Source code for renku.core.management.datasets

# -*- 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 datasets."""

import concurrent.futures
import os
import re
import shutil
import tempfile
import time
import uuid
import warnings
from collections import OrderedDict
from configparser import NoSectionError
from contextlib import contextmanager
from pathlib import Path
from subprocess import PIPE, SubprocessError, run
from urllib import error, parse
from urllib.parse import ParseResult

import attr
import patoolib
import requests
from git import GitCommandError, GitError, Repo
from wcmatch import glob

from renku.core import errors
from renku.core.management.clone import clone
from renku.core.management.config import RENKU_HOME
from renku.core.management.migrate import is_project_unsupported, migrate
from renku.core.models.datasets import Dataset, DatasetFile, DatasetTag, \
    is_dataset_short_name_valid
from renku.core.models.git import GitURL
from renku.core.models.locals import with_reference
from renku.core.models.provenance.agents import Person
from renku.core.models.refs import LinkReference
from renku.core.utils.urls import remove_credentials


[docs]@attr.s class DatasetsApiMixin(object): """Client for handling datasets.""" DATASETS = 'datasets' """Directory for storing dataset metadata in Renku.""" POINTERS = 'pointers' """Directory for storing external pointer files.""" CACHE = 'cache' """Directory to cache transient data.""" @property def renku_datasets_path(self): """Return a ``Path`` instance of Renku dataset metadata folder.""" return self.path / self.renku_home / self.DATASETS @property def renku_pointers_path(self): """Return a ``Path`` instance of Renku pointer files folder.""" path = self.path / self.renku_home / self.POINTERS path.mkdir(exist_ok=True) return path
[docs] def datasets_from_commit(self, commit=None): """Return datasets defined in a commit.""" commit = commit or self.repo.head.commit try: datasets = commit.tree / self.renku_home / self.DATASETS except KeyError: return for tree in datasets: try: blob = tree / self.METADATA except KeyError: continue dataset = Dataset.from_yaml( self.path / Path(blob.path), client=self ) dataset.commit = commit yield dataset
@property def datasets(self): """Return mapping from path to dataset.""" result = {} paths = self.renku_datasets_path.rglob(self.METADATA) for path in paths: result[path] = self.load_dataset_from_path(path) return result
[docs] def load_dataset_from_path(self, path, commit=None): """Return a dataset from a given path.""" path = Path(path) if not path.is_absolute(): path = self.path / path return Dataset.from_yaml(path, client=self, commit=commit)
[docs] def get_dataset_path(self, short_name): """Get dataset path from short_name.""" path = self.renku_datasets_path / short_name / self.METADATA if not path.exists(): try: path = LinkReference( client=self, name='datasets/' + short_name ).reference except errors.ParameterError: return None return path
[docs] def load_dataset(self, short_name=None): """Load dataset reference file.""" if short_name: path = self.get_dataset_path(short_name) if path and path.exists(): return self.load_dataset_from_path(path)
[docs] @contextmanager def with_dataset(self, short_name=None, create=False): """Yield an editable metadata object for a dataset.""" dataset = self.load_dataset(short_name=short_name) clean_up_required = False if dataset is None: if not create: raise errors.DatasetNotFound(name=short_name) clean_up_required = True dataset, path, dataset_ref = self.create_dataset( short_name=short_name ) elif create: raise errors.DatasetExistsError( 'Dataset exists: "{}".'.format(short_name) ) dataset_path = self.path / self.data_dir / dataset.short_name dataset_path.mkdir(parents=True, exist_ok=True) try: yield dataset except Exception: # TODO use a general clean-up strategy # https://github.com/SwissDataScienceCenter/renku-python/issues/736 if clean_up_required: dataset_ref.delete() shutil.rmtree(path.parent, ignore_errors=True) raise dataset.to_yaml()
[docs] def create_dataset( self, short_name=None, title=None, description=None, creators=None, keywords=None, ): """Create a dataset.""" if not short_name: raise errors.ParameterError('Dataset short_name must be provided.') if not is_dataset_short_name_valid(short_name): raise errors.ParameterError( 'Dataset short_name "{}" is not valid.'.format(short_name) ) if self.load_dataset(short_name=short_name): raise errors.DatasetExistsError( 'Dataset exists: "{}".'.format(short_name) ) if not title: title = short_name identifier = str(uuid.uuid4()) path = self.renku_datasets_path / identifier / self.METADATA if path.exists(): raise errors.DatasetExistsError( 'Dataset with reference {} exists'.format(path) ) path.parent.mkdir(parents=True, exist_ok=True) if creators is None: creators = [Person.from_git(self.repo)] keywords = keywords or () with with_reference(path): dataset = Dataset( client=self, identifier=identifier, short_name=short_name, name=title, description=description, creator=creators, keywords=keywords, ) dataset_ref = LinkReference.create( client=self, name='datasets/' + short_name ) dataset_ref.set_reference(path) dataset.path = Path(dataset.path).relative_to(self.path) dataset.to_yaml() return dataset, path, dataset_ref
[docs] def add_data_to_dataset( self, dataset, urls, force=False, overwrite=False, sources=(), destination='', ref=None, external=False, extract=False, all_at_once=False, destination_names=None, progress=None ): """Import the data into the data directory.""" messages = [] warning_messages = [] dataset_datadir = self.path / dataset.data_dir destination = destination or Path('.') destination = self._resolve_path(dataset_datadir, destination) destination = self.path / dataset_datadir / destination if destination.exists() and not destination.is_dir(): raise errors.ParameterError( f'Destination is not a directory: "{destination}"' ) self.check_external_storage() files = [] if all_at_once: # Importing a dataset files = self._add_from_urls( dataset=dataset, urls=urls, destination_names=destination_names, destination=destination, extract=extract, progress=progress ) else: for url in urls: is_remote, is_git = _check_url(url) if is_git and is_remote: # Remote git repo sources = sources or () new_files = self._add_from_git( dataset=dataset, url=url, sources=sources, destination=destination, ref=ref ) else: if sources: raise errors.UsageError( 'Cannot use "--source" with URLs or local files.' ) if not is_remote: # Local path, might be git if is_git: warning_messages.append( 'Adding data from local Git repository: ' + 'Use remote\'s Git URL instead to enable ' + 'lineage information and updates.' ) u = parse.urlparse(url) new_files = self._add_from_local( dataset=dataset, path=u.path, external=external, destination=destination ) else: # Remote URL new_files = self._add_from_url( dataset=dataset, url=url, destination=destination, extract=extract, progress=progress ) files.extend(new_files) # Remove all files that are under a .git directory paths_to_avoid = [ f['path'] for f in files if '.git' in str(f['path']).split(os.path.sep) ] if paths_to_avoid: files = [f for f in files if f['path'] not in paths_to_avoid] warning_messages.append( 'Ignored adding paths under a .git directory:\n ' + '\n '.join(str(p) for p in paths_to_avoid) ) files_to_commit = {str(self.path / f['path']) for f in files} if not force: ignored_files = self.find_ignored_paths(*files_to_commit) if ignored_files: ignored_files = set(ignored_files) files_to_commit = files_to_commit.difference(ignored_files) ignored_sources = [] for file_ in files: if str(self.path / file_['path']) in ignored_files: operation = file_.get('operation') if operation: src, _, _ = operation ignored_sources.append(src) else: ignored_sources.append(file_['path']) files = [ f for f in files if str(self.path / f['path']) in files_to_commit ] warning_messages.append( 'Theses paths are ignored by one of your .gitignore ' + 'files (use "--force" flag if you really want to add ' + 'them):\n ' + '\n '.join([str(p) for p in ignored_sources]) ) # all files at this point can be force-added if not overwrite: existing_files = dataset.find_files(files_to_commit) if existing_files: files_to_commit = files_to_commit.difference(existing_files) files = [ f for f in files if str(self.path / f['path']) in files_to_commit ] warning_messages.append( 'These existing files were not overwritten ' + '(use "--overwrite" flag to overwrite them):\n ' + '\n '.join([str(p) for p in existing_files]) ) for data in files: operation = data.pop('operation', None) if not operation: continue src, dst, action = operation # Remove existing file if any self.remove_file(dst) dst.parent.mkdir(parents=True, exist_ok=True) if action == 'copy': shutil.copy(src, dst) elif action == 'move': shutil.move(src, dst, copy_function=shutil.copy) elif action == 'symlink': self._create_external_file(src, dst) data['external'] = True else: raise errors.OperationError(f'Invalid action {action}') # Track non-symlinks in LFS if self.check_external_storage(): lfs_paths = self.track_paths_in_storage(*files_to_commit) show_message = self.get_value('renku', 'show_lfs_message') if ( lfs_paths and (show_message is None or show_message == 'True') ): messages.append(( 'Adding these files to Git LFS:\n' + '\t{}'.format('\n\t'.join(lfs_paths)) + '\nTo disable this message in the future, run:' + '\n\trenku config show_lfs_message False' )) # Force-add to include possible ignored files self.repo.git.add(*files_to_commit, force=True) self.repo.git.add(self.renku_pointers_path, force=True) staged_files = self.repo.index.diff('HEAD') if staged_files: msg = 'renku dataset: committing {} newly added files'.format( len(files_to_commit) ) skip_hooks = not self.external_storage_requested self.repo.index.commit(msg, skip_hooks=skip_hooks) else: warning_messages.append('No file was added to project') # Generate the DatasetFiles dataset_files = [] for data in files: dataset_file = DatasetFile.from_revision(self, **data) # Set dataset file path relative to root for submodules. if dataset_file.client != self: dataset_file.path = str(data['path']) dataset_files.append(dataset_file) dataset.update_files(dataset_files) return warning_messages, messages
def _check_protected_path(self, path): """Checks if a path is a protected path.""" try: path_in_repo = path.relative_to(self.path) except ValueError: return False for protected_path in self.RENKU_PROTECTED_PATHS: str_path = str(path_in_repo) if re.match('^{}$'.format(protected_path), str_path): return True return False def _add_from_local(self, dataset, path, external, destination): """Add a file or directory from a local filesystem.""" src = Path(os.path.abspath(path)) if not src.exists(): raise errors.ParameterError(f'Cannot find file/directory: {path}') dst = destination / src.name # if we have a directory, recurse if src.is_dir(): if dst.exists() and not dst.is_dir(): raise errors.ParameterError( f'Cannot copy directory to a file: "{dst}"' ) if src == (self.path / dataset.data_dir).resolve(): raise errors.ParameterError( f'Cannot add dataset\'s data directory recursively: {path}' ) if self._check_protected_path(src): raise errors.ProtectedFiles([src]) files = [] for f in src.iterdir(): files.extend( self._add_from_local( dataset=dataset, path=os.path.abspath(f), external=external, destination=dst ) ) return files else: # Check if file is in the project and return it path_in_repo = None if self._is_external_file(src): path_in_repo = path else: try: path_in_repo = src.relative_to(self.path) except ValueError: pass else: if self._check_protected_path(src): raise errors.ProtectedFiles([src]) if path_in_repo: return [{ 'path': path_in_repo, 'url': path_in_repo, 'creator': dataset.creator, 'parent': self }] action = 'symlink' if external else 'copy' return [{ 'path': dst.relative_to(self.path), 'url': 'file://' + os.path.relpath(str(src), str(self.path)), 'creator': dataset.creator, 'parent': self, 'operation': (src, dst, action) }] def _add_from_urls( self, dataset, urls, destination, destination_names, extract, progress ): files = [] max_workers = min(os.cpu_count() - 1, 4) or 1 with concurrent.futures.ThreadPoolExecutor(max_workers) as executor: futures = { executor.submit( self._add_from_url, dataset=dataset, url=url, destination=destination, extract=extract, filename=name, progress=progress ) for url, name in zip(urls, destination_names) } for future in concurrent.futures.as_completed(futures): files.extend(future.result()) return files def _add_from_url( self, dataset, url, destination, extract, filename=None, progress=None ): """Process adding from url and return the location on disk.""" url = self._provider_check(url) try: start = time.time() * 1e+3 tmp_root, paths = self._download( url=url, filename=filename, extract=extract, progress_class=progress ) exec_time = (time.time() * 1e+3 - start) // 1e+3 # If execution time was less or equal to zero seconds, # block the thread a bit to avoid being rate limited. if exec_time == 0: time.sleep(min(os.cpu_count() - 1, 4) or 1) except ( requests.exceptions.HTTPError, error.HTTPError ) as e: # pragma nocover raise errors.OperationError( 'Cannot download from {}'.format(url) ) from e paths = [(src, destination / src.relative_to(tmp_root)) for src in paths if not src.is_dir()] return [{ 'operation': (src, dst, 'move'), 'path': dst.relative_to(self.path), 'url': remove_credentials(url), 'creator': dataset.creator, 'parent': self } for src, dst in paths] def _add_from_git(self, dataset, url, sources, destination, ref): """Process adding resources from another git repository.""" from renku import LocalClient u = parse.urlparse(url) sources = self._resolve_paths(u.path, sources) # Get all files from repo that match sources repo, repo_path = self.prepare_git_repo(url, ref) files = set() used_sources = set() for file in repo.head.commit.tree.traverse(): path = file.path result = self._get_src_and_dst( path, repo_path, sources, destination, used_sources ) if result: files.add(result) unused_sources = set(sources.keys()) - used_sources if unused_sources: unused_sources = {str(s) for s in unused_sources} raise errors.ParameterError( 'No such file or directory', param_hint=unused_sources ) # Create metadata and move files to dataset results = [] remote_client = LocalClient(repo_path) # Pull files from LFS paths = set() for path, src, _ in files: if src.is_dir(): continue if src.is_symlink(): try: path = str(src.resolve().relative_to(repo_path)) except ValueError: # External file pass paths.add(path) self._fetch_lfs_files(repo_path, paths) # Fetch metadata from Renku if any paths = {f[0] for f in files} metadata = self._fetch_files_metadata(remote_client, paths) for path, src, dst in files: if not src.is_dir(): # Use original metadata if it exists based_on = metadata.get(path) if based_on: based_on.url = url based_on.based_on = None creators = based_on.creator else: creators = [] # grab all the creators from the commit history for commit in repo.iter_commits(paths=path): creator = Person.from_commit(commit) if creator not in creators: creators.append(creator) based_on = DatasetFile.from_revision( remote_client, path=src, url=url, creator=creators ) path_in_dst_repo = dst.relative_to(self.path) if remote_client._is_external_file(src): operation = (src.resolve(), dst, 'symlink') else: operation = (src, dst, 'copy') results.append({ 'path': path_in_dst_repo, 'url': remove_credentials(url), 'creator': creators, 'parent': self, 'based_on': based_on, 'operation': operation }) return results @staticmethod def _ensure_dropbox(url): """Ensure dropbox url is set for file download.""" if not isinstance(url, ParseResult): url = parse.urlparse(url) query = url.query or '' if 'dl=0' in url.query: query = query.replace('dl=0', 'dl=1') else: query += 'dl=1' url = url._replace(query=query) return url def _provider_check(self, url): """Check additional provider related operations.""" url = parse.urlparse(url) if 'dropbox.com' in url.netloc: url = self._ensure_dropbox(url) return parse.urlunparse(url) def _resolve_paths(self, root_path, paths): """Check if paths are within a root path and resolve them.""" result = OrderedDict() # Used as an ordered-set for path in paths: r = self._resolve_path(root_path, path) result[r] = None return result def _resolve_path(self, root_path, path): """Check if a path is within a root path and resolve it.""" try: root_path = Path(root_path).resolve() path = os.path.abspath(root_path / path) return Path(path).relative_to(root_path) except ValueError: raise errors.ParameterError( 'File {} is not within path {}'.format(path, root_path) ) def _get_src_and_dst( self, path, repo_path, sources, dst_root, used_sources ): is_wildcard = False if not sources: source = Path('.') else: source = None for s in sources.keys(): try: Path(path).relative_to(s) except ValueError: if glob.globmatch(path, str(s), flags=glob.GLOBSTAR): is_wildcard = True source = path used_sources.add(s) break else: source = s used_sources.add(source) break if not source: return src = repo_path / path source_name = Path(source).name relative_path = Path(path).relative_to(source) if src.is_dir() and is_wildcard: sources[source] = None used_sources.add(source) dst = dst_root / source_name / relative_path return (path, src, dst) def _fetch_lfs_files(self, repo_path, paths): """Fetch and checkout paths that are tracked by Git LFS.""" repo_path = str(repo_path) try: output = run(('git', 'lfs', 'ls-files', '--name-only'), stdout=PIPE, cwd=repo_path, universal_newlines=True) except SubprocessError: return lfs_files = set(output.stdout.split('\n')) files = lfs_files & paths if not files: return try: for path in files: run(['git', 'lfs', 'pull', '--include', path], cwd=repo_path) except KeyboardInterrupt: raise except SubprocessError: pass @staticmethod def _fetch_files_metadata(client, paths): """Return metadata for files from paths.""" files = {} if is_project_unsupported(client): return files migrate(client) for _, dataset in client.datasets.items(): for file_ in dataset.files: path = file_.path if path in paths: files[path] = file_ return files
[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 dataset_commits(self, dataset, max_results=None): """Gets the newest commit for a dataset or its files. Commits are returned sorted from newest to oldest. """ paths = [(self.path / dataset.path / self.METADATA).resolve()] paths.extend(self.path / f.path for f in dataset.files) commits = self.repo.iter_commits(paths=paths, max_count=max_results) return commits
[docs] def add_dataset_tag(self, dataset, tag, description='', force=False): """Adds a new tag to a dataset. Validates if the tag already exists and that the tag follows the same rules as docker tags. See https://docs.docker.com/engine/reference/commandline/tag/ for a documentation of docker tag syntax. :raises: errors.ParameterError """ if len(tag) > 128: raise errors.ParameterError( 'Tags can be at most 128 characters long.' ) if not re.match('^(?![.-])[a-zA-Z0-9_.-]{1,128}$', tag): raise errors.ParameterError(( 'Tag {} is invalid. \n' 'Only characters a-z, A-Z, 0-9, ., - and _ ' 'are allowed. \nTag can\'t start with a . or -' ).format(tag)) if any(t for t in dataset.tags if t.name == tag): if force: # remove duplicate tag dataset.tags = [t for t in dataset.tags if t.name != tag] else: raise errors.ParameterError( 'Tag {} already exists'.format(tag) ) latest_commit = list(self.dataset_commits(dataset, max_results=1))[0] tag = DatasetTag( name=tag, description=description, commit=latest_commit.hexsha, dataset=dataset.name ) dataset.tags.append(tag) return dataset
[docs] def remove_dataset_tags(self, dataset, tags): """Removes tags from a dataset.""" tag_names = {t.name for t in dataset.tags} not_found = set(tags).difference(tag_names) if len(not_found) > 0: raise errors.ParameterError( 'Tags {} not found'.format(', '.join(not_found)) ) dataset.tags = [t for t in dataset.tags if t.name not in tags] return dataset
[docs] def update_dataset_files(self, files, ref, delete=False): """Update files and dataset metadata according to their remotes. :param files: List of files to be updated :param delete: Indicates whether to delete files or not :return: List of files that should be deleted """ from renku import LocalClient visited_repos = {} updated_files = [] deleted_files = [] for file_ in files: if not file_.based_on: continue file_.based_on = DatasetFile.from_jsonld(file_.based_on) based_on = file_.based_on url = based_on.url if url in visited_repos: repo, repo_path, remote_client = visited_repos[url] else: repo, repo_path = self.prepare_git_repo(url, ref) remote_client = LocalClient(repo_path) visited_repos[url] = repo, repo_path, remote_client remote_file = self._fetch_file_metadata( remote_client, based_on.path ) if not remote_file: try: remote_file = DatasetFile.from_revision( remote_client, path=based_on.path, url=url, added=based_on.added ) except KeyError: raise errors.ParameterError( 'Cannot find file {} in the repo {}'.format( based_on.url, url ) ) commit_sha = self._get_commit_sha_from_label(based_on) remote_commit_sha = self._get_commit_sha_from_label(remote_file) if commit_sha != remote_commit_sha: src = Path(repo.working_dir) / based_on.path dst = self.renku_path.parent / file_.path if src.exists(): # Fetch file is it is tracked by Git LFS self._fetch_lfs_files(repo_path, {based_on.path}) if remote_client._is_external_file(src): self.remove_file(dst) self._create_external_file(src.resolve(), dst) else: shutil.copy(src, dst) file_.based_on.commit = remote_file.commit file_.based_on._label = remote_file._label updated_files.append(file_) else: # File was removed or renamed if delete: self.remove_file(dst) deleted_files.append(file_) if not updated_files and (not delete or not deleted_files): # Nothing to commit or update return deleted_files # Commit changes in files file_paths = { str(self.path / f.path) for f in updated_files + deleted_files } # Force-add to include possible ignored files that are in datasets self.repo.git.add(*(file_paths), force=True) skip_hooks = not self.external_storage_requested self.repo.index.commit( 'renku dataset: updated {} files and deleted {} files'.format( len(updated_files), len(deleted_files), skip_hooks=skip_hooks ) ) # Update datasets' metadata modified_datasets = {} for file_ in updated_files: # Re-create list of creators creators = [] # grab all the creators from the commit history for commit in repo.iter_commits(paths=file_.path): creator = Person.from_commit(commit) if creator not in creators: creators.append(creator) new_file = DatasetFile.from_revision( self, path=file_.path, based_on=file_.based_on, creator=creators ) file_.dataset.update_files([new_file]) modified_datasets[file_.dataset.name] = file_.dataset if delete: for file_ in deleted_files: file_.dataset.unlink_file(file_.path) modified_datasets[file_.dataset.name] = file_.dataset for dataset in modified_datasets.values(): dataset.to_yaml() return deleted_files
def _create_external_file(self, src, dst): """Create a new external file.""" try: pointer_file = self._create_pointer_file(target=src) relative = os.path.relpath(pointer_file, dst.parent) os.symlink(relative, dst) except OSError as e: raise errors.OperationError( 'Could not create symbolic link' ) from e def _create_pointer_file(self, target, checksum=None): """Create a new pointer file.""" target = Path(target).resolve() if checksum is None: checksum = self._calculate_checksum(target) while True: filename = '{}-{}'.format(uuid.uuid4(), checksum) path = self.renku_pointers_path / filename if not path.exists(): break try: os.symlink(target, path) except FileNotFoundError: raise errors.ParameterError( 'Cannot find external file {}'.format(target) ) return path def _calculate_checksum(self, filepath): try: return self.repo.git.hash_object(str(filepath)) except GitCommandError: return None
[docs] def update_external_files(self, records): """Update files linked to external storage.""" updated_files_paths = [] updated_datasets = {} for file_ in records: if file_.external: path = self.path / file_.path link = path.parent / os.readlink(path) pointer_file = self.path / link pointer_file = self._update_pointer_file(pointer_file) if pointer_file is not None: relative = os.path.relpath(pointer_file, path.parent) os.remove(path) os.symlink(relative, path) updated_files_paths.append(str(path)) updated_datasets[file_.dataset.short_name] = file_.dataset if not updated_files_paths: return self.repo.git.add(*updated_files_paths, force=True) self.repo.git.add(self.renku_pointers_path, force=True) commit = self.repo.index.commit( 'renku dataset: updated {} external files'.format( len(updated_files_paths) ) ) for dataset in updated_datasets.values(): for file_ in dataset.files: if str(self.path / file_.path) in updated_files_paths: file_.commit = commit file_._label = file_.default_label() dataset.to_yaml()
def _update_pointer_file(self, pointer_file_path): """Update a pointer file.""" try: target = pointer_file_path.resolve(strict=True) except FileNotFoundError: target = pointer_file_path.resolve() raise errors.ParameterError( 'External file not found: {}'.format(target) ) checksum = self._calculate_checksum(target) current_checksum = pointer_file_path.name.split('-')[-1] if checksum == current_checksum: return os.remove(pointer_file_path) return self._create_pointer_file(target, checksum=checksum)
[docs] def remove_file(self, filepath): """Remove a file/symlink and its pointer file (for external files).""" path = Path(filepath) try: link = path.parent / os.readlink(path) except FileNotFoundError: return except OSError: # not a symlink but a normal file os.remove(path) return os.remove(path) try: os.remove(link) except FileNotFoundError: pass
def _is_external_file(self, path): """Checks if a path within repo is an external file.""" if not Path(path).is_symlink() or not self._is_path_within_repo(path): return False pointer = os.readlink(path) return f'{self.renku_home}/{self.POINTERS}' in pointer
[docs] def has_external_files(self): """Return True if project has external files.""" for dataset in self.datasets.values(): for file_ in dataset.files: if file_.external: return True
def _is_path_within_repo(self, path): if not os.path.isabs(path): path = os.path.abspath(path) path = Path(path) try: path.relative_to(self.path) except ValueError: return False else: return True
[docs] def prepare_git_repo(self, url, ref=None): """Clone and cache a Git repo.""" if not url: raise errors.GitError('Invalid URL.') RENKU_BRANCH = 'renku-default-branch' def checkout(repo, ref): try: repo.git.checkout(ref) except GitCommandError: raise errors.ParameterError( 'Cannot find reference "{}" in Git repository: {}'.format( ref, url ) ) ref = ref or RENKU_BRANCH u = GitURL.parse(url) path = u.pathname if u.hostname == 'localhost': path = str(Path(path).resolve()) url = path repo_name = os.path.splitext(os.path.basename(path))[0] path = os.path.dirname(path).lstrip('/') repo_path = ( self.renku_path / self.CACHE / u.hostname / path / repo_name ) if repo_path.exists(): repo = Repo(str(repo_path)) if repo.remotes.origin.url == url: try: repo.git.fetch(all=True) repo.git.checkout(ref) try: repo.git.pull() except GitError: # When ref is not a branch, an error is thrown pass except GitError: # ignore the error and try re-cloning pass else: return repo, repo_path try: shutil.rmtree(str(repo_path)) except PermissionError: raise errors.InvalidFileOperation( 'Cannot delete files in {}: Permission denied'. format(repo_path) ) repo = clone(url, path=str(repo_path), install_githooks=False) # Because the name of the default branch is not always 'master', we # create an alias of the default branch when cloning the repo. It # is used to refer to the default branch later. renku_ref = 'refs/heads/' + RENKU_BRANCH try: repo.git.execute([ 'git', 'symbolic-ref', renku_ref, repo.head.reference.path ]) checkout(repo, ref) except GitCommandError as e: raise errors.GitError( 'Cannot clone remote Git repo: {}'.format(url) ) from e else: return repo, repo_path
@staticmethod def _fetch_file_metadata(client, path): """Return metadata for a single file.""" for _, dataset in client.datasets.items(): for file_ in dataset.files: if file_.path == path: return file_ @staticmethod def _get_commit_sha_from_label(dataset_file): label = dataset_file._label if '@' in label: return label.split('@')[1] return label def _download( self, url, filename, extract, progress_class=None, chunk_size=16384 ): def extract_dataset(filepath): """Extract downloaded file.""" try: tmp = tempfile.mkdtemp() patoolib.extract_archive( str(filepath), outdir=tmp, verbosity=-1 ) except patoolib.util.PatoolError: return filepath.parent, [filepath] else: filepath.unlink() return Path(tmp), [p for p in Path(tmp).rglob('*')] tmp_root = self.renku_path / self.CACHE tmp_root.mkdir(parents=True, exist_ok=True) tmp = tempfile.mkdtemp(dir=tmp_root) with requests.get(url, stream=True) as request: request.raise_for_status() if not filename: u = parse.urlparse(url) filename = Path(u.path).name if not filename: raise errors.ParameterError( f'URL Cannot find a file to download from {url}' ) download_to = Path(tmp) / filename with open(str(download_to), 'wb') as file_: total_size = int(request.headers.get('content-length', 0)) progress_class = progress_class or DownloadProgressCallback progress = progress_class( description=filename, total_size=total_size ) try: for chunk in request.iter_content(chunk_size=chunk_size): if chunk: # ignore keep-alive chunks file_.write(chunk) progress.update(size=len(chunk)) finally: progress.finalize() if extract: return extract_dataset(download_to) return download_to.parent, [download_to]
[docs]class DownloadProgressCallback: """Interface to report various stages of a download.""" def __init__(self, description, total_size): """Default initializer."""
[docs] def update(self, size): """Update the status."""
[docs] def finalize(self): """Called once when the download is finished."""
def _check_url(url): """Check if a url is local/remote and if it contains a git repository.""" u = parse.urlparse(url) if u.scheme not in Dataset.SUPPORTED_SCHEMES: raise errors.UrlSchemeNotSupported( 'Scheme "{}" not supported'.format(u.scheme) ) is_remote = u.scheme not in ('', 'file') or url.startswith('git@') is_git = False if is_remote: is_git = u.path.endswith('.git') else: try: Repo(u.path, search_parent_directories=True) except GitError: pass else: is_git = True return is_remote, is_git DATASET_METADATA_PATHS = [ Path(RENKU_HOME) / Path(DatasetsApiMixin.DATASETS), Path(RENKU_HOME) / Path(DatasetsApiMixin.POINTERS), Path(RENKU_HOME) / Path(LinkReference.REFS), '.gitattributes', ]