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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
Check your local timezone here https://bit.ly/36iVOkX 
 
Please contact support@cyverse.org for any questions, or concerns.

 

 

 

 

 

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About uploading and importing data files and folders using the Discovery Environment

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This section contains:

The root page DEmanual:@self could not be found in space Discovery Environment Manual.

You can upload single files, multiple files, and folders from your desktop using bulk upload or simple upload, and import single or multiple files from URL.

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See Using Special Characters in the DE for notes about file names, folder names, and analysis names.

You also can import test data files from the app's documentation page and download files and folders to your computer. Once imported, you can use the data files for analyses in the Discovery Environment, as well as share data files you own.

If you prefer using the command line, you can manage the data outside of the Discovery Environment in the iPlant Data Store using other tools, as well as upload files directly using iCommands. The method you use depends on the size and number of your data files, as well as your personal preferences.

Method

< 1.9 GB

> 10 GB*

Single File

Multiple Files

Folders

Requires Java

Bulk upload

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Simple upload

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Import from URL

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* Depending on network bandwidth and current load. See Storing and Accessing Your Data in the Data Store for information on larger files and allocation.

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Uploading data files from your desktop

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 upload, or want to upload or import just one file of up to 1.9 GB at a time.
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    There is a maximum total file size of 1.9 GB per upload.

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

Bulk upload

Problem in Chrome on Mac OS X

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Bulk upload in the DE using the Chrome browser on Mac OS X (though 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, use the Safari or Firefox browsers.

  1. Open the Data window.
  2. Click Upload and then click Bulk Upload from Desktop.
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    • 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.
  3. To select a different resource, click the Resource drop-down list and select the resource.
  4. In the Local Files section on the left, browse the folder location, select the file(s) to upload, and then click Add Selected to Queue.
  5. In the Files Queued for Import section, verify that the folder next to Destination is correct.
    To select a different import folder, click Change Destination, navigate to the desired target location, and click Select.
  6. To remove a single file from the Files Queued for Import list, click in the Cancel/Remove column for the file.
    To remove all files from the file queue list, click Clear File Queue.
  7. Click Import Files to begin the import.
  8. When the iDrop Transfer Completed message is displayed, click OK.
  9. To upload another group of files, click Clear File Queue and repeat.
  10. 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.

Simple upload

  1. Open the Data window.
  2. Open the destination folder in your personal Workspace.
  3. Click Upload and then click Simple Upload from Desktop.
  4. In the Upload window, either click Browse to select the first file to upload, or paste the URL in the field.
  5. Repeat for each file to upload.
  6. Click Upload.
    The files are uploaded to the destination folder.

Importing data files from URL

This method is useful when you want to import larger files, have some files you want to upload 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 the Data window, open the destination folder in your personal Workspace. (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 Import from URL.
    The files are imported to the destination folder.

Status updates

As the import progresses, you receive several status updates in the form of popups, notifications, and emails. For more information on notifications, see Viewing and Deleting Notifications. Once you have received notification that your file has been successfully imported, it is available in the specified folder.

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