Fix msg admin none #947
Workflow file for this run
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# name: Qiita CI | |
on: | |
push: | |
branches: [ dev ] | |
pull_request: | |
jobs: | |
# derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml | |
main: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
include: | |
- cover_package: "qiita_db" | |
- cover_package: "qiita_pet qiita_core qiita_ware" | |
services: | |
postgres: | |
# Docker Hub image | |
image: postgres:13.4 | |
env: | |
POSTGRES_DB: postgres | |
POSTGRES_USER: postgres | |
POSTGRES_PASSWORD: postgres | |
COVER_PACKAGE: ${{ matrix.cover_package }} | |
# Set health checks to wait until postgres has started | |
options: >- | |
--health-cmd pg_isready | |
--health-interval 10s | |
--health-timeout 5s | |
--health-retries 5 | |
ports: | |
# based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72 | |
- 5432/tcp | |
steps: | |
# Downloads a copy of the code in your repository before running CI tests | |
- name: Check out repository code | |
uses: actions/checkout@v2 | |
- name: Setup for conda | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
python-version: '3.9' | |
- name: Basic dependencies install | |
env: | |
COVER_PACKAGE: ${{ matrix.cover_package }} | |
shell: bash -l {0} | |
run: | | |
echo "Testing: " $COVER_PACKAGE | |
# pull out the port so we can modify the configuration file easily | |
pgport=${{ job.services.postgres.ports[5432] }} | |
sed -i "s/PORT = 5432/PORT = $pgport/" qiita_core/support_files/config_test.cfg | |
# PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
export PGPASSWORD=postgres | |
# Setting up main qiita conda environment | |
conda config --add channels conda-forge | |
conda deactivate | |
conda create --quiet --yes -n qiita python=3.9 pip libgfortran numpy nginx cython redis | |
conda env list | |
conda activate qiita | |
pip install -U pip | |
pip install sphinx sphinx-bootstrap-theme nose-timer Click coverage | |
# Configuring SSH | |
cp /etc/ssh/sshd_config sshd_config | |
echo "RSAAuthentication yes" > sshd_config | |
echo "PubkeyAuthentication yes" > sshd_config | |
echo "StrictModes no" > sshd_config | |
sudo mv sshd_config /etc/ssh/sshd_config | |
sudo systemctl restart ssh | |
- name: Webdis install | |
shell: bash -l {0} | |
run: | | |
sudo apt-get -y install libevent-dev | |
git clone https://github.com/nicolasff/webdis | |
cd webdis | |
make | |
- name: Main install | |
shell: bash -l {0} | |
run: | | |
conda activate qiita | |
export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
export REDBIOM_HOST="http://localhost:7379" | |
pip install . --no-binary redbiom | |
# 10.2022 | |
# this is for redbiom / biom-format (so fine to delete in the future) | |
pip install future | |
pwd | |
mkdir ~/.qiita_plugins | |
- name: Install plugins | |
shell: bash -l {0} | |
run: | | |
wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-linux-conda.yml | |
conda env create --quiet -n qtp-biom --file qiime2-2022.11-py38-linux-conda.yml | |
rm qiime2-2022.11-py38-linux-conda.yml | |
export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
export REDBIOM_HOST="http://localhost:7379" | |
conda activate qtp-biom | |
pip install -U pip | |
pip install https://github.com/qiita-spots/qiita_client/archive/master.zip | |
pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip | |
# if QIITA_ROOTCA_CERT is appended to certifi's cacert.pem file, | |
# then --server-cert does not need to be specified to any plugin, | |
# including configure_biom. | |
# echo `python -c "import certifi;print(certifi.where())"` | |
configure_biom --env-script "source /home/runner/.profile; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT | |
- name: Starting services | |
shell: bash -l {0} | |
run: | | |
conda activate qiita | |
export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
export REDBIOM_HOST="http://localhost:7379" | |
echo "1. Setting up redis" | |
redis-server --daemonize yes --port 7777 | |
redis-server --daemonize yes --port 6379 | |
echo "2. Starting webdis" | |
pushd webdis | |
./webdis & | |
popd | |
echo "3. Starting redbiom: " $REDBIOM_HOST | |
curl -s http://localhost:7379/FLUSHALL > /dev/null | |
redbiom --version | |
redbiom admin scripts-writable | |
redbiom admin create-context --name "qiita-test" --description "qiita-test context" | |
redbiom admin load-sample-metadata --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
redbiom admin load-sample-metadata-search --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test --tag 4 | |
redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table-for_redbiom_tests.biom --context qiita-test --tag 5 | |
echo "4. Setting up nginx" | |
mkdir -p /usr/share/miniconda/envs/qiita/var/run/nginx/ | |
nginx -c ${PWD}/qiita_pet/nginx_example.conf | |
echo "5. Setting up qiita" | |
conda activate qiita | |
qiita-env make --no-load-ontologies | |
qiita-test-install | |
qiita plugins update | |
echo "6. Starting supervisord => multiple qiita instances" | |
supervisord -c ${PWD}/qiita_pet/supervisor_example.conf | |
sleep 10 | |
cat /tmp/supervisord.log | |
echo "7. Starting plugins" | |
conda deactivate | |
conda activate qtp-biom | |
export QIITA_CLIENT_DEBUG_LEVEL=DEBUG | |
start_biom https://localhost:8383 register ignored | |
conda deactivate | |
echo "8. Setting up SSH" | |
ssh-keygen -t rsa -b 4096 -N '' -f $PWD/qiita_ware/test/test_data/test_key | |
mkdir ~/.ssh/ | |
cp $PWD/qiita_ware/test/test_data/test_key* ~/.ssh/ | |
cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys | |
chmod 600 $PWD/qiita_ware/test/test_data/test_key* | |
chmod 600 ~/.ssh/* | |
chmod 700 ~/.ssh/ | |
echo "Connecting as $USER@localhost" | |
# this line (and the -o StrictHostKeyChecking=no) is so the server | |
# is added to the list of known servers | |
scp -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1 | |
- name: Main tests | |
shell: bash -l {0} | |
env: | |
COVER_PACKAGE: ${{ matrix.cover_package }} | |
run: | | |
conda activate qiita | |
export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
# for testing we only need to have this set, not actually exist | |
export QIITA_JOB_SCHEDULER_EPILOGUE=`/path/to/epilogue/file` | |
export REDBIOM_HOST="http://localhost:7379" | |
nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=${COVER_PACKAGE// / --cover-package=} -e 'test_submit_EBI_parse_EBI_reply_failure' -e 'test_full_submission' | |
# killing the qiita server to run the next commands | |
QIITA_PID=`cat /tmp/supervisord.pid` | |
kill $QIITA_PID | |
sleep 10 | |
# due to qiita_db tests being more complex and taking longer than | |
# the other tests we will only add some extra tests to the run that is | |
# not testing qiita_db | |
if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then | |
# 1. testing that we can add some "dummy" studies to the db via | |
# CLI | |
test_data_studies/commands.sh; | |
# 2. making sure that all qiita cron jobs complete as expected | |
all-qiita-cron-job; | |
# 3. making sure than a production system has the expected rows | |
# in all our tables; steps: a. drop test db, b. change $QIITA_CONFIG_FP | |
# c. create new production system, c. count rows in the db. | |
qiita-env drop; | |
cp $QIITA_CONFIG_FP ${QIITA_CONFIG_FP}.bk | |
sed 's/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/g' ${QIITA_CONFIG_FP}.bk > $QIITA_CONFIG_FP; | |
qiita-env make --no-load-ontologies; | |
export PGPASSWORD=postgres | |
pgport=${{ job.services.postgres.ports[5432] }} | |
row_counts=`psql -h localhost -U postgres -d qiita_test -p $pgport -c "SELECT SUM(c.reltuples) FROM pg_class c JOIN pg_namespace n on n.oid = c.relnamespace WHERE n.nspname = 'qiita' AND c.relkind = 'r' AND n.nspname NOT IN ('information_schema', 'pg_catalog');"` | |
if [[ `echo $row_counts` != *" 0 "* ]]; then | |
echo "***********"; | |
echo "The number of rows in a production system is not what's expected:"; | |
echo $row_counts; | |
echo "***********"; | |
exit 1 | |
fi | |
fi | |
- name: Submit coveralls | |
uses: AndreMiras/coveralls-python-action@develop | |
with: | |
github-token: ${{ secrets.github_token }} | |
flag-name: "${{ matrix.cover_package }}" | |
parallel: true | |
coveralls_finish: | |
needs: main | |
runs-on: ubuntu-latest | |
steps: | |
- name: Coveralls Finished | |
uses: AndreMiras/coveralls-python-action@develop | |
with: | |
github-token: ${{ secrets.github_token }} | |
parallel-finished: true | |
lint: | |
runs-on: ubuntu-latest | |
steps: | |
- name: flake8 | |
uses: actions/setup-python@v2 | |
with: | |
python-version: '3.9' | |
- name: install dependencies | |
run: python -m pip install --upgrade pip | |
- name: Check out repository code | |
uses: actions/checkout@v2 | |
- name: lint | |
run: | | |
pip install -q flake8 | |
flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py |