fw_cloud.mri_export This script can be run anywhere (with appropriate network access, of course) to scrape mri metadata from all v2 and corsica projects on Flywheel and store it in a warehouse database.
fw_cloud.slide_export This script can be run anywhere (with appropriate network access, of course) to scrape histology metadata from cbtn_histology project on Flywheel and store it in a warehouse database.
fw_cloud.report_export: This script can be run anywhere (with appropriate network access, of course) to scrape cbtn report metadata from Flywheel and store it in a warehouse database.
Just run:
- for fw_cloud.mri_export:
pip3 install -r requirements.txt
python3 mri_export.py
-
for fw_cloud.slide_export:
pip3 install -r requirements.txt
python3 slide_export.py
-
for fw_cloud.report_export:
pip3 install -r requirements.txt
python3 report_export.py
Operation currently depends on two environment variables:
| Environment Key | Description |
|---|---|
| FLYWHEEL_API_TOKEN | Your API token for Flywheel. It looks like chop.flywheel.io:<random_alphanum>.D3b has a gsuite service account for this [email protected]. |
| D3B_WAREHOUSE_DB_URL | A user/pass authenticated URL like postgresql://<username>:<password>@<server_uri>/postgres |