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Build # #12880

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travis-ci

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Commit Message

Merge pull request #1067 from CBroz1/master

Add support for insert CSV

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/datajoint/external.py

from pathlib import Path, PurePosixPath, PureWindowsPath
from collections.abc import Mapping
from tqdm import tqdm
import logging
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

logger = logging.getLogger(__name__.split(".")[0])

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 f"{EXTERNAL_TABLE_ROOT}_{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(
                    f"A different version of '{relative_filepath}' has already been placed."
                )
        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
        """

        def _need_checksum(local_filepath, expected_size):
            limit = config.get("filepath_checksum_size_limit")
            actual_size = Path(local_filepath).stat().st_size
            if expected_size != actual_size:
                # this should never happen without outside interference
                raise DataJointError(
                    f"'{local_filepath}' downloaded but size did not match."
                )
            return limit is None or actual_size < limit

        if filepath_hash is not None:
            relative_filepath, contents_hash, size = (
                self & {"hash": filepath_hash}
            ).fetch1("filepath", "contents_hash", "size")
            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 (
                not _need_checksum(local_filepath, size)
                or uuid_from_file(local_filepath) == contents_hash
            )

            if not file_exists:
                self._download_file(external_path, local_filepath)
                if (
                    _need_checksum(local_filepath, size)
                    and uuid_from_file(local_filepath) != contents_hash
                ):
                    # this should never happen without outside interference
                    raise DataJointError(
                        f"'{local_filepath}' downloaded but did not pass checksum."
                    )
            if not _need_checksum(local_filepath, size):
                logger.warning(
                    f"Skipped checksum for file with hash: {contents_hash}, and path: {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	import logging	1✔
5	from .settings import config	1✔
6	from .errors import DataJointError, MissingExternalFile	1✔
7	from .hash import uuid_from_buffer, uuid_from_file	1✔
8	from .table import Table, FreeTable	1✔
9	from .heading import Heading	1✔
10	from .declare import EXTERNAL_TABLE_ROOT	1✔
11	from . import s3	1✔
12	from .utils import safe_write, safe_copy	1✔
13
14	logger = logging.getLogger(__name__.split(".")[0])	1✔
15
16	CACHE_SUBFOLDING = (	1✔
17	2,
18	2,
19	) # (2, 2) means "0123456789abcd" will be saved as "01/23/0123456789abcd"
20	SUPPORT_MIGRATED_BLOBS = True # support blobs migrated from datajoint 0.11.*	1✔
21
22
23	def subfold(name, folds):	1✔
24	"""
25	subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde']
26	"""
27	return (	1✔
28	(name[: folds[0]].lower(),) + subfold(name[folds[0] :], folds[1:])
29	if folds
30	else ()
31	)
32
33
34	class ExternalTable(Table):	1✔
35	"""
36	The table tracking externally stored objects.
37	Declare as ExternalTable(connection, database)
38	"""
39
40	def __init__(self, connection, store, database):	1✔
41	self.store = store	1✔
42	self.spec = config.get_store_spec(store)	1✔
43	self._s3 = None	1✔
44	self.database = database	1✔
45	self._connection = connection	1✔
46	self._heading = Heading(	1✔
47	table_info=dict(
48	conn=connection,
49	database=database,
50	table_name=self.table_name,
51	context=None,
52	)
53	)
54	self._support = [self.full_table_name]	1✔
55	if not self.is_declared:	1✔
56	self.declare()	1✔
57	self._s3 = None	1✔
58	if self.spec["protocol"] == "file" and not Path(self.spec["location"]).is_dir():	1✔
59	raise FileNotFoundError(	×
60	"Inaccessible local directory %s" % self.spec["location"]
61	) from None
62
63	@property	1✔
64	def definition(self):	1✔
65	return """	1✔
66	# external storage tracking
67	hash : uuid # hash of contents (blob), of filename + contents (attach), or relative filepath (filepath)
68	---
69	size :bigint unsigned # size of object in bytes
70	attachment_name=null : varchar(255) # the filename of an attachment
71	filepath=null : varchar(1000) # relative filepath or attachment filename
72	contents_hash=null : uuid # used for the filepath datatype
73	timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp
74	"""
75
76	@property	1✔
77	def table_name(self):	1✔
78	return f"{EXTERNAL_TABLE_ROOT}_{self.store}"	1✔
79
80	@property	1✔
81	def s3(self):	1✔
82	if self._s3 is None:	1✔
83	self._s3 = s3.Folder(**self.spec)	1✔
84	return self._s3	1✔
85
86	# - low-level operations - private
87
88	def _make_external_filepath(self, relative_filepath):	1✔
89	"""resolve the complete external path based on the relative path"""
90	# Strip root
91	if self.spec["protocol"] == "s3":	1✔
92	posix_path = PurePosixPath(PureWindowsPath(self.spec["location"]))	1✔
93	location_path = (	1✔
94	Path(*posix_path.parts[1:])
95	if len(self.spec["location"]) > 0
96	and any(case in posix_path.parts[0] for case in ("\\", ":"))
97	else Path(posix_path)
98	)
99	return PurePosixPath(location_path, relative_filepath)	1✔
100	# Preserve root
101	elif self.spec["protocol"] == "file":	1✔
102	return PurePosixPath(Path(self.spec["location"]), relative_filepath)	1✔
103	else:
104	assert False	×
105
106	def _make_uuid_path(self, uuid, suffix=""):	1✔
107	"""create external path based on the uuid hash"""
108	return self._make_external_filepath(	1✔
109	PurePosixPath(
110	self.database,
111	"/".join(subfold(uuid.hex, self.spec["subfolding"])),
112	uuid.hex,
113	).with_suffix(suffix)
114	)
115
116	def _upload_file(self, local_path, external_path, metadata=None):	1✔
117	if self.spec["protocol"] == "s3":	1✔
118	self.s3.fput(local_path, external_path, metadata)	1✔
119	elif self.spec["protocol"] == "file":	1✔
120	safe_copy(local_path, external_path, overwrite=True)	1✔
121	else:
122	assert False	×
123
124	def _download_file(self, external_path, download_path):	1✔
125	if self.spec["protocol"] == "s3":	1✔
126	self.s3.fget(external_path, download_path)	1✔
127	elif self.spec["protocol"] == "file":	1✔
128	safe_copy(external_path, download_path)	1✔
129	else:
130	assert False	×
131
132	def _upload_buffer(self, buffer, external_path):	1✔
133	if self.spec["protocol"] == "s3":	1✔
134	self.s3.put(external_path, buffer)	1✔
135	elif self.spec["protocol"] == "file":	1✔
136	safe_write(external_path, buffer)	1✔
137	else:
138	assert False	×
139
140	def _download_buffer(self, external_path):	1✔
141	if self.spec["protocol"] == "s3":	1✔
142	return self.s3.get(external_path)	1✔
143	if self.spec["protocol"] == "file":	1✔
144	return Path(external_path).read_bytes()	1✔
145	assert False	×
146
147	def _remove_external_file(self, external_path):	1✔
148	if self.spec["protocol"] == "s3":	1✔
149	self.s3.remove_object(external_path)	1✔
150	elif self.spec["protocol"] == "file":	1✔
151	try:	1✔
152	Path(external_path).unlink()	1✔
153	except FileNotFoundError:	1✔
154	pass	×
155
156	def exists(self, external_filepath):	1✔
157	"""
158	:return: True if the external file is accessible
159	"""
160	if self.spec["protocol"] == "s3":	1✔
161	return self.s3.exists(external_filepath)	1✔
162	if self.spec["protocol"] == "file":	1✔
163	return Path(external_filepath).is_file()	1✔
164	assert False	×
165
166	# --- BLOBS ----
167
168	def put(self, blob):	1✔
169	"""
170	put a binary string (blob) in external store
171	"""
172	uuid = uuid_from_buffer(blob)	1✔
173	self._upload_buffer(blob, self._make_uuid_path(uuid))	1✔
174	# insert tracking info
175	self.connection.query(	1✔
176	"INSERT INTO {tab} (hash, size) VALUES (%s, {size}) ON DUPLICATE KEY "
177	"UPDATE timestamp=CURRENT_TIMESTAMP".format(
178	tab=self.full_table_name, size=len(blob)
179	),
180	args=(uuid.bytes,),
181	)
182	return uuid	1✔
183
184	def get(self, uuid):	1✔
185	"""
186	get an object from external store.
187	"""
188	if uuid is None:	1✔
189	return None	×
190	# attempt to get object from cache
191	blob = None	1✔
192	cache_folder = config.get("cache", None)	1✔
193	if cache_folder:	1✔
194	try:	1✔
195	cache_path = Path(cache_folder, *subfold(uuid.hex, CACHE_SUBFOLDING))	1✔
196	cache_file = Path(cache_path, uuid.hex)	1✔
197	blob = cache_file.read_bytes()	1✔
198	except FileNotFoundError:	1✔
199	pass # not cached	1✔
200	# download blob from external store
201	if blob is None:	1✔
202	try:	1✔
203	blob = self._download_buffer(self._make_uuid_path(uuid))	1✔
204	except MissingExternalFile:	1✔
205	if not SUPPORT_MIGRATED_BLOBS:	1✔
206	raise	×
207	# blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths
208	relative_filepath, contents_hash = (self & {"hash": uuid}).fetch1(	1✔
209	"filepath", "contents_hash"
210	)
211	if relative_filepath is None:	1✔
212	raise	×
213	blob = self._download_buffer(	1✔
214	self._make_external_filepath(relative_filepath)
215	)
216	if cache_folder:	1✔
217	cache_path.mkdir(parents=True, exist_ok=True)	1✔
218	safe_write(cache_path / uuid.hex, blob)	1✔
219	return blob	1✔
220
221	# --- ATTACHMENTS ---
222
223	def upload_attachment(self, local_path):	1✔
224	attachment_name = Path(local_path).name	1✔
225	uuid = uuid_from_file(local_path, init_string=attachment_name + "\0")	1✔
226	external_path = self._make_uuid_path(uuid, "." + attachment_name)	1✔
227	self._upload_file(local_path, external_path)	1✔
228	# insert tracking info
229	self.connection.query(	1✔
230	"""
231	INSERT INTO {tab} (hash, size, attachment_name)
232	VALUES (%s, {size}, "{attachment_name}")
233	ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP""".format(
234	tab=self.full_table_name,
235	size=Path(local_path).stat().st_size,
236	attachment_name=attachment_name,
237	),
238	args=[uuid.bytes],
239	)
240	return uuid	1✔
241
242	def get_attachment_name(self, uuid):	1✔
243	return (self & {"hash": uuid}).fetch1("attachment_name")	1✔
244
245	def download_attachment(self, uuid, attachment_name, download_path):	1✔
246	"""save attachment from memory buffer into the save_path"""
247	external_path = self._make_uuid_path(uuid, "." + attachment_name)	1✔
248	self._download_file(external_path, download_path)	1✔
249
250	# --- FILEPATH ---
251
252	def upload_filepath(self, local_filepath):	1✔
253	"""
254	Raise exception if an external entry already exists with a different contents checksum.
255	Otherwise, copy (with overwrite) file to remote and
256	If an external entry exists with the same checksum, then no copying should occur
257	"""
258	local_filepath = Path(local_filepath)	1✔
259	try:	1✔
260	relative_filepath = str(	1✔
261	local_filepath.relative_to(self.spec["stage"]).as_posix()
262	)
263	except ValueError:	×
264	raise DataJointError(	×
265	"The path {path} is not in stage {stage}".format(
266	path=local_filepath.parent, **self.spec
267	)
268	)
269	uuid = uuid_from_buffer(	1✔
270	init_string=relative_filepath
271	) # hash relative path, not contents
272	contents_hash = uuid_from_file(local_filepath)	1✔
273
274	# check if the remote file already exists and verify that it matches
275	check_hash = (self & {"hash": uuid}).fetch("contents_hash")	1✔
276	if check_hash:	1✔
277	# the tracking entry exists, check that it's the same file as before
278	if contents_hash != check_hash[0]:	1✔
279	raise DataJointError(	1✔
280	f"A different version of '{relative_filepath}' has already been placed."
281	)
282	else:
283	# upload the file and create its tracking entry
284	self._upload_file(	1✔
285	local_filepath,
286	self._make_external_filepath(relative_filepath),
287	metadata={"contents_hash": str(contents_hash)},
288	)
289	self.connection.query(	1✔
290	"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES (%s, {size}, '{filepath}', %s)".format(
291	tab=self.full_table_name,
292	size=Path(local_filepath).stat().st_size,
293	filepath=relative_filepath,
294	),
295	args=(uuid.bytes, contents_hash.bytes),
296	)
297	return uuid	1✔
298
299	def download_filepath(self, filepath_hash):	1✔
300	"""
301	sync a file from external store to the local stage
302
303	:param filepath_hash: The hash (UUID) of the relative_path
304	:return: hash (UUID) of the contents of the downloaded file or Nones
305	"""
306
307	def _need_checksum(local_filepath, expected_size):	1✔
308	limit = config.get("filepath_checksum_size_limit")	1✔
309	actual_size = Path(local_filepath).stat().st_size	1✔
310	if expected_size != actual_size:	1✔
311	# this should never happen without outside interference
312	raise DataJointError(	×
313	f"'{local_filepath}' downloaded but size did not match."
314	)
315	return limit is None or actual_size < limit	1✔
316
317	if filepath_hash is not None:	1✔
318	relative_filepath, contents_hash, size = (	1✔
319	self & {"hash": filepath_hash}
320	).fetch1("filepath", "contents_hash", "size")
321	external_path = self._make_external_filepath(relative_filepath)	1✔
322	local_filepath = Path(self.spec["stage"]).absolute() / relative_filepath	1✔
323
324	file_exists = Path(local_filepath).is_file() and (	1✔
325	not _need_checksum(local_filepath, size)
326	or uuid_from_file(local_filepath) == contents_hash
327	)
328
329	if not file_exists:	1✔
330	self._download_file(external_path, local_filepath)	1✔
331	if (	1✔
332	_need_checksum(local_filepath, size)
333	and uuid_from_file(local_filepath) != contents_hash
334	):
335	# this should never happen without outside interference
336	raise DataJointError(	×
337	f"'{local_filepath}' downloaded but did not pass checksum."
338	)
339	if not _need_checksum(local_filepath, size):	1✔
340	logger.warning(	1✔
341	f"Skipped checksum for file with hash: {contents_hash}, and path: {local_filepath}"
342	)
343	return str(local_filepath), contents_hash	1✔
344
345	# --- UTILITIES ---
346
347	@property	1✔
348	def references(self):	1✔
349	"""
350	:return: generator of referencing table names and their referencing columns
351	"""
352	return (	1✔
353	{k.lower(): v for k, v in elem.items()}
354	for elem in self.connection.query(
355	"""
356	SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name
357	FROM information_schema.key_column_usage
358	WHERE referenced_table_name="{tab}" and referenced_table_schema="{db}"
359	""".format(
360	tab=self.table_name, db=self.database
361	),
362	as_dict=True,
363	)
364	)
365
366	def fetch_external_paths(self, **fetch_kwargs):	1✔
367	"""
368	generate complete external filepaths from the query.
369	Each element is a tuple: (uuid, path)
370
371	:param fetch_kwargs: keyword arguments to pass to fetch
372	"""
373	fetch_kwargs.update(as_dict=True)	1✔
374	paths = []	1✔
375	for item in self.fetch("hash", "attachment_name", "filepath", **fetch_kwargs):	1✔
376	if item["attachment_name"]:	1✔
377	# attachments
378	path = self._make_uuid_path(item["hash"], "." + item["attachment_name"])	×
379	elif item["filepath"]:	1✔
380	# external filepaths
381	path = self._make_external_filepath(item["filepath"])	1✔
382	else:
383	# blobs
384	path = self._make_uuid_path(item["hash"])	1✔
385	paths.append((item["hash"], path))	1✔
386	return paths	1✔
387
388	def unused(self):	1✔
389	"""
390	query expression for unused hashes
391
392	:return: self restricted to elements that are not in use by any tables in the schema
393	"""
394	return self - [	1✔
395	FreeTable(self.connection, ref["referencing_table"]).proj(
396	hash=ref["column_name"]
397	)
398	for ref in self.references
399	]
400
401	def used(self):	1✔
402	"""
403	query expression for used hashes
404
405	:return: self restricted to elements that in use by tables in the schema
406	"""
407	return self & [	×
408	FreeTable(self.connection, ref["referencing_table"]).proj(
409	hash=ref["column_name"]
410	)
411	for ref in self.references
412	]
413
414	def delete(	1✔
415	self,
416	*,
417	delete_external_files=None,
418	limit=None,
419	display_progress=True,
420	errors_as_string=True,
421	):
422	"""
423
424	:param delete_external_files: True or False. If False, only the tracking info is removed from the external
425	store table but the external files remain intact. If True, then the external files themselves are deleted too.
426	:param errors_as_string: If True any errors returned when deleting from external files will be strings
427	:param limit: (integer) limit the number of items to delete
428	:param display_progress: if True, display progress as files are cleaned up
429	:return: if deleting external files, returns errors
430	"""
431	if delete_external_files not in (True, False):	1✔
432	raise DataJointError(	×
433	"The delete_external_files argument must be set to either "
434	"True or False in delete()"
435	)
436
437	if not delete_external_files:	1✔
438	self.unused().delete_quick()	1✔
439	else:
440	items = self.unused().fetch_external_paths(limit=limit)	1✔
441	if display_progress:	1✔
442	items = tqdm(items)	1✔
443	# delete items one by one, close to transaction-safe
444	error_list = []	1✔
445	for uuid, external_path in items:	1✔
446	row = (self & {"hash": uuid}).fetch()	1✔
447	if row.size:	1✔
448	try:	1✔
449	(self & {"hash": uuid}).delete_quick()	1✔
450	except Exception:	×
451	pass # if delete failed, do not remove the external file	×
452	else:
453	try:	1✔
454	self._remove_external_file(external_path)	1✔
455	except Exception as error:	1✔
456	# adding row back into table after failed delete
457	self.insert1(row[0], skip_duplicates=True)	1✔
458	error_list.append(	1✔
459	(
460	uuid,
461	external_path,
462	str(error) if errors_as_string else error,
463	)
464	)
465	return error_list	1✔
466
467
468	class ExternalMapping(Mapping):	1✔
469	"""
470	The external manager contains all the tables for all external stores for a given schema
471	:Example:
472	e = ExternalMapping(schema)
473	external_table = e[store]
474	"""
475
476	def __init__(self, schema):	1✔
477	self.schema = schema	1✔
478	self._tables = {}	1✔
479
480	def __repr__(self):	1✔
481	return "External file tables for schema `{schema}`:\n ".format(	×
482	schema=self.schema.database
483	) + "\n ".join(
484	'"{store}" {protocol}:{location}'.format(store=k, **v.spec)
485	for k, v in self.items()
486	)
487
488	def __getitem__(self, store):	1✔
489	"""
490	Triggers the creation of an external table.
491	Should only be used when ready to save or read from external storage.
492
493	:param store: the name of the store
494	:return: the ExternalTable object for the store
495	"""
496	if store not in self._tables:	1✔
497	self._tables[store] = ExternalTable(	1✔
498	connection=self.schema.connection,
499	store=store,
500	database=self.schema.database,
501	)
502	return self._tables[store]	1✔
503
504	def __len__(self):	1✔
505	return len(self._tables)	×
506
507	def __iter__(self):	1✔
508	return iter(self._tables)	1✔

datajoint / datajoint-python / #12880

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