From a7fa794595b6e54d24ebcbab68d435adad2a5625 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 15 Jun 2020 23:34:36 +0200 Subject: [PATCH 1/3] feat: add age-specific mitigation to schema --- schemas/MitigationAgeSpecificDatum.yml | 22 + schemas/MitigationInterval.yml | 6 + schemas/_SchemaVer.yml | 2 +- src/algorithms/run.ts | 4 + src/algorithms/types/Param.types.ts | 5 +- src/algorithms/types/convert.ts | 41 +- .../types/restricted/ScenarioDatum.ts | 6 + .../utils/suggestNextMitigationInterval.ts | 1 + src/assets/data/scenarios.json | 21358 +--------------- .../MitigationIntervalAgeTable.scss | 53 + .../Mitigation/MitigationIntervalAgeTable.tsx | 188 + src/components/Main/validation/schema.ts | 13 + src/io/serialization/v2.0.0/serialize.ts | 2 +- 13 files changed, 381 insertions(+), 21320 deletions(-) create mode 100644 schemas/MitigationAgeSpecificDatum.yml create mode 100644 src/components/Main/Mitigation/MitigationIntervalAgeTable.scss create mode 100644 src/components/Main/Mitigation/MitigationIntervalAgeTable.tsx diff --git a/schemas/MitigationAgeSpecificDatum.yml b/schemas/MitigationAgeSpecificDatum.yml new file mode 100644 index 000000000..c7b336a51 --- /dev/null +++ b/schemas/MitigationAgeSpecificDatum.yml @@ -0,0 +1,22 @@ +$schema: http://json-schema.org/draft-07/schema +$id: MitigationAgeSpecificDatum +title: MitigationAgeSpecificDatum + +type: object + +additionalProperties: false + +required: + - ageGroup + - enabled + - transmissionReduction + +properties: + ageGroup: + $ref: 'AgeGroup#' + + enabled: + type: boolean + + transmissionReduction: + $ref: 'PercentageRange#' diff --git a/schemas/MitigationInterval.yml b/schemas/MitigationInterval.yml index 51125c120..ef1cd90f1 100644 --- a/schemas/MitigationInterval.yml +++ b/schemas/MitigationInterval.yml @@ -11,6 +11,7 @@ required: - color - timeRange - transmissionReduction + - mitigationAgeSpecificData properties: name: @@ -25,3 +26,8 @@ properties: transmissionReduction: $ref: 'PercentageRange#' + + mitigationAgeSpecificData: + type: array + items: + $ref: 'MitigationAgeSpecificDatum#' diff --git a/schemas/_SchemaVer.yml b/schemas/_SchemaVer.yml index 3b8572df6..592da7dc3 100644 --- a/schemas/_SchemaVer.yml +++ b/schemas/_SchemaVer.yml @@ -3,4 +3,4 @@ $id: _SchemaVer title: _SchemaVer type: string -const: 2.0.0 +const: 2.1.0 diff --git a/src/algorithms/run.ts b/src/algorithms/run.ts index bc567170a..6dc66c66e 100644 --- a/src/algorithms/run.ts +++ b/src/algorithms/run.ts @@ -34,6 +34,10 @@ function simulate( } export async function run({ params, severity, ageDistribution }: RunParams): Promise { + console.log( + JSON.stringify({ 'params.mitigationIntervals.mitigationAgeSpecificData': params.mitigationIntervals }, null, 2), + ) + const tMin: number = new Date(params.simulationTimeRange.begin).getTime() const tMax: number = new Date(params.simulationTimeRange.end).getTime() const ageGroups = ageDistribution.map((d) => d.ageGroup) diff --git a/src/algorithms/types/Param.types.ts b/src/algorithms/types/Param.types.ts index 0a1f017f9..c0cfded66 100644 --- a/src/algorithms/types/Param.types.ts +++ b/src/algorithms/types/Param.types.ts @@ -6,6 +6,7 @@ import type { ScenarioDatum as ScenarioDatumExternal, ScenarioDatumMitigation as ScenarioDatumMitigationExternal, MitigationInterval as MitigationIntervalExternal, + MitigationAgeSpecificDatum as MitigationAgeSpecificDatumExternal, ScenarioDatumEpidemiological, ScenarioDatumPopulation, ScenarioDatumSimulation, @@ -18,6 +19,7 @@ import type { ScenarioDatum, MitigationInterval, ScenarioDatumMitigation, + MitigationAgeSpecificDatum, } from './restricted/ScenarioDatum' export type { @@ -37,7 +39,7 @@ export type { DateRange, NumericRangeNonNegative, PercentageRange } from '../../ export { Convert, AgeGroup } from '../../.generated/latest/types' -export type { ScenarioData, ScenarioDatum, MitigationInterval, ScenarioDatumMitigation } +export type { ScenarioData, ScenarioDatum, MitigationInterval, ScenarioDatumMitigation, MitigationAgeSpecificDatum } export type { ScenarioDatumEpidemiological, ScenarioDatumPopulation, ScenarioDatumSimulation } @@ -47,6 +49,7 @@ export type { ScenarioDatumExternal, ScenarioDatumMitigationExternal, MitigationIntervalExternal, + MitigationAgeSpecificDatumExternal, } export interface ScenarioParameters { diff --git a/src/algorithms/types/convert.ts b/src/algorithms/types/convert.ts index 63a339382..077a49cfb 100644 --- a/src/algorithms/types/convert.ts +++ b/src/algorithms/types/convert.ts @@ -2,14 +2,27 @@ import { omit } from 'lodash' import { uuidv4 } from '../../helpers/uuid' -import { MitigationInterval, MitigationIntervalExternal, ScenarioDatum, ScenarioDatumExternal } from './Param.types' +import { + MitigationAgeSpecificDatum, + MitigationAgeSpecificDatumExternal, + MitigationInterval, + MitigationIntervalExternal, + ScenarioDatum, + ScenarioDatumExternal, +} from './Param.types' -export function addId(interval: MitigationIntervalExternal): MitigationInterval { - return { ...interval, id: uuidv4() } +export function mitigtaionIntervalAgeSpecificToInternal( + mitigationAgeSpecificData: MitigationAgeSpecificDatumExternal[], +): MitigationAgeSpecificDatum[] { + return mitigationAgeSpecificData.map((datum) => ({ ...datum, id: uuidv4() } as MitigationAgeSpecificDatum)) } -export function removeId(interval: MitigationInterval): MitigationIntervalExternal { - return omit(interval, 'id') +export function mitigtaionIntervalToInternal(interval: MitigationIntervalExternal): MitigationInterval { + return { + ...interval, + id: uuidv4(), + mitigationAgeSpecificData: mitigtaionIntervalAgeSpecificToInternal(interval.mitigationAgeSpecificData), + } } export function toInternal(scenario: ScenarioDatumExternal): ScenarioDatum { @@ -18,18 +31,32 @@ export function toInternal(scenario: ScenarioDatumExternal): ScenarioDatum { ...scenario, mitigation: { ...scenario.mitigation, - mitigationIntervals: mitigationIntervals.map(addId), + mitigationIntervals: mitigationIntervals.map(mitigtaionIntervalToInternal), }, } } +export function mitigtaionIntervalAgeSpecificToExternal( + mitigationAgeSpecificData: MitigationAgeSpecificDatum[], +): MitigationAgeSpecificDatumExternal[] { + return mitigationAgeSpecificData.map((datum) => omit(datum, 'id')) +} + +export function mitigationIntervalToExternal(interval: MitigationInterval): MitigationIntervalExternal { + const intervalWithoutId = omit(interval, 'id') + return { + ...intervalWithoutId, + mitigationAgeSpecificData: mitigtaionIntervalAgeSpecificToExternal(intervalWithoutId.mitigationAgeSpecificData), + } +} + export function toExternal(scenario: ScenarioDatum): ScenarioDatumExternal { const { mitigationIntervals } = scenario.mitigation return { ...scenario, mitigation: { ...scenario.mitigation, - mitigationIntervals: mitigationIntervals.map(removeId), + mitigationIntervals: mitigationIntervals.map(mitigationIntervalToExternal), }, } } diff --git a/src/algorithms/types/restricted/ScenarioDatum.ts b/src/algorithms/types/restricted/ScenarioDatum.ts index 9f07dcf6f..a9b78644a 100644 --- a/src/algorithms/types/restricted/ScenarioDatum.ts +++ b/src/algorithms/types/restricted/ScenarioDatum.ts @@ -7,10 +7,16 @@ import type { Merge, StrictOmit } from 'ts-essentials' import type { UUIDv4 } from '../../../helpers/uuid' +import { MitigationAgeSpecificDatumExternal } from '../Param.types' import type { MitigationIntervalExternal, ScenarioDatumExternal, ScenarioDatumMitigationExternal } from '../Param.types' +export interface MitigationAgeSpecificDatum extends MitigationAgeSpecificDatumExternal { + id: UUIDv4 +} + export interface MitigationInterval extends MitigationIntervalExternal { id: UUIDv4 + mitigationAgeSpecificData: MitigationAgeSpecificDatum[] } export interface ScenarioDatumMitigationInternalMutable extends ScenarioDatumMitigationExternal { diff --git a/src/algorithms/utils/suggestNextMitigationInterval.ts b/src/algorithms/utils/suggestNextMitigationInterval.ts index 24429cb65..ba29ffe6c 100644 --- a/src/algorithms/utils/suggestNextMitigationInterval.ts +++ b/src/algorithms/utils/suggestNextMitigationInterval.ts @@ -17,6 +17,7 @@ export function suggestNextMitigationInterval(): MitigationInterval { name: `Intervention from ${tMinMoment.format('D MMM YYYY')}`, timeRange, transmissionReduction: { begin: 10, end: 30 }, + mitigationAgeSpecificData: [], } const color = createColor(interval) diff --git a/src/assets/data/scenarios.json b/src/assets/data/scenarios.json index 1db8a198a..af4e9e6ac 100644 --- a/src/assets/data/scenarios.json +++ b/src/assets/data/scenarios.json @@ -10,8 +10,8 @@ "overflowSeverity": 2.0, "peakMonth": 0, "r0": { - "begin": 2.12, - "end": 2.59 + "begin": 4.08, + "end": 4.98 }, "seasonalForcing": 0.0 }, @@ -21,84 +21,45 @@ "color": "#cccccc", "name": "Intervention 1", "timeRange": { - "begin": "2020-04-02", + "begin": "2020-03-24", "end": "2020-09-01" }, "transmissionReduction": { - "begin": 34.4, - "end": 41.6 - } - } - ] - }, - "population": { - "ageDistributionName": "Afghanistan", - "caseCountsName": "Afghanistan", - "hospitalBeds": 17470, - "icuBeds": 524, - "importsPerDay": 0.1, - "initialNumberOfCases": 58, - "populationServed": 37172386 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-03", - "end": "2020-08-31" - } - } - }, - "name": "Afghanistan" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.42, - "end": 1.73 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-27", - "end": "2020-09-01" + "begin": 73.8, + "end": 84.2 }, - "transmissionReduction": { - "begin": 38.8, - "end": 47.2 - } + "mitigationAgeSpecificData": [ + { "ageGroup": "0-9", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "10-19", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "20-29", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "30-39", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "40-49", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "50-59", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "60-69", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "70-79", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "80+", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } } + ] } ] }, "population": { - "ageDistributionName": "Albania", - "caseCountsName": "Albania", - "hospitalBeds": 7621, - "icuBeds": 228, + "ageDistributionName": "United States of America", + "caseCountsName": "United States of America", + "hospitalBeds": 798288, + "icuBeds": 49499, "importsPerDay": 0.1, - "initialNumberOfCases": 77, - "populationServed": 2866376 + "initialNumberOfCases": 1, + "populationServed": 327167434 }, "simulation": { "numberStochasticRuns": 15, "simulationTimeRange": { - "begin": "2020-02-28", + "begin": "2020-02-08", "end": "2020-08-31" } } }, - "name": "Albania" + "name": "United States of America" }, { "data": { @@ -110,8 +71,8 @@ "overflowSeverity": 2.0, "peakMonth": 0, "r0": { - "begin": 2.46, - "end": 3.01 + "begin": 2.87, + "end": 3.5 }, "seasonalForcing": 0.0 }, @@ -121,21268 +82,45 @@ "color": "#cccccc", "name": "Intervention 1", "timeRange": { - "begin": "2020-03-27", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 52.3, - "end": 63.7 - } - } - ] - }, - "population": { - "ageDistributionName": "Algeria", - "caseCountsName": "Algeria", - "hospitalBeds": 79149, - "icuBeds": 2374, - "importsPerDay": 0.1, - "initialNumberOfCases": 31, - "populationServed": 42228429 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-24", - "end": "2020-08-31" - } - } - }, - "name": "Algeria" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#bf5b17", - "name": "Intervention #1", - "timeRange": { - "begin": "2020-03-17", + "begin": "2020-03-19", "end": "2020-09-01" }, "transmissionReduction": { - "begin": 36.2, - "end": 43.8 - } - }, - { - "color": "#666666", - "name": "Intervention #2", - "timeRange": { - "begin": "2020-03-22", - "end": "2020-09-01" + "begin": 76.0, + "end": 86.0 }, - "transmissionReduction": { - "begin": 54.2, - "end": 65.8 - } + "mitigationAgeSpecificData": [ + { "ageGroup": "0-9", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "10-19", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "20-29", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "30-39", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "40-49", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "50-59", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "60-69", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "70-79", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } }, + { "ageGroup": "80+", "enabled": true, "transmissionReduction": { "begin": 0.33, "end": 0.66 } } + ] } ] }, "population": { "ageDistributionName": "Switzerland", - "caseCountsName": "Andorra", - "hospitalBeds": 160, - "icuBeds": 6, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 77006 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Andorra" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#bf5b17", - "name": "Intervention #1", - "timeRange": { - "begin": "2020-04-04", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 36.2, - "end": 43.8 - } - } - ] - }, - "population": { - "ageDistributionName": "Antigua and Barbuda", - "caseCountsName": "Antigua and Barbuda", - "hospitalBeds": 364, - "icuBeds": 10, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 96286 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Antigua and Barbuda" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.48, - "end": 3.03 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-26", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 48.6, - "end": 59.4 - } - } - ] - }, - "population": { - "ageDistributionName": "Argentina", - "caseCountsName": "Argentina", - "hospitalBeds": 223470, - "icuBeds": 6704, - "importsPerDay": 0.1, - "initialNumberOfCases": 21, - "populationServed": 44494502 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-28", - "end": "2020-08-31" - } - } - }, - "name": "Argentina" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.45, - "end": 1.77 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-31", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 17.8, - "end": 20.2 - } - } - ] - }, - "population": { - "ageDistributionName": "Armenia", - "caseCountsName": "Armenia", - "hospitalBeds": 10253, - "icuBeds": 307, - "importsPerDay": 0.1, - "initialNumberOfCases": 55, - "populationServed": 2951776 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Armenia" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.41, - "end": 2.94 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-23", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 56.2, - "end": 67.8 - } - } - ] - }, - "population": { - "ageDistributionName": "Australia", - "caseCountsName": "Australia", - "hospitalBeds": 95970, - "icuBeds": 2378, + "caseCountsName": "Switzerland", + "hospitalBeds": 30057, + "icuBeds": 1400, "importsPerDay": 0.1, - "initialNumberOfCases": 0, - "populationServed": 24992369 + "initialNumberOfCases": 36, + "populationServed": 8516543 }, "simulation": { "numberStochasticRuns": 15, "simulationTimeRange": { - "begin": "2020-02-08", + "begin": "2020-02-17", "end": "2020-08-31" } } }, - "name": "Australia" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 3.45, - "end": 4.21 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-19", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 71.5, - "end": 82.5 - } - } - ] - }, - "population": { - "ageDistributionName": "Austria", - "caseCountsName": "Austria", - "hospitalBeds": 47920, - "icuBeds": 1833, - "importsPerDay": 0.1, - "initialNumberOfCases": 4, - "populationServed": 8847037 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-19", - "end": "2020-08-31" - } - } - }, - "name": "Austria" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.89, - "end": 2.32 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-04-02", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 30.9, - "end": 37.1 - } - } - ] - }, - "population": { - "ageDistributionName": "Azerbaijan", - "caseCountsName": "Azerbaijan", - "hospitalBeds": 34107, - "icuBeds": 1023, - "importsPerDay": 0.1, - "initialNumberOfCases": 13, - "populationServed": 9942334 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-04", - "end": "2020-08-31" - } - } - }, - "name": "Azerbaijan" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#bf5b17", - "name": "Intervention #1", - "timeRange": { - "begin": "2020-04-09", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 36.2, - "end": 43.8 - } - } - ] - }, - "population": { - "ageDistributionName": "Bahamas", - "caseCountsName": "Bahamas", - "hospitalBeds": 964, - "icuBeds": 28, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 385640 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Bahamas" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#bf5b17", - "name": "Intervention #1", - 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}, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.55, - "end": 3.12 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-31", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 54.2, - "end": 65.8 - } - } - ] - }, - "population": { - "ageDistributionName": "United States of America", - "caseCountsName": "USA-Virginia", - "hospitalBeds": 18115, - "icuBeds": 604, - "importsPerDay": 0.1, - "initialNumberOfCases": 25, - "populationServed": 8626207 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-28", - "end": "2020-08-31" - } - } - }, - "name": "USA-Virginia" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.05, - "end": 2.5 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-17", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 60.1, - "end": 71.9 - } - } - ] - }, - "population": { - "ageDistributionName": "United States of America", - "caseCountsName": "USA-Washington", - "hospitalBeds": 13255, - "icuBeds": 442, - "importsPerDay": 0.1, - "initialNumberOfCases": 253, - "populationServed": 7797095 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-16", - "end": "2020-08-31" - } - } - }, - "name": "USA-Washington" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.25, - "end": 1.52 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#bf5b17", - "name": "Intervention #1", - "timeRange": { - "begin": "2020-04-01", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 18.7, - "end": 21.3 - } - }, - { - "color": "#666666", - "name": "Intervention #2", - "timeRange": { - "begin": "2020-05-26", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 54.2, - "end": 65.8 - } - } - ] - }, - "population": { - "ageDistributionName": "United States of America", - "caseCountsName": "USA-West Virginia", - "hospitalBeds": 6757, - "icuBeds": 225, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 1778070 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-01-17", - "end": "2020-08-31" - } - } - }, - "name": "USA-West Virginia" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.84, - "end": 2.25 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-28", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 41.4, - "end": 50.6 - } - } - ] - }, - "population": { - "ageDistributionName": "United States of America", - "caseCountsName": "USA-Wisconsin", - "hospitalBeds": 12289, - "icuBeds": 410, - "importsPerDay": 0.1, - "initialNumberOfCases": 200, - "populationServed": 5851754 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "USA-Wisconsin" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.74, - "end": 2.13 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-03-31", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 36.2, - "end": 43.8 - } - } - ] - }, - "population": { - "ageDistributionName": "United States of America", - "caseCountsName": "USA-Wyoming", - "hospitalBeds": 1985, - "icuBeds": 66, - "importsPerDay": 0.1, - "initialNumberOfCases": 5, - "populationServed": 567025 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-07", - "end": "2020-08-31" - } - } - }, - "name": "USA-Wyoming" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.53, - "end": 1.86 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [ - { - "color": "#cccccc", - "name": "Intervention 1", - "timeRange": { - "begin": "2020-04-12", - "end": "2020-09-01" - }, - "transmissionReduction": { - "begin": 37.0, - "end": 45.0 - } - } - ] - }, - "population": { - "ageDistributionName": "Uzbekistan", - "caseCountsName": "Uzbekistan", - "hospitalBeds": 98390, - "icuBeds": 2951, - "importsPerDay": 0.1, - "initialNumberOfCases": 25, - "populationServed": 32955400 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-05", - "end": "2020-08-31" - } - } - }, - "name": "Uzbekistan" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [] - }, - "population": { - "ageDistributionName": "Venezuela (Bolivarian Republic of)", - "caseCountsName": "Venezuela (Bolivarian Republic of)", - "hospitalBeds": 25351, - "icuBeds": 760, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 28870195 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Venezuela (Bolivarian Republic of)" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [] - }, - "population": { - "ageDistributionName": "Viet Nam", - "caseCountsName": "Viet Nam", - "hospitalBeds": 252304, - "icuBeds": 7569, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 95540395 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Viet Nam" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [] - }, - "population": { - "ageDistributionName": "Yemen", - "caseCountsName": "Yemen", - "hospitalBeds": 20067, - "icuBeds": 602, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 28667230 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Yemen" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 2.7, - "end": 3.3 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [] - }, - "population": { - "ageDistributionName": "Zambia", - "caseCountsName": "Zambia", - "hospitalBeds": 32890, - "icuBeds": 986, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 17351822 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-03-01", - "end": "2020-08-31" - } - } - }, - "name": "Zambia" - }, - { - "data": { - "epidemiological": { - "hospitalStayDays": 3.0, - "icuStayDays": 14.0, - "infectiousPeriodDays": 3.0, - "latencyDays": 3.0, - "overflowSeverity": 2.0, - "peakMonth": 0, - "r0": { - "begin": 1.1, - "end": 1.35 - }, - "seasonalForcing": 0.0 - }, - "mitigation": { - "mitigationIntervals": [] - }, - "population": { - "ageDistributionName": "Zimbabwe", - "caseCountsName": "Zimbabwe", - "hospitalBeds": 23851, - "icuBeds": 715, - "importsPerDay": 0.1, - "initialNumberOfCases": 10, - "populationServed": 14439018 - }, - "simulation": { - "numberStochasticRuns": 15, - "simulationTimeRange": { - "begin": "2020-02-14", - "end": "2020-08-31" - } - } - }, - "name": "Zimbabwe" + "name": "Switzerland" } ] -} \ No newline at end of file +} diff --git a/src/components/Main/Mitigation/MitigationIntervalAgeTable.scss b/src/components/Main/Mitigation/MitigationIntervalAgeTable.scss new file mode 100644 index 000000000..3f1083c5b --- /dev/null +++ b/src/components/Main/Mitigation/MitigationIntervalAgeTable.scss @@ -0,0 +1,53 @@ +@import '../../../styles/variables'; +@import '../../../styles/mixins'; + +.age-group-parameters { + // 700 = the point at which the titles break for english + // !important because react-grid assigns a width to the table element + table { + min-width: 700px !important; + } + + td, + th { + padding: 0; + } + + td > input { + // otherwise bootstrap makes it too large + height: auto; + padding: 0; + } + + .dx-g-bs4-table-edit-cell { + padding: 0 !important; + } + + td p { + margin: 0; + } + + colgroup col:nth-child(3) { + background-color: #fdbf6f55; + } + + colgroup col:nth-child(4) { + background-color: #fb9a9955; + } + + colgroup col:nth-child(5) { + background-color: #e31a1c55; + } + + colgroup col:nth-child(6) { + background-color: #cab2d655; + } + + colgroup col:nth-child(8) { + background-color: #a6cee355; + } +} + +.age-group-parameters .table-responsive.dx-g-bs4-table-container { + @include horizontal-scroll-shadow(); +} diff --git a/src/components/Main/Mitigation/MitigationIntervalAgeTable.tsx b/src/components/Main/Mitigation/MitigationIntervalAgeTable.tsx new file mode 100644 index 000000000..b5321f764 --- /dev/null +++ b/src/components/Main/Mitigation/MitigationIntervalAgeTable.tsx @@ -0,0 +1,188 @@ +import React from 'react' + +import { omit } from 'lodash' + +import { + ChangeSet, + Column, + DataTypeProvider, + DataTypeProviderProps, + EditingColumnExtension, + EditingState, +} from '@devexpress/dx-react-grid' + +import type { TFunction } from 'i18next' +import { format as d3format } from 'd3-format' +import { FormikErrors, useField } from 'formik' +import { useTranslation } from 'react-i18next' +import { connect } from 'react-redux' +import { Grid, Table, TableHeaderRow, TableInlineCellEditing } from '@devexpress/dx-react-grid-bootstrap4' + +import { AgeGroup } from '../../../algorithms/types/Param.types' +import type { + AgeDistributionDatum, + SeverityDistributionDatum, + ScenarioDatum, +} from '../../../algorithms/types/Param.types' + +import i18n from '../../../i18n/i18n' + +import { + selectAgeDistributionData, + selectScenarioData, + selectSeverityDistributionData, +} from '../../../state/scenario/scenario.selectors' +import { State } from '../../../state/reducer' + +import './MitigationIntervalAgeTable.scss' + +export interface AgeSpecificMitigationDatum { + ageGroup: AgeGroup + enabled: boolean + transmissionReduction: { begin: number; end: number } +} + +export interface AgeSpecificMitigationRow extends AgeSpecificMitigationDatum { + id: string +} + +const columns: Column[] = [ + { name: 'ageGroup', title: i18n.t('Age group') }, + { name: 'enabled', title: i18n.t('Enabled') }, + { + name: 'transmissionReductionBegin', + title: i18n.t('Strength from'), + getCellValue: (row: AgeSpecificMitigationRow) => row.transmissionReduction.begin, + }, + { + name: 'transmissionReductionEnd', + title: i18n.t('Strength to'), + getCellValue: (row: AgeSpecificMitigationRow) => row.transmissionReduction.end, + }, +] + +const columnExtensions: Table.ColumnExtension[] = [ + { columnName: 'ageGroup', align: 'center' }, + { columnName: 'enabled', align: 'center' }, + { columnName: 'strengthFrom', align: 'center' }, + { columnName: 'strengthTo', align: 'center' }, +] + +const editingColumnExtensions: EditingColumnExtension[] = [ + { columnName: 'ageGroup', editingEnabled: false }, // prettier-ignore +] + +const getRowId = (row: AgeSpecificMitigationRow) => row.id + +type HeaderCellProps = Partial & TableHeaderRow.CellProps + +function HeaderCell({ column }: HeaderCellProps) { + const { title } = column + const content = title?.split('\n').map((line, i) => ( +

+ {line} +

+ )) + + return {content} +} + +interface ValueCellProps extends Table.DataCellProps { + onClick?: (e: MouseEvent) => void +} + +const ValueCell = ({ onClick, column, ...props }: ValueCellProps) => { + const editingColumnExtension = editingColumnExtensions.find( + (editingExtension) => column.name === editingExtension.columnName, + ) + const editable = !editingColumnExtension || editingColumnExtension.editingEnabled + return +} + +const DecimalFormatter = ({ value }: DataTypeProvider.ValueFormatterProps) => ( + {d3format('.2')(Number.parseFloat(value))} +) + +const DecimalTypeProvider = (props: DataTypeProviderProps) => ( + +) + +export function getErrorMessages(t: TFunction, errors?: FormikErrors): string[] { + if (!errors) { + return [] + } + + return Object.entries(errors).reduce((result, [i, err]) => { + const rowNum = Number.parseInt(i, 10) + const ageGroup = Object.values(AgeGroup)[rowNum] + + if (err) { + const messages = Object.entries(err).map(([column, message]) => + t('Error in column "{{column}}", row "{{ageGroup}}": {{message}}', { column, ageGroup, message }), + ) + return [...result, ...messages] + } + + return result + }, new Array()) +} + +export interface SeverityTableProps { + scenarioData: ScenarioDatum + ageDistributionData: AgeDistributionDatum[] + severityDistributionData: SeverityDistributionDatum[] +} + +const mapStateToProps = (state: State) => ({ + scenarioData: selectScenarioData(state), + ageDistributionData: selectAgeDistributionData(state), + severityDistributionData: selectSeverityDistributionData(state), +}) + +const mapDispatchToProps = {} + +export const MitigationIntervalAgeTable = connect(mapStateToProps, mapDispatchToProps)(SeverityTableDisconnected) + +function SeverityTableDisconnected({ + scenarioData, + ageDistributionData, + severityDistributionData, +}: SeverityTableProps) { + const { t } = useTranslation() + const [{ value }, { error }, { setValue }] = useField('severity') + const errorMessages = getErrorMessages(t, error) + + if (!value) { + return null + } + + const commitChanges = ({ changed }: ChangeSet) => { + if (!changed) { + return + } + + const newValue = value.map((row) => { + const changedRow = changed[row.id] as AgeSpecificMitigationRow + return changedRow ? { ...row, ...changedRow } : row + }) + + setValue(newValue) + } + + return ( +
+ + + + + + + + {errorMessages.map((message) => ( +
+ {message} +
+ ))} + + ) +} diff --git a/src/components/Main/validation/schema.ts b/src/components/Main/validation/schema.ts index 37088a64c..0ad09765f 100644 --- a/src/components/Main/validation/schema.ts +++ b/src/components/Main/validation/schema.ts @@ -124,6 +124,19 @@ export const schema: yup.Schema = yup transmissionReduction: percentageRange().required(MSG_REQUIRED), name: yup.string().required(MSG_REQUIRED), timeRange: dateRange().required(MSG_REQUIRED), + mitigationAgeSpecificData: yup + .array() + .of( + yup + .object({ + id: (yup.string().required(MSG_REQUIRED) as unknown) as yup.Schema, + ageGroup: yup.string().oneOf(Object.values(AgeGroup)).required(MSG_REQUIRED), + enabled: yup.boolean().required(MSG_REQUIRED), + transmissionReduction: percentageRange().required(MSG_REQUIRED), + }) + .required(MSG_REQUIRED), + ) + .defined(), }) .required(MSG_REQUIRED), ) diff --git a/src/io/serialization/v2.0.0/serialize.ts b/src/io/serialization/v2.0.0/serialize.ts index ff120dd4c..47720f4d9 100644 --- a/src/io/serialization/v2.0.0/serialize.ts +++ b/src/io/serialization/v2.0.0/serialize.ts @@ -11,7 +11,7 @@ import { toExternal, toInternal } from '../../../algorithms/types/convert' import { DeserializationErrorConversionFailed, DeserializationErrorValidationFailed } from '../errors' -const schemaVer = '2.0.0' +const schemaVer = '2.1.0' function serialize(scenarioParameters: ScenarioParameters): string { const shareable: Shareable = { From e5ec50e8ce91f6f274faf0e93a9d04bb8400af63 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 16 Jun 2020 01:12:23 +0200 Subject: [PATCH 2/3] fix: adjust io versioning for schema 2.1.0 --- config/nodemon/dev.json | 1 + config/nodemon/prod.json | 1 + .../{v2.0.0 => v2.1.0}/serialize.ts | 0 src/io/serialization/versioning.ts | 4 ++-- tools/generateTypes.ts | 23 +++++++++++++++---- 5 files changed, 23 insertions(+), 6 deletions(-) rename src/io/serialization/{v2.0.0 => v2.1.0}/serialize.ts (100%) diff --git a/config/nodemon/dev.json b/config/nodemon/dev.json index 62f4e75fb..52cc75322 100644 --- a/config/nodemon/dev.json +++ b/config/nodemon/dev.json @@ -17,6 +17,7 @@ "postcss.config.js", "schemas", "stylelint.config.js", + "tools/generateTypes.ts", "tsconfig.json", "tslint.json", "webpack.config.js", diff --git a/config/nodemon/prod.json b/config/nodemon/prod.json index b823e0cc9..46fbe7f5e 100644 --- a/config/nodemon/prod.json +++ b/config/nodemon/prod.json @@ -19,6 +19,7 @@ "src", "static", "stylelint.config.js", + "tools/generateTypes.ts", "tsconfig.json", "tslint.json", "webpack.config.js", diff --git a/src/io/serialization/v2.0.0/serialize.ts b/src/io/serialization/v2.1.0/serialize.ts similarity index 100% rename from src/io/serialization/v2.0.0/serialize.ts rename to src/io/serialization/v2.1.0/serialize.ts diff --git a/src/io/serialization/versioning.ts b/src/io/serialization/versioning.ts index 42a748fdf..72b442086 100644 --- a/src/io/serialization/versioning.ts +++ b/src/io/serialization/versioning.ts @@ -8,7 +8,7 @@ import type { ScenarioParameters } from '../../algorithms/types/Param.types' import { getOrThrow } from '../../helpers/getOrThrow' -import v2_0_0 from './v2.0.0/serialize' +import v2_1_0 from './v2.1.0/serialize' export type Serializer = (input: ScenarioParameters) => string export type Deserializer = (input: string) => ScenarioParameters @@ -20,7 +20,7 @@ export interface Serializers { export const SERIALIZERS = new Map( Object.entries({ - ...v2_0_0, + ...v2_1_0, }), ) diff --git a/tools/generateTypes.ts b/tools/generateTypes.ts index 48127366d..ca7b25ccb 100644 --- a/tools/generateTypes.ts +++ b/tools/generateTypes.ts @@ -8,13 +8,16 @@ import yaml from 'js-yaml' import path from 'path' import prettier from 'prettier' import { quicktype, InputData, JSONSchema, JSONSchemaInput, JSONSchemaStore, parseJSON } from 'quicktype-core' +import { valid } from 'semver' import util from 'util' import { findModuleRoot } from '../lib/findModuleRoot' +import { get } from 'lodash' const rimraf = util.promisify(rimrafOriginal) const SCHEMA_EXTENSION = '.yml' +const SCHEMA_VER_FILEPATH = 'schemas/_SchemaVer.yml' class Store extends JSONSchemaStore { private schemasRoot: string @@ -42,6 +45,7 @@ function quicktypesAddSources(schemasRoot: string, schemaInput: JSONSchemaInput) async function quicktypesGenerate( lang: string, + schemaVer: string, schemasRoot: string, schemaFilenames: string[], outputPath: string, @@ -56,8 +60,6 @@ async function quicktypesGenerate( const { lines } = await quicktype({ inputData, lang, rendererOptions }) let code = lines.join('\n') - const schemaVer = '2.0.0' - if (lang === 'typescript') { code = prettier.format(code, { parser: 'typescript' }) @@ -105,6 +107,16 @@ async function ajvGenerate(schemasRoot: string, schemaFilenames: string[], outpu return FA.concurrent.forEach(ajvGenerateOne(schemasRoot, ajv, outputDir), schemaFilenames) } +async function getSchemaVer(schemaVerFilepath: string) { + const jsonSchemaString = fs.readFileSync(schemaVerFilepath).toString('utf-8') + const schema = yaml.safeLoad(jsonSchemaString) as Record + const schemaVer = get(schema, 'const') as string + if (!valid(schemaVer)) { + throw new Error(`Expected \`schemaVer\` to be a valid version string but got: "${schemaVer}"`) + } + return schemaVer +} + export default async function generateTypes() { const { moduleRoot } = findModuleRoot() const schemasRoot = path.join(moduleRoot, 'schemas') @@ -112,6 +124,9 @@ export default async function generateTypes() { const pyOutputDir = path.join(moduleRoot, 'data', 'generated') const tsOutput = path.join(tsOutputDir, 'types.ts') const pyOutput = path.join(pyOutputDir, 'types.py') + const schemaVerFilepath = path.join(moduleRoot, SCHEMA_VER_FILEPATH) + + const schemaVer = await getSchemaVer(schemaVerFilepath) let schemaFilenames = await fs.readdir(schemasRoot) schemaFilenames = schemaFilenames.filter((schemaFilename) => schemaFilename.endsWith(SCHEMA_EXTENSION)) @@ -120,12 +135,12 @@ export default async function generateTypes() { await FA.concurrent.forEach(async (d) => fs.mkdirp(d), [tsOutputDir, pyOutputDir]) return Promise.all([ - quicktypesGenerate('typescript', schemasRoot, schemaFilenames, tsOutput, { + quicktypesGenerate('typescript', schemaVer, schemasRoot, schemaFilenames, tsOutput, { 'converters': 'all-objects', 'nice-property-names': 'true', 'runtime-typecheck': 'true', }), - quicktypesGenerate('python', schemasRoot, schemaFilenames, pyOutput, { + quicktypesGenerate('python', schemaVer, schemasRoot, schemaFilenames, pyOutput, { 'python-version': '3.6', 'alphabetize-properties': 'false', }), From a6f3fc39e0442b7e91ec7c1b0055d4d83bd0206f Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Wed, 17 Jun 2020 17:08:31 +0200 Subject: [PATCH 3/3] [WIP] start implementing contact matrix and age-specific interventions --- src/algorithms/initialize.ts | 17 ++++++++++++----- src/algorithms/model.ts | 15 ++++++--------- src/algorithms/types/Result.types.ts | 3 ++- 3 files changed, 20 insertions(+), 15 deletions(-) diff --git a/src/algorithms/initialize.ts b/src/algorithms/initialize.ts index 8c90261ed..8eb053ecc 100644 --- a/src/algorithms/initialize.ts +++ b/src/algorithms/initialize.ts @@ -9,6 +9,10 @@ const monthToDay = (m: number) => { return m * 30 + 15 } +export function sum(arr: number[]): number { + return arr.reduce((a, b) => a + b, 0) +} + const jan2020 = new Date('2020-01-01').valueOf() // time in ms export function withUncertainty(scenario: ScenarioFlat): boolean { @@ -33,13 +37,15 @@ export const msPerDay = 1000 * 60 * 60 * 24 */ export function infectionRate( time: number, - avgInfectionRate: number, + infectedFractionByAge: number[], + contactMatrix: number[][], peakMonth: number, seasonalForcing: number, -): number { +): number[] { // this is super hacky const phase = ((time - jan2020) / msPerDay / 365 - monthToDay(peakMonth) / 365) * 2 * Math.PI - return avgInfectionRate * (1 + seasonalForcing * Math.cos(phase)) + const baseValue = 1 + seasonalForcing * Math.cos(phase) + return contactMatrix.map((v) => baseValue * sum(v.map((d, i) => d * infectedFractionByAge[i]))) } export function getPopulationParams( @@ -88,6 +94,7 @@ export function getPopulationParams( isolated: [], }, rate: { + contactMatrix: Object.keys(AgeGroup).map(() => Object.keys(AgeGroup).map(() => 1.0)), latency: 1 / latencyDays, infection: () => -Infinity, // Dummy infectionRate function. This is set below. recovery: [], @@ -145,8 +152,8 @@ export function getPopulationParams( const avgInfectionRate = tmpR0 / infectiousPeriodDays const containment = containmentRealization.length > 1 ? containmentRealization[i] : containmentRealization[0] - elt.rate.infection = (time: number) => - containment(time) * infectionRate(time, avgInfectionRate, peakMonth, seasonalForcing) + elt.rate.infection = (time: number, infectedFraction: number[]) => + containment(time) * infectionRate(time, infectedFraction, elt.rate.contactMatrix, avgInfectionRate, peakMonth, seasonalForcing) return elt }) diff --git a/src/algorithms/model.ts b/src/algorithms/model.ts index ecd3a983a..7743522ae 100644 --- a/src/algorithms/model.ts +++ b/src/algorithms/model.ts @@ -7,7 +7,7 @@ import { ExportedTimePoint, } from './types/Result.types' -import { msPerDay } from './initialize' +import { msPerDay, sum } from './initialize' const eulerStep = 0.5 export const eulerStepsPerDay = Math.round(1 / eulerStep) @@ -73,10 +73,6 @@ function stepODE(pop: SimulationTimePoint, P: ModelParams, dt: number): Simulati return state } -export function sum(arr: number[]): number { - return arr.reduce((a, b) => a + b, 0) -} - export function gz(x: number): number { return x > 0 ? x : 0 } @@ -294,16 +290,17 @@ function fluxes(time: number, pop: SimulationTimePoint, P: ModelParams): StateFl } // Compute all fluxes (apart from overflow states) barring no hospital bed constraints - const fracInfected = sum(pop.current.infectious) / P.populationServed + const infectionPressure = P.rate.infection( + time, + pop.current.infectious.map((d) => d / P.populationServed), + ) for (let age = 0; age < pop.current.infectious.length; age++) { // Initialize all multi-faceted states with internal arrays flux.exposed[age] = Array(pop.current.exposed[age].length) // Susceptible -> Exposed - flux.susceptible[age] = - P.importsPerDay[age] + - (1 - P.frac.isolated[age]) * P.rate.infection(time) * pop.current.susceptible[age] * fracInfected + flux.susceptible[age] = P.importsPerDay[age] + infectionPressure[age] * pop.current.susceptible[age] // Exposed -> Internal -> Infectious pop.current.exposed[age].forEach((exposed, i, exposedArray) => { diff --git a/src/algorithms/types/Result.types.ts b/src/algorithms/types/Result.types.ts index 0e885e278..ac607306b 100644 --- a/src/algorithms/types/Result.types.ts +++ b/src/algorithms/types/Result.types.ts @@ -56,8 +56,9 @@ export interface ModelFracs { } export interface ModelRates { + contactMatrix: number[][] latency: number - infection: (t: number) => number + infection: (t: number) => number[] recovery: number[] severe: number[] discharge: number[]