@mat3ra/esse 2024.12.19-1 → 2025.4.3-0

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Files changed (107) hide show
  1. package/.pre-commit-config.yaml +3 -2
  2. package/dist/js/schema/core/primitive/integer_positive_single_digit.json +8 -0
  3. package/dist/js/schema/core/reference/modeling/exabyte.json +3 -0
  4. package/dist/js/schema/core/reference/modeling.json +3 -0
  5. package/dist/js/schema/core/reference.json +3 -0
  6. package/dist/js/schema/definitions/constants.json +52 -0
  7. package/dist/js/schema/definitions/units.json +41 -5
  8. package/dist/js/schema/element.json +4 -5
  9. package/dist/js/schema/in_memory_entity/base.json +0 -41
  10. package/dist/js/schema/in_memory_entity/defaultable.json +0 -41
  11. package/dist/js/schema/in_memory_entity/has_consistency_check_has_metadata_named_defaultable.json +74 -0
  12. package/dist/js/schema/in_memory_entity/named.json +0 -41
  13. package/dist/js/schema/in_memory_entity/named_defaultable.json +0 -41
  14. package/dist/js/schema/in_memory_entity/named_defaultable_has_metadata.json +0 -41
  15. package/dist/js/schema/in_memory_entity/named_defaultable_runtime_items.json +0 -41
  16. package/dist/js/schema/job/base.json +9 -41
  17. package/dist/js/schema/job.json +9 -1025
  18. package/dist/js/schema/material/consistency_check.json +40 -0
  19. package/dist/js/schema/material.json +52 -82
  20. package/dist/js/schema/project.json +0 -41
  21. package/dist/js/schema/properties_directory/elemental/atomic_radius.json +4 -5
  22. package/dist/js/schema/properties_directory/non_scalar/average_potential_profile.json +4 -5
  23. package/dist/js/schema/properties_directory/non_scalar/band_structure.json +2 -10
  24. package/dist/js/schema/properties_directory/non_scalar/phonon_dispersions.json +2 -10
  25. package/dist/js/schema/properties_directory/structural/basis/atomic_coordinates.json +4 -5
  26. package/dist/js/schema/properties_directory/structural/basis/atomic_label.json +19 -0
  27. package/dist/js/schema/properties_directory/structural/basis.json +19 -50
  28. package/dist/js/schema/properties_directory/structural/lattice/lattice_bravais.json +12 -6
  29. package/dist/js/schema/properties_directory/structural/lattice/lattice_vectors.json +4 -5
  30. package/dist/js/schema/properties_directory/structural/lattice/type_enum.json +3 -2
  31. package/dist/js/schema/properties_directory/structural/lattice/type_extended_enum.json +3 -2
  32. package/dist/js/schema/properties_directory/structural/lattice.json +16 -16
  33. package/dist/js/schema/property/base.json +0 -41
  34. package/dist/js/schema/property/meta.json +0 -41
  35. package/dist/js/schema/property/raw.json +0 -41
  36. package/dist/js/schema/software/application.json +0 -41
  37. package/dist/js/schema/software/executable.json +0 -41
  38. package/dist/js/schema/software/flavor.json +0 -41
  39. package/dist/js/schema/software/template.json +0 -41
  40. package/dist/js/schema/software_directory/ml/unit/execution/evaluate/cross_validate.json +0 -164
  41. package/dist/js/schema/software_directory/ml/unit/execution/initialize.json +0 -164
  42. package/dist/js/schema/software_directory/ml/unit/execution/score.json +0 -164
  43. package/dist/js/schema/software_directory/ml/unit/execution/train.json +0 -164
  44. package/dist/js/schema/software_directory/ml/unit/execution.json +0 -656
  45. package/dist/js/schema/software_directory/ml/unit/processing/data_transformation/manipulation.json +0 -41
  46. package/dist/js/schema/software_directory/ml/unit/processing/data_transformation/scale_and_reduce.json +0 -41
  47. package/dist/js/schema/software_directory/ml/unit/processing/data_transformation.json +0 -41
  48. package/dist/js/schema/software_directory/ml/unit/processing/feature_selection/filter_based.json +0 -41
  49. package/dist/js/schema/software_directory/ml/unit/processing/feature_selection.json +0 -41
  50. package/dist/js/schema/software_directory/ml/unit/processing.json +0 -82
  51. package/dist/js/schema/software_directory/modeling/deepmd.json +0 -41
  52. package/dist/js/schema/software_directory/modeling/nwchem.json +0 -41
  53. package/dist/js/schema/software_directory/modeling/unit/execution.json +0 -164
  54. package/dist/js/schema/software_directory/modeling/vasp.json +0 -41
  55. package/dist/js/schema/software_directory/scripting/jupyter_lab.json +0 -41
  56. package/dist/js/schema/software_directory/scripting/python.json +0 -41
  57. package/dist/js/schema/software_directory/scripting/shell.json +0 -41
  58. package/dist/js/schema/software_directory/scripting/unit/execution.json +0 -164
  59. package/dist/js/schema/system/_material.json +3 -0
  60. package/dist/js/schema/system/_parent_job.json +3 -0
  61. package/dist/js/schema/system/_project.json +3 -0
  62. package/dist/js/schema/system/consistency_check.json +1 -5
  63. package/dist/js/schema/system/creator.json +3 -0
  64. package/dist/js/schema/system/creator_account.json +3 -0
  65. package/dist/js/schema/system/description.json +1 -1
  66. package/dist/js/schema/system/entity_reference.json +3 -0
  67. package/dist/js/schema/system/has_consistency_check.json +46 -0
  68. package/dist/js/schema/system/in_set.json +3 -0
  69. package/dist/js/schema/system/job_extended.json +6 -0
  70. package/dist/js/schema/system/owner.json +3 -0
  71. package/dist/js/schema/workflow/base.json +0 -41
  72. package/dist/js/schema/workflow/subworkflow/unit.json +0 -410
  73. package/dist/js/schema/workflow/subworkflow.json +0 -451
  74. package/dist/js/schema/workflow/unit/assertion.json +0 -41
  75. package/dist/js/schema/workflow/unit/assignment.json +0 -41
  76. package/dist/js/schema/workflow/unit/base.json +0 -41
  77. package/dist/js/schema/workflow/unit/condition.json +0 -41
  78. package/dist/js/schema/workflow/unit/execution.json +0 -164
  79. package/dist/js/schema/workflow/unit/io.json +0 -41
  80. package/dist/js/schema/workflow/unit/map.json +0 -41
  81. package/dist/js/schema/workflow/unit/processing.json +0 -41
  82. package/dist/js/schema/workflow/unit/reduce.json +0 -41
  83. package/dist/js/schema/workflow/unit/subworkflow.json +0 -41
  84. package/dist/js/schema/workflow/unit.json +0 -492
  85. package/dist/js/schema/workflow.json +0 -984
  86. package/dist/js/schemas.json +1 -1
  87. package/dist/js/types.d.ts +221 -3125
  88. package/package.json +3 -3
  89. package/schema/core/primitive/integer_positive_single_digit.json +8 -0
  90. package/schema/definitions/constants.json +52 -0
  91. package/schema/definitions/units.json +41 -5
  92. package/schema/in_memory_entity/base.json +0 -6
  93. package/schema/in_memory_entity/has_consistency_check_has_metadata_named_defaultable.json +13 -0
  94. package/schema/material/consistency_check.json +22 -0
  95. package/schema/material.json +6 -0
  96. package/schema/properties_directory/non-scalar/band_structure.json +1 -1
  97. package/schema/properties_directory/non-scalar/phonon_dispersions.json +1 -1
  98. package/schema/properties_directory/structural/basis/atomic_label.json +15 -0
  99. package/schema/properties_directory/structural/basis.json +12 -20
  100. package/schema/properties_directory/structural/lattice/lattice_bravais.json +7 -10
  101. package/schema/properties_directory/structural/lattice/type_enum.json +3 -2
  102. package/schema/properties_directory/structural/lattice/type_extended_enum.json +3 -2
  103. package/schema/properties_directory/structural/lattice.json +1 -8
  104. package/schema/system/consistency_check.json +1 -5
  105. package/schema/system/description.json +1 -1
  106. package/schema/system/entity_reference.json +2 -1
  107. package/schema/system/has_consistency_check.json +16 -0
package/dist/js/schema/properties_directory/structural/lattice.json CHANGED
@@ -13,11 +13,6 @@
13
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  "type"
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  ],
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  "properties": {
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- "name": {
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- "enum": [
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- "lattice"
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- ]
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- },
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  "vectors": {
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  "$schema": "http://json-schema.org/draft-07/schema#",
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  "title": "lattice explicit unit",
@@ -37,15 +32,14 @@
37
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  "enum": [
38
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  "km",
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  "m",
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- "pm",
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+ "cm",
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+ "mm",
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+ "um",
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  "nm",
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  "angstrom",
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  "a.u.",
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41
  "bohr",
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- "fractional",
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- "crystal",
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- "cartesian",
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- "alat"
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+ "pm"
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  ]
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  },
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  "a": {
@@ -82,7 +76,7 @@
82
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  },
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  "type": {
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  "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "lattice type schema",
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+ "title": "lattice type enum",
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  "type": "string",
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  "enum": [
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  "CUB",
@@ -99,24 +93,30 @@
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  "TRI",
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  "MCLC",
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  "RHL"
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- ]
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+ ],
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+ "default": "TRI"
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  },
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  "units": {
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+ "title": "Lattice units schema",
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  "type": "object",
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+ "default": {
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+ "length": "angstrom",
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+ "angle": "degree"
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+ },
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  "properties": {
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  "length": {
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- "type": "string",
109
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  "enum": [
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  "angstrom",
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  "bohr"
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- ]
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+ ],
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+ "default": "angstrom"
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  },
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  "angle": {
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- "type": "string",
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  "enum": [
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  "degree",
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  "radian"
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- ]
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+ ],
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+ "default": "degree"
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  }
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  }
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  },
package/dist/js/schema/property/base.json CHANGED
@@ -337,47 +337,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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340
  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
383
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  "type": "string",
package/dist/js/schema/property/meta.json CHANGED
@@ -337,47 +337,6 @@
337
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
347
- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
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  "type": "string",
package/dist/js/schema/property/raw.json CHANGED
@@ -337,47 +337,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
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  "type": "string",
package/dist/js/schema/software/application.json CHANGED
@@ -40,47 +40,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
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  "type": "string",
package/dist/js/schema/software/executable.json CHANGED
@@ -33,47 +33,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
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  "type": "string",
package/dist/js/schema/software/flavor.json CHANGED
@@ -49,47 +49,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
69
- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
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  "schemaVersion": {
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  "description": "entity's schema version. Used to distinct between different schemas.",
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  "type": "string",
package/dist/js/schema/software/template.json CHANGED
@@ -53,47 +53,6 @@
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  "systemName": {
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  "type": "string"
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  },
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- "consistencyChecks": {
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- "type": "array",
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- "items": {
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- "$schema": "http://json-schema.org/draft-07/schema#",
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- "title": "consistency check",
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- "type": "object",
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- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
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- "required": [
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- "key",
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- "name",
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- "severity",
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- "message"
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- ],
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- "properties": {
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- "key": {
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- "type": "string",
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- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
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- },
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- "name": {
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- "enum": [
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- "default",
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- "atomsTooClose",
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- "atomsOverlap"
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- ],
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- "description": "Name of the consistency check that is performed, which is listed in an enum."
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- },
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- "severity": {
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- "enum": [
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- "info",
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- "warning",
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- "error"
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- ],
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- "description": "Severity level of the problem, which is used in UI to differentiate."
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- },
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- "message": {
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- "type": "string",
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- "description": "Message generated by the consistency check describing the problem."
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- }
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- }
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- }
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- },
97
56
  "schemaVersion": {
98
57
  "description": "entity's schema version. Used to distinct between different schemas.",
99
58
  "type": "string",
package/dist/js/schema/software_directory/ml/unit/execution/evaluate/cross_validate.json CHANGED
@@ -72,47 +72,6 @@
72
72
  "systemName": {
73
73
  "type": "string"
74
74
  },
75
- "consistencyChecks": {
76
- "type": "array",
77
- "items": {
78
- "$schema": "http://json-schema.org/draft-07/schema#",
79
- "title": "consistency check",
80
- "type": "object",
81
- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
82
- "required": [
83
- "key",
84
- "name",
85
- "severity",
86
- "message"
87
- ],
88
- "properties": {
89
- "key": {
90
- "type": "string",
91
- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
92
- },
93
- "name": {
94
- "enum": [
95
- "default",
96
- "atomsTooClose",
97
- "atomsOverlap"
98
- ],
99
- "description": "Name of the consistency check that is performed, which is listed in an enum."
100
- },
101
- "severity": {
102
- "enum": [
103
- "info",
104
- "warning",
105
- "error"
106
- ],
107
- "description": "Severity level of the problem, which is used in UI to differentiate."
108
- },
109
- "message": {
110
- "type": "string",
111
- "description": "Message generated by the consistency check describing the problem."
112
- }
113
- }
114
- }
115
- },
116
75
  "schemaVersion": {
117
76
  "description": "entity's schema version. Used to distinct between different schemas.",
118
77
  "type": "string",
@@ -163,47 +122,6 @@
163
122
  "systemName": {
164
123
  "type": "string"
165
124
  },
166
- "consistencyChecks": {
167
- "type": "array",
168
- "items": {
169
- "$schema": "http://json-schema.org/draft-07/schema#",
170
- "title": "consistency check",
171
- "type": "object",
172
- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
173
- "required": [
174
- "key",
175
- "name",
176
- "severity",
177
- "message"
178
- ],
179
- "properties": {
180
- "key": {
181
- "type": "string",
182
- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
183
- },
184
- "name": {
185
- "enum": [
186
- "default",
187
- "atomsTooClose",
188
- "atomsOverlap"
189
- ],
190
- "description": "Name of the consistency check that is performed, which is listed in an enum."
191
- },
192
- "severity": {
193
- "enum": [
194
- "info",
195
- "warning",
196
- "error"
197
- ],
198
- "description": "Severity level of the problem, which is used in UI to differentiate."
199
- },
200
- "message": {
201
- "type": "string",
202
- "description": "Message generated by the consistency check describing the problem."
203
- }
204
- }
205
- }
206
- },
207
125
  "schemaVersion": {
208
126
  "description": "entity's schema version. Used to distinct between different schemas.",
209
127
  "type": "string",
@@ -386,47 +304,6 @@
386
304
  "systemName": {
387
305
  "type": "string"
388
306
  },
389
- "consistencyChecks": {
390
- "type": "array",
391
- "items": {
392
- "$schema": "http://json-schema.org/draft-07/schema#",
393
- "title": "consistency check",
394
- "type": "object",
395
- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
396
- "required": [
397
- "key",
398
- "name",
399
- "severity",
400
- "message"
401
- ],
402
- "properties": {
403
- "key": {
404
- "type": "string",
405
- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
406
- },
407
- "name": {
408
- "enum": [
409
- "default",
410
- "atomsTooClose",
411
- "atomsOverlap"
412
- ],
413
- "description": "Name of the consistency check that is performed, which is listed in an enum."
414
- },
415
- "severity": {
416
- "enum": [
417
- "info",
418
- "warning",
419
- "error"
420
- ],
421
- "description": "Severity level of the problem, which is used in UI to differentiate."
422
- },
423
- "message": {
424
- "type": "string",
425
- "description": "Message generated by the consistency check describing the problem."
426
- }
427
- }
428
- }
429
- },
430
307
  "schemaVersion": {
431
308
  "description": "entity's schema version. Used to distinct between different schemas.",
432
309
  "type": "string",
@@ -611,47 +488,6 @@
611
488
  "systemName": {
612
489
  "type": "string"
613
490
  },
614
- "consistencyChecks": {
615
- "type": "array",
616
- "items": {
617
- "$schema": "http://json-schema.org/draft-07/schema#",
618
- "title": "consistency check",
619
- "type": "object",
620
- "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
621
- "required": [
622
- "key",
623
- "name",
624
- "severity",
625
- "message"
626
- ],
627
- "properties": {
628
- "key": {
629
- "type": "string",
630
- "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
631
- },
632
- "name": {
633
- "enum": [
634
- "default",
635
- "atomsTooClose",
636
- "atomsOverlap"
637
- ],
638
- "description": "Name of the consistency check that is performed, which is listed in an enum."
639
- },
640
- "severity": {
641
- "enum": [
642
- "info",
643
- "warning",
644
- "error"
645
- ],
646
- "description": "Severity level of the problem, which is used in UI to differentiate."
647
- },
648
- "message": {
649
- "type": "string",
650
- "description": "Message generated by the consistency check describing the problem."
651
- }
652
- }
653
- }
654
- },
655
491
  "schemaVersion": {
656
492
  "description": "entity's schema version. Used to distinct between different schemas.",
657
493
  "type": "string",