Merge branch 'main' of https://github.com/genomehubs/goat-data into main

genomehubs · Aug 3, 2023 · ab045cf · ab045cf
2 parents d0ab2e0 + c69866a
commit ab045cf
Showing 1 changed file with 17 additions and 16 deletions.
diff --git a/.github/workflows/test_taxondir.yml b/.github/workflows/test_taxondir.yml
@@ -2,6 +2,7 @@ name: test_taxondir
 on: workflow_dispatch
 env:
   RELEASE: ${{ github.ref_name }}
+  DOCKERVERSION: develop
 
 jobs:
 
@@ -10,14 +11,14 @@ jobs:
     steps:
       - name: Get dockers
         run:  |
-          docker pull genomehubs/genomehubs:latest
+          docker pull genomehubs/genomehubs:$DOCKERVERSION
           docker run --rm genomehubs/genomehubs sh -c 'echo $CONTAINER_VERSION'
       - uses: actions/checkout@v3
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
           fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
       - name: Check es health
-        run:  curl -s "http://es1:9200/_cat/health"
+        run:  curl -s "es1:9200/_cat/health"
       - name: Delete indices for this branch/$RELEASE
         run:  |
           curl -s -X DELETE "es1:9200/*--$RELEASE"
@@ -32,21 +33,21 @@ jobs:
               "rename_pattern" : "--goat--202.*",
               "rename_replacement" : "--goat--${{ env.RELEASE }}"
               }'
-      - name: Add ES index.mapping.nested_objects.limit 100000
+      - name: Add ES index.mapping.nested_objects.limit 1000000
         run:  |
           curl -s -X PUT "es1:9200/taxon--ncbi--goat--${RELEASE}/_settings" \
             -H 'Content-Type: application/json' \
-            -d '{ "index.mapping.nested_objects.limit" : 100000 }'
+            -d '{ "index.mapping.nested_objects.limit" : 1000000 }'
       - name: update config.yaml version
         run:  |
           perl -i -plne 's/^(\s*version:) .*/$1 ${{ env.RELEASE }}/' sources/goat.yaml
       - name: genomehubs index test_taxondir
         run:  |
           docker run --rm --network=host \
             -v `pwd`/sources:/genomehubs/sources \
-            genomehubs/genomehubs:latest bash -c \
+            genomehubs/genomehubs:$DOCKERVERSION bash -c \
               "genomehubs index \
-                --es-host http://es1:9200 \
+                --es-host es1:9200 \
                 --taxonomy-source ncbi \
                 --config-file sources/goat.yaml \
                 --taxon-dir sources/test_taxondir \
@@ -55,28 +56,28 @@ jobs:
         run: |
           docker run --rm --network=host \
             -v `pwd`/sources:/genomehubs/sources \
-            genomehubs/genomehubs:latest bash -c \
+            genomehubs/genomehubs:$DOCKERVERSION bash -c \
               "genomehubs index \
-                --es-host http://es1:9200 \
+                --es-host es1:9200 \
                 --taxonomy-source ncbi \
                 --config-file sources/goat.yaml \
                 --taxon-dir sources/assembly-data-taxon"
       - name: genomehubs fill
         run: |
           docker run --rm --network=host \
             -v `pwd`/sources:/genomehubs/sources \
-            genomehubs/genomehubs:latest bash -c \
+            genomehubs/genomehubs:$DOCKERVERSION bash -c \
               "genomehubs fill \
-                --es-host http://es1:9200 \
+                --es-host es1:9200 \
                 --taxonomy-source ncbi \
                 --config-file sources/goat.yaml \
-                --traverse-root 7711 \
+                --traverse-root 2759 \
                 --traverse-infer-both"
 
       - name: restart dockers
         run: |
           mkdir -p /volumes/docker/logs/$RELEASE
-          docker pull genomehubs/genomehubs-api:latest
+          docker pull genomehubs/genomehubs-api:$DOCKERVERSION
           docker rm -f goat-api
 
           docker run -d \
@@ -86,7 +87,7 @@ jobs:
           --user $UID:$GROUPS \
           -e GH_ORIGINS="http://172.27.18.167:8010 http://172.27.18.167 null http://localhost:8010" \
           -e GH_HUBNAME=goat -e GH_HUBPATH="/genomehubs/resources/" \
-          -e GH_NODE="http://es1:9200" \
+          -e GH_NODE=http://es1:9200 \
           -e GH_RELEASE=$RELEASE \
           -e GH_SOURCE=https://github.com/genomehubs/goat-data/tree/$RELEASE \
           -e GH_ACCESS_LOG=/genomehubs/logs/access.log \
@@ -95,9 +96,9 @@ jobs:
           -v /volumes/docker/logs/$RELEASE:/genomehubs/logs \
           -v /volumes/docker/resources:/genomehubs/resources \
           --name goat-api \
-          genomehubs/genomehubs-api:latest
+          genomehubs/genomehubs-api:$DOCKERVERSION
 
-          docker pull genomehubs/goat:latest
+          docker pull genomehubs/goat:$DOCKERVERSION
           docker rm -f goat-ui
 
           docker run -d --restart always \
@@ -111,4 +112,4 @@ jobs:
           -e GH_SITENAME=GoaT \
           -e GH_ARCHIVE=latest \
           --name goat-ui \
-          genomehubs/goat:latest
+          genomehubs/goat:$DOCKERVERSION