Import from a DRS server

Overview

Seven Bridges Platform/BMS allows you to import and use DRS files from either external sources or Cancer Genomics Cloud powered by Seven Bridges (CGC) environment.

After importing the files, you can then use them as any other file on the Platform. Please note that the actual files physically remain hosted on the source platform and are only linked from Seven Bridges Platform.

Prerequisites

The following are the prerequisites for importing files from a DRS server:

• You need to have a registered account on both Seven Bridges Platform and CGC.
• Multi-factor authentication has to be enabled on both Seven Bridges Platform and CGC.
• You have to connect your Seven Bridges Platform account to the DRS server (CGC). More on this below.

Connect to the DRS server (CGC)

1. Click your username in the upper right corner and then click Account Settings.
2. Click the Dataset Access tab.
3. Locate "Cancer Genomics Cloud Powered by Seven Bridges" section and click Connect.
4. The following pop-up is displayed.

5. Click Yes to complete the procedure.

Once completed, your Seven Bridges Platform account is connected to the CGC and you can start importing files using the import via DRS feature.

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Note

This connection will automatically expire in 30 days. You can disconnect your accounts at any time.

Access the import feature

1. Open the project to which you're importing files.
2. Select the Files tab and then click + Add Files.
3. Click Add Files and choose GA4GH Data Repository Service (DRS), as shown below.

The page for importing files is displayed. The following two options are available:

• Paste DRS URIs - use this option to paste the list of DRS URIs of the files you want to import (see below).
• From a manifest file - use this option to import files by using a manifest (see below).

Import files by pasting DRS URIs

1. Enter DRS URIs into the text area.

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Important notes

The maximum number of links you can put inside the text area is 500. To import again, you will have to wait for 5 minutes.

In addition, please bear in mind that all other API calls you make within this time frame will also count toward this limit. URLs should be entered one per row.

2. (Optional): Enter tags in the Tag files box (see below).
3. Resolve naming conflicts - choose the method for resolving a naming conflict; read more below.
4. Give your consent regarding importing sensitive data by checking the related option.
5. Click Import to start the upload.

Import from a manifest file

To import files from a manifest file:

1. Access your project.
2. Click the Files tab.
3. Click Add files and choose option "GA4GH Data Repository Service (DRS)".

4. Click Browse manifest and choose the manifest file from your computer.

5. (Optional) Tag your files (see below).
6. Choose the method for resolving naming conflicts (see below).
7. Give your consent regarding importing sensitive data by checking the related option.
8. Click Submit.

The files are imported to your project.

Manifest file format

The following rules apply for creating the manifest file.

Add tags to files

To make it easier to visually identify and organize files you can tag them before the import. Separate tags with commas or press enter.

All tags which are already in the selected project are autosuggested in the drop-down menu. Learn more about tagging your files. 

Resolve naming conflicts

Naming conflicts happen when you try to import an item (file or folder) from a DRS server to a project's root folder or subfolder, where an item with the same name already exists. The list below illustrates the possible cases of naming conflicts and the way they are resolved depending on which option is selected in the Resolve naming conflicts dropdown:

1. Importing a file that has the same name as an existing file at the destination path:
   • Skip (default): The file won't be imported. This is the default behavior.
   • Auto-rename: The imported file will be automatically renamed by adding a prefix (underscore and serial number).
   • Overwrite: The existing file will be overwritten by the file imported from the server.
2. Importing a file that has the same name as an existing folder at the destination path:
   • Skip (default): The file won't be imported.
   • Auto-rename: The imported file will be automatically renamed by adding a prefix (underscore and serial number).
   • Overwrite: The file won't be imported.

The following table illustrates the entire naming conflict resolution mechanism:

Check import status

To check the progress of your import, click the notification bell in the upper right corner.

Click Open activity center to see more detailed information about each of the imports.

Click on an import in the left pane, and the right pane will show detailed information about that import including:

• DRS URI - the URI the file was imported from
• Status - the status of the import for each of the files; in case of a failed import, the following information will also be available:
  • Error Code - click to see detailed information about the error code
  • Error Message - the description of the error

Bring your CGC data

To be able to import files from CGC, you will first need to create a connection to CGC environment.

1. Click your username in the upper right corner and select Account Settings.
2. Click the Dataset Access tab.

3. Under "Cancer Genomics Cloud Powered by Seven Bridges" click Connect. 
   
4. If you are not already logged into your CGC account, you will now be asked to log in. Once completed, your Seven Bridges Platform account is connected to CGC and you can start importing files.

This connection will automatically expire in 30 days. You can disconnect your accounts at any time.

The next step is generating a DRS manifest on CGC, after which you will be able to import it to your Seven Bridges project.

Disconnect your account from CGC

Follow the procedure below to disconnect your account from the CGC. Please keep in mind that you will no longer be able to import files. In addition, the files that have been previously imported will no longer be available for use.

1. Click your username in the upper right corner and choose option Account Settings.
2. Click the Dataset Access tab.
3. Find the section for the environment you want to disconnect. 
4. Click the ellipsis menu  and select Deactivate.

Your account is now disconnected from the CGC.