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IMPORTANT: If you use --use-gsutil-for-s3 or GCSURI.USE_GSUTIL_FOR_S3 then you need to update your gsutil. This flag allows a direct transfer between gs:// and s3://. This requires gsutil >= 4.47. See this issue for details.

$ pip install gsutil --upgrade

Autouri

Introduction

It is a Python API for recursively localizing file URIs (e.g. gs://. s3://, http:// and local path) on any target directory URI.

Features:

  • Wraps Python APIs for cloud URIs and URLs.
    • google-cloud-storage for gs:// URIs.
    • boto3 for s3:// URIs.
    • requests for HTTP URLs http:// and https://.
  • Wraps gsutil CLI for direct transfer between gs:// and s3:// URIs.
  • Can presign a bucket URI to get a temporary public URL (e.g. for genome browsers).
  • File locking.
  • MD5 hash checking to prevent unnecessary re-downloading.
  • Localize files on a different URI type.
    • Keeping the original directory structure.
    • Recursively localize all files in CSV/TSV/JSON(value only) files.

Installation

$ pip3 install autouri

Usage

Python API example.

import autouri
from autouri import AutoURI
from autouri import AbsPath


def example():
    """Example for basic functions
    """

    u = AutoURI('gs://test-bucket/hello-world.txt')
    u.write('some text here')

    u.cp('s3://test-bucket/hello-another-world.txt')

    if u.exists:
        u.rm()

    target_s = AutoURI('s3://test-bucket/hello-another-world.txt').read()
    print(target_s)


def example_loc_method1():
    """Example for localization    (method1)
    """
    u = AutoURI('gs://test-bucket/hello-world.json')

    # call directly from AutoURI (or URIBase)
    # loc_prefix defines destination URI directory for localization
    AutoURI.localize(
        'gs://test-bucket/hello-world.json',
        recursive=True,
        loc_prefix='/home/leepc12/loc_cache_dir/')


def example_loc_method2():
    """Example for localization    (method2)
    """
    u = AutoURI('gs://test-bucket/hello-world.json')

    # initialize that class' constant first
    # loc_prefix defines destination URI directory for localization
    AbsPath.init_abspath(
        loc_prefix='/home/leepc12/loc_cache_dir/')

    # call from a specific storage class
    AbsPath.localize(
        'gs://test-bucket/hello-world.json',
        recursive=True)


example()
example_loc_method1()
example_loc_method2()

CLI: Use --help for each sub-command.

$ autouri --help
usage: autouri [-h] {metadata,cp,read,write,rm,loc,presign} ...

positional arguments:
  {metadata,cp,read,write,rm,loc,presign}
    metadata            AutoURI(src).get_metadata(): Get metadata of source.
    cp                  AutoURI(src).cp(target): Copy source to target. target
                        must be a full filename/directory. Target directory
                        must have a trailing directory separator (e.g. /)
    read                AutoURI(src).read(): Read from source.
    write               AutoURI(src).write(text): Write text on source.
    rm                  AutoURI(src).rm(): Delete source.
    loc                 type(target_dir).localize(src): Localize source on
                        target directory (class)
    presign             AutoURI(src).get_presigned_url(). For cloud-based URIs
                        only.

optional arguments:
  -h, --help            show this help message and exit

Requirements

  • Python >= 3.6

    • Packages: requests, dateparser and filelock 
      $ pip3 install requests dateparser filelock

  • Install Google Cloud SDK to get CLIs (gcloud and gsutil).

  • Install google-cloud-storage Python API.

    $ pip3 install google-cloud-storage

  • Install boto3 Python API and AWS CLI.

    $ pip3 install boto3 awscli

Authentication

  • GCS: Use gcloud CLI.

    • Using end-user credentials: You will be asked to enter credentials of your Google account.

      $ gcloud auth application-default login --no-launch-browser

    • Using service account credentials: If you use a service account and a JSON key file associated with it.

      $ gcloud auth activate-service-account --key-file=[YOUR_JSON_KEY.json]
$ GOOGLE_APPLICATION_CREDENTIALS="PATH/FOR/YOUR_JSON_KEY.json"

      Or import and call add_google_app_creds_to_env().

      import autouri
from autouri.gcsuri import add_google_app_creds_to_env

add_google_app_creds_to_env('YOUR_JSON_KEY.json')

    Then set your default project.

    $ gcloud config set project [YOUR_GCP_PROJECT_ID]

  • S3: Use aws CLI. You will be asked to enter credentials of your AWS account.

    $ aws configure

  • URL: Use ~/.netrc file to get access to private URLs. Example .netrc file. You can define credential per site.

    machine www.encodeproject.org
login XXXXXXXX
password abcdefghijklmnop

Using gsutil for direct trasnfer between GCS and S3

Autouri can use gsutil CLI for a direct file transfer between S3 and GCS. Define --use-gsutil-for-s3 in command line arguments or use GCSURI.init_gcsuri(use_gsutil_for_s3=True) in Python. Otherwise, file transfer between GCS and S3 will be streamed through your local machine.

gsutil will take AWS credentials from ~/.aws/credentials file, which is already generated in Authentication.

GCS/S3 bucket configuration

Autouri best works with default bucket configuration for both cloud storages.

GCS (gs://bucket-name)

  • Bucket versioning must be turned off.
    • Check with gsutil versioning get gs://[YOUR_BUCKET_NAME]

S3 (s3://bucket-name)

  • Object versioning must be turned off.