# -*- coding: utf-8 -*-
#
# Copyright 2018-2019 - Swiss Data Science Center (SDSC)
# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
# Eidgenössische Technische Hochschule Zürich (ETHZ).
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Client for handling datasets."""
import os
import shutil
import stat
import warnings
from configparser import NoSectionError
from contextlib import contextmanager
from urllib import error, parse
import attr
import requests
import yaml
from renku import errors
from renku._compat import Path
from renku.models._git import GitURL
from renku.models._jsonld import asjsonld
from renku.models.datasets import Author, Dataset, DatasetFile, NoneType
[docs]@attr.s
class DatasetsApiMixin(object):
"""Client for handling datasets."""
datadir = attr.ib(default='data', converter=str)
"""Define a name of the folder for storing datasets."""
DATASETS = 'datasets'
"""Directory for storing dataset metadata in Renku."""
@property
def renku_datasets_path(self):
"""Return a ``Path`` instance of Renku dataset metadata folder."""
return self.renku_path.joinpath(self.DATASETS)
@property
def datasets(self):
"""Return mapping from path to dataset."""
result = {}
for path in self.renku_datasets_path.rglob(self.METADATA):
with path.open('r') as fp:
result[path] = Dataset.from_jsonld(yaml.load(fp))
return result
[docs] @contextmanager
def with_dataset(self, name=None):
"""Yield an editable metadata object for a dataset."""
from renku.models.refs import LinkReference
with self.lock:
path = None
dataset = None
if name:
path = self.renku_datasets_path / name / self.METADATA
if not path.exists():
path = LinkReference(
client=self, name='datasets/' + name
).reference
if path.exists():
with path.open('r') as f:
source = yaml.load(f) or {}
dataset = Dataset.from_jsonld(source)
if dataset is None:
source = {}
dataset = Dataset(name=name)
path = (
self.renku_datasets_path / dataset.identifier.hex /
self.METADATA
)
path.parent.mkdir(parents=True, exist_ok=True)
if name:
LinkReference.create(
client=self, name='datasets/' + name
).set_reference(path)
dataset_path = self.path / self.datadir / dataset.name
dataset_path.mkdir(parents=True, exist_ok=True)
yield dataset
source.update(**asjsonld(dataset))
# TODO
# if path is None:
# path = dataset_path / self.METADATA
# if path.exists():
# raise ValueError('Dataset already exists')
with path.open('w') as f:
yaml.dump(source, f, default_flow_style=False)
[docs] def add_data_to_dataset(
self, dataset, url, git=False, force=False, **kwargs
):
"""Import the data into the data directory."""
dataset_path = self.path / self.datadir / dataset.name
git = git or check_for_git_repo(url)
target = kwargs.pop('target', None)
if git:
if isinstance(target, (str, NoneType)):
files = self._add_from_git(
dataset, dataset_path, url, target, **kwargs
)
else:
files = {}
for t in target:
files.update(
self._add_from_git(
dataset, dataset_path, url, t, **kwargs
)
)
else:
files = self._add_from_url(dataset, dataset_path, url, **kwargs)
ignored = self.find_ignored_paths(
*[
os.path.relpath(
str(self.renku_datasets_path / dataset.name / key),
start=str(self.path),
) for key in files.keys()
]
)
if ignored:
if force:
self.repo.git.add(*ignored, force=True)
else:
raise errors.IgnoredFiles(ignored)
dataset.files.update(files)
def _add_from_url(self, dataset, path, url, nocopy=False, **kwargs):
"""Process an add from url and return the location on disk."""
u = parse.urlparse(url)
if u.scheme not in Dataset.SUPPORTED_SCHEMES:
raise NotImplementedError(
'{} URLs are not supported'.format(u.scheme)
)
# Respect the directory struture inside the source path.
relative_to = kwargs.pop('relative_to', None)
if relative_to:
dst_path = Path(url).resolve().absolute().relative_to(
Path(relative_to).resolve().absolute()
)
else:
dst_path = os.path.basename(url)
dst = path.joinpath(dst_path).absolute()
if u.scheme in ('', 'file'):
src = Path(u.path).absolute()
# if we have a directory, recurse
if src.is_dir():
files = {}
dst.mkdir(parents=True, exist_ok=True)
for f in src.iterdir():
files.update(
self._add_from_url(
dataset,
dst,
f.absolute().as_posix(),
nocopy=nocopy
)
)
return files
# Make sure the parent directory exists.
dst.parent.mkdir(parents=True, exist_ok=True)
if nocopy:
try:
os.link(str(src), str(dst))
except Exception as e:
raise Exception(
'Could not create hard link '
'- retry without nocopy.'
) from e
else:
shutil.copy(str(src), str(dst))
# Do not expose local paths.
src = None
else:
try:
response = requests.get(url)
dst.write_bytes(response.content)
except error.HTTPError as e: # pragma nocover
raise e
# make the added file read-only
mode = dst.stat().st_mode & 0o777
dst.chmod(mode & ~(stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH))
self.track_paths_in_storage(str(dst.relative_to(self.path)))
dataset_path = self.renku_datasets_path / dataset.name
result = os.path.relpath(str(dst), start=str(dataset_path))
return {
result:
DatasetFile(
path=result,
url=url,
authors=dataset.authors,
dataset=dataset.name,
)
}
def _add_from_git(self, dataset, path, url, target, **kwargs):
"""Process adding resources from another git repository.
The submodules are placed in ``.renku/vendors`` and linked
to the *path* specified by the user.
"""
from git import Repo
# create the submodule
if url.startswith('git@'):
url = 'git+ssh://' + url
u = parse.urlparse(url)
submodule_path = self.renku_path / 'vendors' / (u.netloc or 'local')
# Respect the directory struture inside the source path.
relative_to = kwargs.get('relative_to', None)
if u.scheme in ('', 'file'):
warnings.warn('Importing local git repository, use HTTPS')
# determine where is the base repo path
r = Repo(url, search_parent_directories=True)
src_repo_path = Path(r.git_dir).parent.resolve()
submodule_name = src_repo_path.name
submodule_path = submodule_path / str(src_repo_path).lstrip('/')
# if repo path is a parent, rebase the paths and update url
if src_repo_path != Path(u.path):
top_target = Path(
u.path
).resolve().absolute().relative_to(src_repo_path)
if target:
target = top_target / target
else:
target = top_target
url = src_repo_path.as_posix()
elif u.scheme in {'http', 'https', 'git+https', 'git+ssh'}:
submodule_name = os.path.splitext(os.path.basename(u.path))[0]
submodule_path = submodule_path.joinpath(
os.path.dirname(u.path).lstrip('/'), submodule_name
)
else:
raise NotImplementedError(
'Scheme {} not supported'.format(u.scheme)
)
# FIXME: do a proper check that the repos are not the same
if submodule_name not in (s.name for s in self.repo.submodules):
if u.scheme in {'http', 'https', 'git+https', 'git+ssh'}:
url = self.get_relative_url(url)
# Submodule in python git does some custom magic that does not
# allow for relative URLs, so we call the git function directly
self.repo.git.submodule([
'add', '--force', '--name', submodule_name, url,
submodule_path.relative_to(self.path).as_posix()
])
src = submodule_path / (target or '')
if target and relative_to:
relative_to = Path(relative_to)
if relative_to.is_absolute():
assert u.scheme in {
'', 'file'
}, ('Only relative paths can be used with URLs.')
target = (Path(url).resolve().absolute() / target).relative_to(
relative_to.resolve()
)
else:
# src already includes target so we do not have to append it
target = src.relative_to(submodule_path / relative_to)
# link the target into the data directory
dst = self.path / path / (target or '')
# if we have a directory, recurse
if src.is_dir():
files = {}
dst.mkdir(parents=True, exist_ok=True)
# FIXME get all files from submodule index
for f in src.iterdir():
try:
files.update(
self._add_from_git(
dataset,
path,
url,
target=f.relative_to(submodule_path),
**kwargs
)
)
except ValueError:
pass # skip files outside the relative path
return files
if not dst.parent.exists():
dst.parent.mkdir(parents=True)
os.symlink(os.path.relpath(str(src), str(dst.parent)), str(dst))
# grab all the authors from the commit history
git_repo = Repo(str(submodule_path.absolute()))
authors = []
for commit in git_repo.iter_commits(paths=target):
author = Author.from_commit(commit)
if author not in authors:
authors.append(author)
dataset_path = self.renku_datasets_path / dataset.name
result = os.path.relpath(str(dst), start=str(dataset_path))
if u.scheme in ('', 'file'):
url = None
else:
url = '{}/{}'.format(url, target)
return {
result:
DatasetFile(
path=result,
url=url,
authors=authors,
dataset=dataset.name, # TODO detect original dataset
)
}
[docs] def get_relative_url(self, url):
"""Determine if the repo url should be relative."""
# Check if the default remote of the branch we are on is on
# the same server as the submodule. If so, use a relative path
# instead of an absolute URL.
try:
branch_remote = self.repo.config_reader().get(
'branch "{}"'.format(self.repo.active_branch.name), 'remote'
)
except NoSectionError:
branch_remote = 'origin'
try:
remote = self.repo.remote(branch_remote)
except ValueError:
warnings.warn(
'Remote {} not found, cannot check for relative URL.'.
format(branch_remote)
)
return url
remote_url = GitURL.parse(remote.url)
submodule_url = GitURL.parse(url)
if remote_url.hostname == submodule_url.hostname:
# construct the relative path
url = Path(
'../../{}'.format(submodule_url.owner) if remote_url.owner ==
submodule_url.owner else '..'
)
url = str(url / submodule_url.name)
return url
[docs]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(u.path, search_parent_directories=True)
is_git = True
except InvalidGitRepositoryError:
is_git = False
return is_git