YDA-5225: implement API tests in CI

.github/workflows/api-tests.yml

@@ -0,0 +1,85 @@
+name: Run API tests
+
+on:
+  push:
+    branches:
+    - development
+    - ci-api-tests
+    - yda-5225-api-tests-in-ci
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    if: ${{ ! contains(github.event.head_commit.message, '#noapitests') }}
+    steps:
+
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: Extract branch name
+      shell: bash
+      run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+      id: extract_branch
+
+    - name: Install API test dependencies
+      run: |
+        pip3 install --user -r tests/requirements.txt
+        sudo apt install -y docker-compose
+
+    - name: Clone Yoda repo for Docker Setup
+      run: |
+        git clone -b development --single-branch https://github.com/UtrechtUniversity/yoda.git
+
+    - name: Prepare hosts file for API tests
+      run: |
+        sudo echo "127.0.0.1 portal.yoda eus.yoda data.yoda public.yoda" | sudo tee -a /etc/hosts
+
+    - name: Start Dockerized Yoda
+      run: |
+        cd yoda/docker/compose
+        docker-compose pull
+        ../up.sh -d
+
+    - name: Wait until Dockerized setup is ready
+      shell: bash
+      run: |
+        until $(curl -k --output /dev/null --silent --head --fail https://portal.yoda:8443 ); do printf '.' ; sleep 1; done
+        docker exec provider.yoda sh -c 'while ! pgrep irodsServer > /dev/null  ; do echo Waiting for iRODS to start ...  ; sleep 1; done'
+
+    - name: Pull and install latest version of ruleset
+      shell: bash
+      run: |
+        cd yoda/docker/compose
+        docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo chown irods:irods -R /etc/irods/yoda-ruleset && sudo -u irods git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*" && sudo -u irods git pull && sudo -u irods git status'
+        docker exec provider.yoda sh -c "set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods git checkout ${{ steps.extract_branch.outputs.branch }} && sudo -u irods make && sudo -u irods make install"
+
+    - name: Pull and install latest version of portal
+      shell: bash
+      run: |
+        cd yoda/docker/compose
+        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git config remote.origin.fetch  "+refs/heads/*:refs/remotes/origin/*" && git pull'
+        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git checkout ${{ steps.extract_branch.outputs.branch }} || git checkout development'
+        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git status'
+        docker exec portal.yoda sh -c 'set -x ; touch /var/www/yoda/*.wsgi'
+
+    - name: Run API tests
+      shell: bash
+      run: |
+        cd tests
+        nohup bash -c 'while true ; do sleep 5 ;  ../yoda/docker/run-cronjob.sh copytovault >> ../copytovault.log 2>&1 ; ../yoda/docker/run-cronjob.sh publication >> ../publication.log 2>&1 ; done' &
+        test -d mycache || mkdir -p mycache
+        python3 -m pytest --skip-ui --intake --datarequest -o cache_dir=mycache --environment environments/docker.json
+        cat ../copytovault.log
+        cat ../publication.log
+
+# Uncomment section below when needed for debugging.
+#
+#    - name: Setup tmate session for debugging
+#      uses: mxschmitt/action-tmate@v3
+#      if: ${{ failure() }}
+#      with:
+#        limit-access-to-actor: true

tests/conftest.py

@@ -28,7 +28,10 @@
 intake = False
 archive = False
 sram = False
+skip_api = False
+skip_ui = False
 run_all = False
+verbose_test = False
 
 
 def pytest_addoption(parser):
@@ -37,8 +40,11 @@ def pytest_addoption(parser):
     parser.addoption("--intake", action="store_true", default=False, help="Run intake tests")
     parser.addoption("--archive", action="store_true", default=False, help="Run vault archive tests")
     parser.addoption("--sram", action="store_true", default=False, help="Run group SRAM tests")
+    parser.addoption("--skip-ui", action="store_true", default=False, help="Skip UI tests")
+    parser.addoption("--skip-api", action="store_true", default=False, help="Skip API tests")
     parser.addoption("--all", action="store_true", default=False, help="Run all tests")
     parser.addoption("--environment", action="store", default="environments/development.json", help="Specify configuration file")
+    parser.addoption("--verbose-test", action="store_true", default=False, help="Print additional information for troubleshooting purposes")
 
 
 def pytest_configure(config):
@@ -48,6 +54,8 @@ def pytest_configure(config):
     config.addinivalue_line("markers", "archive: Run vault archive tests")
     config.addinivalue_line("markers", "sram: Run group SRAM tests")
     config.addinivalue_line("markers", "all: Run all tests")
+    config.addinivalue_line("markers", "ui: UI test")
+    config.addinivalue_line("markers", "api: API test")
 
     global environment
     environment = config.getoption("--environment")
@@ -64,18 +72,30 @@ def pytest_configure(config):
     global roles
     roles = configuration.get("roles", {})
 
+    global verbose_test
+    verbose_test = config.getoption("--verbose-test")
+
     # Store cookies for each user.
     for role, user in roles.items():
         csrf, session = login(user["username"], user["password"])
         user_cookies[role] = (csrf, session)
 
-    global datarequest, deposit, intake, archive, sram, run_all
+    global datarequest, deposit, intake, archive, sram, run_all, skip_api, skip_ui
     datarequest = config.getoption("--datarequest")
     deposit = config.getoption("--deposit")
     intake = config.getoption("--intake")
     archive = config.getoption("--archive")
     sram = config.getoption("--sram")
+    skip_ui = config.getoption("--skip-ui")
+    skip_api = config.getoption("--skip-api")
     run_all = config.getoption("--all")
+
+    if skip_ui and run_all:
+        pytest.exit("Error: arguments --skip-ui and --all are incompatible.")
+
+    if skip_api and run_all:
+        pytest.exit("Error: arguments --skip-api and --all are incompatible.")
+
     if run_all:
         datarequest = True
         deposit = True
@@ -103,6 +123,12 @@ def pytest_bdd_apply_tag(tag, function):
         return True
     elif tag == 'sram' and not sram:
         marker = pytest.mark.skip(reason="Skip group SRAM")
+    elif tag == 'api' and skip_api:
+        marker = pytest.mark.skip(reason="Skip API tests")
+        marker(function)
+        return True
+    elif tag == "ui" and skip_ui:
+        marker = pytest.mark.skip(reason="Skip UI tests")
         marker(function)
         return True
     elif tag == "fail":
@@ -135,6 +161,8 @@ def login(user, password):
     urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
 
     url = "{}/user/login".format(portal_url)
+    if verbose_test:
+        print("Login for user {} (retrieve CSRF token) ...".format(user))
 
     client = requests.session()
 
@@ -144,6 +172,8 @@ def login(user, password):
     csrf = p.findall(content)[0]
 
     # Login as user.
+    if verbose_test:
+        print("Login for user {} (main login) ...".format(user))
     login_data = dict(csrf_token=csrf, username=user, password=password, next='/')
     response = client.post(url, data=login_data, headers=dict(Referer=url), verify=False)
     session = client.cookies['__Host-session']
@@ -155,6 +185,8 @@ def login(user, password):
     csrf = p.findall(content)[0]
 
     # Return CSRF and session cookies.
+    if verbose_test:
+        print("Login for user {} completed.".format(user))
     return csrf, session
 
 
@@ -170,6 +202,8 @@ def api_request(user, request, data, timeout=10):
     files = {'csrf_token': (None, csrf), 'data': (None, json.dumps(data))}
     cookies = {'__Host-session': session}
     headers = {'referer': portal_url}
+    if verbose_test:
+        print("Processing API request for user {} with data {}".format(user, json.dumps(data)))
     response = requests.post(url, headers=headers, files=files, cookies=cookies, verify=False, timeout=timeout)
 
     # Remove debug info from response body.
@@ -188,6 +222,8 @@ def upload_data(user, file, folder, file_content="test"):
     urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
 
     # Make POST request.
+    if verbose_test:
+        print("Processing upload for user {} with folder {} and file {}.".format(user, folder, file))
     url = portal_url + "/research/upload"
 
     files = {"csrf_token": (None, csrf),
@@ -217,6 +253,8 @@ def post_form_data(user, request, files):
     urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
 
     # Make POST request.
+    if verbose_test:
+        print("Processing form post for user {} with request {}.".format(user, request))
     url = portal_url + "/" + request
     files['csrf_token'] = (None, csrf)
     cookies = {'__Host-session': session}

tests/features/api/api_browse.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Browse API
 
     Scenario Outline: Browse folder

tests/features/api/api_datarequest.feature

@@ -1,4 +1,4 @@
-@datarequest
+@api @datarequest
 Feature: Datarequest API
 
     Scenario: Datarequest browse

tests/features/api/api_deposit_open.feature

@@ -1,4 +1,4 @@
-@deposit
+@api @deposit
 Feature: Deposit API (open)
 
     Scenario: Deposit created

tests/features/api/api_deposit_restricted.feature

@@ -1,4 +1,4 @@
-@deposit
+@api @deposit
 Feature: Deposit API (restricted)
 
     Scenario: Deposit created

tests/features/api/api_folder.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Folder API
 
     Scenario Outline: Folder lock

tests/features/api/api_group.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Group API
 
     Scenario Outline: Group data

tests/features/api/api_group_sram.feature

@@ -1,4 +1,4 @@
-@sram
+@api @sram
 Feature: Group API
 
     Scenario Outline: Group creation

tests/features/api/api_intake.feature

@@ -1,4 +1,4 @@
-@intake
+@api @intake
 Feature: Intake API
 
     Scenario Outline: Find all studies a user is involved with

tests/features/api/api_meta.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Meta API
 
     Background:

tests/features/api/api_meta_form.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Meta form API
 
     Background:

tests/features/api/api_notifications.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Notifications API
 
     Scenario Outline: Notifications load

tests/features/api/api_provenance.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Provenance API
 
     Scenario Outline: Provenance log

tests/features/api/api_research.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Research API
 
     Background:

tests/features/api/api_research_locked.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Research API (locked)
 
     Background:

tests/features/api/api_resources.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Resources API
 
     Scenario Outline: Get the paginated research groups a user is member or datamanager of

tests/features/api/api_revisions.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Revisions API
 
     Scenario Outline: Search revisions on file name

tests/features/api/api_schema.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Schema API
 
     Scenario Outline: Schema get schemas

tests/features/api/api_schema_transformations.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Schema transformations API
 
     Scenario Outline: Transformation of metadata

tests/features/api/api_search.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Search API
 
     Scenario Outline: Search file

tests/features/api/api_settings.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Settings API
 
     Scenario Outline: Settings Save

tests/features/api/api_token.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Token API
 
     Scenario Outline: Token generate

tests/features/api/api_vault.feature

@@ -1,3 +1,4 @@
+@api
 Feature: Vault API
 
     Scenario Outline: Vault meta form save in vault

tests/features/api/api_vault_archive.feature

@@ -1,4 +1,4 @@
-@archive
+@api @archive
 Feature: Vault Archive API
 
     Scenario Outline: Vault archival status

tests/features/ui/ui_browse.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Browse UI
 
     Scenario Outline: Browsing to a folder in the research space

tests/features/ui/ui_datarequest.feature

@@ -1,4 +1,4 @@
-@datarequest
+@ui @datarequest
 Feature: Datarequest UI
 
     Scenario Outline: Datarequest submit

tests/features/ui/ui_deposit.feature

@@ -1,4 +1,4 @@
-@deposit
+@ui @deposit
 Feature: Deposit UI
 
     Scenario Outline: Deposit open and restricted data package

tests/features/ui/ui_folder.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Folder UI
 
     Scenario Outline: Folder lock

tests/features/ui/ui_group.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Group UI
 
     Scenario Outline: Group member add

tests/features/ui/ui_homepage.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Homepage UI
 
     Scenario Outline: Viewing homepage logged in

tests/features/ui/ui_intake.feature

@@ -1,4 +1,4 @@
-@intake
+@ui @intake
 Feature: Intake UI
 
     @fail

tests/features/ui/ui_login.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Login UI
 
     Scenario Outline: User login flow

tests/features/ui/ui_meta.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Meta UI
 
     Background:

tests/features/ui/ui_publication.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Publication UI
 
     Scenario Outline: Publication of teclab datapackage and test landing page output

tests/features/ui/ui_research.feature

@@ -1,3 +1,4 @@
+@ui
 Feature: Research UI
 
     Background: