_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q15200 | find_release | train | def find_release(package, releases, dependencies=None):
"""Return the best release."""
dependencies = dependencies if dependencies is not None else {}
for release in releases:
url = release['url']
old_priority = dependencies.get(package, {}).get('priority', 0)
for suffix, priority i... | python | {
"resource": ""
} |
q15201 | _safe_path | train | def _safe_path(filepath, can_be_cwl=False):
"""Check if the path should be used in output."""
# Should not be in ignore paths.
if filepath in {'.gitignore', '.gitattributes'}:
return False
# Ignore everything in .renku ...
if filepath.startswith('.renku'):
# ... unless it can be a C... | python | {
"resource": ""
} |
q15202 | tabular | train | def tabular(client, datasets):
"""Format datasets with a tabular output."""
from renku.models._tabulate import tabulate
click.echo(
tabulate(
datasets,
headers=OrderedDict((
('short_id', 'id'),
('name', None),
('created', None)... | python | {
"resource": ""
} |
q15203 | jsonld | train | def jsonld(client, datasets):
"""Format datasets as JSON-LD."""
from renku.models._json import dumps
from renku.models._jsonld import asjsonld
data = [
asjsonld(
dataset,
basedir=os.path.relpath(
'.', start=str(dataset.__reference__.parent)
)
... | python | {
"resource": ""
} |
q15204 | _format_sha1 | train | def _format_sha1(graph, node):
"""Return formatted text with the submodule information."""
try:
submodules = node.submodules
if submodules:
submodule = ':'.join(submodules)
return click.style(submodule, fg='green') + '@' + click.style(
node.commit.hexsha[... | python | {
"resource": ""
} |
q15205 | convert_arguments | train | def convert_arguments(value):
"""Convert arguments from various input formats."""
if isinstance(value, (list, tuple)):
return [
CommandLineBinding(**item) if isinstance(item, dict) else item
for item in value
]
return shlex.split(value) | python | {
"resource": ""
} |
q15206 | cli | train | def cli(ctx, path, renku_home, use_external_storage):
"""Check common Renku commands used in various situations."""
ctx.obj = LocalClient(
path=path,
renku_home=renku_home,
use_external_storage=use_external_storage,
) | python | {
"resource": ""
} |
q15207 | update | train | def update(client, revision, no_output, siblings, paths):
"""Update existing files by rerunning their outdated workflow."""
graph = Graph(client)
outputs = graph.build(revision=revision, can_be_cwl=no_output, paths=paths)
outputs = {node for node in outputs if graph.need_update(node)}
if not output... | python | {
"resource": ""
} |
q15208 | config_path | train | def config_path(path=None, final=False):
"""Return config path."""
if final and path:
return path
if path is None:
path = default_config_dir()
try:
os.makedirs(path)
except OSError as e: # pragma: no cover
if e.errno != errno.EEXIST:
raise
return os.... | python | {
"resource": ""
} |
q15209 | read_config | train | def read_config(path=None, final=False):
"""Read Renku configuration."""
try:
with open(config_path(path, final=final), 'r') as configfile:
return yaml.safe_load(configfile) or {}
except FileNotFoundError:
return {} | python | {
"resource": ""
} |
q15210 | write_config | train | def write_config(config, path, final=False):
"""Write Renku configuration."""
with open(config_path(path, final=final), 'w+') as configfile:
yaml.dump(config, configfile, default_flow_style=False) | python | {
"resource": ""
} |
q15211 | with_config | train | def with_config(f):
"""Add config to function."""
# keep it.
@click.pass_context
def new_func(ctx, *args, **kwargs):
# Invoked with custom config:
if 'config' in kwargs:
return ctx.invoke(f, *args, **kwargs)
if ctx.obj is None:
ctx.obj = {}
conf... | python | {
"resource": ""
} |
q15212 | create_project_config_path | train | def create_project_config_path(
path, mode=0o777, parents=False, exist_ok=False
):
"""Create new project configuration folder."""
# FIXME check default directory mode
project_path = Path(path).absolute().joinpath(RENKU_HOME)
project_path.mkdir(mode=mode, parents=parents, exist_ok=exist_ok)
retur... | python | {
"resource": ""
} |
q15213 | get_project_config_path | train | def get_project_config_path(path=None):
"""Return project configuration folder if exist."""
project_path = Path(path or '.').absolute().joinpath(RENKU_HOME)
if project_path.exists() and project_path.is_dir():
return str(project_path) | python | {
"resource": ""
} |
q15214 | find_project_config_path | train | def find_project_config_path(path=None):
"""Find project config path."""
path = Path(path) if path else Path.cwd()
abspath = path.absolute()
project_path = get_project_config_path(abspath)
if project_path:
return project_path
for parent in abspath.parents:
project_path = get_pr... | python | {
"resource": ""
} |
q15215 | _nodes | train | def _nodes(output, parent=None):
"""Yield nodes from entities."""
# NOTE refactor so all outputs behave the same
entity = getattr(output, 'entity', output)
if isinstance(entity, Collection):
for member in entity.members:
if parent is not None:
member = attr.evolve(me... | python | {
"resource": ""
} |
q15216 | mapped | train | def mapped(cls, key='id', **kwargs):
"""Create list of instances from a mapping."""
kwargs.setdefault('metadata', {})
kwargs['metadata']['jsonldPredicate'] = {'mapSubject': key}
kwargs.setdefault('default', attr.Factory(list))
def converter(value):
"""Convert mapping to a list of instances.... | python | {
"resource": ""
} |
q15217 | CWLClass.from_cwl | train | def from_cwl(cls, data, __reference__=None):
"""Return an instance from CWL data."""
class_name = data.get('class', None)
cls = cls.registry.get(class_name, cls)
if __reference__:
with with_reference(__reference__):
self = cls(
**{k: v
... | python | {
"resource": ""
} |
q15218 | template | train | def template(client, force):
"""Render templated configuration files."""
import pkg_resources
# create the templated files
for tpl_file in CI_TEMPLATES:
tpl_path = client.path / tpl_file
with pkg_resources.resource_stream(__name__, tpl_file) as tpl:
content = tpl.read()
... | python | {
"resource": ""
} |
q15219 | rerun | train | def rerun(client, run, job):
"""Re-run existing workflow or tool using CWL runner."""
from renku.models.provenance import ProcessRun
activity = client.process_commmit()
if not isinstance(activity, ProcessRun):
click.secho('No tool was found.', fg='red', file=sys.stderr)
return
try:... | python | {
"resource": ""
} |
q15220 | _format_default | train | def _format_default(client, value):
"""Format default values."""
if isinstance(value, File):
return os.path.relpath(
str((client.workflow_path / value.path).resolve())
)
return value | python | {
"resource": ""
} |
q15221 | show_inputs | train | def show_inputs(client, workflow):
"""Show workflow inputs and exit."""
for input_ in workflow.inputs:
click.echo(
'{id}: {default}'.format(
id=input_.id,
default=_format_default(client, input_.default),
)
)
sys.exit(0) | python | {
"resource": ""
} |
q15222 | edit_inputs | train | def edit_inputs(client, workflow):
"""Edit workflow inputs."""
types = {
'int': int,
'string': str,
'File': lambda x: File(path=Path(x).resolve()),
}
for input_ in workflow.inputs:
convert = types.get(input_.type, str)
input_.default = convert(
click.p... | python | {
"resource": ""
} |
q15223 | rerun | train | def rerun(client, revision, roots, siblings, inputs, paths):
"""Recreate files generated by a sequence of ``run`` commands."""
graph = Graph(client)
outputs = graph.build(paths=paths, revision=revision)
# Check or extend siblings of outputs.
outputs = siblings(graph, outputs)
output_paths = {no... | python | {
"resource": ""
} |
q15224 | datasets | train | def datasets(ctx, client):
"""Migrate dataset metadata."""
from renku.models._jsonld import asjsonld
from renku.models.datasets import Dataset
from renku.models.refs import LinkReference
from ._checks.location_datasets import _dataset_metadata_pre_0_3_4
for old_path in _dataset_metadata_pre_0_... | python | {
"resource": ""
} |
q15225 | detect_registry_url | train | def detect_registry_url(client, auto_login=True):
"""Return a URL of the Docker registry."""
repo = client.repo
config = repo.config_reader()
# Find registry URL in .git/config
remote_url = None
try:
registry_url = config.get_value('renku', 'registry', None)
except NoSectionError:
... | python | {
"resource": ""
} |
q15226 | JSONEncoder.default | train | def default(self, obj):
"""Encode more types."""
if isinstance(obj, UUID):
return obj.hex
elif isinstance(obj, datetime.datetime):
return obj.isoformat()
return super().default(obj) | python | {
"resource": ""
} |
q15227 | run | train | def run(client, outputs, no_output, success_codes, isolation, command_line):
"""Tracking work on a specific problem."""
working_dir = client.repo.working_dir
mapped_std = _mapped_std_streams(client.candidate_paths)
factory = CommandLineToolFactory(
command_line=command_line,
directory=os... | python | {
"resource": ""
} |
q15228 | log | train | def log(client, revision, format, no_output, paths):
"""Show logs for a file."""
graph = Graph(client)
if not paths:
start, is_range, stop = revision.partition('..')
if not is_range:
stop = start
elif not stop:
stop = 'HEAD'
commit = client.repo.rev_p... | python | {
"resource": ""
} |
q15229 | status | train | def status(ctx, client, revision, no_output, path):
"""Show a status of the repository."""
graph = Graph(client)
# TODO filter only paths = {graph.normalize_path(p) for p in path}
status = graph.build_status(revision=revision, can_be_cwl=no_output)
click.echo('On branch {0}'.format(client.repo.acti... | python | {
"resource": ""
} |
q15230 | validate_name | train | def validate_name(ctx, param, value):
"""Validate a project name."""
if not value:
value = os.path.basename(ctx.params['directory'].rstrip(os.path.sep))
return value | python | {
"resource": ""
} |
q15231 | store_directory | train | def store_directory(ctx, param, value):
"""Store directory as a new Git home."""
Path(value).mkdir(parents=True, exist_ok=True)
set_git_home(value)
return value | python | {
"resource": ""
} |
q15232 | init | train | def init(ctx, client, directory, name, force, use_external_storage):
"""Initialize a project."""
if not client.use_external_storage:
use_external_storage = False
ctx.obj = client = attr.evolve(
client,
path=directory,
use_external_storage=use_external_storage,
)
msg... | python | {
"resource": ""
} |
q15233 | check_missing_files | train | def check_missing_files(client):
"""Find missing files listed in datasets."""
missing = defaultdict(list)
for path, dataset in client.datasets.items():
for file in dataset.files:
filepath = (path.parent / file)
if not filepath.exists():
missing[str(
... | python | {
"resource": ""
} |
q15234 | APIError.from_http_exception | train | def from_http_exception(cls, e):
"""Create ``APIError`` from ``requests.exception.HTTPError``."""
assert isinstance(e, requests.exceptions.HTTPError)
response = e.response
try:
message = response.json()['message']
except (KeyError, ValueError):
message = r... | python | {
"resource": ""
} |
q15235 | UnexpectedStatusCode.return_or_raise | train | def return_or_raise(cls, response, expected_status_code):
"""Check for ``expected_status_code``."""
try:
if response.status_code in expected_status_code:
return response
except TypeError:
if response.status_code == expected_status_code:
ret... | python | {
"resource": ""
} |
q15236 | check_missing_references | train | def check_missing_references(client):
"""Find missing references."""
from renku.models.refs import LinkReference
missing = [
ref for ref in LinkReference.iter_items(client)
if not ref.reference.exists()
]
if not missing:
return True
click.secho(
WARNING + 'Ther... | python | {
"resource": ""
} |
q15237 | get_git_home | train | def get_git_home(path='.'):
"""Get Git path from the current context."""
ctx = click.get_current_context(silent=True)
if ctx and GIT_KEY in ctx.meta:
return ctx.meta[GIT_KEY]
from git import Repo
return Repo(path, search_parent_directories=True).working_dir | python | {
"resource": ""
} |
q15238 | get_git_isolation | train | def get_git_isolation():
"""Get Git isolation from the current context."""
ctx = click.get_current_context(silent=True)
if ctx and GIT_ISOLATION in ctx.meta:
return ctx.meta[GIT_ISOLATION] | python | {
"resource": ""
} |
q15239 | _safe_issue_checkout | train | def _safe_issue_checkout(repo, issue=None):
"""Safely checkout branch for the issue."""
branch_name = str(issue) if issue else 'master'
if branch_name not in repo.heads:
branch = repo.create_head(branch_name)
else:
branch = repo.heads[branch_name]
branch.checkout() | python | {
"resource": ""
} |
q15240 | attrib | train | def attrib(context=None, **kwargs):
"""Create a new attribute with context."""
kwargs.setdefault('metadata', {})
kwargs['metadata'][KEY] = context
return attr.ib(**kwargs) | python | {
"resource": ""
} |
q15241 | _container_attrib_builder | train | def _container_attrib_builder(name, container, mapper):
"""Builder for container attributes."""
context = {'@container': '@{0}'.format(name)}
def _attrib(type, **kwargs):
"""Define a container attribute."""
kwargs.setdefault('metadata', {})
kwargs['metadata'][KEY_CLS] = type
... | python | {
"resource": ""
} |
q15242 | asjsonld | train | def asjsonld(
inst,
recurse=True,
filter=None,
dict_factory=dict,
retain_collection_types=False,
export_context=True,
basedir=None,
):
"""Dump a JSON-LD class to the JSON with generated ``@context`` field."""
jsonld_fields = inst.__class__._jsonld_fields
attrs = tuple(
fi... | python | {
"resource": ""
} |
q15243 | JSONLDMixin.from_jsonld | train | def from_jsonld(cls, data, __reference__=None, __source__=None):
"""Instantiate a JSON-LD class from data."""
if isinstance(data, cls):
return data
if not isinstance(data, dict):
raise ValueError(data)
if '@type' in data:
type_ = tuple(sorted(data['@... | python | {
"resource": ""
} |
q15244 | JSONLDMixin.asjsonld | train | def asjsonld(self):
"""Create JSON-LD with the original source data."""
source = {}
if self.__source__:
source.update(self.__source__)
source.update(asjsonld(self))
return source | python | {
"resource": ""
} |
q15245 | JSONLDMixin.to_yaml | train | def to_yaml(self):
"""Store an instance to the referenced YAML file."""
import yaml
with self.__reference__.open('w') as fp:
yaml.dump(self.asjsonld(), fp, default_flow_style=False) | python | {
"resource": ""
} |
q15246 | send_mail | train | def send_mail(subject, body_text, addr_from, recipient_list,
fail_silently=False, auth_user=None, auth_password=None,
attachments=None, body_html=None, html_message=None,
connection=None, headers=None):
"""
Sends a multipart email containing text and html versions ... | python | {
"resource": ""
} |
q15247 | topological | train | def topological(nodes):
"""Return nodes in a topological order."""
order, enter, state = deque(), set(nodes), {}
def dfs(node):
"""Visit nodes in depth-first order."""
state[node] = GRAY
for parent in nodes.get(node, ()):
color = state.get(parent, None)
if co... | python | {
"resource": ""
} |
q15248 | check_dataset_metadata | train | def check_dataset_metadata(client):
"""Check location of dataset metadata."""
# Find pre 0.3.4 metadata files.
old_metadata = list(_dataset_metadata_pre_0_3_4(client))
if not old_metadata:
return True
click.secho(
WARNING + 'There are metadata files in the old location.'
'\... | python | {
"resource": ""
} |
q15249 | siblings | train | def siblings(client, revision, paths):
"""Show siblings for given paths."""
graph = Graph(client)
nodes = graph.build(paths=paths, revision=revision)
siblings_ = set(nodes)
for node in nodes:
siblings_ |= graph.siblings(node)
paths = {node.path for node in siblings_}
for path in pat... | python | {
"resource": ""
} |
q15250 | inputs | train | def inputs(ctx, client, revision, paths):
r"""Show inputs files in the repository.
<PATHS> Files to show. If no files are given all input files are shown.
"""
from renku.models.provenance import ProcessRun
graph = Graph(client)
paths = set(paths)
nodes = graph.build(revision=revision)
... | python | {
"resource": ""
} |
q15251 | outputs | train | def outputs(ctx, client, revision, paths):
r"""Show output files in the repository.
<PATHS> Files to show. If no files are given all output files are shown.
"""
graph = Graph(client)
filter = graph.build(paths=paths, revision=revision)
output_paths = graph.output_paths
click.echo('\n'.j... | python | {
"resource": ""
} |
q15252 | _context_names | train | def _context_names():
"""Return list of valid context names."""
import inspect
from renku.models import provenance
from renku.models._jsonld import JSONLDMixin
for name in dir(provenance):
cls = getattr(provenance, name)
if inspect.isclass(cls) and issubclass(cls, JSONLDMixin):
... | python | {
"resource": ""
} |
q15253 | print_context_names | train | def print_context_names(ctx, param, value):
"""Print all possible types."""
if not value or ctx.resilient_parsing:
return
click.echo('\n'.join(_context_names()))
ctx.exit() | python | {
"resource": ""
} |
q15254 | _context_json | train | def _context_json(name):
"""Return JSON-LD string for given context name."""
from renku.models import provenance
cls = getattr(provenance, name)
return {
'@context': cls._jsonld_context,
'@type': cls._jsonld_type,
} | python | {
"resource": ""
} |
q15255 | context | train | def context(names):
"""Show JSON-LD context for repository objects."""
import json
contexts = [_context_json(name) for name in set(names)]
if contexts:
click.echo(
json.dumps(
contexts[0] if len(contexts) == 1 else contexts,
indent=2,
)
... | python | {
"resource": ""
} |
q15256 | workflow | train | def workflow(ctx, client):
"""List or manage workflows with subcommands."""
if ctx.invoked_subcommand is None:
from renku.models.refs import LinkReference
names = defaultdict(list)
for ref in LinkReference.iter_items(client, common_path='workflows'):
names[ref.reference.name... | python | {
"resource": ""
} |
q15257 | validate_path | train | def validate_path(ctx, param, value):
"""Detect a workflow path if it is not passed."""
client = ctx.obj
if value is None:
from renku.models.provenance import ProcessRun
activity = client.process_commit()
if not isinstance(activity, ProcessRun):
raise click.BadParameter... | python | {
"resource": ""
} |
q15258 | create | train | def create(client, output_file, revision, paths):
"""Create a workflow description for a file."""
graph = Graph(client)
outputs = graph.build(paths=paths, revision=revision)
output_file.write(
yaml.dump(
ascwl(
graph.ascwl(outputs=outputs),
filter=lam... | python | {
"resource": ""
} |
q15259 | endpoint | train | def endpoint(ctx, config, verbose):
"""Manage set of platform API endpoints."""
if ctx.invoked_subcommand is None:
# TODO default_endpoint = config.get('core', {}).get('default')
for endpoint, values in config.get('endpoints', {}).items():
# TODO is_default = default_endpoint == endp... | python | {
"resource": ""
} |
q15260 | _wrap_path_or_stream | train | def _wrap_path_or_stream(method, mode): # noqa: D202
"""Open path with context or close stream at the end."""
def decorator(path_or_stream):
"""Open the path if needed."""
if isinstance(path_or_stream, (str, Path)):
return method(Path(path_or_stream).open(mode))
return meth... | python | {
"resource": ""
} |
q15261 | doctor | train | def doctor(ctx, client):
"""Check your system and repository for potential problems."""
click.secho('\n'.join(textwrap.wrap(DOCTOR_INFO)) + '\n', bold=True)
from . import _checks
is_ok = True
for attr in _checks.__all__:
is_ok &= getattr(_checks, attr)(client)
if is_ok:
click.... | python | {
"resource": ""
} |
q15262 | DirectoryTree.from_list | train | def from_list(cls, values):
"""Construct a tree from a list with paths."""
self = cls()
for value in values:
self.add(value)
return self | python | {
"resource": ""
} |
q15263 | DirectoryTree.get | train | def get(self, value, default=None):
"""Return a subtree if exists."""
path = value if isinstance(value, Path) else Path(str(value))
subtree = self
for part in path.parts:
try:
subtree = subtree[part]
except KeyError:
return default
... | python | {
"resource": ""
} |
q15264 | DirectoryTree.add | train | def add(self, value):
"""Create a safe directory from a value."""
path = value if isinstance(value, Path) else Path(str(value))
if path and path != path.parent:
destination = self
for part in path.parts:
destination = destination.setdefault(part, Directory... | python | {
"resource": ""
} |
q15265 | default_endpoint_from_config | train | def default_endpoint_from_config(config, option=None):
"""Return a default endpoint."""
default_endpoint = config.get('core', {}).get('default')
project_endpoint = config.get('project',
{}).get('core',
{}).get('default', default_end... | python | {
"resource": ""
} |
q15266 | install_completion | train | def install_completion(ctx, attr, value): # pragma: no cover
"""Install completion for the current shell."""
import click_completion.core
if not value or ctx.resilient_parsing:
return value
shell, path = click_completion.core.install()
click.secho(
'{0} completion installed in {1}... | python | {
"resource": ""
} |
q15267 | default_endpoint | train | def default_endpoint(ctx, param, value):
"""Return default endpoint if specified."""
if ctx.resilient_parsing:
return
config = ctx.obj['config']
endpoint = default_endpoint_from_config(config, option=value)
if endpoint is None:
raise click.UsageError('No default endpoint found.')
... | python | {
"resource": ""
} |
q15268 | validate_endpoint | train | def validate_endpoint(ctx, param, value):
"""Validate endpoint."""
try:
config = ctx.obj['config']
except Exception:
return
endpoint = default_endpoint(ctx, param, value)
if endpoint not in config.get('endpoints', {}):
raise click.UsageError('Unknown endpoint: {0}'.format(e... | python | {
"resource": ""
} |
q15269 | check_siblings | train | def check_siblings(graph, outputs):
"""Check that all outputs have their siblings listed."""
siblings = set()
for node in outputs:
siblings |= graph.siblings(node)
siblings = {node.path for node in siblings}
missing = siblings - {node.path for node in outputs}
if missing:
msg =... | python | {
"resource": ""
} |
q15270 | with_siblings | train | def with_siblings(graph, outputs):
"""Include all missing siblings."""
siblings = set()
for node in outputs:
siblings |= graph.siblings(node)
return siblings | python | {
"resource": ""
} |
q15271 | echo_via_pager | train | def echo_via_pager(*args, **kwargs):
"""Display pager only if it does not fit in one terminal screen.
NOTE: The feature is available only on ``less``-based pager.
"""
try:
restore = 'LESS' not in os.environ
os.environ.setdefault('LESS', '-iXFR')
click.echo_via_pager(*args, **kwa... | python | {
"resource": ""
} |
q15272 | OptionalGroup.parse_args | train | def parse_args(self, ctx, args):
"""Check if the first argument is an existing command."""
if args and args[0] in self.commands:
args.insert(0, '')
super(OptionalGroup, self).parse_args(ctx, args) | python | {
"resource": ""
} |
q15273 | execute | train | def execute(client, output_file, output_paths=None):
"""Run the generated workflow using cwltool library."""
output_paths = output_paths or set()
import cwltool.factory
from cwltool import workflow
from cwltool.context import LoadingContext, RuntimeContext
from cwltool.utils import visit_class
... | python | {
"resource": ""
} |
q15274 | pull | train | def pull(client, revision, auto_login):
"""Pull an existing image from the project registry."""
registry_url = detect_registry_url(client, auto_login=auto_login)
repo = client.repo
sha = repo.rev_parse(revision).hexsha
short_sha = repo.git.rev_parse(sha, short=7)
image = '{registry}:{short_sha... | python | {
"resource": ""
} |
q15275 | tabular | train | def tabular(client, records):
"""Format dataset files with a tabular output.
:param client: LocalClient instance.
:param records: Filtered collection.
"""
from renku.models._tabulate import tabulate
echo_via_pager(
tabulate(
records,
headers=OrderedDict((
... | python | {
"resource": ""
} |
q15276 | jsonld | train | def jsonld(client, records):
"""Format dataset files as JSON-LD.
:param client: LocalClient instance.
:param records: Filtered collection.
"""
from renku.models._json import dumps
from renku.models._jsonld import asjsonld
data = [asjsonld(record) for record in records]
echo_via_pager(d... | python | {
"resource": ""
} |
q15277 | IssueFromTraceback.main | train | def main(self, *args, **kwargs):
"""Catch all exceptions."""
try:
result = super().main(*args, **kwargs)
return result
except Exception:
if HAS_SENTRY:
self._handle_sentry()
if not (sys.stdin.isatty() and sys.stdout.isatty()):
... | python | {
"resource": ""
} |
q15278 | IssueFromTraceback._handle_sentry | train | def _handle_sentry(self):
"""Handle exceptions using Sentry."""
from sentry_sdk import capture_exception, configure_scope
from sentry_sdk.utils import capture_internal_exceptions
with configure_scope() as scope:
with capture_internal_exceptions():
from git im... | python | {
"resource": ""
} |
q15279 | IssueFromTraceback._handle_github | train | def _handle_github(self):
"""Handle exception and submit it as GitHub issue."""
value = click.prompt(
_BUG + click.style(
'1. Open an issue by typing "open";\n',
fg='green',
) + click.style(
'2. Print human-readable information by t... | python | {
"resource": ""
} |
q15280 | IssueFromTraceback._format_issue_body | train | def _format_issue_body(self, limit=-5):
"""Return formatted body."""
from renku import __version__
re_paths = r'(' + r'|'.join([path or os.getcwd()
for path in sys.path]) + r')'
tb = re.sub(re_paths, '[...]', traceback.format_exc(limit=limit))
... | python | {
"resource": ""
} |
q15281 | IssueFromTraceback._format_issue_url | train | def _format_issue_url(self):
"""Format full issue URL."""
query = urlencode({
'title': self._format_issue_title(),
'body': self._format_issue_body(),
})
return self.REPO_URL + self.ISSUE_SUFFIX + '?' + query | python | {
"resource": ""
} |
q15282 | IssueFromTraceback._process_open | train | def _process_open(self):
"""Open link in a browser."""
click.launch(self._format_issue_url())
if not click.confirm('Did it work?', default=True):
click.echo()
self._process_print()
click.secho(
'\nOpen the line manually and copy the text above\... | python | {
"resource": ""
} |
q15283 | pass_local_client | train | def pass_local_client(
method=None,
clean=None,
up_to_date=None,
commit=None,
ignore_std_streams=True,
lock=None,
):
"""Pass client from the current context to the decorated command."""
if method is None:
return functools.partial(
pass_local_client,
clean=... | python | {
"resource": ""
} |
q15284 | _mapped_std_streams | train | def _mapped_std_streams(lookup_paths, streams=('stdin', 'stdout', 'stderr')):
"""Get a mapping of standard streams to given paths."""
# FIXME add device number too
standard_inos = {}
for stream in streams:
try:
stream_stat = os.fstat(getattr(sys, stream).fileno())
key = s... | python | {
"resource": ""
} |
q15285 | _clean_streams | train | def _clean_streams(repo, mapped_streams):
"""Clean mapped standard streams."""
for stream_name in ('stdout', 'stderr'):
stream = mapped_streams.get(stream_name)
if not stream:
continue
path = os.path.relpath(stream, start=repo.working_dir)
if (path, 0) not in repo.in... | python | {
"resource": ""
} |
q15286 | _expand_directories | train | def _expand_directories(paths):
"""Expand directory with all files it contains."""
for path in paths:
path_ = Path(path)
if path_.is_dir():
for expanded in path_.rglob('*'):
yield str(expanded)
else:
yield path | python | {
"resource": ""
} |
q15287 | dataset | train | def dataset(ctx, client, revision, datadir, format):
"""Handle datasets."""
ctx.meta['renku.datasets.datadir'] = datadir
if ctx.invoked_subcommand is not None:
return
if revision is None:
datasets = client.datasets.values()
else:
datasets = client.datasets_from_commit(clien... | python | {
"resource": ""
} |
q15288 | create | train | def create(client, name):
"""Create an empty dataset in the current repo."""
from renku.models.datasets import Author
with client.with_dataset(name=name) as dataset:
click.echo('Creating a dataset ... ', nl=False)
author = Author.from_git(client.repo)
if author not in dataset.author... | python | {
"resource": ""
} |
q15289 | add | train | def add(client, name, urls, link, relative_to, target, force):
"""Add data to a dataset."""
try:
with client.with_dataset(name=name) as dataset:
target = target if target else None
with progressbar(urls, label='Adding data to dataset') as bar:
for url in bar:
... | python | {
"resource": ""
} |
q15290 | ls_files | train | def ls_files(client, names, authors, include, exclude, format):
"""List files in dataset."""
records = _filter(
client, names=names, authors=authors, include=include, exclude=exclude
)
DATASET_FILES_FORMATS[format](client, records) | python | {
"resource": ""
} |
q15291 | unlink | train | def unlink(client, name, include, exclude, yes):
"""Remove matching files from a dataset."""
dataset = client.load_dataset(name=name)
records = _filter(
client, names=[dataset.name], include=include, exclude=exclude
)
if not yes and records:
prompt_text = (
'You are abou... | python | {
"resource": ""
} |
q15292 | _include_exclude | train | def _include_exclude(file_path, include=None, exclude=None):
"""Check if file matches one of include filters and not in exclude filter.
:param file_path: Path to the file.
:param include: Tuple containing patterns to which include from result.
:param exclude: Tuple containing patterns to which exclude ... | python | {
"resource": ""
} |
q15293 | _filter | train | def _filter(client, names=None, authors=None, include=None, exclude=None):
"""Filter dataset files by specified filters.
:param names: Filter by specified dataset names.
:param authors: Filter by authors.
:param include: Include files matching file pattern.
:param exclude: Exclude files matching fi... | python | {
"resource": ""
} |
q15294 | _split_section_and_key | train | def _split_section_and_key(key):
"""Return a tuple with config section and key."""
parts = key.split('.')
if len(parts) > 1:
return 'renku "{0}"'.format(parts[0]), '.'.join(parts[1:])
return 'renku', key | python | {
"resource": ""
} |
q15295 | config | train | def config(client, key, value):
"""Get and set Renku repository and global options."""
if value is None:
cfg = client.repo.config_reader()
click.echo(cfg.get_value(*_split_section_and_key(key)))
else:
with client.repo.config_writer() as cfg:
section, config_key = _split_s... | python | {
"resource": ""
} |
q15296 | check_for_git_repo | train | def check_for_git_repo(url):
"""Check if a url points to a git repository."""
u = parse.urlparse(url)
is_git = False
if os.path.splitext(u.path)[1] == '.git':
is_git = True
elif u.scheme in ('', 'file'):
from git import InvalidGitRepositoryError, Repo
try:
Repo(... | python | {
"resource": ""
} |
q15297 | env | train | def env(config, endpoint):
"""Print RENKU environment variables.
Run this command to configure your Renku client:
$ eval "$(renku env)"
"""
access_token = config['endpoints'][endpoint]['token']['access_token']
click.echo('export {0}={1}'.format('RENKU_ENDPOINT', endpoint))
click.echo(... | python | {
"resource": ""
} |
q15298 | _check_version | train | def _check_version():
"""Check renku version."""
from ._config import APP_NAME
if VersionCache.load(APP_NAME).is_fresh:
return
from pkg_resources import parse_version
from renku.version import __version__
version = parse_version(__version__)
allow_prereleases = version.is_prerelea... | python | {
"resource": ""
} |
q15299 | check_version | train | def check_version(ctx, param, value):
"""Check for latest version of renku on PyPI."""
if ctx.resilient_parsing:
return
if not value and ctx.invoked_subcommand != 'run':
ctx.call_on_close(_check_version) | python | {
"resource": ""
} |
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