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

DISCOVERY ENVIRONMENT USER MANUAL

 

 

 

 

 

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Doc note (Staff view only): Do not rename this page. It's hard coded in the Edit/View Metadata page ("Read more" link next to "Import to User Metadata").

Metadata is data about a data or analysis file or folder that describes its contents and the context of its data. This can be very useful when you need to remember specific information about that file or folder in the future  — such as a tool name, version, or settings you used when submitting an analysis — or when you want to share a file and want the collaborators to understand the context of its data.

A single piece of metadata, or an AVU, is made up of attributes, values, and units. An attribute is a changeable property or characteristic of the file or folder you have selected that can be set to a value. For example, length is an attribute of a file, while 7 is its value, and cms is the unit.  The metadata you enter stays with the file when you share the file or folder with others.

Just like editing any file or folder, you must either have write or own permission to it in order to add, edit, or delete its metadata. You can view, copy, or save the metadata for any file or folder that has been shared with you, regardless of permission level. Another form of metadata that is just for your use is the ability to add tags to a file or folder in the DE.

Other available options are the ability to attach multiple AVUs or metadata templates to the same file or folder, which lists the metadata on the download page that opens from a data link that was sent by the owner to a recipient, download a metadata template as a CSV file, and duplicate a field in a metadata template.

In addition to defining metadata within the DE, you can read and write metadata with iCommands

Adding and editing metadata in the DE

To add or edit metadata to a file or folder, you must have write or own permissions to the item. If saving metadata to multiple files or folders, there is a limit of 1000 items (all files within all subfolders under the parent folder) per save. If you need to save metadata to more than 1000 items, you can either save the metadata to 1000 files at a time until all files have been saved, and then delete the older folder, or use iCommands to do it.

  1. In the Data window, search for the file or folder you own and to which you want to add or edit metadata. To search for a metadata attribute or value, see Searching for Data Items.

  2. Click on the three dots to the right of the file or folder name (or click the checkbox next to the item, click the Metadata menu, and then click Edit/View Metadata):

  3. To add metadata to the data item:

    1. Click Add:

      Tip
      titleAdd button not enabled?

      If the Add button is disabled, you don't have write or own permission. Instead, you can download it to your computer and then upload it to your personal folder.

    2. Double-click in the New Attribute field and enter the attribute for the data item (e.g., length). (Click Help at the top right of the window to view information about attributes and values.)

    3. Tab to the New Value field and enter the value (e.g., 7).

    4. Tab to the Unit field and enter the unit (e.g., cms).
    5. Click Save to save the AVU.
    6. Repeat for each AVU to add.
    7. If done, click Save.
  4. To edit a line of metadata:
    1. Click the three dots at the right side of the item with the metadata to edit.
    2. In the Edit/View Metadata window, click the checkbox for the AVU to edit and then click Edit.
    3. Double-click in the field(s) to edit and make the changes.
    4. Click Save.
  5. To delete a line of metadata or remove a template from a file or folder:
    1. Click the checkbox for the AVU to delete. (Press Shift to select multiple rows.)
    2. Click Delete.
    3. If done, click Save.
  6. To use a metadata template, see the Using Metadata Templates section below.
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  1. In the Data window, click the checkbox for the file or folder to which you want to add a template. (You must have own or write permissions for the item.)
  2. Click Image Removed on the three dots at the right of the row for the item, or click the Metadata menu and then click Edit / View Metadata.
  3. In the User Metadata window, click Select Template:


    Note: To download the template in this window, click .
  4. Select the template to use and click OK.

    Tip

    Click next to the template name to view a description of the template.


    The template window opens, as shown in the following example of the RNA template:


  5. In the template, complete the required fields (noted with a red asterisk).

    Tip

    Click to the left of the attribute name to learn about that field, or click Metadata Term Guide at the top to learn about all attributes in the template.

  6. To duplicate a field, click . (Click to remove the duplicate field.)
  7. When done, click OK. The template's metadata attributes are added to the User Metadata dialog.

  8. Repeat for each additional template to apply to the data item.
  9. When done, click OK.

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  1. Upload the metadata file to the Data Store:
    • If the first column of your metadata file contains only file names (that is, all data files are in the same folder), move the bulk metadata file to the same folder as the location of the data files.
    • If the first column of your metadata file contains the full path to each file (that is, the data files are in different folders), it does not matter where the metadata file is located on the Data Store.
    Note

    If you create the file directly in the DE using the built in text editor, you do not have to upload. Just be sure to save the CSV file in the correct location as specified above.

  2. Apply the metadata to the files:
    1. In the Data window, check the box next to the name of the folder containing the data files to which you want to apply the metadata in bulk.
    2. Click the Metadata menu, point to Apply Bulk Metadata, and then click Select Metadata File.
    3. Browse to the location of the bulk metadata file and select it.
    4. Select the corresponding template from the dropdown menu.
    5. Click Okay.
    6. If the action was successful, you should get a notification. If there is no notification, there was an error in the process and you will need to repeat the process after confirming that your metadata file is formatted correctly.

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