dvuploader 0.3.2

Python library for uploading (bulk) data to Dataverse

Dataverse Uploader

Python equivalent to the DVUploader written in Java. Complements other libraries written in Python and facilitates the upload of files to a Dataverse instance via Direct Upload.

Features

• Parallel direct upload to a Dataverse backend storage
• Files are streamed directly instead of being buffered in memory
• Supports multipart uploads and chunks data accordingly

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https://github.com/gdcc/python-dvuploader/assets/30547301/671131b1-d188-4433-9f77-9ec0ed2af36e

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Getting started

To get started with DVUploader, you can install it via PyPI

python3 -m pip install dvuploader

or by source

git clone https://github.com/gdcc/python-dvuploader.git
cd python-dvuploader
python3 -m pip install .

Quickstart

Programmatic usage

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.

import dvuploader as dv


# Add file individually
files = [
    dv.File(filepath="./small.txt"),
    dv.File(filepath="./tabular.csv", tab_ingest=False),
    dv.File(directory_label="some/dir", filepath="./medium.txt"),
    dv.File(directory_label="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 = 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
)

Command Line Interface

DVUploader ships with a CLI ready to use outside scripts. In order to upload files to a Dataverse instance, simply provide the files of interest, persistent identifier and credentials.

Using arguments

dvuploader my_file.txt my_other_file.txt \
           --pid doi:10.70122/XXX/XXXXX \
           --api-token XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX \
           --dataverse-url https://demo.dataverse.org/ \

Using a config file

Alternatively, you can also supply a config file that contains all necessary information for the uploader. The config file is a JSON/YAML file that contains the following keys:

• persistent_id: Persistent identifier of the dataset to upload to.
• dataverse_url: URL of the Dataverse instance.
• api_token: API token of the Dataverse instance.
• files: List of files to upload. Each file is a dictionary with the following keys:
  • filepath: Path to the file to upload.
  • directory_label: Optional directory label to upload the file to.
  • description: Optional description of the file.
  • mimetype: Mimetype of the file.
  • categories: Optional list of categories to assign to the file.
  • restrict: Boolean to indicate that this is a restricted file. Defaults to False.
  • tabIngest: Boolean to indicate that the file should be ingested as a tab-separated file. Defaults to True.

In the following example, we upload three files to a Dataverse instance. The first file is uploaded to the root directory of the dataset, while the other two files are uploaded to the directory some/dir.

# config.yml
persistent_id: doi:10.70122/XXX/XXXXX
dataverse_url: https://demo.dataverse.org/
api_token: XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
files:
    - filepath: ./small.txt
    - filepath: ./medium.txt
      directory_label: some/dir
    - filepath: ./big.txt
      directory_label: some/dir

The config file can then be used as follows:

dvuploader --config-path config.yml

Environment variables

DVUploader provides several environment variables that allow you to control retry logic and upload size limits. These can be set either through environment variables directly or programmatically using the config function.

Available Environment Variables:

• DVUPLOADER_MAX_RETRIES: Maximum number of retry attempts (default: 15)
• DVUPLOADER_MAX_RETRY_TIME: Maximum wait time between retries in seconds (default: 240)
• DVUPLOADER_MIN_RETRY_TIME: Minimum wait time between retries in seconds (default: 1)
• DVUPLOADER_RETRY_MULTIPLIER: Multiplier for exponential backoff (default: 0.1)
• DVUPLOADER_MAX_PKG_SIZE: Maximum package size in bytes (default: 2GB)
• DVUPLOADER_LOCK_WAIT_TIME: Time to wait between checks for dataset lock (default: 10 seconds)
• DVUPLOADER_LOCK_TIMEOUT: Timeout for dataset lock check in seconds (default: 300 seconds)

Setting via environment:

export DVUPLOADER_MAX_RETRIES=20
export DVUPLOADER_MAX_RETRY_TIME=300
export DVUPLOADER_MIN_RETRY_TIME=2
export DVUPLOADER_RETRY_MULTIPLIER=0.2
export DVUPLOADER_MAX_PKG_SIZE=3221225472  # 3GB
export DVUPLOADER_LOCK_WAIT_TIME=5
export DVUPLOADER_LOCK_TIMEOUT=300

Setting programmatically:

import dvuploader as dv

# Configure the uploader settings
dv.config(
    max_retries=20,
    max_retry_time=300,
    min_retry_time=2,
    retry_multiplier=0.2,
    max_package_size=3 * 1024**3  # 3GB
    lock_wait_time=5,
    lock_timeout=300,
)

# Continue with your upload as normal
files = [dv.File(filepath="./data.csv")]
dvuploader = dv.DVUploader(files=files)
# ... rest of your upload code

The retry logic uses exponential backoff which ensures that subsequent retries will be longer, but won't exceed exceed max_retry_time. This is particularly useful when dealing with native uploads that may be subject to intermediate locks on the Dataverse side.

Troubleshooting

500 error and OptimisticLockException

When uploading multiple tabular files, you might encounter a 500 error and a OptimisticLockException upon the file registration step. This has been discussed in https://github.com/IQSS/dataverse/issues/11265 and is due to the fact that intermediate locks prevent the file registration step from completing.

A workaround is to set the tabIngest flag to False for all files that are to be uploaded. This will cause the files not be ingested but will avoid the intermediate locks.

dv.File(filepath="tab_file.csv", tab_ingest=False)

Please be aware that your tabular files will not be ingested as such but will be uploaded in their native format. You can utilize pyDataverse to ingest the files after they have been uploaded.

Development

To install the development dependencies, run the following command:

pip install poetry
poetry install --with test

Running tests locally

In order to test the DVUploader, you need to have a Dataverse instance running. You can start a local Dataverse instance by following these steps:

1. Start the Dataverse instance

docker compose \
    -f ./docker/docker-compose-base.yml \
    --env-file local-test.env \
    up -d

2. Set up the environment variables

export BASE_URL=http://localhost:8080
export API_TOKEN=XXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
export DVUPLOADER_TESTING=true

3. Run the test(s) with pytest

Run all tests:

poetry run pytest

Run a specific test:

poetry run pytest -k test_native_upload_with_large_file

Run all non-expensive tests:

poetry run pytest -m "not expensive"

Linting

This repository uses ruff to lint the code and codespell to check for spelling mistakes. You can run the linters with the following command:

python -m ruff check
python -m codespell --check-filenames