# -*- coding: utf-8 -*-
#
# Copyright 2018-2020 - 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 a local repository."""
import os
import shutil
import subprocess
import uuid
from collections import defaultdict
from contextlib import contextmanager
from subprocess import check_output
import attr
import filelock
import yaml
from jinja2 import Template
from werkzeug.utils import cached_property, secure_filename
from renku.core import errors
from renku.core.compat import Path
from renku.core.management.config import RENKU_HOME
from renku.core.models.projects import Project
from renku.core.models.refs import LinkReference
from .git import GitCore
[docs]def default_path():
"""Return default repository path."""
from git import InvalidGitRepositoryError
from renku.core.commands.git import get_git_home
try:
return get_git_home()
except InvalidGitRepositoryError:
return '.'
[docs]def path_converter(path):
"""Converter for path in PathMixin."""
return Path(path).resolve()
[docs]@attr.s
class PathMixin:
"""Define a default path attribute."""
path = attr.ib(
default=default_path,
converter=path_converter,
)
@path.validator
def _check_path(self, _, value):
"""Check the path exists and it is a directory."""
if not (value.exists() and value.is_dir()):
raise ValueError('Define an existing directory.')
[docs]@attr.s
class RepositoryApiMixin(GitCore):
"""Client for handling a local repository."""
renku_home = attr.ib(default=RENKU_HOME)
"""Define a name of the Renku folder (default: ``.renku``)."""
renku_path = attr.ib(init=False)
"""Store a ``Path`` instance of the Renku folder."""
parent = attr.ib(default=None)
"""Store a pointer to the parent repository."""
METADATA = 'metadata.yml'
"""Default name of Renku config file."""
LOCK_SUFFIX = '.lock'
"""Default suffix for Renku lock file."""
WORKFLOW = 'workflow'
"""Directory for storing workflow in Renku."""
RENKU_PROTECTED_PATHS = [
'\\.renku/.*', 'Dockerfile', '\\.dockerignore', '\\.gitignore',
'\\.gitattributes', '\\.gitlab-ci\\.yml', 'environment\\.yml',
'requirements\\.txt'
]
def __attrs_post_init__(self):
"""Initialize computed attributes."""
#: Configure Renku path.
path = Path(self.renku_home)
if not path.is_absolute():
path = self.path / path
path.relative_to(path)
self.renku_path = path
self._subclients = {}
super().__attrs_post_init__()
# initialize submodules
if self.repo:
try:
check_output([
'git', 'submodule', 'update', '--init', '--recursive'
],
cwd=str(self.path))
except subprocess.CalledProcessError:
pass
@property
def lock(self):
"""Create a Renku config lock."""
return filelock.FileLock(
str(self.renku_path.with_suffix(self.LOCK_SUFFIX)),
timeout=0,
)
@property
def renku_metadata_path(self):
"""Return a ``Path`` instance of Renku metadata file."""
return self.renku_path.joinpath(self.METADATA)
@property
def workflow_path(self):
"""Return a ``Path`` instance of the workflow folder."""
return self.renku_path / self.WORKFLOW
[docs] @cached_property
def cwl_prefix(self):
"""Return a CWL prefix."""
self.workflow_path.mkdir(parents=True, exist_ok=True) # for Python 3.5
return str(self.workflow_path.resolve().relative_to(self.path))
[docs] @cached_property
def project(self):
"""Return the Project instance."""
if self.renku_metadata_path.exists():
return Project.from_yaml(self.renku_metadata_path, client=self)
@property
def remote(self, remote_name='origin'):
"""Return host, owner and name of the remote if it exists."""
from renku.core.models.git import GitURL
host = owner = name = None
try:
remote_branch = \
self.repo.head.reference.tracking_branch()
if remote_branch is not None:
remote_name = remote_branch.remote_name
except TypeError:
pass
try:
url = GitURL.parse(self.repo.remotes[remote_name].url)
# Remove gitlab. unless running on gitlab.com.
hostname_parts = url.hostname.split('.')
if len(hostname_parts) > 2 and hostname_parts[0] == 'gitlab':
hostname_parts = hostname_parts[1:]
url = attr.evolve(url, hostname='.'.join(hostname_parts))
except IndexError:
url = None
if url:
host = url.hostname
owner = url.owner
name = url.name
return {'host': host, 'owner': owner, 'name': name}
[docs] def process_commit(self, commit=None, path=None):
"""Build an :class:`~renku.core.models.provenance.activities.Activity`.
:param commit: Commit to process. (default: ``HEAD``)
:param path: Process a specific CWL file.
"""
from renku.core.models.cwl.ascwl import CWLClass
from renku.core.models.provenance.activities import Activity
commit = commit or self.repo.head.commit
if len(commit.parents) > 1:
return Activity(commit=commit, client=self)
if path is None:
for file_ in commit.stats.files.keys():
# Find a process (CommandLineTool or Workflow)
if self.is_cwl(file_):
if path is not None:
# Regular activity since it edits multiple CWL files
return Activity(commit=commit, client=self)
path = file_
if path:
data = (commit.tree / path).data_stream.read()
process = CWLClass.from_cwl(
yaml.safe_load(data), __reference__=Path(path)
)
return process.create_run(
commit=commit,
client=self,
process=process,
path=path,
)
return Activity(commit=commit, client=self)
[docs] def is_cwl(self, path):
"""Check if the path is a valid CWL file."""
return path.startswith(self.cwl_prefix) and path.endswith('.cwl')
[docs] def find_previous_commit(self, paths, revision='HEAD', return_first=False):
"""Return a previous commit for a given path starting from ``revision``.
:param revision: revision to start from, defaults to ``HEAD``
:param return_first: show the first commit in the history
:raises KeyError: if path is not present in the given commit
"""
file_commits = list(self.repo.iter_commits(revision, paths=paths))
if not file_commits:
raise KeyError(
'Could not find a file {0} in range {1}'.format(
paths, revision
)
)
return file_commits[-1 if return_first else 0]
[docs] @cached_property
def workflow_names(self):
"""Return index of workflow names."""
names = defaultdict(list)
for ref in LinkReference.iter_items(self, common_path='workflows'):
names[str(ref.reference.relative_to(self.path))].append(ref.name)
return names
[docs] @cached_property
def submodules(self):
"""Return list of submodules it belongs to."""
if self.parent:
client, submodule = self.parent
return client.submodules + [submodule.name]
return []
[docs] def subclients(self, parent_commit):
"""Return mapping from submodule to client."""
if parent_commit in self._subclients:
return self._subclients[parent_commit]
try:
from git import Submodule
submodules = [
submodule for submodule in
Submodule.iter_items(self.repo, parent_commit=parent_commit)
]
except (RuntimeError, ValueError):
# There are no submodules associated with the given commit.
submodules = []
subclients = {}
for submodule in submodules:
subpath = (self.path / submodule.path).resolve()
is_renku = subpath / Path(self.renku_home)
if subpath.exists() and is_renku.exists():
subclients[submodule] = self.__class__(
path=subpath,
parent=(self, submodule),
)
return subclients
[docs] def resolve_in_submodules(self, commit, path):
"""Resolve filename in submodules."""
original_path = self.path / path
in_vendor = str(path).startswith('.renku/vendors')
if original_path.is_symlink() or in_vendor:
original_path = Path(
os.path.realpath(os.path.abspath(str(original_path)))
)
for submodule, subclient in self.subclients(commit).items():
if (Path(submodule.path) / Path('.git')).exists():
try:
subpath = original_path.relative_to(subclient.path)
return (
subclient,
subclient.find_previous_commit(
subpath, revision=submodule.hexsha
),
subpath,
)
except ValueError:
pass
return self, commit, path
[docs] @contextmanager
def with_commit(self, commit):
"""Yield the state of the repo at a specific commit."""
current_branch = None
current_commit = None
try:
current_branch = self.repo.active_branch
except TypeError as e:
# not on a branch, detached head
if 'HEAD is a detached' in str(e):
current_commit = self.repo.head.commit
else:
raise ValueError('Couldn\'t get active branch or commit', e)
self.repo.git.checkout(commit)
try:
yield
finally:
if current_branch:
self.repo.git.checkout(current_branch)
elif current_commit:
self.repo.git.checkout(current_commit)
[docs] @contextmanager
def with_workflow_storage(self):
"""Yield a workflow storage."""
from renku.core.models.cwl.ascwl import ascwl
from renku.core.models.cwl.workflow import Workflow
workflow = Workflow()
yield workflow
for step in workflow.steps:
step_name = '{0}_{1}.cwl'.format(
uuid.uuid4().hex,
secure_filename('_'.join(step.run.baseCommand)),
)
workflow_path = self.workflow_path
if not workflow_path.exists():
workflow_path.mkdir()
step_path = workflow_path / step_name
with step_path.open('w') as step_file:
yaml.dump(
ascwl(
# filter=lambda _, x: not (x is False or bool(x)
step.run,
filter=lambda _, x: x is not None,
basedir=workflow_path,
),
stream=step_file,
default_flow_style=False
)
[docs] def init_repository(self, force=False):
"""Initialize an empty Renku repository."""
from git import Repo
from renku.core.models.provenance.agents import Person
# verify if folder is empty
if self.repo is not None and not force:
raise errors.InvalidFileOperation(
'Folder {0} already contains file. Use --force to overwrite'.
format(self.repo.git_dir)
)
# initialize repo
path = self.path.absolute()
self.repo = Repo.init(str(path))
# verify if author information is available
Person.from_git(self.repo)
[docs] def import_from_template(self, template_path, metadata, force=False):
"""Render template files from a template directory."""
for file in template_path.glob('**/*'):
destination = self.path / file.relative_to(template_path)
try:
# TODO: notify about the expected variables - code stub:
# with file.open() as fr:
# file_content = fr.read()
# # look for the required keys
# env = Environment()
# parsed = env.parse(file_content)
# variables = meta.find_undeclared_variables(parsed)
# parse file and process it
template = Template(file.read_text())
rendered_content = template.render(metadata)
destination.write_text(rendered_content)
except IsADirectoryError:
destination.mkdir(parents=True, exist_ok=True)
except TypeError:
shutil.copy(file, destination)