.circleci/config.yml .coveragerc .dockerignore .github/workflows/dockerimage.yml .github/workflows/gh_release.yml .gitignore CHANGELOG.md Dockerfile Jenkinsfile JenkinsfileWorker LICENSE README.md bin/dev_entrypoint.sh bin/dev_worker.sh bin/entrypoint.sh bin/scheduler.conf bin/worker.conf creator/__init__.py creator/analyses/__init__.py creator/analyses/analyzer.py creator/analyses/apps.py creator/analyses/factories.py creator/analyses/file_types.py creator/analyses/migrations/0001_initial.py creator/analyses/migrations/0002_analysis_error_message.py creator/analyses/migrations/0003_fix_permission_name.py creator/analyses/migrations/__init__.py creator/analyses/models.py creator/analyses/mutations.py creator/analyses/schema.py creator/authentication.py creator/buckets/__init__.py creator/buckets/apps.py creator/buckets/buckets.py creator/buckets/factories.py creator/buckets/migrations/0001_add_buckets.py creator/buckets/migrations/0002_add_custom_permissions.py creator/buckets/migrations/__init__.py creator/buckets/models.py creator/buckets/mutations.py creator/buckets/scanner.py creator/buckets/schema.py creator/data_reviews/__init__.py creator/data_reviews/apps.py creator/data_reviews/factories.py creator/data_reviews/migrations/0001_initial.py creator/data_reviews/migrations/__init__.py creator/data_reviews/models.py creator/data_reviews/mutations.py creator/data_reviews/nodes.py creator/data_reviews/queries.py creator/data_reviews/schema.py creator/data_reviews/signals.py creator/decorators.py creator/dev/__init__.py creator/dev/urls.py creator/dev/views.py creator/email/templates/base.html creator/email/templates/base.txt creator/email/templates/invite.html creator/email/templates/invite.txt creator/events/__init__.py creator/events/apps.py creator/events/migrations/0001_initial.py creator/events/migrations/0002_correct_enums.py creator/events/migrations/0003_project_events.py creator/events/migrations/0004_add_task_events.py creator/events/migrations/0005_add_buckets.py creator/events/migrations/0006_collaborator_events.py creator/events/migrations/0007_add_custom_permissions.py creator/events/migrations/0008_add_sequencing_status.py creator/events/migrations/0009_add_ingestion_status.py creator/events/migrations/0010_add_phenotype_status.py creator/events/migrations/0011_add_referral_tokens_status.py creator/events/migrations/0012_add_slack_events.py creator/events/migrations/0013_updated_event_types.py creator/events/migrations/0014_add_data_review.py creator/events/migrations/__init__.py creator/events/models.py creator/events/schema.py creator/events/signals.py creator/extract_configs/templates/family_trio_config.py creator/extract_configs/templates/genomic_workflow_output_manifest_config.py creator/extract_configs/templates/participant_config.py creator/extract_configs/templates/s3_scrape_config.py creator/extract_configs/views.py creator/fields.py creator/files/__init__.py creator/files/apps.py creator/files/factories.py creator/files/management/__init__.py creator/files/management/commands/__init__.py creator/files/management/commands/fakefiles.py creator/files/migrations/0001_initial.py creator/files/migrations/0002_downloadtoken.py creator/files/migrations/0003_other_file_type.py creator/files/migrations/0004_dev_tokens.py creator/files/migrations/0005_dev_tokens_unique_name.py creator/files/migrations/0006_increase_description_length.py creator/files/migrations/0007_rename_objects_to_versions.py creator/files/migrations/0007_rename_objects_to_versions_squashed.py creator/files/migrations/0008_add_version_description.py creator/files/migrations/0008_update_version_foreign_keys.py creator/files/migrations/0009_add_version_state.py creator/files/migrations/0009_update_version_descriptions.py creator/files/migrations/0010_add_version_file_name.py creator/files/migrations/0010_version_file_names_squashed.py creator/files/migrations/0011_add_creator.py creator/files/migrations/0011_populate_version_file_name.py creator/files/migrations/0012_add_token_creator.py creator/files/migrations/0013_file_tags.py creator/files/migrations/0014_add_dbGaP_type.py creator/files/migrations/0015_add_custom_permissions.py creator/files/migrations/0016_version_mutation_permission.py creator/files/migrations/0017_make_fields_optional.py creator/files/migrations/0018_add_study_to_version.py creator/files/migrations/0019_add_file_type.py creator/files/migrations/0020_version_extract_config_permission.py creator/files/migrations/0021_add_file_types.py creator/files/migrations/0022_add_genomic_workflow_output_type.py creator/files/migrations/__init__.py creator/files/models.py creator/files/mutations/__init__.py creator/files/mutations/download.py creator/files/mutations/file.py creator/files/mutations/version.py creator/files/nodes/__init__.py creator/files/nodes/file.py creator/files/nodes/version.py creator/files/schema/__init__.py creator/files/schema/download.py creator/files/schema/file.py creator/files/schema/version.py creator/files/views.py creator/groups.py creator/jobs/__init__.py creator/jobs/apps.py creator/jobs/migrations/0001_move_jobs.py creator/jobs/migrations/__init__.py creator/jobs/models.py creator/jobs/schema.py creator/jobs/views.py creator/management/commands/permission_tables.py creator/management/commands/schedule_jobs.py creator/management/commands/setup_permissions.py creator/management/commands/setup_test_user.py creator/middleware.py creator/migrations/0001_initial.py creator/migrations/0002_auto_20190321_1936.py creator/migrations/0003_add_user_sub.py creator/migrations/0004_add_user_picture.py creator/migrations/0005_add_subscriptions.py creator/migrations/0006_add_slack_settings.py creator/migrations/0007_add_email_notify.py creator/migrations/0008_nonunique_username.py creator/migrations/0009_add_job.py creator/migrations/0010_list_all_users_permission.py creator/migrations/0011_add_custom_permissions.py creator/migrations/0012_move_jobs.py creator/migrations/__init__.py creator/models.py creator/projects/__init__.py creator/projects/apps.py creator/projects/cavatica.py creator/projects/factories.py creator/projects/migrations/0001_add_projects.py creator/projects/migrations/0002_project_workflow_type.py creator/projects/migrations/0003_project_update_workflows.py creator/projects/migrations/0004_project_deleted_field.py creator/projects/migrations/0005_auto_20200204_1541.py creator/projects/migrations/0006_add_cavatica_permissions.py creator/projects/migrations/__init__.py creator/projects/models.py creator/projects/mutations.py creator/projects/schema.py creator/referral_tokens/__init__.py creator/referral_tokens/apps.py creator/referral_tokens/factories.py creator/referral_tokens/migrations/0001_initial.py creator/referral_tokens/migrations/__init__.py creator/referral_tokens/models.py creator/referral_tokens/mutations.py creator/referral_tokens/schema.py creator/releases/__init__.py creator/releases/apps.py creator/releases/factories.py creator/releases/management/commands/fakereleases.py creator/releases/migrations/0001_initial.py creator/releases/migrations/0002_add_release_events.py creator/releases/migrations/0003_add_release_log.py creator/releases/migrations/0004_remove_delete_cascade.py creator/releases/migrations/__init__.py creator/releases/models.py creator/releases/mutations.py creator/releases/nodes.py creator/releases/queries.py creator/releases/schema.py creator/releases/signals.py creator/releases/slack.py creator/releases/tasks.py creator/releases/validators.py creator/schema.py creator/settings/__init__.py creator/settings/development.py creator/settings/features.py creator/settings/production.py creator/settings/testing.py creator/slack.py creator/status/__init__.py creator/status/apps.py creator/status/banners/__init__.py creator/status/banners/factories.py creator/status/banners/models.py creator/status/banners/mutations.py creator/status/banners/nodes.py creator/status/banners/queries.py creator/status/migrations/0001_add_banners.py creator/status/migrations/__init__.py creator/status/models.py creator/status/schema.py creator/status/settings/__init__.py creator/status/settings/nodes.py creator/status/settings/queries.py creator/studies/__init__.py creator/studies/apps.py creator/studies/dataservice.py creator/studies/factories.py creator/studies/management/commands/.syncstudies.py.swo creator/studies/management/commands/fakestudies.py creator/studies/management/commands/syncstudies.py creator/studies/migrations/0001_initial.py creator/studies/migrations/0002_auto_20190226_1748.py creator/studies/migrations/0003_auto_20190226_2048.py creator/studies/migrations/0004_update_short_name_limit.py creator/studies/migrations/0005_study_name_nullable.py creator/studies/migrations/0006_add_release_date.py creator/studies/migrations/0007_study_description.py creator/studies/migrations/0008_remove_batch.py creator/studies/migrations/0009_study_grant_fields.py creator/studies/migrations/0010_study_deleted.py creator/studies/migrations/0011_add_collaborators.py creator/studies/migrations/0012_add_buckets.py creator/studies/migrations/0013_add_custom_permissions.py creator/studies/migrations/0014_add_sequencing_status.py creator/studies/migrations/0015_add_ingestion_status.py creator/studies/migrations/0016_add_phenotype_status.py creator/studies/migrations/0017_add_slack_channel.py creator/studies/migrations/0018_add_slack_notify.py creator/studies/migrations/0019_add_through_relationship.py creator/studies/migrations/0020_add_collaborator_role.py creator/studies/migrations/0021_add_study_to_version.py creator/studies/migrations/0022_add_investigator_name.py creator/studies/migrations/__init__.py creator/studies/models.py creator/studies/mutations.py creator/studies/nodes.py creator/studies/schema.py creator/studies/views.py creator/tasks.py creator/urls.py creator/users/__init__.py creator/users/apps.py creator/users/factories.py creator/users/mutations.py creator/users/schema.py creator/utils.py creator/version_info.py creator/views.py creator/wsgi.py dev-requirements.txt docker-compose.dataservice.yml docker-compose.email.yml docker-compose.yml docker.env docs/_static/images/email.png docs/_static/images/study_creator.svg docs/_static/study_creator.png docs/auth0.rst docs/authentication.rst docs/authorization.rst docs/bucketservice.rst docs/cavatica.rst docs/concepts.rst docs/conf.py docs/dataservice.rst docs/development/dev_api.rst docs/development/email.rst docs/development/quickstart.rst docs/downloads.rst docs/file_upload/README.md docs/index.rst docs/releases/introduction.rst docs/releases/process.rst docs/study_buckets.rst docs/uploads.rst manage.py pytest.ini release_maker_cfg.json requirements.txt tests/__init__.py tests/analyses/__init__.py tests/analyses/test_create_analysis.py tests/analyses/test_extract_data.py tests/analyses/test_file_formats.py tests/analyses/test_query.py tests/authentication/test_middleware.py tests/authentication/test_service_auth.py tests/buckets/test_bucket_authorization.py tests/buckets/test_buckets.py tests/buckets/test_link_bucket.py tests/buckets/test_scanner.py tests/conftest.py tests/data/SD_ME0WME0W/FV_4DP2P2Y2_clinical.csv tests/data/SD_ME0WME0W/FV_4DP2P2Y2_clinical.tsv tests/data/SD_ME0WME0W/FV_4DP2P2Y2_clinical.txt tests/data/SD_ME0WME0W/FV_4DP2P2Y2_clinical.xls tests/data/SD_ME0WME0W/FV_4DP2P2Y2_clinical.xlsx tests/data/SD_ME0WME0W/s3_scrape.csv tests/data/SD_ME0WME0W/s3_scrape_extra.csv tests/data/SD_ME0WME0W/s3_scrape_partial.csv tests/data/data.csv tests/data/genomic_workflow_output_manifest_config.py tests/data/manifest.txt tests/data/name with spaces.txt tests/data/s3_scrape_config.py tests/data_reviews/test_data_reviews_events.py tests/data_reviews/test_data_reviews_mutations.py tests/data_reviews/test_data_reviews_queries.py tests/data_reviews/test_data_reviews_signals.py tests/decorators.py tests/dev/__init__.py tests/dev/conftest.py tests/dev/test_change_groups.py tests/dev/test_reset_db.py tests/events/test_event_auth.py tests/events/test_files.py tests/events/test_projects.py tests/events/test_studies.py tests/events/test_versions.py tests/files/test_create_file.py tests/files/test_delete.py tests/files/test_dev_tokens.py tests/files/test_downloads.py tests/files/test_extract_config.py tests/files/test_file_type_validation.py tests/files/test_signed_urls.py tests/files/test_update_files.py tests/files/test_update_versions.py tests/files/test_upload.py tests/files/test_valid_types.py tests/jobs/test_models.py tests/keys/jwks.json tests/keys/other_private_key.pem tests/keys/private_key.pem tests/keys/public_key.pem tests/projects/__init__.py tests/projects/fixtures.py tests/projects/test_cavatica.py tests/projects/test_cavatica_sync.py tests/projects/test_import_volume_files.py tests/projects/test_link_project.py tests/projects/test_new_project.py tests/projects/test_query.py tests/projects/test_update_project.py tests/referral_tokens/test_exchange_referral_token.py tests/referral_tokens/test_new_referral_token.py tests/referral_tokens/test_query.py tests/releases/test_cancel_release.py tests/releases/test_check_release.py tests/releases/test_check_task.py tests/releases/test_publish_release.py tests/releases/test_release_cancel_tasks.py tests/releases/test_release_event_queries.py tests/releases/test_release_event_signals.py tests/releases/test_release_initialize_tasks.py tests/releases/test_release_service_mutations.py tests/releases/test_release_service_queries.py tests/releases/test_release_start_tasks.py tests/releases/test_release_task.py tests/releases/test_release_task_queries.py tests/releases/test_releases_queries.py tests/releases/test_scan_releases.py tests/releases/test_slack.py tests/releases/test_start_release.py tests/releases/test_update_release.py tests/releases/test_validators.py tests/status/test_banner_mutations.py tests/status/test_banner_queries.py tests/status/test_status_queries.py tests/studies/test_collaborators.py tests/studies/test_create_study.py tests/studies/test_dataservice.py tests/studies/test_update_ingestion_status.py tests/studies/test_update_phenotype_status.py tests/studies/test_update_sequencing_status.py tests/studies/test_update_study.py tests/tasks/test_analyze_task.py tests/tasks/test_dataservice_sync_task.py tests/tasks/test_import_delivery_files_task.py tests/tasks/test_setup_bucket_task.py tests/tasks/test_setup_cavatica_task.py tests/tasks/test_setup_slack_task.py tests/tasks/test_slack_notify_task.py tests/tasks/test_sync_buckets_task.py tests/tasks/test_sync_cavatica_projects_task.py tests/test_authorized.py tests/test_ego_signing.py tests/test_fields.py tests/test_middleware.py tests/test_models.py tests/test_not_found.py tests/test_query.py tests/test_slack.py tests/test_utils.py tests/test_version_info.py tests/users/test_create.py tests/users/test_groups.py tests/users/test_list.py tests/users/test_membership.py tests/users/test_permissions.py tests/users/test_profile.py tests/users/test_subscriptions.py tests/users/test_update.py <<<<<< network # path=/root/workdir/coverage.xml /root/workdir/creator <<<<<< EOF