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For overview information, see Discovery Environment on the CyVerse website.

DISCOVERY ENVIRONMENT USER MANUAL

Maintenance: Tues, 28 Jan 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
 
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
 
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
 
User Portal                   8:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.
 
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
 
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
 
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar
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Uploading and importing data files and folders within the DE

This page contains:

Uploading data items in the DE

You can upload files from your desktop using two different methods:

  • Bulk upload from Desktop allows you to upload multiple files, including subdirectories, and is known to work reliably for uploads of up to 50 GB and larger. To learn more about downloading and using the Java iDrop desktop applet, see Using iDrop Desktop. We recommend using Java version 6 (version 6 update x). If you experience difficulties using this method, you may want to see which version of Java you are running.
  • Simple Upload from Desktop is useful if you have smaller files up to 1.9 GB per file.

Network bandwidth and current load impacts upload times. For more information on larger files and allocations, see Storing and Accessing Your Data in the Data Store.

You also can import files from URL that are larger than 3-4 GB or are not on your computer.

Prefer command line or have larger files to upload?

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If you prefer using the command line or you have large or many files to upload, you can manage the data outside of the Discovery Environment in the iPlant Data Store, using iDROP Desktop, the iRODS web client, or iCommands. The method you use depends on the size and number of your data files, as well as your personal preferences. For a comparison of the different methods of uploading and downloading data items both within and outside the DE, see Storing and Accessing Your Data in the Data Store.

Using Simple Upload from Desktop

Simple Upload from Desktop is useful when you have smaller files of up to 1.9 GB per file.

  1. Open the Data window.
  2. In your personal folder, open the destination folder for the upload.
  3. Click Upload and then click Simple Upload from Desktop.
  4. Verify the destination folder is correct:

    To change the destination folder, click Cancel, select the correct folder, and then click Upload and Simple Upload from Desktop again.
  5. In the Upload window, click Browse to select the first file to upload.
  6. Repeat for each file to upload.
  7. Click Upload. The files are uploaded to the destination folder.

Using Bulk Upload from Desktop

Bulk Upload from Desktop uses a Java applet to allow you to upload multiple files, folders, and subfolders. It is known to work reliably for uploads of up to 50 GB and larger.

Update your Java version when notified by your operating system, including adjusting security permissions (to allow iDrop to run) when prompted by the Java updater. iDrop is developed using the Java programming language and requires updates to ensure its continued operation. We recommend using Java version 6 (version 6 update x). If you experience difficulties using this method, you may want to see which version of Java you are running, and view the Java Help Center documentation.

Invalid License

License is not configured.

Problem in Chrome on Mac OS X

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Bulk upload in the DE using the Chrome browser on Mac OS X (but not in Windows or Linux) results in Java errors and will not launch. This is due to incompatibility between Chrome and Java. To use bulk upload on Mac OS X, close Chrome and use Safari or Firefox instead.

  1. Open the Data window.
  2. In your personal folder, select the destination folder for the upload.
  3. Click Upload and then click Bulk Upload from Desktop.

    Plugin messages?

    Icon
    • If This plugin is disabled is displayed, click the link, click Enable next to the Java Applet plugin, and then restart your browser.
    • If prompted to allow or deny an applet, click Allow.
    The Upload window opens:
  4. Verify the selected destination folder is correct:
  5. To select a different destination folder, click Change Destination, select the correct folder, and then click Select.
  6. To select a different resource zone (for example, TACC), click the Resource drop-down list at the bottom of the window, and select the resource.
  7. To add a file to the list:
    1. In the Local Files section on the left, expand the Users folder and select your username.
    2. Select the file or files to upload.
    3. Click Add Selected to Queue.
      The file is now listed in the Files Queued for Import list on the right:
    4. Repeat for each file to upload to the selected destination folder.
  8. To remove a file or files from the list:
    • To remove a single file, click in the Cancel/Remove column for the file.
    • To remove all files from the list, click Clear File Queue.
  9. To begin the import, click Import Files.
  10. When the iDrop Transfer Completed message is displayed, click OK.
  11. To upload another group of files, click Clear File Queue and repeat.
  12. When done, close the window by clicking at the top right of the window, and then clicking Yes to the confirmation prompt. The files are uploaded to the destination folder.
     If the window isn't updating...

     It may take up to 30 minutes for the window to be updated. Refresh your browser window to see if the changes have taken effect.

Importing data items using Import From URL

Use Import From URL when you want to import larger files, have some files you want to upload from desktop and some you want to import from URL, or want to import a file to the DE that isn't on your system.

  1. Copy the URL for the first file to import.
  2. In your personal folder, select the destination folder for the import. (To create a new folder, see Creating a Folder.)
  3. Click Upload and then click Import From URL.
  4. Paste the URL for the file to import in the first row.
  5. Repeat for each file to import.
  6. Click the Import from URL button. The files are imported to the destination folder.

Understanding status updates

As the import progresses, you receive several status updates in the form of popups, notifications, and emails. Once you have received notification that your file has been successfully imported, it is available in the destination folder.

 If the window isn't updating...

 It may take up to 30 minutes for the window to be updated. Refresh your browser window to see if the changes have taken effect.

Troubleshooting tips

If you experience issues with uploading or importing in the DE, try the following:

  • Check that the file or folder name does not contain special characters. For more information, see Using Special Characters in the DE.
  • If you are using Chrome on Mac OS X, bulk upload may result in Java errors and not launch, due to incompatibility between Chrome and Java. To use bulk upload on Mac OS X, close Chrome and use Safari or Firefox instead.
  • Go to Ask iPlant and search on upload or import.

For additional assistance, please contact iPlant Support.

See also

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