DSA-Scripts

Python scripts for bulk-managing slides, annotations, and metadata on the Digital Slide Archive (DSA / HistomicsUI) servers:

Server	API URL
Athena (official)	https://athena.rc.ufl.edu/api/v1/
DevAthena (testing)	https://devathena.rc.ufl.edu/api/v1/

All scripts talk to the server through the Girder REST API using the girder-client Python package.

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Scripts

Folder	Script(s)	Purpose
KPMP/annotation_namechange_accesscontrol	annotation_namechange_accesscontrol.py	Rename annotation layers and control which layers non-admin users can see (dry run, backups, undo)
KPMP/annotation_access_control	annotation_access_control.py	Remove specific users from annotation access lists, except for kept layers
KPMP/remove_metadata	remove_metadata.py	Delete user metadata from every item in a folder
KPMP/Metadata	Metadata.py, Metadata.sh, metadata_csv.py, annotations_user_large_metadata.py, common.py	Export metadata, annotations, and files from Athena to HiPerGator and combine metadata into a CSV

Each folder has its own README with full instructions.

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One-time setup (needed for every script)

1. Install Python and the client library

Python 3.8 or newer is required. Check with:

python --version

Install the dependencies:

pip install girder-client pandas

On HiPerGator or a shared system without admin rights, use pip install --user girder-client pandas.

2. Get the code

git clone <this-repo-url>
cd DSA-Scripts/KPMP

3. Get an API key (or use your username/password)

1. Log in to the server in your browser (Athena or DevAthena).
2. Click your name in the top-right corner, then My account.
3. Open the API keys tab and click Create new key.
4. Give it a name and choose Allow all actions, then copy the key.

Treat the key like a password. Never paste it into a file you commit to GitHub. annotation_namechange_accesscontrol.py can also log in with your username and password instead of a key.

4. Find the IDs the scripts ask for

Every object on the server has a 24-character ID (e.g. 69e6919a3c7545c729a39e88).

You need	Where to find it
Folder ID	Open the folder in the server's data browser. The ID is the last part of the URL after folder/. You can also click the folder's ⓘ (info) icon.
Item (slide) ID	Open the slide in HistomicsUI. The ID is the part of the URL after ?image=.
User ID	In the data browser, open Users and click the person. The ID is the part of the URL after user/.

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Ground rules

• Test on DevAthena first, then run on Athena.
• Scripts that change things need the right permissions. Changing access requires admin rights on the annotations (ideally a site admin account). Deleting metadata requires write access to the items.
• All scripts process the given folder and all of its subfolders.
• Keep runs/ and logs/ out of Git (already listed in .gitignore), because they contain user IDs and backups.