Merge pull request #6 from newgene/update-biothing-docker-image

Update ES config with heap size 1G, Update biothing studio build command

.env.example

@@ -3,3 +3,4 @@ export AWS_SECRET_KEY=
 export BIOTHINGS_REPOSITORY=https://github.com/biothings/biothings.api.git
 export BIOTHINGS_VERSION=master
 export PYTHON_VERSION=
+export ES_HEAP_SIZE=

Dockerfile

@@ -231,6 +231,7 @@ ADD ansible_playbook /tmp/ansible_playbook
 ADD inventory /etc/ansible/hosts
 
 COPY --from=build-webapp --chown=root:www-data /build/src/github.com/biothings/biothings_studio/webapp/dist /srv/www/webapp
+ARG ES_HEAP_SIZE
 
 WORKDIR /tmp/ansible_playbook
 RUN if [ -n "$API_NAME" ]; \
@@ -240,12 +241,14 @@ RUN if [ -n "$API_NAME" ]; \
             -e "studio_version=$STUDIO_VERSION" \
             -e "api_name=$API_NAME" \
             -e "api_version=$API_VERSION" \
+            -e "es_heap_size=$ES_HEAP_SIZE" \
             -c local; \
     else \
         ansible-playbook biothings_studio.yml \
             -e "biothings_version=$BIOTHINGS_VERSION" \
             -e "biothings_repository=$BIOTHINGS_REPOSITORY" \
             -e "studio_version=$STUDIO_VERSION" \
+            -e "es_heap_size=$ES_HEAP_SIZE" \
             -c local; \
 fi
 

Makefile

@@ -9,6 +9,7 @@ BIOTHINGS_VERSION ?= master
 BIOTHINGS_REPOSITORY ?= https://github.com/biothings/biothings.api.git
 DOCKER_BUILD_EXTRA_OPTS ?= --force-rm
 PYTHON_VERSION ?=
+ES_HEAP_SIZE ?=
 
 biothings-studio:
 	docker build $(DOCKER_BUILD_EXTRA_OPTS) \
@@ -75,6 +76,7 @@ demohub:
     --build-arg STUDIO_VERSION=$(STUDIO_VERSION) \
     --build-arg BIOTHINGS_VERSION=$(BIOTHINGS_VERSION) \
     --build-arg BIOTHINGS_REPOSITORY=$(BIOTHINGS_REPOSITORY) \
+    --build-arg ES_HEAP_SIZE=512m \
     --build-arg API_VERSION=master \
     --build-arg TEST=1 \
     --build-arg AWS_ACCESS_KEY=$(AWS_ACCESS_KEY) \
@@ -86,6 +88,7 @@ demohub-test:
     --build-arg STUDIO_VERSION=$(STUDIO_VERSION) \
     --build-arg BIOTHINGS_VERSION=$(BIOTHINGS_VERSION) \
     --build-arg BIOTHINGS_REPOSITORY=$(BIOTHINGS_REPOSITORY) \
+    --build-arg ES_HEAP_SIZE=512m \
     --build-arg API_VERSION=master \
     --build-arg TEST=1 \
     --build-arg PYTHON_VERSION=$(PYTHON_VERSION) \

ansible_playbook/configure.yml

@@ -110,8 +110,10 @@
 - name: mongodb data directory
   file: path="{{ software.common_configurations.mongodb.dbpath }}" state=directory owner=mongodb group=mongodb
 
+#- debug: var=software.web_node
+
 - name: biothings (override requirement_web.txt version)
-  git: repo={{ biothings_repository }} dest=/home/biothings/biothings.api version={{ software.web_node.biothings_git_version }}
+  git: repo={{ software.web_node.biothings_repository }} dest=/home/biothings/biothings.api version={{ software.web_node.biothings_git_version }}
   become_user: "biothings"
   become: true
 
@@ -177,3 +179,14 @@
     - {"line": "", "re": "^cluster.initial_master_nodes.*$"}
     - {"line": "xpack.security.enabled: false", "re": "^xpack.security.enabled.*$"}
 
+
+- name: Update /etc/elasticsearch/jvm.options.d/heap.options again replacing min/max heap size
+  when: software.web_node.elasticsearch.heap_size != ''
+  shell:
+    cmd: |
+      cat > /etc/elasticsearch/jvm.options.d/heap.options << EOF
+      -Xms{{ software.web_node.elasticsearch.heap_size }}
+      -Xmx{{ software.web_node.elasticsearch.heap_size }}
+      EOF
+  args:
+    executable: /bin/sh

ansible_playbook/vars/biothings_studio.yml

@@ -13,9 +13,9 @@ software:
       plugin:
         head: "mobz/elasticsearch-head"
         bigdesk: "lukas-vlcek/bigdesk"
-      heap_size: "2g"
+      heap_size: "{{ es_heap_size | default('')}}"
       node_roles: ['data', 'master']
-    biothings_repository: "{{ biothings_repository | default('https://github.com/biothings/biothings.api.git') }}"
+    biothings_repository: "{{ biothings_repository | default('https://github.com/biothings/biothings.api.git', true) }}"
     studio_git_version: "{{ studio_version | default('master')}}"
     biothings_git_version: "{{ biothings_version | default('master')}}"
   common_configurations: