Merge remote-tracking branch 'upstream/main'

Author: sunray1

.github/workflows/docker-publish.yml

@@ -0,0 +1,62 @@
+name: Docker Publish
+
+on:
+  push:
+    branches: [ main ]
+    tags: [ 'v*' ]
+env:
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_BEI_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/bei
+  IMAGE_NAME: portal-react-core-components
+
+jobs:
+  docker-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Google Auth
+        id: 'auth'
+        uses: 'google-github-actions/auth@v2'
+        with:
+          workload_identity_provider: "${{ vars.SHARED_WIF_PROVIDER }}"
+          service_account: "${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}"
+          token_format: 'access_token'
+  
+      - name: Docker Login
+        uses: 'docker/login-action@v3'
+        with:
+          registry: ${{ env.GCP_ARTIFACT_HOST }}
+          username: 'oauth2accesstoken'
+          password: ${{ steps.auth.outputs.access_token }}
+
+      - name: Docker Buildx Setup
+        uses: docker/setup-buildx-action@v3
+
+      - name: Docker Metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.GCP_REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value=v-latest
+            type=ref,event=tag
+            type=sha
+          flavor: |
+            latest=false
+
+      - name: Docker Build
+        uses: docker/bake-action@v6
+        env:
+          REPO: ${{ env.GCP_BEI_REGISTRY }}
+        with:
+          source: .
+          files: |
+            ./docker-bake.hcl
+            ${{ steps.meta.outputs.bake-file }}
+          push: true

bake.Dockerfile

@@ -0,0 +1,50 @@
+#-------------------------------------------------------------------------------
+# Builder container for reproducible build environment
+
+FROM portal-react-apps/node:current AS builder
+
+ENV GENERATE_SOURCEMAP=false
+ENV NODE_OPTIONS=--max_old_space_size=4096
+
+WORKDIR /app
+COPY . ./build-temp/portal-core-components
+
+WORKDIR /app/build-temp/portal-core-components
+RUN npm ci
+RUN npm run build
+RUN mv ./build /app/
+RUN rm -rf /app/build-temp
+
+#-------------------------------------------------------------------------------
+# Build production container with only necessary artifacts
+
+FROM portal-web-server-builder:current AS server-builder-parent
+FROM alpine:3.20
+
+EXPOSE 3006
+
+WORKDIR /opt/go/app
+
+COPY --from=builder /app .
+COPY --from=server-builder-parent /usr/src/app/go-web-server .
+
+# Set app wide env variables
+ENV PORTAL_PORT=3006
+ENV PORTAL_CLIENT_ROUTE="/core-components"
+
+RUN addgroup --gid 1301 portal-react \
+  && adduser -u 444 -D -G portal-react portal-react \
+  && chown -R portal-react:portal-react /opt/go/app \
+  && cd /home/portal-react \
+  && mkdir -p config/portal/apps
+
+USER portal-react
+
+ENTRYPOINT exec ./server \
+  -port=$PORTAL_PORT \
+  -app-client-route=$PORTAL_CLIENT_ROUTE \
+  -app-api-host=$REACT_APP_NEON_API_HOST \
+  -app-web-host=$REACT_APP_NEON_WEB_HOST \
+  -app-api-token=$REACT_APP_NEON_SERVICE_API_TOKEN \
+  -app-auth-silent-type=$REACT_APP_NEON_AUTH_SILENT_TYPE \
+  -app-cookie-domain=$PORTAL_SERVER_APP_COOKIE_DOMAIN

docker-bake.hcl

@@ -0,0 +1,34 @@
+variable "NODE_VERSION" {
+  default = "22.5"
+}
+
+# Populated from GitHub Action
+variable "REPO" {
+  default = ""
+}
+
+group "default" {
+  targets = [
+    "portal-core-components",
+  ]
+}
+
+# Populated from GitHub Action
+target "docker-metadata-action" {
+  tags = []
+}
+
+target "bootstrap" {
+  platforms = [ "linux/amd64" ]
+  no-cache = true
+}
+
+target "portal-core-components" {
+  inherits = ["bootstrap", "docker-metadata-action"]
+  tags = [for tag in target.docker-metadata-action.tags : tag]
+  dockerfile = "bake.Dockerfile"
+  contexts = {
+    "portal-web-server-builder:current" = "docker-image://${REPO}/portal-web-server-builder:v2.0.0"
+    "portal-react-apps/node:current" = "docker-image://node:${NODE_VERSION}-alpine"
+  }
+}

lib/components/ExternalHost/ExternalHost.js

@@ -281,7 +281,7 @@ const externalHosts = {
     id: 'BOLD',
     name: 'BOLD',
     projectTitle: 'BOLD (Barcode of Life Datasystem)',
-    url: 'http://www.barcodinglife.com/',
+    url: 'https://boldsystems.org/',
     hostType: HOST_TYPES.ADDITIONAL_DATA,
     linkType: LINK_TYPES.BY_PRODUCT,
     hostDataVariety: 'Raw sequence data',
@@ -292,7 +292,7 @@ const externalHosts = {
       }
       return externalProducts[productCode].searches.map(search => ({
         key: search.query,
-        node: renderExternalHostLink("http://www.boldsystems.org/index.php/Public_SearchTerms?query=".concat(search.query), search.title, 'BOLD', productCode)
+        node: renderExternalHostLink("https://portal.boldsystems.org/recordset/".concat(search.query), search.title, 'BOLD', productCode)
       }));
     }
   },

lib/components/NeonEnvironment/NeonEnvironment.d.ts

@@ -10,6 +10,7 @@ export declare const requiredEnvironmentVars: string[];
 export declare const optionalEnvironmentVars: string[];
 export interface NeonServerData {
     NeonPublicAPIHost: Undef<string>;
+    NeonPublicAPIHostAllowInternal: Undef<boolean>;
     NeonWebHost: Undef<string>;
     NeonPublicAPITokenHeader: Undef<string>;
     NeonPublicAPIToken: Undef<string>;

lib/components/NeonEnvironment/NeonEnvironment.js

@@ -150,12 +150,13 @@ const NeonEnvironment = {
   getNeonServerDataApiHost: () => {
     const serverData = NeonEnvironment.getNeonServerData();
     if (serverData && typeof serverData.NeonPublicAPIHost === 'string') {
+      const allowInternal = typeof serverData.NeonPublicAPIHostAllowInternal === 'boolean' ? serverData.NeonPublicAPIHostAllowInternal : false;
       const apiHost = serverData.NeonPublicAPIHost;
       try {
         const {
           hostname: apiHostname
         } = new URL(apiHost);
-        if (NeonEnvironment.isApiHostValid(apiHostname)) {
+        if (NeonEnvironment.isApiHostValid(apiHostname) || allowInternal) {
           return apiHost;
         }
       } catch (e) {

lib/components/SiteMap/SiteMapFeature.js

@@ -1436,7 +1436,7 @@ const SiteMapFeature = props => {
       }
       if (state.map.zoomedIcons[featureKey] !== null) {
         const baseIcon = state.map.zoomedIcons[featureKey];
-        const selection = isSelectable && isSelected ? _SiteMapUtils.SELECTION_STATUS.SELECTED : _SiteMapUtils.SELECTION_STATUS.UNSELECTED;
+        const selection = isSelectable && isSelected && (0, _typeUtil.exists)(baseIcon) && (0, _typeUtil.exists)(baseIcon[_SiteMapUtils.SELECTION_STATUS.SELECTED]) ? _SiteMapUtils.SELECTION_STATUS.SELECTED : _SiteMapUtils.SELECTION_STATUS.UNSELECTED;
         const initialHighlight = isHighlighted ? _SiteMapUtils.HIGHLIGHT_STATUS.HIGHLIGHT : _SiteMapUtils.HIGHLIGHT_STATUS.NONE;
         if (baseIcon && baseIcon[selection]) {
           icon = baseIcon[selection][initialHighlight];
@@ -1489,12 +1489,14 @@ const SiteMapFeature = props => {
           };
         }
       }
-      marker = /*#__PURE__*/_react.default.createElement(_reactLeaflet.Marker, _extends({
-        key: "".concat(key, "-marker"),
-        position: position,
-        title: key,
-        icon: icon
-      }, interaction), renderedPopup);
+      if ((0, _typeUtil.exists)(icon)) {
+        marker = /*#__PURE__*/_react.default.createElement(_reactLeaflet.Marker, _extends({
+          key: "".concat(key, "-marker"),
+          position: position,
+          title: key,
+          icon: icon
+        }, interaction), renderedPopup);
+      }
     }
     switch (featureShape) {
       case 'Marker':

lib/components/SiteMap/SiteMapUtils.js

@@ -9,6 +9,7 @@ var _cloneDeep = _interopRequireDefault(require("lodash/cloneDeep"));
 var _leaflet = _interopRequireDefault(require("leaflet"));
 var _Theme = require("../Theme/Theme");
 var _RouteService = _interopRequireDefault(require("../../service/RouteService"));
+var _typeUtil = require("../../util/typeUtil");
 var _iconPlaceholder = _interopRequireDefault(require("./svg/icon-placeholder.svg"));
 var _iconShapeCircleShadow = _interopRequireDefault(require("./svg/icon-shape-circle-shadow.svg"));
 var _iconShapeCircleSelect = _interopRequireDefault(require("./svg/icon-shape-circle-select.svg"));
@@ -1789,13 +1790,16 @@ const getZoomedIcon = function () {
   } = shadow[highlight] || {};
   // Adjust icon, size, and anchor if selected (and a different "selected" icon is available)
   if (featureHasIcon && selection === SELECTION_STATUS.SELECTED && feature.iconSelectedSvg) {
-    iconUrl = feature.iconSelectedSvg;
+    iconUrl = (0, _typeUtil.exists)(feature.iconSelectedSvg) ? feature.iconSelectedSvg : _iconPlaceholder.default;
     iconSize = iconSize.map(d => d + SELECTED_ICON_OFFSET);
     iconAnchor = iconAnchor.map(d => d + SELECTED_ICON_OFFSET / 2);
     shadowSize = shadowUrl ? shadowSize.map(d => d + SELECTED_ICON_OFFSET) : null;
     shadowAnchor = shadowUrl ? shadowAnchor.map(d => d + SELECTED_ICON_OFFSET / 2) : null;
     popupAnchor[1] -= SELECTED_ICON_OFFSET / 2;
   }
+  if (!(0, _typeUtil.exists)(iconUrl)) {
+    iconUrl = _iconPlaceholder.default;
+  }
   // Determine Icon Scale
   // Normalize the scale to a range of at least 0.2 to 0.5 (but as big as 0.2 to 1) based on
   // current zoom and feature zoom bounds, then multiply by any feature icon scale