├── .github └── workflows │ ├── ci.yaml │ ├── integration_tests.yaml │ └── wool.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .secrets.baseline ├── Dockerfile ├── Jenkinsfile.performance ├── LICENSE ├── NOTICE ├── README.md ├── azure-devops-pipeline.yaml ├── bin ├── confighelper.py ├── settings.py ├── setup_psqlgraph.py ├── setup_test_database.py └── setup_transactionlogs.py ├── deployment ├── scripts │ └── postgresql │ │ └── postgresql_test_init.sql └── wsgi │ └── gunicorn.conf.py ├── dockerrun.bash ├── docs ├── Gen3 graph data flow.png ├── Makefile ├── SPHINX-LICENSE.txt ├── _config.yml ├── api_reference │ ├── index.rst │ ├── sheepdog.auth.rst │ ├── sheepdog.blueprint.rst │ ├── sheepdog.dictionary.rst │ ├── sheepdog.errors.rst │ ├── sheepdog.globals.rst │ ├── sheepdog.models.rst │ ├── sheepdog.rst │ ├── sheepdog.transactions.rst │ ├── sheepdog.utils.rst │ └── substitutions.rst ├── azure_devops_pipeline.md ├── azure_devops_pipeline_config_1.png ├── azure_devops_pipeline_config_2.png ├── azure_devops_pipeline_config_3.png ├── build │ ├── doctrees │ │ ├── api_reference │ │ │ ├── index.doctree │ │ │ ├── sheepdog.auth.doctree │ │ │ ├── sheepdog.blueprint.doctree │ │ │ ├── sheepdog.dictionary.doctree │ │ │ ├── sheepdog.doctree │ │ │ ├── sheepdog.errors.doctree │ │ │ ├── sheepdog.globals.doctree │ │ │ ├── sheepdog.models.doctree │ │ │ ├── sheepdog.transactions.doctree │ │ │ └── sheepdog.utils.doctree │ │ ├── contents.doctree │ │ ├── entities │ │ │ └── index.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── requests │ │ │ └── index.doctree │ └── html │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── api_reference │ │ ├── index.html │ │ ├── sheepdog.auth.html │ │ ├── sheepdog.blueprint.html │ │ ├── sheepdog.dictionary.html │ │ ├── sheepdog.errors.html │ │ ├── sheepdog.globals.html │ │ ├── sheepdog.html │ │ ├── sheepdog.models.html │ │ ├── sheepdog.transactions.html │ │ └── sheepdog.utils.html │ │ ├── contents.html │ │ ├── entities │ │ └── index.html │ │ ├── genindex-A.html │ │ ├── genindex-B.html │ │ ├── genindex-C.html │ │ ├── genindex-D.html │ │ ├── genindex-E.html │ │ ├── genindex-F.html │ │ ├── genindex-G.html │ │ ├── genindex-H.html │ │ ├── genindex-I.html │ │ ├── genindex-J.html │ │ ├── genindex-L.html │ │ ├── genindex-M.html │ │ ├── genindex-N.html │ │ ├── genindex-O.html │ │ ├── genindex-P.html │ │ ├── genindex-R.html │ │ ├── genindex-S.html │ │ ├── genindex-T.html │ │ ├── genindex-U.html │ │ ├── genindex-V.html │ │ ├── genindex-W.html │ │ ├── genindex-X.html │ │ ├── genindex-all.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── requests │ │ └── index.html │ │ ├── search.html │ │ └── searchindex.js ├── conf.py ├── contents.rst ├── entities │ └── index.rst ├── index.html ├── index.rst ├── local_dev_environment.md └── requests │ └── index.rst ├── openapi ├── README.md ├── __init__.py ├── app_info.py ├── definitions.py ├── docstring_parser.py └── swagger.yml ├── poetry.lock ├── pyproject.toml ├── run.py ├── run_tests.bash ├── sample_usage.py ├── sheepdog ├── __init__.py ├── api.py ├── auth │ └── __init__.py ├── blueprint │ ├── __init__.py │ └── routes │ │ ├── __init__.py │ │ ├── route_utils.py │ │ └── views │ │ ├── __init__.py │ │ └── program │ │ ├── __init__.py │ │ └── project.py ├── config.py ├── dev_settings.py ├── errors.py ├── globals.py ├── sanity_checks.py ├── test_settings.py ├── transactions │ ├── __init__.py │ ├── close │ │ └── __init__.py │ ├── deletion │ │ ├── __init__.py │ │ ├── entity.py │ │ └── transaction.py │ ├── entity_base.py │ ├── release │ │ ├── __init__.py │ │ └── transaction.py │ ├── review │ │ ├── __init__.py │ │ └── transaction.py │ ├── submission │ │ ├── __init__.py │ │ ├── entity.py │ │ └── transaction.py │ ├── transaction_base.py │ └── upload │ │ ├── __init__.py │ │ ├── entity.py │ │ ├── entity_factory.py │ │ ├── sub_entities.py │ │ └── transaction.py ├── utils │ ├── __init__.py │ ├── manifest.py │ ├── parse.py │ ├── s3.py │ ├── scheduling.py │ └── transforms │ │ ├── __init__.py │ │ ├── bcr_xml_to_json.py │ │ └── graph_to_doc.py └── version_data.py └── tests ├── __init__.py ├── ci_commands_script.sh ├── ci_setup.sh ├── conftest.py ├── integration ├── README.md ├── __init__.py ├── api.py ├── conftest.py ├── datadict │ ├── __init__.py │ ├── conftest.py │ ├── schemas │ │ └── dictionary.json │ ├── submission │ │ ├── __init__.py │ │ ├── data │ │ │ ├── aliquot.json │ │ │ ├── all_props.gql │ │ │ ├── all_samples_props.gql │ │ │ ├── analyte.json │ │ │ ├── annotation.json │ │ │ ├── bcr_example1.xml │ │ │ ├── bcr_invalid1.xml │ │ │ ├── bcr_invalid_schema_location1.xml │ │ │ ├── bcr_invalid_schema_location2.xml │ │ │ ├── bcr_invalid_structure.xml │ │ │ ├── biospec1.json │ │ │ ├── biospec2.json │ │ │ ├── biospecimen_props_and_links.gql │ │ │ ├── bulk1.json │ │ │ ├── case.json │ │ │ ├── clinical1.xml │ │ │ ├── clinical2.xml │ │ │ ├── clinical3.xml │ │ │ ├── databundle1.json │ │ │ ├── demographic.json │ │ │ ├── diagnosis.json │ │ │ ├── diagnosis.tsv │ │ │ ├── dump.json │ │ │ ├── experiment.1.json │ │ │ ├── experiment.2.json │ │ │ ├── experimental_metadata.json │ │ │ ├── experimental_metadata.tsv │ │ │ ├── exposure.json │ │ │ ├── file.json │ │ │ ├── file_empty_link.tsv │ │ │ ├── files.tsv │ │ │ ├── just_ids.gql │ │ │ ├── portion.json │ │ │ ├── program.json │ │ │ ├── project.json │ │ │ ├── read_group.json │ │ │ ├── read_group_invalid.json │ │ │ ├── sample.json │ │ │ ├── samples1.csv │ │ │ ├── samples1.tsv │ │ │ ├── samples2.tsv │ │ │ ├── samples_invalid.csv │ │ │ ├── single_case_tree.gql │ │ │ ├── single_case_tree_with_fragments.gql │ │ │ ├── submitted_unaligned_reads.json │ │ │ ├── submitted_unaligned_reads_invalid.json │ │ │ ├── treatment.json │ │ │ └── whitespace.tsv │ │ ├── test_admin_endpoints.py │ │ ├── test_bcr_xml_to_json.py │ │ ├── test_endpoints.py │ │ ├── test_upload.py │ │ └── utils.py │ ├── system_test.py │ └── test_ssl_and_isolation_level.py ├── datadictwithobjid │ ├── __init__.py │ ├── conftest.py │ ├── schemas │ │ └── dictionary.json │ ├── submission │ │ ├── __init__.py │ │ ├── data │ │ │ ├── aliquot.json │ │ │ ├── all_props.gql │ │ │ ├── all_samples_props.gql │ │ │ ├── analyte.json │ │ │ ├── annotation.json │ │ │ ├── bcr_example1.xml │ │ │ ├── bcr_invalid1.xml │ │ │ ├── bcr_invalid_schema_location1.xml │ │ │ ├── bcr_invalid_schema_location2.xml │ │ │ ├── bcr_invalid_structure.xml │ │ │ ├── biospec1.json │ │ │ ├── biospec2.json │ │ │ ├── biospecimen_props_and_links.gql │ │ │ ├── bulk1.json │ │ │ ├── case.json │ │ │ ├── clinical1.xml │ │ │ ├── clinical2.xml │ │ │ ├── clinical3.xml │ │ │ ├── databundle1.json │ │ │ ├── demographic.json │ │ │ ├── diagnosis.json │ │ │ ├── diagnosis.tsv │ │ │ ├── dump.json │ │ │ ├── experiment.1.json │ │ │ ├── experiment.2.json │ │ │ ├── experiment.json │ │ │ ├── experimental_metadata.json │ │ │ ├── experimental_metadata.tsv │ │ │ ├── experimental_metadata_bad_link.tsv │ │ │ ├── exposure.json │ │ │ ├── file.json │ │ │ ├── file_empty_link.tsv │ │ │ ├── files.tsv │ │ │ ├── just_ids.gql │ │ │ ├── portion.json │ │ │ ├── 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