Before uploading a file to the CSSI DCC portal, consult the ISA-Tab specification  . This specification describes how to structure your investigation data to create an Investigation-Study-Assay (ISA) archive. This may involve configuring it using open-source software  made for this purpose.

The following pages describe how to upload ISA Archives.

Globus is a service that enables large file transfers securely. You must have an account with Globus before you use it to upload investigation files to CSSI DCC. If you do not already have an account, you are prompted to create one when you start the upload process. 

To upload files using Globus   

1. Begin uploading your ISA archive by creating a folder in CSSI DCC:
   1. Log in to the CSSI DCC Portal, as described in Logging In to the CSSI DCC Portal.

   2. Select Investigations > Upload. The Upload ISA Archives page appears.
      

   3. Enter a unique name for your new folder. Note that this name can differ from the title within the ISA archive.

   4. Click Create. The File Upload section appears, with the new folder name above it.
       

      
      

2. On the Upload ISA Archives page, click  Upload with Globus. If you have not yet logged into Globus, a log in page appears.
    

   Globus Documentation and Support

   For more information about using Globus, consult their documentation and/or support:

   • https://docs.globus.org/
   • https://support.globus.org/

   After you successfully log in, the Globus File Manager page appears. The system has already populated the destination endpoint on the right (/_upload_target/...), which is the folder you selected in DCC. 
    

3. On the left, select the starting endpoint and select the file or files you want to upload. Navigate to the file or files, if necessary. 
   

4. Click the Start button that points to the destination to begin the transfer request. A message briefly appears on the screen when the transfer request is submitted successfully. When the transfer succeeds, Globus sends a notification email message.

    

5. In the DCC Upload ISA Archives page, notice that a new folder appears in the list of folders at the top of the page. Click Open in the row for that folder. At this point, the new folder contains only one investigation version.  
   
    

6. If needed now or later, to change the folder name, click the icon next to the folder name. 

7. If needed now or later, to edit the metadata of an investigation version, click View/Edit Metadata in the row for that version. The edit metadata page for that investigation version appears. For details, refer to Editing Investigation Metadata.
8. Consider making this version available to all CSSI DCC users by requesting open access for this version. For instructions, refer to Requesting Open Access for an Investigation. 

The CSSI DCC Portal validates uploaded ISA archives using standards and conventions described in the ISA-Tab specification . The ISA tools site provides additional technical information about validating ISA archives.

If your ISA archive does not meet those standards and conventions, you may encounter an error when you upload it to the CSSI DCC Portal. Your ISA archive will likely process successfully but the application will detail the error in the Status column. You may then want to address the error and upload again. A sample error message follows:

Missing Data Files: File processed successfully. 1 files referenced in the assay(s) were not found. Click here to view the missing file lists (limited to 1000 entries each).

CSSI DCC looks for errors in three types of files that are commonly in an ISA archive:

• Data files: If there are more than 1000 missing data files for an assay file, only the first 1000 will be listed.
• Additional files: If files are found in your uploaded archive, but were not referenced in the metadata, they are listed.
• External file references: The upload summary lists all of the external file references in your uploaded archive and notes whether or not they are verified.

After the upload completes, the error message appears in the Status column of the File Upload area on the Upload Single ISA Archive tab. It provides an overview of the error and a link to the details.

 

Click the link in the status message. A page opens that details the status of the three types of files in the uploaded ISA archive.

The Missing Files section details each missing data file referenced in the metadata of the assays:

The Additional Files sections details files you uploaded that you didn't reference in the archive's metadata.

The External File References section lists external file references in your uploaded archive and notes whether they are verified or not.

If the portal can detect that the URL is valid without authenticating it, it appears in this list as “Verified.”

In all other cases, it appears as “Not Verified.”

When uploading an ISA archive to a CSSI DCC folder, you can specify who can access its investigation data. You can do this before or after you request open access for your data. You can control access to the entire investigation or only selected assays and studies.

You must have the role of uploader or higher to control data access. Your administrator determines your role.

When you assign access, you assign it to one or more groups rather than individual users, though a single group could contain a single user. Anyone with upload privileges can create and manage these groups, but you must create the group(s) before you upload.

The following page family describes how to control access to investigation data.

If you have requested open access for an investigation, and if your request had an incorrect embargo date, you can change the embargo date after an administrator has approved the open access request. You can also remove the embargo date, which means you want the system to make the investigation open access immediately when the administrator approves it again. 

1. Wait until an administrator has approved the open access request. On the Upload ISA Archives page, the system changes the status of the investigation version to Open Access approved, Embargoed.
   
2. On the Upload ISA Archives page, next to the investigation version that has the incorrect embargo date, click Preview. The Open Access Preview page appears. 
3. Click Request Open Access. The Request Open Access dialog box appears.
   
4. Next to the Embargo Release Date, click Edit. The Embargo Release Date becomes editable.
5. If you want to change the date, enter the date when the embargo should be released. If you want the system to make the investigation open access immediately, delete the date.

6. In the Comments field, provide any comments you want to associate with this request. 
   

7. Click Submit. The system changes the status of the investigation version to Request pending as of <date time>. An administrator processes your new request. 

When that administrator has approved your new request, the system changes the status of the investigation version (on the Upload ISA Archives page) back to Open Access approved, Embargoed.

When system has made the investigation version open access, the system sends you an email notification with "CSSI DCC Portal Investigation Granted Open Access" as the subject line. 

The first time you upload an ISA archive to a new folder, it becomes the first version of that folder (investigation). You are an owner of the folder you created. 

While you should associate only one investigation with a folder, you can upload multiple versions of an investigation file to that folder, and then request open access for one of those versions.  You may want to do this if you change your investigation data or need to fix it due to an upload error. Each time you upload a new investigation file to a folder, the version number increases by one. Each folder can have only one open access version.

Each time an administrator or the system makes an investigation version open access, the system automatically removes the open access status from the version that previously had that status. Here are some examples:

• If version 1 of your investigation currently has open access status, and then an administrator makes version 5 open access, the system automatically removes the open access status from version 1.
• Or, if version 5 currently has open access status, and then an administrator makes version 1 open access, the system automatically removes the open access status from version 5. 

CSSI DCC tracks the date and time each time an administrator makes an investigation version open access. Use the history timeline to switch between current and previous versions of the investigation file. You can download a previous version. You can view the history for investigation files to which you have access.

To view the history of an investigation file

1. Browse or search for an investigation. For instructions, refer to Browsing Investigations or Searching Investigation Data. The Investigation Details page appears. 
   
2. Scroll down to the History section of the page. Consider taking the following actions:
   
   • The current version number appears above the timeline. You can hover over the version number to see the date when this version became the current version.  In this example, Version 1 became current on 6/9/2017. 
     
      

   • When an investigation has multiple versions, they appear on the timeline as well. The version that is currently selected is always green. In the example below, the current version is selected, so it appears in green. The current version is also open-ended to the future until another version has the open access status.

     The white space between versions, as in the example below, indicate times when no version of the investigation file was open access.

     
     
      

   • To select a previous version, hover the mouse over the timeline. If the version you want to select is not immediately visible, move the scroll wheel on the mouse down to move left and up to move right until you see a previous version.  In this example, a previous version was current only on 6/22/2017. 
     
      
   • Click the previous version to select it.  The Investigation Details page appears. The top of the page displays the selected version number and a link to the current version. You can download this previous version, as described in Downloading Investigation Data.