Remove external dependency from test

GMOD · Oct 21, 2024 · 00d6606 · 00d6606
1 parent 3bd302b
commit 00d6606
Show file tree

Hide file tree

Showing 8 changed files with 8 additions and 8 deletions.
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -40,6 +40,7 @@ jobs:
         working-directory: packages/jbrowse-plugin-apollo
       - name: Start apollo
         run: |
+          yarn --cwd packages/apollo-collaboration-server/test/data/ serve --listen 3131 &
           yarn --cwd packages/apollo-shared start &
           ALLOW_ROOT_USER=true ROOT_USER_NAME=admin ROOT_USER_PASSWORD=pass yarn --cwd packages/apollo-collaboration-server start &
       - name: Run CLI tests

diff --git a/.github/workflows/reload_demo_data.yml b/.github/workflows/reload_demo_data.yml
@@ -89,16 +89,14 @@ jobs:
             /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz \
             --fai /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.fai \
             --gzi /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.gzi \
-            --assembly 'Schistosoma haematobium' \
-            --not-editable
+            --assembly 'Schistosoma haematobium'
 
           apollo assembly \
             add-from-fasta \
             /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz \
             --fai /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.fai \
             --gzi /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.gzi \
-            --assembly 'Schistosoma mansoni' \
-            --not-editable
+            --assembly 'Schistosoma mansoni'
 
           apollo feature \
             import \

diff --git a/packages/apollo-cli/test/test.py b/packages/apollo-cli/test/test.py
@@ -299,10 +299,7 @@ def testAddAssemblyFromLocalFasta(self):
 
     def testAddAssemblyFromExternalFasta(self):
         p = shell(
-            f"""{apollo} assembly add-from-fasta {P} -a vv1 -f \
-                https://raw.githubusercontent.com/GMOD/Apollo3/main/packages/apollo-collaboration-server/test/data/volvox.fa \
-                -x https://raw.githubusercontent.com/GMOD/Apollo3/main/packages/apollo-collaboration-server/test/data/volvox.fa.fai
-                  """
+            f"{apollo} assembly add-from-fasta {P} -a vv1 -f http://localhost:3131/volvox.fa.gz"
         )
         out = json.loads(p.stdout)
         self.assertTrue("fa" in out["externalLocation"].keys())

diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json
@@ -109,6 +109,7 @@
     "jest": "^29.6.2",
     "mongodb": "^4.7.0",
     "rimraf": "^3.0.2",
+    "serve": "^14.0.1",
     "source-map-support": "^0.5.20",
     "supertest": "^6.1.3",
     "ts-jest": "^29.1.1",

diff --git a/packages/apollo-collaboration-server/test/data/volvox.fa.gz b/packages/apollo-collaboration-server/test/data/volvox.fa.gz
diff --git a/packages/apollo-collaboration-server/test/data/volvox.fa.gz.fai b/packages/apollo-collaboration-server/test/data/volvox.fa.gz.fai
@@ -0,0 +1,2 @@
+ctgA	50001	22	60	61
+ctgB	6079	50879	100	101
diff --git a/packages/apollo-collaboration-server/test/data/volvox.fa.gz.gzi b/packages/apollo-collaboration-server/test/data/volvox.fa.gz.gzi
diff --git a/yarn.lock b/yarn.lock
@@ -428,6 +428,7 @@ __metadata:
     rimraf: "npm:^3.0.2"
     rxjs: "npm:^7.4.0"
     sanitize-filename: "npm:^1.6.3"
+    serve: "npm:^14.0.1"
     socket.io: "npm:^4.5.3"
     source-map-support: "npm:^0.5.20"
     stream-concat: "npm:^1.0.0"