diff --git a/.github/workflows/build_cli.yml b/.github/workflows/build_cli.yml deleted file mode 100644 index 8bba198..0000000 --- a/.github/workflows/build_cli.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: Build binaries - -on: [push] - -jobs: - build: - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - max-parallel: 1 - matrix: - os: ['windows-latest', 'ubuntu-latest', 'macos-latest'] - - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: "3.10" - - run: pip install . - - run: pip install pyinstaller - - run: pyinstaller -F ./dvuploader/cli.py -n dvuploader-${{ matrix.os }} --distpath ./bin - - name: Push - run: | - git config --global user.name "Build Bot" - git config --global user.email "build.bot@bot.com" - - git pull - git add ./bin/\* - git commit -a -m "šŸ¤– Built DVUploader for ${{ matrix.os }}" - git push diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..5ba90f6 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,17 @@ +name: Build and publish + +on: + release: + types: [released] + +jobs: + deploy: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: "Build and publish to PyPi" + uses: JRubics/poetry-publish@v1.17 + with: + pypi_token: ${{ secrets.PYPI_TOKEN }} \ No newline at end of file diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..d4b0229 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,36 @@ +name: Integration Tests + +on: [push] + +jobs: + build: + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: ['3.8', '3.9', '3.10', '3.11'] + + env: + PORT: 8080 + steps: + - name: "Checkout" + uses: "actions/checkout@v4" + - name: Run Dataverse Action + id: dataverse + uses: gdcc/dataverse-action@main + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python3 -m pip install --upgrade pip + python3 -m pip install poetry + poetry install --with test + - name: Test with pytest + env: + API_TOKEN: ${{ steps.dataverse.outputs.api_token }} + BASE_URL: ${{ steps.dataverse.outputs.base_url }} + DVUPLOADER_TESTING: "true" + run: | + python3 -m poetry run pytest diff --git a/README.md b/README.md index 9ba5fa8..93dac14 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,9 @@ -

-

Python DVUploader

-

+

+ Dataverse Uploader
+ PyPI version + Build Badge + Build Badge +

Python equivalent to the [DVUploader](https://github.com/GlobalDataverseCommunityConsortium/dataverse-uploader) written in Java. Complements other libraries written in Python and facilitates the upload of files to a Dataverse instance via [Direct Upload](https://guides.dataverse.org/en/latest/developers/s3-direct-upload-api.html). @@ -12,9 +15,7 @@ Python equivalent to the [DVUploader](https://github.com/GlobalDataverseCommunit ----- -

- -

+https://github.com/gdcc/python-dvuploader/assets/30547301/671131b1-d188-4433-9f77-9ec0ed2af36e ----- @@ -41,23 +42,27 @@ python3 -m pip install . In order to perform a direct upload, you need to have a Dataverse instance running and a cloud storage provider. The following example shows how to upload files to a Dataverse instance. Simply provide the files of interest and utilize the `upload` method of a `DVUploader` instance. ```python -from dvuploader import DVUploader, File +import dvuploader as dv + +# Add file individually files = [ - File(filepath="./small.txt"), - File(directoryLabel="some/dir", filepath="./medium.txt"), - File(directoryLabel="some/dir", filepath="./big.txt"), + dv.File(filepath="./small.txt"), + dv.File(directoryLabel="some/dir", filepath="./medium.txt"), + dv.File(directoryLabel="some/dir", filepath="./big.txt"), + *dv.add_directory("./data"), # Add an entire directory ] DV_URL = "https://demo.dataverse.org/" API_TOKEN = "XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX" PID = "doi:10.70122/XXX/XXXXX" -dvuploader = DVUploader(files=files) +dvuploader = dv.DVUploader(files=files) dvuploader.upload( api_token=API_TOKEN, dataverse_url=DV_URL, persistent_id=PID, + n_parallel_uploads=2, # Whatever your instance can handle ) ``` @@ -109,7 +114,3 @@ The `config` file can then be used as follows: ```bash dvuploader --config-path config.yml ``` - -#### CLI Binaries - -DVUploader ships with binaries for Linux, MacOS and Windows. You can download the binaries from the `bin` [directory](./bin) and use them in a similar fashion as described above. diff --git a/bin/dvuploader-macos-latest b/bin/dvuploader-macos-latest deleted file mode 100755 index 0432c26..0000000 Binary files a/bin/dvuploader-macos-latest and /dev/null differ diff --git a/bin/dvuploader-ubuntu-latest b/bin/dvuploader-ubuntu-latest deleted file mode 100755 index 7416ce1..0000000 Binary files a/bin/dvuploader-ubuntu-latest and /dev/null differ diff --git a/bin/dvuploader-windows-latest.exe b/bin/dvuploader-windows-latest.exe deleted file mode 100644 index 1b5c8fc..0000000 Binary files a/bin/dvuploader-windows-latest.exe and /dev/null differ diff --git a/dvuploader/__init__.py b/dvuploader/__init__.py index d908381..279f1f1 100644 --- a/dvuploader/__init__.py +++ b/dvuploader/__init__.py @@ -1,2 +1,7 @@ from .dvuploader import DVUploader from .file import File +from .utils import add_directory + +import nest_asyncio + +nest_asyncio.apply() diff --git a/dvuploader/checksum.py b/dvuploader/checksum.py index 595c832..f5f5d50 100644 --- a/dvuploader/checksum.py +++ b/dvuploader/checksum.py @@ -3,11 +3,22 @@ import os from typing import Callable -from pydantic import BaseModel, Field +from pydantic import BaseModel, ConfigDict, Field + + +from enum import Enum +import hashlib class ChecksumTypes(Enum): - """Enum class representing different types of checksums.""" + """Enum class representing different types of checksums. + + Attributes: + SHA1: Represents the SHA-1 checksum algorithm. + MD5: Represents the MD5 checksum algorithm. + SHA256: Represents the SHA-256 checksum algorithm. + SHA512: Represents the SHA-512 checksum algorithm. + """ SHA1 = ("SHA-1", hashlib.sha1) MD5 = ("MD5", hashlib.md5) @@ -23,8 +34,7 @@ class Checksum(BaseModel): value (str): The value of the checksum. """ - class Config: - allow_population_by_field_name = True + model_config = ConfigDict(populate_by_name=True) type: str = Field(..., alias="@type") value: str = Field(..., alias="@value") @@ -62,7 +72,6 @@ def _chunk_checksum(fpath: str, hash_fun: Callable, blocksize=2**20) -> str: Returns: str: A string representing the checksum of the file. """ - m = hash_fun() with open(fpath, "rb") as f: while True: diff --git a/dvuploader/chunkstream.py b/dvuploader/chunkstream.py deleted file mode 100644 index b05435c..0000000 --- a/dvuploader/chunkstream.py +++ /dev/null @@ -1,40 +0,0 @@ -class ChunkStream: - """ - A class used to represent a Chunk Stream. - - ... - - Attributes: - read_limit (int) - The maximum amount of data to be read from the file - amount_seen (int) - The amount of data already read from the file - file_obj (BufferedReader) - The file to read from - len (int) - the length of the data to be read, same as read_limit - """ - - def __init__(self, file_obj, read_limit, file_size): - """ - Constructs all the necessary attributes for the ChunkStream object. - - Args: - file_obj (BufferedReader) - The file to read from - read_limit (int) - the maximum amount of data to be read from the file - """ - self.read_limit = read_limit - self.amount_seen = 0 - self.file_obj = file_obj - - # So that requests doesn't try to chunk the upload but will instead stream it: - self.len = min(file_size, read_limit) - - def read(self, amount=-1): - if self.amount_seen >= self.read_limit: - return b"" - - remaining_amount = self.read_limit - self.amount_seen - - if amount < 0: - amount = remaining_amount - - data = self.file_obj.read(min(amount, remaining_amount)) - self.amount_seen += len(data) - return data diff --git a/dvuploader/cli.py b/dvuploader/cli.py index 5429cea..1086011 100644 --- a/dvuploader/cli.py +++ b/dvuploader/cli.py @@ -2,7 +2,7 @@ import typer from pydantic import BaseModel -from typing import List, Tuple +from typing import List, Optional from dvuploader import DVUploader, File @@ -11,12 +11,13 @@ class CliInput(BaseModel): dataverse_url: str persistent_id: str files: List[File] + n_jobs: int = 1 app = typer.Typer() -def _parse_yaml_config(path: str) -> Tuple[List[File], str, str, str]: +def _parse_yaml_config(path: str) -> CliInput: """ Parses a configuration file and returns a Class instance containing a list of File objects, a persistent ID, a Dataverse URL, @@ -32,7 +33,7 @@ def _parse_yaml_config(path: str) -> Tuple[List[File], str, str, str]: Raises: ValueError: If the configuration file is invalid. """ - return CliInput(**yaml.safe_load(open(path))) + return CliInput(**yaml.safe_load(open(path))) # type: ignore def _validate_inputs( @@ -40,9 +41,23 @@ def _validate_inputs( pid: str, dataverse_url: str, api_token: str, - config_path: str, + config_path: Optional[str], ) -> None: - if config_path and len(filepaths) > 0: + """ + Validates the inputs for the dvuploader command. + + Args: + filepaths (List[str]): List of filepaths to be uploaded. + pid (str): Persistent identifier of the dataset. + dataverse_url (str): URL of the Dataverse instance. + api_token (str): API token for authentication. + config_path (Optional[str]): Path to the configuration file. + + Raises: + typer.BadParameter: If both a configuration file and a list of filepaths are specified. + typer.BadParameter: If neither a configuration file nor metadata parameters are specified. + """ + if config_path is not None and len(filepaths) > 0: raise typer.BadParameter( "Cannot specify both a JSON/YAML file and a list of filepaths." ) @@ -80,15 +95,27 @@ def main( default=None, help="The URL of the Dataverse repository.", ), - config_path: str = typer.Option( + config_path: Optional[str] = typer.Option( default=None, help="Path to a JSON/YAML file containing specifications for the files to upload. Defaults to None.", ), n_jobs: int = typer.Option( - default=-1, + default=1, help="The number of parallel jobs to run. Defaults to -1.", ), ): + """ + Uploads files to a Dataverse repository. + + Args: + filepaths (List[str]): A list of filepaths to upload. + pid (str): The persistent identifier of the Dataverse dataset. + api_token (str): The API token for the Dataverse repository. + dataverse_url (str): The URL of the Dataverse repository. + config_path (Optional[str]): Path to a JSON/YAML file containing specifications for the files to upload. Defaults to None. + n_jobs (int): The number of parallel jobs to run. Defaults to -1. + """ + _validate_inputs( filepaths=filepaths, pid=pid, @@ -113,9 +140,9 @@ def main( persistent_id=cli_input.persistent_id, dataverse_url=cli_input.dataverse_url, api_token=cli_input.api_token, - n_jobs=n_jobs, + n_parallel_uploads=n_jobs, ) if __name__ == "__main__": - typer.run(main) + app() diff --git a/dvuploader/directupload.py b/dvuploader/directupload.py index 6e35213..8952bdd 100644 --- a/dvuploader/directupload.py +++ b/dvuploader/directupload.py @@ -1,98 +1,169 @@ +import asyncio +from io import BytesIO import json import os -from typing import Dict, List +from typing import Dict, List, Optional, Tuple from urllib.parse import urljoin - -import grequests -import requests -from dotted_dict import DottedDict -from requests.exceptions import HTTPError -from tqdm import tqdm -from tqdm.utils import CallbackIOWrapper +import aiofiles +import aiohttp from dvuploader.file import File -from dvuploader.chunkstream import ChunkStream from dvuploader.utils import build_url -global MAX_RETRIES +TESTING = bool(os.environ.get("DVUPLOADER_TESTING", False)) -MAX_RETRIES = 10 TICKET_ENDPOINT = "/api/datasets/:persistentId/uploadurls" ADD_FILE_ENDPOINT = "/api/datasets/:persistentId/addFiles" UPLOAD_ENDPOINT = "/api/datasets/:persistentId/add?persistentId=" REPLACE_ENDPOINT = "/api/files/{FILE_ID}/replace" -def direct_upload( +async def direct_upload( + files: List[File], + dataverse_url: str, + api_token: str, + persistent_id: str, + progress, + pbars, + n_parallel_uploads: int, +) -> None: + """ + Perform parallel direct upload of files to the specified Dataverse repository. + + Args: + files (List[File]): A list of File objects to be uploaded. + dataverse_url (str): The URL of the Dataverse repository. + api_token (str): The API token for the Dataverse repository. + persistent_id (str): The persistent identifier of the Dataverse dataset. + progress: The progress object to track the upload progress. + pbars: A list of progress bars to display the upload progress for each file. + n_parallel_uploads (int): The number of parallel uploads to perform. + + Returns: + None + """ + + headers = { + "X-Dataverse-key": api_token, + } + params = { + "headers": headers, + "connector": aiohttp.TCPConnector(limit=n_parallel_uploads), + } + async with aiohttp.ClientSession(**params) as session: + tasks = [ + _upload_to_store( + session=session, + file=file, + dataverse_url=dataverse_url, + api_token=api_token, + persistent_id=persistent_id, + pbar=pbar, + progress=progress, + delay=0.0, + ) + for pbar, file in zip(pbars, files) + ] + + upload_results = await asyncio.gather(*tasks) + + for status, file in upload_results: + if status is True: + continue + + print(f"āŒ Failed to upload file '{file.fileName}' to the S3 storage") + + connector = aiohttp.TCPConnector(limit=4) + pbar = progress.add_task("ā•°ā”€ā”€ [bold white]Registering files", total=len(files)) + results = [] + async with aiohttp.ClientSession( + headers=headers, + connector=connector, + ) as session: + for file in files: + results.append( + await _add_file_to_ds( + session=session, + file=file, + dataverse_url=dataverse_url, + pid=persistent_id, + ) + ) + + progress.update(pbar, advance=1) + + for file, status in zip(files, results): + if status is False: + print(f"āŒ Failed to register file '{file.fileName}' at Dataverse") + + +async def _upload_to_store( + session: aiohttp.ClientSession, file: File, persistent_id: str, dataverse_url: str, api_token: str, - position: int, - n_parallel_uploads: int, -) -> bool: + pbar, + progress, + delay: float, +): """ Uploads a file to a Dataverse collection using direct upload. Args: + session (aiohttp.ClientSession): The aiohttp client session. file (File): The file object to upload. persistent_id (str): The persistent identifier of the Dataverse dataset to upload to. dataverse_url (str): The URL of the Dataverse instance to upload to. api_token (str): The API token to use for authentication. - position (int): The position of the file in the list of files to upload. - n_parallel_uploads (int): The number of parallel uploads to perform. + pbar: The progress bar object. + progress: The progress object. + delay (float): The delay in seconds before starting the upload. Returns: - bool: True if the upload was successful, False otherwise. + tuple: A tuple containing the upload status (bool) and the file object. """ + await asyncio.sleep(delay) + assert file.fileName is not None, "File name is None" assert os.path.exists(file.filepath), f"File {file.filepath} does not exist" file_size = os.path.getsize(file.filepath) - pbar = _setup_pbar(file.filepath, position) - response = _request_ticket( + ticket = await _request_ticket( + session=session, dataverse_url=dataverse_url, api_token=api_token, file_size=file_size, persistent_id=persistent_id, ) - if not "urls" in response: - file.storageIdentifier = _upload_singlepart( - response=response, + if not "urls" in ticket: + status, storage_identifier = await _upload_singlepart( + session=session, + ticket=ticket, filepath=file.filepath, pbar=pbar, + progress=progress, ) + else: - file.storageIdentifier = _upload_multipart( - response=response, + status, storage_identifier = await _upload_multipart( + session=session, + response=ticket, filepath=file.filepath, dataverse_url=dataverse_url, - api_token=api_token, pbar=pbar, - n_parallel_uploads=n_parallel_uploads, + progress=progress, ) - result = _add_file_to_ds( - dataverse_url, - persistent_id, - api_token, - file, - n_parallel_uploads, - ) + file.storageIdentifier = storage_identifier - if result is True: - pbar.bar_format = f"ā”œā”€ā”€ {file.filepath} uploaded!" - else: - pbar.bar_format = f"ā”œā”€ā”€ {file.filepath} failed to upload!" + return status, file - pbar.close() - return True - - -def _request_ticket( +async def _request_ticket( + session: aiohttp.ClientSession, dataverse_url: str, api_token: str, persistent_id: str, @@ -100,139 +171,187 @@ def _request_ticket( ) -> Dict: """Requests a ticket from a Dataverse collection to perform an upload. - This method will return a URL and storageIdentifier that later on is - used to perform the direct upload. - - Please note, your Dataverse installation and collection should have - enabled Direct Upload to an S3 bucket to perform the upload. + This method will send a request to the Dataverse API to obtain a ticket + for performing a direct upload to an S3 bucket. The ticket contains a URL + and storageIdentifier that will be used later to perform the upload. Args: - dataverse_url (str): URL to the Dataverse installation - api_token (str): API Token used to access the dataset. - persistent_id (str): Persistent identifier of the dataset of interest. + session (aiohttp.ClientSession): The aiohttp client session to use for the request. + dataverse_url (str): The URL of the Dataverse installation. + api_token (str): The API token used to access the dataset. + persistent_id (str): The persistent identifier of the dataset of interest. + file_size (int): The size of the file to be uploaded. Returns: - Dict: Response from the Dataverse API + Dict: The response from the Dataverse API, containing the ticket information. """ - - # Build request URL - query = build_url( - endpoint=TICKET_ENDPOINT, - dataverse_url=dataverse_url, + url = build_url( + endpoint=urljoin(dataverse_url, TICKET_ENDPOINT), key=api_token, persistentId=persistent_id, size=file_size, ) - # Send HTTP request - response = requests.get(query) - - if response.status_code != 200: - raise HTTPError( - f"Could not request a ticket for dataset '{persistent_id}' at '{dataverse_url}' \ - \n\n{json.dumps(response.json(), indent=2)}" - ) # type: ignore + async with session.get(url) as response: + response.raise_for_status() + payload = await response.json() + return payload["data"] - return DottedDict(response.json()["data"]) - -def _upload_singlepart( - response: Dict, +async def _upload_singlepart( + session: aiohttp.ClientSession, + ticket: Dict, filepath: str, - pbar: tqdm, -) -> str: + pbar, + progress, +) -> Tuple[bool, str]: """ Uploads a single part of a file to a remote server using HTTP PUT method. Args: - response (Dict): A dictionary containing the response from the server. + session (aiohttp.ClientSession): The aiohttp client session used for the upload. + ticket (Dict): A dictionary containing the response from the server. filepath (str): The path to the file to be uploaded. pbar (tqdm): A progress bar object to track the upload progress. + progress: The progress object used to update the progress bar. Returns: - str: The storage identifier of the uploaded file. + Tuple[bool, str]: A tuple containing the status of the upload (True for success, False for failure) + and the storage identifier of the uploaded file. """ + assert "url" in ticket, "Couldnt find 'url'" - assert "url" in response, "Couldnt find 'url'" + if TESTING: + ticket["url"] = ticket["url"].replace("localstack", "localhost", 1) - headers = {"x-amz-tagging": "dv-state=temp"} - storage_identifier = response.storageIdentifier # type: ignore - wrapped_file = CallbackIOWrapper(pbar.update, open(filepath, "rb")) - resp = requests.put( - response.url, # type: ignore - data=wrapped_file, # type: ignore - stream=True, - headers=headers, - ) + storage_identifier = ticket["storageIdentifier"] + params = { + "url": ticket["url"], + "data": open(filepath, "rb"), + } - if resp.status_code != 200: - raise HTTPError( - f"Could not upload file \ - \n\n{resp.headers}" - ) # type: ignore + async with session.put(**params) as response: + status = response.status == 200 - return storage_identifier + if status: + progress.update(pbar, advance=os.path.getsize(filepath)) + return status, storage_identifier -def _upload_multipart( + +async def _upload_multipart( + session: aiohttp.ClientSession, response: Dict, filepath: str, dataverse_url: str, - api_token: str, - pbar: tqdm, - n_parallel_uploads: int, + pbar, + progress, ): """ Uploads a file to Dataverse using multipart upload. Args: + session (aiohttp.ClientSession): The aiohttp client session. response (Dict): The response from the Dataverse API containing the upload ticket information. filepath (str): The path to the file to be uploaded. dataverse_url (str): The URL of the Dataverse instance. - api_token (str): The API token for the Dataverse instance. pbar (tqdm): A progress bar to track the upload progress. - n_parallel_uploads (int): The number of parallel uploads to perform. + progress: The progress callback function. Returns: - str: The storage identifier for the uploaded file. + Tuple[bool, str]: A tuple containing a boolean indicating the success of the upload and the storage identifier for the uploaded file. """ _validate_ticket_response(response) - abort = response.abort # type: ignore - complete = response.complete # type: ignore - part_size = response.partSize # type: ignore - urls = response.urls # type: ignore - storage_identifier = response.storageIdentifier # type: ignore + abort = response["abort"] + complete = response["complete"] + part_size = response["partSize"] + urls = iter(response["urls"].values()) + storage_identifier = response["storageIdentifier"] # Chunk file and retrieve paths and urls - chunks = _chunk_file(filepath, part_size, urls) - tasks = [{"file": streamer, "url": url} for streamer, url in chunks] + chunk_size = int(part_size) try: - rs = ( - grequests.put( - task["url"], - data=CallbackIOWrapper(pbar.update, task["file"], "read"), - stream=True, - ) - for task in tasks + e_tags = await _chunked_upload( + filepath=filepath, + session=session, + urls=urls, + chunk_size=chunk_size, + pbar=pbar, + progress=progress, + ) + except Exception as e: + print(f"āŒ Failed to upload file '{filepath}' to the S3 storage") + await _abort_upload( + session=session, + url=abort, + dataverse_url=dataverse_url, ) + raise e + + await _complete_upload( + session=session, + url=complete, + dataverse_url=dataverse_url, + e_tags=e_tags, + ) + + return True, storage_identifier + + +async def _chunked_upload( + filepath: str, + session: aiohttp.ClientSession, + urls, + chunk_size: int, + pbar, + progress, +): + """ + Uploads a file in chunks to multiple URLs using the provided session. + + Args: + filepath (str): The path of the file to upload. + session (aiohttp.ClientSession): The aiohttp client session to use for the upload. + urls: An iterable of URLs to upload the file chunks to. + chunk_size (int): The size of each chunk in bytes. + pbar (tqdm): The progress bar to update during the upload. + progress: The progress object to track the upload progress. - # Execute upload - responses = grequests.map( - requests=rs, - size=n_parallel_uploads, + Returns: + List[str]: A list of ETags returned by the server for each uploaded chunk. + """ + e_tags = [] + async with aiofiles.open(filepath, "rb") as f: + chunk = await f.read(chunk_size) + e_tags.append( + await _upload_chunk( + session=session, + url=next(urls), + file=BytesIO(chunk), + ) ) - e_tags = [response.headers["ETag"] for response in responses] - except Exception as e: - _abort_upload(abort, dataverse_url, api_token) - raise e + progress.update(pbar, advance=len(chunk)) + + while chunk: + chunk = await f.read(chunk_size) + progress.update(pbar, advance=len(chunk)) - _complete_upload(complete, dataverse_url, e_tags, api_token) + if not chunk: + break + else: + e_tags.append( + await _upload_chunk( + session=session, + url=next(urls), + file=BytesIO(chunk), + ) + ) - return storage_identifier + return e_tags def _validate_ticket_response(response: Dict) -> None: @@ -245,105 +364,119 @@ def _validate_ticket_response(response: Dict) -> None: assert "storageIdentifier" in response, "Could not find 'storageIdentifier'" -def _chunk_file( - path: str, - chunk_size: int, - urls: Dict, -) -> List[str]: +async def _upload_chunk( + session: aiohttp.ClientSession, + url: str, + file: BytesIO, +): """ - Breaks a file into chunks of a specified size and saves them to disk. - Returns a list of tuples containing the path to each chunk and its corresponding upload URL. + Uploads a chunk of data to the specified URL using the provided session. Args: - path (str): The path to the file to be chunked. - chunk_size (int): The size of each chunk in bytes. - urls (Dict): A dictionary containing the upload URLs for each chunk. - chunk_dir (str, optional): The directory to save the chunks in. Defaults to "./chunks". + session (aiohttp.ClientSession): The session to use for the upload. + url (str): The URL to upload the chunk to. + file (ChunkStream): The chunk of data to upload. + pbar: The progress bar to update during the upload. Returns: - List[str]: A list of tuples containing the path to each chunk and its corresponding upload URL. + str: The ETag value of the uploaded chunk. """ - # os.makedirs(chunk_dir, exist_ok=True) - - start = 0 - uploads = [] - - for url in urls.values(): - size = min(chunk_size, os.stat(path).st_size - start) - file = open(path, "rb") - file.seek(start) + if TESTING: + url = url.replace("localstack", "localhost", 1) - uploads.append((ChunkStream(file, chunk_size, size), url)) + params = { + "url": url, + "data": file, + } - start += chunk_size + async with session.put(**params) as response: + response.raise_for_status() + return response.headers.get("ETag") - return uploads - -def _complete_upload( +async def _complete_upload( + session: aiohttp.ClientSession, url: str, dataverse_url: str, - e_tags: List[str], - api_token: str, + e_tags: List[Optional[str]], ) -> None: - """Completes the upload by sending the E tags""" + """Completes the upload by sending the E tags + + Args: + session (aiohttp.ClientSession): The aiohttp client session. + url (str): The URL to send the PUT request to. + dataverse_url (str): The base URL of the Dataverse instance. + e_tags (List[str]): The list of E tags to send in the payload. + + Raises: + aiohttp.ClientResponseError: If the response status code is not successful. + """ - headers = {"X-Dataverse-key": api_token} payload = json.dumps({str(index + 1): e_tag for index, e_tag in enumerate(e_tags)}) - response = requests.put(urljoin(dataverse_url, url), data=payload, headers=headers) - if response.status_code != 200: - raise HTTPError( - f"Could not complete upload \ - \n\n{json.dumps(response.json(), indent=2)}" - ) # type: ignore + async with session.put(urljoin(dataverse_url, url), data=payload) as response: + response.raise_for_status() -def _abort_upload( +async def _abort_upload( + session: aiohttp.ClientSession, url: str, dataverse_url: str, - api_token: str, ): - headers = {"X-Dataverse-key": api_token} - requests.delete(urljoin(dataverse_url, url), headers=headers) + """ + Aborts an ongoing upload by sending a DELETE request to the specified URL. + + Args: + session (aiohttp.ClientSession): The aiohttp client session. + url (str): The URL to send the DELETE request to. + dataverse_url (str): The base URL of the Dataverse instance. + + Raises: + aiohttp.ClientResponseError: If the DELETE request fails. + """ + async with session.delete(urljoin(dataverse_url, url)) as response: + response.raise_for_status() -def _add_file_to_ds( +async def _add_file_to_ds( + session: aiohttp.ClientSession, dataverse_url: str, pid: str, - api_token: str, file: File, -): - headers = {"X-Dataverse-key": api_token} +) -> bool: + """ + Adds a file to a Dataverse dataset. + + Args: + session (aiohttp.ClientSession): The aiohttp client session. + dataverse_url (str): The URL of the Dataverse instance. + pid (str): The persistent identifier of the dataset. + file (File): The file to be added. + Returns: + bool: True if the file was added successfully, False otherwise. + """ if not file.to_replace: url = urljoin(dataverse_url, UPLOAD_ENDPOINT + pid) else: url = build_url( dataverse_url=dataverse_url, - endpoint=REPLACE_ENDPOINT.format(FILE_ID=file.file_id), + endpoint=urljoin( + dataverse_url, + REPLACE_ENDPOINT.format(FILE_ID=file.file_id), + ), ) - payload = {"jsonData": file.json(by_alias=True, exclude={"to_replace", "file_id"})} - - for _ in range(MAX_RETRIES): - response = requests.post(url, headers=headers, files=payload) - if response.status_code == 200: - return True - - return False + json_data = file.model_dump_json( + by_alias=True, + exclude={"to_replace", "file_id"}, + indent=2, + ) + with aiohttp.MultipartWriter("form-data") as writer: + json_part = writer.append(json_data) + json_part.set_content_disposition("form-data", name="jsonData") -def _setup_pbar(fpath: str, position: int, pre: str = "ā”œā”€ā”€ "): - return tqdm( - total=os.stat(fpath).st_size, - unit="B", - unit_scale=True, - unit_divisor=1024, - ascii=" >=", - desc=pre + f"{fpath} ", - bar_format="{l_bar}{bar:20}{r_bar}{bar:-10b}", - position=position, - leave=True, - ) + async with session.post(url, data=writer) as response: + return response.status == 200 diff --git a/dvuploader/dvuploader.py b/dvuploader/dvuploader.py index 5b8f157..c2a412c 100644 --- a/dvuploader/dvuploader.py +++ b/dvuploader/dvuploader.py @@ -1,21 +1,22 @@ -import grequests +import asyncio +from urllib.parse import urljoin import requests import os +import rich from typing import Dict, List, Optional from pydantic import BaseModel -from joblib import Parallel, delayed -from dotted_dict import DottedDict +from rich.progress import Progress, TaskID +from rich.table import Table +from rich.console import Console from dvuploader.directupload import ( TICKET_ENDPOINT, - _abort_upload, - _validate_ticket_response, direct_upload, ) from dvuploader.file import File from dvuploader.nativeupload import native_upload -from dvuploader.utils import build_url, retrieve_dataset_files +from dvuploader.utils import build_url, retrieve_dataset_files, setup_pbar class DVUploader(BaseModel): @@ -38,7 +39,6 @@ def upload( persistent_id: str, dataverse_url: str, api_token: str, - n_jobs: int = -1, n_parallel_uploads: int = 1, ) -> None: """ @@ -48,12 +48,17 @@ def upload( persistent_id (str): The persistent identifier of the Dataverse dataset. dataverse_url (str): The URL of the Dataverse repository. api_token (str): The API token for the Dataverse repository. - n_jobs (int): The number of parallel jobs to run. Defaults to -1. n_parallel_uploads (int): The number of parallel uploads to execute. In the case of direct upload, this restricts the amount of parallel chunks per upload. Please use n_jobs to control parallel files. Returns: None """ + rich.print("\n") + + # Validate and hash files + progress = Progress() + with progress: + asyncio.run(self._validate_and_hash_files(progress=progress)) # Check for duplicates self._check_duplicates( @@ -66,11 +71,11 @@ def upload( files = sorted( self.files, key=lambda x: os.path.getsize(x.filepath), - reverse=True, + reverse=False, ) if not self.files: - print("\nāŒ No files to upload\n") + rich.print("\n[bold italic white]āŒ No files to upload\n") return # Check if direct upload is supported @@ -79,29 +84,74 @@ def upload( api_token=api_token, persistent_id=persistent_id, ) - print("\nāš ļø Direct upload not supported. Falling back to Native API.") - print(f"\nšŸš€ Uploading files") + if not has_direct_upload: + print("\nāš ļø Direct upload not supported. Falling back to Native API.") + + rich.print(f"\n[bold italic white]šŸš€ Uploading files") + + progress, pbars = self.setup_progress_bars(files=files) if not has_direct_upload: - self._execute_native_uploads( - files=files, - dataverse_url=dataverse_url, - api_token=api_token, - persistent_id=persistent_id, - n_parallel_uploads=n_parallel_uploads, - ) + with progress: + asyncio.run( + native_upload( + files=files, + dataverse_url=dataverse_url, + api_token=api_token, + persistent_id=persistent_id, + n_parallel_uploads=n_parallel_uploads, + progress=progress, + pbars=pbars, + ) + ) else: - self._parallel_direct_upload( - files=files, - dataverse_url=dataverse_url, - api_token=api_token, - persistent_id=persistent_id, - n_jobs=n_jobs, - n_parallel_uploads=n_parallel_uploads, + with progress: + asyncio.run( + direct_upload( + files=files, + dataverse_url=dataverse_url, + api_token=api_token, + persistent_id=persistent_id, + pbars=pbars, + progress=progress, + n_parallel_uploads=n_parallel_uploads, + ) + ) + + print("\nšŸŽ‰ Done!\n") + + async def _validate_and_hash_files( + self, + progress: Progress, + ): + """ + Validates and hashes the files to be uploaded. + + Returns: + None + """ + + task = progress.add_task( + "[italic white]šŸ“ Preparing upload", + total=len(self.files), + ) + + tasks = [ + self._validate_and_hash_file( + file=file, + progress=progress, + task=task, ) + for file in self.files + ] + + await asyncio.gather(*tasks) - print("šŸŽ‰ Done!\n") + @staticmethod + async def _validate_and_hash_file(file: File, progress: Progress, task: TaskID): + file.extract_filename_hash_file() + progress.update(task, advance=1) def _check_duplicates( self, @@ -126,7 +176,15 @@ def _check_duplicates( api_token=api_token, ) - print("\nšŸ”Ž Checking dataset files") + print("\n") + + table = Table( + title="[bold white]šŸ”Ž Checking dataset files", + title_justify="left", + ) + table.add_column("File", style="cyan", no_wrap=True) + table.add_column("Status") + table.add_column("Action") to_remove = [] @@ -136,12 +194,14 @@ def _check_duplicates( ) if has_same_hash and file.checksum: - print( - f"ā”œā”€ā”€ File '{file.fileName}' already exists with same {file.checksum.type} hash - Skipping upload." + table.add_row( + file.fileName, "[bright_black]Same hash", "[bright_black]Skip" ) to_remove.append(file) else: - print(f"ā”œā”€ā”€ File '{file.fileName}' is new - Uploading.") + table.add_row( + file.fileName, "[spring_green3]New", "[spring_green3]Upload" + ) # If present in dataset, replace file file.file_id = self._get_file_id(file, ds_files) @@ -150,12 +210,13 @@ def _check_duplicates( for file in to_remove: self.files.remove(file) - print("šŸŽ‰ Done") + console = Console() + console.print(table) @staticmethod def _get_file_id( file: File, - ds_files: List[DottedDict], + ds_files: List[Dict], ) -> Optional[str]: """ Get the file ID for a given file in a dataset. @@ -174,14 +235,14 @@ def _get_file_id( # Find the file that matches label and directoryLabel for ds_file in ds_files: - dspath = os.path.join(ds_file.get("directoryLabel", ""), ds_file.label) + dspath = os.path.join(ds_file.get("directoryLabel", ""), ds_file["label"]) fpath = os.path.join(file.directoryLabel, file.fileName) # type: ignore if dspath == fpath: - return ds_file.dataFile.id + return ds_file["dataFile"]["id"] @staticmethod - def _check_hashes(file: File, dsFile: DottedDict): + def _check_hashes(file: File, dsFile: Dict): """ Checks if a file has the same checksum as a file in the dataset. @@ -196,7 +257,7 @@ def _check_hashes(file: File, dsFile: DottedDict): if not file.checksum: return False - hash_algo, hash_value = tuple(dsFile.dataFile.checksum.values()) + hash_algo, hash_value = tuple(dsFile["dataFile"]["checksum"].values()) return file.checksum.value == hash_value and file.checksum.type == hash_algo @@ -209,110 +270,35 @@ def _has_direct_upload( """Checks if the response from the ticket request contains a direct upload URL""" query = build_url( - endpoint=TICKET_ENDPOINT, - dataverse_url=dataverse_url, + endpoint=urljoin(dataverse_url, TICKET_ENDPOINT), key=api_token, persistentId=persistent_id, size=1024, ) # Send HTTP request - response = requests.get(query).json() - expected_error = "Direct upload not supported for files in this dataset" + response = requests.get(query) - if "message" in response and expected_error in response["message"]: + if response.status_code == 404: return False + else: + return True - # Abort test upload for now, if direct upload is supported - data = DottedDict(response.json()["data"]) - _validate_ticket_response(data) - _abort_upload( - data.abort, - dataverse_url, - api_token, - ) - - return True - - @staticmethod - def _execute_native_uploads( - files: List[File], - dataverse_url: str, - api_token: str, - persistent_id: str, - n_parallel_uploads: int, - ): + def setup_progress_bars(self, files: List[File]): """ - Executes native uploads for the given files in parallel. - - Args: - files (List[File]): The list of File objects to be uploaded. - dataverse_url (str): The URL of the Dataverse repository. - api_token (str): The API token for the Dataverse repository. - persistent_id (str): The persistent identifier of the Dataverse dataset. - n_parallel_uploads (int): The number of parallel uploads to execute. + Sets up progress bars for each file in the uploader. Returns: - List[requests.Response]: The list of responses for each file upload. + A list of progress bars, one for each file in the uploader. """ + progress = Progress() tasks = [ - native_upload( - file=file, - dataverse_url=dataverse_url, - api_token=api_token, - persistent_id=persistent_id, - position=position, + setup_pbar( + fpath=file.filepath, + progress=progress, ) - for position, file in enumerate(files) + for file in files ] - # Execute tasks - responses = grequests.map(tasks, size=n_parallel_uploads) - - if not all(map(lambda x: x.status_code == 200, responses)): - errors = "\n".join( - ["\n\nāŒ Failed to upload files:"] - + [ - f"ā”œā”€ā”€ File '{file.fileName}' could not be uploaded: {response.status_code} {response.json()['message']}" - for file, response in zip(files, responses) - if response.status_code != 200 - ] - ) - - print(errors, "\n") - - @staticmethod - def _parallel_direct_upload( - files: List[File], - dataverse_url: str, - api_token: str, - persistent_id: str, - n_parallel_uploads: int, - n_jobs: int = -1, - ) -> None: - """ - Perform parallel direct upload of files to the specified Dataverse repository. - - Args: - files (List[File]): A list of File objects to be uploaded. - dataverse_url (str): The URL of the Dataverse repository. - api_token (str): The API token for the Dataverse repository. - persistent_id (str): The persistent identifier of the Dataverse dataset. - n_jobs (int): The number of parallel jobs to run. Defaults to -1. - - Returns: - None - """ - - Parallel(n_jobs=n_jobs, backend="threading")( - delayed(direct_upload)( - file=file, - dataverse_url=dataverse_url, - api_token=api_token, - persistent_id=persistent_id, - position=position, - n_parallel_uploads=n_parallel_uploads, - ) - for position, file in enumerate(files) - ) + return progress, tasks diff --git a/dvuploader/file.py b/dvuploader/file.py index b0b0940..f98216c 100644 --- a/dvuploader/file.py +++ b/dvuploader/file.py @@ -1,47 +1,82 @@ import os from typing import List, Optional -from pydantic import BaseModel, Field, validator +from pydantic import BaseModel, Field, model_validator +import rich from dvuploader.checksum import Checksum, ChecksumTypes class File(BaseModel): + """ + Represents a file with its properties and methods. + + Attributes: + filepath (str): The path to the file. + description (str): The description of the file. + directoryLabel (str): The label of the directory where the file is stored. + mimeType (str): The MIME type of the file. + categories (List[str]): The categories associated with the file. + restrict (bool): Indicates if the file is restricted. + checksum_type (ChecksumTypes): The type of checksum used for the file. + storageIdentifier (Optional[str]): The identifier of the storage where the file is stored. + fileName (Optional[str]): The name of the file. + checksum (Optional[Checksum]): The checksum of the file. + to_replace (bool): Indicates if the file should be replaced. + file_id (Optional[str]): The ID of the file. + + Methods: + _validate_filepath(path): Validates if the file path exists and is a file. + _extract_filename_hash_file(): Extracts the filename from the filepath and calculates the file's checksum. + + """ + filepath: str = Field(..., exclude=True) description: str = "" directoryLabel: str = "" mimeType: str = "text/plain" categories: List[str] = ["DATA"] restrict: bool = False - checksum_type: ChecksumTypes = Field( - default=ChecksumTypes.MD5, - exclude=True, - ) + checksum_type: ChecksumTypes = Field(default=ChecksumTypes.MD5, exclude=True) storageIdentifier: Optional[str] = None fileName: Optional[str] = None checksum: Optional[Checksum] = None to_replace: bool = False file_id: Optional[str] = None + def extract_filename_hash_file(self): + """ + Extracts the filename and calculates the hash of the file. + + Returns: + self: The current instance of the class. + """ + self._validate_filepath(self.filepath) + self.fileName = os.path.basename(self.filepath) + + # Hash file + hash_algo, hash_fun = self.checksum_type.value + self.checksum = Checksum.from_file( + fpath=self.filepath, + hash_fun=hash_fun, + hash_algo=hash_algo, + ) + + return self + @staticmethod def _validate_filepath(path): + """ + Validates if the given filepath exists and is a file. + + Args: + path (str): The filepath to be validated. + + Raises: + FileNotFoundError: If the filepath does not exist. + TypeError: If the filepath is not a file. + """ if not os.path.exists(path): raise FileNotFoundError(f"Filepath {path} does not exist.") elif not os.path.isfile(path): - raise TypeError(f"Filepath {path} is not a file.") - elif not os.access(path, os.R_OK): - raise TypeError(f"Filepath {path} is not readable.") - - return path - - @validator("fileName", always=True) - def _extract_filename(cls, v, values): - return os.path.basename(values["filepath"]) - - @validator("checksum", always=True) - def _calculate_hash(cls, v, values): - cls._validate_filepath(values["filepath"]) - fpath = values["filepath"] - hash_algo, hash_fun = values["checksum_type"].value - - return Checksum.from_file(fpath=fpath, hash_fun=hash_fun, hash_algo=hash_algo) + raise IsADirectoryError(f"Filepath {path} is not a file.") diff --git a/dvuploader/nativeupload.py b/dvuploader/nativeupload.py index 9a7a0f8..8af3766 100644 --- a/dvuploader/nativeupload.py +++ b/dvuploader/nativeupload.py @@ -1,52 +1,103 @@ +import asyncio import json import os -import grequests -from dvuploader.directupload import _setup_pbar -from dvuploader.file import File -from dvuploader.utils import build_url, retrieve_dataset_files -from tqdm.utils import CallbackIOWrapper +from typing import List +import aiohttp +from dvuploader.file import File +from dvuploader.utils import build_url +MAX_RETRIES = os.environ.get("DVUPLOADER_MAX_RETRIES", 15) NATIVE_UPLOAD_ENDPOINT = "/api/datasets/:persistentId/add" NATIVE_REPLACE_ENDPOINT = "/api/files/{FILE_ID}/replace" +assert isinstance(MAX_RETRIES, int), "DVUPLOADER_MAX_RETRIES must be an integer" -def native_upload( - file: File, + +async def native_upload( + files: List[File], dataverse_url: str, api_token: str, persistent_id: str, - position: int, + n_parallel_uploads: int, + pbars, + progress, +): + """ + Executes native uploads for the given files in parallel. + + Args: + files (List[File]): The list of File objects to be uploaded. + dataverse_url (str): The URL of the Dataverse repository. + api_token (str): The API token for the Dataverse repository. + persistent_id (str): The persistent identifier of the Dataverse dataset. + n_parallel_uploads (int): The number of parallel uploads to execute. + + Returns: + List[requests.Response]: The list of responses for each file upload. + """ + + session_params = { + "base_url": dataverse_url, + "headers": {"X-Dataverse-key": api_token}, + "connector": aiohttp.TCPConnector( + limit=n_parallel_uploads, + force_close=True, + ), + } + + async with aiohttp.ClientSession(**session_params) as session: + tasks = [ + _single_native_upload( + session=session, + file=file, + persistent_id=persistent_id, + pbar=pbar, # type: ignore + progress=progress, + ) + for pbar, file in zip(pbars, files) + ] + + responses = await asyncio.gather(*tasks) + + for (status, response), file in zip(responses, files): + if status == 200: + continue + + print(f"āŒ Failed to upload file '{file.fileName}': {response['message']}") + + +async def _single_native_upload( + session: aiohttp.ClientSession, + file: File, + persistent_id: str, + pbar, + progress, ): """ Uploads a file to a Dataverse repository using the native upload method. Args: + session (aiohttp.ClientSession): The aiohttp client session. file (File): The file to be uploaded. - dataverse_url (str): The URL of the Dataverse repository. - api_token (str): The API token for authentication. persistent_id (str): The persistent identifier of the dataset. - position (int): The position of the file within the dataset. + pbar: The progress bar object. + progress: The progress object. Returns: - Response: The response object from the upload request. + tuple: A tuple containing the status code and the JSON response from the upload request. """ - pbar = _setup_pbar(file.filepath, position) - if not file.to_replace: - url = build_url( - dataverse_url=dataverse_url, + endpoint = build_url( endpoint=NATIVE_UPLOAD_ENDPOINT, persistentId=persistent_id, ) else: - url = build_url( - dataverse_url=dataverse_url, + endpoint = build_url( endpoint=NATIVE_REPLACE_ENDPOINT.format(FILE_ID=file.file_id), ) - header = {"X-Dataverse-key": api_token} json_data = { "description": file.description, "forceReplace": "true", @@ -56,24 +107,32 @@ def native_upload( "forceReplace": True, } - files = { - "jsonData": json.dumps(json_data), - "file": ( - os.path.basename(file.filepath), - CallbackIOWrapper(pbar.update, open(file.filepath, "rb"), "read"), - ), - } + for _ in range(MAX_RETRIES): + with aiohttp.MultipartWriter("form-data") as writer: + json_part = writer.append(json.dumps(json_data)) + json_part.set_content_disposition("form-data", name="jsonData") + + file_part = writer.append(open(file.filepath, "rb")) + file_part.set_content_disposition( + "form-data", + name="file", + filename=file.fileName, + ) + async with session.post(endpoint, data=writer) as response: + status = response.status + + if status == 200: + progress.update( + pbar, + advance=os.path.getsize(file.filepath), + ) + + # Wait to avoid rate limiting + await asyncio.sleep(0.7) + + return status, await response.json() + + # Wait to avoid rate limiting + await asyncio.sleep(1.0) - def _response_hook(response, *args, **kwargs): - filesize = os.path.getsize(file.filepath) - pbar.reset(filesize / 1024) - pbar.update(filesize / 1024) - pbar.close() - return response - - return grequests.post( - url=url, - headers=header, - files=files, - hooks=dict(response=_response_hook), - ) + return False, {"message": "Failed to upload file"} diff --git a/dvuploader/utils.py b/dvuploader/utils.py index b7ecb8f..c66696b 100644 --- a/dvuploader/utils.py +++ b/dvuploader/utils.py @@ -1,23 +1,41 @@ import json +import os +import pathlib +import re +from typing import List from urllib.parse import urljoin -from requests import PreparedRequest import requests -from dotted_dict import DottedDict +from rich.progress import Progress + +from dvuploader.file import File +import os def build_url( - dataverse_url: str, endpoint: str, **kwargs, ) -> str: - """Builds a URL string, given access points and credentials""" + """Builds a URL string, given access points and credentials + + Args: + endpoint (str): The base endpoint of the URL + **kwargs: Additional key-value pairs to be included as query parameters + + Returns: + str: The complete URL string with query parameters + """ - req = PreparedRequest() - req.prepare_url(urljoin(dataverse_url, endpoint), kwargs) + if not isinstance(endpoint, str): + raise TypeError("Endpoint must be a string") - assert req.url is not None, f"Could not build URL for '{dataverse_url}'" + assert all(isinstance(v, str) for v in kwargs.keys()), "All keys must be strings" - return req.url + queries = "&".join([f"{k}={str(v)}" for k, v in kwargs.items()]) + + if kwargs == {}: + return endpoint + + return f"{endpoint}?{queries}" def retrieve_dataset_files( @@ -39,17 +57,116 @@ def retrieve_dataset_files( HTTPError: If the request to the Dataverse repository fails. """ - DATASET_ENDPOINT = "/api/datasets/:persistentId/?persistentId={0}" + DATASET_ENDPOINT = f"/api/datasets/:persistentId/?persistentId={persistent_id}" response = requests.get( - urljoin(dataverse_url, DATASET_ENDPOINT.format(persistent_id)), + urljoin(dataverse_url, DATASET_ENDPOINT), headers={"X-Dataverse-key": api_token}, ) - if response.status_code != 200: - raise requests.HTTPError( - f"Could not download dataset '{persistent_id}' at '{dataverse_url}' \ - \n\n{json.dumps(response.json(), indent=2)}" - ) # type: ignore + response.raise_for_status() + + return response.json()["data"]["latestVersion"]["files"] + + +def add_directory( + directory: str, + ignore: List[str] = [r"^\."], + directory_label: str = "", +): + """ + Recursively adds all files in the specified directory to a list of File objects. + + Args: + directory (str): The directory path. + ignore (List[str], optional): A list of regular expressions to ignore certain files or directories. Defaults to [r"^\."]. + directory_label (str, optional): The label to be added to the directory path of each file. Defaults to "". + + Returns: + List[File]: A list of File objects representing the files in the directory. + """ + files = [] + + # Part of the path to remove from the directory + for file in pathlib.Path(directory).rglob("*"): + if not file.is_file(): + continue + if part_is_ignored(str(file.name), ignore): + continue + if any(part_is_ignored(part, ignore) for part in list(file.parts)): + continue + + directoryLabel = _truncate_path( + file.parent, + pathlib.Path(directory), + ) + + files.append( + File( + filepath=str(file), + directoryLabel=os.path.join( + directory_label, + directoryLabel, + ), + ) + ) + + return files + + +def _truncate_path(path: pathlib.Path, to_remove: pathlib.Path): + """ + Truncate a path by removing a substring from the beginning. + + Args: + path (str): The path to truncate. + to_remove (str): The substring to remove from the beginning of the path. + + Returns: + str: The truncated path. + """ + + parts = path.parts[len(to_remove.parts) :] + + if len(parts) 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+ +[tool.pytest.ini_options] +addopts = ["-v", "--cov=dvuploader"] +asyncio_mode = "auto" \ No newline at end of file diff --git a/static/demo.gif b/static/demo.gif index 8058fbb..b266341 100644 Binary files a/static/demo.gif and b/static/demo.gif differ diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..376bac9 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,69 @@ +import os +import pytest +import requests + + +@pytest.fixture +def credentials(): + """Returns the credentials for the Dataverse server.""" + BASE_URL = os.environ.get("BASE_URL") + API_TOKEN = os.environ.get("API_TOKEN") + + assert BASE_URL, "BASE_URL environment variable must be set" + assert API_TOKEN, "API_TOKEN environment variable must be set" + + return BASE_URL, API_TOKEN + + +def create_dataset( + parent: str, + server_url: str, + api_token: str, +): + """ + Creates a dataset in a Dataverse. + + Args: + parent (str): The parent Dataverse identifier. + server_url (str): The URL of the Dataverse server. + api_token (str): The API token for authentication. + + Returns: + str: The persistent identifier of the created dataset. + """ + if server_url.endswith("/"): + server_url = server_url[:-1] + + url = f"{server_url}/api/dataverses/{parent}/datasets" + response = requests.post( + url=url, + headers={"X-Dataverse-key": api_token}, + data=open("./tests/fixtures/create_dataset.json", "rb"), + ) + + response.raise_for_status() + + return response.json()["data"]["persistentId"] + + +def create_mock_file( + directory: str, + name: str, + size: int = 100, +): + """Create a file with the specified size in megabytes. + + Args: + directory (str): The directory where the file will be created. + name (str): The name of the file. + size (int, optional): Size of the file in megabytes. Defaults to 100. + """ + + path = os.path.join(directory, name) + size = size * 1024 * 1024 + + with open(path, "wb") as f: + f.seek(size - 1) # 1 GB + f.write(b"\0") + + return path diff --git a/tests/fixtures/add_dir_files/.hidden b/tests/fixtures/add_dir_files/.hidden new file mode 100644 index 0000000..e69de29 diff --git a/tests/fixtures/add_dir_files/__to_ignore_dir__/subfile_in_ignore.txt b/tests/fixtures/add_dir_files/__to_ignore_dir__/subfile_in_ignore.txt new file mode 100644 index 0000000..b603905 --- /dev/null +++ b/tests/fixtures/add_dir_files/__to_ignore_dir__/subfile_in_ignore.txt @@ -0,0 +1 @@ +This file is part of an ignored dir \ No newline at end of file diff --git a/tests/fixtures/add_dir_files/anotherfile.txt b/tests/fixtures/add_dir_files/anotherfile.txt new file mode 100644 index 0000000..ca79e48 --- /dev/null +++ b/tests/fixtures/add_dir_files/anotherfile.txt @@ -0,0 +1 @@ +This is another test \ No newline at end of file diff --git a/tests/fixtures/add_dir_files/somefile.txt b/tests/fixtures/add_dir_files/somefile.txt new file mode 100644 index 0000000..793aa68 --- /dev/null +++ b/tests/fixtures/add_dir_files/somefile.txt @@ -0,0 +1 @@ +This is a test \ No newline at end of file diff --git a/tests/fixtures/add_dir_files/subdir/subfile.txt b/tests/fixtures/add_dir_files/subdir/subfile.txt new file mode 100644 index 0000000..5d7cce2 --- /dev/null +++ b/tests/fixtures/add_dir_files/subdir/subfile.txt @@ -0,0 +1 @@ +This is a subfile \ No newline at end of file diff --git a/tests/fixtures/add_dir_files/to_ignore.txt b/tests/fixtures/add_dir_files/to_ignore.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/fixtures/cli_input.yaml b/tests/fixtures/cli_input.yaml new file mode 100644 index 0000000..7d1826a --- /dev/null +++ b/tests/fixtures/cli_input.yaml @@ -0,0 +1,7 @@ +persistent_id: doi:10.70122/XXX/XXXXX +dataverse_url: https://demo.dataverse.org/ +api_token: XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX +files: + - filepath: ./tests/fixtures/add_dir_files/somefile.txt + - filepath: ./tests/fixtures/add_dir_files/anotherfile.txt + directoryLabel: some/dir \ No newline at end of file diff --git a/tests/fixtures/create_dataset.json b/tests/fixtures/create_dataset.json new file mode 100644 index 0000000..1aff3ef --- /dev/null +++ b/tests/fixtures/create_dataset.json @@ -0,0 +1,76 @@ +{ + "datasetVersion": { + "metadataBlocks": { + "citation": { + "fields": [ + { + "multiple": false, + "typeClass": "primitive", + "typeName": "title", + "value": "My dataset" + }, + { + "multiple": true, + "typeClass": "controlledVocabulary", + "typeName": "subject", + "value": [ + "Other" + ] + }, + { + "multiple": true, + "typeClass": "compound", + "typeName": "author", + "value": [ + { + "authorName": { + "multiple": false, + "typeClass": "primitive", + "typeName": "authorName", + "value": "John Doe" + } + } + ] + }, + { + "multiple": true, + "typeClass": "compound", + "typeName": "datasetContact", + "value": [ + { + "datasetContactName": { + "multiple": false, + "typeClass": "primitive", + "typeName": "datasetContactName", + "value": "John Doe" + }, + "datasetContactEmail": { + "multiple": false, + "typeClass": "primitive", + "typeName": "datasetContactEmail", + "value": "john@doe.com" + } + } + ] + }, + { + "multiple": true, + "typeClass": "compound", + "typeName": "dsDescription", + "value": [ + { + "dsDescriptionValue": { + "multiple": false, + "typeClass": "primitive", + "typeName": "dsDescriptionValue", + "value": "This is a description of the dataset" + } + } + ] + } + ] + } + } + } + } + \ No newline at end of file diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/test_native_upload.py b/tests/integration/test_native_upload.py new file mode 100644 index 0000000..31b7a49 --- /dev/null +++ b/tests/integration/test_native_upload.py @@ -0,0 +1,55 @@ +import tempfile + +import pytest +from dvuploader.dvuploader import DVUploader + +from dvuploader.utils import add_directory, retrieve_dataset_files +from tests.conftest import create_dataset, create_mock_file + + +class TestNativeUpload: + def test_native_upload( + self, + credentials, + ): + BASE_URL, API_TOKEN = credentials + + with tempfile.TemporaryDirectory() as directory: + # Arrange + create_mock_file(directory, "small_file.txt", size=1) + create_mock_file(directory, "mid_file.txt", size=50) + create_mock_file(directory, "large_file.txt", size=200) + + # Add all files in the directory + files = add_directory(directory=directory) + + # Create Dataset + pid = create_dataset( + parent="Root", + server_url=BASE_URL, + api_token=API_TOKEN, + ) + + # Act + uploader = DVUploader(files=files) + uploader.upload( + persistent_id=pid, + api_token=API_TOKEN, + dataverse_url=BASE_URL, + n_parallel_uploads=1, + ) + + # Assert + expected_files = [ + "small_file.txt", + "mid_file.txt", + "large_file.txt", + ] + files = retrieve_dataset_files( + dataverse_url=BASE_URL, + persistent_id=pid, + api_token=API_TOKEN, + ) + + assert len(files) == 3 + assert sorted([file["label"] for file in files]) == sorted(expected_files) diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/test_cli.py b/tests/unit/test_cli.py new file mode 100644 index 0000000..7888288 --- /dev/null +++ b/tests/unit/test_cli.py @@ -0,0 +1,91 @@ +import tempfile +from typer.testing import CliRunner +import yaml +from dvuploader.cli import _parse_yaml_config, app +from tests.conftest import create_dataset + +runner = CliRunner() + + +class TestParseYAMLConfig: + def test_full_input(self): + # Assert + fpath = "tests/fixtures/cli_input.yaml" + + # Act + cli_input = _parse_yaml_config(fpath) + [file.extract_filename_hash_file() for file in cli_input.files] + + # Assert + expected_files = [ + ("", "somefile.txt"), + ("some/dir", "anotherfile.txt"), + ] + + assert cli_input.api_token == "XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX" + assert cli_input.dataverse_url == "https://demo.dataverse.org/" + assert cli_input.persistent_id == "doi:10.70122/XXX/XXXXX" + + assert len(cli_input.files) == 2 + assert sorted( + [(file.directoryLabel, file.fileName) for file in cli_input.files] + ) == sorted(expected_files) + + +class TestCLIMain: + def test_kwarg_arg_input(self, credentials): + # Arrange + BASE_URL, API_TOKEN = credentials + pid = create_dataset( + parent="Root", + server_url=BASE_URL, + api_token=API_TOKEN, + ) + + # Act + result = runner.invoke( + app, + [ + "./tests/fixtures/add_dir_files/somefile.txt", + "--pid", + pid, + "--api-token", + API_TOKEN, + "--dataverse-url", + BASE_URL, + ], + ) + assert result.exit_code == 0 + + def test_yaml_input(self, credentials): + # Arrange + BASE_URL, API_TOKEN = credentials + pid = create_dataset( + parent="Root", + server_url=BASE_URL, + api_token=API_TOKEN, + ) + + with tempfile.NamedTemporaryFile(suffix=".yaml") as file: + upload_params = { + "api_token": API_TOKEN, + "dataverse_url": BASE_URL, + "persistent_id": pid, + "files": [ + { + "filepath": "./tests/fixtures/add_dir_files/somefile.txt", + "directoryLabel": "", + } + ], + } + + with open(file.name, "w") as f: + yaml.dump(upload_params, f) + + # Act + result = runner.invoke(app, ["--config-path", file.name]) + assert result.exit_code == 0 + + def test_no_input(self): + result = runner.invoke(app, []) + assert result.exit_code == 2 diff --git a/tests/unit/test_directupload.py b/tests/unit/test_directupload.py new file mode 100644 index 0000000..658f290 --- /dev/null +++ b/tests/unit/test_directupload.py @@ -0,0 +1,86 @@ +from urllib.parse import urljoin +import aiohttp +import pytest +from dvuploader.directupload import ( + _add_file_to_ds, + UPLOAD_ENDPOINT, + REPLACE_ENDPOINT, + _validate_ticket_response, +) + +from dvuploader.file import File + + +class Test_AddFileToDs: + # Should successfully add a file to a Dataverse dataset with a valid file path + @pytest.mark.asyncio + async def test_successfully_add_file_with_valid_filepath(self, mocker): + # Mock the session.post method to return a response with status code 200 + mock_post = mocker.patch("aiohttp.ClientSession.post") + mock_post.return_value.__aenter__.return_value.status = 200 + + # Initialize the necessary variables + session = aiohttp.ClientSession() + dataverse_url = "https://example.com" + pid = "persistent_id" + fpath = "tests/fixtures/add_dir_files/somefile.txt" + file = File(filepath=fpath) + + # Invoke the function + result = await _add_file_to_ds(session, dataverse_url, pid, file) + + # Assert that the response status is 200 and the result is True + assert mock_post.called_with( + urljoin(dataverse_url, UPLOAD_ENDPOINT + pid), data=mocker.ANY + ) + assert result is True + + @pytest.mark.asyncio + async def test_successfully_replace_file_with_valid_filepath(self, mocker): + # Mock the session.post method to return a response with status code 200 + mock_post = mocker.patch("aiohttp.ClientSession.post") + mock_post.return_value.__aenter__.return_value.status = 200 + + # Initialize the necessary variables + session = aiohttp.ClientSession() + dataverse_url = "https://example.com" + pid = "persistent_id" + fpath = "tests/fixtures/add_dir_files/somefile.txt" + file = File(filepath=fpath, file_id="0") + + # Invoke the function + result = await _add_file_to_ds(session, dataverse_url, pid, file) + + # Assert that the response status is 200 and the result is True + assert mock_post.called_with( + urljoin(dataverse_url, REPLACE_ENDPOINT.format(FILE_ID=file.file_id)), + data=mocker.ANY, + ) + assert result is True + + +class Test_ValidateTicketResponse: + # Function does not raise any exceptions when all necessary fields are present + def test_no_exceptions_when_fields_present(self): + response = { + "abort": "abort_url", + "complete": "complete_url", + "partSize": 100, + "urls": {"url1": "url1", "url2": "url2"}, + "storageIdentifier": "storage_id", + } + try: + _validate_ticket_response(response) + except AssertionError: + pytest.fail("AssertionError raised when all necessary fields are present") + + # Function raises AssertionError when 'abort' field is missing + def test_raises_assertion_error_when_abort_field_missing(self): + response = { + "complete": "complete_url", + "partSize": 100, + "urls": {"url1": "url1", "url2": "url2"}, + "storageIdentifier": "storage_id", + } + with pytest.raises(AssertionError): + _validate_ticket_response(response) diff --git a/tests/unit/test_file.py b/tests/unit/test_file.py new file mode 100644 index 0000000..695c506 --- /dev/null +++ b/tests/unit/test_file.py @@ -0,0 +1,45 @@ +import pytest +from dvuploader.file import File + + +class TestFile: + def test_read_file(self): + # Arrange + fpath = "tests/fixtures/add_dir_files/somefile.txt" + + # Act + file = File( + filepath=fpath, + directoryLabel="", + ) + + file.extract_filename_hash_file() + + # Assert + assert file.fileName == "somefile.txt" + + def test_read_non_existent_file(self): + # Arrange + fpath = "tests/fixtures/add_dir_files/non_existent.txt" + + # Act + with pytest.raises(FileNotFoundError): + file = File( + filepath=fpath, + directoryLabel="", + ) + + file.extract_filename_hash_file() + + def test_read_non_file(self): + # Arrange + fpath = "tests/fixtures/add_dir_files" + + # Act + with pytest.raises(IsADirectoryError): + file = File( + filepath=fpath, + directoryLabel="", + ) + + file.extract_filename_hash_file() diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py new file mode 100644 index 0000000..81dbe32 --- /dev/null +++ b/tests/unit/test_utils.py @@ -0,0 +1,219 @@ +import requests +import pytest + +from rich.progress import Progress +from dvuploader.utils import ( + add_directory, + build_url, + retrieve_dataset_files, + setup_pbar, +) + + +class TestAddDirectory: + def test_all_files_added_except_hidden(self): + # Arrange + directory = "tests/fixtures/add_dir_files" + + # Act + files = add_directory(directory) + [file.extract_filename_hash_file() for file in files] + + # Assert + expected_files = [ + ("", "somefile.txt"), + ("", "anotherfile.txt"), + ("", "to_ignore.txt"), + ("subdir", "subfile.txt"), + ("__to_ignore_dir__", "subfile_in_ignore.txt"), + ] + + assert len(files) == len(expected_files), "Wrong number of files" + + for directory_label, filename in expected_files: + assert any( + file.fileName == filename for file in files + ), f"File {filename} not found in files" + + file = next(filter(lambda file: file.fileName == filename, files)) + assert ( + file.directoryLabel == directory_label + ), f"File {filename} has wrong directory label" + + def test_all_files_added_except_hidden_and_dunder(self): + # Arrange + directory = "tests/fixtures/add_dir_files" + + # Act + files = add_directory(directory, ignore=[r"^\.", "__.*__"]) + [file.extract_filename_hash_file() for file in files] + + # Assert + expected_files = [ + ("", "somefile.txt"), + ("", "anotherfile.txt"), + ("", "to_ignore.txt"), + ("subdir", "subfile.txt"), + ] + + assert len(files) == len(expected_files), "Wrong number of files" + + for directory_label, filename in expected_files: + assert any( + file.fileName == filename for file in files + ), f"File {filename} not found in files" + + file = next(filter(lambda file: file.fileName == filename, files)) + assert ( + file.directoryLabel == directory_label + ), f"File {filename} has wrong directory label" + + +class TestBuildUrl: + # Returns the endpoint if no query parameters are provided + def test_returns_endpoint_if_no_query_parameters(self): + # Arrange + endpoint = "https://example.com/api" + + # Act + result = build_url(endpoint) + + # Assert + assert result == endpoint + + # Returns the complete URL string with query parameters if valid query parameters are provided + def test_returns_complete_URL_with_query_parameters(self): + # Arrange + endpoint = "https://example.com/api" + query_params = {"param1": "value1", "param2": "value2"} + + # Act + result = build_url(endpoint, **query_params) + + # Assert + assert result == "https://example.com/api?param1=value1¶m2=value2" + + # Handles query parameters with integer values + def test_handles_query_parameters_with_integer_values(self): + # Arrange + endpoint = "https://example.com/api" + query_params = {"param1": 123, "param2": 456} + + # Act + result = build_url(endpoint, **query_params) + + # Assert + assert result == "https://example.com/api?param1=123¶m2=456" + + # Returns the endpoint without a question mark if an empty dictionary is provided as query parameters + def test_returns_endpoint_without_question_mark_if_empty_dictionary(self): + # Arrange + endpoint = "https://example.com/api" + query_params = {} + + # Act + result = build_url(endpoint, **query_params) + + # Assert + assert result == "https://example.com/api" + + # Raises a TypeError if the endpoint is not a string + def test_raises_TypeError_if_endpoint_not_string(self): + # Arrange + endpoint = 123 + query_params = {"param1": "value1", "param2": "value2"} + + # Act and Assert + with pytest.raises(TypeError): + build_url(endpoint, **query_params) # type: ignore + + # Raises a TypeError if any of the query parameter keys are not strings + def test_raises_TypeError_if_query_parameter_keys_not_strings(self): + # Arrange + endpoint = "https://example.com/api" + query_params = {123: "value1", "param2": "value2"} + + # Act and Assert + with pytest.raises(TypeError): + build_url(endpoint, **query_params) # type: ignore + + +class TestRetrieveDatasetFiles: + # Retrieve files of a dataset with valid dataverse_url, persistent_id, and api_token. + def test_valid_parameters_with_dotted_dict(self, mocker): + # Mock the requests.get function + mocker.patch("requests.get") + + # Set up mock response + mock_response = mocker.Mock() + mock_response.json.return_value = { + "data": { + "latestVersion": { + "files": [ + {"filename": "file1.txt"}, + {"filename": "file2.txt"}, + ] + } + } + } + requests.get.return_value = mock_response + + # Call the function under test + result = retrieve_dataset_files("http://example.com", "12345", "token") + + # Assert the result + assert result == [ + {"filename": "file1.txt"}, + {"filename": "file2.txt"}, + ] + + # Assert that requests.get was called with the correct parameters + requests.get.assert_called_once_with( + "http://example.com/api/datasets/:persistentId/?persistentId=12345", + headers={"X-Dataverse-key": "token"}, + ) + + # Return a list of files in the dataset. + def test_return_files_list(self, mocker): + # Mock the requests.get function + mocker.patch("requests.get") + + # Set up mock response + mock_response = mocker.Mock() + mock_response.json.return_value = { + "data": { + "latestVersion": { + "files": [{"filename": "file1.txt"}, {"filename": "file2.txt"}] + } + } + } + requests.get.return_value = mock_response + + # Call the function under test + result = retrieve_dataset_files("http://example.com", "12345", "token") + + # Assert the result + assert result == [{"filename": "file1.txt"}, {"filename": "file2.txt"}] + + # Raise HTTPError if the request to the Dataverse repository fails. + def test_raise_http_error(self, mocker): + # Mock the requests.get function to raise an exception + mocker.patch("requests.get", side_effect=requests.exceptions.HTTPError) + + # Call the function under test and assert that it raises an HTTPError + with pytest.raises(requests.exceptions.HTTPError): + retrieve_dataset_files("http://example.com", "12345", "token") + + +class TestSetupPbar: + def test_returns_progress_bar_object(self): + # Arrange + fpath = "tests/fixtures/add_dir_files/somefile.txt" + progress = Progress() + + # Act + result = setup_pbar(fpath=fpath, progress=progress) + + # Assert + assert isinstance(result, int) + assert result == 0