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Implement header for base properties #58

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merged 6 commits into from
Aug 22, 2023
Merged

Implement header for base properties #58

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004695c
Update base schema
bgyori Aug 15, 2023
120d52e
Update petrinet and regnet schemas
bgyori Aug 15, 2023
8f66195
Update petrinet examples with header
bgyori Aug 15, 2023
b8222ae
Update regnet examples
bgyori Aug 15, 2023
088ad0b
Fix base schema
bgyori Aug 15, 2023
18671ac
Add header in all sub-models
bgyori Aug 15, 2023
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50 changes: 31 additions & 19 deletions base_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,23 +2,37 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Name of the model."
},
"description": {
"type": "string",
"description": "A description of the model."
},
"schema": {
"type": "string",
"format": "uri",
"description": "URI of a JSON schema document that describes the model stored in the 'model' parameter."
"header": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Name of the model."
},
"description": {
"type": "string",
"description": "A description of the model."
},
"schema": {
"type": "string",
"format": "uri",
"description": "URI of a JSON schema document that describes the model stored in the 'model' parameter."
},
"schema_name": {
"type": "string",
"description": "The ID of the schema name. E.g. `petrinet`"
},
"model_version": {
"type": "string",
"description": "The version of the model."
}
},
"required": [
"name",
"description",
"schema"
]
},
"schema_name": {
"type": "string",
"description": "The ID of the schema name. E.g. `petrinet`"
},
"model": {
"type": "object",
"description": "JSON representation of a model. This should contain everything needed to fully run the model, including all rates/initial parameters/distributions/etc."
Expand All @@ -33,9 +47,7 @@
}
},
"required": [
"name",
"description",
"schema",
"header",
"model"
]
}
20 changes: 12 additions & 8 deletions petrinet/examples/flux_typed.json
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@@ -1,8 +1,10 @@
{
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah. Modified by Patrick.",
"model_version": "0.1",
"header": {
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah. Modified by Patrick.",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -41,10 +43,12 @@
"ode": {},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
20 changes: 12 additions & 8 deletions petrinet/examples/flux_typed_aug.json
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
{
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah",
"model_version": "0.1",
"header": {
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -73,10 +75,12 @@
"ode": {},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
10 changes: 6 additions & 4 deletions petrinet/examples/ont_pop_vax.json
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
{
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
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12 changes: 7 additions & 5 deletions petrinet/examples/sir.json
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@@ -1,9 +1,11 @@
{
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "SIR model",
"schema_name": "petrinet",
"model_version": "0.1",
"header": {
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "SIR model",
"schema_name": "petrinet",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
50 changes: 30 additions & 20 deletions petrinet/examples/sir_flux_span.json
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
{
"name": "SIR-Two-City-Flux Stratified Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "SIR disease model stratified spatially between two cities model created by Patrick",
"model_version": "0.1",
"header": {
"name": "SIR-Two-City-Flux Stratified Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "SIR disease model stratified spatially between two cities model created by Patrick",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -154,10 +156,12 @@
"span": [
{
"system": {
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1",
"header": {
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -316,10 +320,12 @@
},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -473,10 +479,12 @@
},
{
"system": {
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah",
"model_version": "0.1",
"header": {
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -547,10 +555,12 @@
"ode": {},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
22 changes: 13 additions & 9 deletions petrinet/examples/sir_typed.json
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
{
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"schema_name": "petrinet",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1",
"header": {
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"schema_name": "petrinet",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -146,10 +148,12 @@
},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
20 changes: 12 additions & 8 deletions petrinet/examples/sir_typed_aug.json
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@@ -1,8 +1,10 @@
{
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1",
"header": {
"name": "SIR Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Typed SIR model created by Nelson, derived from the one by Ben, Micah, Brandon",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down Expand Up @@ -161,10 +163,12 @@
},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"header": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1"
},
"model": {
"states": [
{
Expand Down
38 changes: 22 additions & 16 deletions petrinet/petrinet_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,27 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"name": {
"type": "string"
},
"schema": {
"type": "string",
"format": "uri"
},
"schema_name": {
"type": "string"
},
"description": {
"type": "string"
},
"model_version": {
"type": "string"
"header": {
"type": "object",
"properties": {
"name": {
"type": "string"
},
"schema": {
"type": "string",
"format": "uri"
},
"schema_name": {
"type": "string"
},
"description": {
"type": "string"
},
"model_version": {
"type": "string"
}
},
"required": ["name", "schema", "description"]
},
"properties": {
"type": "object"
Expand Down Expand Up @@ -377,5 +383,5 @@
}
},
"additionalProperties": true,
"required": ["name", "description", "schema", "model"]
"required": ["header", "model"]
}
12 changes: 7 additions & 5 deletions regnet/examples/lotka_volterra.json
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@@ -1,9 +1,11 @@
{
"name": "Lotka Volterra",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.1/regnet/regnet_schema.json",
"schema_name": "regnet",
"description": "Lotka Volterra model",
"model_version": "0.1",
"header": {
"name": "Lotka Volterra",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.1/regnet/regnet_schema.json",
"schema_name": "regnet",
"description": "Lotka Volterra model",
"model_version": "0.1"
},
"model": {
"vertices": [
{
Expand Down
12 changes: 7 additions & 5 deletions regnet/examples/syntax_edge_cases.json
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@@ -1,9 +1,11 @@
{
"name": "Syntax Edge Cases",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.1/regnet/regnet_schema.json",
"schema_name": "regnet",
"description": "A regulatory network to demonstrate syntactic edge cases of the JSON Schema of RegNets.",
"model_version": "0.1",
"header": {
"name": "Syntax Edge Cases",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.1/regnet/regnet_schema.json",
"schema_name": "regnet",
"description": "A regulatory network to demonstrate syntactic edge cases of the JSON Schema of RegNets.",
"model_version": "0.1"
},
"model": {
"vertices": [
{
Expand Down
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