Start Apollo from existing JBrowse config

.github/workflows/deploy/httpd.conf

@@ -549,7 +549,7 @@ SSLRandomSeed startup builtin
 SSLRandomSeed connect builtin
 </IfModule>
 
-ProxyPass "/config.json" "http://apollo-collaboration-server:3999/jbrowse/config.json"
-ProxyPassReverse "/config.json" "http://apollo-collaboration-server:3999/jbrowse/config.json"
+ProxyPass "/config.json" "http://apollo-collaboration-server:3999/config.json"
+ProxyPassReverse "/config.json" "http://apollo-collaboration-server:3999/config.json"
 ProxyPassMatch "^/apollo/(.*)$" "http://apollo-collaboration-server:3999/$1" connectiontimeout=3600 timeout=3600
 ProxyPassReverse "/apollo/" "http://apollo-collaboration-server:3999/"

.github/workflows/pull_request.yml

@@ -132,11 +132,17 @@ jobs:
           cache: yarn
       - name: Install
         run: yarn --immutable
+      # Use the JBrowse build matching the @jbrowse/core version the plugin is
+      # built against
       - name: Get JBrowse
         run: |
           version=$(yarn info @jbrowse/core --json | jq -r '.children.Version')
           yarn run jbrowse create --branch "v$version" .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
+      # The server seeds its assemblies from these config files at startup
+      - name: Copy JBrowse test fixtures
+        run: yarn run copy-jbrowse-test-fixtures
+        working-directory: packages/jbrowse-plugin-apollo
       - name: Start MongoDB
         uses: supercharge/mongodb-github-action@1.12.1
         with:
@@ -260,11 +266,17 @@ jobs:
           cache: yarn
       - name: Install
         run: yarn --immutable
+      # Use the JBrowse build matching the @jbrowse/core version the plugin is
+      # built against
       - name: Get JBrowse
         run: |
           version=$(yarn info @jbrowse/core --json | jq -r '.children.Version')
           yarn run jbrowse create --branch "v$version" .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
+      # The server creates the "example" assembly from these at startup
+      - name: Copy JBrowse test fixtures
+        run: yarn run copy-jbrowse-test-fixtures
+        working-directory: packages/apollo-plugin-example
       - name: Start MongoDB
         uses: supercharge/mongodb-github-action@1.12.1
         with:
@@ -452,11 +464,35 @@ jobs:
           tags: apollo-cli:test
           cache-from: type=gha,scope=cli
           cache-to: type=gha,mode=max,scope=cli
+      # The server creates its assemblies from the JBrowse config in
+      # JBROWSE_DIR when it starts
+      - name: Make JBrowse config
+        run: |
+          mkdir docker-jbrowse
+          cp packages/apollo-collaboration-server/test/data/tiny.fasta* docker-jbrowse/
+          cat > docker-jbrowse/config.json <<'EOF'
+          {
+            "assemblies": [
+              {
+                "name": "vv1",
+                "sequence": {
+                  "adapter": {
+                    "type": "IndexedFastaAdapter",
+                    "fastaLocation": { "uri": "tiny.fasta" },
+                    "faiLocation": { "uri": "tiny.fasta.fai" }
+                  }
+                }
+              }
+            ]
+          }
+          EOF
       - name: Start MongoDB and apollo-collaboration-server
         run: |
           docker network create apollo
           docker run --detach --name mongo --network apollo mongo:8
           docker run --detach --name apollo --network apollo --publish 3999:3999 \
+            --volume "$PWD/docker-jbrowse:/data/jbrowse" \
+            --env JBROWSE_DIR=/data/jbrowse \
             --env NAME="Docker test" \
             --env URL=http://localhost:3999 \
             --env MONGODB_URI=mongodb://mongo:27017/apolloDb \
@@ -485,8 +521,9 @@ jobs:
           apollo config accessType root
           apollo config rootPassword pass
           apollo login
-          apollo assembly add-from-gff /data/tiny.fasta.gff3 --assembly vv1
           apollo assembly get --assembly vv1 | grep vv1
+          apollo feature import /data/tiny.fasta.gff3 --assembly vv1
+          apollo feature get --assembly vv1 | grep ctgA
       # The server exits with 0 when it shuts down cleanly on SIGTERM, and
       # Docker kills it (exit code 137) if it takes too long
       - name: Stop apollo-collaboration-server

.gitignore

@@ -123,6 +123,7 @@ test/data/downloaded
 test/uploaded
 test/downloaded
 packages/apollo-collaboration-server/test/uploaded
+packages/apollo-collaboration-server/test/embedded-db
 
 # Vim
 *.swp

CONTRIBUTING.md

@@ -13,7 +13,7 @@ You'll need `yarn` to be installed.
 You then have two options to start Apollo3 for development purposes. In both
 cases, the instance is then accessible via
 
-http://localhost:3000/?config=http://localhost:3999/jbrowse/config.json
+http://localhost:3000/?config=http://localhost:3999/test_data/config.json
 
 ## In a container via Visual Studio Code
 
@@ -52,9 +52,20 @@ start-mongodb:
 
 # open in browser
 open:
-    xdg-open http://localhost:3000/?config=http://localhost:3999/jbrowse/config.json
+    xdg-open http://localhost:3000/?config=http://localhost:3999/test_data/config.json
 ```
 
+### Without installing MongoDB
+
+To try things out without installing MongoDB, start the collaboration server
+with `yarn workspace @apollo-annotation/collaboration-server start:embedded-db`
+instead. This uses the `.embedded.env` configuration, which is the same as
+`.development.env` but starts an embedded MongoDB that stores its data in
+`packages/apollo-collaboration-server/test/embedded-db/`. The first start
+downloads a MongoDB binary (about 100 MB). Don't set `MONGODB_URI` in
+`.development.local.env` if you use this, since only one MongoDB option can be
+set.
+
 ## Local configuration overrides
 
 The collaboration server's development configuration lives in