Merge branch 'master' into bugfix/improve-db-sessions

Conflicts:
	datagateway_api/src/main.py
	poetry.lock

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,13 +3,13 @@ This PR will close #{issue number}
 ## Description
 Enter a description of the changes here
 
-## Testing instructions
+## Testing Instructions
 Add a set up instructions describing how the reviewer should test the code
 
 - [ ] Review code
-- [ ] Check Travis build
+- [ ] Check GitHub Actions build
 - [ ] Review changes to test coverage
 - [ ] {more steps here}
 
-## Agile board tracking
-connect to #{issue number}
+## Agile Board Tracking
+Connect to #{issue number}

.github/workflows/ci-build.yml

@@ -0,0 +1,157 @@
+name: CI
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+jobs:
+  tests:
+    runs-on: ubuntu-16.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.6', '3.7', '3.8', '3.9']
+    name: Python ${{ matrix.python-version }} Build & Tests
+    steps:
+    - name: Add apt repo
+      run: sudo add-apt-repository universe
+
+    # Setup Java & Python
+    - name: Setup Java
+      uses: actions/setup-java@v1
+      with:
+        java-version: 8
+        java-package: jdk
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: x64
+
+    # ICAT Ansible clone and install dependencies
+    - name: Checkout icat-ansible
+      uses: actions/checkout@v2
+      with:
+        repository: icatproject-contrib/icat-ansible
+        ref: change-payara-setup-script-url
+        path: icat-ansible
+    - name: Install Ansible
+      run: pip install -r icat-ansible/requirements.txt
+
+    # Prep for running the playbook
+    - name: Create hosts file
+      run: echo -e "[icatdb-minimal-hosts]\nlocalhost ansible_connection=local" > icat-ansible/hosts
+    - name: Prepare vault pass
+      run: echo -e "icattravispw" > icat-ansible/vault_pass.txt
+    - name: Move vault to directory it'll get detected by Ansible
+      run: mv icat-ansible/vault.yml icat-ansible/group_vars/all
+    - name: Replace default payara user with Actions user
+      run: |
+        sed -i -e "s/^payara_user: \"glassfish\"/payara_user: \"runner\"/" icat-ansible/group_vars/all/vars.yml
+
+    # Create local instance of ICAT
+    - name: Run ICAT Ansible Playbook
+      run: |
+        ansible-playbook icat-ansible/icatdb-minimal-hosts.yml -i icat-ansible/hosts --vault-password-file icat-ansible/vault_pass.txt -vv
+
+    - name: Checkout DataGateway API
+      uses: actions/checkout@v2
+      with:
+        path: datagateway-api
+
+    # Prep for using the API for tests
+    - name: Create log file
+      run: touch logs.log
+    - name: Configure log file location
+      run: echo "`jq -r --arg REPO_DIR "$GITHUB_WORKSPACE/logs.log" \
+        '.log_location=$REPO_DIR' datagateway-api/config.json.example`" > datagateway-api/config.json.example
+    - name: Create config.json
+      run: cp datagateway-api/config.json.example datagateway-api/config.json
+
+    # Install Nox, Poetry and API's dependencies
+    - name: Install Nox
+      run: pip install nox==2020.8.22
+    - name: Install Poetry
+      run: pip install poetry==1.1.4
+    - name: Install dependencies
+      run: cd datagateway-api/ && poetry install
+
+    - name: Add dummy data to icatdb
+      run: |
+        cd datagateway-api && poetry run python -m util.icat_db_generator -s 4 -y 3
+
+    # Run Nox tests session, saves and uploads a coverage report to codecov
+    - name: Run Nox tests session
+      run: nox -s tests -f datagateway-api/noxfile.py -- --cov=datagateway_api --cov-report=xml
+    - name: Upload code coverage report
+      if: matrix.python-version == '3.6'
+      uses: codecov/codecov-action@v1
+      with:
+        directory: ./datagateway-api
+
+  linting:
+    runs-on: ubuntu-16.04
+    name: Linting
+    steps:
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.6'
+        architecture: x64
+    - name: Checkout DataGateway API
+      uses: actions/checkout@v2
+      with:
+        path: datagateway-api
+
+    - name: Install Nox
+      run: pip install nox==2020.8.22
+    - name: Install Poetry
+      run: pip install poetry==1.1.4
+
+    - name: Run Nox lint session
+      run: nox -s lint -f datagateway-api/noxfile.py
+
+  formatting:
+    runs-on: ubuntu-16.04
+    name: Code Formatting
+    steps:
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.6'
+        architecture: x64
+    - name: Checkout DataGateway API
+      uses: actions/checkout@v2
+      with:
+        path: datagateway-api
+
+    - name: Install Nox
+      run: pip install nox==2020.8.22
+    - name: Install Poetry
+      run: pip install poetry==1.1.4
+
+    - name: Run Nox black session
+      run: nox -s black -f datagateway-api/noxfile.py
+
+  safety:
+    runs-on: ubuntu-16.04
+    name: Dependency Safety
+    steps:
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.6'
+        architecture: x64
+    - name: Checkout DataGateway API
+      uses: actions/checkout@v2
+      with:
+        path: datagateway-api
+
+    - name: Install Nox
+      run: pip install nox==2020.8.22
+    - name: Install Poetry
+      run: pip install poetry==1.1.4
+
+    - name: Run Nox safety session
+      run: nox -s safety -f datagateway-api/noxfile.py

.gitignore

@@ -7,3 +7,4 @@ config.json
 .nox/
 .python-version
 .coverage
+coverage.xml

README.md

@@ -1,3 +1,8 @@
+[![Build Status](https://github.com/ral-facilities/datagateway-api/workflows/CI/badge.svg?branch=master)](https://github.com/ral-facilities/datagateway-api/actions?query=workflow%3A%22CI%22)
+[![Codecov](https://codecov.io/gh/ral-facilities/datagateway-api/branch/master/graph/badge.svg)](https://codecov.io/gh/ral-facilities/datagateway-api)
+
+
+
 # DataGateway API
 This is a Flask-based API that fetches data from an ICAT instance, to interface with
 [DataGateway](https://github.com/ral-facilities/datagateway). This API uses two ways
@@ -90,6 +95,7 @@ version needs to be downloaded and built individually:
 pyenv install 3.6.8
 pyenv install 3.7.7
 pyenv install 3.8.2
+pyenv install 3.9.0
 ```
 
 To verify the installation commands worked:
@@ -98,6 +104,7 @@ To verify the installation commands worked:
 python3.6 --version
 python3.7 --version
 python3.8 --version
+python3.9 --version
 ```
 
 These Python versions need to be made available to local version of the repository. They
@@ -106,7 +113,7 @@ following command will create a `.python-version` file inside the repo (this fil
 currently listed in `.gitignore`):
 
 ```bash
-pyenv local 3.6.8 3.7.7 3.8.2
+pyenv local 3.6.8 3.7.7 3.8.2 3.9.0
 ```
 
 

config.json.example

@@ -1,10 +1,10 @@
 {
   "backend": "db",
-  "DB_URL": "mysql+pymysql://root:rootpw@localhost:13306/icatdb",
-  "ICAT_URL": "https://localhost.localdomain:8181",
+  "DB_URL": "mysql+pymysql://icatdbuser:icatdbuserpw@localhost:3306/icatdb",
+  "ICAT_URL": "https://localhost:8181",
   "icat_check_cert": false,
   "log_level": "WARN",
-  "log_location": "/home/user1/datagateway-api/logs.log",
+  "log_location": "/home/runner/work/datagateway-api/datagateway-api/logs.log",
   "debug_mode": false,
   "generate_swagger": false,
   "host": "127.0.0.1",

datagateway_api/common/constants.py

@@ -5,7 +5,6 @@
 
 class Constants:
     DATABASE_URL = config.get_db_url()
-    ACCEPTED_DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
     PYTHON_ICAT_DISTNCT_CONDITION = "!= null"
     ICAT_PROPERTIES = config.get_icat_properties()
     TEST_MOD_CREATE_DATETIME = datetime(2000, 1, 1)