def test_get_workflows_scope(app_client, client_auth_method, user1, user1_auth,
user2, user2_auth):
logger.debug("The first user: %r", user1['user'])
logger.debug("Number of workflows user1: %r", len(user1['workflows']))
logger.debug("The second user: %r", user2['user'])
logger.debug("Number of workflows user1: %r", len(user2['workflows']))
assert user1_auth != user2_auth, "Invalid credentials"
assert len(user1['workflows']) > len(user2['workflows'])
# get workflows registered by user1
response = app_client.get(utils.build_workflow_path(), headers=user1_auth)
assert response.status_code == 200, "Error getting workflows user 1"
user1_workflows = json.loads(response.data)['items']
logger.info(user1_workflows)
# get registered workflows by reader
response = app_client.get(utils.build_workflow_path(), headers=user2_auth)
assert response.status_code == 200, "Error getting workflows user 2"
user2_workflows = json.loads(response.data)['items']
logger.info(user2_workflows)
# when the query is performed by the registry, we get all workflows in the registry
if client_auth_method == ClientAuthenticationMethod.CLIENT_CREDENTIALS:
assert len(user2_workflows) == len(
user1_workflows), "Unexpected number of workflows"
else:
assert len(user2_workflows) == 2, "Unexpected number of workflows"
assert len(user2_workflows) < len(
user1_workflows), "Unexpected number of workflows"
def test_get_workflow_latest_version(app_client, client_auth_method, user1,
user1_auth, valid_workflow):
workflow = utils.pick_workflow(user1, valid_workflow)
wv1 = workflow.copy()
wv2 = workflow.copy()
wv1['version'] = "1"
wv2['version'] = "2"
utils.register_workflow(user1, wv1)
utils.register_workflow(user1, wv2)
response = app_client.get(utils.build_workflow_path(), headers=user1_auth)
utils.assert_status_code(200, response.status_code)
workflows = json.loads(response.data)
logger.debug("Workflows: %r", workflows)
url = f"{utils.build_workflow_path()}/{workflow['uuid']}?previous_versions=true"
logger.debug("URL: %r", url)
response = app_client.get(url, headers=user1_auth)
logger.debug(response)
utils.assert_status_code(200, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['uuid'] == workflow['uuid'], "Unexpected workflow ID"
assert data['version'][
'version'] == "2", "Unexpected workflow version number: it should the latest (=2)"
assert "previous_versions" in data, "Unable to find the versions field"
assert "1" in [_['version'] for _ in data['previous_versions']
], "Previous version not defined"
def test_workflow_registration_generic_link(app_client, client_auth_method,
user1, user1_auth,
client_credentials_registry,
valid_workflow):
logger.debug("User: %r", user1)
logger.debug("headers: %r", user1_auth)
workflow = {
'uuid': str(uuid.uuid4()),
'version': '1',
'roc_link':
"http://webserver:5000/download?file=ro-crate-galaxy-sortchangecase.crate.zip",
'name': 'Galaxy workflow from Generic Link',
'testing_service_type': 'jenkins',
'authorization': app_client.application.config['WEB_SERVER_AUTH_TOKEN']
}
logger.debug("Selected workflow: %r", workflow)
logger.debug("Using oauth2 user: %r", user1)
assert workflow['name'] is not None, "MMMMM"
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user1_auth)
logger.debug("The actual response: %r", response.data)
utils.assert_status_code(201, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['wf_uuid'] == workflow['uuid'] and data['wf_version'] == workflow['version'], \
"Response should be equal to the workflow UUID"
def test_empty_workflows(app_client, client_auth_method, user1, user1_auth):
response = app_client.get(utils.build_workflow_path(), headers=user1_auth)
utils.assert_status_code(200, response.status_code)
assert response.data, "Empty response"
data = json.loads(response.data)
logger.debug("Response %r", data)
assert len(data['items']) == 0, "Invalid number of workflows"
def test_get_workflow_version(app_client, client_auth_method, user1,
user1_auth, valid_workflow):
workflow = utils.pick_workflow(user1, valid_workflow)
wv1 = workflow.copy()
wv2 = workflow.copy()
wv1['version'] = "1"
wv2['version'] = "2"
utils.register_workflow(user1, wv1)
utils.register_workflow(user1, wv2)
response = app_client.get(utils.build_workflow_path(), headers=user1_auth)
utils.assert_status_code(response.status_code, 200)
workflows = json.loads(response.data)
logger.debug("Workflows: %r", workflows)
# Check version 1 and 2
for v_id in (1, 2):
url = f"{utils.build_workflow_path()}/{workflow['uuid']}/{v_id}"
logger.debug("URL: %r", url)
response = app_client.get(url, headers=user1_auth)
logger.debug(response)
utils.assert_status_code(response.status_code, 200)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['uuid'] == workflow['uuid'], "Unexpected workflow ID"
assert data['version'][
'version'] == f"{v_id}", "Unexpected workflow version number: it should the latest (=2)"
assert data['version']['is_latest'] is (v_id == 2), \
"It shouldn't be the latest version"
def test_workflow_registration_same_workflow_by_different_users(
app_client, client_auth_method, user1, user1_auth, user2, user2_auth,
client_credentials_registry):
original_workflow = utils.pick_workflow(user1, name='sort-and-change-case')
assert len(models.Workflow.all()) == 0, "Unexpected number of workflows"
for user, user_auth in [(user1, user1_auth), (user2, user2_auth)]:
workflow = original_workflow.copy()
logger.debug("Selected workflow: %r", workflow)
logger.debug("User: %r", user)
logger.debug("headers: %r", user_auth)
logger.debug("Using oauth2 user: %r", user)
# When the client is a registry and it uses the ClientCredentials auth flow,
# it must provide the submitter ID
if client_auth_method == ClientAuthenticationMethod.CLIENT_CREDENTIALS:
workflow['submitter_id'] = \
list(user1["user"].oauth_identity.values())[0].provider_user_id
elif client_auth_method in [
ClientAuthenticationMethod.AUTHORIZATION_CODE,
ClientAuthenticationMethod.API_KEY
]:
workflow['registry'] = client_credentials_registry.uri
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user_auth)
logger.debug("The actual response: %r", response.data)
if user == user1:
utils.assert_status_code(201, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['wf_uuid'] == workflow['uuid'] and data['wf_version'] == workflow['version'], \
"Response should be equal to the workflow UUID"
else:
utils.assert_status_code(409, response.status_code)
def test_workflow_registration_by_external_id_auto_roc_link(
app_client, client_auth_method, user1, user1_auth,
client_credentials_registry, valid_workflow):
logger.debug("User: %r", user1)
logger.debug("headers: %r", user1_auth)
workflow = utils.pick_workflow(user1, valid_workflow)
logger.debug("Selected workflow: %r", workflow)
logger.debug("Using oauth2 user: %r", user1)
# Remove the UUID and set the external identifier
workflow['identifier'] = workflow['external_id']
wf_uuid = workflow['uuid']
del workflow['uuid']
del workflow['roc_link']
# When the client is a registry and it uses the ClientCredentials auth flow,
# it must provide the submitter ID
if client_auth_method == ClientAuthenticationMethod.CLIENT_CREDENTIALS: # ClientCredentials case
workflow['submitter_id'] = \
list(user1["user"].oauth_identity.values())[0].provider_user_id
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user1_auth)
logger.debug("The actual response: %r", response.data)
utils.assert_status_code(201, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['wf_uuid'] == wf_uuid and data['wf_version'] == workflow['version'], \
"Response should be equal to the workflow UUID"
def test_delete_workflows(app_client, client_auth_method, user1, user1_auth):
workflows = WorkflowVersion.all()
assert len(workflows) > 0, "Unexpected number of workflows"
for w in [x for x in user1['workflows'] if x['name'] in [_.name for _ in workflows]]:
logger.debug("User1 Auth Headers: %r", user1_auth)
r = app_client.delete(utils.build_workflow_path(w, version_as_subpath=True), headers=user1_auth)
logger.debug("Delete Response: %r", r.data)
assert r.status_code == 204, f"Error when deleting the workflow {w}"
assert len(WorkflowVersion.all()) == 0, "Unexpected number of workflow after delete"
def test_workflow_registration_default_name(app_client, client_auth_method,
user1, user1_auth,
client_credentials_registry,
valid_workflow):
logger.debug("User: %r", user1)
logger.debug("headers: %r", user1_auth)
workflow = utils.pick_workflow(user1, valid_workflow)
logger.debug("Selected workflow: %r", workflow)
logger.debug("Using oauth2 user: %r", user1)
# When the client is a registry and it uses the ClientCredentials auth flow,
# it must provide the submitter ID
if client_auth_method == ClientAuthenticationMethod.CLIENT_CREDENTIALS:
workflow['submitter_id'] = \
list(user1["user"].oauth_identity.values())[0].provider_user_id
elif client_auth_method in [
ClientAuthenticationMethod.AUTHORIZATION_CODE,
ClientAuthenticationMethod.API_KEY
]:
workflow['registry'] = client_credentials_registry.uri
del workflow['name']
assert not hasattr(workflow,
'name'), "Name should not be defined by the user"
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user1_auth)
logger.debug("The actual response: %r", response.data)
utils.assert_status_code(201, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['wf_uuid'] == workflow['uuid'] and data['wf_version'] == workflow['version'], \
"Response should be equal to the workflow UUID"
# check name
response = app_client.get(utils.build_workflow_path(workflow),
headers=user1_auth)
utils.assert_status_code(200, response.status_code)
data = json.loads(response.data)
assert data['name'] == valid_workflow, "Invalid workflow name"
def test_workflow_registration_without_roc_link(app_client, client_auth_method,
user1, user1_auth,
client_credentials_registry,
valid_workflow):
logger.debug("User: %r", user1)
logger.debug("headers: %r", user1_auth)
workflow = utils.pick_workflow(user1, valid_workflow)
logger.debug("Selected workflow: %r", workflow)
logger.debug("Using oauth2 user: %r", user1)
del workflow['roc_link']
workflow['registry'] = workflow['registry_uri']
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user1_auth)
# if the client is not a registry client
# the roc_link MUST be provided to register the workflow
logger.debug("The actual response: %r", response.data)
utils.assert_status_code(500, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
def test_workflow_registration_by_registry_uuid(app_client, client_auth_method,
user1, user1_auth,
client_credentials_registry,
valid_workflow):
logger.debug("User: %r", user1)
logger.debug("headers: %r", user1_auth)
workflow = utils.pick_workflow(user1, valid_workflow)
logger.debug("Selected workflow: %r", workflow)
logger.debug("Using oauth2 user: %r", user1)
# Set the registry reference
workflow['registry'] = client_credentials_registry.uuid
logger.debug("The BODY: %r", workflow)
response = app_client.post(utils.build_workflow_path(),
json=workflow,
headers=user1_auth)
logger.debug("The actual response: %r", response.data)
utils.assert_status_code(201, response.status_code)
data = json.loads(response.data)
logger.debug("Response data: %r", data)
assert data['wf_uuid'] == workflow['uuid'] and data['wf_version'] == workflow['version'], \
"Response should be equal to the workflow UUID"
def test_get_workflow_not_authorized(app_client, client_auth_method, user1,
user1_auth):
workflow = utils.pick_workflow(user1)
response = app_client.get(utils.build_workflow_path(workflow))
logger.debug(response.data)
utils.assert_status_code(401, response.status_code)
