Merge pull request #58 from DARPA-ASKEM/header

Implement header for base properties
DARPA-ASKEM · Aug 22, 2023 · f2c90f1 · f2c90f1
2 parents 14d9eb8 + 18671ac
commit f2c90f1
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Showing 12 changed files with 185 additions and 125 deletions.
diff --git a/base_schema.json b/base_schema.json
@@ -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."
@@ -33,9 +47,7 @@
     }
   },
   "required": [
-    "name",
-    "description",
-    "schema",
+    "header",
     "model"
   ]
 }
diff --git a/petrinet/examples/flux_typed.json b/petrinet/examples/flux_typed.json
@@ -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": [
       {
@@ -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": [
             {

diff --git a/petrinet/examples/flux_typed_aug.json b/petrinet/examples/flux_typed_aug.json
@@ -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": [
       {
@@ -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": [
             {

diff --git a/petrinet/examples/ont_pop_vax.json b/petrinet/examples/ont_pop_vax.json
@@ -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": [
       {

diff --git a/petrinet/examples/sir.json b/petrinet/examples/sir.json
@@ -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": [
       {

diff --git a/petrinet/examples/sir_flux_span.json b/petrinet/examples/sir_flux_span.json
@@ -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": [
       {
@@ -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": [
               {
@@ -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": [
                     {
@@ -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": [
               {
@@ -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": [
                     {

diff --git a/petrinet/examples/sir_typed.json b/petrinet/examples/sir_typed.json
@@ -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": [
       {
@@ -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": [
             {

diff --git a/petrinet/examples/sir_typed_aug.json b/petrinet/examples/sir_typed_aug.json
@@ -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": [
       {
@@ -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": [
             {

diff --git a/petrinet/petrinet_schema.json b/petrinet/petrinet_schema.json
@@ -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"
@@ -377,5 +383,5 @@
     }
   },
   "additionalProperties": true,
-  "required": ["name", "description", "schema", "model"]
+  "required": ["header", "model"]
 }
diff --git a/regnet/examples/lotka_volterra.json b/regnet/examples/lotka_volterra.json
@@ -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": [
       {

diff --git a/regnet/examples/syntax_edge_cases.json b/regnet/examples/syntax_edge_cases.json
@@ -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": [
       {