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sourcecache.py
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/
sourcecache.py
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__authors__ = "Johannes Köster"
__copyright__ = "Copyright 2022, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import hashlib
from pathlib import Path
import re
import os
from snakemake import utils
import tempfile
import io
from abc import ABC, abstractmethod
from datetime import datetime
from snakemake.common import (
ON_WINDOWS,
is_local_file,
get_appdirs,
parse_uri,
smart_join,
)
from snakemake.exceptions import WorkflowError, SourceFileError
from snakemake.io import git_content, split_git_path
from snakemake.logging import logger
def _check_git_args(tag: str = None, branch: str = None, commit: str = None):
n_refs = sum(1 for ref in (tag, branch, commit) if ref is not None)
if n_refs != 1:
raise SourceFileError(
"exactly one of tag, branch, or commit must be specified."
)
class SourceFile(ABC):
@abstractmethod
def get_path_or_uri(self):
...
@abstractmethod
def is_persistently_cacheable(self):
...
def get_uri_hash(self):
urihash = hashlib.sha256()
urihash.update(self.get_path_or_uri().encode())
return urihash.hexdigest()
def get_basedir(self):
path = os.path.dirname(self.get_path_or_uri())
return self.__class__(path)
@abstractmethod
def get_filename(self):
...
def join(self, path):
if isinstance(path, SourceFile):
path = path.get_path_or_uri()
return self.__class__(smart_join(self.get_path_or_uri(), path))
def mtime(self):
"""If possible, return mtime of the file. Otherwise, return None."""
return None
def __hash__(self):
return self.get_path_or_uri().__hash__()
def __eq__(self, other):
if isinstance(other, SourceFile):
return self.get_path_or_uri() == other.get_path_or_uri()
return False
def __str__(self):
return self.get_path_or_uri()
def simplify_path(self):
return self
class GenericSourceFile(SourceFile):
def __init__(self, path_or_uri):
self.path_or_uri = path_or_uri
def get_path_or_uri(self):
return self.path_or_uri
def get_filename(self):
return os.path.basename(self.path_or_uri)
def is_persistently_cacheable(self):
return False
class LocalSourceFile(SourceFile):
def __init__(self, path):
self.path = path
def get_path_or_uri(self):
return self.path
def is_persistently_cacheable(self):
return False
def get_filename(self):
return os.path.basename(self.path)
def abspath(self):
return LocalSourceFile(os.path.abspath(self.path))
def isabs(self):
return os.path.isabs(self.path)
def simplify_path(self):
return utils.simplify_path(self.path)
def mtime(self):
return os.stat(self.path).st_mtime
def __fspath__(self):
return self.path
class LocalGitFile(SourceFile):
def __init__(
self, repo_path, path: str, tag: str = None, ref: str = None, commit: str = None
):
_check_git_args(tag, ref, commit)
self.tag = tag
self.commit = commit
self._ref = ref
self.repo_path = repo_path
self.path = path
def get_path_or_uri(self):
return "git+{}/{}@{}".format(self.repo_path, self.path, self.ref)
def join(self, path):
return LocalGitFile(
self.repo_path,
"/".join((self.path, path)),
tag=self.tag,
ref=self.ref,
commit=self.commit,
)
def is_persistently_cacheable(self):
return False
def get_filename(self):
return os.path.basename(self.path)
@property
def ref(self):
return self.tag or self.commit or self._ref
class HostingProviderFile(SourceFile):
"""Marker for denoting github source files from releases."""
valid_repo = re.compile("^.+/.+$")
def __init__(
self,
repo: str = None,
path: str = None,
tag: str = None,
branch: str = None,
commit: str = None,
):
if repo is None:
raise SourceFileError("repo must be given")
if not self.__class__.valid_repo.match(repo):
raise SourceFileError(
"repo {} is not a valid repo specification (must be given as owner/name)."
)
_check_git_args(tag, branch, commit)
if path is None:
raise SourceFileError("path must be given")
if not all(
isinstance(item, str)
for item in (repo, path, tag, branch, commit)
if item is not None
):
raise SourceFileError("arguments must be given as str.")
self.repo = repo
self.tag = tag
self.commit = commit
self.branch = branch
self.path = path.strip("/")
def is_persistently_cacheable(self):
return self.tag or self.commit
def get_filename(self):
return os.path.basename(self.path)
@property
def ref(self):
return self.tag or self.commit or self.branch
def get_basedir(self):
return self.__class__(
repo=self.repo,
path=os.path.dirname(self.path),
tag=self.tag,
commit=self.commit,
branch=self.branch,
)
def join(self, path):
path = os.path.normpath("{}/{}".format(self.path, path))
if ON_WINDOWS:
# convert back to URL separators
# (win specific separators are introduced by normpath above)
path = path.replace("\\", "/")
return self.__class__(
repo=self.repo,
path=path,
tag=self.tag,
commit=self.commit,
branch=self.branch,
)
class GithubFile(HostingProviderFile):
def get_path_or_uri(self):
return "https://github.com/{}/raw/{}/{}".format(self.repo, self.ref, self.path)
class GitlabFile(HostingProviderFile):
def __init__(
self,
repo: str,
path: str,
tag: str = None,
branch: str = None,
commit: str = None,
host: str = None,
):
super().__init__(repo, path, tag, branch, commit)
self.host = host
def get_path_or_uri(self):
return "https://{}/{}/-/raw/{}/{}".format(
self.host or "gitlab.com", self.repo, self.ref, self.path
)
def infer_source_file(path_or_uri, basedir: SourceFile = None):
if isinstance(path_or_uri, SourceFile):
if basedir is None or isinstance(path_or_uri, HostingProviderFile):
return path_or_uri
else:
path_or_uri = path_or_uri.get_path_or_uri()
if isinstance(path_or_uri, Path):
path_or_uri = str(path_or_uri)
if not isinstance(path_or_uri, str):
raise SourceFileError(
"must be given as Python string or one of the predefined source file marker types (see docs)"
)
if is_local_file(path_or_uri):
# either local file or relative to some remote basedir
for schema in ("file://", "file:"):
if path_or_uri.startswith(schema):
path_or_uri = path_or_uri[len(schema) :]
break
if not os.path.isabs(path_or_uri) and basedir is not None:
return basedir.join(path_or_uri)
return LocalSourceFile(path_or_uri)
if path_or_uri.startswith("git+file:"):
root_path, file_path, ref = split_git_path(path_or_uri)
return LocalGitFile(root_path, file_path, ref=ref)
# something else
return GenericSourceFile(path_or_uri)
class SourceCache:
cache_whitelist = [
"https://raw.githubusercontent.com/snakemake/snakemake-wrappers/\d+\.\d+.\d+"
] # TODO add more prefixes for uris that are save to be cached
def __init__(self, runtime_cache_path=None):
self.cache = Path(
os.path.join(get_appdirs().user_cache_dir, "snakemake/source-cache")
)
os.makedirs(self.cache, exist_ok=True)
if runtime_cache_path is None:
runtime_cache_parent = self.cache / "runtime-cache"
os.makedirs(runtime_cache_parent, exist_ok=True)
self.runtime_cache = tempfile.TemporaryDirectory(
suffix="snakemake-runtime-source-cache",
dir=runtime_cache_parent,
)
self._runtime_cache_path = None
else:
self._runtime_cache_path = runtime_cache_path
self.runtime_cache = None
self.cacheable_prefixes = re.compile("|".join(self.cache_whitelist))
@property
def runtime_cache_path(self):
return self._runtime_cache_path or self.runtime_cache.name
def lock_cache(self, entry):
from filelock import FileLock
return FileLock(entry.with_suffix(".lock"))
def open(self, source_file, mode="r"):
cache_entry = self._cache(source_file)
return self._open(cache_entry, mode)
def exists(self, source_file):
try:
self._cache(source_file)
except Exception:
return False
return True
def get_path(self, source_file, mode="r"):
cache_entry = self._cache(source_file)
return cache_entry
def _cache_entry(self, source_file):
urihash = source_file.get_uri_hash()
# TODO add git support to smart_open!
if source_file.is_persistently_cacheable():
# check cache
return self.cache / urihash
else:
# check runtime cache
return Path(self.runtime_cache_path) / urihash
def _cache(self, source_file):
cache_entry = self._cache_entry(source_file)
with self.lock_cache(cache_entry):
if not cache_entry.exists():
self._do_cache(source_file, cache_entry)
return cache_entry
def _do_cache(self, source_file, cache_entry):
# open from origin
with self._open(source_file.get_path_or_uri(), "rb") as source, open(
cache_entry, "wb"
) as cache_source:
cache_source.write(source.read())
mtime = source_file.mtime()
if mtime is not None:
# Set to mtime of original file
# In case we don't have that mtime, it is fine
# to just keep the time at the time of caching
# as mtime.
os.utime(cache_entry, times=(mtime, mtime))
def _open(self, path_or_uri, mode):
from smart_open import open
if isinstance(path_or_uri, LocalGitFile):
import git
return io.BytesIO(
git.Repo(path_or_uri.repo_path)
.git.show("{}:{}".format(path_or_uri.ref, path_or_uri.path))
.encode()
)
if isinstance(path_or_uri, SourceFile):
path_or_uri = path_or_uri.get_path_or_uri()
try:
return open(path_or_uri, mode)
except Exception as e:
raise WorkflowError("Failed to open source file {}".format(path_or_uri), e)