Skip to content
Python package for interacting with NDA web services. Used to validate, submit, and download data to and from NDA.
Python
Branch: master
Clone or download
David Obenshain
David Obenshain Merge pull request #58 in WSCLIENT/nda-tools-python from release/Down…
…load_Manager_Refresh_2 to master

* commit 'e73ffa03b8f94a4c71ae93ed388432e5cf1e3d7a': (38 commits)
  Removed incorrect change from changelog.
  Updated version for prod deploy to PyPI.
  Updated changelog.
  Merge pull request #56 in WSCLIENT/nda-tools-python from feature/NDA-5359-add-integration-tests to develop
  Merge pull request #54 in WSCLIENT/nda-tools-python from feature/NDA-5324-remove-duplicate-credential-handling to develop
  Using @patch instead of instead of mock.patch function. Removed copy of parse_local_files and replace with call to actual function.
  Increment Test PyPI version.
  Added missing parameter for skip local file check.
  Removed unit test classes for other modules. Added filepath function testing for Utils.
  NDA-5154 * Added try to catch exception for file not existing when attempting to locate the file in multiple directories. * Added progress on matching files to directories to debug log.
  NDA-5154 - Updating version for Test PyPI
  NDA-5154 - Addressing bug where parse_local_files will use local instance of Configuration class, which does not have the skip_local_file_check that is set in vtcmd.py and instance of Submission.py on resuming a submission.
  Added tests for configuration.
  Added missing Configuration variable for aws_access_key.
  Init test files
  Moved s3 resource into S3Auth.
  Corrected case where file_size is less than 9999 which results in invalid chunk size of 0.
  Moved s3 client creation to S3Auth class.
  Renamed Authorization to S3Authentication. Class handles s3 client session creation. Multipart sessions are still handled by Submission.
  Revert to getpass instead of input.
  ...
Latest commit 50f9cb1 Oct 31, 2019

README.md

nda-tools

In order to submit data to the National Institute of Mental Health Data Archives (NDA), users must validate their data to ensure it complies with the required format. This is done using the NDA validation tool. Additionally, users can package and download data from NDA as well. If associated data is downloaded from S3, temporary federated AWS tokens are required. A python package and command line clients have been developed to allow users to programmatically validate, package, submit, and/or download data. The package and clients interact with the Validation, Submission Package, and Data Submission web services.

Getting Started

Installing Python

You will need a python distribution to use the client. Run the following from a terminal/command-prompt to determine if python is installed:

python --version

If python is installed you should see output indicating the version of Python that is installed.

If python is not available, you will need to download and install it from Python.org. Please also consult the documentation: Python2, Python3

Notes:

  • You may need administrative rights, root, or sudo privileges to install a python distribution.
  • Python may be installed but not available on the system path, please consult python installation and usage documentation

Installing pip

Since Python 2.7.9 pip is released with python, you can check the version like this:

pip --version

If pip is installed you should see version information, if not you should install pip. First download it from https://bootstrap.pypa.io/get-pip.py, then run the following to install for your user.

python get-pip.py --user

Notes:

  • Pip may be installed but not available on the system path, please consult python installation and usage documentation

Installing the client

These instructions will help you get setup to run the client.

Simply enter the following command into your terminal or command prompt to install nda-tools:

pip install nda-tools

Thi will automatically install the nda-tools package, including the command line scripts and required packages.

Credentials

While not needed for just validation, if you would like to create a package and submit your data to the NDA, you must have an active account with us. This can be requested from the NDA website. You can read more about what is needed for contributing data into NDA here.

You are now ready to run the client.

Please note that if you encounter SSL errors when running the client, you may need to re-run pip installation of requests, with pip install requests[secure] which will install some additional packages with more support for SSL connections.

Using the Client

To view options available for the validation tool python client, enter the following command:

vtcmd -h

or to view options available for the download python client, enter:

downloadcmd -h

Configuring the Client

  • If your command-line inputs have special characters (i.e., passwords) or spaces (i.e, in directory/filenames), you may need to enclose them in quotations.
    • If you are using windows, use double-quotes: ""
    • If you are using Mac OSX or Linux, use single-quotes: ''
  • Upon your first run, the client will prompt you to enter your username and password, which it will store in the settings file at ~/.NDATools/settings.cfg. You may go back and edit your credentials at any time.

The settings.cfg file provided with the client contains configurable options for Endpoints, Files, and User information.

Typically there will be no need to change entries in the 'Endpoints' section, however you may wish to modify the 'Files' and 'User' section with preferred locations for validation results, user login, and AWS credentials information.

  • While arguments are not positional, you should make your list of files to validate the first argument.
    • The list of files has no command-line switch so it can get interpreted as part of a preceding argument.
    • For example there is no way to differentiate whether the csv file is part of the -l argument or a second argument:
    vtcmd -l "Users/[youruser]/Documents/MultipleDataTypes" \
    "Users/[youruser]/Documents/MultipleDataTypes/Stage_Testing_BigFiles_genomics_sample03.csv" 
    

Files for Validation

It is important that you know the full path to the csv files that you will be validating. Furthermore, if your data also includes manifests and/or associated files (ie. genomics files, imaging files), you must also know the full path to these files, which should be entered as an optional command-line argument. Otherwise, the client will prompt you to enter a list of directories where any of the associated files are located. You can also list a bucket, optional prefix, and your AWS credentials if your associated files are located in AWS.

Please note: When listing the directory for associated files, include the folder up to but not including the file name listed in the csv file.

Example:

If the associated file name is Users/[youruser]/Documents/MultipleDataTypes/data/1G_file.fastq and is listed in your csv file as:

data/1G_file.fastq

then the directory you will enter is:

Users/[youruser]/Documents/MultipleDataTypes

You should not include the 'data/' folder as part of the directory name.

To start validation, you must enter a list of files (or file path if not in current directory), separated by a space:

vtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv 

If your data includes manifest files, you must enter the directories where the manifest files are found, separated by a space:

vtcmd submission_data/sample_imagingcollection01.csv  -m submission_data/Manifests

If there are associated files, enter the directories where they are found, separated by a space:

vtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -l MultipleDataTypes testdata/with_associated_files 

If the files are located somewhere other than the current working directory, then you must enter the full path to the files:

vtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -l Users/[youruser]/Downloads/SubmissionData testdata/with_associated_files

If your associated files are located in S3, then you must include the bucket name, access key, and secret key. The access and secret key can be stored in the settings.cfg file as well.

vtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -s3 my_bucket -ak XXXXXXXXXXXXXX -sk XXXXXXXXXXXXXX

Note: You can also upload associated files saved locally and in s3. Just make sure to include the directory where the local files are saved (-l path/to/local/associated/files)

To create a package, enter "-b" at the end of your command line argument. You can also enter your username, password, AWS credentials, collection ID or alternate endpoint title, and the title and description of your submission, or you can enter this information later when prompted by the client. Until all your files are validated and all associated files have been located on your local drive or in S3, the client will not begin building the submission package.

When package submission and upload is complete, you will receive an email in your inbox from NDA confirming your submission was successful.

If your file upload was disrupted, you may restart your submission from where if left off if you have the submission ID, which is provided to you when the submission is first created. To restart the submission using the client, enter the following command:

vtcmd <submissionID> -r

You can optionally include your username, password, AWS credentials, and directory list at this point as well, or enter it if/when prompted by the client.

Downloading Data

To download data, you should use the downloadcmd command. This provides several options to download your NDA packaged data or a subset of the data. All files are downloaded automatically to the ~/AWS_downloads folder, but you can change this by indicating a new directory in the command line to save files.

Please note, the maximum transfer limit of data is 5TB at one time.

All Package Data

All packaged data can be downloaded by passing the package ID:

downloadcmd <packageID> -dp

Note: it will NOT download associated files unless you created your NDA package with associated files. Steps to download associated files are below.

Downloading .txt Files

The downloadcmd command has two options for downloading data inside .txt files. If you have downloaded your NDA package, you will find meta-data .txt files, many of which represent data measures. Genomics, imaging, and other associated data will be listed in these .txt files as s3 links. If you would like to download all the s3 links in your .txt file, you can indicate so by passing the -ds flag.

downloadcmd path/to/data/structure/file/image03.txt -ds

Another option is to create your own .txt file listing any and all S3 links you would like to download from NDA. This can be a subset of the data you want, or a list of everything.

downloadcmd path/to/all/s3/txt/file/alls3.txt -t

Restart Download

Often times, your download may be interrupted. To restart a download process, enter the same command you did for the original run, but include the -r flag and the directory where all the files were being downloaded:

downloadcmd path/to/all/s3/txt/file/alls3.txt -t -r /Users/<your_user>/AWS_downloads

Further Assistance

If you have any problems with this validation tool python client, or would like to provide feedback/comments, please email us at NDAHelp@mail.nih.gov.

nda-tools

You can’t perform that action at this time.