aced-idp/nvidia-collaboration

OHSU CEDAR Cyclic IF and H&E images

nvidia-collaboration

OHSU CEDAR Cyclic IF and H&E images

Getting started

Setup python environment

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/*

nvidia-collaboration's Issues

Task (Assay) code, categories

As an ACED user, in order to identify assay type, I need Task's category and code set to the correct ontology values.

Quench values in Observation

As an ACED researcher, in order to accurately query data, "quench" values must be coded correctly.

Distinct Patient (Cell line)

As an ACED researcher, in order to accurately query data, I need to correlate specimen to patient.

(Patient/Cell line is currently unknown, assume each tissue comes from different patient)

Sifter implementation

As an ACED engineer, in order to reproduce graph(s), I need to incorporate sifter.

Replace/enhance transform with sifter

File Attributes

As an aced researcher, in order to accurately query data, DocumentReference's attachment should have file md5 and size attributes