@macrostrat/column-views 2.1.3 → 2.2.0

package/src/facets/fossils/provider.ts

@@ -1,10 +1,14 @@
-import { group } from "d3-array";
-import { createAPIContext, useAPIResult } from "@macrostrat/ui-components";
+import { group, InternMap } from "d3-array";
+import {
+  createAPIContext,
+  useAPIResult,
+  useAsyncMemo,
+} from "@macrostrat/ui-components";
 
 const responseUnwrapper = (d) => d.records;
 
 const pbdbAPIContext = createAPIContext({
-  baseURL: "https://training.paleobiodb.org/data1.2",
+  baseURL: "https://paleobiodb.org/data1.2",
   unwrapResponse: responseUnwrapper,
 });
 
@@ -26,10 +30,13 @@ export function usePBDBFossilData(
   });
 }
 
-export interface PBDBCollection {
+export interface PBDBIdentifier {
   unit_id: number;
   col_id: number;
   cltn_id: number;
+}
+
+export interface PBDBCollection extends PBDBIdentifier {
   cltn_name: string;
   pbdb_occs: number;
   t_age: number;
@@ -37,44 +44,133 @@ export interface PBDBCollection {
   [key: string]: any; // Allow for additional properties
 }
 
-function useMacrostratFossilData({ col_id }): PBDBCollection[] | null {
-  return useAPIResult("/fossils", { col_id });
+export interface PBDBOccurrence extends PBDBIdentifier {
+  occ_id: number;
+  cltn_id: number;
+  taxon_name: string;
+  best_name: string;
+  [key: string]: any; // Allow for additional properties
+}
+
+export function useFossilData(
+  col_id: number,
+  type = FossilDataType.Collections,
+) {
+  // Fossil links are stored in both Macrostrat and PBDB, depending on how the link was assembled. Here
+  // we create a unified view of data over both sources.
+  return useAsyncMemo(async () => {
+    if (col_id == null) return null;
+    return await fetchFossilData(col_id, type);
+  }, [col_id, type]);
+}
+
+async function fetchMacrostratFossilData(
+  col_id: number,
+  type: FossilDataType,
+): Promise<PBDBCollection[]> {
+  if (type !== FossilDataType.Collections) {
+    // Macrostrat API only supports collections
+    return [];
+  }
+
+  // Fetch fossil collections linked to columns from the Macrostrat API
+  const resp = await fetch(
+    `https://macrostrat.org/api/fossils?col_id=${col_id}`,
+  );
+  const res = await resp.json();
+  // Create collections from Macrostrat data
+  return res.success.data;
+}
+
+async function fetchPDBDFossilData(
+  col_id: number,
+  type: FossilDataType,
+): Promise<PBDBCollection[]> {
+  const resp = await fetch(
+    `https://paleobiodb.org/data1.2/${type}/list.json?ms_column=${col_id}&show=mslink,full`,
+  );
+  const res = await resp.json();
+  return res.records.map(
+    type == FossilDataType.Collections
+      ? createMacrostratCollection
+      : preprocessOccurrence,
+  );
+}
+
+async function fetchFossilData(
+  colID: number,
+  type: FossilDataType,
+): Promise<InternMap<number, PBDBOccurrence[] | PBDBCollection[]>> {
+  const [macrostratData, pbdbData] = await Promise.all([
+    fetchMacrostratFossilData(colID, type),
+    fetchPDBDFossilData(colID, type),
+  ]);
+
+  const data = [...macrostratData, ...pbdbData];
+
+  return group(data, (d) => d.unit_id);
+}
+
+function preprocessOccurrence(d): PBDBOccurrence {
+  /* Preprocess data for an occurrence into a Macrostrat-like format */
+  // Standardize names of Macrostrat units and columns
+  const unit_id = parseInt(d.msu.replace(/^\w+:/, ""));
+  const col_id = parseInt(d.msc.replace(/^\w+:/, ""));
+
+  // taxon names may be stored in different fields
+  const occ_id = parseInt(d.oid.replace(/^occ:/, ""));
+  const cltn_id = parseInt(d.cid.replace(/^col:/, ""));
+
+  return {
+    ...d,
+    unit_id,
+    col_id,
+    taxon_name: d.tna,
+    best_name: d.idn ?? d.tna,
+    occ_id,
+    cltn_id,
+    cltn_name: d.nam,
+  };
 }
 
 function createMacrostratCollection(d): PBDBCollection {
+  /* Preprocess data for a collection into a Macrostrat-like format */
   let unit_id = null;
   let col_id = null;
   // Standardize names of Macrostrat units and columns
-  if (d.msu !== null) {
+  if (d.msu != null) {
     unit_id = parseInt(d.msu.replace(/^\w+:/, ""));
   }
-  if (d.msc !== null) {
+  if (d.msc != null) {
     col_id = parseInt(d.msc.replace(/^\w+:/, ""));
   }
 
+  // taxon names may be stored in different fields
+  let taxon_name = d.tna;
+  let occ_id = null;
+  if (d.oid != null && d.oid.startsWith("occ:")) {
+    occ_id = parseInt(d.oid.replace(/^occ:/, ""));
+  }
+  if (d.idn != null) {
+    taxon_name = d.idn;
+  }
+
+  let cltn_id = d.cltn_id;
+  if (d.oid != null && d.oid.startsWith("col:")) {
+    cltn_id = parseInt(d.oid.replace(/^col:/, ""));
+  } else if (d.cid != null && d.cid.startsWith("col:")) {
+    cltn_id = parseInt(d.cid.replace(/^col:/, ""));
+  }
+
   return {
     ...d,
     unit_id,
     col_id,
-    cltn_id: parseInt(d.oid.replace(/^col:/, "")),
+    taxon_name,
+    occ_id,
+    cltn_id,
     cltn_name: d.nam,
     t_age: d.t_age,
     b_age: d.b_age,
   };
 }
-
-export function useFossilData({ col_id }) {
-  // Fossil links are stored in both Macrostrat and PBDB, depending on how the link was assembled. Here
-  // we create a unified view of data over both sources.
-
-  const r1 = usePBDBFossilData(FossilDataType.Collections, { col_id });
-
-  const r2 = useMacrostratFossilData({ col_id });
-
-  if (r1 == null || r2 == null) return null;
-  const r1a = r1.map(createMacrostratCollection);
-
-  const data = [...r1a, ...r2];
-
-  return group(data, (d) => d.unit_id);
-}

package/src/facets/index.ts

@@ -1,3 +1,5 @@
 export * from "./fossils";
 export * from "./detrital-zircon";
 export * from "./carbon-isotopes";
+export * from "./measurements";
+export * from "./base-sample-column";

package/src/facets/measurements/index.ts

@@ -0,0 +1,38 @@
+import h from "@macrostrat/hyper";
+import { useAPIResult } from "@macrostrat/ui-components";
+import { BaseMeasurementsColumn, TruncatedList } from "../base-sample-column";
+
+function useSGPData({ col_id }) {
+  const res = useAPIResult(
+    "https://dev.macrostrat.org/api/pg/sgp_unit_matches",
+    {
+      col_id: `eq.${col_id}`,
+    },
+    (d) => d,
+  );
+  return res;
+}
+
+export function SGPMeasurementsColumn({ columnID, color = "magenta" }) {
+  const data = useSGPData({ col_id: columnID });
+
+  if (data == null) return null;
+
+  return h(BaseMeasurementsColumn, {
+    data,
+    noteComponent: SGPSamplesNote,
+  });
+}
+
+function SGPSamplesNote(props) {
+  const { note } = props;
+  const sgp_samples = note?.data?.sgp_samples;
+
+  if (sgp_samples == null || sgp_samples.length === 0) return null;
+
+  return h(TruncatedList, {
+    className: "sgp-samples",
+    data: sgp_samples,
+    itemRenderer: (p) => h("span", p.data.name),
+  });
+}

package/src/facets/measurements/provider.ts

@@ -0,0 +1,80 @@
+import { group } from "d3-array";
+import { createAPIContext, useAPIResult } from "@macrostrat/ui-components";
+
+const responseUnwrapper = (d) => d.records;
+
+const pbdbAPIContext = createAPIContext({
+  baseURL: "https://training.paleobiodb.org/data1.2",
+  unwrapResponse: responseUnwrapper,
+});
+
+export enum FossilDataType {
+  Occurrences = "occs",
+  Collections = "colls",
+}
+
+export function usePBDBFossilData(
+  type: FossilDataType,
+  { col_id },
+): any[] | null {
+  const params = {
+    ms_column: col_id,
+    show: "full,mslink",
+  };
+  return useAPIResult(`/${type}/list.json`, params, {
+    context: pbdbAPIContext,
+  });
+}
+
+export interface PBDBCollection {
+  unit_id: number;
+  col_id: number;
+  cltn_id: number;
+  cltn_name: string;
+  pbdb_occs: number;
+  t_age: number;
+  b_age: number;
+  [key: string]: any; // Allow for additional properties
+}
+
+function useMacrostratFossilData({ col_id }): PBDBCollection[] | null {
+  return useAPIResult("/fossils", { col_id });
+}
+
+function createMacrostratCollection(d): PBDBCollection {
+  let unit_id = null;
+  let col_id = null;
+  // Standardize names of Macrostrat units and columns
+  if (d.msu !== null) {
+    unit_id = parseInt(d.msu.replace(/^\w+:/, ""));
+  }
+  if (d.msc !== null) {
+    col_id = parseInt(d.msc.replace(/^\w+:/, ""));
+  }
+
+  return {
+    ...d,
+    unit_id,
+    col_id,
+    cltn_id: parseInt(d.oid.replace(/^col:/, "")),
+    cltn_name: d.nam,
+    t_age: d.t_age,
+    b_age: d.b_age,
+  };
+}
+
+export function useFossilData({ col_id }) {
+  // Fossil links are stored in both Macrostrat and PBDB, depending on how the link was assembled. Here
+  // we create a unified view of data over both sources.
+
+  const r1 = usePBDBFossilData(FossilDataType.Collections, { col_id });
+
+  const r2 = useMacrostratFossilData({ col_id });
+
+  if (r1 == null || r2 == null) return null;
+  const r1a = r1.map(createMacrostratCollection);
+
+  const data = [...r1a, ...r2];
+
+  return group(data, (d) => d.unit_id);
+}