def test_validate_config_when_is_valid_shell_selections(self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'echo "Hello, world!"',
'shell': 'bash'
})
self.assertTrue(result[0])
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'echo "Hello, world!"',
'shell': 'sh'
})
self.assertTrue(result[0])
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'echo "Hello, world!"',
'shell': 'zsh'
})
self.assertTrue(result[0])
def test_validate_config_when_is_not_valid_missing_commands(self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
})
self.assertFalse(result[0])
self.assertTrue('Missing attribute \'commands\'' in result[1])
def test_validate_config_when_is_not_valid_commands_wrong_type(self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': True
})
self.assertFalse(result[0])
self.assertTrue('Attribute \'commands\' must be a str' in result[1])
async def list_connectable_repos_by_org(owner: str, token: str, timeout: int = 15) -> List[dict]:
headers = {
"Authorization": f"token {token}",
"Accept": "application/vnd.github.mercy-preview+json" # so repo topics will be returned
}
async with httpx.AsyncClient(headers=headers, timeout=timeout) as client:
workflows = []
org_repos = await list_repositories(owner, token)
# TODO refactor to send reqs in parallel
for repository in org_repos:
branches = await list_repo_branches(owner, repository['name'], token)
for branch in branches:
response = await client.get(
f"https://raw.githubusercontent.com/{owner}/{repository['name']}/{branch['name']}/plantit.yaml",
headers={
"Authorization": f"token {token}",
"Accept": "application/vnd.github.mercy-preview+json" # so repo topics will be returned
})
if response.status_code == 404:
logger.debug(f"No plantit.yaml in {owner}/{repository['name']}/{branch['name']}")
continue
if response.status_code != 200:
logger.warning(f"Failed to retrieve plantit.yaml from {owner}/{repository['name']}/{branch['name']}")
continue
else: logger.debug(f"Found plantit.yaml in {owner}/{repository['name']}/{branch['name']}")
repository['organization'] = owner
try:
config = yaml.safe_load(response.text)
valid, errors = validate_workflow_configuration(config)
workflows.append({
'repo': repository,
'config': config,
'branch': branch,
'validation': {
'is_valid': valid,
'errors': errors
},
'example': owner == 'Computational-Plant-Science' and 'example' in repository['name'].lower()
})
except Exception:
workflows.append({
'repo': repository,
'config': {},
'branch': branch,
'validation': {
'is_valid': False,
'errors': [traceback.format_exc()]
},
'example': False
})
return workflows
def test_validate_config_when_is_valid_with_no_input_and_empty_output(
self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'echo "Hello, world!"',
'output': {}
})
self.assertTrue(result[0])
def test_validate_config_when_is_not_valid_mount_empty(self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': True,
'commands': 'echo "Hello, world!"',
'mount': [],
})
self.assertFalse(result[0])
self.assertTrue('Attribute \'mount\' must not be empty' in result[1])
def test_validate_config_when_is_not_valid_missing_name(self):
valid, errors = validate_workflow_configuration({
'author':
'Computational Plant Science Lab',
'image':
'docker://alpine',
'commands':
'echo "Hello, world!"'
})
self.assertFalse(valid)
self.assertTrue('Missing attribute \'name\'' in errors)
def test_validate_config_when_is_not_valid_missing_image(self):
result = validate_workflow_configuration({
'name':
'Test Flow',
'author':
'Computational Plant Science Lab',
'commands':
'echo "Hello, world!"'
})
self.assertFalse(result[0])
self.assertTrue('Missing attribute \'image\'' in result[1])
def test_validate_config_when_is_valid_with_no_input_path_and_empty_output(
self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'cat $INPUT',
'input': {
'kind': 'file'
},
'output': {}
})
self.assertTrue(result[0])
def test_validate_config_when_is_valid_and_input_kind_matches_path(self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'cat $INPUT',
'input': {
'path':
'/iplant/home/shared/iplantcollaborative/testing_tools/cowsay/cowsay.txt',
'kind': 'file'
},
'output': {}
})
self.assertTrue(result[0])
async def get_repo_bundle(owner: str, name: str, branch: str, github_token: str, cyverse_token: str) -> dict:
tasks = [get_repo(owner, name, github_token), get_repo_config(owner, name, github_token, branch)]
responses = await asyncio.gather(*tasks, return_exceptions=True)
repo = responses[0]
config = responses[1]
valid, errors = validate_workflow_configuration(config)
return {
'repo': repo,
'config': config,
'validation': {
'is_valid': valid,
'errors': errors
}
}
def test_validate_config_when_is_not_valid_unsupported_shell(self):
result = validate_workflow_configuration({
'name':
'Test Flow',
'author':
'Computational Plant Science Lab',
'image':
'docker://alpine',
'commands':
'echo "Hello, world!"',
'shell':
'not a supported shell'
})
self.assertFalse(result[0])
self.assertTrue(
'Attribute \'shell\' must be \'sh\', \'bash\', or \'zsh\'' in
result[1])
def test_validate_config_when_is_valid_with_input_directory_and_nonempty_output(
self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'ls "$INPUT" | tee output.txt',
'input': {
'path':
'/iplant/home/shared/iplantcollaborative/testing_tools/cowsay',
'kind': 'directory'
},
'output': {
'path': 'outputdir'
}
})
self.assertTrue(result)
def test_validate_config_when_is_valid_with_input_file_and_empty_output(
self):
result = validate_workflow_configuration({
'name': 'Test Flow',
'author': 'Computational Plant Science Lab',
'image': 'docker://alpine',
'commands': 'echo "Hello, world!"',
'input': {
'path':
'/iplant/home/shared/iplantcollaborative/testing_tools/cowsay/cowsay.txt',
'kind': 'file'
},
'output': {
'path': ''
}
})
self.assertTrue(result)
