How to guide: The CODI Desktop Uploader

How to guide: The CODI Desktop Uploader

Tool view


Purpose of tool 

The CODI Desktop Uploader is a tool created to ease the transition between NimOS and CODI. The main objective of the application is to facilitate the uploading of NimOS generated datasets to the CODI cloud platform. It complements NimOS by reading the folder structure of NimOS datasets, making it easy to visualize NimOS data with previews and metadata information.


Contents 

Download the Desktop Uploader 
Log in to the desktop uploader
Upload datasets to the Cloud
Collaboration, Tags and Key Value tags
Technical specifications

Download the Desktop Uploader 

You can download the CODI Desktop Uploader via CODI directly, from the upload section. 



Log in to the desktop uploader

To launch the Desktop Uploader, click on its desktop shortcut icon. 


The Desktop Uploader interface will appear on the login page. As with the CODI web application, log in to the Desktop Uploader with your CODI credentials. Please note: each dataset uploaded via the open session will be imported into the current user account space in CODI. So make sure the open session is linked to your account.




Upload dataset to the Cloud

Select a folder containing your acquisition files. 
  1. The Desktop Uploader will look for each acquisition file located in the selected folder and its subfolders, up to 5 sublayers.
  2. You can change the number of sublayers of folders.
  3. This is the main gallery. You can view all datasets in the selected folder and its subfolders, thanks to their thumbnail generated by NimOS. A dataset with the "Cloud" icon has already been uploaded to CODI while a dataset with the "Desktop" icon has not yet been uploaded to CODI.
  4. You can use the filtering options to sort your datasets.
  5. Select the datasets you want to upload to the cloud and visualize a dataset’s metadata by clicking on it. 
  6. View the metadata, thumbnail and files information of the selected dataset on the left-hand side panel. 
  7. Define the tags and key-value tags that will be applied to each imported dataset, and select a Collaboration to upload your dataset to.
  8. Upload your dataset selection to the cloud !


Collaboration, tags and Key Value tags

Using the Desktop Uploader, you can automatically tag all your datasets and upload them directly into a Collaboration.
Similarly to CODI, you can set single tags and/or key-value tags which  will be applied to every dataset uploaded into CODI from the Desktop Uploader. Using tags, you will be able to organize your data within your personal or shared dataset space or more specifically inside your Collaborations. You can select your target collaboration from the settings (see picture below).




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