Merge branch 'lexicon-rework'

* lexicon-rework:
  Updated page breadcrumbs somewhat
  Created a basic admin component
  Started putting in place a page console
  Starting point for extractions management

packages/settings/index.ts

@@ -45,6 +45,8 @@ export const macrostratInstance = getRuntimeConfig("MACROSTRAT_INSTANCE");
 
 export const elevationLayerURL = getRuntimeConfig("ELEVATION_LAYER_URL");
 
+export const enableAdmin = getRuntimeConfig("ENABLE_ADMIN", true);
+
 /** Legacy settings object */
 export const SETTINGS = {
   cdrPrefix,

pages/+Layout.ts

@@ -3,6 +3,7 @@ import { ReactNode } from "react";
 
 import { AuthProvider } from "~/_providers/auth";
 import { usePageContext } from "vike-react/usePageContext";
+import { enableAdmin } from "@macrostrat-web/settings";
 
 import "~/styles/blueprint-core";
 import "~/styles/_theme.styl";
@@ -11,6 +12,8 @@ import "~/styles/padding.css";
 //
 import h from "./layout.module.sass";
 
+import { PageAdminConsole } from "~/components";
+
 export default function Layout({ children }: { children: ReactNode }) {
   const pageContext = usePageContext();
   const { exports = {}, config, user } = pageContext;
@@ -23,7 +26,12 @@ export default function Layout({ children }: { children: ReactNode }) {
     h(
       supportsDarkMode ? DarkModeProvider : NoOpDarkModeProvider,
       { followSystem: true },
-      h("div.app-shell", { className: pageStyle + "-page" }, children)
+      h("div.app-shell", { className: pageStyle + "-page" }, [
+        children,
+        h.if(enableAdmin)(PageAdminConsole, {
+          className: "page-admin-container",
+        }),
+      ])
     )
   );
 }

pages/+Page.mdx

@@ -1,14 +1,9 @@
 export { ContentPage as default } from "~/layouts";
 import { macrostratInstance } from "@macrostrat-web/settings";
-import { PageHeader } from "~/components";
+import { PageHeaderV2 } from "~/components";
 import { LinkCard } from "~/components/cards";
 
-<PageHeader title="Macrostrat">
-  <span className="subtitle">
-    <span className="secondary">v2</span>{" "}
-    <span className="tertiary">{macrostratInstance}</span>
-  </span>
-</PageHeader>
+<PageHeaderV2 title="Macrostrat"></PageHeaderV2>
 
 <LinkCard href="/map" title="Map interface">
   Macrostrat's main map interface showing a harmonized view of the Earth's crust

pages/dev/xdd-extractions/+Page.ts

@@ -0,0 +1,82 @@
+import h from "@macrostrat/hyper";
+import { PostgrestClient } from "@supabase/postgrest-js";
+
+import { ContentPage } from "~/layouts";
+import { PageHeaderV2 } from "~/components";
+import { postgrestPrefix } from "@macrostrat-web/settings";
+import { useEffect, useState } from "react";
+
+const postgrest = new PostgrestClient(postgrestPrefix);
+
+function usePostgresQuery(query) {
+  const [data, setData] = useState(null);
+  useEffect(() => {
+    postgrest
+      .from(query)
+      .select("n_matches,citation,paper_id")
+      .order("n_matches", { ascending: false })
+      .limit(100)
+      .then((res) => {
+        setData(res.data);
+      });
+  }, [query]);
+  return data;
+}
+
+export function Page() {
+  return h(ContentPage, [h(PageMain)]);
+}
+
+function PageMain() {
+  return h("div", [
+    h(PageHeaderV2, { title: "Stratigraphic name extractions" }),
+    h(ExtractionIndex),
+  ]);
+}
+
+function ExtractionIndex() {
+  const data = usePostgresQuery("kg_publication_entities");
+  if (data == null) {
+    return h("div", "Loading...");
+  }
+
+  return h([
+    h(
+      data.map((d) => {
+        return h("div", [
+          h(xDDCitation, {
+            citation: d.citation,
+            href: `/dev/xdd-extractions/${d.paper_id}`,
+          }),
+          h("p", `${d.n_matches} stratigraphic name matches`),
+        ]);
+      })
+    ),
+  ]);
+}
+
+function pruneEmptyCitationElements(citation): any {
+  const keys = [
+    "title",
+    "author",
+    "doi",
+    "journal",
+    "identifier",
+    "volume",
+    "number",
+    "year",
+  ];
+  let newCitation = {};
+  for (let key of keys) {
+    if (citation[key] != null && citation[key] !== "") {
+      newCitation[key] = citation[key];
+    }
+  }
+  return newCitation;
+}
+
+function xDDCitation({ citation, href }) {
+  const newCitation = pruneEmptyCitationElements(citation);
+  const { title } = newCitation;
+  return h("div", [h("h2.title", h("a", { href }, title))]);
+}

pages/dev/xdd-extractions/+config.ts

@@ -0,0 +1,10 @@
+export default {
+  meta: {
+    Page: {
+      env: {
+        client: true,
+        server: false,
+      },
+    },
+  },
+};

pages/dev/xdd-extractions/@paperId/+Page.ts

@@ -0,0 +1,113 @@
+import h from "@macrostrat/hyper";
+import { PostgrestClient } from "@supabase/postgrest-js";
+
+import { ContentPage } from "~/layouts";
+import { PageBreadcrumbs } from "~/components";
+import { postgrestPrefix } from "@macrostrat-web/settings";
+import { useEffect, useState } from "react";
+import { usePageContext } from "vike-react/usePageContext";
+import { JSONView } from "@macrostrat/ui-components";
+
+const postgrest = new PostgrestClient(postgrestPrefix);
+
+function usePostgresQuery(query, { paperId }) {
+  const [data, setData] = useState(null);
+  useEffect(() => {
+    postgrest
+      .from(query)
+      .select()
+      .filter("paper_id", "eq", paperId)
+      .then((res) => {
+        setData(res.data);
+      });
+  }, [query]);
+  return data;
+}
+
+export function Page() {
+  return h(ContentPage, [h(PageBreadcrumbs), h(PageMain)]);
+}
+
+function PageMain() {
+  return h("div", [
+    h("h1", "xDD stratigraphic name extractions"),
+    h(ExtractionIndex),
+  ]);
+}
+
+function ExtractionIndex() {
+  const { routeParams } = usePageContext();
+  const { paperId } = routeParams;
+
+  const data = usePostgresQuery("kg_context_entities", { paperId });
+  if (data == null) {
+    return h("div", "Loading...");
+  }
+
+  return h(data.map((d) => h(ExtractionContext, { data: d })));
+}
+
+function ExtractionContext({ data }) {
+  return h("div", [
+    h("p", data.paragraph_text),
+    h(
+      "ul.entities",
+      data.entities.map((d) => h(ExtractionInfo, { data: d }))
+    ),
+  ]);
+}
+
+type Match = any;
+
+interface Entity {
+  id: number;
+  name: string;
+  type: "strat_name" | "lith" | "lith_att";
+  indices: [number, number];
+  children: Entity[];
+  match?: Match;
+}
+
+function ExtractionInfo({ data }: { data: Entity }) {
+  const children = data.children ?? [];
+
+  const match = data.match ?? null;
+
+  console.log(data);
+
+  return h("li.entity", { className: data.type }, [
+    h("span.name", data.name),
+    h(Match, { data: match }),
+    h.if(children.length > 0)([
+      h(
+        "ul.children",
+        children.map((d) => h(ExtractionInfo, { data: d }))
+      ),
+    ]),
+  ]);
+}
+
+function Match({ data }) {
+  if (data == null) return null;
+  const href = buildHref(data);
+  return h([" ", h("a.match", { href }, data.name)]);
+}
+
+function buildHref(match) {
+  /** Build a URL for a matched term */
+  if (match == null) return null;
+
+  if (match.strat_name_id != null) {
+    return `/lex/strat-names/${match.strat_name_id}`;
+  }
+
+  if (match.lith_id != null) {
+    return `/lex/lithologies`;
+  }
+
+  if (match.lith_att_id != null) {
+    return `/lex/lithologies`;
+  }
+
+  return null;
+}

pages/layout.module.sass

@@ -4,4 +4,12 @@
 :global(.in-page-transition)
   height: 100vh
   overflow: hidden
-  position: relative
+  position: relative
+
+// An admin console for the page
+.page-admin-container
+  position: fixed
+  top: 0
+  right: 0
+  margin: 1em
+  z-index: 5000

pages/lex/strat-names/+Page.ts

@@ -154,39 +154,3 @@ function StratNamesList({ data }) {
     data.map((d) => h(StratNameItem, { data: d, key: d.id })),
   ]);
 }
-
-const ranks = {
-  Fm: "Formation",
-  Mbr: "Member",
-  Gp: "Group",
-  Sgp: "Supergroup",
-};
-
-function StratNameItem({ data }) {
-  const { kg_liths, liths, units, id } = data;
-  return h("div.strat-name", {}, [
-    h(
-      Link,
-      { href: `/lex/strat-names/${id}` },
-      h("h2.strat-name", [
-        data.strat_name,
-        " ",
-        h("span", ranks[data.rank] ?? data.rank),
-      ])
-    ),
-    h("p", [`in ${units.length} columns`]),
-    h("div.strat-name-details", [h(Liths, { liths })]),
-    h.if(kg_liths != null)("div.strat-name-details", [
-      h(Liths, { liths: kg_liths, candidate: true }),
-    ]),
-  ]);
-}
-
-function Liths({ liths, candidate = false }) {
-  return h(
-    "p.liths",
-    liths.map((lith, i) => {
-      return h(AttributedLithTag, { key: i, lith, candidate });
-    })
-  );
-}

pages/lex/strat-names/@id/+Page.ts

@@ -4,7 +4,6 @@ import { Link, PageHeader } from "~/components";
 import { AttributedLithTag } from "~/components";
 import { AnchorButton, Icon, InputGroup, Tag } from "@blueprintjs/core";
 import { GDDReferenceCard, CollapseCard } from "@macrostrat/ui-components";
-import { useState } from "react";
 import styles from "./main.module.sass";
 
 const h = hyper.styled(styles);

pages/map/map-interface/map-page/index.ts

@@ -3,7 +3,7 @@ import { Suspense, useCallback, useEffect, useRef } from "react";
 import { Spinner } from "@blueprintjs/core";
 import loadable from "@loadable/component";
 import { mapPagePrefix } from "@macrostrat-web/settings";
-import { MapAreaContainer } from "@macrostrat/map-interface";
+import { MapAreaContainer, MapBottomControls } from "@macrostrat/map-interface";
 import classNames from "classnames";
 import { useSelector } from "react-redux";
 import { Route, Routes } from "react-router-dom";
@@ -18,6 +18,8 @@ import Searchbar from "../components/navbar";
 import MapContainer from "./map-view";
 import { MenuPage } from "./menu";
 import h from "./main.module.styl";
+import { PageAdminButton, PageAdminConsole } from "~/components";
+import MapControls from "../../../../packages/sift/src/js/components/MapControls";
 
 const ElevationChart = loadable(() => import("../components/elevation-chart"));
 const InfoDrawer = loadable(() => import("../components/info-drawer"));
@@ -79,6 +81,7 @@ function MapPage({
       detailPanel: h(InfoDrawerHolder),
       detailPanelStyle: "floating",
       bottomPanel: h(ElevationChart, null),
+      mapControls: h(MapBottomControls, [h(PageAdminButton)]),
       contextPanelOpen: contextPanelOpen || inputFocus,
       detailPanelOpen: infoDrawerOpen,
       className: classNames(