def publish_snapshot(self):
if self.deposition is None:
self.create_new_deposition()
self.update_metadata_from_yaml()
else:
if self.is_last_deposition_published():
self.create_new_version()
self.delete_previous_file()
self.update_metadata()
self.upload_new_file()
r = requests.get(self.baseurl, params=self.params)
config = pu.read_config()
try:
deposition_id = r.json()[0]['id']
except (KeyError, IndexError):
pu.fail("No previously unpublished records exist.")
url = '{}/{}/actions/publish'.format(self.baseurl, deposition_id)
r = requests.post(url, params=self.params)
if r.status_code == 202:
doi = r.json()['doi']
doi_url = r.json()['doi_url']
pu.info("Snapshot has been successfully published with DOI "
"{} and the DOI URL {}".format(doi, doi_url))
config['metadata']['zenodo_doi'] = doi
config['metadata']['zenodo_doi_url'] = doi_url
pu.write_config(config)
else:
pu.fail("Status {}: Failed to publish the record.".format(
r.status_code))
def cli(ctx, pipeline):
"""Add a pipeline to your repository from the existing popperized
repositories on github. The pipeline argument is provided as owner/repo/
pipeline. For example, popper add popperized/quiho-popper/single-node
adds the single-node pipeline from the quiho-popper repository.
"""
try:
owner, repo, pipeline_name = pipeline.split('/')
except ValueError:
pu.fail("See popper add --help for more info.")
project_root = pu.get_project_root()
path = os.path.join(project_root, 'pipelines')
if os.path.exists(path):
pass
else:
os.chdir(project_root)
os.mkdir('pipelines')
dirname = pipeline_name
url = ('https://api.github.com/repos/{}/{}/contents/pipelines/{}'
.format(owner, repo, pipeline_name))
repo_config = get_config(owner, repo)
save_directory(path, dirname, url)
path = os.path.join(path, pipeline_name)
update_config(owner, repo, pipeline_name, path, repo_config)
pu.info("Pipeline {} successfully added.".format(pipeline_name)
+ " It can be viewed in the pipelines directory.",
fg="green")
def cli(ctx):
"""Resets a popper repository completely, removing all existing
pipelines and folders, leaving behind a newly created .popper.yml file.
Note: It only removes those files inside a pipeline folder that are also
tracked by git. Untracked files will not be deleted.
"""
msg = (
"This will remove all the pipeline files in this "
" project, do you want to continue?"
)
if(not click.confirm(msg, abort=False)):
sys.exit(0)
project_root = pu.get_project_root()
if project_root != os.getcwd():
msg = 'This command can only be executed from the project root folder'
pu.fail(msg)
config = pu.read_config()
for _, p in config['pipelines'].items():
pu.exec_cmd('git rm -r {}'.format(p['path']))
pu.write_config(pu.init_config)
content = pt.ReadMe()
content.init_project()
pu.info("Reset complete", fg="cyan")
def cli(ctx, pipeline, add, rm):
"""Manipulates the environments that are associated to a pipeline. An
environment is a docker image where a pipeline runs when 'popper run' is
executed. The 'host' environment is a special case that corresponds to
the running directly on the environment where the 'popper' command runs,
i.e. running directly on the host without docker. When a new pipeline is
created using, the default environment is 'host' (see 'popper init --help'
for more).
Examples:
popper env mypipeline # show environments for pipeline
popper env mypipeline --add ubuntu-xenial,centos-7.2
popper env mypipeline --rm host
"""
config = pu.read_config()
if not add and not rm:
pu.info(str(config['pipelines'][pipeline]['envs']))
if add:
config['pipelines'][pipeline]['envs'] += add.split(',')
if rm:
for e in rm.split(','):
config['pipelines'][pipeline]['envs'].remove(e)
pu.write_config(config)
def docker_create(self, img):
env_vars = self.action.get('env', {})
for s in self.action.get('secrets', []):
env_vars.update({s: os.environ[s]})
for e, v in self.env.items():
env_vars.update({e: v})
env_vars.update({'HOME': os.environ['HOME']})
env_flags = [" -e {}='{}'".format(k, v) for k, v in env_vars.items()]
docker_cmd = 'docker create '
docker_cmd += ' --name={}'.format(self.cid)
docker_cmd += ' --volume {0}:{0}'.format(self.workspace)
docker_cmd += ' --volume {0}:{0}'.format(os.environ['HOME'])
docker_cmd += ' --volume {0}:{0}'.format('/var/run/docker.sock')
docker_cmd += ' --workdir={} '.format(self.workspace)
docker_cmd += ''.join(env_flags)
if self.action.get('runs', None):
docker_cmd += ' --entrypoint={} '.format(self.action['runs'])
docker_cmd += ' {}'.format(img)
docker_cmd += ' {}'.format(' '.join(self.action.get('args', '')))
pu.info('{}[{}] docker create {} {}\n'.format(
self.msg_prefix, self.action['name'], img,
' '.join(self.action.get('args', ''))))
pu.exec_cmd(docker_cmd, debug=self.debug, dry_run=self.dry_run)
def cli(ctx, add, rm):
"""Manipulates the metadata associated to a Popper repository. A metadata
entry is an arbitrary key-value pair. Without any options, it displays all
the existing metadata entries.
Examples:
popper metadata # show all entries
popper metadata --add author='Jane Doe' --add year=2018
popper metadata --rm author
"""
config = pu.read_config()
if not add and not rm:
pu.info(str(config['metadata']))
if add:
for kv_str in add:
kv_list = kv_str.split('=')
config['metadata'][kv_list[0]] = kv_list[1]
if rm:
for k in rm:
config['metadata'].pop(k)
pu.write_config(config)
def run(self, reuse=False):
cmd = self.action.get('runs', ['entrypoint.sh'])
cmd[0] = os.path.join('./', cmd[0])
cmd.extend(self.action.get('args', ''))
cwd = os.getcwd()
if not self.dry_run:
if 'repo_dir' in self.action:
os.chdir(self.action['repo_dir'])
else:
os.chdir(os.path.join(cwd, self.action['uses']))
os.environ.update(self.action.get('env', {}))
pu.info('{}[{}] {}\n'.format(self.msg_prefix, self.action['name'],
' '.join(cmd)))
_, ecode = pu.exec_cmd(' '.join(cmd),
verbose=(not self.quiet),
debug=self.debug,
ignore_error=True,
log_file=self.log_filename,
dry_run=self.dry_run)
for i in self.action.get('env', {}):
os.environ.pop(i)
os.chdir(cwd)
if ecode != 0:
pu.fail("\n\nAction '{}' failed.\n.".format(self.action['name']))
def cli(ctx):
"""Synchronize your pipelines and popper.yml file if any pipeline or stage
has been deleted.
"""
pipeline_dir = os.path.join(pu.get_project_root(), 'pipelines')
popper_config = pu.read_config()
pipelines = {}
for pipeline in os.listdir(pipeline_dir):
envs = popper_config['pipelines'][pipeline]['envs']
relative_path = popper_config['pipelines'][pipeline]['path']
defined_stages = popper_config['pipelines'][pipeline]['stages']
existing_stages = []
for stage in defined_stages:
os.chdir(os.path.join(pipeline_dir, pipeline))
if os.path.exists(stage+'.sh') or os.path.exists(stage):
existing_stages.append(stage)
pipelines[pipeline] = {
'envs': envs,
'path': relative_path,
'stages': existing_stages
}
popper_config['pipelines'] = pipelines
pu.write_config(popper_config)
pu.info("\nYour popper.yml file has been updated! Run git diff to see "
"the differences.", fg="white")
def cli(ctx, service, key):
"""Creates a archive of the repository on the provided service using an
access token. Reports an error if archive creation is not successful.
Currently supported services are Zenodo and Figshare.
"""
services = {'zenodo': Zenodo, 'figshare': Figshare}
environment_variables = {
'zenodo': 'POPPER_ZENODO_API_TOKEN',
'figshare': 'POPPER_FIGSHARE_API_TOKEN'
}
if service not in services:
pu.fail("The service {} is not supported. See popper archive "
"--help for more info.".format(service))
if not key:
try:
key = os.environ[environment_variables[service]]
except KeyError:
key = get_access_token(service)
archive = services[service](key)
archive.publish_snapshot()
pu.info("Done..!")
def execute(self, cmd, log_tag):
time_limit = time.time() + self.timeout
sleep_time = 0.25
log_tag = log_tag.replace(' ', '_')
out_fname = os.path.join(os.environ['WORKSPACE'], log_tag + '.out')
err_fname = os.path.join(os.environ['WORKSPACE'], log_tag + '.err')
with open(out_fname, "w") as outf, open(err_fname, "w") as errf:
p = subprocess.Popen(cmd,
stdout=outf,
stderr=errf,
shell=True,
preexec_fn=os.setsid)
while p.poll() is None:
if self.timeout != 0.0 and time.time() > time_limit:
os.killpg(os.getpgid(p.pid), signal.SIGTERM)
sys.stdout.write(' time out!')
break
if sleep_time < 300:
sleep_time *= 2
for i in range(int(sleep_time)):
if i % 10 == 0:
pu.info('.')
time.sleep(sleep_time)
pu.info('\n')
return p.poll()
def download_actions(self):
"""Clone actions that reference a repository."""
infoed = False
for _, a in self.wf['action'].items():
if 'docker://' in a['uses'] or './' in a['uses']:
continue
user = a['uses'].split('/')[0]
repo = a['uses'].split('/')[1]
if '@' in a['uses']:
action_dir = '/'.join(a['uses'].split('@')[0].split('/')[2:])
version = a['uses'].split('@')[1]
else:
action_dir = '/'.join(a['uses'].split('/')[2:])
version = None
action_dir = os.path.join('./', action_dir)
repo_parent_dir = os.path.join(self.actions_cache_path, user)
if not os.path.exists(repo_parent_dir):
os.makedirs(repo_parent_dir)
if not infoed:
pu.info('[popper] cloning actions from repositories\n')
infoed = True
scm.clone(user, repo, repo_parent_dir, version)
a['repo_dir'] = os.path.join(repo_parent_dir, repo)
a['action_dir'] = action_dir
def update_badge(status):
if pu.is_repo_empty():
pu.warn('No commit log found. Skipping badge server update.')
return
remote_url = pu.get_remote_url()
if not remote_url:
pu.warn('No remote url found. Skipping badge server update.')
return
baseurl = pu.read_config().get('badge-server-url',
'http://badges.falsifiable.us')
org, repo = remote_url.split('/')[-2:]
badge_server_url = '{}/{}/{}'.format(baseurl, org, repo)
branch_name = check_output(['git', 'rev-parse', '--abbrev-ref',
'HEAD'])[:-1]
data = {
'timestamp': int(time.time()),
'commit_id': pu.get_head_commit(),
'status': status,
'branch': branch_name,
}
try:
r = requests.post(badge_server_url, data=data)
if r.status_code != 201 and r.status_code != 200:
pu.warn("Could not create a record on the badge server.")
else:
pu.info(r.json()['message'], fg="green")
except requests.exceptions.RequestException:
pu.warn("Could not communicate with the badge server.")
def publish_snapshot(self):
if self.deposition is None:
self.create_new_deposition()
else:
if self.is_last_deposition_published():
self.create_new_version()
self.delete_previous_file()
self.upload_new_file()
self.update_metadata()
url = '{}/{}/publish'.format(
self.baseurl, self.deposition['id']
)
r = requests.post(url, params=self.params)
if r.status_code == 201:
url = r.json()['location']
r = requests.get(url, params=self.params)
doi = r.json()['doi']
doi_url = 'https://doi.org/{}'.format(doi)
pu.info(
"Snapshot has been successfully published with DOI "
"{} and the DOI URL {}".format(doi, doi_url)
)
config = pu.read_config()
config['metadata']['figshare_doi'] = doi
config['metadata']['figshare_doi_url'] = doi_url
pu.write_config(config)
else:
pu.fail(
"Status {}: Failed to publish the record."
.format(r.status_code)
)
def cli(ctx, pipeline):
"""Remove a popper pipeline from the user's repository effectively
to keep the pipelines folder and the .popper.yml files in sync.
"""
project_root = pu.get_project_root()
pipelines = pu.read_config()['pipelines']
if pipeline in pipelines:
path = pipelines[pipeline]['path']
pipeline_dir = os.path.join(
project_root,
path)
else:
pu.fail("Pipeline '{}' not in this project".format(pipeline))
if os.path.isdir(pipeline_dir):
shutil.rmtree(pipeline_dir)
popper_config = pu.read_config()
del popper_config['pipelines'][pipeline]
pu.info("Pipeline '{}' removed successfully".format(pipeline),
fg="blue")
pu.write_config(popper_config)
else:
pu.fail("Path '{}' is not a folder".format(pipeline))
def get_access_token(service, cwd):
"""Tries to read the access token from a key file. If not present,
prompts the user for a key and also stores the key in a key file
if the user wishes."""
os.chdir(cwd)
try:
with open('.{}.key'.format(service), 'r') as keyfile:
encrypted_access_token = keyfile.read().strip().encode()
passphrase = click.prompt(
'Please enter your passphrase for {}'.format(service),
hide_input=True).encode()
f = Fernet(generate_key(passphrase))
try:
access_token = f.decrypt(encrypted_access_token).decode("utf8")
except InvalidToken:
pu.fail("Invalid passphrase. Please use the same passphrase "
"used at the time of encrypting the access_token.")
except FileNotFoundError:
pu.info('No access token found for {}'.format(service))
access_token = click.prompt(
'Please enter your access token for {}'.format(service))
if click.confirm('Would you like to store this key?'):
passphrase = click.prompt('Enter a strong passphrase',
hide_input=True).encode()
f = Fernet(generate_key(passphrase))
encrypted_access_token = f.encrypt(access_token.encode())
with open('.{}.key'.format(service), 'w') as keyfile:
keyfile.writelines(encrypted_access_token.decode("utf8"))
pu.info('Your key is stored in .{}.key'.format(service))
return access_token
def run_in_docker(project_root, pipe_n, pipe_d, env, timeout, skip,
ignore_errors, output_dir, env_vars, args):
abs_path = '{}/{}'.format(project_root, pipe_d['path'])
docker_cmd = 'docker run --rm -v {0}:{0}'.format(project_root)
docker_cmd += ' --workdir={} '.format(abs_path)
docker_cmd += ' '.join(args)
docker_cmd += ''.join(
[' -e {0}="{1}"'.format(k, env_vars[k])
for k in env_vars]) if env_vars else ''
if '/' in env:
img = env
else:
img = 'falsifiable/popper:{}'.format(env)
docker_cmd += ' {} run '.format(img)
popper_flags = ' --timeout={}'.format(timeout)
popper_flags += ' --skip {}'.format(','.join(skip)) if skip else ''
popper_flags += ' --output {}'.format(output_dir)
popper_flags += ' --ignore-errors' if ignore_errors else ''
cmd = '{} {}'.format(docker_cmd, popper_flags)
pu.info('Running in Docker with: {}'.format(cmd))
check_output(cmd, shell=True)
with open(os.path.join(abs_path, output_dir, 'popper_status'), 'r') as f:
status = f.read()
return status
def cli(ctx, pipeline):
"""Remove a popper pipeline from the user's repository effectively
to keep the pipelines folder and the .popper.yml files in sync.
"""
project_root = pu.get_project_root()
if pipeline == 'paper':
pipeline_dir = project_root
else:
pipeline_dir = os.path.join(project_root, 'pipelines')
pipeline_path = os.path.join(pipeline_dir, pipeline)
if os.path.isdir(pipeline_path):
shutil.rmtree(pipeline_path)
popper_config = pu.read_config()
del popper_config['pipelines'][pipeline]
pu.info("Pipeline {} removed successfully".format(pipeline),
fg="green")
pu.write_config(popper_config)
else:
pu.fail("Pipeline {} doesn't exists".format(pipeline))
def cli(ctx, wfile, recursive):
"""
Creates a graph in the .dot format representing the workflow
"""
wfile_list = list()
if recursive:
wfile_list = pu.find_recursive_wfile()
else:
wfile_list.append(pu.find_default_wfile(wfile))
for wfile in wfile_list:
pipeline = Workflow(wfile, False, False, False, False)
graph = list()
wf = pipeline.wf
workflow_name = list(wf['workflow'].keys())[0]
action = wf['resolves'][0]
last_action = get_first_action(wf)
for act in last_action:
graph.append("\t{} -> {};\n".format(
workflow_name.replace(' ', '_').replace('-', '_'),
act.replace(' ', '_').replace('-', '_')))
parent_action = cur_action = action
graph = add(parent_action, cur_action, wf['action'], graph)
graph = ''.join(list(set(graph)))
graph = "digraph G {\n" + graph + "}\n"
pu.info(graph)
def cli(ctx):
"""Synchronize your pipelines and popper.yml file if any pipeline or stage
has been deleted.
"""
popper_config = pu.read_config()
project_root = pu.get_project_root()
pipelines = popper_config['pipelines']
# Removing nonexistent pipelines from .popper.yml
for p in list(pipelines):
pipeline = pipelines[p]
pipe_path = os.path.join(project_root, pipeline['path'])
# Checking if the pipeline exists
if os.path.exists(pipe_path):
# Synchronizing stages
stages = [
x[:-3] for x in os.listdir(pipe_path) if x.endswith(".sh")
]
pipelines[p]['stages'] = stages
else:
del pipelines[p]
popper_config['pipelines'] = pipelines
pu.write_config(popper_config)
pu.info(
"\nYour popper.yml file has been updated! Run git diff to see "
"the differences.",
fg="white")
def initialize_repo(project_root):
"""This function is used for initializing a popper repository."""
if pu.is_popperized():
pu.fail('Repository has already been popperized')
return
config = {
'metadata': {
'access_right': "open",
'license': "CC-BY-4.0",
'upload_type': "publication",
'publication_type': "article"
},
'pipelines': {},
'popperized': ["github/popperized"]
}
pu.write_config(config)
with open(os.path.join(project_root, '.gitignore'), 'a') as f:
f.write('.cache\n')
f.write('popper_logs\n')
f.write('popper_status\n')
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def get_access_token(service):
"""Tries to read the access token from a key file. If not present,
prompts the user for a key and also stores the key in a key file
if the user wishes."""
project_root = pu.get_project_root()
os.chdir(project_root)
try:
with open('.{}.key'.format(service), 'r') as keyfile:
encrypted_access_token = keyfile.read().strip()
passphrase = click.prompt(
'Please enter your passphrase for {}'.format(service),
hide_input=True).encode()
aes = pyaes.AESModeOfOperationCTR(generate_key(passphrase))
try:
access_token = aes.decrypt(encrypted_access_token).decode()
except UnicodeDecodeError:
pu.fail("Invalid passphrase. Please use the same passphrase "
"used at the time of encrypting the access_token.")
except FileNotFoundError:
pu.info('No access token found for {}'.format(service))
access_token = click.prompt(
'Please enter your access token for {}'.format(service))
if click.confirm('Would you like to store this key?'):
passphrase = click.prompt('Enter a strong passphrase',
hide_input=True).encode()
aes = pyaes.AESModeOfOperationCTR(generate_key(passphrase))
encrypted_access_token = aes.encrypt(access_token)
with open('.{}.key'.format(service), 'w') as keyfile:
keyfile.writelines('{}'.format(''.join(
chr(b) for b in encrypted_access_token)))
pu.info('Your key is stored in .{}.key'.format(service))
return access_token
def upload_snapshot(service_url, params, filename):
"""Receives the service_url and the required paramters and the filename to
be uploaded and uploads the deposit, but the deposit is not published
at this step. Returns the deposition id."""
# Create the deposit
pu.info("Uploading the snapshot...")
headers = {'Content-Type': "application/json"}
r = requests.post(service_url, params=params, json={}, headers=headers)
if r.status_code == 401:
pu.fail("Your access token is invalid. "
"Please enter a valid access token.")
deposition_id = r.json()['id']
upload_url = service_url + '/{}/files'.format(deposition_id)
files = {'file': open(filename, 'rb')}
data = {'filename': filename}
# Upload the file
r = requests.post(upload_url, data=data, files=files, params=params)
response = {'status_code': r.status_code}
if r.status_code == 201:
file_id = r.json()['id']
response['deposition_id'] = deposition_id
pu.info(
"Snapshot has been successfully uploaded. Your deposition id is "
"{} and the file id is {}.".format(deposition_id, file_id))
else:
pu.fail("Status {}: Failed to upload your snapshot. Please "
"try again.".format(r.status_code))
return deposition_id
def run_pipeline(project_root, pipeline, timeout, skip):
abs_path = os.path.join(project_root, pipeline['path'])
pu.info("Executing " + os.path.basename(abs_path), fg='blue',
bold=True, blink=True)
os.chdir(abs_path)
check_output('rm -rf popper_logs/ popper_status', shell=True)
check_output('mkdir -p popper_logs/', shell=True)
STATUS = "SUCCESS"
with click.progressbar(pipeline['stages'], show_eta=False,
label="Current stage: ", item_show_func=str,
bar_template='[%(bar)s] %(label)s %(info)s',
show_percent=False) as stages:
for stage in stages:
if os.path.isfile(stage):
stage_file = stage
elif os.path.isfile(stage + '.sh'):
stage_file = stage + '.sh'
else:
continue
if skip and stage in skip.split(','):
continue
ecode = execute(stage_file, timeout, stages)
if ecode != 0:
pu.info("Stage {} failed.".format(stage), fg='red',
bold=True, blink=True)
STATUS = "FAIL"
pu.info(".err and .out output for {}:".format(stage), fg='red')
for t in ['.err', '.out']:
logfile = 'popper_logs/{}{}'.format(stage_file, t)
with open(logfile, 'r') as f:
pu.info(f.read())
break
if 'valid' in stage:
STATUS = "GOLD"
with open('popper_logs/validate.sh.out', 'r') as f:
validate_output = f.readlines()
if len(validate_output) == 0:
STATUS = "SUCCESS"
for line in validate_output:
if '[true]' not in line:
STATUS = "SUCCESS"
with open('popper_status', 'w') as f:
f.write(STATUS + '\n')
pu.info('status : ' + STATUS, fg='green', bold=True)
sys.stdout.write('\n')
return STATUS
def initialize_repo(project_root):
if pu.is_popperized():
pu.fail('Repository has already been popperized')
with open(os.path.join(project_root, '.popper.yml'), 'w') as f:
f.write('{ metadata: { }, pipelines: { } }\n')
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def cli(ctx, service, history, inplace):
"""Generates markdown for the badge of a service. Currently available
services are: CloudLab, Chameleon, Google Cloud Engine and Popper.
"""
if history and service:
raise BadArgumentUsage("--history can't be combined with other flags.")
remote_url = pu.get_remote_url()
if not remote_url:
pu.fail("Failed to infer remote URL for git repository.")
org, repo = remote_url.split('/')[-2:]
if history:
baseurl = pu.read_config().get('badge-server-url',
'http://badges.falsifiable.us')
try:
r = requests.get('{}/{}/{}/list'.format(baseurl, org, repo))
if r.json():
pu.print_yaml(r.json())
else:
pu.info("No records to show")
except requests.exceptions.RequestException:
pu.fail("Could not communicate with the badge server")
sys.exit(0)
if not service and inplace:
raise BadArgumentUsage("--inplace must be given with --service")
if service is None:
pu.fail('Please specify a service name.')
if service not in services:
pu.fail('Unknown service {}.'.format(service))
if service == 'popper':
org, repo = remote_url.split('/')[-2:]
markup = '[]({})'.format(
services[service][0], services[service][1].format(org, repo),
services[service][2])
else:
markup = '[]({})'.format(*services[service])
if not inplace:
pu.info(markup)
sys.exit(0)
try:
os.chdir(pu.get_project_root())
with open('README.md', 'r+') as f:
content = f.read()
f.seek(0, 0)
f.write(markup + '\n\n' + content)
except IOError as e:
if e.errno == ENOENT:
pu.fail("README.md does not exist at the root of the project")
def cli(ctx, name, stages, envs, existing, infer_stages):
"""Initializes a repository or a pipeline. Without an argument, this
command initializes a popper repository. If an argument is given, a
pipeline or paper folder is initialized. If the given name is 'paper',
then a 'paper' folder is created. Otherwise, a pipeline named NAME is
created and initialized inside the 'pipelines' folder.
By default, the stages of a pipeline are: setup, run, post-run, validate
and teardown. To override these, the `--stages` flag can be provided, which
expects a comma-separated list of stage names.
The teardown stage is to be provided at the end if the --stages flag is
being used.
If the --existing flag is given, the NAME argument is treated as a path to
a folder, which is assumed to contain bash scripts. --stages must be given.
"""
# check if the the teardown stage is the last stage of the pipeline
if stages and 'teardown' in stages and stages.split(',')[-1] != 'teardown':
raise BadArgumentUsage(
'--stages = Teardown should be the last stage.' +
' Consider renaming it or putting it at the end.')
project_root = pu.get_project_root()
# init repo
if name is None:
initialize_repo(project_root)
return
if not pu.is_popperized():
pu.fail("Repository has not been popperized yet. See 'init --help'")
if isdir(os.path.join(project_root, name)) and existing:
# existing pipeline
abs_path = os.path.join(project_root, name)
relative_path = name
if infer_stages:
stages = ",".join(
map(lambda x: x[:-3], sorted(glob.glob1(abs_path, '*.sh'))))
else:
initialize_existing_pipeline(abs_path, stages, envs)
elif name == 'paper':
# create a paper pipeline
abs_path = os.path.join(project_root, 'paper')
relative_path = os.path.join('paper')
initialize_paper(abs_path, envs)
else:
# new pipeline
abs_path = os.path.join(project_root, 'pipelines', name)
relative_path = os.path.join('pipelines', name)
initialize_new_pipeline(abs_path, stages, envs)
pu.update_config(name, stages, envs, relative_path)
pu.info('Initialized pipeline ' + name, fg='blue', bold=True)
def create_archive(project_root, project_name):
"""Creates a git archive of the popperized repository and returns the
filename."""
pu.info("Creating the archive...")
os.chdir(project_root)
archive_file = project_name + '.tar.gz'
command = 'git archive master | gzip > ' + archive_file
subprocess.call(command, shell=True)
return archive_file
def docker_start(self):
pu.info('{}[{}] docker start \n'.format(self.msg_prefix,
self.action['name']))
cmd = 'docker start --attach {}'.format(self.cid)
_, ecode = pu.exec_cmd(
cmd, verbose=(not self.quiet), debug=self.debug,
log_file=self.log_filename, dry_run=self.dry_run)
return ecode
def cli(ctx, pipeline, add, rm):
"""Define or remove executions of a pipeline."""
config, pipeline_config = pu.read_config(pipeline)
if add and rm:
raise UsageError("Both add and rm cannot be given at the same time. "
"See popper env-vars --help for more information.")
if add:
env_vars = pipeline_config.get('vars', [])
vars_add = {}
for var in add:
key, val = var.split('=')
vars_add[key] = val
env_vars.append(vars_add)
pu.update_config(pipeline, vars=env_vars)
elif rm:
env_vars = pipeline_config.get('vars', None)
if not env_vars:
pu.fail("No environment variables defined for this pipeline.")
vars_del = {}
for var in rm:
key, val = var.split('=')
vars_del[key] = val
index = -1
for vars in env_vars:
if len(vars.keys()) != len(vars_del.keys()):
continue
else:
successful = True
for key in vars_del:
if vars[key] != vars_del[key]:
successful = False
if successful:
index = env_vars.index(vars)
break
if index != -1:
env_vars.pop(index)
pu.update_config(pipeline, vars=env_vars)
else:
pu.fail("The environment variable list does "
"not exist for this pipeline.")
else:
try:
env_vars = pipeline_config['vars']
if len(env_vars) == 0:
raise KeyError
pu.print_yaml(env_vars)
except KeyError:
pu.info("No environment variables defined for this pipeline.")
def cli(ctx, action, wfile, timeout, workspace):
"""Executes one or more pipelines and reports on their status.
"""
pipeline = Workflow(wfile)
pipeline.workspace = workspace
pipeline.timeout = timeout
pipeline.run(action)
if action:
pu.info('\nAction "{}" finished successfully.\n\n'.format(action))
else:
pu.info('\nWorkflow finished successfully.\n\n')
