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update: Change time window on Location & Situation Report component to rely on API calls #633

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update: Change time window on Location & Situation Report component to rely on API calls #633

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c321111
update: location report with date params
olekkorob Feb 14, 2023
ff62af2
update: location report
olekkorob Feb 15, 2023
add22b7
chore: update location map, table
olekkorob Feb 15, 2023
3478a08
update: situation report
olekkorob Feb 16, 2023
b1672a4
chore: update report summary
olekkorob Feb 27, 2023
578927f
fix: location report issue
olekkorob Feb 27, 2023
19ee667
chore: report summary minor update
olekkorob Feb 27, 2023
f7b12b1
fix: default date range issue
olekkorob Mar 14, 2023
571b199
fix: default date range
olekkorob Mar 23, 2023
1e97a13
fix: not read from query
olekkorob Mar 23, 2023
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200 changes: 174 additions & 26 deletions web/src/api/genomics.js
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Original file line number Diff line number Diff line change
Expand Up @@ -590,6 +590,8 @@ export const getReportData = (
totalThreshold,
ndays,
defaultLocations = ['USA', 'USA_US-CA'],
minDate = '',
maxDate = '',
) => {
store.state.admin.reportloading = true;

Expand Down Expand Up @@ -634,10 +636,25 @@ export const getReportData = (
getCharacteristicMutations(apiurl, lineageString),
getMutationDetails(apiurl, mutationArr),
getMutationsByLineage(apiurl, mutationArr),
getCumPrevalences(apiurl, queryStr, locations, totalThreshold),
getSublineageTotals(apiurl, md, location),
getTemporalPrevalence(apiurl, location, queryStr, null),
getSublineagePrevalence(apiurl, md, location),
getCumPrevalences(
apiurl,
queryStr,
locations,
totalThreshold,
minDate,
maxDate,
),
getSublineageTotals(apiurl, md, location, minDate, maxDate),
getTemporalPrevalence(
apiurl,
location,
queryStr,
null,
true,
minDate,
maxDate,
),
getSublineagePrevalence(apiurl, md, location, minDate, maxDate),
getPositiveLocations(apiurl, queryStr, 'Worldwide'),
getPositiveLocations(apiurl, queryStr, 'USA'),
getLocationPrevalence(apiurl, queryStr, location, ndays),
Expand Down Expand Up @@ -736,11 +753,25 @@ export const updateChoroData = (
);
};

export const getSublineageTotals = (apiurl, md, location) => {
export const getSublineageTotals = (
apiurl,
md,
location,
minDate = '',
maxDate = '',
) => {
if (md && md.pango_descendants) {
const queryStr = `pangolin_lineage=${md.pango_descendants.join(',')}`;

return getCumPrevalence(apiurl, queryStr, location, 0).pipe(
return getCumPrevalence(
apiurl,
queryStr,
location,
0,
true,
minDate,
maxDate,
).pipe(
map((results) => {
// sort in descending order of frequency
results.sort((a, b) => b.lineage_count - a.lineage_count);
Expand All @@ -767,10 +798,24 @@ export const getSublineageTotals = (apiurl, md, location) => {
return of([]);
};

export const getSublineagePrevalence = (apiurl, md, location) => {
export const getSublineagePrevalence = (
apiurl,
md,
location,
minDate = '',
maxDate = '',
) => {
if (md) {
const queryStr = `pangolin_lineage=${md.pango_descendants.join(',')}`;
return getTemporalPrevalence(apiurl, location, queryStr).pipe(
return getTemporalPrevalence(
apiurl,
location,
queryStr,
false,
true,
minDate,
maxDate,
).pipe(
map((results) => {
results = results.filter((d) => d);

Expand Down Expand Up @@ -837,6 +882,8 @@ export const updateLocationData = (
location,
totalThreshold,
ndays,
minDate,
maxDate,
) => {
// lookup WHO name in curated dictionary
const filtered = CURATED.filter(
Expand Down Expand Up @@ -870,11 +917,26 @@ export const updateLocationData = (

return forkJoin([
findAllLocationMetadata(apiurl, locations, location),
getTemporalPrevalence(apiurl, location, queryStr, null),
getTemporalPrevalence(
apiurl,
location,
queryStr,
null,
true,
minDate,
maxDate,
),
getLocationPrevalence(apiurl, queryStr, location, ndays),
getCumPrevalences(apiurl, queryStr, locations, totalThreshold),
getSublineageTotals(apiurl, md, location),
getSublineagePrevalence(apiurl, md, location),
getCumPrevalences(
apiurl,
queryStr,
locations,
totalThreshold,
minDate,
maxDate,
),
getSublineageTotals(apiurl, md, location, minDate, maxDate),
getSublineagePrevalence(apiurl, md, location, minDate, maxDate),
]).pipe(
map(
([
Expand Down Expand Up @@ -1007,7 +1069,22 @@ export const getCharacteristicMutations = (
prevalenceThreshold = store.state.genomics.characteristicThreshold,
returnFlat = true,
includeSublineages = false,
genes = ["5UTR", "ORF1a", "ORF1b", "S", "ORF3a", "E", "M", "ORF6", "ORF7a", "ORF7b", "ORF8", "N", "ORF10", "3UTR"],
genes = [
'5UTR',
'ORF1a',
'ORF1b',
'S',
'ORF3a',
'E',
'M',
'ORF6',
'ORF7a',
'ORF7b',
'ORF8',
'N',
'ORF10',
'3UTR',
],
) => {
if (!lineage) return of([]);

Expand Down Expand Up @@ -1163,10 +1240,20 @@ export const getCumPrevalences = (
queryStr,
locations,
totalThreshold,
minDate = '',
maxDate = '',
) => {
return forkJoin(
...locations.map((d) =>
getCumPrevalence(apiurl, queryStr, d, totalThreshold),
getCumPrevalence(
apiurl,
queryStr,
d,
totalThreshold,
true,
minDate,
maxDate,
),
),
).pipe(
map((results) => {
Expand Down Expand Up @@ -1195,11 +1282,21 @@ export const getCumPrevalenceQueryLoop = (
queries,
location,
totalThreshold,
minDate,
maxDate,
) => {
if (queries.length) {
return forkJoin(
...queries.map((queryStr) =>
getCumPrevalence(apiurl, queryStr, location, totalThreshold),
getCumPrevalence(
apiurl,
queryStr,
location,
totalThreshold,
true,
minDate,
maxDate,
),
),
).pipe(
map((results) => {
Expand Down Expand Up @@ -1256,11 +1353,13 @@ export const getCumPrevalence = (
location,
totalThreshold,
returnFlat = true,
minDate = '',
maxDate = '',
) => {
const url =
location === 'Worldwide'
? `${apiurl}prevalence-by-location?cumulative=true&${queryStr}`
: `${apiurl}prevalence-by-location?${queryStr}&location_id=${location}&cumulative=true`;
? `${apiurl}prevalence-by-location?cumulative=true&${queryStr}&max_date=${maxDate}&min_date=${minDate}`
: `${apiurl}prevalence-by-location?${queryStr}&location_id=${location}&cumulative=true&max_date=${maxDate}&min_date=${minDate}`;
return from(
axios.get(url, {
headers: {
Expand Down Expand Up @@ -1531,13 +1630,15 @@ export const getTemporalPrevalence = (
queryStr,
indivCall = false,
returnFlat = true,
minDate = '',
maxDate = '',
) => {
store.state.admin.reportloading = true;
let url;
if (location === 'Worldwide') {
url = `${apiurl}prevalence-by-location?${queryStr}`;
url = `${apiurl}prevalence-by-location?${queryStr}&min_date=${minDate}&max_date=${maxDate}`;
} else {
url = `${apiurl}prevalence-by-location?${queryStr}&location_id=${location}`;
url = `${apiurl}prevalence-by-location?${queryStr}&location_id=${location}&min_date=${minDate}&max_date=${maxDate}`;
}

return from(
Expand Down Expand Up @@ -1816,8 +1917,10 @@ export const getCumPrevalenceAllLineages = (
nday_threshold,
ndays,
window,
minDate,
maxDate,
) => {
let url = `${apiurl}prevalence-by-location-all-lineages?location_id=${location}&other_threshold=${other_threshold}&nday_threshold=${nday_threshold}&ndays=${ndays}&window=${window}&ndays=${ndays}&cumulative=true`;
let url = `${apiurl}prevalence-by-location-all-lineages?location_id=${location}&other_threshold=${other_threshold}&nday_threshold=${nday_threshold}&ndays=${ndays}&window=${window}&ndays=${ndays}&cumulative=true&min_date=${minDate}&max_date=${maxDate}`;

return from(
axios.get(url, {
Expand Down Expand Up @@ -1859,10 +1962,12 @@ export const getPrevalenceAllLineages = (
other_threshold,
nday_threshold,
ndays,
minDate = '',
maxDate = '',
) => {
const dateThreshold = new Date('2020-03-14');

let url = `${apiurl}prevalence-by-location-all-lineages?location_id=${location}&other_threshold=${other_threshold}&nday_threshold=${nday_threshold}&ndays=${ndays}`;
let url = `${apiurl}prevalence-by-location-all-lineages?location_id=${location}&other_threshold=${other_threshold}&nday_threshold=${nday_threshold}&ndays=${ndays}&max_date=${maxDate}&min_date=${minDate}`;

return from(
axios.get(url, {
Expand Down Expand Up @@ -1997,6 +2102,8 @@ export const getLocationReportData = (
nday_threshold,
ndays,
window,
minDate = '',
maxDate = '',
) => {
store.state.genomics.locationLoading2 = true;

Expand All @@ -2009,6 +2116,8 @@ export const getLocationReportData = (
nday_threshold,
ndays,
window,
minDate,
maxDate,
).pipe(
mergeMap((results) =>
getMutationsOfInterestPrevalence(apiurl, results.recentDomain).pipe(
Expand Down Expand Up @@ -2036,6 +2145,8 @@ export const getLocationLineagePrevalences = (
nday_threshold,
ndays,
window,
minDate,
maxDate,
) => {
return forkJoin([
getPrevalenceAllLineages(
Expand All @@ -2044,6 +2155,8 @@ export const getLocationLineagePrevalences = (
other_threshold,
nday_threshold,
ndays,
minDate,
maxDate,
),
getCumPrevalenceAllLineages(
apiurl,
Expand All @@ -2052,6 +2165,8 @@ export const getLocationLineagePrevalences = (
nday_threshold,
ndays,
window,
minDate,
maxDate,
),
]).pipe(
map(([lineagesByDay, mostRecentLineages]) => {
Expand Down Expand Up @@ -2206,6 +2321,8 @@ export const getLocationTable = (
location,
mutations,
totalThreshold,
minDate = '',
maxDate = '',
) => {
store.state.genomics.locationLoading3 = true;
const pangos = mutations
Expand All @@ -2220,8 +2337,23 @@ export const getLocationTable = (
const variantQueries = mutations.map((d) => d.query);

return forkJoin([
getCumPrevalence(apiurl, pangoQuery, location, totalThreshold),
getCumPrevalenceQueryLoop(apiurl, variantQueries, location, totalThreshold),
getCumPrevalence(
apiurl,
pangoQuery,
location,
totalThreshold,
true,
minDate,
maxDate,
),
getCumPrevalenceQueryLoop(
apiurl,
variantQueries,
location,
totalThreshold,
minDate,
maxDate,
),
]).pipe(
map(([lineages, variants]) => {
let results = lineages.concat(variants);
Expand Down Expand Up @@ -2272,12 +2404,14 @@ export const getEpiMutationPrevalence = (
locationID,
mutations,
epiFields = 'location_id,date,confirmed,mostRecent,confirmed_numIncrease,confirmed_rolling,dead_numIncrease,dead_rolling',
minDate = '',
maxDate = '',
) => {
store.state.genomics.locationLoading4 = true;

return forkJoin([
getEpiTraces(epiurl, [locationID], epiFields),
getAllTemporalPrevalences(apiurl, locationID, mutations),
getAllTemporalPrevalences(apiurl, locationID, mutations, minDate, maxDate),
]).pipe(
map(([epi, mutationTraces]) => {
epi = epi.length ? epi[0].value : [];
Expand All @@ -2300,11 +2434,25 @@ export const getEpiMutationPrevalence = (
);
};

export const getAllTemporalPrevalences = (apiurl, locationID, mutations) => {
export const getAllTemporalPrevalences = (
apiurl,
locationID,
mutations,
minDate = '',
maxDate = '',
) => {
if (mutations.length) {
return forkJoin(
...mutations.map((mutation) =>
getTemporalPrevalence(apiurl, locationID, mutation.query),
getTemporalPrevalence(
apiurl,
locationID,
mutation.query,
false,
true,
minDate,
maxDate,
),
),
).pipe(
map((results) => {
Expand Down
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