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Using Allas storage service to receive sensitive research data

Allas storage service is a general purpose data storage service maintained by CSC. It provides free-of-charge storage space for academic research projects at Finnish universities and research institutes. Allas can be used for storing any kind of research data during the active working phase of a research project. Allas is however not intended for data archiving. You must remove your data from Allas when the research project ends.

There is no automatic backup processes in Allas. In technical level Allas is very reliable and fault-tolerant, but if you, or some of your project members, remove or overwrite some data in Allas, it is permanently lost. Thus, you might consider making a backup copy of your data to some other location.

This document provides an example of how a research group can use Allas service to receive sensitive data from external data provider like a sequencing center.

The steps 1 (Obtaining storage space in Allas), and 2 (Generating encryption keys) require some work, but they need to be done only once. Once you have the keys in place you can move directly to step 3 when you need to prepare a new shared bucket.

1. Obtaining a storage space in Allas

If you are already using Allas service, you can skip this chapter and start from chapter 2. Otherwise, do following steps to get access to Allas.

Step 1.1. Create a user account

If you are not yet CSC customer, register yourself to CSC. You can do these steps in the CSC’s customer portal MyCSC.

Create a CSC account by logging in to MyCSC with Haka or Virtu.

Step 1.2. Create or join a project

In addition to CSC user account, new users must either join a CSC computing project or set up a new computing project. You can use the same project to access other CSC services too like Puhti, cPouta, or SD desktop.

Create a CSC project in MyCSC and apply access to Allas. See if you are eligible to act as a project manager. If your work belongs to any of the free-of-charge use cases, select 'Academic' as the project type. As a project manager, you can invite other users as members to your project.

If you wish to be joined to an existing project, please ask the project manager to add your CSC user account to the project member list.

Step 1.3. Add Allas access for your project

Add Allas service to your project in MyCSC. Only the project manager can add services. After you have added Allas to the project, the other project members need to login to MyCSC and approve the terms of use for the service before getting access to Allas.

After these steps, your project has 10 TB storage space available in Allas. Please contact CSC Service Desk if you need more storage space. The data in Allas can be downloaded to your local environment or to CSC computers. More information about different ways to access data in Allas can be found from Allas user guide.

2. Generating keys for encrypting sensitive data

2.1 What are encryption keys for?

In case of sensitive research data, for example human nucleotide sequence data, the data needs to be properly encrypted before it can be uploaded to Allas. The CSC Sensitive Data Services encrypts data by default with CSC specific key that can be used only in the CSC environment. If you want to use your sensitive data in other locations too you need to create a Crypt4GH compatible key pair consisting of secret key and public key for your own use. You can use the same key pair several times, and normally it is practical to use the same keys for all data of a project so that key management does not get too complicated.

Below you can find step-by-step instructions to create encryption keys using the Cryp4GH graphical user interface or via the command line.

Once the keys have been generated, you can send the public key to all data producers, so that they can then encrypt the data that they will send for you. After that, only the owners of the private key, i.e. project members, can decrypt the data.

The potential danger with data encryption is that if the secret key or its password is lost, the data can’t be decrypted by any means anymore. Thus, you should store the keys and password so that the information will be preserved also when servers and project members change. On the other hand, the secret key should be moved only to those places where decryption is done, and the password should remain unreachable for non-project members.

CSC does not provide an encryption key management system at the moment. If you don't have access to a proper key management system, one solution is to store the secret key and a text file containing the password to CSC Sensitive Data environment using SD Connect interface. The interface encrypts this data with CSC public key, after which the project members, and only them, can use SD Desktop service to check, what were the keys and passwords the project uses.

CSC Sensitive Data environment uses Crypt4GH encryption tool that allows encryption with several public keys. Data encrypted with this way can be opened with several secure keys. If you utilize sensitive data services of CSC it is handy to use both project's public key and CSC public key in encryption. This way the data can be used both in users local environment and in the sensitive data services of CSC.

Creating crypt4gh compatible keys via grafical user interface

  1. Generate your encryption key pair (secret key and public key) with the Crypt4GH application (you can skip this paragraph if you already have a key pair).

    • Install the Crypt4GH application:

    CSC has developed a simple application that will allow you to generate your encryption keys and decrypt data when necessary. Download the version specific to your operating system from the GitHub repository:

    Please check that the tool for Windows has been digitally signed by CSC - IT Center for Science. After the download, you can find the Crypt4GH application in your downloads folder.

    • When you open the application for the first time, you might encounter an error message. In this case, click on More info and verify that the publisher is CSC-IT Center for Science (or in Finnish CSC-Tieteen tietotekniikan keskus Oy) and then click on Run anyway.

    • Generate your encryption keys:

      • Open the Crypt4GH application and click on Generate Keys (in the top right corner).
      • The tool will open a new window and ask you to insert a password (Private Key Passphrase). This password will be associated with your secret key. Please, use a strong password.
      • When you click on OK, the tool will generate a key pair consisting of a secret key (username_crypt4gh.key) and a public key (username_crypt4gh.pub).

      • The keys/file names will be displayed in the Activity Log with the following message:

        Key pair has been generated, your private key will be auto-loaded the next time you launch this tool:
Private key: username_crypt4gh.key
Public key: username_crypt4gh.pub
All the fields must be filled before file encryption will be started

        The keys will be generated and saved to the same folder in which the application resides.

      Note

      • If you lose or forget your secret key, or the password, you will be unable to decrypt the files.
      • Do not share your secret key or your password.
      • You need to create your keys only once and use them for all your encryption needs, but you can of course, choose to generate separate keys for encryption as you wish.

Cretating encryption keys via command line tools

In this example, we first generate your key pair (a password-protected private key and a public key that can be shared with collaborators). Next, we encrypt a file with public keys of two different collaborators (research group A and research group B).

Python 3.6+ is required to use the Crypt4GH encryption utility. If you need help installing Python, please follow these instructions.

  1. Install the Crypt4GH encryption CLI tool

    You can install Crypt4GH directly with pip tool:

    pip install crypt4gh

    or, if you prefer the latest sources from GitHub:

    pip install -r crypt4gh/requirements.txt
pip install ./crypt4gh

    or even:

    pip install git+https://github.com/EGA-archive/crypt4gh.git

    The usual -h flag shows you the different options that the tool accepts:

    $ crypt4gh -h

Utility for the cryptographic GA4GH standard, reading from stdin and outputting to stdout.

Usage:
   {PROG} [-hv] [--log <file>] encrypt [--sk <path>] --recipient_pk <path> [--recipient_pk <path>]... [--range <start-end>]
   {PROG} [-hv] [--log <file>] decrypt [--sk <path>] [--sender_pk <path>] [--range <start-end>]
   {PROG} [-hv] [--log <file>] rearrange [--sk <path>] --range <start-end>
   {PROG} [-hv] [--log <file>] reencrypt [--sk <path>] --recipient_pk <path> [--recipient_pk <path>]... [--trim]

Options:
   -h, --help             Prints this help and exit
   -v, --version          Prints the version and exits
   --log <file>           Path to the logger file (in YML format)
   --sk <keyfile>         Curve25519-based Private key.
                        When encrypting, if neither the private key nor C4GH_SECRET_KEY are specified, we generate a new key
   --recipient_pk <path>  Recipient's Curve25519-based Public key
   --sender_pk <path>     Peer's Curve25519-based Public key to verify provenance (akin to signature)
   --range <start-end>    Byte-range either as  <start-end> or just <start> (Start included, End excluded)
   -t, --trim             Keep only header packets that you can decrypt

Environment variables:
   C4GH_LOG         If defined, it will be used as the default logger
   C4GH_SECRET_KEY  If defined, it will be used as the default secret key (ie --sk ${C4GH_SECRET_KEY})

    You may notice that crypt4gh uses --sk option for the private key. This might seem odd but apparently, crypt4gh uses term secure key for private key, hence sk, and consequently pk refers to public key instead of the private key.

  2. Generate your public-private key pair

    You use crypt4gh-keygen command to create your private and public keys:

    $ crypt4gh-keygen --sk mykey.sec --pk mykey.pub
Generating public/private Crypt4GH key pair.
Enter passphrase for meykey.sec (empty for no passphrase): 
Enter passphrase for mykey.sec (again): 
Your private key has been saved in mykey.sec
Your public key has been saved in mykey.pub

    where --sk mykey.sec is your private (secret, sk) key and --pk mykey.pub is your public key (pk). The tool will ask you to enter a password (passphrase) for your private key. For security reasons, the password is not shown when you type it, so the tool will ask you to enter it a second time to make sure you made no typing errors (or, you make the same errors twice). Please, use a strong password!

    Note

    If you lose or forget your private key, or the password to it, you will be unable to decrypt the files. Do not share your private key or your password.

    Note

    You need to create your keys only once and use them for all your encryption needs, but you can of course, choose to generate separate keys for encryption as you wish.

3. Project key generation example

3.1 Generating keys

In the example below, researcher Tiina Tutkija wants to use Allas to receive and store human sequence data that she will use in her new research project. The project is called AniMINE. It will last several years, and it will include several researchers and data sources. Tiina Tutkija already has a customer project with Allas access at CSC.

Now she creates and stores encryption keys for the project. Tiina has cryp4gh-gui encryption program installed on her laptop. She uses the Generate Keys option to create a new key pair that is protected with password (in this case H8koGN3lzkke).
The key files generated are named based on the user account of the creator (secret key: ttutkija_crypt4gh.key, public key: ttutkija_crypt4gh.pub). As the keys will be used by several members of the project, Tiina renames the key files accordingly: animine_crypt4gh.key and animine_crypt4gh.pub.

3.2 Storing keys with SD Connect

Next, Tiina Tutkija logs in to SD Connect web user interface. Tiina uses Chrome for best experience.

After connecting she checks that Select project dropdown at the top left refers to the CSC project that AniMINE project will be using. After that she clicks the Create folder (in the UI buckets are called folders) button to create a new folder called animine_keys. Then she uses the same button to create another folder called animine_pub.

Now SD Connect contains two new empty folders. Tiina opens the folder amimine_keys and uses Upload button. Then she uses Select files to select both keys to be uploaded and starts the upload process by clicking button Upload.

When the upload is ready, Tiina navigates to the other folder animine_pub. She clicks the Upload button and she uploads ONLY the public key (animine_crypt4gh.pub) to this folder.

Finally, she opens a simple text editor to create short instructions file about the keys. The content of the file, named as animine_key_instructions.txt, is as follows:

---------------------------------------------------------------------------------------------------------
AniMINE  encryption keys created on 16.3. 2022 by project manager Tiina Tutkija.
Following key files are used to encrypt sensitive data used by AniMINE project.
Keys are used with crypt4gh encryption tool.
Public key:   animine_crypt4gh.pub
Secret key:   animine_crypt4gh.key
The password of the secret key is:  H8koGN3lzkke
Note that the secret key and password should never be given or shown to 
users that are not members of this project.

You can find a readable copy of the public key in SD Connect in location
    animine_pub/animine_crypt4gh.pub

You can freely download and send this public key to persons and organizations 
that provide data for AniMINE project. If you want to use data, that has 
been protected using this key pair, locally, please contact project manager 
Tiina Tutkija to get your own copy of the secret key and instructions for 
local decryption. Please use this document, that is readable only in the 
SD Desktop environment of this project, as the only written reference 
for the password. 

Delete the local copy of the secret key when it is no longer actively used. 
------------------------------------------------

She uploads this text file to the animine_keys folder on and then deletes the file from her local computer.

Now the folders animine_keys contain files:

  • data/animine_crypt4gh.pub.c4gh
  • data/animine_crypt4gh.key.c4gh
  • data/animine_key_instructions.txt.c4gh

And folder animine_pub contains files:

  • data/animine_crypt4gh.pub

4. Opening a storage bucket for importing data from data producer

Once you have access to Allas, you can create a new data bucket there and share this bucket with the data producer. This approach requires that the data producer too has a project at CSC. Usually the Finnish academic data producers, like sequencing centers, have a CSC project. You can copy the public key of your project to the shared bucket or sent the public key to the data producer by some other means.

We recommend that you ask the data producer to encrypt your data with CSC public key and with the key of your project. This way you can use the data both in your local secure environment and in CSC Sensitive Data Services.

4.1 Using Puhti to create a shared bucket

If you know the project number of the data producer, you can easily create a shared Allas bucket using a-tools commands in Puhti. First open terminal connection to puhti.csc.fi (use SSH, PuTTY, or terminal connection from Puhti web interface).

In chapter 2.2 we had researcher Tiina Tutkija who created encryption keys and stored them to Allas. In her case a shared bucket could be created with following commands.

First Tiina Tutkija opens a connection to Puhti. In a browser, she moves to URL https://puhti.csc.fi and logs in with her CSC account. Once the web interface of Puhti is open she opens a terminal with tool:

Tools/Login node shell

This tool provides terminal connection to Puhti.

In the terminal, Tiina activates connection to Allas:

module load allas
allas-conf

Then she creates a new shared bucket with command:

make-shared-bucket

This tool creates a new bucket and shares it with the collaborator. The command asks first for the name of the bucket to be created. In this case Tiina uses bucket name animine_data_import_1.

Then the command asks for the project that should have access to the bucket. The project name of data producer is in this example project_2000111.

Then she downloads the public key to Puhti:

a-get animine_pub/data/animine_crypt4gh.pub

And uploads the key to the shared bucket:

a-put animine_crypt4gh.pub -b animine_data_import_1

Finally, Tiina sends the name of the shared bucket to the data producer and ask them to encrypt the data to be uploaded with both the public key that they can find from the bucket and the CSC public key.

4.2 Revoke bucket sharing after data transport

Moving large datasets (several terabytes) of data to Allas can take a long time. After few days, data producer tells Tiina that all data has been imported to the shared animine_data_import_1 bucket in Allas. Tiina can now remove the external access rights from the bucket with command:

a-access -rw project_2000111 animine_data_import_1

5. Using encrypted data

The data stored to CSC using the procedure above is accessible only to the members of the research group. The data is encrypted with both CSC public key and research group's own public key. If the data is accessed through SD Desktop the decryption of data is done automatically by the Data Gateway tool when data is used in the working environment.

If the data is used in other environments, decryption must be done by the user.

In SD Connect service the shared bucket, in this example animine_data_import_1, needs some preparations before the uploaded data can be downloaded.

First, user must share the bucket to her own project too. After that the uploaded data can be accessed, not through the normal data Browser view, but through the Shared view of SD Connect.

In the example above, researcher Tiina Tutkija shared a data bucket animine_data_import_1 in Allas service to receive data from sequencing center. The sequencing center uploaded file run_12_R1.fastq.c4gh to the bucket. Tiina can now use SD Connect to download this file to her local computer.

  • First, Tiina checks the Project Identifier string of her project and copies it to the clip board.
  • Then, on the Browser view of SD Connect she presses the Share button of the bucket (animine_data_import_1). This opens the Bucket sharing page. Here, Tiina turns on read and write permissions and adds her Project Identifier (shown in the user information page of SD Connect) to the field: Project Identifiers to share with. The sharing is activated by clicking the Share button.
  • Next, Tiina moves to the Shared to the project view which now includes bucket animine_data_import_1.

She can now open the bucket and start downloading the data.

However, after downloading the file is still in encrypted format. To decrypt the file Tiina opens the cryp4gh-gui encryption tool that she previously installed to her computer to create the encryption keys.

Now she uses this tool to decrypt the data. In crypt4gh interface she first clicks Load My Private Key and the selects the animine_crypt4gh.key that is the secret key used by her research project. Then she uses Select File to select the file run_12_R1.fastq.c4gh she just downloaded to her computer. Next she clicks Decrypt File boutton. crypt4gh-gui will now ask the password of the secret key (H8koGN3lzkke in this case) after which a decrypted version of the file, run_12_R1.fastq, is created next to the encryprted file. Tiina can now remove run_12_R1.fastq.c4gh from her local computer and start working with the run_12_R1.fastq file.