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Use Case #4: Find and Send Files from the ELITE Portal to CAVATICA

In Use Case #1: Find and Download Files Associated With a Selected Study, we look at how to download files from the web using the Download Cart.

An alternative to downloading files to your local work environment is to “send” the data to a data commons. A data commons is a cloud-based platform that lets researchers manage and analyze data and collaborate within the community to facilitate new scientific collaborations. The ELITE Portal is integrated with CAVATICA to enable this service.

The ELITE Portal and CAVATICA use the Global Alliance for Genomics and Health (GA4GH) standard Data Repository Service (DRS) to enable researchers to access, combine, and analyze data no matter where it is stored. We create a unique mapping - the DRS Uniform Resource Identifier (URI) - to identify each cloud-based resource on the ELITE Portal. This DRS URI is basically a reference link, similar to a URL, that points us to where the data is stored. CAVATICA uses DRS URIs when we “send” data from the ELITE Portal to CAVATICA for analysis.

Users do not pay for storage of the source files when using this service and are solely responsible for paying compute costs in CAVATICA. Members of the Exceptional Longevity Consortia are also eligible for Pilot Funds on CAVATICA.

Link Your Synapse and CAVATICA Accounts

  1. Log into the portal.

  2. Follow instructions for Gaining Access to CAVATICA, including Logging In to CAVATICA and Link Your Synapse Account.

Find Data Associated with a Selected Study and Request Access to Files

Follow steps from Use Case #1 to Find Data Associated with a Selected Study and Request Access to Files.

Send Selected Files to CAVATICA

  1. Once you have narrowed down the data table to only the files you are interested in, you can initiate sending them to CAVATICA. Use the labelled images below as reference while following these next steps.

    1. Click the Send to CAVATICA icon (1) above the visualization section.

    2. Notice that this brings up a new dialog box that displays the requirements that must be met before data can be sent. These include (2) connecting your CAVATICA and Synapse accounts and (3) completing all data access requirements.

      1. The Send to CAVATICA button will be disabled if there are any unfinished actions.

    3. Once all requirements are complete, the Send to CAVATICA button in the bottom right (4) will be enabled. Click the Send to CAVATICA button. You will be redirected to cavatica.sbgenomics.com to complete the process.

  2. Once you are on the cavatica.sbgenomics.com site, complete the following fields on the “Importing DRS data” landing page (5):

    1. Destination project: Create a new project or select an existing project folder to save your data.

    2. Resolve naming conflicts: Naming conflicts happen when you try to import an item from a DRS server to a project’s root folder where an item with the same name already exists. If you select “Skip” (default), then the file won’t be imported. If you select “Auto-rename”, the imported file will be automatically renamed by adding a prefix. Learn more about resolving naming conflicts.

    3. Add tags: Tags make it easier to visually identify and organize files. Separate tags with a comma, enter, or tab key. Learn more about tagging your files.

    4. Agree to the terms and conditions of acceptable use.

  3. Click the Import data button.

  4. The confirmation page will notify you that the import started successfully (6). Click Done to close the confirmation page.

  5. Follow the import progress by clicking on the bell icon in the navigation bar (7). Once your files are imported successfully, they will display in the project folder as shown.

Visit the Seven Bridges Knowledge Center for more details on how to Import from a DRS server.

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