├── .env.example ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── backend_dev.yml │ ├── backend_prod.yml │ ├── frontend_dev.yml │ ├── frontend_prod.yml │ ├── kill_idle_cons.yml │ ├── refresh_counts.yml │ ├── refresh_db.yml │ ├── refresh_from_datasets.yml │ ├── refresh_voc.yml │ ├── resolve_fetch_failures_0_members.yml │ ├── resolve_fetch_failures_excess_items.yml │ ├── test_backend_e2e_and_unit_and_qc.yml │ ├── test_frontend_e2e_live_dev.yml │ ├── test_frontend_e2e_live_dev_running_local.yml │ ├── test_frontend_e2e_live_prod.yml │ └── test_frontend_unit_and_qc.yml ├── .gitignore ├── .gitmodules ├── .psqlrc.example ├── .run ├── backend.run.xml └── test-onto-api.run.xml ├── LICENSE ├── Procfile ├── README.md ├── backend.sh ├── backend ├── README.md ├── __init__.py ├── api_logger.py ├── app.py ├── config.py ├── db │ ├── README.md │ ├── __init__.py │ ├── ad_hoc_omop_vocab_version.py │ ├── analysis.py │ ├── config.py │ ├── ddl-1-column_types.jinja.sql │ ├── ddl-1-functions.sql │ ├── ddl-10-codeset_counts.jinja.sql │ ├── ddl-11-all_csets.jinja.sql │ ├── ddl-12-all_csets_view.jinja.sql │ ├── ddl-13-concepts_with_counts_ungrouped.jinja.sql │ ├── ddl-14-concepts_with_counts.jinja.sql │ ├── ddl-15-concept_relationship_plus.jinja.sql │ ├── ddl-16-concept_ancestor_plus.jinja.sql │ ├── ddl-17-add-service-user-to-researcher.sql │ ├── ddl-18-apirun_groups.jinja.sql │ ├── ddl-19-concept_graph.jinja.sql │ ├── ddl-2-primary_keys.jinja.sql │ ├── ddl-20-concept_set_json.jinja.sql │ ├── ddl-3-indexes.jinja.sql │ ├── ddl-4-concept_set_members.jinja.sql │ ├── ddl-5-concept_set_container.jinja.sql │ ├── ddl-6-cset_members_items.jinja.sql │ ├── ddl-9-members_items_summary.jinja.sql │ ├── initialize.py │ ├── load.py │ ├── my-temp.cnf │ ├── my.cnf │ ├── my.cnf.example │ ├── queries.py │ ├── queries.sql │ ├── refresh.py │ ├── refresh_dataset_group_tables.py │ ├── refresh_from_datasets.py │ ├── resolve_fetch_failures_0_members.py │ ├── resolve_fetch_failures_excess_items.py │ └── utils.py ├── gunicorn_config.py ├── routes │ ├── cset_crud.py │ ├── db.py │ ├── graph.py │ └── oak.py └── utils.py ├── db_backup.sh ├── docs ├── backend │ └── db │ │ └── analysis.md ├── call_graph.md ├── developer.md ├── eileen_sop_2023-01-31.pdf ├── future.md ├── graph-examples │ ├── graph-example-common-ancestor-nodes.dot │ ├── graph-example-common-ancestor-nodes.svg │ ├── graph-example-common-ancestor-roots.dot │ ├── graph-example-common-ancestor-roots.svg │ ├── graph-example-simple.dot │ ├── graph-example-simple.svg │ ├── graph-examples.dot │ └── graph-examples.svg ├── graph-testing.md ├── graph.md ├── index.md ├── refresh.md ├── refresh_failure_history.md └── screen-shots │ ├── 5f80bfba-malignant-cancer.png │ ├── 5f80bfba-many-small.png │ ├── 9f6f82b-many-small.png │ ├── backwards-dfs.png │ ├── eb27fa7-many-small.png │ ├── gap-filling-algorithm.png │ └── large-to-small_many-small.png ├── enclave_wrangler ├── N3C_recommended_counts_for_AMIA_poster.py ├── README.md ├── actions_api.py ├── actions_old_palantir3file_api.py ├── api_call.py ├── config.py ├── curl-stuff │ ├── actionTypes.json │ ├── actionTypes.sh │ ├── api-get.sh │ ├── concept_descendants.sh │ ├── linkTypesForObjectTypes.sh │ ├── objectTypes.json │ ├── objectTypes.sh │ └── whoami.sh ├── dataset_upload.py ├── datasets.py ├── models.py ├── nameBasedEndpoints.json ├── objects_api.py ├── reviving_ontology_api_stuff.py └── utils.py ├── frontend ├── .babelrc ├── README.md ├── index.html ├── jest.config.js ├── jest.setup.js ├── package.json ├── playwright.config.js ├── public │ ├── athena.ico │ ├── atlas.ico │ ├── favicon.ico │ ├── logo192.png │ ├── logo512.png │ ├── manifest.json │ ├── react-favicon.ico │ └── robots.txt ├── src │ ├── .prettierignore │ ├── App.css │ ├── App.jsx │ ├── __mocks__ │ │ ├── @floating-ui │ │ │ └── react-dom-interactions.js │ │ ├── react-markdown.js │ │ └── react-merge-refs.js │ ├── assets │ │ └── IndentedListIcon.jsx │ ├── components │ │ ├── AboutPage.jsx │ │ ├── AddConcepts.tsx │ │ ├── AlertMessages.jsx │ │ ├── ConceptSetCard.jsx │ │ ├── Concepts.jsx │ │ ├── CsetComparisonPage.jsx │ │ ├── Csets.jsx │ │ ├── CsetsDataTable.jsx │ │ ├── FlexibleContainer.jsx │ │ ├── GraphPlayground.jsx.HOLD │ │ ├── MuiAppBar.jsx │ │ ├── N3CRecommended.jsx │ │ ├── NewCset.jsx │ │ ├── Popover.jsx │ │ ├── Tooltip.jsx │ │ ├── UploadCsv.jsx │ │ ├── UsageReport.jsx │ │ └── dataTableUtils.jsx │ ├── env.dev.js │ ├── env.js │ ├── env.local.js │ ├── env.prod.js │ ├── index.tsx │ ├── logo.svg │ ├── popover_styles.css │ ├── reportWebVitals.js │ ├── state │ │ ├── AppState.jsx │ │ ├── DataCache.jsx │ │ ├── DataGetter.jsx │ │ ├── GraphState.jsx │ │ └── StorageProvider.jsx │ └── utils.jsx ├── static.json ├── staticwebapp.config.json ├── tests │ ├── jest │ │ ├── graph_algorithm.test.js │ │ └── index.OLDtest.jsx │ ├── playwright │ │ ├── README.md │ │ ├── basic-functions.test.js │ │ ├── comparison.todo.js │ │ ├── large-cset-handling.test.js │ │ ├── n3c-recommended.test.js │ │ ├── performance │ │ │ ├── .keep │ │ │ ├── performance-tests-2024-10-01T17.35.csv │ │ │ └── performance-tests-2024-10-01T17.36.csv │ │ ├── setup-test-environments.js │ │ └── test-reporter.js │ ├── test-data │ │ ├── asthmaExampleGraphData.json │ │ ├── diagramCase.json │ │ ├── manySmallGraphContainerGraphData.json │ │ └── singleSmallGraph.json │ └── testUtils.js ├── tsconfig.json ├── vite-env.d.ts ├── vite.config.mjs └── yarn.lock ├── gunicorn_config.py ├── makefile ├── misc ├── ad_hoc │ ├── amia_paper_2024 │ │ └── stats.py │ └── rxnorm_medication_csets │ │ ├── med-csets.csv │ │ ├── medication_csets_from_rxnorm_to_pg.py │ │ └── rxnorm_csets_for_tanner.csv ├── data-and-python-notebooks └── future_features │ ├── octo-stuff │ ├── octo-data.py │ └── octo-sample-data.json │ ├── sssom_map │ ├── README.md │ └── sample_mapping_files │ │ ├── sample1_icd10cm_omop.csv │ │ └── sample2_icd10cm2omop_sssom_mapping.csv │ └── vsac_wrangler │ ├── config.py │ └── google_sheets.py ├── requirements-alt.txt ├── requirements-unlocked.txt ├── requirements.txt ├── runtime.txt ├── startup.txt ├── test ├── __init__.py ├── test_backend │ ├── __init__.py │ ├── all_subsumes_tuples_2022_12_21.pickle │ ├── db │ │ ├── input │ │ │ └── test_refresh_dataset_group_tables │ │ │ │ ├── counts │ │ │ │ ├── concept_set_counts_clamped.csv │ │ │ │ └── deidentified_term_usage_by_domain_clamped.csv │ │ │ │ └── vocab │ │ │ │ ├── concept.csv │ │ │ │ ├── concept_ancestor.csv │ │ │ │ ├── concept_relationship.csv │ │ │ │ └── relationship.csv │ │ ├── test_config.py │ │ ├── test_refresh_dataset_group_tables.py │ │ └── test_utils.py │ ├── routes │ │ ├── __init__.py │ │ ├── static │ │ │ └── concept_graph │ │ │ │ ├── Sulfonylureas.json │ │ │ │ ├── _base_case_hash.txt │ │ │ │ ├── antibiotics 1.json │ │ │ │ ├── autoimmune 1.json │ │ │ │ ├── autoimmune 2.json │ │ │ │ ├── many-small.json │ │ │ │ ├── single-small-second-time.json │ │ │ │ └── single-small.json │ │ └── test_graph.py │ ├── test_backend.py │ └── test_resolve_fetch_failures.py ├── test_database.py ├── test_enclave_wrangler │ ├── __init__.py │ ├── input │ │ ├── test_csets_and_members_enclave_to_db │ │ │ └── objects.pkl │ │ ├── test_dataset_upload_old_palantir3file │ │ │ ├── code_sets.csv │ │ │ ├── concept_set_container_edited.csv │ │ │ └── concept_set_version_item_rv_edited.csv │ │ ├── test_get_link_types │ │ │ └── input.json │ │ ├── test_get_object_types │ │ │ └── input.json │ │ ├── test_upload_cset_container_from_csv │ │ │ └── new_container.csv │ │ ├── test_upload_cset_version_from_csv │ │ │ └── type-2-diabetes-mellitus.csv │ │ └── test_upload_cset_version_from_csv2 │ │ │ ├── new_version.csv │ │ │ └── unused │ │ │ ├── new_version - alternative - not sure if working.csv │ │ │ └── new_version_that_throws_error.csv │ ├── test_actions_api.py │ ├── test_dataset_upload.py │ └── test_objects_api.py ├── utils.py └── utils_db_refresh_test_wrapper.py └── token-life.sh 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