OHSU CEDAR Cyclic IF and H&E images
source venv/bin/activate
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements-dev.txt
python3 -m pip install -e .
The input directory:
tests/fixtures-new/
├── HandE
├── RegisteredImages
│ ├── 17633-6-Scene-001
│ ├── 18538-6-Scene-001
│ ├── 19142-6-Scene-001
│ ├── 24952-6-Scene-001
│ ├── 30411-6-Scene-001
│ ├── 31022-6-Scene-001
│ ├── 31480-6-Scene-001
│ ├── 33548-6-Scene-001
│ ├── 38592-6-Scene-001
│ ├── 48411-6-Scene-001
│ ├── 54774-4-Scene-001
│ ├── 57494-6-Scene-001
│ └── 57658-6-Scene-001
└── annotations
will produce:
gen3_util meta import dir tests/fixtures/ tmp/output --project_id aced-nvidia --plugin_path gen3_util_plugin_nvidia --remove_path_prefix tests/fixtures/
summary:
ResearchStudy:
count: 1
ResearchSubject:
count: 13
Patient:
count: 13
Specimen:
count: 13
DocumentReference:
count: 738
size: 74437
msg: OK
Output files:
tmp/output
├── DocumentReference.ndjson
├── Patient.ndjson
├── ResearchStudy.ndjson
├── ResearchSubject.ndjson
└── Specimen.ndjson
Identifiers:
$ cat tmp/output/*.ndjson | jq -rc '. as $r | .identifier[]? | [$r.resourceType, .value]'
["Patient","P1"]
["Specimen","T1"]
pytest tests/
- PyPi
# update pypi
# pypi credentials - see https://twine.readthedocs.io/en/stable/#environment-variables
export TWINE_USERNAME= # the username to use for authentication to the repository.
export TWINE_PASSWORD= # the password to use for authentication to the repository.
# this could be maintained as so: export $(cat .env | xargs)
rm -r dist/
python3 setup.py sdist bdist_wheel
twine upload dist/*