Files

precisionFDA allows users to upload files from thier computer, generate them by running apps, or share them with the precisionFDA community.

Files & Folders

Every file has an ID starting with file-. This ID is used throughout the precisionFDA system.

Creating a Folder

To add a folder click the Add folder button to create a sub-folder in the current location, then enter a name.

Selected Items

Each file or folder has a checkbox on the left. Select one or more items to perform an action on them. By using the Actions dropdown (top right)

Actions

When one or more items are selected, click Actions (top right) to:

• Move them to another folder.
• Publish them (and any files inside selected folders).
• Delete them (a confirmation dialog will appear).
• Download them (a dialog will allow you to download each file individually).
• ...more

Moving Items

You can organize files into folders to keep related items together.

• Move files into a folder by selecting files or folders and dragging them onto a folder. Alternativy you can use Move action form the Actions dropdown, and picking a destination folder.

Uploading files

You can upload small files directly from your web browser by clicking "Add files". Choose the files you want to upload, and click "Upload all" to begin the upload to cloud storage. To ensure integrity, your web browser will automatically calculate a checksum of the uploaded content and ensure that it matches the checksum calculated on the cloud side.

Once the upload is complete, the system will perform some additional finalization. This process usually takes a few seconds, during which the file is in a "closing" state. After finalization is completed, the file becomes "closed" and can now be used within precisionFDA (downloaded, published, or provided as input in apps). Its contents can never be changed, and it is given a unique, immutable id of the form "file-Bk0kjkQ0ZP01x1KJqQyqJ7yq" to distinguish it across the whole site.

If the upload gets interrupted for any reason, you will see the partially-uploaded file in your list of files, marked with an "open" state. Please delete the file and reupload it. Periodically, the precisionFDA system may automatically clean up partially uploaded files.

For large files that are accessible over the Internet, we suggest running the "Fetch file from URL" app, which has been provided by the precisionFDA team. The app allows you to fetch a file from a given URL.

For large files that are on your computer, we suggest using the precisionFDA CLI, a command-line tool capable of uploading with multiple threads and more resilient to transient errors. The precisionFDA CLI can be used for both files and app assets, and it's available through the CLI docs page.

Visit that page and download the precisionFDA CLI for your operating system and architecture by clicking the respective button under "Step 3".

The tool requires an "authorization key" in order to authenticate the client against the precisionFDA system. You can get a key by clicking the respective button under "Step 4" in the "Add Assets" page. Copy the key from that page and paste it in the command below where it says KEY. For your security, the key is valid for 24h.

Run ./pfda upload-file -key KEY -file /path/to/filein a Unix/Linux environment, or "C:\path\to\pfda\executable\pfda.exe" upload-file -key KEY -file "C:\path\to\filename" for a Windows environment. This command will upload the file to precisionFDA.

The CLI can do a lot more than uploading assets, please see the Command Line Interface documentation page

Examining file origin

The system automatically records the origin of files. The "origin" column describes how each file got introduced to precisionFDA; it is set to "Uploaded" if the file was directly uploaded; otherwise it points to a job if the file was generated by running an app. Further information can be obtained using the tracking feature.

File details

Clicking on a filename in the files list (or on other file links that appear in certain precisionFDA areas) takes you to the file details page, which shows information such as filename, unique id, size, creation time, and origin. In addition, if the file has been used as input to any comparisons or has been attached to any notes, those will also be visible in respective sub-sections.

This page shows one or more action buttons, depending on the file state and your permissions: