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 __init__(self, access_token):
super(Figshare, self).__init__()
self.baseurl = 'https://api.figshare.com/v2/account/articles'
self.params = {'access_token': access_token}
r = requests.get(self.baseurl, params=self.params)
if r.status_code == 200:
depositions = r.json()
remote_url = pu.get_remote_url()
for deposition in depositions:
deposition_id = deposition['id']
url = '{}/{}'.format(self.baseurl, deposition_id)
r = requests.get(url, params=self.params)
deposition = r.json()
if remote_url in deposition['references']:
self.deposition = deposition
break
elif r.status_code == 403:
pu.fail(
"The access token provided was invalid. "
"Please provide a valid access_token."
)
else:
pu.fail(
"Status {}: Could not fetch the depositions."
"Try again later.".format(r.status_code)
)
def __init__(self, access_token):
super(Zenodo, self).__init__()
self.baseurl = 'https://zenodo.org/api/deposit/depositions'
self.params = {'access_token': access_token}
r = requests.get(self.baseurl, params=self.params)
try:
depositions = r.json()
remote_url = pu.get_remote_url()
for deposition in depositions:
metadata = deposition['metadata']
try:
identifiers = metadata['related_identifiers']
if identifiers[0]['identifier'] == remote_url:
self.deposition = deposition
except KeyError:
pass
except TypeError:
if r.status_code == 401:
pu.fail(
"The access token provided was invalid. "
"Please provide a valid access_token."
)
else:
pu.fail(
"Status {}: Could not fetch the depositions."
"Try again later.".format(r.status_code)
)
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 __init__(self):
"""The __init__ method of the base class is responsible for checking
if there are no unstaged changes in the repository and fail otherwise.
The __init__ method of the derived classes should call this method
using the super function. The __init__ method of the derived class,
however, is responsible for getting the previous relevant deposition
from the service url, using the OAuth access token.
"""
self.remote_url = pu.get_remote_url()
if not self.remote_url:
pu.fail(
"Failed to fetch remote url for git repository. The "
"'archive' commands relies on having"
)
def update_metadata(self):
"""Reads required metatdata from .popper.yml and updates the
metadata for the record. This will only be called when no previous
deposition is found.
Args:
deposition_id (str): The deposition id whose metadata will
be updated
"""
deposition_id = self.deposition['id']
config = pu.read_config()['metadata']
data = {}
required_data = ['title', 'abstract', 'categories', 'keywords']
metadata_is_valid = True
for req in required_data:
if req not in config:
metadata_is_valid = False
break
if not metadata_is_valid:
pu.fail(
"Metadata is not defined properly in .popper.yml. "
"See the documentation for proper metadata format."
)
# Change abstract to description, if present
data['description'] = config['abstract']
# Collect the authors in a sorted manner
authors = []
for key in sorted(list(config.keys())):
if 'author' in key:
name, email, affiliation = map(
lambda x: x.strip(), config[key].split(',')
)
authors.append({'name': name})
if len(authors) != 0:
data['authors'] = authors
# Change the keywords to a list from string of comma separated values
data['tags'] = list(
map(lambda x: x.strip(), config['keywords'].split(','))
)
categories = []
try:
categories.append(int(config['categories']))
except ValueError:
categories = list(
map(lambda x: int(x.strip()), config['categories'].split(','))
)
data['categories'] = categories
data['references'] = [pu.get_remote_url()]
url = '{}/{}'.format(self.baseurl, deposition_id)
r = requests.put(
url, data=json.dumps(data), params=self.params
)
if r.status_code != 205:
pu.fail(
"Status {}: Failed to update metadata.".format(r.status_code)
)
def update_metadata_from_yaml(self):
"""Reads required metatdata from .popper.yml and updates the
metadata for the record. This will only be called when no previous
deposition is found.
Args:
deposition_id (str): The deposition id whose metadata will
be updated
"""
deposition_id = self.deposition['id']
config = pu.read_config()['metadata']
data = {}
required_data = ['title', 'upload_type', 'abstract', 'author1']
metadata_is_valid = True
for req in required_data:
if req not in config:
metadata_is_valid = False
break
if not metadata_is_valid:
pu.fail(
"Metadata is not defined properly in .popper.yml. "
"See the documentation for proper metadata format."
)
data['title'] = config['title']
# Change abstract to description, if present
data['description'] = '<p>' + config['abstract'] + '</p>'
# Collect the authors in a sorted manner
creators = []
for key in sorted(list(config.keys())):
if 'author' in key:
name, email, affiliation = map(
lambda x: x.strip(), config[key].split(',')
)
if len(name.split()) == 2:
name = ', '.join(name.split()[::-1])
creators.append({'name': name, 'affiliation': affiliation})
data['creators'] = creators
# Change the keywords to a list from string of comma separated values
if 'keywords' in config:
data['keywords'] = list(
map(lambda x: x.strip(), config['keywords'].split(','))
)
data['related_identifiers'] = [{
"identifier": pu.get_remote_url(),
"relation": "hasPart",
"scheme": "url"
}]
data['upload_type'] = config['upload_type']
if config['upload_type'] == 'publication':
data['publication_type'] = config['publication_type']
data = {'metadata': data}
url = '{}/{}'.format(self.baseurl, deposition_id)
r = requests.put(
url, data=json.dumps(data), params=self.params,
headers={'Content-Type': "application/json"}
)
if r.status_code != 200:
pu.fail(
"Status {}: Failed to update metadata.".format(r.status_code)
)
def init_pipeline(self, pipeline_path, stages, envs):
""" Generates a README template for the newly initialized
pipeline.
Args:
pipeline_path (str): The absolute path of the pipeline.
stages (str): Contains all the stages of the pipeline separated
by comma.
envs (list): Contains a list of the environments on which the
pipeline can be executed.
"""
pipeline_name = pipeline_path.split('/')[-1]
content = """# `{}`
<!--
NOTE TO AUTHORS: replace all the **TODO** marks with your own content.
-->
"""
content = content.format(pipeline_name)
if (len(stages)) > 0:
content += """
**TODO**: insert high-level description of the pipeline.
The pipeline consists of the following stages:
"""
for i, stage in enumerate(stages.split(',')):
content += """
* [`{0}`](./{0}.sh). **TODO**: describe `{0}` stage.
"""
content = content.format(stage)
content += """
# Obtaining the pipeline
To add this pipeline to your project using the
[`popper` CLI tool](https://github.com/systemslab/popper):
```bash
cd your-repo
popper add {0}/{1}/{2}
```
{3}
# Running the pipeline
To run the pipeline using the
[`popper` CLI tool](https://github.com/systemslab/popper):
```bash
cd {1}
popper run {2}
```
"""
url = pu.get_remote_url()
if url:
if 'https://' in url:
org = os.path.basename(os.path.dirname(url))
else:
org = url.split(':')[1]
todomark = ''
else:
org = '<org>'
todomark = '**TODO**: replace `org` appropriately.'
content = content.format(org, self.repo_name, pipeline_name, todomark)
content += """
The pipeline is executed on the following environment(s): `{}`. In addition,
the following environment variables are expected:
* `<ENV_VAR1>`. Description of variable.
* `<ENV_VAR2>`. Another description.
> **TODO**: rename or remove ENV_VAR1 and ENV_VAR2 appropiately.
For example, the following is an execution with all expected
variables:
"""
content = content.format(','.join(envs))
content += """
```bash
export <ENV_VAR1>=value-for-<ENV_VAR_1>
export <ENV_VAR2>=value-for-<ENV_VAR_2>
popper run {}
```
> **TODO**: rename or remove `export` statements above appropriately.
"""
content = content.format(pipeline_name)
content += """
# Dependencies
**TODO**: add list of dependencies, for example:
* Python.
* C++ compiler.
* [Docker](https://docker.com) (for generating plots).
* etc.
"""
self.write_readme(content, pipeline_path)