@mat3ra/esse 2024.12.19-1 → 2025.4.3-0

package/.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
         name: Regenerate data modules classes from static assets
         # yamllint disable rule:line-length
         entry: |
-          bash -c 'if [ "$(git diff --cached --name-only | grep "schema/")" ]; then echo "Skipping model generation because schemas were not changed."; exit 0; fi && \
+          bash -c 'if [ ! "$(git diff --cached --name-only | grep schema)" ]; then echo "Skipping model generation because schemas were not changed."; exit 0; fi && \
             datamodel-codegen \
                 --input ./dist/js/schema/ \
                 --input-file-type jsonschema \
@@ -24,7 +24,8 @@ repos:
                 --enable-version-header \
                 --use-title-as-name \
                 --class-name ESSE \
-                --disable-timestamp && \
+                --disable-timestamp \
+                --use-default && \
             # Move 3rd party modules to a separate directory with a PEP8 compliant name
             rm -rf ./dist/py/third_party && \
             mv ./dist/py/3pse ./dist/py/third_party'

package/dist/js/schema/core/primitive/integer_positive_single_digit.json

@@ -0,0 +1,8 @@
+{
+    "$id": "core/primitive/integer-positive-single-digit",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "integer positive single digit",
+    "type": "integer",
+    "minimum": 1,
+    "maximum": 9
+}

package/dist/js/schema/core/reference/modeling/exabyte.json

@@ -27,6 +27,9 @@
             "$schema": "http://json-schema.org/draft-07/schema#",
             "title": "entity reference schema",
             "type": "object",
+            "required": [
+                "_id"
+            ],
             "properties": {
                 "_id": {
                     "description": "entity identity",

package/dist/js/schema/core/reference/modeling.json

@@ -26,6 +26,9 @@
                     "$schema": "http://json-schema.org/draft-07/schema#",
                     "title": "entity reference schema",
                     "type": "object",
+                    "required": [
+                        "_id"
+                    ],
                     "properties": {
                         "_id": {
                             "description": "entity identity",

package/dist/js/schema/core/reference.json

@@ -30,6 +30,9 @@
                             "$schema": "http://json-schema.org/draft-07/schema#",
                             "title": "entity reference schema",
                             "type": "object",
+                            "required": [
+                                "_id"
+                            ],
                             "properties": {
                                 "_id": {
                                     "description": "entity identity",

package/dist/js/schema/definitions/constants.json

@@ -0,0 +1,52 @@
+{
+    "$id": "definitions/constants",
+    "title": "fundamental constants",
+    "description": "Fundamental physical constants, 2022 NIST CODATA (https://doi.org/10.48550/arXiv.2409.03787)",
+    "type": "object",
+    "required": [
+        "c",
+        "h",
+        "e",
+        "G",
+        "me",
+        "eps0",
+        "mu0"
+    ],
+    "properties": {
+        "c": {
+            "description": "speed of light in vacuum, \"units\": \"m/s\"",
+            "type": "number",
+            "default": 299792458
+        },
+        "h": {
+            "description": "Planck constant, \"units\": \"J s\"",
+            "type": "number",
+            "default": 6.62607015e-34
+        },
+        "e": {
+            "description": "elementary charge, \"units\": \"C\"",
+            "type": "number",
+            "default": 1.602176634e-19
+        },
+        "G": {
+            "description": "Newtonian constant of gravitation, \"units\": \"m^3/kg/s^2\"",
+            "type": "number",
+            "default": 6.6743015e-11
+        },
+        "me": {
+            "description": "electron mass \"units\": \"kg\"",
+            "type": "number",
+            "default": 9.109383713928e-31
+        },
+        "eps0": {
+            "description": "vacuum permittivity, \"units\": \"F/m\"",
+            "type": "number",
+            "default": 8.854187818814e-12
+        },
+        "mu0": {
+            "description": "vacuum permeability, \"units\": \"N/A^2\"",
+            "type": "number",
+            "default": 0.000001256637061272
+        }
+    }
+}

package/dist/js/schema/definitions/units.json

@@ -1,20 +1,48 @@
 {
     "$id": "definitions/units",
+    "title": "all units definitions",
+    "angle": {
+        "enum": [
+            "degree",
+            "radian"
+        ],
+        "default": "degree"
+    },
+    "coordinates_basis": {
+        "enum": [
+            "crystal",
+            "cartesian"
+        ],
+        "default": "crystal"
+    },
+    "coordinates_lattice_reciprocal": {
+        "enum": [
+            "crystal",
+            "cartesian"
+        ],
+        "default": "crystal"
+    },
     "length": {
         "enum": [
             "km",
             "m",
-            "pm",
+            "cm",
+            "mm",
+            "um",
             "nm",
             "angstrom",
             "a.u.",
             "bohr",
-            "fractional",
-            "crystal",
-            "cartesian",
-            "alat"
+            "pm"
         ]
     },
+    "length_atomic": {
+        "enum": [
+            "angstrom",
+            "bohr"
+        ],
+        "default": "angstrom"
+    },
     "energy": {
         "enum": [
             "kJ/mol",
@@ -26,6 +54,14 @@
             "eV/atom"
         ]
     },
+    "energy_atomic": {
+        "enum": [
+            "eV",
+            "hartree",
+            "rydberg"
+        ],
+        "default": "eV"
+    },
     "surface_energy": {
         "enum": [
             "eV/A^2"

package/dist/js/schema/element.json

@@ -31,15 +31,14 @@
                                 "enum": [
                                     "km",
                                     "m",
-                                    "pm",
+                                    "cm",
+                                    "mm",
+                                    "um",
                                     "nm",
                                     "angstrom",
                                     "a.u.",
                                     "bohr",
-                                    "fractional",
-                                    "crystal",
-                                    "cartesian",
-                                    "alat"
+                                    "pm"
                                 ]
                             },
                             "value": {

package/dist/js/schema/in_memory_entity/base.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/in_memory_entity/defaultable.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/in_memory_entity/has_consistency_check_has_metadata_named_defaultable.json

@@ -0,0 +1,74 @@
+{
+    "$id": "in-memory-entity/has-consistency-check-has-metadata-named-defaultable",
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "has consistency check has metadata named defaultable in-memory entity schema",
+    "type": "object",
+    "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.",
+    "properties": {
+        "_id": {
+            "description": "entity identity",
+            "type": "string"
+        },
+        "slug": {
+            "description": "entity slug",
+            "type": "string"
+        },
+        "systemName": {
+            "type": "string"
+        },
+        "schemaVersion": {
+            "description": "entity's schema version. Used to distinct between different schemas.",
+            "type": "string",
+            "default": "2022.8.16"
+        },
+        "name": {
+            "description": "entity name",
+            "type": "string"
+        },
+        "isDefault": {
+            "description": "Identifies that entity is defaultable",
+            "type": "boolean",
+            "default": false
+        },
+        "metadata": {
+            "type": "object"
+        },
+        "consistencyChecks": {
+            "type": "array",
+            "items": {
+                "$schema": "http://json-schema.org/draft-07/schema#",
+                "title": "consistency check",
+                "type": "object",
+                "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.",
+                "required": [
+                    "key",
+                    "name",
+                    "severity",
+                    "message"
+                ],
+                "properties": {
+                    "key": {
+                        "type": "string",
+                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
+                    },
+                    "name": {
+                        "type": "string",
+                        "description": "Name of the consistency check that is performed, which is listed in an enum."
+                    },
+                    "severity": {
+                        "enum": [
+                            "info",
+                            "warning",
+                            "error"
+                        ],
+                        "description": "Severity level of the problem, which is used in UI to differentiate."
+                    },
+                    "message": {
+                        "type": "string",
+                        "description": "Message generated by the consistency check describing the problem."
+                    }
+                }
+            }
+        }
+    }
+}

package/dist/js/schema/in_memory_entity/named.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/in_memory_entity/named_defaultable.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/in_memory_entity/named_defaultable_has_metadata.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/in_memory_entity/named_defaultable_runtime_items.json

@@ -15,47 +15,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",

package/dist/js/schema/job/base.json

@@ -217,6 +217,9 @@
             "$schema": "http://json-schema.org/draft-07/schema#",
             "title": "entity reference schema",
             "type": "object",
+            "required": [
+                "_id"
+            ],
             "properties": {
                 "_id": {
                     "description": "entity identity",
@@ -236,6 +239,9 @@
             "$schema": "http://json-schema.org/draft-07/schema#",
             "title": "entity reference schema",
             "type": "object",
+            "required": [
+                "_id"
+            ],
             "properties": {
                 "_id": {
                     "description": "entity identity",
@@ -255,6 +261,9 @@
             "$schema": "http://json-schema.org/draft-07/schema#",
             "title": "entity reference schema",
             "type": "object",
+            "required": [
+                "_id"
+            ],
             "properties": {
                 "_id": {
                     "description": "entity identity",
@@ -316,47 +325,6 @@
         "systemName": {
             "type": "string"
         },
-        "consistencyChecks": {
-            "type": "array",
-            "items": {
-                "$schema": "http://json-schema.org/draft-07/schema#",
-                "title": "consistency check",
-                "type": "object",
-                "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.",
-                "required": [
-                    "key",
-                    "name",
-                    "severity",
-                    "message"
-                ],
-                "properties": {
-                    "key": {
-                        "type": "string",
-                        "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
-                    },
-                    "name": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose",
-                            "atomsOverlap"
-                        ],
-                        "description": "Name of the consistency check that is performed, which is listed in an enum."
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ],
-                        "description": "Severity level of the problem, which is used in UI to differentiate."
-                    },
-                    "message": {
-                        "type": "string",
-                        "description": "Message generated by the consistency check describing the problem."
-                    }
-                }
-            }
-        },
         "schemaVersion": {
             "description": "entity's schema version. Used to distinct between different schemas.",
             "type": "string",