/usr/lib/python3/dist-packages/reprounzip/common.py is in python3-reprounzip 1.0.10-1.
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# This file is part of ReproZip which is released under the Revised BSD License
# See file LICENSE for full license details.
# This file is shared:
# reprozip/reprozip/common.py
# reprounzip/reprounzip/common.py
"""Common functions between reprozip and reprounzip.
This module contains functions that are specific to the reprozip software and
its data formats, but that are shared between the reprozip and reprounzip
packages. Because the packages can be installed separately, these functions are
in a separate module which is duplicated between the packages.
As long as these are small in number, they are not worth putting in a separate
package that reprozip and reprounzip would both depend on.
"""
from __future__ import division, print_function, unicode_literals
import atexit
import contextlib
import copy
from datetime import datetime
from distutils.version import LooseVersion
import functools
import logging
import logging.handlers
import os
from rpaths import PosixPath, Path
import sys
import tarfile
import usagestats
import yaml
from .utils import iteritems, itervalues, unicode_, stderr, UniqueNames, \
escape, CommonEqualityMixin, optional_return_type, hsize, join_root, \
copyfile
FILE_READ = 0x01
FILE_WRITE = 0x02
FILE_WDIR = 0x04
FILE_STAT = 0x08
FILE_LINK = 0x10
class File(CommonEqualityMixin):
"""A file, used at some point during the experiment.
"""
comment = None
def __init__(self, path, size=None):
self.path = path
self.size = size
def __eq__(self, other):
return (isinstance(other, File) and
self.path == other.path)
def __hash__(self):
return hash(self.path)
class Package(CommonEqualityMixin):
"""A distribution package, containing a set of files.
"""
def __init__(self, name, version, files=None, packfiles=True, size=None):
self.name = name
self.version = version
self.files = list(files) if files is not None else []
self.packfiles = packfiles
self.size = size
def add_file(self, file_):
self.files.append(file_)
def __unicode__(self):
return '%s (%s)' % (self.name, self.version)
__str__ = __unicode__
# Pack format history:
# 1: used by reprozip 0.2 through 0.7. Single tar.gz file, metadata under
# METADATA/, data under DATA/
# 2: pack is usually not compressed, metadata under METADATA/, data in another
# DATA.tar.gz (files inside it still have the DATA/ prefix for ease-of-use
# in unpackers)
#
# Pack metadata history:
# 0.2: used by reprozip 0.2
# 0.2.1:
# config: comments directories as such in config
# trace database: adds executed_files.workingdir, adds processes.exitcode
# data: packs dynamic linkers
# 0.3:
# config: don't list missing (unpacked) files in config
# trace database: adds opened_files.is_directory
# 0.3.1: no change
# 0.3.2: no change
# 0.4:
# config: adds input_files, output_files, lists parent directories
# 0.4.1: no change
# 0.5: no change
# 0.6: no change
# 0.7:
# moves input_files and output_files from run to global scope
# adds processes.is_thread column to trace database
# 0.8: adds 'id' field to run
class RPZPack(object):
"""Encapsulates operations on the RPZ pack format.
"""
def __init__(self, pack):
self.pack = Path(pack)
self.tar = tarfile.open(str(self.pack), 'r:*')
f = self.tar.extractfile('METADATA/version')
version = f.read()
f.close()
if version.startswith(b'REPROZIP VERSION '):
try:
version = int(version[17:].rstrip())
except ValueError:
version = None
if version in (1, 2):
self.version = version
self.data_prefix = PosixPath(b'DATA')
else:
raise ValueError(
"Unknown format version %r (maybe you should upgrade "
"reprounzip? I only know versions 1 and 2" % version)
else:
raise ValueError("File doesn't appear to be a RPZ pack")
if self.version == 1:
self.data = self.tar
elif version == 2:
self.data = tarfile.open(
fileobj=self.tar.extractfile('DATA.tar.gz'),
mode='r:*')
else:
assert False
def remove_data_prefix(self, path):
if not isinstance(path, PosixPath):
path = PosixPath(path)
components = path.components[1:]
if not components:
return path.__class__('')
return path.__class__(*components)
def open_config(self):
"""Gets the configuration file.
"""
return self.tar.extractfile('METADATA/config.yml')
def extract_config(self, target):
"""Extracts the config to the specified path.
It is up to the caller to remove that file once done.
"""
member = copy.copy(self.tar.getmember('METADATA/config.yml'))
member.name = str(target.components[-1])
self.tar.extract(member,
path=str(Path.cwd() / target.parent))
target.chmod(0o644)
assert target.is_file()
@contextlib.contextmanager
def with_config(self):
"""Context manager that extracts the config to a temporary file.
"""
fd, tmp = Path.tempfile(prefix='reprounzip_')
os.close(fd)
self.extract_config(tmp)
yield tmp
tmp.remove()
def extract_trace(self, target):
"""Extracts the trace database to the specified path.
It is up to the caller to remove that file once done.
"""
target = Path(target)
if self.version == 1:
member = self.tar.getmember('METADATA/trace.sqlite3')
elif self.version == 2:
try:
member = self.tar.getmember('METADATA/trace.sqlite3.gz')
except KeyError:
member = self.tar.getmember('METADATA/trace.sqlite3')
else:
assert False
member = copy.copy(member)
member.name = str(target.components[-1])
self.tar.extract(member,
path=str(Path.cwd() / target.parent))
target.chmod(0o644)
assert target.is_file()
@contextlib.contextmanager
def with_trace(self):
"""Context manager that extracts the trace database to a temporary file.
"""
fd, tmp = Path.tempfile(prefix='reprounzip_')
os.close(fd)
self.extract_trace(tmp)
yield tmp
tmp.remove()
def list_data(self):
"""Returns tarfile.TarInfo objects for all the data paths.
"""
return [copy.copy(m)
for m in self.data.getmembers()
if m.name.startswith('DATA/')]
def data_filenames(self):
"""Returns a set of filenames for all the data paths.
Those paths begin with a slash / and the 'DATA' prefix has been
removed.
"""
return set(PosixPath(m.name[4:])
for m in self.data.getmembers()
if m.name.startswith('DATA/'))
def get_data(self, path):
"""Returns a tarfile.TarInfo object for the data path.
Raises KeyError if no such path exists.
"""
path = PosixPath(path)
path = join_root(PosixPath(b'DATA'), path)
return copy.copy(self.data.getmember(path))
def extract_data(self, root, members):
"""Extracts the given members from the data tarball.
The members must come from get_data().
"""
self.data.extractall(str(root), members)
def copy_data_tar(self, target):
"""Copies the file in which the data lies to the specified destination.
"""
if self.version == 1:
self.pack.copyfile(target)
elif self.version == 2:
with target.open('wb') as fp:
data = self.tar.extractfile('DATA.tar.gz')
copyfile(data, fp)
data.close()
def close(self):
if self.data is not self.tar:
self.data.close()
self.tar.close()
self.data = self.tar = None
class InvalidConfig(ValueError):
"""Configuration file is invalid.
"""
def read_files(files, File=File):
if files is None:
return []
return [File(PosixPath(f)) for f in files]
def read_packages(packages, File=File, Package=Package):
if packages is None:
return []
new_pkgs = []
for pkg in packages:
pkg['files'] = read_files(pkg['files'], File)
new_pkgs.append(Package(**pkg))
return new_pkgs
Config = optional_return_type(['runs', 'packages', 'other_files'],
['inputs_outputs', 'additional_patterns',
'format_version'])
@functools.total_ordering
class InputOutputFile(object):
def __init__(self, path, read_runs, write_runs):
self.path = path
self.read_runs = read_runs
self.write_runs = write_runs
def __eq__(self, other):
return ((self.path, self.read_runs, self.write_runs) ==
(other.path, other.read_runs, other.write_runs))
def __lt__(self, other):
return self.path < other.path
def __repr__(self):
return "<InputOutputFile(path=%r, read_runs=%r, write_runs=%r)>" % (
self.path, self.read_runs, self.write_runs)
def load_iofiles(config, runs):
"""Loads the inputs_outputs part of the configuration.
This tests for duplicates, merge the lists of executions, and optionally
loads from the runs for reprozip < 0.7 compatibility.
"""
files_list = config.get('inputs_outputs') or []
# reprozip < 0.7 compatibility: read input_files and output_files from runs
if 'inputs_outputs' not in config:
for i, run in enumerate(runs):
for rkey, wkey in (('input_files', 'read_by_runs'),
('output_files', 'written_by_runs')):
for k, p in iteritems(run.pop(rkey, {})):
files_list.append({'name': k,
'path': p,
wkey: [i]})
files = {} # name:str: InputOutputFile
paths = {} # path:PosixPath: name:str
required_keys = set(['name', 'path'])
optional_keys = set(['read_by_runs', 'written_by_runs'])
uniquenames = UniqueNames()
for i, f in enumerate(files_list):
keys = set(f)
if (not keys.issubset(required_keys | optional_keys) or
not keys.issuperset(required_keys)):
raise InvalidConfig("File #%d has invalid keys")
name = f['name']
path = PosixPath(f['path'])
readers = sorted(f.get('read_by_runs', []))
writers = sorted(f.get('written_by_runs', []))
if name in files:
if files[name].path != path:
old_name, name = name, uniquenames(name)
logging.warning("File name appears multiple times: %s\n"
"Using name %s instead",
old_name, name)
else:
uniquenames.insert(name)
if path in paths:
if paths[path] == name:
logging.warning("File appears multiple times: %s", name)
else:
logging.warning("Two files have the same path (but different "
"names): %s, %s\nUsing name %s",
name, paths[path], paths[path])
name = paths[path]
files[name].read_runs.update(readers)
files[name].write_runs.update(writers)
else:
paths[path] = name
files[name] = InputOutputFile(path, readers, writers)
return files
def load_config(filename, canonical, File=File, Package=Package):
"""Loads a YAML configuration file.
`File` and `Package` parameters can be used to override the classes that
will be used to hold files and distribution packages; useful during the
packing step.
`canonical` indicates whether a canonical configuration file is expected
(in which case the ``additional_patterns`` section is not accepted). Note
that this changes the number of returned values of this function.
"""
with filename.open(encoding='utf-8') as fp:
config = yaml.safe_load(fp)
ver = LooseVersion(config['version'])
keys_ = set(config)
if 'version' not in keys_:
raise InvalidConfig("Missing version")
# Accepts versions from 0.2 to 0.8 inclusive
elif not LooseVersion('0.2') <= ver < LooseVersion('0.9'):
pkgname = (__package__ or __name__).split('.', 1)[0]
raise InvalidConfig("Loading configuration file in unknown format %s; "
"this probably means that you should upgrade "
"%s" % (ver, pkgname))
unknown_keys = keys_ - set(['pack_id', 'version', 'runs',
'inputs_outputs',
'packages', 'other_files',
'additional_patterns',
# Deprecated
'input_files', 'output_files'])
if unknown_keys:
logging.warning("Unrecognized sections in configuration: %s",
', '.join(unknown_keys))
runs = config.get('runs') or []
packages = read_packages(config.get('packages'), File, Package)
other_files = read_files(config.get('other_files'), File)
inputs_outputs = load_iofiles(config, runs)
# reprozip < 0.7 compatibility: set inputs/outputs on runs (for plugins)
for i, run in enumerate(runs):
run['input_files'] = dict((n, f.path)
for n, f in iteritems(inputs_outputs)
if i in f.read_runs)
run['output_files'] = dict((n, f.path)
for n, f in iteritems(inputs_outputs)
if i in f.write_runs)
# reprozip < 0.8 compatibility: assign IDs to runs
for i, run in enumerate(runs):
if run.get('id') is None:
run['id'] = "run%d" % i
record_usage_package(runs, packages, other_files,
inputs_outputs,
pack_id=config.get('pack_id'))
kwargs = {'format_version': ver,
'inputs_outputs': inputs_outputs}
if canonical:
if 'additional_patterns' in config:
raise InvalidConfig("Canonical configuration file shouldn't have "
"additional_patterns key anymore")
else:
kwargs['additional_patterns'] = config.get('additional_patterns') or []
return Config(runs, packages, other_files,
**kwargs)
def write_file(fp, fi, indent=0):
fp.write("%s - \"%s\"%s\n" % (
" " * indent,
escape(unicode_(fi.path)),
' # %s' % fi.comment if fi.comment is not None else ''))
def write_package(fp, pkg, indent=0):
indent_str = " " * indent
fp.write("%s - name: \"%s\"\n" % (indent_str, escape(pkg.name)))
fp.write("%s version: \"%s\"\n" % (indent_str, escape(pkg.version)))
if pkg.size is not None:
fp.write("%s size: %d\n" % (indent_str, pkg.size))
fp.write("%s packfiles: %s\n" % (indent_str, 'true' if pkg.packfiles
else 'false'))
fp.write("%s files:\n"
"%s # Total files used: %s\n" % (
indent_str, indent_str,
hsize(sum(fi.size
for fi in pkg.files
if fi.size is not None))))
if pkg.size is not None:
fp.write("%s # Installed package size: %s\n" % (
indent_str, hsize(pkg.size)))
for fi in sorted(pkg.files, key=lambda fi_: fi_.path):
write_file(fp, fi, indent + 1)
def save_config(filename, runs, packages, other_files, reprozip_version,
inputs_outputs=None,
canonical=False, pack_id=None):
"""Saves the configuration to a YAML file.
`canonical` indicates whether this is a canonical configuration file
(no ``additional_patterns`` section).
"""
dump = lambda x: yaml.safe_dump(x, encoding='utf-8', allow_unicode=True)
with filename.open('w', encoding='utf-8', newline='\n') as fp:
# Writes preamble
fp.write("""\
# ReproZip configuration file
# This file was generated by reprozip {version} at {date}
{what}
# Run info{pack_id}
version: "{format!s}"
""".format(pack_id=(('\npack_id: "%s"' % pack_id) if pack_id is not None
else ''),
version=escape(reprozip_version),
format='0.8',
date=datetime.now().isoformat(),
what=("# It was generated by the packer and you shouldn't need to "
"edit it" if canonical
else "# You might want to edit this file before running the "
"packer\n# See 'reprozip pack -h' for help")))
fp.write("runs:\n")
for i, run in enumerate(runs):
# Remove reprozip < 0.7 compatibility fields
run = dict((k, v) for k, v in iteritems(run)
if k not in ('input_files', 'output_files'))
fp.write("# Run %d\n" % i)
fp.write(dump([run]).decode('utf-8'))
fp.write("\n")
fp.write("""\
# Input and output files
# Inputs are files that are only read by a run; reprounzip can replace these
# files on demand to run the experiment with custom data.
# Outputs are files that are generated by a run; reprounzip can extract these
# files from the experiment on demand, for the user to examine.
# The name field is the identifier the user will use to access these files.
inputs_outputs:""")
for n, f in iteritems(inputs_outputs):
fp.write("""\
- name: {name}
path: {path}
written_by_runs: {writers}
read_by_runs: {readers}""".format(name=n, path=unicode_(f.path),
readers=repr(f.read_runs),
writers=repr(f.write_runs)))
fp.write("""\
# Files to pack
# All the files below were used by the program; they will be included in the
# generated package
# These files come from packages; we can thus choose not to include them, as it
# will simply be possible to install that package on the destination system
# They are included anyway by default
packages:
""")
# Writes files
for pkg in sorted(packages, key=lambda p: p.name):
write_package(fp, pkg)
fp.write("""\
# These files do not appear to come with an installed package -- you probably
# want them packed
other_files:
""")
for f in sorted(other_files, key=lambda fi: fi.path):
write_file(fp, f)
if not canonical:
fp.write("""\
# If you want to include additional files in the pack, you can list additional
# patterns of files that will be included
additional_patterns:
# Example:
# - /etc/apache2/** # Everything under apache2/
# - /var/log/apache2/*.log # Log files directly under apache2/
# - /var/lib/lxc/*/rootfs/home/**/*.py # All Python files of all users in
# # that container
""")
class LoggingDateFormatter(logging.Formatter):
"""Formatter that puts milliseconds in the timestamp.
"""
converter = datetime.fromtimestamp
def formatTime(self, record, datefmt=None):
ct = self.converter(record.created)
t = ct.strftime("%H:%M:%S")
s = "%s.%03d" % (t, record.msecs)
return s
def setup_logging(tag, verbosity):
"""Sets up the logging module.
"""
levels = [logging.CRITICAL, logging.WARNING, logging.INFO, logging.DEBUG]
console_level = levels[min(verbosity, 3)]
file_level = logging.INFO
min_level = min(console_level, file_level)
# Create formatter, with same format as C extension
fmt = "[%s] %%(asctime)s %%(levelname)s: %%(message)s" % tag
formatter = LoggingDateFormatter(fmt)
# Console logger
handler = logging.StreamHandler()
handler.setLevel(console_level)
handler.setFormatter(formatter)
# Set up logger
logger = logging.root
logger.setLevel(min_level)
logger.addHandler(handler)
# File logger
dotrpz = Path('~/.reprozip').expand_user()
try:
if not dotrpz.is_dir():
dotrpz.mkdir()
filehandler = logging.handlers.RotatingFileHandler(str(dotrpz / 'log'),
mode='a',
delay=False,
maxBytes=400000,
backupCount=5)
except (IOError, OSError):
logging.warning("Couldn't create log file %s", dotrpz / 'log')
else:
filehandler.setFormatter(formatter)
filehandler.setLevel(file_level)
logger.addHandler(filehandler)
filehandler.emit(logging.root.makeRecord(
__name__.split('.', 1)[0],
logging.INFO,
"(log start)", 0,
"Log opened %s %s",
(datetime.now().strftime("%Y-%m-%d"), sys.argv),
None))
_usage_report = None
def setup_usage_report(name, version):
"""Sets up the usagestats module.
"""
global _usage_report
certificate_file = get_reprozip_ca_certificate()
_usage_report = usagestats.Stats(
'~/.reprozip/usage_stats',
usagestats.Prompt(enable='%s usage_report --enable' % name,
disable='%s usage_report --disable' % name),
os.environ.get('REPROZIP_USAGE_URL',
'https://stats.reprozip.org/'),
version='%s %s' % (name, version),
unique_user_id=True,
env_var='REPROZIP_USAGE_STATS',
ssl_verify=certificate_file.path)
try:
os.getcwd().encode('ascii')
except (UnicodeEncodeError, UnicodeDecodeError):
record_usage(cwd_ascii=False)
else:
record_usage(cwd_ascii=True)
def enable_usage_report(enable):
"""Enables or disables usage reporting.
"""
if enable:
_usage_report.enable_reporting()
stderr.write("Thank you, usage reports will be sent automatically "
"from now on.\n")
else:
_usage_report.disable_reporting()
stderr.write("Usage reports will not be collected nor sent.\n")
def record_usage(**kwargs):
"""Records some info in the current usage report.
"""
if _usage_report is not None:
_usage_report.note(kwargs)
def record_usage_package(runs, packages, other_files,
inputs_outputs,
pack_id=None):
"""Records the info on some pack file into the current usage report.
"""
if _usage_report is None:
return
for run in runs:
record_usage(argv0=run['argv'][0])
record_usage(pack_id=pack_id or '',
nb_packages=len(packages),
nb_package_files=sum(len(pkg.files)
for pkg in packages),
packed_packages=sum(1 for pkg in packages
if pkg.packfiles),
nb_other_files=len(other_files),
nb_input_outputs_files=len(inputs_outputs),
nb_input_files=sum(1 for f in itervalues(inputs_outputs)
if f.read_runs),
nb_output_files=sum(1 for f in itervalues(inputs_outputs)
if f.write_runs))
def submit_usage_report(**kwargs):
"""Submits the current usage report to the usagestats server.
"""
_usage_report.submit(kwargs,
usagestats.OPERATING_SYSTEM,
usagestats.SESSION_TIME,
usagestats.PYTHON_VERSION)
def get_reprozip_ca_certificate():
"""Gets the ReproZip CA certificate filename.
"""
fd, certificate_file = Path.tempfile(prefix='rpz_stats_ca_', suffix='.pem')
with certificate_file.open('wb') as fp:
fp.write(usage_report_ca)
os.close(fd)
atexit.register(os.remove, certificate_file.path)
return certificate_file
usage_report_ca = b'''\
-----BEGIN CERTIFICATE-----
MIIDzzCCAregAwIBAgIJAMmlcDnTidBEMA0GCSqGSIb3DQEBCwUAMH4xCzAJBgNV
BAYTAlVTMREwDwYDVQQIDAhOZXcgWW9yazERMA8GA1UEBwwITmV3IFlvcmsxDDAK
BgNVBAoMA05ZVTERMA8GA1UEAwwIUmVwcm9aaXAxKDAmBgkqhkiG9w0BCQEWGXJl
cHJvemlwLWRldkB2Z2MucG9seS5lZHUwHhcNMTQxMTA3MDUxOTA5WhcNMjQxMTA0
MDUxOTA5WjB+MQswCQYDVQQGEwJVUzERMA8GA1UECAwITmV3IFlvcmsxETAPBgNV
BAcMCE5ldyBZb3JrMQwwCgYDVQQKDANOWVUxETAPBgNVBAMMCFJlcHJvWmlwMSgw
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-----END CERTIFICATE-----
'''
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