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gorzellgorzell
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Merge pull request #1 from covid-modeling/gorzell/only-pass-modelinput
api: Remove runner related infromation from ModelInput.
2 parents 7404475 + 5af7dbe commit 910ccce

27 files changed

+381
-327
lines changed

‎packages/api/package-lock.json

Lines changed: 1 addition & 1 deletion
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‎packages/api/package.json

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@@ -1,6 +1,6 @@
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{
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"name": "@covid-modeling/api",
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"version": "0.8.2",
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"version": "0.9.0",
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"main": "dist/src/index",
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"types": "dist/src/index.d.ts",
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"scripts": {

‎packages/api/schema/input.json

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@@ -1,5 +1,5 @@
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{
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"$ref": "#/definitions/RequestInput",
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"$ref": "#/definitions/ModelInput",
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"$schema": "http://json-schema.org/draft-07/schema#",
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"definitions": {
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"ISODate": {
@@ -47,29 +47,10 @@
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],
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"type": "object"
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},
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"Model": {
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"additionalProperties": false,
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"properties": {
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"imageURL": {
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"type": "string"
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},
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"slug": {
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"$ref": "#/definitions/ModelSlug"
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}
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},
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"required": [
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"slug",
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"imageURL"
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],
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"type": "object"
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},
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"ModelInput": {
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"additionalProperties": false,
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"description": "A generalized description of the input to an epidemiological model.",
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"properties": {
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"model": {
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"$ref": "#/definitions/Model"
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},
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"parameters": {
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"$ref": "#/definitions/ModelParameters"
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},
@@ -81,7 +62,6 @@
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}
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},
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"required": [
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"model",
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"region",
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"parameters"
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],
@@ -125,47 +105,6 @@
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"interventionPeriods"
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],
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"type": "object"
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},
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"ModelSlug": {
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"enum": [
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"mrc-ide-covid-sim",
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"basel",
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"mc19"
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],
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"type": "string"
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},
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"RequestInput": {
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"additionalProperties": false,
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"properties": {
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"callbackURL": {
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"type": [
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"string",
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"null"
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]
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},
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"configuration": {
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"$ref": "#/definitions/ModelInput"
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},
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"id": {
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"type": [
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"string",
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"number"
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]
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},
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"models": {
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"items": {
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"$ref": "#/definitions/Model"
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},
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"type": "array"
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}
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},
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"required": [
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"id",
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"models",
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"configuration",
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"callbackURL"
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],
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"type": "object"
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}
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}
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}

‎packages/api/schema/output.json

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Original file line numberDiff line numberDiff line change
@@ -47,29 +47,10 @@
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],
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"type": "object"
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},
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"Model": {
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"additionalProperties": false,
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"properties": {
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"imageURL": {
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"type": "string"
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},
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"slug": {
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"$ref": "#/definitions/ModelSlug"
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}
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},
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"required": [
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"slug",
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"imageURL"
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],
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"type": "object"
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},
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"ModelInput": {
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"additionalProperties": false,
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"description": "A generalized description of the input to an epidemiological model.",
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"properties": {
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"model": {
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"$ref": "#/definitions/Model"
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},
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"parameters": {
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"$ref": "#/definitions/ModelParameters"
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},
@@ -81,7 +62,6 @@
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}
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},
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"required": [
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"model",
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"region",
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"parameters"
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],
@@ -188,14 +168,6 @@
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],
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"type": "object"
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},
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"ModelSlug": {
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"enum": [
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"mrc-ide-covid-sim",
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"basel",
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"mc19"
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],
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"type": "string"
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},
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"SeverityMetrics": {
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"additionalProperties": false,
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"properties": {

‎packages/api/schema/runner.json

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{
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"$ref": "#/definitions/RequestInput",
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"$schema": "http://json-schema.org/draft-07/schema#",
4+
"definitions": {
5+
"ISODate": {
6+
"type": "string"
7+
},
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"Intensity": {
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"enum": [
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"mild",
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"moderate",
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"aggressive"
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],
14+
"type": "string"
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},
16+
"InterventionPeriod": {
17+
"additionalProperties": false,
18+
"properties": {
19+
"caseIsolation": {
20+
"$ref": "#/definitions/Intensity",
21+
"description": "The level to which individuals with symptoms self-isolate."
22+
},
23+
"reductionPopulationContact": {
24+
"description": "The estimated reduction in population contact resulting from\nall of the above interventions. Some models require this generalized\nparameter instead of the individual interventions.",
25+
"type": "number"
26+
},
27+
"schoolClosure": {
28+
"$ref": "#/definitions/Intensity",
29+
"description": "The level of school closure in the region."
30+
},
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"socialDistancing": {
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"$ref": "#/definitions/Intensity",
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"description": "The level of social distancing in the region."
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},
35+
"startDate": {
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"$ref": "#/definitions/ISODate",
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"description": "An ISO-8601 string encoding the date that these interventions begin."
38+
},
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"voluntaryHomeQuarantine": {
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"$ref": "#/definitions/Intensity",
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"description": "The level to which entire households self-isolate when one member\nof the household has symptoms."
42+
}
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},
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"required": [
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"startDate",
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"reductionPopulationContact"
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],
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"type": "object"
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},
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"Model": {
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"additionalProperties": false,
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"properties": {
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"imageURL": {
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"type": "string"
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},
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"slug": {
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"$ref": "#/definitions/ModelSlug"
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}
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},
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"required": [
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"slug",
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"imageURL"
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],
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"type": "object"
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},
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"ModelInput": {
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"additionalProperties": false,
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"description": "A generalized description of the input to an epidemiological model.",
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"properties": {
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"parameters": {
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"$ref": "#/definitions/ModelParameters"
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},
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"region": {
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"type": "string"
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},
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"subregion": {
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"type": "string"
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}
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},
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"required": [
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"region",
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"parameters"
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],
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"type": "object"
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},
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"ModelParameters": {
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"additionalProperties": false,
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"properties": {
89+
"calibrationCaseCount": {
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"description": "The total number of confirmed cases in the region before the calibration date.",
91+
"type": "number"
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},
93+
"calibrationDate": {
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"$ref": "#/definitions/ISODate",
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"description": "An ISO-8601 string encoding the date of the most recent case data in the region."
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},
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"calibrationDeathCount": {
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"description": "The total number of deaths in the region before the calibration date.",
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"type": "number"
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},
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"interventionPeriods": {
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"description": "A list of time periods, each with a different set of interventions.",
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"items": {
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"$ref": "#/definitions/InterventionPeriod"
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},
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"type": "array"
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},
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"r0": {
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"description": "The assumed reproduction number for the virus. If this is null, then each\nmodel will use its own default value.",
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"type": [
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"number",
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"null"
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]
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}
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},
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"required": [
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"calibrationDate",
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"calibrationCaseCount",
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"calibrationDeathCount",
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"r0",
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"interventionPeriods"
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],
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"type": "object"
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},
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"ModelSlug": {
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"enum": [
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"mrc-ide-covid-sim",
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"basel",
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"mc19"
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],
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"type": "string"
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},
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"RequestInput": {
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"additionalProperties": false,
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"properties": {
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"callbackURL": {
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"type": [
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"string",
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"null"
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]
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},
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"configuration": {
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"$ref": "#/definitions/ModelInput"
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},
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"id": {
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"type": [
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"string",
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"number"
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]
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},
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"models": {
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"items": {
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"$ref": "#/definitions/Model"
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},
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"type": "array"
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}
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},
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"required": [
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"id",
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"models",
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"configuration",
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"callbackURL"
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],
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"type": "object"
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}
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}
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}

‎packages/api/script/generate-schema

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22

33
set -e
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5+
echo Generating runner schema
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ts-json-schema-generator --path src/index.ts --type RequestInput --out schema/runner.json
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echo Generating input schema
6-
ts-json-schema-generator --path src/index.ts --type RequestInput --out schema/input.json
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ts-json-schema-generator --path src/index.ts --type ModelInput --out schema/input.json
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echo Generating output schema
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ts-json-schema-generator --path src/index.ts --type ModelOutput --out schema/output.json

‎packages/api/src/model-input.ts

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import { Model } from './index'
2-
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/**
42
* A generalized description of the input to an epidemiological model.
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*/
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export interface ModelInput {
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model: Model
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region: string
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subregion?: string
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parameters: ModelParameters

‎packages/model-runner/Makefile

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.PHONY: test
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test: build
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# FIXME: uncomment this when there are some actual tests
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#npm run test
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npm run test
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.PHONY: integration-test
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integration-test: build
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# FIXME: uncomment this when there are some actual tests
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#npm run integration-test
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npm run integration-test
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.PHONY: release
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release:
@@ -44,6 +42,4 @@ run-local: build
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4543
.PHONY: run-remote
4644
run-remote:
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./bin/submit-run ~/.github/covid_pat.json test/test-job-mrc-ide-covidsim.json
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./bin/submit-run ~/.github/covid_pat.json test/test-job-basel.json
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./bin/submit-run ~/.github/covid_pat.json test/test-job-mc19.json
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./bin/submit-run ~/.github/covid_pat.json test/test-job-matrix.json

‎packages/model-runner/package.json

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{
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"name": "@covid-modeling/model-runner",
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"version": "0.8.0",
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"version": "1.1.0",
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"main": "dist/index.js",
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"scripts": {
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"test": "PATH=$PATH:../../node_modules/.bin && mocha --debug-brk --ui tdd -r ts-node/register test/unit/*-test.ts",
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"dependencies": {
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"@azure/identity": "^1.1.0-preview1",
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"@azure/storage-blob": "^12.1.1",
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"@covid-modeling/api": "0.8.*",
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"@covid-modeling/api": "0.9.*",
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"archiver": "^4.0.1",
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"d3": "^5.15.0",
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"dockerode": "^3.2.0",

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