...

An ISA-Tab archive file is a compressed (.ZIP) file containing multiple text files and data files. Each tab-delimited text file in an ISA-Tab file describes the structure, meaning the column headers and row values when considered in spreadsheet format, of the investigation, study, and assay components of the archive. The data files correspond to each assay and are included in the archive in their native format, for example, Microsoft Excel. An ISA-Tab archive file may also contain images and other files.

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.

...

ISA-Tab files that you upload must be in .zip format. Use Globus to upload files larger than 10 GB.

To upload ISA-Tab files

1. Log in to the CSSI DCC Portal.
2. Select Investigations > Upload.
   The Upload ISA TAB Files page appears.
   

3. 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.

   
   
   

4. 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.

5. 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.

6. 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.

7. 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. 
   

...

Publishing ISA-Tab Files to CSSI DCC

1.  Upload  at least one ISA-Tab file to a project.

2. 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.   

3. Click the Preview button next to that version.

   

   The Publish Preview page appears.
   
   
   

4. 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.

   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 the ISA-Tab specification  Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include  . The ISA tools site Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include  provides additional technical information about validating ISA-Tab files.

5. 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.
   
   

...