Merge branch 'main' into parentage-viewer

soybase · Jan 2, 2025 · 13ef39a · 13ef39a
2 parents 30feb64 + aefb773
commit 13ef39a
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Showing 5 changed files with 75 additions and 22 deletions.
diff --git a/.github/workflows/build-deploy.yml b/.github/workflows/build-deploy.yml
@@ -59,7 +59,7 @@ jobs:
         id: restore-cache-jbrowse
         with:
           path: ./_site/assets/js/jbrowse
-          key: jbrowse-${{ hashFiles('_data/datastore-metadata/**', '_scripts/jbrowse-tracks.sh', 'Makefile', 'assets/js/jbrowse-config.json') }}
+          key: jbrowse-${{ hashFiles('_data/datastore-metadata/**', '_config.yml', '_scripts/jbrowse-tracks.sh', '_themes/jekyll-theme-legumeinfo/_includes/analytics.html', 'Makefile', 'assets/js/jbrowse-config.json') }}
       - uses: actions/setup-node@v4
         if: steps.restore-cache-jbrowse.outputs.cache-hit != 'true'
         with:
@@ -69,13 +69,13 @@ jobs:
         run: |
           make jbrowse
           rm -rf assets/js/jbrowse/test_data
-          mv assets/js/jbrowse _site/assets/js
+          bundle exec jekyll build --profile --trace # process assets/js/jbrowse/index.html as liquid
       - uses: actions/cache/save@v4
         id: save-cache-jbrowse
         if: steps.restore-cache-jbrowse.outputs.cache-hit != 'true'
         with:
           path: ./_site/assets/js/jbrowse
-          key: jbrowse-${{ hashFiles('_data/datastore-metadata/**', '_scripts/jbrowse-tracks.sh', 'Makefile', 'assets/js/jbrowse-config.json') }}
+          key: jbrowse-${{ hashFiles('_data/datastore-metadata/**', '_config.yml', '_scripts/jbrowse-tracks.sh', '_themes/jekyll-theme-legumeinfo/_includes/analytics.html', 'Makefile', 'assets/js/jbrowse-config.json') }}
       # create artifact.tar from ./_site directory & upload as artifact named 'github-pages'
       - name: Upload Pages artifact
         uses: actions/upload-pages-artifact@v3

diff --git a/Makefile b/Makefile
@@ -50,7 +50,7 @@ else # assume dev container
   PYTHON_VENV_ACTIVATE = true # no-op
 endif
 
-JBROWSE_VERSION = 2.15.4
+JBROWSE_VERSION = 2.18.0
 PA11YCI_VERSION = 3.1.X
 
 serve: mostlyclean setup
@@ -74,9 +74,14 @@ pa11y: setup
 
 
 # JBrowse CLI will already be installed globally if using a dev container
+# Ensure JBrowse index.html is parsed by jekyll & inline GA script
 jbrowse: setup
 	if ! { command -v jbrowse || npm ls @jbrowse/cli ; } >/dev/null 2>&1; then npm install $(NPM_INSTALL_OPTIONS) @jbrowse/cli@${JBROWSE_VERSION}; fi
-	if ! [ -d ./assets/js/jbrowse ]; then npx jbrowse create assets/js/jbrowse --tag=v${JBROWSE_VERSION}; fi
+	if ! [ -d ./assets/js/jbrowse ]; then \
+      npx jbrowse create assets/js/jbrowse --tag=v${JBROWSE_VERSION}; \
+      sed -i.bak -e 's/^/---\n---\n/' -e 's/>/>\n/g' assets/js/jbrowse/index.html; \
+      sed -i.bak -e '/<\/script>/r ./_themes/jekyll-theme-legumeinfo/_includes/analytics.html' assets/js/jbrowse/index.html; \
+    fi
 	cp assets/js/jbrowse-config.json assets/js/jbrowse/config.json
 	npm exec -c '_scripts/jbrowse-tracks.sh'
 

diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ Changes made to other file types (e.g., data and config files) may only be refle
 
 
 ```sh
-make jbrowse # (optional) install JBrowse dependencies if needed
+make jbrowse # (optional; slow!) install JBrowse dependencies if needed
              # & run _scripts/jbrowse-tracks.sh to generate JBrowse config.json
 make         # install dependencies if needed & start jekyll server listening on localhost:4000
 ... CTRL-C ...

diff --git a/_scripts/jbrowse-tracks.sh b/_scripts/jbrowse-tracks.sh
@@ -48,13 +48,46 @@ do
   (
     eval $(yaml2sh ${readme})
     datastore_dir_url=${DATASTORE_URL}/$(dirname ${readme#_data/datastore-metadata/})
+    trackId=${identifier%.*}
+    assemblyNames=${identifier%.ann[0-9].*}
+    if grep -q jbrowse-index ${readme%/*}/MANIFEST.*.yml
+    then
+      config=$(printf '
+      {
+        "displays": [{"displayId":"%s","renderer":{"maxHeight":3000}}],
+        "textSearching": {
+          "textSearchAdapter": {
+            "type": "TrixTextSearchAdapter",
+            "textSearchAdapterId": "%s-index",
+            "ixFilePath": {
+              "uri": "https://data.soybase.org/jbrowse-index/trix/%s.ix",
+              "locationType": "UriLocation"
+            },
+            "ixxFilePath": {
+              "uri": "https://data.soybase.org/jbrowse-index/trix/%s.ixx",
+              "locationType": "UriLocation"
+            },
+            "metaFilePath": {
+              "uri": "https://data.soybase.org/jbrowse-index/trix/%s_meta.json",
+              "locationType": "UriLocation"
+            },
+            "assemblyNames": [
+              "%s"
+            ]
+          }
+        }
+      }' "${trackId}" "${trackId}" "${trackId}" "${trackId}" "${trackId}" "${assemblyNames}")
+    else
+      config=$(printf '{"displays":[{"displayId":"%s","renderer":{"maxHeight":3000}}]}' "${identifier%.*}")
+    fi
+
     jbrowse add-track \
       ${datastore_dir_url}/${scientific_name_abbrev}.${identifier}.gene_models_main.gff3.gz \
-      --assemblyNames=${identifier%.ann[0-9].*} \
+      --assemblyNames=${assemblyNames} \
       --category='Genes' \
-      --trackId=${identifier%.*} \
+      --trackId=${trackId} \
       --description="${synopsis}<br /><br /><b>more info:</b> ${datastore_dir_url}/" \
-      --config=$(printf '{"displays":[{"displayId":"%s","renderer":{"maxHeight":3000}}]}' "${identifier%.*}") \
+      --config="${config}" \
       --out=assets/js/jbrowse
   )
 done
@@ -64,12 +97,38 @@ do
   (
     eval $(yaml2sh ${readme})
     datastore_dir_url=${DATASTORE_URL}/$(dirname ${readme#_data/datastore-metadata/})
+    assemblyNames=${identifier%.mrk.*}
+    config=$(printf '
+    {
+      "textSearching": {
+        "textSearchAdapter": {
+          "type": "TrixTextSearchAdapter",
+          "textSearchAdapterId": "%s-index",
+          "ixFilePath": {
+            "uri": "https://data.soybase.org/jbrowse-index/trix/%s.ix",
+            "locationType": "UriLocation"
+          },
+          "ixxFilePath": {
+            "uri": "https://data.soybase.org/jbrowse-index/trix/%s.ixx",
+            "locationType": "UriLocation"
+          },
+          "metaFilePath": {
+            "uri": "https://data.soybase.org/jbrowse-index/trix/%s_meta.json",
+            "locationType": "UriLocation"
+          },
+          "assemblyNames": [
+            "%s"
+          ]
+        }
+      }
+    }' "${identifier}" "${identifier}" "${identifier}" "${identifier}" "${assemblyNames}")
     jbrowse add-track \
       ${datastore_dir_url}/${scientific_name_abbrev}.${identifier}.gff3.gz \
-      --assemblyNames=${identifier%.mrk.*} \
+      --assemblyNames=${assemblyNames} \
       --category='Markers' \
       --name=${identifier##*.} \
       --trackId=${identifier} \
+      --config="${config}" \
       --description="${synopsis}<br /><br /><b>more info:</b> ${datastore_dir_url}/" \
       --out=assets/js/jbrowse
   )
@@ -159,15 +218,3 @@ do
         --out=assets/js/jbrowse/
     done
 done
-
-
-
-
-
-
-# FIXME: too big & slow to generate for testing
-# https://github.com/GMOD/jbrowse-components/issues/3019
-#npx jbrowse text-index \
-#  --perTrack \
-#  --tracks='...' \
-#  --attributes='Name'
diff --git a/assets/js/jbrowse-config.json b/assets/js/jbrowse-config.json
@@ -1,5 +1,6 @@
 {
   "configuration": {
+      "disableAnalytics": true,
       "hierarchical": {
         "defaultCollapsed": {
           "subCategories": true