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feat: import samples additional attributes - flash point and refractive index #4019

feat: import samples additional attributes - flash point and refractive index

feat: import samples additional attributes - flash point and refractive index #4019

Workflow file for this run

name: Continuous Integration
on:
workflow_dispatch:
pull_request:
push:
branches:
- main
jobs:
linting:
if: github.event.pull_request && (github.triggering_actor != 'dependabot[bot]')
runs-on: ubuntu-latest
env:
PRONTO_PULL_REQUEST_ID: ${{ github.event.pull_request.number }}
steps:
- name: checkout repository
uses: actions/checkout@v4
- run: |
git fetch --no-tags --prune --unshallow origin +refs/heads/*:refs/remotes/origin/*
- uses: ruby/setup-ruby@v1
with:
ruby-version: '3.3.0'
- name: install linting dependencies
run: gem install rubocop pronto pronto-rubocop rubocop-rspec rubocop-rails rubocop-performance
- name: run Pronto
run: pronto run -f github_status github_pr_review -c origin/${{ github.base_ref }}
env:
PRONTO_GITHUB_ACCESS_TOKEN: "${{ github.token }}"
if: github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name # don't run on PRs from forks because of missing write permission: https://github.com/orgs/community/discussions/26829
- name: run Pronto on fork
# We cannot use the `github_status` formatter on forks in order to report the linting status,
# since the formatter requires write access, which isn't the default on forks.
# This is why we're using the `--exit-code` flag, which causes Pronto to propagate non-zero exit codes,
# i.e., we can use the `--exit-code` flag to fail the linting job in case Pronto reports warning or errors (https://github.com/prontolabs/pronto).
run: pronto run --exit-code -f text -c origin/${{ github.base_ref }}
if: github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
testing:
needs: [linting]
if: always() && (needs.linting.result == 'success' || needs.linting.result == 'skipped') # https://github.com/actions/runner/issues/491
runs-on: ubuntu-latest
defaults:
run:
shell: bash
container: complat/chemotion_eln_runner:main
services:
postgres:
image: postgres:16 # https://hub.docker.com/_/postgres
env:
POSTGRES_PASSWORD: postgres # env variable required by postgres Docker container
POSTGRES_USER: chemotion # optional env variable used in conjunction with POSTGRES_PASSWORD to set a user and their password
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
steps:
- name: checkout repository
uses: actions/checkout@v3
- name: create user for datacollectors testing
run: |
useradd testuser -m -s /bin/bash
mkdir /home/testuser/.ssh
chown testuser:testuser /home/testuser/.ssh
chmod 700 /home/testuser/.ssh
- name: configure ssh for datacollectors testing
run: |
service ssh restart
mkdir -p $HOME/.ssh
chmod 700 $HOME/.ssh
ssh-keygen -t ed25519 -f $HOME/.ssh/id_test -N ""
# echo "$(<$HOME/.ssh/id_test.pub)" >> $HOME/.ssh/authorized_keys
echo "$(<$HOME/.ssh/id_test.pub)" | sudo tee -a /home/testuser/.ssh/authorized_keys
eval `ssh-agent`
ssh-add $HOME/.ssh/id_test
ssh-keyscan -H 127.0.0.1 >> $HOME/.ssh/known_hosts
- name: configure repository
run: |
mv public/welcome-message-sample.md public/welcome-message.md
cd config
cp database.yml.gitlab database.yml
cp -f datacollectors.yml.example datacollectors.yml
cp -f profile_default.yml.example profile_default.yml
cp -f shrine.yml.example shrine.yml
cp -f storage.yml.example storage.yml
cp -f radar.yml.example radar.yml
touch klasses.json
bundle config set without ''
- name: configure postgres
env:
PG_ROLE: chemotion_test
PG_ROLE_PASSWORD: 123456
PG_DATABASE: chemotion_test
PGPASSWORD: postgres # env variable required by psql client
run: | # host is service container name
psql -h postgres -U chemotion -c "CREATE ROLE $PG_ROLE LOGIN CREATEDB NOSUPERUSER PASSWORD '$PG_ROLE_PASSWORD';"
psql -h postgres -U chemotion -c "CREATE DATABASE $PG_DATABASE OWNER $PG_ROLE;"
psql -d postgresql://$PG_ROLE:$PG_ROLE_PASSWORD@postgres/$PG_DATABASE -c 'CREATE EXTENSION IF NOT EXISTS "pg_trgm"; CREATE EXTENSION IF NOT EXISTS "hstore"; CREATE EXTENSION IF NOT EXISTS "uuid-ossp";'
- name: bundle install
run: bundle install
- name: yarn install
run: yarn install --production=false
- name: prepare postgres
run: |
RAILS_ENV=test bundle exec rake db:migrate
RAILS_ENV=test bundle exec rake db:test:prepare
RAILS_ENV=test bundle exec rake db:seed
- name: npm test
run: npm test
- name: rspec unit
run: |
eval `ssh-agent`
ssh-add $HOME/.ssh/id_test
RAILS_ENV=test bundle exec rspec --exclude-pattern spec/{features}/**/*_spec.rb spec
- name: coverage rspec unit
if: github.event.pull_request && (github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name) && (github.triggering_actor != 'dependabot[bot]') # don't run on PRs from forks because of missing write permission: https://github.com/orgs/community/discussions/26829
uses: zgosalvez/github-actions-report-lcov@v1
with:
coverage-files: coverage/lcov/${{ github.event.repository.name }}.lcov
minimum-coverage: 57
artifact-name: code-coverage-report
github-token: ${{ secrets.GITHUB_TOKEN }}
# - name: precompile
# run: RAILS_ENV=test bundle exec rake webpacker:compile
# - name: rspec acceptance
# continue-on-error: true # don't fail job because this step; TODO: fix flaky acceptance tests...
# run: RAILS_ENV=test bundle exec rspec spec/features