.travis.yml

language: python

matrix:
  include:

    # Here you can add or remove specific builds, and Python versions. You
    # should currently be able to use Python 2.6, 2.7, or 3.3 or later. The
    # NUMPY and SCIPY versions are set here as an example, but you can
    # add/remove environment variables, and use them below during the install.

    - python: 3.10

services:
  - mysql

addons:
  postgresql: "12"
  apt:
    packages:
      - postgresql-12
      - postgresql-client-12
env:
  global:
    - PGPORT=5433
    - CODECOV_TOKEN="50dd5c2e-4259-4cfa-97a7-b4429e0d179e"

before_install:

  # Increase size of database drive
  - sudo mount -o remount,size=50% /var/ramfs

  # Set up the databases - install seqrepo and UTA
  - mysql -e 'CREATE DATABASE validator;'
  - df -h

  # seqrepo needs bgzip from htslib, in ubuntu this is included in the tabix package
  - sudo apt-get -y install tabix

  ## prep psql, get and load vvta db dump
  # fix auth (taken from https://alphahydrae.com/2021/02/how-to-run-postgresql-13-on-travis-ci/)
  - sudo sed -i  -e '/local.*peer/s/postgres/all/' -e 's/peer\|md5/trust/g' /etc/postgresql/12/main/pg_hba.conf

  # Restart the PostgreSQL service:
  - sudo service postgresql@12-main restart
  - sleep 3
  - createuser -e --createdb  uta_admin

  ### for local use we probably just need to add -P to createuser and use uta_admin, but that spawns an interactive prompt
  ### also we need to test that the database works with only public permissions too, as should be for any web attached user
  - createdb -e vvta -O uta_admin
  - psql -d vvta -U postgres -c "CREATE USER ta_user WITH PASSWORD 'read_only'"
  - wget --output-document=vvta_2022_11_noseq.sql.gz  https://www528.lamp.le.ac.uk/vvdata/vvta/vvta_2022_11_noseq.sql.gz
  - gunzip -c vvta_2022_11.noseq.psql.gz | psql --quiet vvta
  - psql -d vvta -U postgres -c 'GRANT SELECT ON vvta_2022_11.gene TO public;'
  - psql -d vvta -U postgres -c 'GRANT SELECT ON ALL TABLES IN SCHEMA public TO ta_user;'

  # Access to materialzed views
  - psql -d vvta -U postgres -c 'GRANT SELECT ON vvta_2022_11.tx_def_summary_v TO ta_user;'
  - psql -d vvta -U postgres -c 'GRANT SELECT ON vvta_2022_11.tx_exon_aln_v TO ta_user;'
  - psql -d vvta -U postgres -c 'GRANT SELECT ON vvta_2022_11.transcript_lengths_v TO ta_user;'
  - psql -d vvta -U postgres -c 'GRANT SELECT ON vvta_2022_11.exon_set TO ta_user;'

  # Copy configuration file
  - cp configuration/travis.ini "$HOME"/.variantvalidator

  # Get validator database
  - wget --output-document=validator_2022_11.sql.gz https://www528.lamp.le.ac.uk/vvdata/validator/validator_2022_11.sql.gz
  - gunzip validator_2022_11.sql.gz

install:

  # Test dependencies
  - pip install -r requirements_dev.txt
  - pip install -e .

  ## get seqrepo data and load it into now installed seqrepo
  - mkdir "$HOME"/vvta_seqrepo
  - wget --output-document="$HOME"/vvta_seqrepo/VV_SR_2022_11.tar https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_2022_11.tar
  - cd "$HOME"/vvta_seqrepo/
  - tar -xvf VV_SR_2022_11.tar
  - cd -

  # Set up validator database
  - mysql validator < validator_2022_11.sql
  - rm validator_2022_11.sql

  #  - update_vdb.py
  - df -h

script:

  - pytest --cov-report=term --cov=VariantValidator/ # will run all tests in the package

after_script:
  - codecov