As with all systems, precisionFDA relies on files to store data. Files can be uploaded from your computer or generated by running apps, and can be shared with the precisionFDA community.
Clicking on "Files" at the top navigation bar takes you to the a page that lists all the files accessible by your account. Files owned by you are shown under "My Files" Members' contributions (including yours) are shown under "Explore". You can further filter files (for example, search for a given filename keyword) by clicking on the "eye" icon, which will reveal a filter bar. Choose any filters and apply them by clicking on the "funnel" icon.
The precisionFDA system also allows users to organize files into folders, putting similar files together. Users may generate a new folder in the current folder, which will prompt the user for the name of the folder to use. Files can be moved into a folder by selecting them, and using the button in the top right to move into a folder.
You can multiselect files to perform an operation on each of them. All files and folders have a checkbox on the left, checking that will select that file. If an individual file is selected, you can rename the file. With one or more file or folder selected, you can move the selected objects into another folder. In addition to that, you can publish the selected files and any files inside the folders you have selected. A dialog will pop up to confirm the files you have selected. You can also delete these file, which will similarly show a dialog to confirm all the files. Finally, you can download these files, which will show a dialog allowing you to download each individual file. Due to the size of files, generating a tarball is not possible at this time.
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 uploader, a command-line tool capable of uploading with multiple threads and more resilient to transient errors. The precisionFDA uploader can be used for both files and app assets, and it's available through the Create Assets page.
Visit that page and download the precisionFDA uploader by clicking the respective button under "Step 3". (NOTE: The uploader requires Python 2.7, as well as the python 'requests' and 'futures' packages, so ensure you have those available in your environment).
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.
./pfda upload-file --auth KEY /path/to/file. This command will upload the file to precisionFDA.
$HOME/.config/precision-fda/config.json, so after you have run it once, you don't need to specify the key in subsequent invocations.
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.
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:
|Click...||In order to...|
|Attach to...||Attach the file to a note. See the notes section for more info.|
|Open||Open the file inline in your browser (if your browser supports it). Use this action to see the content of text files, PDF files, images, etc.|
|Download||Download the file right away via your browser.|
|Authorized URL||Generate an authorized URL via which the file can be downloaded non-interactively.|
|Track||Display a graph tracking the file's provenance. See Tracking for more info.|
|Publish||Publicly contribute the file to the precisionFDA community. See Publishing for more info.|
|Delete||Permanently remove the file from precisionFDA.|