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<a href="https://github.com/datajoint/datajoint-python/commit/<a class=hub.com/datajoint/datajoint-python/commit/30b599fb6f835b7fccbfd198c8b2b15d9847e59a">30b599fb6<a href="https://github.com/datajoint/datajoint-python/commit/30b599fb6f835b7fccbfd198c8b2b15d9847e59a">">Merge </a><a class="double-link" href="https://github.com/datajoint/datajoint-python/commit/<a class="double-link" href="https://github.com/datajoint/datajoint-python/commit/e8d09cddeabecbc47d1e56902b31ea274a6c3021">e8d09cdde</a>">e8d09cdde</a><a href="https://github.com/datajoint/datajoint-python/commit/30b599fb6f835b7fccbfd198c8b2b15d9847e59a"> into 0ff34f283">0ff34f283</a>

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90.09

/datajoint/external.py

from pathlib import Path, PurePosixPath, PureWindowsPath
from collections.abc import Mapping
from tqdm import tqdm
from .settings import config
from .errors import DataJointError, MissingExternalFile
from .hash import uuid_from_buffer, uuid_from_file
from .table import Table, FreeTable
from .heading import Heading
from .declare import EXTERNAL_TABLE_ROOT
from . import s3
from .utils import safe_write, safe_copy

CACHE_SUBFOLDING = (
    2,
    2,
)  # (2, 2) means  "0123456789abcd" will be saved as "01/23/0123456789abcd"
SUPPORT_MIGRATED_BLOBS = True  # support blobs migrated from datajoint 0.11.*


def subfold(name, folds):
    """
    subfolding for external storage:   e.g.  subfold('aBCdefg', (2, 3))  -->  ['ab','cde']
    """
    return (
        (name[: folds[0]].lower(),) + subfold(name[folds[0] :], folds[1:])
        if folds
        else ()
    )


class ExternalTable(Table):
    """
    The table tracking externally stored objects.
    Declare as ExternalTable(connection, database)
    """

    def __init__(self, connection, store, database):
        self.store = store
        self.spec = config.get_store_spec(store)
        self._s3 = None
        self.database = database
        self._connection = connection
        self._heading = Heading(
            table_info=dict(
                conn=connection,
                database=database,
                table_name=self.table_name,
                context=None,
            )
        )
        self._support = [self.full_table_name]
        if not self.is_declared:
            self.declare()
        self._s3 = None
        if self.spec["protocol"] == "file" and not Path(self.spec["location"]).is_dir():
            raise FileNotFoundError(
                "Inaccessible local directory %s" % self.spec["location"]
            ) from None

    @property
    def definition(self):
        return """
        # external storage tracking
        hash  : uuid    #  hash of contents (blob), of filename + contents (attach), or relative filepath (filepath)
        ---
        size      :bigint unsigned     # size of object in bytes
        attachment_name=null : varchar(255)  # the filename of an attachment
        filepath=null : varchar(1000)  # relative filepath or attachment filename
        contents_hash=null : uuid      # used for the filepath datatype
        timestamp=CURRENT_TIMESTAMP  :timestamp   # automatic timestamp
        """

    @property
    def table_name(self):
        return "{external_table_root}_{store}".format(
            external_table_root=EXTERNAL_TABLE_ROOT, store=self.store
        )

    @property
    def s3(self):
        if self._s3 is None:
            self._s3 = s3.Folder(**self.spec)
        return self._s3

    # - low-level operations - private

    def _make_external_filepath(self, relative_filepath):
        """resolve the complete external path based on the relative path"""
        # Strip root
        if self.spec["protocol"] == "s3":
            posix_path = PurePosixPath(PureWindowsPath(self.spec["location"]))
            location_path = (
                Path(*posix_path.parts[1:])
                if len(self.spec["location"]) > 0
                and any(case in posix_path.parts[0] for case in ("\\", ":"))
                else Path(posix_path)
            )
            return PurePosixPath(location_path, relative_filepath)
        # Preserve root
        elif self.spec["protocol"] == "file":
            return PurePosixPath(Path(self.spec["location"]), relative_filepath)
        else:
            assert False

    def _make_uuid_path(self, uuid, suffix=""):
        """create external path based on the uuid hash"""
        return self._make_external_filepath(
            PurePosixPath(
                self.database,
                "/".join(subfold(uuid.hex, self.spec["subfolding"])),
                uuid.hex,
            ).with_suffix(suffix)
        )

    def _upload_file(self, local_path, external_path, metadata=None):
        if self.spec["protocol"] == "s3":
            self.s3.fput(local_path, external_path, metadata)
        elif self.spec["protocol"] == "file":
            safe_copy(local_path, external_path, overwrite=True)
        else:
            assert False

    def _download_file(self, external_path, download_path):
        if self.spec["protocol"] == "s3":
            self.s3.fget(external_path, download_path)
        elif self.spec["protocol"] == "file":
            safe_copy(external_path, download_path)
        else:
            assert False

    def _upload_buffer(self, buffer, external_path):
        if self.spec["protocol"] == "s3":
            self.s3.put(external_path, buffer)
        elif self.spec["protocol"] == "file":
            safe_write(external_path, buffer)
        else:
            assert False

    def _download_buffer(self, external_path):
        if self.spec["protocol"] == "s3":
            return self.s3.get(external_path)
        if self.spec["protocol"] == "file":
            return Path(external_path).read_bytes()
        assert False

    def _remove_external_file(self, external_path):
        if self.spec["protocol"] == "s3":
            self.s3.remove_object(external_path)
        elif self.spec["protocol"] == "file":
            try:
                Path(external_path).unlink()
            except FileNotFoundError:
                pass

    def exists(self, external_filepath):
        """
        :return: True if the external file is accessible
        """
        if self.spec["protocol"] == "s3":
            return self.s3.exists(external_filepath)
        if self.spec["protocol"] == "file":
            return Path(external_filepath).is_file()
        assert False

    # --- BLOBS ----

    def put(self, blob):
        """
        put a binary string (blob) in external store
        """
        uuid = uuid_from_buffer(blob)
        self._upload_buffer(blob, self._make_uuid_path(uuid))
        # insert tracking info
        self.connection.query(
            "INSERT INTO {tab} (hash, size) VALUES (%s, {size}) ON DUPLICATE KEY "
            "UPDATE timestamp=CURRENT_TIMESTAMP".format(
                tab=self.full_table_name, size=len(blob)
            ),
            args=(uuid.bytes,),
        )
        return uuid

    def get(self, uuid):
        """
        get an object from external store.
        """
        if uuid is None:
            return None
        # attempt to get object from cache
        blob = None
        cache_folder = config.get("cache", None)
        if cache_folder:
            try:
                cache_path = Path(cache_folder, *subfold(uuid.hex, CACHE_SUBFOLDING))
                cache_file = Path(cache_path, uuid.hex)
                blob = cache_file.read_bytes()
            except FileNotFoundError:
                pass  # not cached
        # download blob from external store
        if blob is None:
            try:
                blob = self._download_buffer(self._make_uuid_path(uuid))
            except MissingExternalFile:
                if not SUPPORT_MIGRATED_BLOBS:
                    raise
                # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths
                relative_filepath, contents_hash = (self & {"hash": uuid}).fetch1(
                    "filepath", "contents_hash"
                )
                if relative_filepath is None:
                    raise
                blob = self._download_buffer(
                    self._make_external_filepath(relative_filepath)
                )
            if cache_folder:
                cache_path.mkdir(parents=True, exist_ok=True)
                safe_write(cache_path / uuid.hex, blob)
        return blob

    # --- ATTACHMENTS ---

    def upload_attachment(self, local_path):
        attachment_name = Path(local_path).name
        uuid = uuid_from_file(local_path, init_string=attachment_name + "\0")
        external_path = self._make_uuid_path(uuid, "." + attachment_name)
        self._upload_file(local_path, external_path)
        # insert tracking info
        self.connection.query(
            """
        INSERT INTO {tab} (hash, size, attachment_name)
        VALUES (%s, {size}, "{attachment_name}")
        ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP""".format(
                tab=self.full_table_name,
                size=Path(local_path).stat().st_size,
                attachment_name=attachment_name,
            ),
            args=[uuid.bytes],
        )
        return uuid

    def get_attachment_name(self, uuid):
        return (self & {"hash": uuid}).fetch1("attachment_name")

    def download_attachment(self, uuid, attachment_name, download_path):
        """save attachment from memory buffer into the save_path"""
        external_path = self._make_uuid_path(uuid, "." + attachment_name)
        self._download_file(external_path, download_path)

    # --- FILEPATH ---

    def upload_filepath(self, local_filepath):
        """
        Raise exception if an external entry already exists with a different contents checksum.
        Otherwise, copy (with overwrite) file to remote and
        If an external entry exists with the same checksum, then no copying should occur
        """
        local_filepath = Path(local_filepath)
        try:
            relative_filepath = str(
                local_filepath.relative_to(self.spec["stage"]).as_posix()
            )
        except ValueError:
            raise DataJointError(
                "The path {path} is not in stage {stage}".format(
                    path=local_filepath.parent, **self.spec
                )
            )
        uuid = uuid_from_buffer(
            init_string=relative_filepath
        )  # hash relative path, not contents
        contents_hash = uuid_from_file(local_filepath)

        # check if the remote file already exists and verify that it matches
        check_hash = (self & {"hash": uuid}).fetch("contents_hash")
        if check_hash:
            # the tracking entry exists, check that it's the same file as before
            if contents_hash != check_hash[0]:
                raise DataJointError(
                    "A different version of '{file}' has already been placed.".format(
                        file=relative_filepath
                    )
                )
        else:
            # upload the file and create its tracking entry
            self._upload_file(
                local_filepath,
                self._make_external_filepath(relative_filepath),
                metadata={"contents_hash": str(contents_hash)},
            )
            self.connection.query(
                "INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES (%s, {size}, '{filepath}', %s)".format(
                    tab=self.full_table_name,
                    size=Path(local_filepath).stat().st_size,
                    filepath=relative_filepath,
                ),
                args=(uuid.bytes, contents_hash.bytes),
            )
        return uuid

    def download_filepath(self, filepath_hash):
        """
        sync a file from external store to the local stage

        :param filepath_hash: The hash (UUID) of the relative_path
        :return: hash (UUID) of the contents of the downloaded file or Nones
        """
        if filepath_hash is not None:
            relative_filepath, contents_hash = (self & {"hash": filepath_hash}).fetch1(
                "filepath", "contents_hash"
            )
            external_path = self._make_external_filepath(relative_filepath)
            local_filepath = Path(self.spec["stage"]).absolute() / relative_filepath
            file_exists = (
                Path(local_filepath).is_file()
                and uuid_from_file(local_filepath) == contents_hash
            )
            if not file_exists:
                self._download_file(external_path, local_filepath)
                checksum = uuid_from_file(local_filepath)
                if (
                    checksum != contents_hash
                ):  # this should never happen without outside interference
                    raise DataJointError(
                        "'{file}' downloaded but did not pass checksum'".format(
                            file=local_filepath
                        )
                    )
            return str(local_filepath), contents_hash

    # --- UTILITIES ---

    @property
    def references(self):
        """
        :return: generator of referencing table names and their referencing columns
        """
        return (
            {k.lower(): v for k, v in elem.items()}
            for elem in self.connection.query(
                """
        SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name
        FROM information_schema.key_column_usage
        WHERE referenced_table_name="{tab}" and referenced_table_schema="{db}"
        """.format(
                    tab=self.table_name, db=self.database
                ),
                as_dict=True,
            )
        )

    def fetch_external_paths(self, **fetch_kwargs):
        """
        generate complete external filepaths from the query.
        Each element is a tuple: (uuid, path)

        :param fetch_kwargs: keyword arguments to pass to fetch
        """
        fetch_kwargs.update(as_dict=True)
        paths = []
        for item in self.fetch("hash", "attachment_name", "filepath", **fetch_kwargs):
            if item["attachment_name"]:
                # attachments
                path = self._make_uuid_path(item["hash"], "." + item["attachment_name"])
            elif item["filepath"]:
                # external filepaths
                path = self._make_external_filepath(item["filepath"])
            else:
                # blobs
                path = self._make_uuid_path(item["hash"])
            paths.append((item["hash"], path))
        return paths

    def unused(self):
        """
        query expression for unused hashes

        :return: self restricted to elements that are not in use by any tables in the schema
        """
        return self - [
            FreeTable(self.connection, ref["referencing_table"]).proj(
                hash=ref["column_name"]
            )
            for ref in self.references
        ]

    def used(self):
        """
        query expression for used hashes

        :return: self restricted to elements that in use by tables in the schema
        """
        return self & [
            FreeTable(self.connection, ref["referencing_table"]).proj(
                hash=ref["column_name"]
            )
            for ref in self.references
        ]

    def delete(
        self,
        *,
        delete_external_files=None,
        limit=None,
        display_progress=True,
        errors_as_string=True
    ):
        """

        :param delete_external_files: True or False. If False, only the tracking info is removed from the external
                store table but the external files remain intact. If True, then the external files themselves are deleted too.
        :param errors_as_string: If True any errors returned when deleting from external files will be strings
        :param limit: (integer) limit the number of items to delete
        :param display_progress: if True, display progress as files are cleaned up
        :return: if deleting external files, returns errors
        """
        if delete_external_files not in (True, False):
            raise DataJointError(
                "The delete_external_files argument must be set to either "
                "True or False in delete()"
            )

        if not delete_external_files:
            self.unused().delete_quick()
        else:
            items = self.unused().fetch_external_paths(limit=limit)
            if display_progress:
                items = tqdm(items)
            # delete items one by one, close to transaction-safe
            error_list = []
            for uuid, external_path in items:
                row = (self & {"hash": uuid}).fetch()
                if row.size:
                    try:
                        (self & {"hash": uuid}).delete_quick()
                    except Exception:
                        pass  # if delete failed, do not remove the external file
                    else:
                        try:
                            self._remove_external_file(external_path)
                        except Exception as error:
                            # adding row back into table after failed delete
                            self.insert1(row[0], skip_duplicates=True)
                            error_list.append(
                                (
                                    uuid,
                                    external_path,
                                    str(error) if errors_as_string else error,
                                )
                            )
            return error_list


class ExternalMapping(Mapping):
    """
    The external manager contains all the tables for all external stores for a given schema
    :Example:
        e = ExternalMapping(schema)
        external_table = e[store]
    """

    def __init__(self, schema):
        self.schema = schema
        self._tables = {}

    def __repr__(self):
        return "External file tables for schema `{schema}`:\n    ".format(
            schema=self.schema.database
        ) + "\n    ".join(
            '"{store}" {protocol}:{location}'.format(store=k, **v.spec)
            for k, v in self.items()
        )

    def __getitem__(self, store):
        """
        Triggers the creation of an external table.
        Should only be used when ready to save or read from external storage.

        :param store: the name of the store
        :return: the ExternalTable object for the store
        """
        if store not in self._tables:
            self._tables[store] = ExternalTable(
                connection=self.schema.connection,
                store=store,
                database=self.schema.database,
            )
        return self._tables[store]

    def __len__(self):
        return len(self._tables)

    def __iter__(self):
        return iter(self._tables)

1	from pathlib import Path, PurePosixPath, PureWindowsPath	1✔
2	from collections.abc import Mapping	1✔
3	from tqdm import tqdm	1✔
4	from .settings import config	1✔
5	from .errors import DataJointError, MissingExternalFile	1✔
6	from .hash import uuid_from_buffer, uuid_from_file	1✔
7	from .table import Table, FreeTable	1✔
8	from .heading import Heading	1✔
9	from .declare import EXTERNAL_TABLE_ROOT	1✔
10	from . import s3	1✔
11	from .utils import safe_write, safe_copy	1✔
12
13	CACHE_SUBFOLDING = (	1✔
14	2,
15	2,
16	) # (2, 2) means "0123456789abcd" will be saved as "01/23/0123456789abcd"
17	SUPPORT_MIGRATED_BLOBS = True # support blobs migrated from datajoint 0.11.*	1✔
18
19
20	def subfold(name, folds):	1✔
21	"""
22	subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde']
23	"""
24	return (	1✔
25	(name[: folds[0]].lower(),) + subfold(name[folds[0] :], folds[1:])
26	if folds
27	else ()
28	)
29
30
31	class ExternalTable(Table):	1✔
32	"""
33	The table tracking externally stored objects.
34	Declare as ExternalTable(connection, database)
35	"""
36
37	def __init__(self, connection, store, database):	1✔
38	self.store = store	1✔
39	self.spec = config.get_store_spec(store)	1✔
40	self._s3 = None	1✔
41	self.database = database	1✔
42	self._connection = connection	1✔
43	self._heading = Heading(	1✔
44	table_info=dict(
45	conn=connection,
46	database=database,
47	table_name=self.table_name,
48	context=None,
49	)
50	)
51	self._support = [self.full_table_name]	1✔
52	if not self.is_declared:	1✔
53	self.declare()	1✔
54	self._s3 = None	1✔
55	if self.spec["protocol"] == "file" and not Path(self.spec["location"]).is_dir():	1✔
56	raise FileNotFoundError(	×
57	"Inaccessible local directory %s" % self.spec["location"]
58	) from None
59
60	@property	1✔
61	def definition(self):	1✔
62	return """	1✔
63	# external storage tracking
64	hash : uuid # hash of contents (blob), of filename + contents (attach), or relative filepath (filepath)
65	---
66	size :bigint unsigned # size of object in bytes
67	attachment_name=null : varchar(255) # the filename of an attachment
68	filepath=null : varchar(1000) # relative filepath or attachment filename
69	contents_hash=null : uuid # used for the filepath datatype
70	timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp
71	"""
72
73	@property	1✔
74	def table_name(self):	1✔
75	return "{external_table_root}_{store}".format(	1✔
76	external_table_root=EXTERNAL_TABLE_ROOT, store=self.store
77	)
78
79	@property	1✔
80	def s3(self):	1✔
81	if self._s3 is None:	1✔
82	self._s3 = s3.Folder(**self.spec)	1✔
83	return self._s3	1✔
84
85	# - low-level operations - private
86
87	def _make_external_filepath(self, relative_filepath):	1✔
88	"""resolve the complete external path based on the relative path"""
89	# Strip root
90	if self.spec["protocol"] == "s3":	1✔
91	posix_path = PurePosixPath(PureWindowsPath(self.spec["location"]))	1✔
92	location_path = (	1✔
93	Path(*posix_path.parts[1:])
94	if len(self.spec["location"]) > 0
95	and any(case in posix_path.parts[0] for case in ("\\", ":"))
96	else Path(posix_path)
97	)
98	return PurePosixPath(location_path, relative_filepath)	1✔
99	# Preserve root
100	elif self.spec["protocol"] == "file":	1✔
101	return PurePosixPath(Path(self.spec["location"]), relative_filepath)	1✔
102	else:
103	assert False	×
104
105	def _make_uuid_path(self, uuid, suffix=""):	1✔
106	"""create external path based on the uuid hash"""
107	return self._make_external_filepath(	1✔
108	PurePosixPath(
109	self.database,
110	"/".join(subfold(uuid.hex, self.spec["subfolding"])),
111	uuid.hex,
112	).with_suffix(suffix)
113	)
114
115	def _upload_file(self, local_path, external_path, metadata=None):	1✔
116	if self.spec["protocol"] == "s3":	1✔
117	self.s3.fput(local_path, external_path, metadata)	1✔
118	elif self.spec["protocol"] == "file":	1✔
119	safe_copy(local_path, external_path, overwrite=True)	1✔
120	else:
121	assert False	×
122
123	def _download_file(self, external_path, download_path):	1✔
124	if self.spec["protocol"] == "s3":	1✔
125	self.s3.fget(external_path, download_path)	1✔
126	elif self.spec["protocol"] == "file":	1✔
127	safe_copy(external_path, download_path)	1✔
128	else:
129	assert False	×
130
131	def _upload_buffer(self, buffer, external_path):	1✔
132	if self.spec["protocol"] == "s3":	1✔
133	self.s3.put(external_path, buffer)	1✔
134	elif self.spec["protocol"] == "file":	1✔
135	safe_write(external_path, buffer)	1✔
136	else:
137	assert False	×
138
139	def _download_buffer(self, external_path):	1✔
140	if self.spec["protocol"] == "s3":	1✔
141	return self.s3.get(external_path)	1✔
142	if self.spec["protocol"] == "file":	1✔
143	return Path(external_path).read_bytes()	1✔
144	assert False	×
145
146	def _remove_external_file(self, external_path):	1✔
147	if self.spec["protocol"] == "s3":	1✔
148	self.s3.remove_object(external_path)	1✔
149	elif self.spec["protocol"] == "file":	1✔
150	try:	1✔
151	Path(external_path).unlink()	1✔
152	except FileNotFoundError:	1✔
153	pass	×
154
155	def exists(self, external_filepath):	1✔
156	"""
157	:return: True if the external file is accessible
158	"""
159	if self.spec["protocol"] == "s3":	1✔
160	return self.s3.exists(external_filepath)	1✔
161	if self.spec["protocol"] == "file":	1✔
162	return Path(external_filepath).is_file()	1✔
163	assert False	×
164
165	# --- BLOBS ----
166
167	def put(self, blob):	1✔
168	"""
169	put a binary string (blob) in external store
170	"""
171	uuid = uuid_from_buffer(blob)	1✔
172	self._upload_buffer(blob, self._make_uuid_path(uuid))	1✔
173	# insert tracking info
174	self.connection.query(	1✔
175	"INSERT INTO {tab} (hash, size) VALUES (%s, {size}) ON DUPLICATE KEY "
176	"UPDATE timestamp=CURRENT_TIMESTAMP".format(
177	tab=self.full_table_name, size=len(blob)
178	),
179	args=(uuid.bytes,),
180	)
181	return uuid	1✔
182
183	def get(self, uuid):	1✔
184	"""
185	get an object from external store.
186	"""
187	if uuid is None:	1✔
188	return None	×
189	# attempt to get object from cache
190	blob = None	1✔
191	cache_folder = config.get("cache", None)	1✔
192	if cache_folder:	1✔
193	try:	1✔
194	cache_path = Path(cache_folder, *subfold(uuid.hex, CACHE_SUBFOLDING))	1✔
195	cache_file = Path(cache_path, uuid.hex)	1✔
196	blob = cache_file.read_bytes()	1✔
197	except FileNotFoundError:	1✔
198	pass # not cached	1✔
199	# download blob from external store
200	if blob is None:	1✔
201	try:	1✔
202	blob = self._download_buffer(self._make_uuid_path(uuid))	1✔
203	except MissingExternalFile:	1✔
204	if not SUPPORT_MIGRATED_BLOBS:	1✔
205	raise	×
206	# blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths
207	relative_filepath, contents_hash = (self & {"hash": uuid}).fetch1(	1✔
208	"filepath", "contents_hash"
209	)
210	if relative_filepath is None:	1✔
211	raise	×
212	blob = self._download_buffer(	1✔
213	self._make_external_filepath(relative_filepath)
214	)
215	if cache_folder:	1✔
216	cache_path.mkdir(parents=True, exist_ok=True)	1✔
217	safe_write(cache_path / uuid.hex, blob)	1✔
218	return blob	1✔
219
220	# --- ATTACHMENTS ---
221
222	def upload_attachment(self, local_path):	1✔
223	attachment_name = Path(local_path).name	1✔
224	uuid = uuid_from_file(local_path, init_string=attachment_name + "\0")	1✔
225	external_path = self._make_uuid_path(uuid, "." + attachment_name)	1✔
226	self._upload_file(local_path, external_path)	1✔
227	# insert tracking info
228	self.connection.query(	1✔
229	"""
230	INSERT INTO {tab} (hash, size, attachment_name)
231	VALUES (%s, {size}, "{attachment_name}")
232	ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP""".format(
233	tab=self.full_table_name,
234	size=Path(local_path).stat().st_size,
235	attachment_name=attachment_name,
236	),
237	args=[uuid.bytes],
238	)
239	return uuid	1✔
240
241	def get_attachment_name(self, uuid):	1✔
242	return (self & {"hash": uuid}).fetch1("attachment_name")	1✔
243
244	def download_attachment(self, uuid, attachment_name, download_path):	1✔
245	"""save attachment from memory buffer into the save_path"""
246	external_path = self._make_uuid_path(uuid, "." + attachment_name)	1✔
247	self._download_file(external_path, download_path)	1✔
248
249	# --- FILEPATH ---
250
251	def upload_filepath(self, local_filepath):	1✔
252	"""
253	Raise exception if an external entry already exists with a different contents checksum.
254	Otherwise, copy (with overwrite) file to remote and
255	If an external entry exists with the same checksum, then no copying should occur
256	"""
257	local_filepath = Path(local_filepath)	1✔
258	try:	1✔
259	relative_filepath = str(	1✔
260	local_filepath.relative_to(self.spec["stage"]).as_posix()
261	)
262	except ValueError:	×
263	raise DataJointError(	×
264	"The path {path} is not in stage {stage}".format(
265	path=local_filepath.parent, **self.spec
266	)
267	)
268	uuid = uuid_from_buffer(	1✔
269	init_string=relative_filepath
270	) # hash relative path, not contents
271	contents_hash = uuid_from_file(local_filepath)	1✔
272
273	# check if the remote file already exists and verify that it matches
274	check_hash = (self & {"hash": uuid}).fetch("contents_hash")	1✔
275	if check_hash:	1✔
276	# the tracking entry exists, check that it's the same file as before
277	if contents_hash != check_hash[0]:	1✔
278	raise DataJointError(	1✔
279	"A different version of '{file}' has already been placed.".format(
280	file=relative_filepath
281	)
282	)
283	else:
284	# upload the file and create its tracking entry
285	self._upload_file(	1✔
286	local_filepath,
287	self._make_external_filepath(relative_filepath),
288	metadata={"contents_hash": str(contents_hash)},
289	)
290	self.connection.query(	1✔
291	"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES (%s, {size}, '{filepath}', %s)".format(
292	tab=self.full_table_name,
293	size=Path(local_filepath).stat().st_size,
294	filepath=relative_filepath,
295	),
296	args=(uuid.bytes, contents_hash.bytes),
297	)
298	return uuid	1✔
299
300	def download_filepath(self, filepath_hash):	1✔
301	"""
302	sync a file from external store to the local stage
303
304	:param filepath_hash: The hash (UUID) of the relative_path
305	:return: hash (UUID) of the contents of the downloaded file or Nones
306	"""
307	if filepath_hash is not None:	1✔
308	relative_filepath, contents_hash = (self & {"hash": filepath_hash}).fetch1(	1✔
309	"filepath", "contents_hash"
310	)
311	external_path = self._make_external_filepath(relative_filepath)	1✔
312	local_filepath = Path(self.spec["stage"]).absolute() / relative_filepath	1✔
313	file_exists = (	1✔
314	Path(local_filepath).is_file()
315	and uuid_from_file(local_filepath) == contents_hash
316	)
317	if not file_exists:	1✔
318	self._download_file(external_path, local_filepath)	1✔
319	checksum = uuid_from_file(local_filepath)	1✔
320	if (	1✔
321	checksum != contents_hash
322	): # this should never happen without outside interference
323	raise DataJointError(	×
324	"'{file}' downloaded but did not pass checksum'".format(
325	file=local_filepath
326	)
327	)
328	return str(local_filepath), contents_hash	1✔
329
330	# --- UTILITIES ---
331
332	@property	1✔
333	def references(self):	1✔
334	"""
335	:return: generator of referencing table names and their referencing columns
336	"""
337	return (	1✔
338	{k.lower(): v for k, v in elem.items()}
339	for elem in self.connection.query(
340	"""
341	SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name
342	FROM information_schema.key_column_usage
343	WHERE referenced_table_name="{tab}" and referenced_table_schema="{db}"
344	""".format(
345	tab=self.table_name, db=self.database
346	),
347	as_dict=True,
348	)
349	)
350
351	def fetch_external_paths(self, **fetch_kwargs):	1✔
352	"""
353	generate complete external filepaths from the query.
354	Each element is a tuple: (uuid, path)
355
356	:param fetch_kwargs: keyword arguments to pass to fetch
357	"""
358	fetch_kwargs.update(as_dict=True)	1✔
359	paths = []	1✔
360	for item in self.fetch("hash", "attachment_name", "filepath", **fetch_kwargs):	1✔
361	if item["attachment_name"]:	1✔
362	# attachments
363	path = self._make_uuid_path(item["hash"], "." + item["attachment_name"])	×
364	elif item["filepath"]:	1✔
365	# external filepaths
366	path = self._make_external_filepath(item["filepath"])	1✔
367	else:
368	# blobs
369	path = self._make_uuid_path(item["hash"])	1✔
370	paths.append((item["hash"], path))	1✔
371	return paths	1✔
372
373	def unused(self):	1✔
374	"""
375	query expression for unused hashes
376
377	:return: self restricted to elements that are not in use by any tables in the schema
378	"""
379	return self - [	1✔
380	FreeTable(self.connection, ref["referencing_table"]).proj(
381	hash=ref["column_name"]
382	)
383	for ref in self.references
384	]
385
386	def used(self):	1✔
387	"""
388	query expression for used hashes
389
390	:return: self restricted to elements that in use by tables in the schema
391	"""
392	return self & [	×
393	FreeTable(self.connection, ref["referencing_table"]).proj(
394	hash=ref["column_name"]
395	)
396	for ref in self.references
397	]
398
399	def delete(	1✔
400	self,
401	*,
402	delete_external_files=None,
403	limit=None,
404	display_progress=True,
405	errors_as_string=True
406	):
407	"""
408
409	:param delete_external_files: True or False. If False, only the tracking info is removed from the external
410	store table but the external files remain intact. If True, then the external files themselves are deleted too.
411	:param errors_as_string: If True any errors returned when deleting from external files will be strings
412	:param limit: (integer) limit the number of items to delete
413	:param display_progress: if True, display progress as files are cleaned up
414	:return: if deleting external files, returns errors
415	"""
416	if delete_external_files not in (True, False):	1✔
417	raise DataJointError(	×
418	"The delete_external_files argument must be set to either "
419	"True or False in delete()"
420	)
421
422	if not delete_external_files:	1✔
423	self.unused().delete_quick()	1✔
424	else:
425	items = self.unused().fetch_external_paths(limit=limit)	1✔
426	if display_progress:	1✔
427	items = tqdm(items)	1✔
428	# delete items one by one, close to transaction-safe
429	error_list = []	1✔
430	for uuid, external_path in items:	1✔
431	row = (self & {"hash": uuid}).fetch()	1✔
432	if row.size:	1✔
433	try:	1✔
434	(self & {"hash": uuid}).delete_quick()	1✔
435	except Exception:	×
436	pass # if delete failed, do not remove the external file	×
437	else:
438	try:	1✔
439	self._remove_external_file(external_path)	1✔
440	except Exception as error:	1✔
441	# adding row back into table after failed delete
442	self.insert1(row[0], skip_duplicates=True)	1✔
443	error_list.append(	1✔
444	(
445	uuid,
446	external_path,
447	str(error) if errors_as_string else error,
448	)
449	)
450	return error_list	1✔
451
452
453	class ExternalMapping(Mapping):	1✔
454	"""
455	The external manager contains all the tables for all external stores for a given schema
456	:Example:
457	e = ExternalMapping(schema)
458	external_table = e[store]
459	"""
460
461	def __init__(self, schema):	1✔
462	self.schema = schema	1✔
463	self._tables = {}	1✔
464
465	def __repr__(self):	1✔
466	return "External file tables for schema `{schema}`:\n ".format(	×
467	schema=self.schema.database
468	) + "\n ".join(
469	'"{store}" {protocol}:{location}'.format(store=k, **v.spec)
470	for k, v in self.items()
471	)
472
473	def __getitem__(self, store):	1✔
474	"""
475	Triggers the creation of an external table.
476	Should only be used when ready to save or read from external storage.
477
478	:param store: the name of the store
479	:return: the ExternalTable object for the store
480	"""
481	if store not in self._tables:	1✔
482	self._tables[store] = ExternalTable(	1✔
483	connection=self.schema.connection,
484	store=store,
485	database=self.schema.database,
486	)
487	return self._tables[store]	1✔
488
489	def __len__(self):	1✔
490	return len(self._tables)	×
491
492	def __iter__(self):	1✔
493	return iter(self._tables)	1✔

datajoint / datajoint-python / #12398

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