@mat3ra/esse 2023.12.25-2

package/schema/core/reference/literature/name.json

@@ -0,0 +1,24 @@
+{
+    "$id": "core/reference/literature/name",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "experiment author schema",
+    "type": "object",
+    "properties": {
+        "first": {
+            "type": "string"
+        },
+        "middle": {
+            "type": "string"
+        },
+        "last": {
+            "type": "string"
+        },
+        "affiliation": {
+            "type": "string"
+        }
+    },
+    "required": [
+        "first",
+        "last"
+    ]
+}

package/schema/core/reference/literature/pages.json

@@ -0,0 +1,17 @@
+{
+    "$id": "core/reference/literature/pages",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "pages schema",
+    "type": "object",
+    "properties": {
+        "start": {
+            "type": "string"
+        },
+        "end": {
+            "type": "string"
+        }
+    },
+    "required": [
+        "start"
+    ]
+}

package/schema/core/reference/literature.json

@@ -0,0 +1,82 @@
+{
+    "$id": "core/reference/literature",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "literature reference schema",
+    "properties": {
+        "type": {
+            "enum": [
+                "literature"
+            ]
+        },
+        "doi": {
+            "type": "string",
+            "description": "Digital Object Identifier of the reference."
+        },
+        "isbn": {
+            "type": "string",
+            "description": "International Standard Book Number of the reference."
+        },
+        "issn": {
+            "type": "string",
+            "description": "International Standard Serial Number of the reference."
+        },
+        "url": {
+            "type": "string",
+            "description": "Internet address of the reference."
+        },
+        "title": {
+            "type": "string",
+            "description": "Title of the work."
+        },
+        "publisher": {
+            "type": "string",
+            "description": "Publisher of the work."
+        },
+        "journal": {
+            "type": "string",
+            "description": "Journal in which the work appeared."
+        },
+        "volume": {
+            "type": "string",
+            "description": "Volume of the series in which the work appeared."
+        },
+        "year": {
+            "type": "string",
+            "description": "Year in which the reference was published."
+        },
+        "issue": {
+            "type": "string",
+            "description": "Issue of the collection in which the work appeared."
+        },
+        "pages": {
+            "type": "object",
+            "description": "Start and end pages of the work.",
+            "allOf": [
+                {
+                    "$ref": "literature/pages.json"
+                }
+            ]
+        },
+        "authors": {
+            "type": "array",
+            "description": "List of authors of the work.",
+            "items": {
+                "$ref": "literature/name.json"
+            }
+        },
+        "editors": {
+            "type": "array",
+            "description": "List of editors of the work.",
+            "items": {
+                "$ref": "literature/name.json"
+            }
+        },
+        "reference": {
+            "type": "array",
+            "items": {
+                "type": "object"
+            },
+            "description": "References cited by the work. Reference objects can nest as deeply as needed. This is useful, for example, when tracking the history of a value referenced in a scholarly article; the top level reference would contain information about where the data was accessed while the nested reference would contain information about where it was originally published."
+        }
+    }
+}

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

@@ -0,0 +1,30 @@
+{
+    "$id": "core/reference/modeling/exabyte",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "info for characteristic obtained by exabyte calculation",
+    "properties": {
+        "type": {
+            "enum": [
+                "exabyte"
+            ]
+        },
+        "title": {
+            "description": "Human-readable title of the job",
+            "type": "string",
+            "maxLength": 300
+        },
+        "_id": {
+            "description": "job identifier",
+            "type": "string"
+        },
+        "owner": {
+            "description": "owner entity reference",
+            "$ref": "../../../system/entity_reference.json"
+        }
+    },
+    "required": [
+        "title",
+        "_id",
+        "owner"
+    ]
+}

package/schema/core/reference/modeling.json

@@ -0,0 +1,10 @@
+{
+    "$id": "core/reference/modeling",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "info for property obtained by modeling, only supports exabyte-originated data atm, but easily extendable",
+    "oneOf": [
+        {
+            "$ref": "modeling/exabyte.json"
+        }
+    ]
+}

package/schema/core/reference.json

@@ -0,0 +1,16 @@
+{
+    "$id": "core/reference",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "reference schema (using `anyOf` instead of `oneOf` below b/c current reference schemas overlap)",
+    "anyOf": [
+        {
+            "$ref": "reference/modeling.json"
+        },
+        {
+            "$ref": "reference/experiment.json"
+        },
+        {
+            "$ref": "reference/literature.json"
+        }
+    ]
+}

package/schema/core/reusable/atomic_data/per_orbital.json

@@ -0,0 +1,22 @@
+{
+    "$id": "core/reusable/atomic-data/per-orbital",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital",
+    "description": "Atomic properties per orbital e.g., Hubbard U parameters.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "integer",
+            "description": "Site number or index in the lattice"
+        },
+        "atomicSpecies": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co1, Mn"
+        },
+        "orbitalName": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        }
+    }
+}

package/schema/core/reusable/atomic_data/per_orbital_pair.json

@@ -0,0 +1,39 @@
+{
+    "$id": "core/reusable/atomic-data/per-orbital-pair",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital pair",
+    "description": "Atomic properties per orbital pair e.g., Hubbard V parameters.",
+    "type": "object",
+    "properties": {
+        "id": {
+            "type": "integer",
+            "description": "Site number or index in the lattice"
+        },
+        "id2": {
+            "type": "integer",
+            "description": "Site number or index in the lattice of second site"
+        },
+        "atomicSpecies": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co1, Mn"
+        },
+        "atomicSpecies2": {
+            "type": "string",
+            "pattern": "^[a-zA-Z]{1,2}[\\d+]?$",
+            "description": "Example: Co2, O"
+        },
+        "orbitalName": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        },
+        "orbitalName2": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        },
+        "distance": {
+            "type": "number",
+            "description": "Distance between two sites in Bohr."
+        }
+    }
+}

package/schema/core/reusable/atomic_data/value_number.json

@@ -0,0 +1,13 @@
+{
+    "$id": "core/reusable/atomic-data/value-number",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data numeric properties",
+    "description": "Numeric value specific to atomic data",
+    "type": "object",
+    "properties": {
+        "value": {
+            "type": "number",
+            "description": "Value related to a specific property, e.g., Hubbard U, V etc."
+        }
+    }
+}

package/schema/core/reusable/atomic_data/value_string.json

@@ -0,0 +1,13 @@
+{
+    "$id": "core/reusable/atomic-data/string-value",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data string properties",
+    "description": "String value specific to atomic data",
+    "type": "object",
+    "properties": {
+        "value": {
+            "type": "string",
+            "description": "String value specific to atomic data"
+        }
+    }
+}

package/schema/core/reusable/atomic_data_per_orbital_numeric.json

@@ -0,0 +1,15 @@
+{
+    "$id": "core/reusable/atomic-data-per-orbital-numeric",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital numeric",
+    "description": "Atomic properties per orbital pair with numeric value e.g., Hubbard V parameters.",
+    "type": "object",
+    "allOf":[
+        {
+            "$ref": "atomic_data/per_orbital.json"
+        },
+        {
+            "$ref": "atomic_data/value_number.json"
+        }
+    ]
+}

package/schema/core/reusable/atomic_data_per_orbital_pair_numeric.json

@@ -0,0 +1,15 @@
+{
+    "$id": "core/reusable/atomic-data-per-orbital-pair-numeric",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Atomic data per orbital pair numeric",
+    "description": "Atomic properties per orbital pair with numeric value e.g., Hubbard V parameters.",
+    "type": "object",
+    "allOf":[
+        {
+            "$ref": "atomic_data/per_orbital_pair.json"
+        },
+        {
+            "$ref": "atomic_data/value_number.json"
+        }
+    ]
+}

package/schema/core/reusable/atomic_orbital.json

@@ -0,0 +1,32 @@
+{
+    "$id": "core/reusable/atomic-orbital",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic orbital schema",
+    "type": "object",
+    "properties": {
+        "orbitalName": {
+            "type": "string",
+            "pattern": "^[1-7][sSpPdDfF]$"
+        },
+        "orbitalIndex": {
+            "type": "integer",
+            "minimum": 1
+        },
+        "principalNumber": {
+            "type": "integer",
+            "minimum": 1,
+            "maximum": 7
+        },
+        "angularMomentum": {
+            "type": "integer",
+            "minimum": 0,
+            "maximum": 3
+        },
+        "occupation": {
+            "type": "number",
+            "description": "Shell occupation",
+            "minimum": 0,
+            "maximum": 14
+        }
+    }
+}

package/schema/core/reusable/atomic_scalars.json

@@ -0,0 +1,17 @@
+{
+    "$id": "core/reusable/atomic-scalars",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic scalars vectors schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/array_of_ids.json"
+        }
+    ],
+    "items": {
+        "properties": {
+            "value": {
+                "$ref": "../primitive/scalar.json"
+            }
+        }
+    }
+}

package/schema/core/reusable/atomic_strings.json

@@ -0,0 +1,17 @@
+{
+    "$id": "core/reusable/atomic-strings",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic strings vectors schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/array_of_ids.json"
+        }
+    ],
+    "items": {
+        "properties": {
+            "value": {
+                "type": "string"
+            }
+        }
+    }
+}

package/schema/core/reusable/atomic_vectors.json

@@ -0,0 +1,17 @@
+{
+    "$id": "core/reusable/atomic-vectors",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "atomic vectors schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/array_of_ids.json"
+        }
+    ],
+    "items": {
+        "properties": {
+            "value": {
+                "$ref": "../abstract/vector.json"
+            }
+        }
+    }
+}

package/schema/core/reusable/band_gap.json

@@ -0,0 +1,44 @@
+{
+    "$id": "core/reusable/band-gap",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "band gap schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "kpointConduction": {
+            "description": "kpoint inside conduction band in crystal coordinates",
+            "$ref": "../abstract/point.json"
+        },
+        "kpointValence": {
+            "description": "kpoint inside valence band in crystal coordinates",
+            "$ref": "../abstract/point.json"
+        },
+        "eigenvalueConduction": {
+            "description": "eigenvalue at k-point in conduction band",
+            "type": "number"
+        },
+        "eigenvalueValence": {
+            "description": "eigenvalue at k-point in valence band",
+            "type": "number"
+        },
+        "spin": {
+            "type": "number"
+        },
+        "type": {
+            "type": "string",
+            "enum": [
+                "direct",
+                "indirect"
+            ]
+        },
+        "units": {
+            "$ref": "../../definitions/units.json#/energy"
+        }
+    },
+    "required": [
+        "type"
+    ]
+}

package/schema/core/reusable/categories.json

@@ -0,0 +1,29 @@
+{
+    "$id": "core/reusable/categories",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "categories",
+    "description": "Used to categorize entities such as models and methods",
+    "type": "object",
+    "properties": {
+        "tier1": {
+            "description": "top-level category",
+            "$ref": "../primitive/slugified_entry_or_slug.json"
+        },
+        "tier2": {
+            "description": "second level category",
+            "$ref": "../primitive/slugified_entry_or_slug.json"
+        },
+        "tier3": {
+            "description": "third level category",
+            "$ref": "../primitive/slugified_entry_or_slug.json"
+        },
+        "type": {
+            "description": "general type of the entity",
+            "$ref": "../primitive/slugified_entry_or_slug.json"
+        },
+        "subtype": {
+            "description": "general subtype of the entity",
+            "$ref": "../primitive/slugified_entry_or_slug.json"
+        }
+    }
+}

package/schema/core/reusable/category_path.json

@@ -0,0 +1,7 @@
+{
+    "$id": "core/reusable/category-path",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "category path schema",
+    "description": "TODO: Use regex once schema draft version has been updated",
+    "type": "string"
+}

package/schema/core/reusable/dielectric_tensor_component.json

@@ -0,0 +1,28 @@
+{
+    "$id": "core/reusable/dielectric-tensor-component",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Dielectric Tensor",
+    "allOf": [
+        {
+            "$ref": "./frequency_function_matrix.json"
+        }
+    ],
+    "properties": {
+        "part": {
+            "description": "Real or imaginary part of the dielectric tensor component",
+            "type": "string",
+            "enum": [
+                "real",
+                "imaginary"
+            ]
+        },
+        "spin": {
+            "type": "number"
+        }
+    },
+    "required": [
+        "part",
+        "frequencies",
+        "components"
+    ]
+}

package/schema/core/reusable/energy.json

@@ -0,0 +1,29 @@
+{
+    "$id": "core/reusable/energy",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "energy schema",
+    "allOf": [
+        {
+            "$ref": "../primitive/scalar.json"
+        }
+    ],
+    "properties": {
+        "name": {
+            "type": "string"
+        },
+        "units": {
+            "anyOf": [
+                {
+                    "$ref": "../../definitions/units.json#/energy"
+                },
+                {
+                    "$ref": "../../definitions/units.json#/surface_energy"
+                }
+            ]
+        }
+    },
+    "required": [
+        "name",
+        "units"
+    ]
+}

package/schema/core/reusable/file_metadata.json

@@ -0,0 +1,20 @@
+{
+    "$id": "core/reusable/file-metadata",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "file_metadata",
+    "properties": {
+        "pathname": {
+            "description": "Relative path to the directory that contains the file.",
+            "type": "string"
+        },
+        "basename": {
+            "description": "Basename of the file",
+            "type": "string",
+            "$comment": "isGenerative:true"
+        },
+        "filetype": {
+            "description": "What kind of file this is, e.g. image / text",
+            "type": "string"
+        }
+    }
+}

package/schema/core/reusable/frequency_function_matrix.json

@@ -0,0 +1,23 @@
+{
+    "$id": "core/reusable/frequency-function-matrix",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "",
+    "description": "Schema for a function of frequency yielding a nx3 matrix",
+    "type": "object",
+    "properties": {
+        "frequencies": {
+            "description": "Frequencies",
+            "type": "array",
+            "items": {
+                "type": "number"
+            }
+        },
+        "components": {
+            "description": "Matrix with 3 columns, e.g. x, y, z",
+            "type": "array",
+            "items": {
+                "$ref": "../primitive/array_of_3_numbers.json"
+            }
+        }
+    }
+}

package/schema/core/reusable/object_storage_container_data.json

@@ -0,0 +1,37 @@
+{
+    "$id": "core/reusable/object-storage-container-data",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Object Storage Container Data",
+    "properties": {
+        "CONTAINER": {
+            "description": "Object storage container for the file",
+            "type": "string"
+        },
+        "NAME": {
+            "description": "Name of the file inside the object storage bucket",
+            "type": "string"
+        },
+        "PROVIDER": {
+            "description": "Object storage provider",
+            "type": "string"
+        },
+        "REGION": {
+            "description": "Region for the object container specified in Container",
+            "type": "string"
+        },
+        "SIZE": {
+            "description": "Size of the file in bytes",
+            "type": "integer"
+        },
+        "TIMESTAMP": {
+            "description": "Unix timestamp showing when the file was last modified",
+            "type": "string"
+        }
+    },
+    "required": [
+        "CONTAINER",
+        "NAME",
+        "PROVIDER",
+        "REGION"
+    ]
+}