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5 adding schema for individual components #25

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merged 4 commits into from
Feb 15, 2024
Merged

5 adding schema for individual components #25

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93712c4
Added Schemas
SmithRWORNL Feb 14, 2024
5ac4fa7
Changed parameter schema number
SmithRWORNL Feb 15, 2024
54e9366
Parameter number schema expansion
SmithRWORNL Feb 15, 2024
3767cbd
Removed scidata schema validation
SmithRWORNL Feb 15, 2024
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26 changes: 22 additions & 4 deletions .github/workflows/actions.yml
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Expand Up @@ -27,10 +27,28 @@ jobs:
run: |
python -m pip install check-jsonschema

- name: Run Unit schema validation
- name: Run JSON schema validation
run: |
check-jsonschema -o json --schemafile schema/basisset.json examples/sections/basisset.jsonld
check-jsonschema -o json --schemafile schema/calculation.json examples/sections/calculation.jsonld
check-jsonschema -o json --schemafile schema/chemical.json examples/sections/chemical.jsonld
check-jsonschema -o json --schemafile schema/computer.json examples/sections/computer.jsonld
check-jsonschema -o json --schemafile schema/dataseries.json examples/sections/dataseries.jsonld
check-jsonschema -o json --schemafile schema/dataset.json examples/sections/dataset.jsonld
check-jsonschema -o json --schemafile schema/framework_outline.json examples/sections/framework_outline.jsonld
check-jsonschema -o json --schemafile schema/framework_plus.json examples/sections/framework_plus.jsonld
check-jsonschema -o json --schemafile schema/framework.json examples/sections/framework.jsonld
check-jsonschema -o json --schemafile schema/measurement.json examples/sections/measurement.jsonld
check-jsonschema -o json --schemafile schema/methodology.json examples/sections/methodology_cc.jsonld
check-jsonschema -o json --schemafile schema/methodology.json examples/sections/methodology_exp.jsonld
check-jsonschema -o json --schemafile schema/mixture.json examples/sections/mixture.jsonld
check-jsonschema -o json --schemafile schema/molsystem.json examples/sections/molsystem.jsonld
check-jsonschema -o json --schemafile schema/parameter.json examples/sections/parameter.jsonld
check-jsonschema -o json --schemafile schema/procedure.json examples/sections/procedure.jsonld
check-jsonschema -o json --schemafile schema/resource.json examples/sections/resource.jsonld
check-jsonschema -o json --schemafile schema/software.json examples/sections/software.jsonld
check-jsonschema -o json --schemafile schema/substance.json examples/sections/substance.jsonld
check-jsonschema -o json --schemafile schema/system.json examples/sections/system_cc.jsonld
check-jsonschema -o json --schemafile schema/system.json examples/sections/system_exp.jsonld
check-jsonschema -o json --schemafile schema/unit.json examples/sections/unit.jsonld

- name: Run Value schema validation
run: |
check-jsonschema -o json --schemafile schema/value.json examples/sections/value.jsonld
4 changes: 2 additions & 2 deletions examples/sections/basisset.jsonld
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Expand Up @@ -5,7 +5,7 @@
"dct": "http://purl.org/dc/terms/",
"gc": "http://purl.org/gc/",
"obo": "http://purl.obolibrary.org/obo/",
"wd": "http://www.wikidata.org/entity/",
"wd": "http://www.wikidata.org/entity/"
},
{"@base": "https://stuchalk.github.io/scidata/examples/sections/basisset/"}
],
Expand Down Expand Up @@ -72,4 +72,4 @@
]
}
]
}
}
6 changes: 3 additions & 3 deletions examples/sections/measurement.jsonld
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Expand Up @@ -2,8 +2,8 @@
"@context": [
"https://stuchalk.github.io/scidata/contexts/crg_measurement.jsonld",
{
"sdo": "https://stuchalk.github.io/scidata/ontology/scidata.owl#"
"cao": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl#",
"sdo": "https://stuchalk.github.io/scidata/ontology/scidata.owl#",
"cao": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl#"
},
{"@base": "https://stuchalk.github.io/scidata/examples/sections/measurement"}
],
Expand Down Expand Up @@ -91,4 +91,4 @@
}
}
]
}
}
4 changes: 2 additions & 2 deletions examples/sections/procedure.jsonld
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Expand Up @@ -4,7 +4,7 @@
{
"afr": "http://purl.allotrope.org/ontologies/result#",
"afre": "http://purl.allotrope.org/ontologies/realizable",
"repome": "https://w3id.org/reproduceme#",
"repome": "https://w3id.org/reproduceme#"
},
{"@base": "https://stuchalk.github.io/scidata/examples/procedure/"}
],
Expand Down Expand Up @@ -70,4 +70,4 @@
],
"notes": "If the electrode is not in 'Good condition' repeat the calibration procedure. If it is still not showing 'Good condition' report to your supervisor and obtain a replacement."
}
}
}
39 changes: 39 additions & 0 deletions schema/basisset.json
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@@ -0,0 +1,39 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Basis Set Schema",
"description": "JSON schema for a basis set",
"type": "object",
"properties": {
"@id": { "type": "string" },
"title": { "type": "string" },
"description": { "type": "string" },
"format": { "type": "string" },
"setType": { "type": "string" },
"harmonicType": { "type": "string" },
"contractionType": { "type": "string" },
"sets": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"symbol": { "type": "string" },
"contractions": {
"shell": { "type": "string" },
"matrix": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"datatype": { "type": "string" },
"rows": { "type": "number" },
"columns": { "type": "number" },
"delimiter": { "type": "string" },
"values": { "type": "string" }
}
}
}
}
}
}
}
}
27 changes: 27 additions & 0 deletions schema/calculation.json
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@@ -0,0 +1,27 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Calculation Schema",
"description": "JSON schema for a calculation",
"type": "object",
"properties": {
"@id": { "type": "string" },
"approach": { "type": "string" },
"calcclass": { "type": "string" },
"calcType": { "type": "string" },
"submethod": { "type": "string" },
"calculations": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"class": { "type": "string" },
"calcType": { "type": "string" },
"referenceState": { "type": "string" },
"determinant": { "type": "string" },
"spin#": { "type": "string" }
}
}
}
}
}
17 changes: 17 additions & 0 deletions schema/chemical.json
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{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Methodology CC Schema",
"description": "JSON schema for a methodology",
"type": "object",
"properties": {
"@id": { "type": "string" },
"name": { "type": "string" },
"sourcetype": { "type": "string" },
"vendor": { "type": "string" },
"grade": { "type": "string" },
"properties": {
"type": "array",
"items": {"$ref": "parameter.json"}
}
}
}
38 changes: 38 additions & 0 deletions schema/computer.json
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@@ -0,0 +1,38 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Calculation Schema",
"description": "JSON schema for a calculation",
"type": "object",
"properties": {
"@id": { "type": "string" },
"architecture": { "type": "string" },
"cpu": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"opmodes": { "type": "string" },
"count": { "type": "number" },
"speed": { "type": "string" },
"vendorid": { "type": "string" },
"family": { "type": "string" },
"model": { "type": "string" },
"modelname": { "type": "string" }
}
},
"byteorder": { "type": "string" },
"threadspercore": { "type": "number" },
"corespersocket": { "type": "number" },
"sockets": { "type": "number" },
"cache": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"l1datacache": { "type": "string" },
"l1instcache": { "type": "string" },
"l2cache": { "type": "string" },
"l3cache": { "type": "string" }
}
},
"ram": { "type": "string" }
}
}
34 changes: 34 additions & 0 deletions schema/dataseries.json
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{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Data Series Schema",
"description": "JSON schema for a data series",
"type": "object",
"properties": {
"@id": { "type": "string" },
"label": { "type": "string" },
"axis": { "type": "string" },
"uid": { "type": "string" },
"parameter": {
"type": "object",
"required": [ "@id" ],
"properties": {
"@id": { "type": "string" },
"datatype": { "type": "string" },
"numberarray": {
"type": "array",
"items": {
"type": "number"
}
},
"quantity": { "type": "string" },
"valuearray": {
"@id": { "type": "string" },
"textarray": {
"type": "array",
"items": { "type": "string" }
}
}
}
}
}
}
64 changes: 64 additions & 0 deletions schema/dataset.json
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{
"$schema": "http://json-schema.org/draft-04/schema#",
"title": "Data Set Schema",
"description": "JSON schema for a data set",
"type": "object",
"properties": {
"@id": { "type": "string" },
"datapoint": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"scope": { "type": "string" },
"quantity": { "type": "string" },
"property": { "type": "string" },
"value": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"number": { "type": "string" },
"unitstr": { "type": "string" }
}
}
}
}
},
"datagroup": {
"type": "array",
"items": {"$ref": "#/definitions/datagroup"}
}
},
"definitions": {
"datagroup" : {
"type": "object",
"items": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"scope": { "type": "string" },
"group": { "type": "string" },
"attributes": {
"type": "array",
"items": {
"type": "object",
"properties": {
"@id": { "type": "string" },
"number": { "type": "number" }
}
}
},
"dataseries": {
"type": "array",
"items": {"$ref": "dataseries.json"}
},
"datagroup": {
"type": "array",
"items": {"$ref": "#/definitions/datagroup"}
}
}
}
}
}
}
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