From 7dc50784a381254f16be2a97ca2cb3e35a0ebdf7 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 03:05:49 +0200 Subject: [PATCH 01/19] Azure implementation for multipart upload --- cognite/cdffs/spec.py | 151 +++++++++++++++++++++++++++++++++--------- 1 file changed, 120 insertions(+), 31 deletions(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 42de466..f7c0c64 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -1,11 +1,15 @@ """File System Specification for CDF Files.""" +import base64 import logging import time +from concurrent.futures import ThreadPoolExecutor +from io import BytesIO from pathlib import Path from typing import Any, Dict, List, Optional, Tuple, Union +import requests from cognite.client import ClientConfig, CogniteClient -from cognite.client.data_classes.files import FileMetadata +from cognite.client.data_classes.files import FileMetadata, FileMetadataUpdate from cognite.client.exceptions import ( CogniteAPIError, CogniteAuthError, @@ -16,6 +20,7 @@ from fsspec import AbstractFileSystem from fsspec.caching import AllBytes from fsspec.spec import AbstractBufferedFile +from fsspec.utils import DEFAULT_BLOCK_SIZE from .credentials import get_connection_config from .file_handler import FileException, FileHandler @@ -461,7 +466,7 @@ def open( self, path: str, mode: str = "rb", - block_size: str = "default", + block_size: int = DEFAULT_BLOCK_SIZE, cache_options: Optional[Dict[Any, Any]] = None, **kwargs: Optional[Any], ) -> "CdfFile": @@ -612,7 +617,7 @@ def __init__( directory: str, external_id: str, mode: str = "rb", - block_size: str = "default", + block_size: int = DEFAULT_BLOCK_SIZE, cache_options: Optional[Union[Dict[Any, Any], None]] = None, **kwargs: Optional[Any], ) -> None: @@ -625,7 +630,7 @@ def __init__( directory (str): Root directory for the file. external_id (str): External Id for the file. mode (str): Mode to work with the file. - block_size (str): Block size to read/write the file. + block_size (int): Block size to read/write the file. cache_options (str): Additional caching options for the file. **kwargs (Optional[Any]): Set of keyword arguments to read/write the file contents. """ @@ -634,11 +639,33 @@ def __init__( self.external_id: str = external_id self.all_bytes_caching: bool = "cache_type" in kwargs and kwargs["cache_type"] == "all" self.file_metadata: FileMetadata = FileMetadata(metadata={}) + self.block_ids: List[str] = list() # User can use a file metadata for each file when they write the files. if isinstance(kwargs.get("file_metadata"), FileMetadata) and mode != "rb": self.file_metadata = kwargs.pop("file_metadata") + self.file_descriptor = self.cognite_client.post( + f"/api/v1/projects/{self.cognite_client.config.project}/files?overwrite=true", + json={ + "externalId": Path(self.external_id).name, + "name": Path(self.external_id).name, + "directory": self.root_dir, + "source": self.file_metadata.source or fs.file_metadata.source, + "assetIds": self.file_metadata.asset_ids or fs.file_metadata.asset_ids, + "dataSetId": self.file_metadata.data_set_id or fs.file_metadata.data_set_id, + "mimeType": self.file_metadata.mime_type or fs.file_metadata.mime_type, + "geoLocation": self.file_metadata.geo_location or fs.file_metadata.geo_location, + "metadata": { + **self.file_metadata.dump()["metadata"], + **fs.file_metadata.metadata, + }, + }, + ).json() + + self.session = requests.Session() + self.index = 0 + super().__init__( fs, path, @@ -648,6 +675,35 @@ def __init__( **kwargs, ) + def _merge_blocks(self) -> None: + """Merge all uploaded blocks into the final blob.""" + # Commit the blocks + commit_url = f"{self.file_descriptor['uploadUrl']}&comp=blocklist" + block_list_xml = '' + for block_id in self.block_ids: + block_list_xml += f"{block_id}" + block_list_xml += "" + + response = self.session.put( + commit_url, + data=block_list_xml, + headers={ + "x-ms-blob-content-type": "application/xml", + "Content-Length": str(len(block_list_xml)), + "x-ms-version": "2019-12-12", + }, + ) + response.raise_for_status() + + self.cognite_client.files.update( + item=FileMetadataUpdate(id=self.file_descriptor["id"]) + .metadata() + .set({"size": (len(self.block_ids) - 1) * self.blocksize + self.buffer.getbuffer().nbytes}) + ) + + # Clear block ids + self.block_ids.clear() + def _upload_chunk(self, final: bool = False) -> bool: """Upload file contents to CDF. @@ -660,37 +716,70 @@ def _upload_chunk(self, final: bool = False) -> bool: Raises: RuntimeError: When an unexpected error occurred. """ - try: - if final: - file_metadata = self.file_metadata.metadata or self.fs.file_metadata.metadata - file_metadata = ( - dict(file_metadata, **{"size": self.buffer.getbuffer().nbytes}) - if file_metadata - else {"size": self.buffer.getbuffer().nbytes} - ) - response = self.cognite_client.files.upload_bytes( - content=self.buffer.getbuffer(), - name=Path(self.external_id).name, - external_id=self.external_id, - directory=self.root_dir, - source=self.file_metadata.source or self.fs.file_metadata.source, - asset_ids=self.file_metadata.asset_ids or self.fs.file_metadata.asset_ids, - data_set_id=self.file_metadata.data_set_id or self.fs.file_metadata.data_set_id, - mime_type=self.file_metadata.mime_type or self.fs.file_metadata.mime_type, - geo_location=self.file_metadata.geo_location or self.fs.file_metadata.geo_location, - metadata=file_metadata, - overwrite=True, - ) - self.fs.cache_path( - self.root_dir, - self.external_id, - int(response.metadata.get("size")) if response.metadata.get("size") else -1, + def generate_block_blob_block_id(block_name_prefix: str, index: int) -> str: + while len(block_name_prefix) < 19: + block_name_prefix += "x" + block_id = f"{block_name_prefix[:19]}{index:05}".encode("utf-8") + + return base64.b64encode(block_id).decode("utf-8") + + def upload_block(block_data: bytes, block_id: str) -> None: + """Uploads a single block.""" + try: + url = self.file_descriptor["uploadUrl"].split("?") + upload_block_url = f"{url[0]}?blockid={block_id}&comp=block&{url[1]}" + response = self.session.put( + upload_block_url, + data=block_data, + headers={ + "Accept": "application/xml", + "Content-Type": "application/octet-stream", + "Content-Length": str(len(block_data)), + "x-ms-version": "2019-12-12", + }, ) + response.raise_for_status() + logging.info(f"Finished uploading block {block_id}. Took {response.elapsed.total_seconds()} sec") + except Exception as ex: + logging.warning("Failed to upload on of the blocks: {ex}", exc_info=ex) + raise + + try: + buffer_length = self.buffer.getbuffer().nbytes + blocks = [self.buffer.getbuffer()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] + + # Only consider blocks of full size for uploading + full_blocks = [b for b in blocks if len(b) == self.blocksize] + + logging.info(f"{len(full_blocks)} full blocks discovered") + + # Upload blocks in parallel using ThreadPoolExecutor + with ThreadPoolExecutor(max_workers=5) as executor: + block_ids = [ + generate_block_blob_block_id(self.external_id, index) + for index in range(self.index, self.index + len(full_blocks)) + ] + self.block_ids.extend(block_ids) + + list(executor.map(upload_block, full_blocks, block_ids)) + + # Reset buffer to only contain the leftover data (less than blocksize) + leftover_data = b"".join(blocks[len(full_blocks) :]) + self.buffer: BytesIO = BytesIO(leftover_data) + + # Update the index + self.index += len(full_blocks) + + # If it's the final block, then send a merge request + if final: + upload_block(leftover_data, generate_block_blob_block_id(self.external_id, self.index)) + self._merge_blocks() return final - except _COMMON_EXCEPTIONS as cognite_exp: - raise RuntimeError from cognite_exp + + except (requests.exceptions.RequestException, _COMMON_EXCEPTIONS) as error: # type: ignore + raise RuntimeError from error def _fetch_range(self, start: int, end: int) -> Any: """Read file contents from CDF. From d832f4dcd9740abd094b9df991f8694cca7e4cc1 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 09:23:32 +0200 Subject: [PATCH 02/19] Some bug fixes --- cognite/cdffs/spec.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index f7c0c64..03cb316 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -697,7 +697,7 @@ def _merge_blocks(self) -> None: self.cognite_client.files.update( item=FileMetadataUpdate(id=self.file_descriptor["id"]) - .metadata() + .metadata .set({"size": (len(self.block_ids) - 1) * self.blocksize + self.buffer.getbuffer().nbytes}) ) @@ -761,8 +761,8 @@ def upload_block(block_data: bytes, block_id: str) -> None: for index in range(self.index, self.index + len(full_blocks)) ] self.block_ids.extend(block_ids) - - list(executor.map(upload_block, full_blocks, block_ids)) + for arg in zip(full_blocks, block_ids): + executor.submit(upload_block, arg[0], arg[1]) # Reset buffer to only contain the leftover data (less than blocksize) leftover_data = b"".join(blocks[len(full_blocks) :]) @@ -773,7 +773,9 @@ def upload_block(block_data: bytes, block_id: str) -> None: # If it's the final block, then send a merge request if final: - upload_block(leftover_data, generate_block_blob_block_id(self.external_id, self.index)) + block_id = generate_block_blob_block_id(self.external_id, self.index) + upload_block(leftover_data, block_id) + self.block_ids.append(block_id) self._merge_blocks() return final From 64af25d19a2a90211492b697cb59053d4d1b4b3c Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 09:58:24 +0200 Subject: [PATCH 03/19] Add zip example --- examples/zip.py | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 examples/zip.py diff --git a/examples/zip.py b/examples/zip.py new file mode 100644 index 0000000..f19d17c --- /dev/null +++ b/examples/zip.py @@ -0,0 +1,49 @@ +import re +import zipfile +from pathlib import Path + +import fsspec +from cognite.client.data_classes import FileMetadata + +from cognite import cdffs # noqa + + +def clean_filename(path): + # Replace multiple slashes or colons with a single underscore + cleaned = re.sub(r'[:/]+', '_', path) + return cleaned + + +def main(): + source_fs = fsspec.filesystem("file") + target_fs = fsspec.filesystem("cdffs") + + BUFFER_SIZE = 1 * 1024 * 1024 # 1MB + + source_files = [ + f + for f in source_fs.glob(f"{Path(__file__).parent.parent.absolute()}/**/*") + if Path(f).is_file() + ] + + with target_fs.open( + f"test.zip", + "wb", + file_metadata=FileMetadata( + source="test", + directory="/archive/", + data_set_id=8576667485598960, + mime_type="application/zip", + metadata={"test": "test"} + ), + block_size=BUFFER_SIZE, + ) as target_file: + with zipfile.ZipFile(target_file, 'w') as zipf: + for source_path in source_files: + with source_fs.open(source_path, "rb") as source_file: + zip_file_name = clean_filename(source_path) + zipf.writestr(zip_file_name, source_file.read()) + + +if __name__ == '__main__': + main() From 9021ce2664209dc0b0beb409789bf46ed06c22e6 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 10:15:23 +0200 Subject: [PATCH 04/19] Propagate mime type --- cognite/cdffs/spec.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 03cb316..3f5e2ee 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -688,7 +688,8 @@ def _merge_blocks(self) -> None: commit_url, data=block_list_xml, headers={ - "x-ms-blob-content-type": "application/xml", + "x-ms-blob-content-type": self.file_metadata.mime_type, + "Content-Type": "application/xml", "Content-Length": str(len(block_list_xml)), "x-ms-version": "2019-12-12", }, From 8edc408814e815c907aa7db5e13072abd5be7d4e Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 20:47:41 +0200 Subject: [PATCH 05/19] More progress --- cognite/cdffs/az_upload_strategy.py | 72 +++++++++++++ cognite/cdffs/gcp_upload_strategy.py | 54 ++++++++++ cognite/cdffs/memory_upload_strategy.py | 33 ++++++ cognite/cdffs/spec.py | 128 +++++------------------- cognite/cdffs/upload_strategy.py | 66 ++++++++++++ examples/zip.py | 32 +++--- 6 files changed, 264 insertions(+), 121 deletions(-) create mode 100644 cognite/cdffs/az_upload_strategy.py create mode 100644 cognite/cdffs/gcp_upload_strategy.py create mode 100644 cognite/cdffs/memory_upload_strategy.py create mode 100644 cognite/cdffs/upload_strategy.py diff --git a/cognite/cdffs/az_upload_strategy.py b/cognite/cdffs/az_upload_strategy.py new file mode 100644 index 0000000..81ad022 --- /dev/null +++ b/cognite/cdffs/az_upload_strategy.py @@ -0,0 +1,72 @@ +"""Azure native file upload strategy.""" +import base64 +import logging + +from cognite.client import CogniteClient +from cognite.client.data_classes import FileMetadata + +from .upload_strategy import UploadStrategy + + +class AzureUploadStrategy(UploadStrategy): + """Azure implementation for upload strategy.""" + + def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): + """Initializer.""" + super().__init__(metadata, cognite_client) + + def _generate_block_blob_block_id(self, index: int, block_name_prefix: str = __file__.__str__()) -> str: + while len(block_name_prefix) < 19: + block_name_prefix += "x" + block_id = f"{block_name_prefix[:19]}{index:05}".encode("utf-8") + + return base64.b64encode(block_id).decode("utf-8") + + def upload_chunk(self, data: bytes, index: int) -> None: + """Uploads a single block.""" + try: + url = self.params["upload_url"].split("?") + block_id = self._generate_block_blob_block_id(index=index) + upload_block_url = f"{url[0]}?blockid={block_id}&comp=block&{url[1]}" + response = self.session.put( + upload_block_url, + data=data, + headers={ + "Accept": "application/xml", + "Content-Type": "application/octet-stream", + "Content-Length": str(len(data)), + "x-ms-version": "2019-12-12", + }, + ) + response.raise_for_status() + with self.lock: + self.indexes.append(index) + logging.info(f"Finished uploading block {index}. Took {response.elapsed.total_seconds()} sec") + except Exception as ex: + logging.warning("Failed to upload on of the blocks: {ex}", exc_info=ex) + raise + + def merge_chunks(self) -> None: + """Merge all uploaded blocks into the final blob.""" + try: + upload_url = self.params["upload_url"] + commit_url = f"{upload_url}&comp=blocklist" + block_list_xml = '' + for index in sorted(self.indexes): + block_list_xml += f"{self._generate_block_blob_block_id(index)}" + block_list_xml += "" + + response = self.session.put( + commit_url, + data=block_list_xml, + headers={ + "x-ms-blob-content-type": self.params["mime_type"], + "Content-Type": "application/xml", + "Content-Length": str(len(block_list_xml)), + "x-ms-version": "2019-12-12", + }, + ) + response.raise_for_status() + except Exception as ex: + logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) + raise diff --git a/cognite/cdffs/gcp_upload_strategy.py b/cognite/cdffs/gcp_upload_strategy.py new file mode 100644 index 0000000..b4708a1 --- /dev/null +++ b/cognite/cdffs/gcp_upload_strategy.py @@ -0,0 +1,54 @@ +"""Google native file upload strategy.""" +import logging +from collections import OrderedDict +from typing import Dict + +from cognite.client import CogniteClient +from cognite.client.data_classes import FileMetadata + +from .upload_strategy import UploadStrategy + + +class GoogleUploadStrategy(UploadStrategy): + """Google implementation for upload strategy.""" + + def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): + """Initializer.""" + super().__init__(metadata, cognite_client) + self.chunk_cache: Dict = OrderedDict() # Store chunks in the order received + self.last_written_index = -1 # The last consecutive chunk index that was written + self.last_written_byte = -1 # The last byte position that was written + + def _write_chunk(self, index: int, data: bytes) -> None: + start_byte = self.last_written_byte + 1 + end_byte = start_byte + len(data) - 1 + + headers = {"Content-Length": str(len(data)), "Content-Range": f"bytes {start_byte}-{end_byte}/*"} + + response = self.session.put(self.params["upload_url"], headers=headers, data=data) + response.raise_for_status() + + with self.lock: + self.indexes.append(index) + + logging.info(f"Finished uploading chunk {index}. Took {response.elapsed.total_seconds()} sec") + + # Update the last written byte position + self.last_written_byte = end_byte + + def upload_chunk(self, data: bytes, index: int) -> None: + """Uploads a single chunk.""" + with self.lock: + self.chunk_cache[index] = data + + # Check for consecutive chunks in cache and write them + while self.last_written_index + 1 in self.chunk_cache: + next_index = self.last_written_index + 1 + self._write_chunk(next_index, self.chunk_cache[next_index]) + del self.chunk_cache[next_index] # Remove the written chunk from cache + self.last_written_index = next_index + + logging.info(f"Received chunk {index}. Cache size: {len(self.chunk_cache)} chunks") + + def merge_chunks(self) -> None: + """Google Cloud Storage handles merging internally. So, this method is a no-op for the GCS strategy.""" diff --git a/cognite/cdffs/memory_upload_strategy.py b/cognite/cdffs/memory_upload_strategy.py new file mode 100644 index 0000000..ed69462 --- /dev/null +++ b/cognite/cdffs/memory_upload_strategy.py @@ -0,0 +1,33 @@ +"""Inmemory file upload strategy.""" +import logging +import threading +from typing import Dict + +from cognite.client import CogniteClient +from cognite.client.data_classes import FileMetadata + +from .upload_strategy import UploadStrategy + + +class InMemoryUploadStrategy(UploadStrategy): + """Inmemory implementation for upload strategy.""" + + def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): + """Initializer.""" + super().__init__(metadata, cognite_client) + self.blocks: Dict[int, bytes] = {} + self.lock = threading.Lock() + + def upload_chunk(self, data: bytes, index: int) -> None: + """Upload single chunk.""" + with self.lock: + self.blocks[index] = data + + def merge_chunks(self) -> None: + """Merge all uploaded blocks into the final blob.""" + try: + content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) + self.cognite_client.files.upload_bytes(content=content, id=self.params["id"]) + except Exception as ex: + logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) + raise diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 3f5e2ee..67bfb19 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -1,15 +1,13 @@ """File System Specification for CDF Files.""" -import base64 import logging import time from concurrent.futures import ThreadPoolExecutor -from io import BytesIO from pathlib import Path from typing import Any, Dict, List, Optional, Tuple, Union import requests from cognite.client import ClientConfig, CogniteClient -from cognite.client.data_classes.files import FileMetadata, FileMetadataUpdate +from cognite.client.data_classes.files import FileMetadata from cognite.client.exceptions import ( CogniteAPIError, CogniteAuthError, @@ -22,8 +20,12 @@ from fsspec.spec import AbstractBufferedFile from fsspec.utils import DEFAULT_BLOCK_SIZE +from .az_upload_strategy import AzureUploadStrategy from .credentials import get_connection_config from .file_handler import FileException, FileHandler +from .gcp_upload_strategy import GoogleUploadStrategy +from .memory_upload_strategy import InMemoryUploadStrategy +from .upload_strategy import UploadStrategy logger = logging.getLogger(__name__) _COMMON_EXCEPTIONS = (CogniteAuthError, CogniteConnectionError, CogniteConnectionRefused, CogniteAPIError) @@ -53,6 +55,7 @@ def __init__( self, connection_config: Optional[ClientConfig] = None, file_metadata: FileMetadata = FileMetadata(metadata={}), + upload_strategy: str = "inmemory", **kwargs: Optional[Any], ) -> None: """Initialize the CdfFileSystem and creates a connection to CDF. @@ -83,6 +86,7 @@ def __init__( self.download_retries: bool = kwargs.get("download_retries", True) # type: ignore self.file_cache: Dict[str, Dict[str, Any]] = {} self.file_handler: FileHandler = FileHandler() + self.upload_strategy = upload_strategy # Create a connection to Cdf self.do_connect(connection_config, **kwargs) @@ -634,37 +638,25 @@ def __init__( cache_options (str): Additional caching options for the file. **kwargs (Optional[Any]): Set of keyword arguments to read/write the file contents. """ + self.index = 0 self.cognite_client: CogniteClient = cognite_client self.root_dir: str = directory self.external_id: str = external_id self.all_bytes_caching: bool = "cache_type" in kwargs and kwargs["cache_type"] == "all" self.file_metadata: FileMetadata = FileMetadata(metadata={}) - self.block_ids: List[str] = list() # User can use a file metadata for each file when they write the files. if isinstance(kwargs.get("file_metadata"), FileMetadata) and mode != "rb": self.file_metadata = kwargs.pop("file_metadata") - self.file_descriptor = self.cognite_client.post( - f"/api/v1/projects/{self.cognite_client.config.project}/files?overwrite=true", - json={ - "externalId": Path(self.external_id).name, - "name": Path(self.external_id).name, - "directory": self.root_dir, - "source": self.file_metadata.source or fs.file_metadata.source, - "assetIds": self.file_metadata.asset_ids or fs.file_metadata.asset_ids, - "dataSetId": self.file_metadata.data_set_id or fs.file_metadata.data_set_id, - "mimeType": self.file_metadata.mime_type or fs.file_metadata.mime_type, - "geoLocation": self.file_metadata.geo_location or fs.file_metadata.geo_location, - "metadata": { - **self.file_metadata.dump()["metadata"], - **fs.file_metadata.metadata, - }, - }, - ).json() - - self.session = requests.Session() - self.index = 0 + self.write_strategy: UploadStrategy + + if self.fs.upload_strategy == "google": + self.write_strategy = GoogleUploadStrategy(self.file_metadata, self.cognite_client) + elif self.fs.upload_strategy == "azure": + self.write_strategy = AzureUploadStrategy(self.file_metadata, self.cognite_client) + else: + self.write_strategy = InMemoryUploadStrategy(self.file_metadata, self.cognite_client) super().__init__( fs, @@ -675,36 +667,6 @@ def __init__( **kwargs, ) - def _merge_blocks(self) -> None: - """Merge all uploaded blocks into the final blob.""" - # Commit the blocks - commit_url = f"{self.file_descriptor['uploadUrl']}&comp=blocklist" - block_list_xml = '' - for block_id in self.block_ids: - block_list_xml += f"{block_id}" - block_list_xml += "" - - response = self.session.put( - commit_url, - data=block_list_xml, - headers={ - "x-ms-blob-content-type": self.file_metadata.mime_type, - "Content-Type": "application/xml", - "Content-Length": str(len(block_list_xml)), - "x-ms-version": "2019-12-12", - }, - ) - response.raise_for_status() - - self.cognite_client.files.update( - item=FileMetadataUpdate(id=self.file_descriptor["id"]) - .metadata - .set({"size": (len(self.block_ids) - 1) * self.blocksize + self.buffer.getbuffer().nbytes}) - ) - - # Clear block ids - self.block_ids.clear() - def _upload_chunk(self, final: bool = False) -> bool: """Upload file contents to CDF. @@ -718,66 +680,26 @@ def _upload_chunk(self, final: bool = False) -> bool: RuntimeError: When an unexpected error occurred. """ - def generate_block_blob_block_id(block_name_prefix: str, index: int) -> str: - while len(block_name_prefix) < 19: - block_name_prefix += "x" - block_id = f"{block_name_prefix[:19]}{index:05}".encode("utf-8") - - return base64.b64encode(block_id).decode("utf-8") - - def upload_block(block_data: bytes, block_id: str) -> None: - """Uploads a single block.""" - try: - url = self.file_descriptor["uploadUrl"].split("?") - upload_block_url = f"{url[0]}?blockid={block_id}&comp=block&{url[1]}" - response = self.session.put( - upload_block_url, - data=block_data, - headers={ - "Accept": "application/xml", - "Content-Type": "application/octet-stream", - "Content-Length": str(len(block_data)), - "x-ms-version": "2019-12-12", - }, - ) - response.raise_for_status() - logging.info(f"Finished uploading block {block_id}. Took {response.elapsed.total_seconds()} sec") - except Exception as ex: - logging.warning("Failed to upload on of the blocks: {ex}", exc_info=ex) - raise + def strategy_submit(data: bytes, index: int) -> None: + self.write_strategy.upload_chunk(data, index) try: - buffer_length = self.buffer.getbuffer().nbytes - blocks = [self.buffer.getbuffer()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] - - # Only consider blocks of full size for uploading - full_blocks = [b for b in blocks if len(b) == self.blocksize] + buffer_length = len(self.buffer.getvalue()) + blocks = [self.buffer.getvalue()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] - logging.info(f"{len(full_blocks)} full blocks discovered") + logging.info(f"{len(blocks)} full blocks discovered") # Upload blocks in parallel using ThreadPoolExecutor with ThreadPoolExecutor(max_workers=5) as executor: - block_ids = [ - generate_block_blob_block_id(self.external_id, index) - for index in range(self.index, self.index + len(full_blocks)) - ] - self.block_ids.extend(block_ids) - for arg in zip(full_blocks, block_ids): - executor.submit(upload_block, arg[0], arg[1]) - - # Reset buffer to only contain the leftover data (less than blocksize) - leftover_data = b"".join(blocks[len(full_blocks) :]) - self.buffer: BytesIO = BytesIO(leftover_data) + for arg in zip(blocks, range(self.index, self.index + len(blocks))): + executor.submit(strategy_submit, arg[0], arg[1]) # Update the index - self.index += len(full_blocks) + self.index += len(blocks) # If it's the final block, then send a merge request if final: - block_id = generate_block_blob_block_id(self.external_id, self.index) - upload_block(leftover_data, block_id) - self.block_ids.append(block_id) - self._merge_blocks() + self.write_strategy.merge_chunks() return final diff --git a/cognite/cdffs/upload_strategy.py b/cognite/cdffs/upload_strategy.py new file mode 100644 index 0000000..967fe20 --- /dev/null +++ b/cognite/cdffs/upload_strategy.py @@ -0,0 +1,66 @@ +"""Abstract upload strategy.""" +import abc +import threading +from pathlib import Path +from typing import Dict, List + +import requests +from cognite.client import CogniteClient +from cognite.client.data_classes import FileMetadata + + +class UploadStrategy(abc.ABC): + """File upload strategy interface to work with a specific file. + + Provides an interface to upload single data chunk or command to finalize the upload. Works with unbounded files. + """ + + def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): + """Initialize the Strategy. + + Args: + metadata (FileMetadata): File Metadata that a user can use when opening a file to write. + cognite_client (ClientClient): Cognite client to work with Cdf. + """ + self.session = requests.Session() + self.lock = threading.Lock() + self.indexes: List[int] = list() + self.cognite_client = cognite_client + self.params = self.init_uploader(metadata) + + def init_uploader(self, metadata: FileMetadata) -> Dict: + """Initialize the upload. + + Args: + metadata (FileMetadata): File Metadata that a user can use when opening a file to write. + + Returns: + Dictionary with unpacked parameters + """ + file_descriptor = self.cognite_client.post( + f"/api/v1/projects/{self.cognite_client.config.project}/files?overwrite=true", + json={ + "externalId": Path(metadata.external_id).name, + "name": Path(metadata.external_id).name, + "directory": metadata.directory, + "source": metadata.source or None, + "assetIds": metadata.asset_ids or None, + "dataSetId": metadata.data_set_id or None, + "mimeType": metadata.mime_type or None, + "geoLocation": metadata.geo_location or None, + "metadata": metadata.metadata or None, + }, + ).json() + return { + "id": file_descriptor["id"], + "mime_type": metadata.mime_type, + "upload_url": file_descriptor["uploadUrl"], + } + + @abc.abstractmethod + def upload_chunk(self, data: bytes, index: int) -> None: + """Upload single chunk.""" + + @abc.abstractmethod + def merge_chunks(self) -> None: + """Finalize the upload.""" diff --git a/examples/zip.py b/examples/zip.py index f19d17c..b882574 100644 --- a/examples/zip.py +++ b/examples/zip.py @@ -10,7 +10,7 @@ def clean_filename(path): # Replace multiple slashes or colons with a single underscore - cleaned = re.sub(r'[:/]+', '_', path) + cleaned = re.sub(r"[:/]+", "_", path) return cleaned @@ -20,30 +20,26 @@ def main(): BUFFER_SIZE = 1 * 1024 * 1024 # 1MB - source_files = [ - f - for f in source_fs.glob(f"{Path(__file__).parent.parent.absolute()}/**/*") - if Path(f).is_file() - ] + source_files = [f for f in source_fs.glob(f"{Path(__file__).parent.parent.absolute()}/**/*") if Path(f).is_file()] with target_fs.open( - f"test.zip", - "wb", - file_metadata=FileMetadata( - source="test", - directory="/archive/", - data_set_id=8576667485598960, - mime_type="application/zip", - metadata={"test": "test"} - ), - block_size=BUFFER_SIZE, + "test.zip", + "wb", + file_metadata=FileMetadata( + source="test", + directory="/archive/", + mime_type="application/zip", + metadata={"test": "test"}, + ), + block_size=BUFFER_SIZE, ) as target_file: - with zipfile.ZipFile(target_file, 'w') as zipf: + with zipfile.ZipFile(target_file, "w") as zipf: for source_path in source_files: + print(source_path) with source_fs.open(source_path, "rb") as source_file: zip_file_name = clean_filename(source_path) zipf.writestr(zip_file_name, source_file.read()) -if __name__ == '__main__': +if __name__ == "__main__": main() From c1b184a62fea9a0f70483f0e9f4cb2db5712425f Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 20:53:20 +0200 Subject: [PATCH 06/19] More progress --- cognite/cdffs/memory_upload_strategy.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cognite/cdffs/memory_upload_strategy.py b/cognite/cdffs/memory_upload_strategy.py index ed69462..9ca9a45 100644 --- a/cognite/cdffs/memory_upload_strategy.py +++ b/cognite/cdffs/memory_upload_strategy.py @@ -17,6 +17,7 @@ def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): super().__init__(metadata, cognite_client) self.blocks: Dict[int, bytes] = {} self.lock = threading.Lock() + self.metadata = metadata def upload_chunk(self, data: bytes, index: int) -> None: """Upload single chunk.""" @@ -27,7 +28,7 @@ def merge_chunks(self) -> None: """Merge all uploaded blocks into the final blob.""" try: content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) - self.cognite_client.files.upload_bytes(content=content, id=self.params["id"]) + self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump()) except Exception as ex: logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) raise From 3bcce775c00ace31b1b8beb6085823953c8f4217 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Wed, 25 Oct 2023 22:01:03 +0200 Subject: [PATCH 07/19] Final touches --- cognite/cdffs/az_upload_strategy.py | 6 ++++- cognite/cdffs/gcp_upload_strategy.py | 3 ++- cognite/cdffs/memory_upload_strategy.py | 4 ++- cognite/cdffs/spec.py | 33 +++++++++++++++++++------ cognite/cdffs/upload_strategy.py | 7 +++--- examples/zip.py | 10 +++++--- 6 files changed, 46 insertions(+), 17 deletions(-) diff --git a/cognite/cdffs/az_upload_strategy.py b/cognite/cdffs/az_upload_strategy.py index 81ad022..52e50ca 100644 --- a/cognite/cdffs/az_upload_strategy.py +++ b/cognite/cdffs/az_upload_strategy.py @@ -14,6 +14,7 @@ class AzureUploadStrategy(UploadStrategy): def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): """Initializer.""" super().__init__(metadata, cognite_client) + self.total_size = 0 def _generate_block_blob_block_id(self, index: int, block_name_prefix: str = __file__.__str__()) -> str: while len(block_name_prefix) < 19: @@ -39,6 +40,7 @@ def upload_chunk(self, data: bytes, index: int) -> None: }, ) response.raise_for_status() + self.total_size += len(data) # track total object size with self.lock: self.indexes.append(index) logging.info(f"Finished uploading block {index}. Took {response.elapsed.total_seconds()} sec") @@ -46,7 +48,7 @@ def upload_chunk(self, data: bytes, index: int) -> None: logging.warning("Failed to upload on of the blocks: {ex}", exc_info=ex) raise - def merge_chunks(self) -> None: + def merge_chunks(self) -> int: """Merge all uploaded blocks into the final blob.""" try: upload_url = self.params["upload_url"] @@ -67,6 +69,8 @@ def merge_chunks(self) -> None: }, ) response.raise_for_status() + + return self.total_size except Exception as ex: logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) raise diff --git a/cognite/cdffs/gcp_upload_strategy.py b/cognite/cdffs/gcp_upload_strategy.py index b4708a1..bc32052 100644 --- a/cognite/cdffs/gcp_upload_strategy.py +++ b/cognite/cdffs/gcp_upload_strategy.py @@ -50,5 +50,6 @@ def upload_chunk(self, data: bytes, index: int) -> None: logging.info(f"Received chunk {index}. Cache size: {len(self.chunk_cache)} chunks") - def merge_chunks(self) -> None: + def merge_chunks(self) -> int: """Google Cloud Storage handles merging internally. So, this method is a no-op for the GCS strategy.""" + return self.last_written_byte + 1 diff --git a/cognite/cdffs/memory_upload_strategy.py b/cognite/cdffs/memory_upload_strategy.py index 9ca9a45..79cdfa7 100644 --- a/cognite/cdffs/memory_upload_strategy.py +++ b/cognite/cdffs/memory_upload_strategy.py @@ -24,11 +24,13 @@ def upload_chunk(self, data: bytes, index: int) -> None: with self.lock: self.blocks[index] = data - def merge_chunks(self) -> None: + def merge_chunks(self) -> int: """Merge all uploaded blocks into the final blob.""" try: content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump()) + return len(content) + except Exception as ex: logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) raise diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 67bfb19..53096f0 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -7,7 +7,7 @@ import requests from cognite.client import ClientConfig, CogniteClient -from cognite.client.data_classes.files import FileMetadata +from cognite.client.data_classes.files import FileMetadata, FileMetadataUpdate from cognite.client.exceptions import ( CogniteAPIError, CogniteAuthError, @@ -643,19 +643,28 @@ def __init__( self.root_dir: str = directory self.external_id: str = external_id self.all_bytes_caching: bool = "cache_type" in kwargs and kwargs["cache_type"] == "all" - self.file_metadata: FileMetadata = FileMetadata(metadata={}) + self.file_metadata: FileMetadata = FileMetadata( + name=Path(path).name, + external_id=self.external_id, + directory=self.root_dir, + ) # User can use a file metadata for each file when they write the files. if isinstance(kwargs.get("file_metadata"), FileMetadata) and mode != "rb": - self.file_metadata = kwargs.pop("file_metadata") + self.file_metadata = FileMetadata( + **{ + **kwargs.pop("file_metadata").dump(), # type: ignore + **self.file_metadata.dump(), + } + ) self.write_strategy: UploadStrategy - if self.fs.upload_strategy == "google": + if fs.upload_strategy == "google" and mode != "rb": self.write_strategy = GoogleUploadStrategy(self.file_metadata, self.cognite_client) - elif self.fs.upload_strategy == "azure": + elif fs.upload_strategy == "azure" and mode != "rb": self.write_strategy = AzureUploadStrategy(self.file_metadata, self.cognite_client) - else: + elif mode != "rb": self.write_strategy = InMemoryUploadStrategy(self.file_metadata, self.cognite_client) super().__init__( @@ -699,7 +708,17 @@ def strategy_submit(data: bytes, index: int) -> None: # If it's the final block, then send a merge request if final: - self.write_strategy.merge_chunks() + total_size = self.write_strategy.merge_chunks() + + self.cognite_client.files.update( + item=FileMetadataUpdate(external_id=self.external_id).metadata.set({"size": total_size}) + ) + + self.fs.cache_path( + self.root_dir, + self.external_id, + total_size, + ) return final diff --git a/cognite/cdffs/upload_strategy.py b/cognite/cdffs/upload_strategy.py index 967fe20..6066112 100644 --- a/cognite/cdffs/upload_strategy.py +++ b/cognite/cdffs/upload_strategy.py @@ -1,7 +1,6 @@ """Abstract upload strategy.""" import abc import threading -from pathlib import Path from typing import Dict, List import requests @@ -40,8 +39,8 @@ def init_uploader(self, metadata: FileMetadata) -> Dict: file_descriptor = self.cognite_client.post( f"/api/v1/projects/{self.cognite_client.config.project}/files?overwrite=true", json={ - "externalId": Path(metadata.external_id).name, - "name": Path(metadata.external_id).name, + "externalId": metadata.external_id, + "name": metadata.name, "directory": metadata.directory, "source": metadata.source or None, "assetIds": metadata.asset_ids or None, @@ -62,5 +61,5 @@ def upload_chunk(self, data: bytes, index: int) -> None: """Upload single chunk.""" @abc.abstractmethod - def merge_chunks(self) -> None: + def merge_chunks(self) -> int: """Finalize the upload.""" diff --git a/examples/zip.py b/examples/zip.py index b882574..357e4b1 100644 --- a/examples/zip.py +++ b/examples/zip.py @@ -16,18 +16,18 @@ def clean_filename(path): def main(): source_fs = fsspec.filesystem("file") - target_fs = fsspec.filesystem("cdffs") + target_fs = fsspec.filesystem("cdffs", upload_strategy="azure") BUFFER_SIZE = 1 * 1024 * 1024 # 1MB source_files = [f for f in source_fs.glob(f"{Path(__file__).parent.parent.absolute()}/**/*") if Path(f).is_file()] with target_fs.open( - "test.zip", + "archive/test.zip", "wb", file_metadata=FileMetadata( source="test", - directory="/archive/", + data_set_id=8576667485598960, mime_type="application/zip", metadata={"test": "test"}, ), @@ -40,6 +40,10 @@ def main(): zip_file_name = clean_filename(source_path) zipf.writestr(zip_file_name, source_file.read()) + with target_fs.open("archive/test.zip", mode="rb") as source: + with source_fs.open("test.zip", mode="wb") as destination: + destination.write(source.read()) + if __name__ == "__main__": main() From 26ca47cc8df209bfe8c806c96c3b861d26476577 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 10:08:48 +0200 Subject: [PATCH 08/19] Add some documentation --- CHANGELOG.md | 5 +++++ cognite/cdffs/__init__.py | 2 +- docs/source/cdffs.rst | 6 +++++- docs/source/examples.rst | 7 +++++++ pyproject.toml | 2 +- 5 files changed, 19 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dcf7252..b176eeb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -136,3 +136,8 @@ Changes are grouped as follows - Dependency updates for docs & source code. [unreleased]: + +## [0.2.9] - 2023-10-26 + +### Added +- Support for native multipart file upload for CDF in Azure and Google. diff --git a/cognite/cdffs/__init__.py b/cognite/cdffs/__init__.py index 49204a2..e7d4329 100644 --- a/cognite/cdffs/__init__.py +++ b/cognite/cdffs/__init__.py @@ -3,7 +3,7 @@ from .spec import CdfFileSystem -__version__ = "0.2.8" +__version__ = "0.2.9" __all__ = ["CdfFileSystem"] fsspec.register_implementation(CdfFileSystem.protocol, CdfFileSystem) diff --git a/docs/source/cdffs.rst b/docs/source/cdffs.rst index e1161c8..9f809e1 100644 --- a/docs/source/cdffs.rst +++ b/docs/source/cdffs.rst @@ -146,5 +146,9 @@ Supported configurations when working with `cdffs`. - `Optional` - Flag to indicate enable/disable download retries. Default is True. - + * - `upload_strategy` + - `Optional` + - Flag to configure various file upload strategies. Possible values: [`azure`, `google`, `inmemory`]. Default is `inmemory`. + `azure`: will use multipart upload expecting CDF in Azure. `google` will use multipart upload expecting CDF in Google. + `inmemory` is a default upload strategy, where entire file is cached and uploaded as a single call to CDF. diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 5800e8b..565efff 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -38,3 +38,10 @@ the files from/to CDF Files. .. literalinclude:: ./../../examples/geopandas_parquet.py :language: python + +zip file +^^^^^^^^^ +Example to read folder from local filesystem and write `zip` file to CDF Files using `ZipFile` package. + +.. literalinclude:: ./../../examples/zip.py + :language: python diff --git a/pyproject.toml b/pyproject.toml index 957db1c..a8b78ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "cognite-cdffs" -version = "0.2.8" +version = "0.2.9" description = "File System Interface for CDF Files" license = "Apache-2.0" authors = ["Infant Alex "] From 33e39fbb4acd2905ff54ae3e13f55c2252171b44 Mon Sep 17 00:00:00 2001 From: Infant Alex Date: Thu, 26 Oct 2023 18:10:20 +0200 Subject: [PATCH 09/19] fixing unit tests --- cognite/cdffs/memory_upload_strategy.py | 2 +- tests/test_spec.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cognite/cdffs/memory_upload_strategy.py b/cognite/cdffs/memory_upload_strategy.py index 79cdfa7..82786e1 100644 --- a/cognite/cdffs/memory_upload_strategy.py +++ b/cognite/cdffs/memory_upload_strategy.py @@ -28,7 +28,7 @@ def merge_chunks(self) -> int: """Merge all uploaded blocks into the final blob.""" try: content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) - self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump()) + self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump(), overwrite=True) return len(content) except Exception as ex: diff --git a/tests/test_spec.py b/tests/test_spec.py index 8f5eaaf..2d0aed4 100644 --- a/tests/test_spec.py +++ b/tests/test_spec.py @@ -131,7 +131,7 @@ def mock_files_upload_response(request): "uploadUrl": "https://azure.blob-test.com/uploaddata", } - wirte_url_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files?overwrite=True" + wirte_url_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files" azure_upload_url_pattern = "https://azure.blob-test.com/uploaddata" response.assert_all_requests_are_fired = False From 77b97c20607727754277360083ae50f2324d694e Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 18:32:59 +0200 Subject: [PATCH 10/19] Use dataset for deletion --- cognite/cdffs/spec.py | 85 ++++++++++++++++++---------------- tests/test_spec_integration.py | 2 +- 2 files changed, 45 insertions(+), 42 deletions(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 53096f0..d4fdedc 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -52,11 +52,11 @@ class CdfFileSystem(AbstractFileSystem): protocol: str = "cdffs" def __init__( - self, - connection_config: Optional[ClientConfig] = None, - file_metadata: FileMetadata = FileMetadata(metadata={}), - upload_strategy: str = "inmemory", - **kwargs: Optional[Any], + self, + connection_config: Optional[ClientConfig] = None, + file_metadata: FileMetadata = FileMetadata(metadata={}), + upload_strategy: str = "inmemory", + **kwargs: Optional[Any], ) -> None: """Initialize the CdfFileSystem and creates a connection to CDF. @@ -105,9 +105,9 @@ def _strip_protocol(cls, path: str) -> str: return stripped_path def do_connect( - self, - connection_config: ClientConfig, - **kwargs: Optional[Any], + self, + connection_config: ClientConfig, + **kwargs: Optional[Any], ) -> None: """Connect to CDF using the connection configurations provided by the user. @@ -160,7 +160,7 @@ def split_path(self, path: str, validate_suffix: bool = True) -> Tuple[str, str, elif self._suffix_exists(path): external_id_prefix = [x for x in Path(path).parts if Path(x).suffix][0] root_dir = path[: path.find(external_id_prefix)].strip("/") - external_id = path[path.find(external_id_prefix) :] + external_id = path[path.find(external_id_prefix):] elif Path(path).parts and not validate_suffix: external_id_prefix = "" @@ -312,9 +312,9 @@ def ls(self, path: str, detail: bool = False, **kwargs: Optional[Any]) -> Union[ inp_key = str(Path(root_dir, external_id_prefix)).lstrip("/") if limit != -1 or not ( - inp_key in self.dircache - and inp_key in self.cdf_list_cache - and time.time() - self.cdf_list_cache[inp_key] < self.cdf_list_expiry_time + inp_key in self.dircache + and inp_key in self.cdf_list_cache + and time.time() - self.cdf_list_cache[inp_key] < self.cdf_list_expiry_time ): self._ls(root_dir, external_id_prefix, limit=limit) # type: ignore @@ -432,12 +432,12 @@ def exists(self, path: str) -> bool: return bool(self.cognite_client.files.retrieve(external_id=external_id)) if external_id else False def mv( - self, - source_path: str, - destination_path: str, - recursive: bool = False, - maxdepth: Union[int, None] = None, - **kwargs: Optional[Any], + self, + source_path: str, + destination_path: str, + recursive: bool = False, + maxdepth: Union[int, None] = None, + **kwargs: Optional[Any], ) -> None: """Move the files and directories at a path given to a new path. @@ -467,12 +467,12 @@ def cd(self, path: str, **kwargs: Optional[Any]) -> None: raise NotImplementedError def open( - self, - path: str, - mode: str = "rb", - block_size: int = DEFAULT_BLOCK_SIZE, - cache_options: Optional[Dict[Any, Any]] = None, - **kwargs: Optional[Any], + self, + path: str, + mode: str = "rb", + block_size: int = DEFAULT_BLOCK_SIZE, + cache_options: Optional[Dict[Any, Any]] = None, + **kwargs: Optional[Any], ) -> "CdfFile": """Open the file for reading and writing. @@ -501,7 +501,7 @@ def open( ) def read_file( - self, external_id: str, start_byte: Union[int, None] = None, end_byte: Union[int, None] = None + self, external_id: str, start_byte: Union[int, None] = None, end_byte: Union[int, None] = None ) -> Any: """Open and read the contents of a file. @@ -540,7 +540,7 @@ def read_file( raise FileNotFoundError from cognite_exp def cat( - self, path: Union[str, list], recursive: bool = False, on_error: str = "raise", **kwargs: Optional[Any] + self, path: Union[str, list], recursive: bool = False, on_error: str = "raise", **kwargs: Optional[Any] ) -> Union[bytes, Any, Dict[str, bytes]]: """Open and read the contents of a file(s). @@ -614,16 +614,16 @@ class CdfFile(AbstractBufferedFile): """ def __init__( - self, - fs: CdfFileSystem, - cognite_client: CogniteClient, - path: str, - directory: str, - external_id: str, - mode: str = "rb", - block_size: int = DEFAULT_BLOCK_SIZE, - cache_options: Optional[Union[Dict[Any, Any], None]] = None, - **kwargs: Optional[Any], + self, + fs: CdfFileSystem, + cognite_client: CogniteClient, + path: str, + directory: str, + external_id: str, + mode: str = "rb", + block_size: int = DEFAULT_BLOCK_SIZE, + cache_options: Optional[Union[Dict[Any, Any], None]] = None, + **kwargs: Optional[Any], ) -> None: """Initialize the CdfFile. @@ -644,17 +644,20 @@ def __init__( self.external_id: str = external_id self.all_bytes_caching: bool = "cache_type" in kwargs and kwargs["cache_type"] == "all" self.file_metadata: FileMetadata = FileMetadata( - name=Path(path).name, - external_id=self.external_id, - directory=self.root_dir, + **{ + **fs.file_metadata.dump(), + "name": Path(path).name, + "external_id": self.external_id, + "directory": self.root_dir + } ) # User can use a file metadata for each file when they write the files. if isinstance(kwargs.get("file_metadata"), FileMetadata) and mode != "rb": self.file_metadata = FileMetadata( **{ - **kwargs.pop("file_metadata").dump(), # type: ignore **self.file_metadata.dump(), + **kwargs.pop("file_metadata").dump(), # type: ignore } ) @@ -694,7 +697,7 @@ def strategy_submit(data: bytes, index: int) -> None: try: buffer_length = len(self.buffer.getvalue()) - blocks = [self.buffer.getvalue()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] + blocks = [self.buffer.getvalue()[i: i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] logging.info(f"{len(blocks)} full blocks discovered") diff --git a/tests/test_spec_integration.py b/tests/test_spec_integration.py index d5557d9..a7b29fb 100644 --- a/tests/test_spec_integration.py +++ b/tests/test_spec_integration.py @@ -88,7 +88,7 @@ def verify_file_status(cognite_client, source, external_ids): def delete_files(cognite_client): for source in _SOURCES: - list_of_ids = [x.external_id for x in cognite_client.files.list(source=source, limit=-1)] + list_of_ids = [x.external_id for x in cognite_client.files.list(data_set_external_ids=["dataset:integration_tests"], limit=-1)] print(list_of_ids) if list_of_ids: try: From 9c1aeb5cb4b22ddfd9b6da49e2d35478c8727827 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 18:33:09 +0200 Subject: [PATCH 11/19] pre-commit --- cognite/cdffs/spec.py | 76 +++++++++++++++++----------------- tests/test_spec_integration.py | 5 ++- 2 files changed, 42 insertions(+), 39 deletions(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index d4fdedc..420af5c 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -52,11 +52,11 @@ class CdfFileSystem(AbstractFileSystem): protocol: str = "cdffs" def __init__( - self, - connection_config: Optional[ClientConfig] = None, - file_metadata: FileMetadata = FileMetadata(metadata={}), - upload_strategy: str = "inmemory", - **kwargs: Optional[Any], + self, + connection_config: Optional[ClientConfig] = None, + file_metadata: FileMetadata = FileMetadata(metadata={}), + upload_strategy: str = "inmemory", + **kwargs: Optional[Any], ) -> None: """Initialize the CdfFileSystem and creates a connection to CDF. @@ -105,9 +105,9 @@ def _strip_protocol(cls, path: str) -> str: return stripped_path def do_connect( - self, - connection_config: ClientConfig, - **kwargs: Optional[Any], + self, + connection_config: ClientConfig, + **kwargs: Optional[Any], ) -> None: """Connect to CDF using the connection configurations provided by the user. @@ -160,7 +160,7 @@ def split_path(self, path: str, validate_suffix: bool = True) -> Tuple[str, str, elif self._suffix_exists(path): external_id_prefix = [x for x in Path(path).parts if Path(x).suffix][0] root_dir = path[: path.find(external_id_prefix)].strip("/") - external_id = path[path.find(external_id_prefix):] + external_id = path[path.find(external_id_prefix) :] elif Path(path).parts and not validate_suffix: external_id_prefix = "" @@ -312,9 +312,9 @@ def ls(self, path: str, detail: bool = False, **kwargs: Optional[Any]) -> Union[ inp_key = str(Path(root_dir, external_id_prefix)).lstrip("/") if limit != -1 or not ( - inp_key in self.dircache - and inp_key in self.cdf_list_cache - and time.time() - self.cdf_list_cache[inp_key] < self.cdf_list_expiry_time + inp_key in self.dircache + and inp_key in self.cdf_list_cache + and time.time() - self.cdf_list_cache[inp_key] < self.cdf_list_expiry_time ): self._ls(root_dir, external_id_prefix, limit=limit) # type: ignore @@ -432,12 +432,12 @@ def exists(self, path: str) -> bool: return bool(self.cognite_client.files.retrieve(external_id=external_id)) if external_id else False def mv( - self, - source_path: str, - destination_path: str, - recursive: bool = False, - maxdepth: Union[int, None] = None, - **kwargs: Optional[Any], + self, + source_path: str, + destination_path: str, + recursive: bool = False, + maxdepth: Union[int, None] = None, + **kwargs: Optional[Any], ) -> None: """Move the files and directories at a path given to a new path. @@ -467,12 +467,12 @@ def cd(self, path: str, **kwargs: Optional[Any]) -> None: raise NotImplementedError def open( - self, - path: str, - mode: str = "rb", - block_size: int = DEFAULT_BLOCK_SIZE, - cache_options: Optional[Dict[Any, Any]] = None, - **kwargs: Optional[Any], + self, + path: str, + mode: str = "rb", + block_size: int = DEFAULT_BLOCK_SIZE, + cache_options: Optional[Dict[Any, Any]] = None, + **kwargs: Optional[Any], ) -> "CdfFile": """Open the file for reading and writing. @@ -501,7 +501,7 @@ def open( ) def read_file( - self, external_id: str, start_byte: Union[int, None] = None, end_byte: Union[int, None] = None + self, external_id: str, start_byte: Union[int, None] = None, end_byte: Union[int, None] = None ) -> Any: """Open and read the contents of a file. @@ -540,7 +540,7 @@ def read_file( raise FileNotFoundError from cognite_exp def cat( - self, path: Union[str, list], recursive: bool = False, on_error: str = "raise", **kwargs: Optional[Any] + self, path: Union[str, list], recursive: bool = False, on_error: str = "raise", **kwargs: Optional[Any] ) -> Union[bytes, Any, Dict[str, bytes]]: """Open and read the contents of a file(s). @@ -614,16 +614,16 @@ class CdfFile(AbstractBufferedFile): """ def __init__( - self, - fs: CdfFileSystem, - cognite_client: CogniteClient, - path: str, - directory: str, - external_id: str, - mode: str = "rb", - block_size: int = DEFAULT_BLOCK_SIZE, - cache_options: Optional[Union[Dict[Any, Any], None]] = None, - **kwargs: Optional[Any], + self, + fs: CdfFileSystem, + cognite_client: CogniteClient, + path: str, + directory: str, + external_id: str, + mode: str = "rb", + block_size: int = DEFAULT_BLOCK_SIZE, + cache_options: Optional[Union[Dict[Any, Any], None]] = None, + **kwargs: Optional[Any], ) -> None: """Initialize the CdfFile. @@ -648,7 +648,7 @@ def __init__( **fs.file_metadata.dump(), "name": Path(path).name, "external_id": self.external_id, - "directory": self.root_dir + "directory": self.root_dir, } ) @@ -697,7 +697,7 @@ def strategy_submit(data: bytes, index: int) -> None: try: buffer_length = len(self.buffer.getvalue()) - blocks = [self.buffer.getvalue()[i: i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] + blocks = [self.buffer.getvalue()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] logging.info(f"{len(blocks)} full blocks discovered") diff --git a/tests/test_spec_integration.py b/tests/test_spec_integration.py index a7b29fb..43a970c 100644 --- a/tests/test_spec_integration.py +++ b/tests/test_spec_integration.py @@ -88,7 +88,10 @@ def verify_file_status(cognite_client, source, external_ids): def delete_files(cognite_client): for source in _SOURCES: - list_of_ids = [x.external_id for x in cognite_client.files.list(data_set_external_ids=["dataset:integration_tests"], limit=-1)] + list_of_ids = [ + x.external_id + for x in cognite_client.files.list(data_set_external_ids=["dataset:integration_tests"], limit=-1) + ] print(list_of_ids) if list_of_ids: try: From 14d1e52ee12f0b2a384309d52f5c4fca8f43236f Mon Sep 17 00:00:00 2001 From: Infant Alex Date: Thu, 26 Oct 2023 18:43:13 +0200 Subject: [PATCH 12/19] fixing integration tests --- tests/test_spec_integration.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tests/test_spec_integration.py b/tests/test_spec_integration.py index 43a970c..1a616e6 100644 --- a/tests/test_spec_integration.py +++ b/tests/test_spec_integration.py @@ -79,7 +79,10 @@ def verify_file_status(cognite_client, source, external_ids): while True: if ( upload_status := [ - x.uploaded for x in cognite_client.files.list(external_id_prefix=external_ids, source=source) + x.uploaded + for x in cognite_client.files.list( + external_id_prefix=external_ids, data_set_external_ids=["dataset:integration_tests"] + ) ] ) and all(upload_status): break From 97e584e24eae2d49f60e84941c4b2b5967bb53f3 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 18:52:45 +0200 Subject: [PATCH 13/19] Fix metadata --- cognite/cdffs/spec.py | 2 +- tests/test_spec_integration.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index 420af5c..efc794b 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -714,7 +714,7 @@ def strategy_submit(data: bytes, index: int) -> None: total_size = self.write_strategy.merge_chunks() self.cognite_client.files.update( - item=FileMetadataUpdate(external_id=self.external_id).metadata.set({"size": total_size}) + item=FileMetadataUpdate(external_id=self.external_id).metadata.add({"size": total_size}) ) self.fs.cache_path( diff --git a/tests/test_spec_integration.py b/tests/test_spec_integration.py index 1a616e6..b5fbcf3 100644 --- a/tests/test_spec_integration.py +++ b/tests/test_spec_integration.py @@ -93,7 +93,7 @@ def delete_files(cognite_client): for source in _SOURCES: list_of_ids = [ x.external_id - for x in cognite_client.files.list(data_set_external_ids=["dataset:integration_tests"], limit=-1) + for x in cognite_client.files.list(source=source, limit=-1) ] print(list_of_ids) if list_of_ids: From 85e1bb89f2a6506286758995a12dc0c0acbb7954 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 20:01:35 +0200 Subject: [PATCH 14/19] fix zarr test --- tests/test_spec_integration.py | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/tests/test_spec_integration.py b/tests/test_spec_integration.py index b5fbcf3..ef00143 100644 --- a/tests/test_spec_integration.py +++ b/tests/test_spec_integration.py @@ -3,6 +3,7 @@ import json import os +import random import time import dask.dataframe as dd @@ -90,17 +91,18 @@ def verify_file_status(cognite_client, source, external_ids): def delete_files(cognite_client): + list_of_ids = set() for source in _SOURCES: - list_of_ids = [ - x.external_id - for x in cognite_client.files.list(source=source, limit=-1) - ] - print(list_of_ids) - if list_of_ids: - try: - cognite_client.files.delete(external_id=list_of_ids) - except (CogniteNotFoundError, CogniteDuplicatedError): - pass + list_of_ids.update([x.external_id for x in cognite_client.files.list(source=source, limit=-1)]) + list_of_ids.update( + [x.external_id for x in cognite_client.files.list(data_set_external_ids="dataset:integration_tests", limit=-1)] + ) + print(list_of_ids) + if list_of_ids: + try: + cognite_client.files.delete(external_id=list(list_of_ids)) + except (CogniteNotFoundError, CogniteDuplicatedError): + pass @pytest.fixture(scope="session", autouse=True) @@ -197,15 +199,17 @@ def test_xarray_zarr(cognite_client, client_config, data_set_id): file_metadata = FileMetadata( source="test_int_xarray_zarr", mime_type="application/octet-stream", data_set_id=data_set_id ) + random.seed() + uuid = random.randint(0, 100) inp_ds.to_zarr( - "cdffs://tests/integration/xarray/zarr/test_int_xarray.zarr", + f"cdffs://tests/integration/xarray/zarr/test_int_xarray_{uuid}.zarr", storage_options={"connection_config": client_config, "file_metadata": file_metadata}, ) - verify_file_status(cognite_client, "test_int_xarray_zarr", "test_int_xarray.zarr") + verify_file_status(cognite_client, "test_int_xarray_zarr", f"test_int_xarray_{uuid}.zarr") res_da = xr.open_zarr( - "cdffs://tests/integration/xarray/zarr/test_int_xarray.zarr", + f"cdffs://tests/integration/xarray/zarr/test_int_xarray_{uuid}.zarr", storage_options={"connection_config": client_config}, ) assert inp_ds.dims == res_da.dims From 8e39932c059fb48633b5342945d905593def8cb6 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 20:03:35 +0200 Subject: [PATCH 15/19] final touch --- cognite/cdffs/upload_strategy.py | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/cognite/cdffs/upload_strategy.py b/cognite/cdffs/upload_strategy.py index 6066112..12ba7d4 100644 --- a/cognite/cdffs/upload_strategy.py +++ b/cognite/cdffs/upload_strategy.py @@ -38,17 +38,7 @@ def init_uploader(self, metadata: FileMetadata) -> Dict: """ file_descriptor = self.cognite_client.post( f"/api/v1/projects/{self.cognite_client.config.project}/files?overwrite=true", - json={ - "externalId": metadata.external_id, - "name": metadata.name, - "directory": metadata.directory, - "source": metadata.source or None, - "assetIds": metadata.asset_ids or None, - "dataSetId": metadata.data_set_id or None, - "mimeType": metadata.mime_type or None, - "geoLocation": metadata.geo_location or None, - "metadata": metadata.metadata or None, - }, + json=metadata.dump(camel_case=True), ).json() return { "id": file_descriptor["id"], From c9517c3bee17d1b14074642b3aa085cb30ecabd6 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 22:10:53 +0200 Subject: [PATCH 16/19] Test uploaders --- tests/conftest.py | 52 ++++++++++++++++++++++++++++++++- tests/test_spec.py | 72 ++++++++++++++++++++++++++++++---------------- 2 files changed, 99 insertions(+), 25 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index a007638..498b836 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,10 @@ from unittest import mock import pytest -from cognite.client import CogniteClient +from cognite.client import ClientConfig, CogniteClient +from cognite.client.credentials import Token + +from cognite.cdffs import CdfFileSystem @pytest.fixture @@ -17,3 +20,50 @@ def mock_cognite_client(): def mock_unset_env(): with mock.patch.dict(os.environ, values={}, clear=True): yield + + +@pytest.mark.usefixtures("mock_cognite_client") +@pytest.fixture(scope="function") +def fs(): + inp = { + "connection_config": ClientConfig( + client_name="foobar", + base_url="https://foobar.cognitedata.com", + project="foobar", + credentials=Token("dummy-token"), + ) + } + fs = CdfFileSystem(**inp) + return fs + + +@pytest.mark.usefixtures("mock_cognite_client") +@pytest.fixture(scope="function") +def az_fs(): + inp = { + "connection_config": ClientConfig( + client_name="foobar", + base_url="https://foobar.cognitedata.com", + project="foobar", + credentials=Token("dummy-token"), + ), + "upload_strategy": "azure", + } + fs = CdfFileSystem(**inp) + return fs + + +@pytest.mark.usefixtures("mock_cognite_client") +@pytest.fixture(scope="function") +def gcp_fs(): + inp = { + "connection_config": ClientConfig( + client_name="foobar", + base_url="https://foobar.cognitedata.com", + project="foobar", + credentials=Token("dummy-token"), + ), + "upload_strategy": "google", + } + fs = CdfFileSystem(**inp) + return fs diff --git a/tests/test_spec.py b/tests/test_spec.py index 2d0aed4..9e7e13b 100644 --- a/tests/test_spec.py +++ b/tests/test_spec.py @@ -13,21 +13,6 @@ global_config.disable_pypi_version_check = True -@pytest.mark.usefixtures("mock_cognite_client") -@pytest.fixture(scope="function") -def fs(): - inp = { - "connection_config": ClientConfig( - client_name="foobar", - base_url="https://foobar.cognitedata.com", - project="foobar", - credentials=Token("dummy-token"), - ) - } - fs = CdfFileSystem(**inp) - return fs - - @pytest.fixture def mock_files_ls_response(request): with responses.RequestsMock() as response: @@ -131,17 +116,39 @@ def mock_files_upload_response(request): "uploadUrl": "https://azure.blob-test.com/uploaddata", } - wirte_url_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files" + update_response_body = { + "items": [ + { + "externalId": "df.csv", + "name": "df.csv", + "directory": "/sample_data/out/sample/", + "source": "test", + "mimeType": "text/plain", + "metadata": {"size": 100}, + "dataSetId": 783443182507908, + "id": 783443232507908, + "uploaded": True, + "uploadedTime": 1667464449, + "labels": [], + "createdTime": 1667464449, + "lastUpdatedTime": 1667464449, + } + ] + } + + write_url_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files" azure_upload_url_pattern = "https://azure.blob-test.com/uploaddata" + file_update_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files/update" response.assert_all_requests_are_fired = False if request.param == "successful": - response.add(response.POST, wirte_url_pattern, status=200, json=upload_response_body) + response.add(response.POST, write_url_pattern, status=200, json=upload_response_body) response.add(response.PUT, azure_upload_url_pattern, status=200, json={}) + response.add(response.POST, file_update_pattern, status=200, json=update_response_body) else: response.add( response.POST, - wirte_url_pattern, + write_url_pattern, status=500, json={}, ) @@ -533,23 +540,40 @@ def test_makedirs_exception(fs, exist_ok_flag, test_input, expected_result): @pytest.mark.parametrize( - "test_path, test_mode, test_data, expected_len, mock_files_upload_response", + "fs, test_path, test_mode, test_data, expected_len, mock_files_upload_response", [ ( + "fs", "/sample_data/out/sample/df.csv", "wb", ",A,B\n0,1,2\n1,4,5\n", 17, "successful", - ) + ), + ( + "az_fs", + "/sample_data/out/sample/df.csv", + "wb", + ",A,B\n0,1,2\n1,4,5\n", + 17, + "successful", + ), + ( + "gcp_fs", + "/sample_data/out/sample/df.csv", + "wb", + ",A,B\n0,1,2\n1,4,5\n", + 17, + "successful", + ), ], - indirect=["mock_files_upload_response"], + indirect=["mock_files_upload_response", "fs"], ) @pytest.mark.usefixtures("mock_files_upload_response") def test_open_write(fs, test_path, test_mode, test_data, expected_len): - fs.file_metadata = FileMetadata(metadata={}) - cdf_file = fs.open(test_path, mode=test_mode) - test_len = cdf_file.write(test_data.encode("utf-8")) + with fs.open(test_path, mode=test_mode, file_metadata=FileMetadata(metadata={})) as cdf_file: + test_len = cdf_file.write(test_data.encode("utf-8")) + assert test_len == expected_len From 8eed3bb7f70667b592b200a986215d6f435e4502 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Thu, 26 Oct 2023 22:55:38 +0200 Subject: [PATCH 17/19] Fix fixtures --- cognite/cdffs/gcp_upload_strategy.py | 4 +--- cognite/cdffs/spec.py | 10 ++++++++-- tests/conftest.py | 5 +++++ tests/test_spec.py | 9 +++++---- 4 files changed, 19 insertions(+), 9 deletions(-) diff --git a/cognite/cdffs/gcp_upload_strategy.py b/cognite/cdffs/gcp_upload_strategy.py index bc32052..8523650 100644 --- a/cognite/cdffs/gcp_upload_strategy.py +++ b/cognite/cdffs/gcp_upload_strategy.py @@ -27,9 +27,7 @@ def _write_chunk(self, index: int, data: bytes) -> None: response = self.session.put(self.params["upload_url"], headers=headers, data=data) response.raise_for_status() - - with self.lock: - self.indexes.append(index) + self.indexes.append(index) logging.info(f"Finished uploading chunk {index}. Took {response.elapsed.total_seconds()} sec") diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index efc794b..e299b5b 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -28,7 +28,13 @@ from .upload_strategy import UploadStrategy logger = logging.getLogger(__name__) -_COMMON_EXCEPTIONS = (CogniteAuthError, CogniteConnectionError, CogniteConnectionRefused, CogniteAPIError) +_COMMON_EXCEPTIONS = ( + CogniteAuthError, + CogniteConnectionError, + CogniteConnectionRefused, + CogniteAPIError, + requests.exceptions.RequestException, +) _CACHE_SLEEP_INTERVAL = 5 @@ -725,7 +731,7 @@ def strategy_submit(data: bytes, index: int) -> None: return final - except (requests.exceptions.RequestException, _COMMON_EXCEPTIONS) as error: # type: ignore + except _COMMON_EXCEPTIONS as error: # type: ignore raise RuntimeError from error def _fetch_range(self, start: int, end: int) -> Any: diff --git a/tests/conftest.py b/tests/conftest.py index 498b836..84e1f27 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -67,3 +67,8 @@ def gcp_fs(): } fs = CdfFileSystem(**inp) return fs + + +@pytest.fixture +def filesystem(request): + return request.getfixturevalue(request.param) diff --git a/tests/test_spec.py b/tests/test_spec.py index 9e7e13b..dbbac8a 100644 --- a/tests/test_spec.py +++ b/tests/test_spec.py @@ -144,6 +144,7 @@ def mock_files_upload_response(request): if request.param == "successful": response.add(response.POST, write_url_pattern, status=200, json=upload_response_body) response.add(response.PUT, azure_upload_url_pattern, status=200, json={}) + response.add(response.PUT, f"{azure_upload_url_pattern}&comp=blocklist", status=200, json={}) response.add(response.POST, file_update_pattern, status=200, json=update_response_body) else: response.add( @@ -540,7 +541,7 @@ def test_makedirs_exception(fs, exist_ok_flag, test_input, expected_result): @pytest.mark.parametrize( - "fs, test_path, test_mode, test_data, expected_len, mock_files_upload_response", + "filesystem, test_path, test_mode, test_data, expected_len, mock_files_upload_response", [ ( "fs", @@ -567,11 +568,11 @@ def test_makedirs_exception(fs, exist_ok_flag, test_input, expected_result): "successful", ), ], - indirect=["mock_files_upload_response", "fs"], + indirect=["filesystem", "mock_files_upload_response"], ) @pytest.mark.usefixtures("mock_files_upload_response") -def test_open_write(fs, test_path, test_mode, test_data, expected_len): - with fs.open(test_path, mode=test_mode, file_metadata=FileMetadata(metadata={})) as cdf_file: +def test_open_write(filesystem, test_path, test_mode, test_data, expected_len): + with filesystem.open(test_path, mode=test_mode, file_metadata=FileMetadata(metadata={}), block_size=5) as cdf_file: test_len = cdf_file.write(test_data.encode("utf-8")) assert test_len == expected_len From b8d46d9d4f4a1ba62dd9c5be289485c944f39c9d Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Fri, 27 Oct 2023 09:55:50 +0200 Subject: [PATCH 18/19] mimic storage behvaiour better --- tests/test_spec.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tests/test_spec.py b/tests/test_spec.py index dbbac8a..8a76702 100644 --- a/tests/test_spec.py +++ b/tests/test_spec.py @@ -1,6 +1,7 @@ # type: ignore # pylint: disable=missing-function-docstring import os +import re import pytest import responses @@ -99,6 +100,8 @@ def mock_files_ls_error_response(): @pytest.fixture def mock_files_upload_response(request): with responses.RequestsMock() as response: + azure_upload_url_pattern = "https://azure.blob-test.com/uploaddata" + upload_response_body = { "externalId": "df.csv", "name": "df.csv", @@ -113,7 +116,7 @@ def mock_files_upload_response(request): "labels": [], "createdTime": 1667464449, "lastUpdatedTime": 1667464449, - "uploadUrl": "https://azure.blob-test.com/uploaddata", + "uploadUrl": f"{azure_upload_url_pattern}?token=123", } update_response_body = { @@ -137,14 +140,12 @@ def mock_files_upload_response(request): } write_url_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files" - azure_upload_url_pattern = "https://azure.blob-test.com/uploaddata" file_update_pattern = "https://foobar.cognitedata.com/api/v1/projects/foobar/files/update" response.assert_all_requests_are_fired = False if request.param == "successful": response.add(response.POST, write_url_pattern, status=200, json=upload_response_body) - response.add(response.PUT, azure_upload_url_pattern, status=200, json={}) - response.add(response.PUT, f"{azure_upload_url_pattern}&comp=blocklist", status=200, json={}) + response.add(response.PUT, re.compile(rf"{azure_upload_url_pattern}\?.*"), status=201, json={}) response.add(response.POST, file_update_pattern, status=200, json=update_response_body) else: response.add( From f9ea02f562437b1500f5bfcdb5b6fbd097385e17 Mon Sep 17 00:00:00 2001 From: Pavel Zubarev Date: Fri, 27 Oct 2023 10:46:46 +0200 Subject: [PATCH 19/19] Be smart about number of code lines --- .pre-commit-config.yaml | 2 +- cognite/cdffs/az_upload_strategy.py | 84 +- cognite/cdffs/memory_upload_strategy.py | 12 +- cognite/cdffs/spec.py | 49 +- poetry.lock | 2469 +++++++++++------------ pyproject.toml | 1 + 6 files changed, 1272 insertions(+), 1345 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6e9e9c5..a41af78 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: hooks: - id: mypy exclude: ^(tests/|examples/|docs/) - additional_dependencies: ["types-requests"] + additional_dependencies: ["types-requests", "types-retry"] - repo: https://github.com/pycqa/flake8 rev: 6.1.0 hooks: diff --git a/cognite/cdffs/az_upload_strategy.py b/cognite/cdffs/az_upload_strategy.py index 52e50ca..f1509b8 100644 --- a/cognite/cdffs/az_upload_strategy.py +++ b/cognite/cdffs/az_upload_strategy.py @@ -17,60 +17,50 @@ def __init__(self, metadata: FileMetadata, cognite_client: CogniteClient): self.total_size = 0 def _generate_block_blob_block_id(self, index: int, block_name_prefix: str = __file__.__str__()) -> str: - while len(block_name_prefix) < 19: - block_name_prefix += "x" - block_id = f"{block_name_prefix[:19]}{index:05}".encode("utf-8") + block_id = f"{block_name_prefix.ljust(19, 'x')[:19]}{index:05}".encode("utf-8") return base64.b64encode(block_id).decode("utf-8") def upload_chunk(self, data: bytes, index: int) -> None: """Uploads a single block.""" - try: - url = self.params["upload_url"].split("?") - block_id = self._generate_block_blob_block_id(index=index) - upload_block_url = f"{url[0]}?blockid={block_id}&comp=block&{url[1]}" - response = self.session.put( - upload_block_url, - data=data, - headers={ - "Accept": "application/xml", - "Content-Type": "application/octet-stream", - "Content-Length": str(len(data)), - "x-ms-version": "2019-12-12", - }, - ) - response.raise_for_status() - self.total_size += len(data) # track total object size - with self.lock: - self.indexes.append(index) - logging.info(f"Finished uploading block {index}. Took {response.elapsed.total_seconds()} sec") - except Exception as ex: - logging.warning("Failed to upload on of the blocks: {ex}", exc_info=ex) - raise + url = self.params["upload_url"].split("?") + block_id = self._generate_block_blob_block_id(index=index) + upload_block_url = f"{url[0]}?blockid={block_id}&comp=block&{url[1]}" + response = self.session.put( + upload_block_url, + data=data, + headers={ + "Accept": "application/xml", + "Content-Type": "application/octet-stream", + "Content-Length": str(len(data)), + "x-ms-version": "2019-12-12", + }, + ) + response.raise_for_status() + self.total_size += len(data) # track total object size + with self.lock: + self.indexes.append(index) + logging.info(f"Finished uploading block {index}. Took {response.elapsed.total_seconds()} sec") def merge_chunks(self) -> int: """Merge all uploaded blocks into the final blob.""" - try: - upload_url = self.params["upload_url"] - commit_url = f"{upload_url}&comp=blocklist" - block_list_xml = '' - for index in sorted(self.indexes): - block_list_xml += f"{self._generate_block_blob_block_id(index)}" - block_list_xml += "" + upload_url = self.params["upload_url"] + commit_url = f"{upload_url}&comp=blocklist" + block_list_xml = '' + for index in sorted(self.indexes): + block_list_xml += f"{self._generate_block_blob_block_id(index)}" + block_list_xml += "" - response = self.session.put( - commit_url, - data=block_list_xml, - headers={ - "x-ms-blob-content-type": self.params["mime_type"], - "Content-Type": "application/xml", - "Content-Length": str(len(block_list_xml)), - "x-ms-version": "2019-12-12", - }, - ) - response.raise_for_status() + response = self.session.put( + commit_url, + data=block_list_xml, + headers={ + "x-ms-blob-content-type": self.params["mime_type"], + "Content-Type": "application/xml", + "Content-Length": str(len(block_list_xml)), + "x-ms-version": "2019-12-12", + }, + ) + response.raise_for_status() - return self.total_size - except Exception as ex: - logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) - raise + return self.total_size diff --git a/cognite/cdffs/memory_upload_strategy.py b/cognite/cdffs/memory_upload_strategy.py index 82786e1..3566170 100644 --- a/cognite/cdffs/memory_upload_strategy.py +++ b/cognite/cdffs/memory_upload_strategy.py @@ -1,5 +1,4 @@ """Inmemory file upload strategy.""" -import logging import threading from typing import Dict @@ -26,11 +25,6 @@ def upload_chunk(self, data: bytes, index: int) -> None: def merge_chunks(self) -> int: """Merge all uploaded blocks into the final blob.""" - try: - content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) - self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump(), overwrite=True) - return len(content) - - except Exception as ex: - logging.warning("Failed to merge all blocks: {ex}", exc_info=ex) - raise + content = b"".join([self.blocks[key] for key in sorted(self.blocks.keys())]) + self.cognite_client.files.upload_bytes(content=content, **self.metadata.dump(), overwrite=True) + return len(content) diff --git a/cognite/cdffs/spec.py b/cognite/cdffs/spec.py index e299b5b..6a5b4e8 100644 --- a/cognite/cdffs/spec.py +++ b/cognite/cdffs/spec.py @@ -19,6 +19,7 @@ from fsspec.caching import AllBytes from fsspec.spec import AbstractBufferedFile from fsspec.utils import DEFAULT_BLOCK_SIZE +from retry import retry from .az_upload_strategy import AzureUploadStrategy from .credentials import get_connection_config @@ -685,6 +686,7 @@ def __init__( **kwargs, ) + @retry(exceptions=_COMMON_EXCEPTIONS, tries=2) def _upload_chunk(self, final: bool = False) -> bool: """Upload file contents to CDF. @@ -698,41 +700,38 @@ def _upload_chunk(self, final: bool = False) -> bool: RuntimeError: When an unexpected error occurred. """ + @retry(tries=3, logger=logging.getLogger("upload_chunk")) def strategy_submit(data: bytes, index: int) -> None: self.write_strategy.upload_chunk(data, index) - try: - buffer_length = len(self.buffer.getvalue()) - blocks = [self.buffer.getvalue()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] - - logging.info(f"{len(blocks)} full blocks discovered") + buffer_length = len(self.buffer.getvalue()) + blocks = [self.buffer.getvalue()[i : i + self.blocksize] for i in range(0, buffer_length, self.blocksize)] - # Upload blocks in parallel using ThreadPoolExecutor - with ThreadPoolExecutor(max_workers=5) as executor: - for arg in zip(blocks, range(self.index, self.index + len(blocks))): - executor.submit(strategy_submit, arg[0], arg[1]) + logging.info(f"{len(blocks)} full blocks discovered") - # Update the index - self.index += len(blocks) + # Upload blocks in parallel using ThreadPoolExecutor + with ThreadPoolExecutor(max_workers=5) as executor: + for arg in zip(blocks, range(self.index, self.index + len(blocks))): + executor.submit(strategy_submit, arg[0], arg[1]) - # If it's the final block, then send a merge request - if final: - total_size = self.write_strategy.merge_chunks() + # Update the index + self.index += len(blocks) - self.cognite_client.files.update( - item=FileMetadataUpdate(external_id=self.external_id).metadata.add({"size": total_size}) - ) + # If it's the final block, then send a merge request + if final: + total_size = self.write_strategy.merge_chunks() - self.fs.cache_path( - self.root_dir, - self.external_id, - total_size, - ) + self.cognite_client.files.update( + item=FileMetadataUpdate(external_id=self.external_id).metadata.add({"size": total_size}) + ) - return final + self.fs.cache_path( + self.root_dir, + self.external_id, + total_size, + ) - except _COMMON_EXCEPTIONS as error: # type: ignore - raise RuntimeError from error + return final def _fetch_range(self, start: int, end: int) -> Any: """Read file contents 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pydantic-settings = "^2.0.3" +retry = "^0.9.2" [tool.poetry.dev-dependencies]