CURATION-VSCODE-INTEGRATIONS

These dots provide project code integration with VS Code post DC-1820.

1. .env - defines the environmental variables for running tests. Currently tests are run within the host's virtual env. This is a vscode limitation. Instead, tests can be run using DC-1820 curation.sh script (or the powershell equiv.) if you wish to run tests within docker.

2. .vscode contains the launch.json and tasks.json files for running curation in docker. Furthermore, settings.json defines the configuration for running python tests (discovery, execution, and debugging)

Configuration

For the .env file, fill out the following information.

Personal details:

USERNAME=<FIRST_INITIAL_LASTNAME>
GH_USERNAME=<GITHUB_USERNAME>

The following path variables must point to host locations. PYTHONPATH must point to the data_steward folder (an incorrect path will cause project import errors during test execution).

GOOGLE_APPLICATION_CREDENTIALS=/PATH/TO/CREDENTIALS/aou-res-curation-test.json
PYTHONPATH=/PATH/TO/PROJECT/curation/data_steward

Define buckets and datasets:

DRC_BUCKET_NAME=<YOUR_NAME>_drc
BUCKET_NAME_FAKE=<YOUR_NAME>_fake
BUCKET_NAME_NYC=<YOUR_NAME>_nyc
BUCKET_NAME_PITT=<YOUR_NAME>_pitt
BUCKET_NAME_CHS=<YOUR_NAME>_chs
BUCKET_NAME_UNIONED_EHR=<YOUR_NAME>_drc

BIGQUERY_DATASET_ID=<YOUR_NAME>_ehr
RDR_DATASET_ID=<YOUR_NAME>_rdr
COMBINED_DATASET_ID=<YOUR_NAME>_combined
UNIONED_DATASET_ID=<YOUR_NAME>_unioned
COMBINED_DEID_DATASET_ID=<YOUR_NAME>_deid

Setting up tasks.json only requires personal details, dataset names, and bucket names.

"env": {
    // These values are configured for the container environment
    // and should not be modified
    "PYTHONPATH": "/home/curation/project/curation/curation_venv/lib/python3.7/site-packages",
    "GOOGLE_APPLICATION_CREDENTIALS": "/home/curation/project/curation/aou-res-curation-test.json",
    "APPLICATION_ID": "aou-res-curation-test",
    "GOOGLE_CLOUD_PROJECT": "aou-res-curation-test",
    "VOCABULARY_DATASET": "vocabulary20201008",
    // These values are for you to configure
    "GH_USERNAME": "<GITHUB_USERNAME>",
    "USERNAME": "<FIRST_INITIAL_LASTNAME>",
    "DRC_BUCKET_NAME": "<YOUR_NAME>_drc",
    "BUCKET_NAME_FAKE": "<YOUR_NAME>_fake",
    "BUCKET_NAME_NYC": "<YOUR_NAME>_nyc",
    "BUCKET_NAME_PITT": "<YOUR_NAME>_pitt",
    "BUCKET_NAME_CHS": "<YOUR_NAME>_chs",
    "BUCKET_NAME_UNIONED_EHR": "<YOUR_NAME>_drc",
    "BIGQUERY_DATASET_ID": "<YOUR_NAME>_ehr",
    "RDR_DATASET_ID": "<YOUR_NAME>_rdr",
    "COMBINED_DATASET_ID": "<YOUR_NAME>_combined",
    "UNIONED_DATASET_ID": "<YOUR_NAME>_unioned",
    "COMBINED_DEID_DATASET_ID": "<YOUR_NAME>_deid"
}

finally, define your entrypoint in tasks.json:

"python": {
    // Define your entrypoint here
    // NOTE: this is a path within the container.
    // It must start with /home/curation/project/curation/
    "file": "/home/curation/project/curation/data_steward/main.py",
}