├── .dockerignore ├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── Dockerfile ├── Dockerfile-dev ├── README.md ├── cerberus1 ├── __init__.py ├── cerberus.py ├── errors.py ├── platform.py ├── schema.py └── utils.py ├── data ├── Final_gene_map_oncopanel.v1.txt ├── genes.csv ├── genes.oncopanel.csv ├── oncotree_file.txt ├── tcga.clinical.pkl ├── tcga.genomic.pkl └── tcga │ └── matchminer │ ├── clinical.bson │ ├── clinical.metadata.json │ ├── filter.bson │ ├── filter.metadata.json │ ├── genomic.bson │ ├── genomic.metadata.json │ ├── trial.bson │ ├── trial.metadata.json │ ├── user.bson │ └── user.metadata.json ├── docker-compose.yml ├── elasticsearch ├── elasticsearch.yml ├── mapping.json ├── settings.json └── synonyms.txt ├── email.config.json ├── filters_config ├── filters_config.json └── plugins │ ├── DFCIFilterMatchDocumentCreator.py │ ├── DFCIQueryNodeContainerTransformer.py │ ├── DFCIQueryNodeTransformer.py │ └── DFCIQueryTransformers.py ├── gunicorn.conf.py ├── matchminer ├── __init__.py ├── components │ ├── __init__.py │ ├── gi │ │ ├── __init__.py │ │ └── data_model.py │ └── oncore │ │ ├── __init__.py │ │ ├── oncore_app.py │ │ ├── oncore_utilities.py │ │ └── templates │ │ └── curateInterface.html ├── constants.py ├── custom.py ├── data │ └── tumor_tree.txt ├── data_model.py ├── database.py ├── elasticsearch.py ├── event_hooks │ ├── __init__.py │ ├── clinical.py │ ├── event_utils.py │ ├── genomic.py │ ├── hipaa.py │ ├── immunoprofile.py │ ├── match.py │ ├── patient_view.py │ ├── public_stats.py │ ├── statistics.py │ ├── status.py │ ├── trial.py │ ├── trial_match.py │ └── user.py ├── events.py ├── hooks │ ├── UtilHooks.py │ └── __init__.py ├── matchengine_v1 │ ├── README │ ├── data │ │ └── tumor_tree.txt │ ├── engine.py │ ├── schema.py │ ├── settings.py │ ├── sort.py │ ├── utilities.py │ └── validation.py ├── miner.py ├── security.py ├── settings.py ├── settings_dev.py ├── settings_prod.py ├── templates │ ├── __init__.py │ ├── emails │ │ ├── __init__.py │ │ └── emails.py │ └── templates │ │ ├── attrs.html │ │ ├── base.html │ │ ├── index.html │ │ └── match.html ├── trial_search.py ├── utilities.py └── validation.py ├── pymm_run.py ├── requirements.in ├── requirements.txt ├── secrets_json_dev.json ├── secrets_json_dev_nodocker.json ├── secrets_json_test_nodocker.json ├── setup.sh ├── tests ├── __init__.py ├── data │ ├── __init__.py │ ├── clinical.bson │ ├── clinical.metadata.json │ ├── genomic.bson │ ├── genomic.metadata.json │ ├── mock │ │ ├── __init__.py │ │ └── trial.py │ ├── oncotree_file.txt │ ├── scaffolds │ │ └── normalize.bson │ ├── yaml │ │ ├── 00-001.yml │ │ ├── 00-002.yml │ │ ├── 00-003.yml │ │ └── bad.yml │ └── yaml_schema.py ├── test_cbioengine │ ├── __init__.py │ └── test_ioutils.py ├── test_matchminer │ ├── __init__.py │ ├── filters_config │ │ ├── filters_config.json │ │ └── plugins │ │ │ ├── DFCIFilterMatchDocumentCreator.py │ │ │ ├── DFCIQueryNodeContainerTransformer.py │ │ │ ├── DFCIQueryNodeTransformer.py │ │ │ └── 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