![]() |
Page History
...
Only users who have registered for and logged in to the CSSI DCC Portal can upload investigation data. During registration, you must also select the I would like to upload Investigation data checkbox and be approved. For more information, see Chapter 3: Uploading and Publishing Investigation Data.
Uploading ISA-Tab Files
Before uploading a file to the CSSI DCC portal, consult the ISA-Tab specification
Multiexcerpt include | ||||||
---|---|---|---|---|---|---|
|
Multiexcerpt include | ||||||
---|---|---|---|---|---|---|
|
...
- Log in to the CSSI DCC Portal.
- Select Investigations > Upload.
The Upload ISA TAB Files page appears.
Click New Project.
The Project Properties page appears.Info A project is simply a container for the ISA-Tab file. It allows you to track multiple versions of ISA-Tab file uploads to this project.
It is a best practice for each investigation to have its own project.
- Enter a title for your new project. Note that this title and that of the ISA-Tab file that the project contains can be different.
Click Save Project.
The new project is listed under Investigation Projects.
Info If the File Upload section of the page is not visible, click Open next to the project name to show it.
Info title Changing the Project Name If needed now or later, click Edit to change the project name. Depending on your privileges, you may not see the Delete button.
Select the file you want to upload to this project in one of the following ways:
Drag and drop the ISA-Tab archive file from your computer to the Drop your files here box surrounded by the dashed lines:
Click the Drop your files here box image and browse to where the file is stored.
The file is listed in the File Upload area and the status is listed as Ready.
If the file is smaller than 10 GB, click Upload selected files. If the file is larger than 10 GB, use Globus instead.
The file begins processing and the status moves through the following stages:
- Uploading
- Processing Queued
- Queued
- Preparing uploaded files
- Parsing ISA TAB Metadata
- Preparing Data Files
- Validating assay files and file sizes
- File processed successfully
Success: file processed successfully
Once an administrator approves the upload request, the uploaded, unpublished file appears in the Investigation Projects section of the page. It is not yet published, so you must now publish it to use it in CSSI DCC.
Uploading Large Files with Globus
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.
...
- Begin uploading your ISA-Tab file by creating a project in CSSI DCC and selecting a file. For more information on this process, go to Uploading ISA-Tab Files.
On the Upload ISA TAB Files page, click
If you have not yet logged into Globus, a log in page appears.
.Info title Globus Documentation and Support For more information about using Globus, consult their documentation
and/or supportMultiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
.Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include After you successfully log in, the Globus Transfer Files page appears. One of the Endpoints you configured is already populated, though you can change it.
Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.
Confirm or change the destination endpoint (on the right).
Click the right arrow button that points to the destination to begin the transfer request.
A message appears on the screen when the transfer request is submitted successfully. You receive an email when the request is granted and the transfer succeeds.
Once an administrator approves the upload request, the uploaded, unpublished file appears in the Investigation Projects section of the page.Since you have not yet published the uploaded file, you must publish it to use it in CSSI DCC.
Understanding Upload Errors
Include Page Understanding Upload Errors Understanding Upload Errors
Controlling Access to Investigation Data
Include Page Controlling Access to Investigation Data Controlling Access to Investigation Data
Publishing ISA-Tab Files to the CSSI DCC Portal
Include Page | ||||
---|---|---|---|---|
|
Viewing Publish History
The first time you upload an ISA-Tab file to a new project, it is the first version of that file.
...
- Browse or search for an investigation.
The Investigation Details page appears. - Click History to show the timeline.
- 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 a file 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 you publish another version.
Info The white space between versions, as in the example below, indicate times when no version of the investigation file was published.
- 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, showing the selected version number at the top. You can download the full data or selected metadata of this previous version. You cannot download selected data of a previous version.
- 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.
Unpublishing ISA-Tab Files
After publishing a file, you may want to unpublish a version of it to remove that version completely from the CSSI DCC server.
...