# nvidia-collaboration
OHSU CEDAR Cyclic IF and H&E images
## Getting started
### Setup python environment
```commandline
source venv/bin/activate
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements-dev.txt
python3 -m pip install -e .
```
## Run meta import with --plugin_path
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
```
### expected results
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"]
```
## Run the tests
```
pytest tests/
```
## Distribution
- 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/*
```
Raw data
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"description": "# nvidia-collaboration\nOHSU CEDAR Cyclic IF and H&E images\n\n## Getting started\n\n### Setup python environment\n\n```commandline\nsource venv/bin/activate\npython3 -m pip install -r requirements.txt\npython3 -m pip install -r requirements-dev.txt \npython3 -m pip install -e .\n```\n\n## Run meta import with --plugin_path\n\nThe input directory:\n\n```\ntests/fixtures-new/\n\u251c\u2500\u2500 HandE\n\u251c\u2500\u2500 RegisteredImages\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 17633-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 18538-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 19142-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 24952-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 30411-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 31022-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 31480-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 33548-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 38592-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 48411-6-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 54774-4-Scene-001\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 57494-6-Scene-001\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 57658-6-Scene-001\n\u2514\u2500\u2500 annotations\n\n```\n\nwill produce:\n\n```\ngen3_util meta import dir tests/fixtures/ tmp/output --project_id aced-nvidia --plugin_path gen3_util_plugin_nvidia --remove_path_prefix tests/fixtures/\nsummary:\n ResearchStudy:\n count: 1\n ResearchSubject:\n count: 13\n Patient:\n count: 13\n Specimen:\n count: 13\n DocumentReference:\n count: 738\n size: 74437\nmsg: OK\n\n\n```\n\n### expected results\n\nOutput files:\n\n```\ntmp/output\n\u251c\u2500\u2500 DocumentReference.ndjson\n\u251c\u2500\u2500 Patient.ndjson\n\u251c\u2500\u2500 ResearchStudy.ndjson\n\u251c\u2500\u2500 ResearchSubject.ndjson\n\u2514\u2500\u2500 Specimen.ndjson\n```\n\nIdentifiers:\n\n```\n$ cat tmp/output/*.ndjson | jq -rc '. as $r | .identifier[]? | [$r.resourceType, .value]'\n[\"Patient\",\"P1\"]\n[\"Specimen\",\"T1\"]\n```\n\n\n## Run the tests\n\n```\npytest tests/\n```\n## Distribution\n\n- PyPi\n\n```\n# update pypi\n\n# pypi credentials - see https://twine.readthedocs.io/en/stable/#environment-variables\n\nexport TWINE_USERNAME= # the username to use for authentication to the repository.\nexport TWINE_PASSWORD= # the password to use for authentication to the repository.\n\n# this could be maintained as so: export $(cat .env | xargs)\n\nrm -r dist/\npython3 setup.py sdist bdist_wheel\ntwine upload dist/*\n```\n\n\n",
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