Merge pull request #698 from PecanProject/release/5.3.0

Release/5.3.0

Author: robkooper

.github/workflows/ci.yml

@@ -0,0 +1,81 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+    tags:
+      - '*'
+
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        ruby: 
+          - 2.4
+          - 2.5
+          - 2.6
+          # - 2.7 is not supported, results in error
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        ports: 
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/cache@v1
+        with:
+          path: vendor/bundle
+          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-gems-
+      - name: Set up Ruby ${{ matrix.ruby }}
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby }}
+      - name: Install libraries
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libgeos-dev
+      - name: Install gems
+        run: |
+          gem install bundler -v 1.17.3
+          bundle config path vendor/bundle
+          bundle config without 'javascript_testing'
+          bundle config with 'docker'
+          bundle config
+          bundle install --jobs 4 --retry 3
+      - name: Build and test with Rake
+        env:
+          RAILS_ENV: test
+        run: |
+          cp config/database.yml.gh config/database.yml
+          psql -h localhost -U postgres -c "CREATE USER bety WITH SUPERUSER CREATEDB UNENCRYPTED PASSWORD 'bety'";
+          psql -h localhost -U postgres -c "DROP DATABASE IF EXISTS test;"
+          psql -h localhost -U postgres -c "CREATE DATABASE test WITH OWNER bety;"
+          psql -h localhost -U bety -d test -c "CREATE EXTENSION postgis;"
+          #bundle exec rails db:create
+          # bundle exec rails db:migrate
+          bundle exec rake db:structure:load
+          bundle exec rake db:fixtures:load
+          mkdir -p spec/tmp
+          bundle exec rails test
+          bundle exec rspec --tag ~js
+
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build image
+        run: docker build --tag image --file Dockerfile .

.github/workflows/dbdump.yml

@@ -0,0 +1,70 @@
+name: DB Dump
+
+on:
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  sync:
+    if: github.repository == 'PecanProject/bety'
+
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        ports: 
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Database
+        run: |
+          psql -h localhost -U postgres -c "CREATE ROLE bety WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'bety'"
+          psql -h localhost -U postgres -c "CREATE DATABASE bety WITH OWNER bety"
+          psql -h localhost -U postgres -d bety -c "CREATE EXTENSION postgis;"
+
+      - name: Sync with EBI
+        run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 0 -c -w https://ebi-forecast.igb.illinois.edu/pecan/dump/bety.tar.gz
+
+      - name: Sync with BU
+        run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 1
+
+      - name: Sync with BNL
+        run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 2 -w ftp://anon:[email protected]/outgoing/betydb/bety.tar.gz
+
+      - name: Sync with Wisconsin
+        run: script/load.bety.sh -a "postgres" -p "-h localhost" -d "bety" -o bety -m 99 -r 5 -w http://tree.aos.wisc.edu:6480/sync/dump/bety.tar.gz
+
+      - name: Dump Database
+        run: pg_dump -h localhost -U postgres -F c bety > initdb/db.dump
+
+      - name: Build Docker with Database dump
+        run: |
+          cd initdb
+          docker build --tag image --file Dockerfile .
+
+      - name: Login into registry
+        run: |
+          echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+          if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then
+            echo "${{ secrets.DOCKERHUB_PASSWORD }}" | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
+          fi
+
+      - name: Push docker image
+        run: |
+          IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/db
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+          for T in $(date +'%Y-%V') 'latest'; do
+            docker tag image $IMAGE_ID:$T
+            docker push $IMAGE_ID:$T
+            if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then
+              docker tag image pecan/db:$T
+              docker push pecan/db:$T
+            fi
+          done

.github/workflows/release.yml

@@ -0,0 +1,71 @@
+name: Release
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+    tags:
+      - '*'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build image
+        run: |
+          docker build \
+          --build-arg BETY_GIT_TAGS="$(git log --pretty=format:%d -1)" \
+          --build-arg BETY_GIT_BRANCH="$(git rev-parse --abbrev-ref HEAD)" \
+          --build-arg BETY_GIT_CHECKSUM="$(git log --pretty=format:%H -1)" \
+          --build-arg BETY_GIT_DATE="$(git log --pretty=format:%ad -1)" \
+          --tag image --file Dockerfile .
+      - name: Login into registry
+        run: |
+          echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+          if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then
+            echo "${{ secrets.DOCKERHUB_PASSWORD }}" | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
+          fi
+      - name: Push image
+        run: |
+          # image all lowercase
+          IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/bety
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "master" ] && VERSION=latest
+
+          # all tags we will apply
+          TMPVERSION="${VERSION}"
+          OLDVERSION=""
+          TAGS=""
+          while [ "$OLDVERSION" != "$TMPVERSION" ]; do
+            TAGS="${TAGS} ${TMPVERSION}"
+            OLDVERSION="${TMPVERSION}"
+            TMPVERSION=$(echo ${OLDVERSION} | sed 's/\.[0-9]*$//')
+          done 
+          if [ "${TAGS}" == "" ]; then
+            TAGS="test"
+          fi
+          if [ "${TAGS}" == "master" ]; then
+            TAGS="latest"
+          fi
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+          echo TAGS=$TAGS
+
+          # push all images
+          for T in $TAGS; do
+            docker tag image $IMAGE_ID:$T
+            docker push $IMAGE_ID:$T
+            if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" -a -n "${{ secrets.DOCKERHUB_PASSWORD }}" ]; then
+              docker tag image pecan/bety:$T
+              docker push pecan/bety:$T
+            fi
+          done

.gitignore

@@ -20,5 +20,8 @@ config/initializers/site_keys.rb
 .Rproj.user
 public/assets
 
+docker-compose.override.yml
+docker-compose.override.yaml
+
 # Ignore encrypted secrets key file.
 config/secrets.yml.key

.travis.yml

@@ -5,12 +5,38 @@ section for the next release.
 
 For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
 
+## Migrations
+
+Some of the changes require a migration. Depending on how you run BETY you can use one of the following options. No matter what, make sure you have a backup of your database before you do the migration, just in case.
+
+### Native Install
+
+You will need to install the latest version of BETY (or the version you want to migrate to), and run `rake db:migrate SKIP_SCHEMASPY=YES`.
+
+### Docker (with docker compose)
+
+In this case you can simply pull down the version you want, and run `docker-compose bety migrate`.
+
 ## [Unreleased]
 
-### Fixes
+## [5.3.0] - 2020-04-15
 
+### Fixes
+- #696 : actually now uses environment variable SECRET_KEY_BASE. If this was set, unset otherwise you can not login to BETY.
+- #551 : remove GUnload message from console on page change.
 - #672 : Added activemodel-serializers-xml Gem to restore functionality of "original" API XML endpoints.
 - #674 : Upgraded comma Gem to restore CSV file downloads.
+- use actual information in database for load and dump scripts.
+- update doi links http://dx.doi.org --> https://doi.org
+- fixed functions to explicitly add public. to function call and table reference. (this will require a migration)
+- upgrade rake to 13.0.1 (dependbot fix)
+- upgrade nokogiri to 1.10.8 (dependbot fix)
+
+### Added
+- script to add new users to bety
+- dockerfile to dump database in docker image for faster restore of database.
+- switched to github actions instead of Travis
+- cronjob on github actions to create pecan/db docker image nightly, will safe also with year-weak (i.e 2020-15)
 
 ## [5.2.2] - 2019-12-06
 

CHANGELOG.md

@@ -1,7 +1,7 @@
 ## Software
 
 Scott Rohde; Carl Crott; Patrick Mulroony; Jeremy Kemball; David LeBauer; Jimmy Chen; Rob Kooper; Yilin Dong; Andrew Shirk; Zhengqi Yang; Uday Saraf; Michael Dietze. 
-2014. BETYdb 3.2.3. [doi:10.5281/zenodo.11792](http://dx.doi.org/10.5281/zenodo.11792)
+2014. BETYdb 3.2.3. [doi:10.5281/zenodo.11792](https://doi.org/10.5281/zenodo.11792)
 
 ## Data
 

CITATION

@@ -45,7 +45,7 @@ ENV LOCAL_SERVER=99 \
     INITIALIZE_URL="-w https://ebi-forecast.igb.illinois.edu/pecan/dump/all/bety.tar.gz" \
     RAILS_ENV="production" \
     RAILS_RELATIVE_URL_ROOT="" \
-    SECRET_KEY_BASE="ThisIsNotReallySuchAGreatSecret" \
+    SECRET_KEY_BASE="thisisnotasecret" \
     UNICORN_WORKER_PROCESSES="3" \
     UNICORN_PORT="8000" \
     BETY_GIT_TAGS=${BETY_GIT_TAGS} \

Dockerfile

@@ -113,14 +113,14 @@ GEM
     memoist (0.16.0)
     method_source (0.9.0)
     mini_mime (1.0.0)
-    mini_portile2 (2.3.0)
+    mini_portile2 (2.4.0)
     minitest (5.11.3)
     multi_json (1.13.1)
     mustache (1.0.5)
     narray (0.6.0.4)
     nio4r (2.3.0)
-    nokogiri (1.8.5)
-      mini_portile2 (~> 2.3.0)
+    nokogiri (1.10.8)
+      mini_portile2 (~> 2.4.0)
     passenger (5.3.4)
       rack
       rake (>= 0.8.1)
@@ -138,7 +138,7 @@ GEM
     public_suffix (3.0.2)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
-    rack (2.0.7)
+    rack (2.0.8)
     rack-test (1.0.0)
       rack (>= 1.0, < 3)
     railroad (0.5.0)
@@ -171,7 +171,7 @@ GEM
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     raindrops (0.19.0)
-    rake (12.3.1)
+    rake (13.0.1)
     rb-fsevent (0.10.3)
     rb-inotify (0.9.10)
       ffi (>= 0.5.0, < 2)