc_runtime/site/translation/submission_portal_translator.py +616 -162
  89. nmdc_runtime/site/translation/translator.py +73 -3
  90. nmdc_runtime/site/util.py +26 -7
  91. nmdc_runtime/site/validation/emsl.py +1 -0
  92. nmdc_runtime/site/validation/gold.py +1 -0
  93. nmdc_runtime/site/validation/util.py +16 -12
  94. nmdc_runtime/site/workspace.yaml +13 -0
  95. nmdc_runtime/static/NMDC_logo.svg +1073 -0
  96. nmdc_runtime/static/ORCID-iD_icon_vector.svg +4 -0
  97. nmdc_runtime/static/README.md +5 -0
  98. nmdc_runtime/static/favicon.ico +0 -0
  99. nmdc_runtime/util.py +236 -192
  100. nmdc_runtime-2.12.0.dist-info/METADATA +45 -0
  101. nmdc_runtime-2.12.0.dist-info/RECORD +131 -0
  102. {nmdc_runtime-1.3.1.dist-info → nmdc_runtime-2.12.0.dist-info}/WHEEL +1 -2
  103. {nmdc_runtime-1.3.1.dist-info → nmdc_runtime-2.12.0.dist-info}/entry_points.txt +0 -1
  104. nmdc_runtime/containers.py +0 -14
  105. nmdc_runtime/core/db/Database.py +0 -15
  106. nmdc_runtime/core/exceptions/__init__.py +0 -23
  107. nmdc_runtime/core/exceptions/base.py +0 -47
  108. nmdc_runtime/core/exceptions/token.py +0 -13
  109. nmdc_runtime/domain/users/queriesInterface.py +0 -18
  110. nmdc_runtime/domain/users/userSchema.py +0 -37
  111. nmdc_runtime/domain/users/userService.py +0 -14
  112. nmdc_runtime/infrastructure/database/db.py +0 -3
  113. nmdc_runtime/infrastructure/database/models/user.py +0 -10
  114. nmdc_runtime/lib/__init__.py +0 -1
  115. nmdc_runtime/lib/extract_nmdc_data.py +0 -41
  116. nmdc_runtime/lib/load_nmdc_data.py +0 -121
  117. nmdc_runtime/lib/nmdc_dataframes.py +0 -829
  118. nmdc_runtime/lib/nmdc_etl_class.py +0 -402
  119. nmdc_runtime/lib/transform_nmdc_data.py +0 -1117
  120. nmdc_runtime/site/drsobjects/ingest.py +0 -93
  121. nmdc_runtime/site/drsobjects/registration.py +0 -131
  122. nmdc_runtime/site/terminusdb/generate.py +0 -198
  123. nmdc_runtime/site/terminusdb/ingest.py +0 -44
  124. nmdc_runtime/site/terminusdb/schema.py +0 -1671
  125. nmdc_runtime/site/translation/emsl.py +0 -42
  126. nmdc_runtime/site/translation/gold.py +0 -53
  127. nmdc_runtime/site/translation/jgi.py +0 -31
  128. nmdc_runtime/site/translation/util.py +0 -132
  129. nmdc_runtime/site/validation/jgi.py +0 -42
  130. nmdc_runtime-1.3.1.dist-info/METADATA +0 -181
  131. nmdc_runtime-1.3.1.dist-info/RECORD +0 -81
  132. nmdc_runtime-1.3.1.dist-info/top_level.txt +0 -1
  133. /nmdc_runtime/{client → api}/__init__.py +0 -0
  134. /nmdc_runtime/{core → api/boot}/__init__.py +0 -0
  135. /nmdc_runtime/{core/db → api/core}/__init__.py +0 -0
  136. /nmdc_runtime/{domain → api/db}/__init__.py +0 -0
  137. /nmdc_runtime/{domain/users → api/endpoints}/__init__.py +0 -0
  138. /nmdc_runtime/{infrastructure → api/endpoints/lib}/__init__.py +0 -0
  139. /nmdc_runtime/{infrastructure/database → api/models}/__init__.py +0 -0
  140. /nmdc_runtime/{infrastructure/database/models → api/models/lib}/__init__.py +0 -0
  141. /nmdc_runtime/{site/drsobjects/__init__.py → api/models/minter.py} +0 -0
  142. /nmdc_runtime/site/{terminusdb → repair}/__init__.py +0 -0
  143. {nmdc_runtime-1.3.1.dist-info → nmdc_runtime-2.12.0.dist-info/licenses}/LICENSE +0 -0
nmdc_runtime/site/translation/neon_utils.py CHANGED
@@ -22,7 +22,11 @@ def _get_value_or_none(data: pd.DataFrame, column_name: str) -> Union[str, float
22
22
  ):
23
23
  if column_name == "horizon":
24
24
  return f"{data[column_name].values[0]} horizon"
25
- elif column_name == "qaqcStatus":
25
+ elif (
26
+ column_name == "qaqcStatus"
27
+ or column_name == "extrQaqcStatus"
28
+ or column_name == "seqQaqcStatus"
29
+ ):
26
30
  return data[column_name].values[0].lower()
27
31
  elif column_name == "sampleTopDepth":
28
32
  return float(data[column_name].values[0]) / 100
@@ -46,7 +50,14 @@ def _create_controlled_identified_term_value(
46
50
  """
47
51
  if id is None or name is None:
48
52
  return None
49
- return nmdc.ControlledIdentifiedTermValue(term=nmdc.OntologyClass(id=id, name=name))
53
+ return nmdc.ControlledIdentifiedTermValue(
54
+ term=nmdc.OntologyClass(
55
+ id=id,
56
+ name=name,
57
+ type="nmdc:OntologyClass",
58
+ ),
59
+ type="nmdc:ControlledIdentifiedTermValue",
60
+ )
50
61
 
51
62
 
52
63
  def _create_controlled_term_value(name: str = None) -> nmdc.ControlledTermValue:
@@ -60,7 +71,10 @@ def _create_controlled_term_value(name: str = None) -> nmdc.ControlledTermValue:
60
71
  """
61
72
  if name is None:
62
73
  return None
63
- return nmdc.ControlledTermValue(has_raw_value=name)
74
+ return nmdc.ControlledTermValue(
75
+ has_raw_value=name,
76
+ type="nmdc:ControlledTermValue",
77
+ )
64
78
 
65
79
 
66
80
  def _create_timestamp_value(value: str = None) -> nmdc.TimestampValue:
@@ -73,7 +87,7 @@ def _create_timestamp_value(value: str = None) -> nmdc.TimestampValue:
73
87
  """
74
88
  if value is None:
75
89
  return None
76
- return nmdc.TimestampValue(has_raw_value=value)
90
+ return nmdc.TimestampValue(has_raw_value=value, type="nmdc:TimestampValue")
77
91
 
78
92
 
79
93
  def _create_quantity_value(
@@ -90,7 +104,9 @@ def _create_quantity_value(
90
104
  """
91
105
  if numeric_value is None or math.isnan(numeric_value):
92
106
  return None
93
- return nmdc.QuantityValue(has_numeric_value=float(numeric_value), has_unit=unit)
107
+ return nmdc.QuantityValue(
108
+ has_numeric_value=float(numeric_value), has_unit=unit, type="nmdc:QuantityValue"
109
+ )
94
110
 
95
111
 
96
112
  def _create_text_value(value: str = None) -> nmdc.TextValue:
@@ -102,7 +118,7 @@ def _create_text_value(value: str = None) -> nmdc.TextValue:
102
118
  """
103
119
  if value is None:
104
120
  return None
105
- return nmdc.TextValue(has_raw_value=value)
121
+ return nmdc.TextValue(has_raw_value=value, type="nmdc:TextValue")
106
122
 
107
123
 
108
124
  def _create_double_value(value: str = None) -> nmdc.Double:
@@ -115,7 +131,7 @@ def _create_double_value(value: str = None) -> nmdc.Double:
115
131
  """
116
132
  if value is None or math.isnan(value):
117
133
  return None
118
- return nmdc.Double(value)
134
+ return nmdc.Double(value, type="nmdc:Double")
119
135
 
120
136
 
121
137
  def _create_geolocation_value(
@@ -143,4 +159,5 @@ def _create_geolocation_value(
143
159
  return nmdc.GeolocationValue(
144
160
  latitude=nmdc.DecimalDegree(latitude),
145
161
  longitude=nmdc.DecimalDegree(longitude),
162
+ type="nmdc:GeolocationValue",
146
163
  )