 |
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.
Registering to Use the CSSI DCC Portal
...
- Navigate to the CSSI DCC Portal.
The home page appears.
- Click Login.
The Please Sign In page appears.
Enter your email address and password you specified when you registered.
Info To reset your password, click Forgot Password? In the window that appears, enter your email address to request a password reset email.
- Click Sign In.
The CSSI DCC portal home page appears.
...
- 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.
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
The uploaded 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.
Info title Large Files If the file is larger than 10 GB, use Globus instead.
...
- If you haven't already, start Globus Connect Personal.
- 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 Support If you have trouble logging in, go to Globus Support
or send an email to support@globus.org.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 when you installed Globus Connect Personal 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 arrow button in the direction of the source pointing 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.
The Once an administrator approves the upload request, the uploaded, unpublished file appears in the Investigation Projects section of the page.
You can now publish this file when you are ready.
Validating the Upload
Publishing ISA-Tab Files to CSSI DCC
Upload at least one ISA-Tab file to a project.
Info title Upload Errors You may encounter an upload error. 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).The CSSI DCC Portal validates uploaded ISA-Tab files using standards and conventions described in
...
.Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
...
The ISA tools site
provides additional technical information about validating ISA-Tab files.Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
Publishing ISA-Tab Files to CSSI DCC
- Upload at least one ISA-Tab file to a project.
- If you have uploaded multiple versions of the file to the project, decide which version of the ISA-Tab file you want to publish to CSSI DCC.
Click the Preview button next to that version.
The Publish Preview page appears.
Review the uploaded file by exploring the investigation details. If you are satisfied with the content of this version, request its publication by clicking Publish this Version. If you are not satisfied or the upload generated an error, click Return to go back to your project and upload a new version of the ISA-Tab file.
Check your inbox for an email with the subject line "Investigation Published." You can also confirm the published state of your file by checking the value of the Published Version field (the number should equal the number of the version you intended to publish) and the Published field (should be true) on the Upload ISA TAB Files page.
...
