GDC Models

Git repository centrally stores and serves GDC data models defined in static YAML files.

GDC Models

Update the data models

Sync

Syncing is the process of updating the models with any properties which may be derived from external sources, normalizing keywords, as well as insuring all default mapping values are set. This process should be run after the gdcdictionary is updated and when any new property is added to the viz indices.

The process can be run for any index (-i) and any of its doc-types (-d). Multiple can be specified on the command line and if none are provided for either all of the respective type are run.

Install

pip-compile --extra=sync
--index-url=https://nexus.osdc.io/repository/pypi-gdc-releases/simple
--output-file=requirements-sync.txt
--strip-extras
--upgrade pip install -r requirements-sync.txt

Examples

Run all indices/doc-types:

sync-models

Run all associated doc-types:

sync-models -i gdc_from_graph -i case_centric

Run a singular doc-type:

sync-models -i gdc_from_graph -d file

After Syncing

Once the sync has been run, review and commit the generated models. These should contain all new properties from the graph (graph indices) and all keywords should have the clinical normalizer applied if appropriate.

WARNING: YAML & Pre-Commit Hook

Edit the YAML files as usual, then commit changes to git. A pre-commit hook will validate YAML and ensure it's well formatted. It is important to keep YAML file formatted consistently, such as using 2 whitespaces for indentation, across all revisions. This will make change tracking much easier.

If a YAML validation issue is reported, you will need to commit again.

The pre-commit hook will automatically format all new or changed YAML files. A copy of unchanged original YAML file is kept with .bak suffix. Before proceed with retrying git commit, please diff your original YAML and the automatically formatted one to ensure YAML formatting did not create any error.

Use the data models

Import ES models into Python code

from gdcmodels import get_es_models

es_models = get_es_models()

Initialize Elasticsearch index settings and mappings using command line script

# get usage information by: python init_index.py -h
# initialize Elasticsearch indexes: case_set and file_set, add prefix 'gdc_r52' to index name
python init_index.py --index case_set file_set --host localhost --prefix gdc_r52

Setup pre-commit hook to check for secrets and format YAML

We use pre-commit to setup pre-commit hooks for this repo. We use detect-secrets to search for secrets being committed into the repo.

To install the pre-commit hook, run

pre-commit install

To update the .secrets.baseline file run

detect-secrets scan --update .secrets.baseline

.secrets.baseline contains all the string that were caught by detect-secrets but are not stored in plain text. Audit the baseline to view the secrets .

detect-secrets audit .secrets.baseline