def _find_tables(
db: audformat.Database,
db_root: str,
version: str,
deps: Dependencies,
verbose: bool,
) -> typing.List[str]:
r"""Update tables."""
# release dependencies to removed tables
db_tables = [f'db.{table}.csv' for table in db.tables]
for file in set(deps.tables) - set(db_tables):
deps._drop(file)
tables = []
for table in audeer.progress_bar(
db.tables,
desc='Find tables',
disable=not verbose,
):
file = f'db.{table}.csv'
checksum = audbackend.md5(os.path.join(db_root, file))
if file not in deps or checksum != deps.checksum(file):
deps._add_meta(file, version, table, checksum)
tables.append(table)
return tables
def job(table: str):
file = f'db.{table}.csv'
full_file = os.path.join(db_root, file)
if not os.path.exists(full_file):
tables.append(file)
else:
checksum = audbackend.md5(full_file)
# if the table already exists
# we have to compare checksum
# in case it was altered by flavor
if checksum != deps.checksum(file): # pragma: no cover
tables.append(file)
def _find_media(
db: audformat.Database,
db_root: str,
version: str,
deps: Dependencies,
archives: typing.Mapping[str, str],
verbose: bool,
) -> typing.Set[str]:
# release dependencies to removed media
# and select according archives for upload
media = set()
db_media = db.files
for file in set(deps.media) - set(db_media):
media.add(deps.archive(file))
deps._drop(file)
# update version of altered media and insert new ones
for file in audeer.progress_bar(
db_media,
desc='Find media',
disable=not verbose,
):
path = os.path.join(db_root, file)
if file not in deps:
checksum = audbackend.md5(path)
if file in archives:
archive = archives[file]
else:
archive = audeer.uid(from_string=file.replace('\\', '/'))
deps._add_media(db_root, file, version, archive, checksum)
elif not deps.removed(file):
checksum = audbackend.md5(path)
if checksum != deps.checksum(file):
archive = deps.archive(file)
deps._add_media(db_root, file, version, archive, checksum)
return media
def publish(
db_root: str,
version: str,
repository: Repository,
*,
archives: typing.Mapping[str, str] = None,
previous_version: typing.Optional[str] = 'latest',
cache_root: str = None,
num_workers: typing.Optional[int] = 1,
verbose: bool = True,
) -> Dependencies:
r"""Publish database.
A database can have dependencies
to files of an older version of itself.
E.g. you might add a few new files to an existing database
and publish as a new version.
:func:`audb.publish` will upload then only the new files
and store dependencies on the already published files.
To allow for dependencies
you first have to load the version of the database
that the new version should depend on
with :func:`audb.load_to` to ``db_root``.
Afterwards you make your changes to that folder
and run :func:`audb.publish`.
:func:`audb.publish` will then check
that the version of the files inside that folder
match the version given by ``previous_version``.
Setting ``previous_version=None`` allows you
to start from scratch and upload all files
even if an older versions exist.
In this case you don't call :func:`audb.load_to`
before running :func:`audb.publish`.
Args:
db_root: root directory of database
version: version string
repository: name of repository
archives: dictionary mapping files to archive names.
Can be used to bundle files into archives.
Archive name must not include an extension
previous_version: specifies the version
this publication should be based on.
If ``'latest'``
it will use automatically the latest published version
or ``None``
if no version was published.
If ``None`` it assumes you start from scratch.
cache_root: cache folder where databases are stored.
If not set :meth:`audb.default_cache_root` is used.
Only used to read the dependencies of the previous version
num_workers: number of parallel jobs or 1 for sequential
processing. If ``None`` will be set to the number of
processors on the machine multiplied by 5
verbose: show debug messages
Returns:
dependency object
Raises:
RuntimeError: if version already exists
RuntimeError: if database tables reference non-existing files
RuntimeError: if database in ``db_root`` depends on other version
as indicated by ``previous_version``
RuntimeError: if database is not portable,
see :meth:`audformat.Database.is_portable`
"""
db = audformat.Database.load(db_root, load_data=False)
backend = audbackend.create(
repository.backend,
repository.host,
repository.name,
)
remote_header = backend.join(db.name, define.HEADER_FILE)
versions = backend.versions(remote_header)
if version in versions:
raise RuntimeError('A version '
f"'{version}' "
'already exists for database '
f"'{db.name}'.")
if previous_version == 'latest':
if len(versions) > 0:
previous_version = versions[-1]
else:
previous_version = None
# load database and dependencies
deps_path = os.path.join(db_root, define.DEPENDENCIES_FILE)
deps = Dependencies()
if os.path.exists(deps_path):
deps.load(deps_path)
# check if database folder depends on the right version
# dependencies shouldn't be there
if previous_version is None and len(deps) > 0:
raise RuntimeError(
f"You did not set a dependency to a previous version, "
f"but you have a '{define.DEPENDENCIES_FILE}' file present "
f"in {db_root}.")
# dependencies missing
if previous_version is not None and len(deps) == 0:
raise RuntimeError(
f"You want to depend on '{previous_version}' "
f"of {db.name}, "
f"but you don't have a '{define.DEPENDENCIES_FILE}' file present "
f"in {db_root}. "
f"Did you forgot to call "
f"'audb.load_to({db_root}, {db.name}, "
f"version={previous_version}?")
# dependencies do not match version
if previous_version is not None and len(deps) > 0:
with tempfile.TemporaryDirectory() as tmp_dir:
previous_deps_path = os.path.join(
tmp_dir,
define.DEPENDENCIES_FILE,
)
previous_deps = dependencies(
db.name,
version=previous_version,
cache_root=cache_root,
)
previous_deps.save(previous_deps_path)
if audbackend.md5(deps_path) != audbackend.md5(previous_deps_path):
raise RuntimeError(
f"You want to depend on '{previous_version}' "
f"of {db.name}, "
f"but the MD5 sum of your "
f"'{define.DEPENDENCIES_FILE}' file "
f"in {db_root} "
f"does not match the MD5 sum of the corresponding file "
f"for the requested version in the repository. "
f"Did you forgot to call "
f"'audb.load_to({db_root}, {db.name}, "
f"version='{previous_version}') "
f"or modified the file manually?")
# load database from folder
db = audformat.Database.load(db_root)
if not db.is_portable:
raise RuntimeError("Some files in the tables have absolute paths "
"or use '.' or '..' to address a folder. "
"Please replace those paths by relative paths "
"and use folder names instead of dots.")
# check all files referenced in a table exists
missing_files = [
f for f in db.files if not os.path.exists(os.path.join(db_root, f))
]
if len(missing_files) > 0:
number_of_presented_files = 20
error_msg = (
f'{len(missing_files)} files are referenced in tables '
'that cannot be found. '
f"Missing files are: '{missing_files[:number_of_presented_files]}")
if len(missing_files) <= number_of_presented_files:
error_msg += "'."
else:
error_msg += ", ...'."
raise RuntimeError(error_msg)
# make sure all tables are stored in CSV format
for table_id, table in db.tables.items():
table_path = os.path.join(db_root, f'db.{table_id}')
table_ext = audformat.define.TableStorageFormat.CSV
if not os.path.exists(table_path + f'.{table_ext}'):
table.save(table_path, storage_format=table_ext)
# check archives
archives = archives or {}
# publish tables
tables = _find_tables(db, db_root, version, deps, verbose)
_put_tables(tables, db_root, db.name, version, backend, num_workers,
verbose)
# publish media
media = _find_media(db, db_root, version, deps, archives, verbose)
_put_media(media, db_root, db.name, version, deps, backend, num_workers,
verbose)
# publish dependencies and header
deps.save(deps_path)
archive_file = backend.join(db.name, define.DB)
backend.put_archive(
db_root,
define.DEPENDENCIES_FILE,
archive_file,
version,
)
try:
local_header = os.path.join(db_root, define.HEADER_FILE)
remote_header = db.name + '/' + define.HEADER_FILE
backend.put_file(local_header, remote_header, version)
except Exception: # pragma: no cover
# after the header is published
# the new version becomes visible,
# so if something goes wrong here
# we better clean up
if backend.exists(remote_header, version):
backend.remove_file(remote_header, version)
return deps
def load_to(
root: str,
name: str,
*,
version: str = None,
cache_root: str = None,
num_workers: typing.Optional[int] = 1,
verbose: bool = True,
) -> audformat.Database:
r"""Load database to directory.
Loads the original state of the database
to a custom directory.
No conversion or filtering will be applied.
If the target folder already contains
some version of the database,
it will upgrade to the requested version.
Unchanged files will be skipped.
Args:
root: target directory
name: name of database
version: version string, latest if ``None``
cache_root: cache folder where databases are stored.
If not set :meth:`audb.default_cache_root` is used.
Only used to read the dependencies of the requested version
num_workers: number of parallel jobs or 1 for sequential
processing. If ``None`` will be set to the number of
processors on the machine multiplied by 5
verbose: show debug messages
Returns:
database object
"""
if version is None:
version = latest_version(name)
db_root = audeer.safe_path(root)
db_root_tmp = database_tmp_folder(db_root)
# remove files with a wrong checksum
# to ensure we load correct version
update = os.path.exists(db_root) and os.listdir(db_root)
audeer.mkdir(db_root)
deps = dependencies(name, version=version, cache_root=cache_root)
if update:
for file in deps.files:
full_file = os.path.join(db_root, file)
if os.path.exists(full_file):
checksum = audbackend.md5(full_file)
if checksum != deps.checksum(file):
os.remove(full_file)
# load database header without tables from backend
db_header, backend = load_header(
db_root_tmp,
name,
version,
overwrite=True,
)
# get altered and new tables
db_header.save(db_root_tmp, header_only=True)
tables = _find_tables(db_header, db_root, deps, num_workers, verbose)
_get_tables(tables, db_root, db_root_tmp, name, deps, backend, num_workers,
verbose)
# load database
# move header to root and load database ...
_move_file(db_root_tmp, db_root, define.HEADER_FILE)
try:
db = audformat.Database.load(
db_root,
num_workers=num_workers,
verbose=verbose,
)
except (KeyboardInterrupt, Exception): # pragma: no cover
# make sure to remove header if user interrupts
os.remove(os.path.join(db_root, define.HEADER_FILE))
raise
# afterwards remove header to avoid the database
# can be loaded before download is complete
os.remove(os.path.join(db_root, define.HEADER_FILE))
# get altered and new media files
media = _find_media(db, db_root, deps, num_workers, verbose)
_get_media(media, db_root, db_root_tmp, name, deps, backend, num_workers,
verbose)
# save dependencies
dep_path_tmp = os.path.join(db_root_tmp, define.DEPENDENCIES_FILE)
deps.save(dep_path_tmp)
_move_file(db_root_tmp, db_root, define.DEPENDENCIES_FILE)
# save database and remove the temporal directory
# to signal all files were correctly loaded
_save_database(db, db_root, db_root_tmp, num_workers, verbose)
try:
_remove_empty_dirs(db_root_tmp)
except OSError: # pragma: no cover
raise RuntimeError('Could not remove temporary directory, '
'probably there are some leftover files.'
'This should not happen.')
return db
def test_publish(version):
db = audformat.Database.load(DB_ROOT_VERSION[version])
print(db.is_portable)
print(db.files)
if not audb.versions(DB_NAME):
with pytest.raises(RuntimeError):
audb.latest_version(DB_NAME)
archives = db['files']['speaker'].get().dropna().to_dict()
deps = audb.publish(
DB_ROOT_VERSION[version],
version,
pytest.PUBLISH_REPOSITORY,
archives=archives,
previous_version=None,
num_workers=pytest.NUM_WORKERS,
verbose=False,
)
backend = audb.core.utils.lookup_backend(DB_NAME, version)
number_of_files = len(set(archives.keys()))
number_of_archives = len(set(archives.values()))
assert len(deps.files) - len(deps.archives) == (number_of_files -
number_of_archives)
for archive in set(archives.values()):
assert archive in deps.archives
db = audb.load(
DB_NAME,
version=version,
full_path=False,
num_workers=pytest.NUM_WORKERS,
)
assert db.name == DB_NAME
versions = audb.versions(DB_NAME)
latest_version = audb.latest_version(DB_NAME)
assert version in versions
assert latest_version == versions[-1]
df = audb.available(only_latest=False)
assert DB_NAME in df.index
assert set(df[df.index == DB_NAME]['version']) == set(versions)
df = audb.available(only_latest=True)
assert DB_NAME in df.index
assert df[df.index == DB_NAME]['version'][0] == latest_version
for file in db.files:
name = archives[file] if file in archives else file
file_path = backend.join(db.name, 'media', name)
backend.exists(file_path, version)
path = os.path.join(DB_ROOT_VERSION[version], file)
assert deps.checksum(file) == audbackend.md5(path)
if deps.format(file) in [
audb.core.define.Format.WAV,
audb.core.define.Format.FLAC,
]:
assert deps.bit_depth(file) == audiofile.bit_depth(path)
assert deps.channels(file) == audiofile.channels(path)
assert deps.duration(file) == audiofile.duration(path)
assert deps.sampling_rate(file) == audiofile.sampling_rate(path)