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Prevalent Taxa Fix #384

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Merged
davenquinn merged 2 commits into from
Oct 14, 2025
Merged

Prevalent Taxa Fix #384

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ceb6e22
Use cltn_id not column id for liths
davidsklar99 Sep 19, 2025
0e3c26c
Update rest
davidsklar99 Sep 19, 2025
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16 changes: 4 additions & 12 deletions pages/columns/groups/@group/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,17 +1,19 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const col_group_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);

// Await all API calls
const [resData, colData, refs1, refs2] = await Promise.all([
const [resData, colData, fossilsData, refs1, refs2] = await Promise.all([
fetchAPIData("/defs/groups", { col_group_id }),
fetchAPIData("/columns", {
col_group_id,
response: "long",
format: "geojson",
}),
fetchAPIData("/fossils", { col_group_id, format: "geojson" }),
fetchAPIRefs("/fossils", { col_group_id }),
fetchAPIRefs("/columns", { col_group_id }),
]);
Expand All @@ -20,17 +22,7 @@ export async function data(pageContext) {
const refValues2 = Object.values(refs2);
const refs = [...refValues1, ...refValues2];

const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
taxaData = await response.json();
}
const taxaData = await getPrevalentTaxa(fossilsData);

return { resData: resData[0], colData, taxaData, refs };
}
16 changes: 4 additions & 12 deletions pages/dev/columns-test/groups/@group/+data.ts
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,19 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const col_group_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);

// Await all API calls
const [resData, colData, refs1, refs2] = await Promise.all([
const [resData, colData, fossilsData,refs1, refs2] = await Promise.all([
fetchAPIData("/defs/groups", { col_group_id }),
fetchAPIData("/columns", {
col_group_id,
response: "long",
format: "geojson",
}),
fetchAPIData("/fossils", { col_group_id, format: "geojson" }),
fetchAPIRefs("/fossils", { col_group_id }),
fetchAPIRefs("/columns", { col_group_id }),
]);
Expand All @@ -20,17 +22,7 @@ export async function data(pageContext) {
const refValues2 = Object.values(refs2);
const refs = [...refValues1, ...refValues2];

const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
taxaData = await response.json();
}
const taxaData = await getPrevalentTaxa(fossilsData);

return { resData: resData[0], colData, taxaData, refs };
}
22 changes: 2 additions & 20 deletions pages/lex/economics/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const econ_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand Down Expand Up @@ -42,26 +43,7 @@ export async function data(pageContext) {
const refValues2 = refs2 ? Object.values(refs2) : [];
const refs = [...refValues1, ...refValues2];

// Build column ID list for PBDB taxa fetch
const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
try {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
if (response.ok) {
taxaData = await response.json();
} else {
console.warn("PBDB taxa fetch failed with status", response.status);
}
} catch (err) {
console.warn("Error fetching PBDB taxa data:", err);
}
}
const taxaData = await getPrevalentTaxa(fossilsData);

return {
resData: resData?.[0] ?? null,
Expand Down
17 changes: 2 additions & 15 deletions pages/lex/environments/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const environ_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand Down Expand Up @@ -48,21 +49,7 @@ export async function data(pageContext) {
?.join(",");

// Fetch PBDB fossil prevalence data
let taxaData = null;
if (cols) {
try {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
if (response.ok) {
taxaData = await response.json();
} else {
console.warn("PBDB taxa fetch failed with status", response.status);
}
} catch (err) {
console.warn("Error fetching PBDB taxa data:", err);
}
}
const taxaData = await getPrevalentTaxa(fossilsData);

return {
resData: resData?.[0] ?? null,
Expand Down
23 changes: 2 additions & 21 deletions pages/lex/intervals/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const int_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand Down Expand Up @@ -42,27 +43,7 @@ export async function data(pageContext) {
const refValues2 = refs2 ? Object.values(refs2) : [];
const refs = [...refValues1, ...refValues2];

// Extract column IDs
const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

// Optional: Fetch PBDB taxa data
let taxaData = null;
if (cols) {
try {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
if (response.ok) {
taxaData = await response.json();
} else {
console.warn("PBDB taxa fetch failed with status", response.status);
}
} catch (err) {
console.warn("Error fetching PBDB taxa data:", err);
}
}
const taxaData = await getPrevalentTaxa(fossilsData);

return {
resData: resData?.[0] ?? null,
Expand Down
2 changes: 1 addition & 1 deletion pages/lex/lithologies/@id/+Page.client.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ export function Page() {
const features = colData?.features || [];
const timescales = resData?.timescales || [];

console.log("resData:", resData);
console.log("fossil Data:", fossilsData);

const children = [
h(ColumnsTable, {
Expand Down
22 changes: 2 additions & 20 deletions pages/lex/lithologies/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const lith_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand Down Expand Up @@ -43,26 +44,7 @@ export async function data(pageContext) {
const refValues2 = refs2 ? Object.values(refs2) : [];
const refs = [...refValues1, ...refValues2];

// Extract column IDs to fetch taxa data (PBDB)
const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
try {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
if (response.ok) {
taxaData = await response.json();
} else {
console.warn("PBDB taxa fetch failed with status", response.status);
}
} catch (err) {
console.warn("Error fetching taxa data from PBDB:", err);
}
}
const taxaData = await getPrevalentTaxa(fossilsData);

return {
resData: resData?.[0] ?? null,
Expand Down
13 changes: 2 additions & 11 deletions pages/lex/strat-concepts/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { apiDomain, pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const concept_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand All @@ -21,17 +22,7 @@ export async function data(pageContext) {
const refValues2 = refs2 ? Object.values(refs2) : [];
const refs = [...refValues1, ...refValues2];

const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
taxaData = await response.json();
}
const taxaData = await getPrevalentTaxa(fossilsData);

return { resData: resData[0], refs, fossilsData, colData, taxaData, unitsData };
}
13 changes: 2 additions & 11 deletions pages/lex/strat-names/@id/+data.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import { pbdbDomain } from "@macrostrat-web/settings";
import { fetchAPIData, fetchAPIRefs } from "~/_utils";
import { getPrevalentTaxa } from "~/components/lex/data-helper";

export async function data(pageContext) {
const strat_name_id = parseInt(pageContext.urlParsed.pathname.split("/")[3]);
Expand All @@ -24,17 +25,7 @@ export async function data(pageContext) {
const refValues2 = Object.values(refs2);
const refs = [...refValues1, ...refValues2];

const cols = colData?.features
?.map((feature) => feature.properties.col_id)
?.join(",");

let taxaData = null;
if (cols) {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${cols}`
);
taxaData = await response.json();
}
const taxaData = await getPrevalentTaxa(fossilsData);

return {
resData: resData[0],
Expand Down
24 changes: 24 additions & 0 deletions src/components/lex/data-helper.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
import { pbdbDomain } from "@macrostrat-web/settings";

export async function getPrevalentTaxa(fossilsData) {
// Extract cltn IDs to fetch taxa data (PBDB)
const collectionIds = fossilsData?.features
?.map((feature) => feature.properties.cltn_id)

let taxaData = null;
if (collectionIds && collectionIds.length > 0) {
try {
const response = await fetch(
`${pbdbDomain}/data1.2/occs/prevalence.json?limit=5&coll_id=${collectionIds.join(",")}`
);
if (response.ok) {
taxaData = await response.json();
} else {
console.warn("PBDB taxa fetch failed with status", response.status);
}
} catch (err) {
console.warn("Error fetching taxa data from PBDB:", err);
}
}
return taxaData;
}