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safinea-COVIDmodel 2024_2025_1_COVID #224

safinea-COVIDmodel 2024_2025_1_COVID

safinea-COVIDmodel 2024_2025_1_COVID #224

name: Validate Submissions
# Activate the validation process on pull-requests for model-output data submissions or on meta-data changes
on:
pull_request_target:
branches:
- main
paths:
- 'model-output/**'
- 'model-metadata/*'
- '!**README**'
- '!**.md'
- '!**.MD'
jobs:
validate-submission_job:
runs-on: ubuntu-latest
outputs:
changed_files: ${{ steps.get_changed_files.outputs.all_changed_files }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
PR_NUMBER: ${{ github.event.pull_request.number }}
steps:
# Setup R env
# ---------------------------------
- uses: r-lib/actions/setup-r@v2
with:
install-r: false
use-public-rspm: true
# Install hubValidations package from HubVerse
# ----------------------------------------------
- uses: r-lib/actions/setup-r-dependencies@v2
with:
packages: hubverse-org/hubValidations, any::sessioninfo
# Install System dependencies
# ---------------------------------
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install libcurl4-openssl-dev libv8-dev
# Install Pyton env and lib
# ---------------------------
- uses: actions/setup-python@v4
with:
python-version: '3.10'
- run: pip install pandas pyarrow
# checkout the repository with reference to the SHA of the HEAD
# commit of the branch that is being merged into the Base
# ------------------------------------------------------------------
- name: Checkout repository
uses: actions/checkout@v3
with:
ref: ${{ github.event.pull_request.head.sha }}
fetch-depth: 1
# Get changes from pull request for later use
# --------------------------------------------
- name: Get changes
id: get_changed_files
uses: tj-actions/changed-files@v41
# Checkout the python tools repo
# -------------------------------------------
- name: checkout python tools repo
uses: actions/checkout@v3
with:
repository: 'european-modelling-hubs/hub-tools'
ref: 'main'
path: './tools/'
# Trace changes
# ---------------------------------
- name: List all changed files
run: |
for file in ${{ steps.get_changed_files.outputs.all_changed_files }}; do
echo "$file was changed"
done
# Validate data submission
# ---------------------------------
- name: Run validations
env:
files: ${{ steps.get_changed_files.outputs.all_changed_files }}
PR_NUMBER: ${{ github.event.number }}
run: |
library("hubValidations")
v <- hubValidations::validate_pr(
gh_repo = Sys.getenv("GITHUB_REPOSITORY"),
pr_number = Sys.getenv("PR_NUMBER"),
skip_submit_window_check = FALSE,
derived_task_ids = c("target_end_date", "pop_group")
)
hubValidations::check_for_errors(v, verbose = TRUE)
shell: Rscript {0}
# Validate derived_task_ids since their validation
# is currently skipped in the validate_pr
- name: Validate derived task ids
env:
input_list: ${{ steps.get_changed_files.outputs.all_changed_files }}
run: |
python ./tools/code/validate_derived_task_ids.py
# Eventually comment on it
# ---------------------------
- name: Comment PR
uses: thollander/actions-comment-pull-request@v2
with:
message: |
All validation checks completed successfully.
pr_number: ${{ github.event.pull_request.number }}
# Approve the pull request
# ---------------------------
- name: Approve Pull Request
uses: juliangruber/[email protected]
with:
github-token: ${{ secrets.GITHUB_TOKEN }}
number: ${{ github.event.pull_request.number }}
# And then finally do the merge
# -------------------------------
- name: Merge the pull request
id: merge_pr
run: |
echo ">>> Merging PR URL: ${{ github.event.pull_request.html_url }}"
gh pr merge --auto --squash $PR_URL
env:
PR_URL: ${{ github.event.pull_request.html_url }}
GH_TOKEN: ${{ github.token }}
# As a last step, call a job that persists changes from the pull-request
# to a json db for further upload to the web-server platform
call-persisting-wf_job:
needs: validate-submission_job
uses: european-modelling-hubs/RespiCompass/.github/workflows/persist_changes.yml@main
with:
changes-list: ${{ needs.validate-submission_job.outputs.changed_files }}
secrets:
envPAT: ${{ secrets.GITHUB_TOKEN }}