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        "description": "# nda-tools\n\nIn order to submit data to the National Institute of Mental Health Data Archives (NDA), users must\nvalidate their data to ensure it complies with the required format. This is done using the NDA\nvalidation tool. Additionally, users can package and download data from NDA as well. If associated data is downloaded \nfrom S3, temporary federated AWS tokens are required. A python package and command line clients have been developed to \nallow users to programmatically validate, package, submit, and/or download data. The package and clients interact with \nthe  [Validation](https://nda.nih.gov/api/validation/docs/swagger-ui.html), \n[Submission Package](https://nda.nih.gov/api/submission-package/docs/swagger-ui.html#!), and\n[Data Submission](http://nda.nih.gov/api/submission/docs/swagger-ui.html#!) web services.\n\n\n## Getting Started\n\n### Installing Python\nYou will need a python distribution to use the client. Run the following from a terminal/command-prompt to determine if python is installed:\n```\npython --version\n```\nIf python is installed you should see output indicating the version of Python that is installed.\n\nIf python is not available, you will need to download and install it from [Python.org](https://www.python.org/). Please also consult the documentation: [Python2](https://docs.python.org/2/using/), [Python3](https://docs.python.org/3/using/)\n\n**Notes:** \n- You may need administrative rights, root, or sudo privileges to install a python distribution.\n- Python may be installed but not available on the system path, please consult python installation and usage documentation\n\n### Installing pip\nSince Python 2.7.9 pip is released with python, you can check the version like this:\n```\npip --version\n```\nIf 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](https://bootstrap.pypa.io/get-pip.py), then run the following to install for your user.\n```\npython get-pip.py --user\n```\n\n**Notes:** \n- Pip may be installed but not available on the system path, please consult python installation and usage documentation\n\n### Installing the client\n\nThese instructions will help you get setup to run the client. \n\nSimply enter the following command into your terminal or command prompt to install nda-tools:\n\n```pip install nda-tools```\n\nThi will automatically install the nda-tools package, including the command line scripts and required packages. \n\n\n### Credentials\nWhile not needed for just validation, if you would like to create a package and submit your data to the NDA, you must \nhave an active account with us. This can be requested from the [NDA website](https://nda.nih.gov/user/create_account.html).\nYou can read more about what is needed for contributing data into NDA [here](https://nda.nih.gov/contribute.html). \n\n##### You are now ready to run the client.\n\nPlease note that if you encounter SSL errors when running the client, you may need to re-run pip installation of requests, with\n`pip install requests[secure]` which will install some additional packages with more support for SSL connections.\n\n## Using the Client\nTo view options available for the validation tool python client, enter the following command:\n\n`vtcmd -h`\n\nor to view options available for the download python client, enter:\n\n`downloadcmd -h`\n\n### Configuring the Client\n- 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.\n  - If you are using windows, use double-quotes: \"\"\n  - If you are using Mac OSX or Linux, use single-quotes: ''\n- Upon your first run, the client will prompt you to enter your username and password, which it will store in the settings file\nat ~/.NDATools/settings.cfg. You may go back and edit your credentials at any time.\n\nThe settings.cfg file provided with the client contains configurable options for Endpoints, Files, and User information.\n\nTypically 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.\n\n- While arguments are not positional, you should make your list of files to validate the first argument.\n  - The list of files has no command-line switch so it can get interpreted as part of a preceding argument.\n  - For example there is no way to differentiate whether the csv file is part of the -l argument or a second argument: \n  ```\n  vtcmd -l \"Users/[youruser]/Documents/MultipleDataTypes\" \\\n  \"Users/[youruser]/Documents/MultipleDataTypes/Stage_Testing_BigFiles_genomics_sample03.csv\" \n  ```  \n\n\n### Files for Validation\nIt is important that you know the full path to the csv files that you will be validating. Furthermore, if your data\nalso includes manifests and/or associated files (ie. genomics files, imaging files), you must also know the full path to these files,\nwhich should be entered as an optional command-line argument. Otherwise, the client will prompt you to enter a list of \ndirectories where any of the associated files are located. You can also list a bucket, optional prefix, and your AWS \ncredentials if your associated files are located in AWS.\n\n**Please note:** When listing the directory for associated files, include the folder **up to but not including**\nthe file name listed in the csv file.\n\n##### Example:\nIf the associated file name is Users/[youruser]/Documents/MultipleDataTypes/data/1G_file.fastq and is listed in your csv file as:\n\n>data/1G_file.fastq\n\nthen the directory you will enter is:\n >Users/[youruser]/Documents/MultipleDataTypes \n\nYou should **not** include the 'data/' folder as part of the directory name.\n\nTo start validation, you must enter a list of files (or file path if not in current directory), separated by a space:\n\n```\nvtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv \n```\nIf your data includes manifest files, you must enter the directories where the manifest files are found, separated by a space:\n\n```\nvtcmd submission_data/sample_imagingcollection01.csv  -m submission_data/Manifests\n```\n\n\nIf there are associated files, enter the directories where they are found, separated by a space:\n\n```\nvtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -l MultipleDataTypes testdata/with_associated_files \n```\n\nIf the files are located somewhere other than the current working directory, then you must enter the full\npath to the files:\n\n```\nvtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -l Users/[youruser]/Downloads/SubmissionData testdata/with_associated_files\n```\n\nIf your associated files are located in S3, then you must include the bucket name, access key, and secret key. \nThe access and secret key can be stored in the settings.cfg file as well.\n\n```\nvtcmd MultipleDataTypes/genomics_sample03.csv testdata/with_associated_files/genomics_sample03.csv -s3 my_bucket -ak XXXXXXXXXXXXXX -sk XXXXXXXXXXXXXX\n```\n\nNote: You can also upload associated files saved locally and in s3. Just make sure to include the directory where the \nlocal files are saved (-l path/to/local/associated/files)\n\nTo create a package, enter \"-b\" at the end of your command line argument. You can also enter your username, password, \nAWS credentials, collection ID or alternate endpoint title, and the title and description of your submission, or you can enter this\ninformation later when prompted by the client. Until all your files are validated and all associated files have been\nlocated on your local drive or in S3, the client will not begin building the submission package.\n\nWhen package submission and upload is complete, you will receive an email in your inbox from NDA confirming your \nsubmission was successful. \n\nIf your file upload was disrupted, you may restart your submission from where if left off if you have the submission ID,\nwhich is provided to you when the submission is first created. To restart the submission using the client, enter the \nfollowing command:\n\n```\nvtcmd <submissionID> -r\n```\n\nYou can optionally include your username, password, AWS credentials, and directory list at this point as well, or enter it if/when prompted\nby the client.\n\n## Downloading Data\n\nTo download data, you should use the downloadcmd command. This provides several options to download your NDA packaged data \nor a subset of the data. All files are downloaded automatically to the ~/AWS_downloads folder, but you can change this by\nindicating a new directory in the command line to save files. \n\nPlease note, the maximum transfer limit of data is 5TB at one time. \n\n#### All Package Data\nAll packaged data can be downloaded by passing the package ID:\n\n`downloadcmd <packageID> -dp`\n\nNote: it will NOT download associated files *unless you created your NDA package with associated files*. Steps to download associated \nfiles are below.\n\n#### Downloading .txt Files\nThe downloadcmd command has two options for downloading data inside .txt files. If you have downloaded your NDA package, you will find\nmeta-data .txt files, many of which represent data measures. Genomics, imaging, and other associated data will be listed in these .txt files\nas 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.\n\n`downloadcmd path/to/data/structure/file/image03.txt -ds`\n\nAnother option is to create your own .txt file listing any and all S3 links you would like to download from NDA. This can\nbe a subset of the data you want, or a list of everything.\n\n`downloadcmd path/to/all/s3/txt/file/alls3.txt -t`\n\n\n#### Restart Download\n\nOften times, your download may be interrupted. To restart a download process, enter the same command you did for the original\nrun, but include the -r flag and the directory where all the files were being downloaded:\n\n`downloadcmd path/to/all/s3/txt/file/alls3.txt -t -r /Users/<your_user>/AWS_downloads`\n\n\n\n## Further Assistance\nIf you have any problems with this validation tool python client, or would like to provide feedback/comments,\nplease email us at NDAHelp@mail.nih.gov.\n# nda-tools\n\n\n",
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