Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __call__() (chat_protocol.HandleError method) (mdvtools.dbutils.safe_mdv_app.PrefixMiddleware method) __table_args__ (mdvtools.dbutils.dbmodels.Project attribute) __tablename__ (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.SharedObject attribute) (mdvtools.dbutils.dbmodels.User attribute) (mdvtools.dbutils.dbmodels.UserPreference attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) _add_dimension_reductions() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _add_dims() (in module mdvtools.conversions) _add_layers() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _add_unstructured_data() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_anndata() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_chunked_sparse_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_dense_sparse_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_dt_heatmap() (in module mdvtools.conversions) _create_edge_case_anndata() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_expression_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_incremental_csr_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_moderately_sparse_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_obs_data() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_single_sparse_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_skeleton_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_var_data() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _create_very_sparse_matrix() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _ensure_log_file_exists() (chatlog.ChatLogger method) _generate_fast_chunk_indices() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _generate_realistic_expression_values() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _generate_unique_chunk_indices() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) _get_h5_handle() (mdvtools.mdvproject.MDVProject method) _get_optimal_chunk_size() (mdvtools.mdvproject.MDVProject method) _initialize_oauth() (mdvtools.auth.auth0_provider.Auth0Provider method) _jwks_cache (in module mdvtools.auth.auth0_provider) _jwks_cache_expiry (in module mdvtools.auth.auth0_provider) _lint_code_with_ruff() (in module code_manipulation) _lock (mdvtools.mdvproject.MDVProject attribute) A abundance_box_plot module AbundanceBoxPlot (class in abundance_box_plot) access_level (mdvtools.dbutils.dbmodels.Project attribute) accessed_timestamp (mdvtools.dbutils.dbmodels.Project attribute) active_projects_cache (in module mdvtools.auth.authutils) add_annotations() (mdvtools.mdvproject.MDVProject method) add_centroid_plots() (in module mdvtools.spatial) add_column_to_group() (in module mdvtools.mdvproject) add_datasource() (mdvtools.mdvproject.MDVProject method) add_genome_browser() (mdvtools.mdvproject.MDVProject method) add_image_set() (mdvtools.mdvproject.MDVProject method) add_images_to_datasource() (mdvtools.mdvproject.MDVProject method) add_new_project() (mdvtools.dbutils.dbservice.ProjectService static method) add_or_update_file_in_project() (mdvtools.dbutils.dbservice.FileService static method) add_or_update_image_datasource() (mdvtools.mdvproject.MDVProject method) add_or_update_user() (mdvtools.dbutils.dbservice.UserService static method) add_or_update_user_project() (mdvtools.dbutils.dbservice.UserProjectService static method) add_refseq_track() (mdvtools.mdvproject.MDVProject method) add_region_images() (mdvtools.mdvproject.MDVProject method) add_rows_as_columns_link() (mdvtools.mdvproject.MDVProject method) add_rows_as_columns_subgroup() (mdvtools.mdvproject.MDVProject method) add_safe_headers() (in module mdvtools.server_utils) add_viv_images() (mdvtools.mdvproject.MDVProject method) add_viv_viewer() (mdvtools.mdvproject.MDVProject method) administrator (mdvtools.dbutils.dbmodels.User attribute) all_users_cache (in module mdvtools.auth.authutils) app (in module mdvtools.dbutils.mdv_server_app) (in module mdvtools.dbutils.safe_mdv_app) (in module mdvtools.mdv_desktop) (in module mdvtools.querytools.app) (mdvtools.auth.dummy_provider.DummyAuthProvider attribute) (mdvtools.auth.shibboleth_provider.ShibbolethProvider attribute) (mdvtools.dbutils.safe_mdv_app.PrefixMiddleware attribute) (mdvtools.project_router.SingleProjectShim attribute) (mdvtools.server_extension.MDVServerOptions attribute) args (in module mdvtools.csv_to_static) ask_question() (chat_protocol.ProjectChatProtocol method) AskQuestionResult (class in chat_protocol) assign_permissions() (in module manage_project_permissions) Auth0Provider (class in mdvtools.auth.auth0_provider) auth_id (mdvtools.dbutils.dbmodels.User attribute) AuthProvider (class in mdvtools.auth.auth_provider) B backend_db (mdvtools.mdvproject.MDVProject attribute) (mdvtools.server_extension.MDVServerOptions attribute) BASE_DELAY (in module mdvtools.auth.auth0_provider) base_plot module basename (in module mdvtools.csv_to_static) BasePlot (class in base_plot) batch_assign_from_file() (in module manage_project_permissions) before_request() (mdvtools.project_router.ProjectBlueprint method) (mdvtools.project_router.ProjectBlueprintProtocol method) (mdvtools.project_router.SingleProjectShim method) before_request_funcs (mdvtools.project_router.ProjectBlueprint attribute) blueprints (mdvtools.project_router.ProjectBlueprint attribute) box_plot module BoxPlot (class in box_plot) C cache_last_updated (in module mdvtools.auth.authutils) CACHE_REFRESH_INTERVAL (in module mdvtools.auth.authutils) cache_user_projects() (in module mdvtools.auth.authutils) can_read (mdvtools.dbutils.dbmodels.UserProject attribute) can_write (mdvtools.dbutils.dbmodels.UserProject attribute) change_project_access() (mdvtools.dbutils.dbservice.ProjectService static method) chart_prototypes (in module mdvtools.chart_prototypes) chart_types_md (in module markdown_utils) ChartKeys (in module mdvtools.chart_prototypes) chat_enabled (in module chat_protocol) chat_extension (in module chat_server_extension) chat_protocol module chat_server_extension module chatlog module ChatLogger (class in chatlog) ChatLogItem (class in chatlog) ChatRequest (class in chat_protocol) ChatSocketAPI (class in chatlog) ChatSocketIOHandler (class in chatlog) check_columns_exist() (mdvtools.mdvproject.MDVProject method) check_htslib() (in module mdvtools.mdvproject) chrom_sizes (mdvtools.dbutils.dbmodels.Genome attribute) chunked_log1p_normalization() (in module mdvtools.tests.mock_anndata) chunked_zscore_normalization() (in module mdvtools.tests.mock_anndata) class_name (mdvtools.dbutils.dbmodels.Job attribute) cli() (in module mdvtools.cli) code (chat_protocol.AskQuestionResult attribute) code_execution module code_manipulation module col_types (in module mdvtools.csv_to_static) Cols (in module mdvtools.mdvproject) ColumnName (in module mdvtools.mdvproject) COMMIT_HASH (in module github_utils) compute_vcf_end() (in module mdvtools.conversions) config (in module mdvtools.mdv_desktop) config_file (in module mdvtools.mdv_desktop) confirmed_at (mdvtools.dbutils.dbmodels.User attribute) connections (mdvtools.dbutils.dbmodels.Genome attribute) context (chatlog.ChatLogItem attribute) contribution_heatmap_proto (in module mdvtools.chart_prototypes) conversation_id (chat_protocol.ChatRequest attribute) (chatlog.ChatLogItem attribute) convert_data_to_binary() (in module mdvtools.csv_to_static) (mdvtools.mdvproject.MDVProject method) convert_mudata() (in module mdvtools.cli) convert_mudata_to_mdv() (in module mdvtools.conversions) convert_plot_to_json() (mdvtools.mdvproject.MDVProject method) convert_scanpy() (in module mdvtools.cli) convert_scanpy_to_mdv() (in module mdvtools.conversions) convert_to_static_page() (mdvtools.mdvproject.MDVProject method) convert_vcf() (in module mdvtools.cli) convert_vcf_to_df() (in module mdvtools.conversions) convert_vcf_to_mdv() (in module mdvtools.conversions) copy_images() (mdvtools.mdvproject.MDVProject method) crawl_github_repo() (in module github_utils) crawl_local_repo() (in module local_files_utils) create_app() (in module mdvtools.server) (in module mdvtools.serverlite) create_auth_provider() (in module mdvtools.auth.authutils) create_base_directory() (in module mdvtools.dbutils.mdv_server_app) create_bed_gz_file() (in module mdvtools.mdvproject) create_column_markdown() (in module markdown_utils) create_datasource_template() (mdvtools.mdvproject.MDVProject method) create_edge_case_anndata() (in module mdvtools.tests.mock_anndata) create_edge_cases() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_error_markdown() (in module markdown_utils) create_extreme_anndata() (in module mdvtools.tests.mock_anndata) create_extreme_dataset() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_fast_large_anndata() (in module mdvtools.tests.mock_anndata) create_flask_app() (in module mdvtools.dbutils.mdv_server_app) create_image_view_prototype() (in module mdvtools.image_view_prototype) create_interaction_matrix_view() (in module mdvtools.spatial) create_large() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_large_anndata() (in module mdvtools.tests.mock_anndata) create_massive_anndata() (in module mdvtools.tests.mock_anndata) create_massive_dataset() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_memory_efficient_large() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_memory_efficient_large_anndata() (in module mdvtools.tests.mock_anndata) create_minimal() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_minimal_anndata() (in module mdvtools.tests.mock_anndata) create_project_markdown() (in module markdown_utils) create_realistic() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) create_realistic_anndata() (in module mdvtools.tests.mock_anndata) create_regulamentary_project() (in module mdvtools.conversions) create_regulamentary_project_from_pipeline() (in module mdvtools.conversions) create_roi_interaction_view() (in module mdvtools.spatial) create_skeleton_anndata() (in module mdvtools.tests.mock_anndata) create_suggested_questions_prompt() (in module markdown_utils) create_table_plot() (mdvtools.mdvproject.MDVProject method) create_with_specific_features() (mdvtools.tests.mock_anndata.MockAnnDataFactory method) created_timestamp (mdvtools.dbutils.dbmodels.Project attribute) D data (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.UserPreference attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) database (mdvtools.dbutils.dbmodels.Genome attribute) DATABASE_URL (in module mdvtools.querytools.app) DataSourceName (in module mdvtools.mdvproject) datasources (mdvtools.mdvproject.MDVProject property) dataSources (view.View attribute) datasourcesfile (mdvtools.mdvproject.MDVProject attribute) datatype_mappings (in module mdvtools.mdvproject) date_added (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) date_made_public (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) date_modified (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) date_shared (mdvtools.dbutils.dbmodels.SharedObject attribute) db (in module mdvtools.dbutils.dbmodels) default_ds (in module mdvtools.image_view_prototype) default_image_name (in module mdvtools.image_view_prototype) delete() (mdvtools.mdvproject.MDVProject method) delete_datasource() (mdvtools.mdvproject.MDVProject method) delete_files_by_project() (mdvtools.dbutils.dbservice.FileService static method) delete_uploaded_image() (mdvtools.mdvproject.MDVProject method) deleted_timestamp (mdvtools.dbutils.dbmodels.Project attribute) density_scatter_plot module DensityScatterPlot (class in density_scatter_plot) description (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) df (in module mdvtools.csv_to_static) dir (mdvtools.mdvproject.MDVProject attribute) DIRECTORY_PATH (in module local_files_utils) dispatch_request() (mdvtools.project_router.ProjectBlueprint method) dot_plot module DotPlot (class in dot_plot) DummyAuthProvider (class in mdvtools.auth.dummy_provider) E email (mdvtools.dbutils.dbmodels.User attribute) emit() (chatlog.ChatSocketIOHandler method) ENABLE_AUTH (in module mdvtools.dbutils.mdv_server_app) ensure_regions_fields() (mdvtools.mdvproject.MDVProject method) error (chat_protocol.AskQuestionResult attribute) (chatlog.ChatLogItem attribute) error_message (chat_protocol.ProjectChatProtocol attribute) escape_markdown() (in module markdown_utils) estimate_memory_usage() (in module mdvtools.tests.mock_anndata) event_name (chatlog.ChatSocketIOHandler attribute) example_basic_usage() (in module mdvtools.tests.example_mock_usage) example_conversion_testing() (in module mdvtools.tests.example_mock_usage) example_factory_usage() (in module mdvtools.tests.example_mock_usage) example_intents_md (in module markdown_utils) example_stress_testing() (in module mdvtools.tests.example_mock_usage) example_validation_and_summary() (in module mdvtools.tests.example_mock_usage) execute_code() (in module code_execution) execute_plt_test() (in module code_execution) execute_query() (in module mdvtools.querytools.app) extensions (mdvtools.server_extension.MDVServerOptions attribute) extract_code_from_response() (in module code_manipulation) extract_python_code_from_ipynb() (in module github_utils) (in module local_files_utils) extract_python_code_from_py() (in module github_utils) (in module local_files_utils) F failed_projects (mdvtools.dbutils.dbservice.ProjectService attribute) feature_import_proto (in module mdvtools.chart_prototypes) fields (mdvtools.dbutils.dbmodels.ViewSet attribute) File (class in mdvtools.dbutils.dbmodels) file (in module chatlog) file_exists_in_project() (mdvtools.dbutils.dbservice.FileService static method) file_path (mdvtools.dbutils.dbmodels.File attribute) filename (in module mdvtools.csv_to_static), [1] files (mdvtools.dbutils.dbmodels.Project attribute) FileService (class in mdvtools.dbutils.dbservice) finished_on (mdvtools.dbutils.dbmodels.Job attribute) first_name (mdvtools.dbutils.dbmodels.User attribute) from_dict() (chatlog.ChatLogItem class method) G generate_id() (base_plot.BasePlot method) GeneSet (class in mdvtools.dbutils.dbmodels) Genome (class in mdvtools.dbutils.dbmodels) genome (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) get_active_projects() (mdvtools.dbutils.dbservice.ProjectService static method) get_anndata_summary() (in module mdvtools.tests.mock_anndata) get_auth_provider() (in module mdvtools.auth.authutils) get_byte_data() (mdvtools.mdvproject.MDVProject method) get_centroid_plot() (mdvtools.mdvproject.MDVProject method) get_column() (mdvtools.mdvproject.MDVProject method) get_column_groups() (in module mdvtools.csv_to_static) get_column_info() (in module mdvtools.mdvproject) get_column_metadata() (mdvtools.mdvproject.MDVProject method) get_column_type() (in module mdvtools.csv_to_static) get_configs() (mdvtools.mdvproject.MDVProject method) get_conversation_logs() (chatlog.ChatLogger method) get_createproject_prompt_RAG() (in module templates) get_datasource() (in module mdvtools.csv_to_static) get_datasource_as_dataframe() (mdvtools.mdvproject.MDVProject method) get_datasource_metadata() (mdvtools.mdvproject.MDVProject method) get_datasource_names() (mdvtools.mdvproject.MDVProject method) get_db_connection() (in module mdvtools.querytools.app) get_file_by_path_and_project() (mdvtools.dbutils.dbservice.FileService static method) get_file_size_gb() (in module mdvtools.convert_anndata) get_files_by_project() (mdvtools.dbutils.dbservice.FileService static method) get_genome_browser() (mdvtools.mdvproject.MDVProject method) get_image() (mdvtools.mdvproject.MDVProject method) get_image_plot() (mdvtools.mdvproject.MDVProject method) get_interaction_matrix() (mdvtools.mdvproject.MDVProject method) get_json() (in module mdvtools.mdvproject) get_links() (mdvtools.mdvproject.MDVProject method) get_logger() (in module mdvtools.logging_config) get_logs() (chatlog.ChatLogger method) get_matrix() (in module mdvtools.conversions) get_memory_usage() (in module memory) get_next_project_id() (mdvtools.dbutils.dbservice.ProjectService static method) get_project_by_id() (mdvtools.dbutils.dbservice.ProjectService static method) get_project_by_name() (in module manage_project_permissions) get_projects() (in module mdvtools.querytools.app) get_quantiles() (in module mdvtools.csv_to_static) get_random_string() (in module mdvtools.mdvproject) get_range() (in module mdvtools.server_utils) get_selection_dialog() (mdvtools.mdvproject.MDVProject method) get_server_options_for_db_projects() (in module mdvtools.dbutils.server_options) get_state() (in module mdvtools.csv_to_static) get_subgroup_bytes() (in module mdvtools.mdvproject) get_suggested_questions() (chat_protocol.ProjectChatProtocol method) get_text_indices() (in module mdvtools.csv_to_static) get_token() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) get_user() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) get_user_by_email() (in module manage_project_permissions) get_user_project_permissions() (mdvtools.dbutils.dbservice.UserProjectService static method) get_view() (mdvtools.mdvproject.MDVProject method) get_views() (in module mdvtools.csv_to_static) GITHUB_REPO (in module github_utils) GITHUB_TOKEN (in module github_utils) github_utils module H h5file (mdvtools.mdvproject.MDVProject attribute) handle_callback() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) handle_error (chat_protocol.ChatRequest attribute) HandleError (class in chat_protocol) has_images (in module mdvtools.csv_to_static) heatmap_plot module HeatmapPlot (class in heatmap_plot) histogram_plot module HistogramPlot (class in histogram_plot) I icon (mdvtools.dbutils.dbmodels.Genome attribute) id (chat_protocol.ChatRequest attribute) (chatlog.ChatSocketIOHandler attribute) (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.SharedObject attribute) (mdvtools.dbutils.dbmodels.User attribute) (mdvtools.dbutils.dbmodels.UserPreference attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) (mdvtools.mdvproject.MDVProject attribute) image_chart() (in module mdvtools.chart_prototypes) imagefolder (mdvtools.mdvproject.MDVProject attribute) index() (in module mdvtools.querytools.app) indir (in module mdvtools.csv_to_static) init_error (chat_protocol.ProjectChatProtocol attribute) initialCharts (view.View attribute) initialize_json_log() (in module chatlog) inputs (mdvtools.dbutils.dbmodels.Job attribute) insert_link() (mdvtools.mdvproject.MDVProject method) institution (mdvtools.dbutils.dbmodels.User attribute) is_active (mdvtools.dbutils.dbmodels.User attribute) is_admin (mdvtools.dbutils.dbmodels.User attribute) is_authenticated() (in module mdvtools.auth.authutils) is_deleted (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) is_owner (mdvtools.dbutils.dbmodels.UserProject attribute) is_public (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) is_token_valid() (mdvtools.auth.auth0_provider.Auth0Provider method) is_valid_mdv_project() (in module mdvtools.dbutils.mdv_server_app) J Job (class in mdvtools.dbutils.dbmodels) jobs (mdvtools.dbutils.dbmodels.User attribute) json_keyfile_path (in module chatlog) json_string (in module mdvtools.image_view_prototype) JWKS_CACHE_DURATION (in module mdvtools.auth.auth0_provider) L label (mdvtools.dbutils.dbmodels.Genome attribute) LangchainLoggingHandler (class in chatlog) last_name (mdvtools.dbutils.dbmodels.User attribute) layout (view.Panel attribute) level (mdvtools.dbutils.dbmodels.SharedObject attribute) links (view.View attribute) load_config() (in module mdvtools.dbutils.mdv_server_app) local_files_utils module lock() (mdvtools.mdvproject.MDVProject method) log (chatlog.LangchainLoggingHandler attribute) (in module chatlog) log() (chat_protocol.ProjectChatProtocol method) (chatlog.ChatSocketAPI method) (in module mdvtools.server) (in module mdvtools.websocket) log_chat() (chatlog.ChatLogger method) log_chat_item() (in module chatlog) log_file_path (chatlog.ChatLogger attribute) log_memory_usage() (in module memory) log_to_json() (in module chatlog) logger (chatlog.ChatSocketAPI attribute) (chatlog.LangchainLoggingHandler attribute) (in module chat_server_extension) (in module chatlog) (in module mdvtools.auth.authutils) (in module mdvtools.auth.dummy_provider) (in module mdvtools.auth.project_auth) (in module mdvtools.auth.register_auth_routes) (in module mdvtools.auth.shibboleth_provider) (in module mdvtools.dbutils.dbservice) (in module mdvtools.dbutils.mdv_server_app) (in module mdvtools.dbutils.routes) (in module mdvtools.dbutils.safe_mdv_app) (in module mdvtools.mdvproject) (in module mdvtools.project_router) (in module mdvtools.server) login() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) login_url (mdvtools.auth.shibboleth_provider.ShibbolethProvider attribute) logout() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) logout_url (mdvtools.auth.shibboleth_provider.ShibbolethProvider attribute) M main() (in module manage_project_permissions) (in module mdvtools.csv_to_static) (in module mdvtools.tests.example_mock_usage) make_chart() (in module mdvtools.chart_prototypes) manage_project_permissions module markdown_utils module MAX_DELAY (in module mdvtools.auth.auth0_provider) MAX_RETRIES (in module mdvtools.auth.auth0_provider) mdv_socketio() (in module mdvtools.websocket) MDVProject (class in mdvtools.mdvproject) MDVProjectChatServerExtension (class in chat_server_extension) MDVProjectServerExtension (class in mdvtools.server_extension) MDVServerOptions (class in mdvtools.server_extension) mdvtools module mdvtools.auth module mdvtools.auth.auth0_provider module mdvtools.auth.auth_provider module mdvtools.auth.authutils module mdvtools.auth.dummy_provider module mdvtools.auth.project_auth module mdvtools.auth.register_auth_routes module mdvtools.auth.shibboleth_provider module mdvtools.chart_prototypes module mdvtools.cli module mdvtools.conversions module mdvtools.convert_anndata module mdvtools.csv_to_static module mdvtools.dbutils module mdvtools.dbutils.dbmodels module mdvtools.dbutils.dbservice module mdvtools.dbutils.mdv_server_app module mdvtools.dbutils.routes module mdvtools.dbutils.safe_mdv_app module mdvtools.dbutils.server_options module mdvtools.dbutils.test module mdvtools.dbutils.test.integration module mdvtools.dbutils.test.unit module mdvtools.image_view_prototype module mdvtools.logging_config module mdvtools.mdv_desktop module mdvtools.mdvproject module mdvtools.project_router module mdvtools.querytools module mdvtools.querytools.app module mdvtools.server module mdvtools.server_extension module mdvtools.server_utils module mdvtools.serverlite module mdvtools.spatial module mdvtools.tests module mdvtools.tests.example_mock_usage module mdvtools.tests.mock_anndata module mdvtools.websocket module memory module message (chat_protocol.AskQuestionResult attribute) (chat_protocol.ChatRequest attribute) MockAnnDataFactory (class in mdvtools.tests.mock_anndata) module abundance_box_plot base_plot box_plot chat_protocol chat_server_extension chatlog code_execution code_manipulation density_scatter_plot dot_plot github_utils heatmap_plot histogram_plot local_files_utils manage_project_permissions markdown_utils mdvtools mdvtools.auth mdvtools.auth.auth0_provider mdvtools.auth.auth_provider mdvtools.auth.authutils mdvtools.auth.dummy_provider mdvtools.auth.project_auth mdvtools.auth.register_auth_routes mdvtools.auth.shibboleth_provider mdvtools.chart_prototypes mdvtools.cli mdvtools.conversions mdvtools.convert_anndata mdvtools.csv_to_static mdvtools.dbutils mdvtools.dbutils.dbmodels mdvtools.dbutils.dbservice mdvtools.dbutils.mdv_server_app mdvtools.dbutils.routes mdvtools.dbutils.safe_mdv_app mdvtools.dbutils.server_options mdvtools.dbutils.test mdvtools.dbutils.test.integration mdvtools.dbutils.test.unit mdvtools.image_view_prototype mdvtools.logging_config mdvtools.mdv_desktop mdvtools.mdvproject mdvtools.project_router mdvtools.querytools mdvtools.querytools.app mdvtools.server mdvtools.server_extension mdvtools.server_utils mdvtools.serverlite mdvtools.spatial mdvtools.tests mdvtools.tests.example_mock_usage mdvtools.tests.mock_anndata mdvtools.websocket memory multi_line_plot pie_chart ring_chart row_chart row_summary_box_plot sankey_plot scatter_plot scatter_plot_3D selection_dialog_plot stacked_row_plot table_plot templates text_box_plot view violin_plot wordcloud_plot msg (in module chat_protocol) multi_line_plot module multi_line_proto (in module mdvtools.chart_prototypes) MultiLinePlot (class in multi_line_plot) mutate_state_json() (chat_server_extension.MDVProjectChatServerExtension method) (mdvtools.server_extension.MDVProjectServerExtension method) mypath (in module chatlog) (in module local_files_utils) N name (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) (mdvtools.project_router.ProjectBlueprint attribute) namespace (chatlog.ChatSocketIOHandler attribute) needs_cache_refresh() (in module mdvtools.auth.authutils) numpy_dtypes (in module mdvtools.mdvproject) O oauth (in module mdvtools.dbutils.mdv_server_app), [1] object_id (mdvtools.dbutils.dbmodels.SharedObject attribute) on_chain_end() (chatlog.LangchainLoggingHandler method) on_chain_start() (chatlog.LangchainLoggingHandler method) on_chat_model_start() (chatlog.LangchainLoggingHandler method) on_llm_end() (chatlog.LangchainLoggingHandler method) open_browser (mdvtools.server_extension.MDVServerOptions attribute) outdir (in module mdvtools.csv_to_static), [1] outputs (mdvtools.dbutils.dbmodels.Job attribute) owner (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.SharedObject attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) P packages_functions (in module templates) Panel (class in view) panelWidth (view.Panel attribute) parent (mdvtools.dbutils.dbmodels.Project attribute) parse_multitext (in module mdvtools.csv_to_static) parse_permission() (in module manage_project_permissions) parse_view_name() (in module code_manipulation) parser (in module mdvtools.convert_anndata) (in module mdvtools.csv_to_static) password (mdvtools.dbutils.dbmodels.User attribute) patch_viewname() (in module code_manipulation) path (in module mdvtools.mdvproject) (in module mdvtools.serverlite) (mdvtools.dbutils.dbmodels.Project attribute) pie_chart module PieChart (class in pie_chart) plot_data (base_plot.BasePlot attribute) plt_code (in module code_execution) port (mdvtools.server_extension.MDVServerOptions attribute) preference (mdvtools.dbutils.dbmodels.UserPreference attribute) preferences (mdvtools.dbutils.dbmodels.User attribute) prefix (mdvtools.dbutils.safe_mdv_app.PrefixMiddleware attribute) PrefixMiddleware (class in mdvtools.dbutils.safe_mdv_app) prepare_code() (in module code_manipulation) progress_name (chatlog.ChatSocketAPI attribute) project (chatlog.ChatSocketAPI attribute) Project (class in mdvtools.dbutils.dbmodels) project_dir (in module mdvtools.mdv_desktop) project_id (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) project_namespace (chatlog.ChatSocketAPI attribute) PROJECT_PATH_1 (in module github_utils) PROJECT_PATH_2 (in module github_utils) project_pre_dispatch_checks() (in module mdvtools.auth.project_auth) ProjectBlueprint (class in mdvtools.project_router) ProjectBlueprintProtocol (class in mdvtools.project_router) ProjectChat (in module chat_protocol) ProjectChatProtocol (class in chat_protocol) projects (in module mdvtools.mdv_desktop) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.User attribute) ProjectService (class in mdvtools.dbutils.dbservice) prompt_data (in module templates) prompt_template (chatlog.ChatLogItem attribute) Q query (chatlog.ChatLogItem attribute) R read_secret() (in module mdvtools.dbutils.mdv_server_app) register_app() (mdvtools.project_router.ProjectBlueprint static method) register_auth_routes() (in module mdvtools.auth.register_auth_routes) register_before_request_auth() (in module mdvtools.auth.authutils) register_routes() (chat_server_extension.MDVProjectChatServerExtension method) (in module mdvtools.dbutils.routes) (mdvtools.server_extension.MDVProjectServerExtension method) remove_column() (mdvtools.mdvproject.MDVProject method) remove_user_from_project() (mdvtools.dbutils.dbservice.UserProjectService static method) rename_columns() (in module mdvtools.csv_to_static) replace_text_values() (in module mdvtools.csv_to_static) response (chatlog.ChatLogItem attribute) restore_datasource() (mdvtools.mdvproject.MDVProject method) retry_with_exponential_backoff() (in module mdvtools.auth.auth0_provider) ring_chart module RingChart (class in ring_chart) room (chat_protocol.ChatRequest attribute) (chatlog.ChatSocketAPI attribute) (chatlog.ChatSocketIOHandler attribute) route() (mdvtools.project_router.ProjectBlueprint method) (mdvtools.project_router.ProjectBlueprintProtocol method) (mdvtools.project_router.SingleProjectShim method) routes (in module mdvtools.server) (mdvtools.project_router.ProjectBlueprint attribute) row_chart module row_summary_box_plot module RowChart (class in row_chart) RowSummaryBox (class in row_summary_box_plot) run_subprocess() (in module code_execution) running (in module mdvtools.mdv_desktop) S safe_file_save (mdvtools.mdvproject.MDVProject attribute) sankey_plot module SankeyPlot (class in sankey_plot) save_json() (in module mdvtools.mdvproject) save_json_atomic() (in module mdvtools.mdvproject) save_state() (mdvtools.mdvproject.MDVProject method) scatter_plot module scatter_plot_3D module ScatterPlot (class in scatter_plot) ScatterPlot3D (class in scatter_plot_3D) selection_chart() (in module mdvtools.chart_prototypes) selection_chart_proto (in module mdvtools.chart_prototypes) selection_dialog_plot module SelectionDialogPlot (class in selection_dialog_plot) send_file() (in module mdvtools.server_utils) sent_on (mdvtools.dbutils.dbmodels.Job attribute) separator (in module mdvtools.csv_to_static) serve() (in module mdvtools.cli) (mdvtools.mdvproject.MDVProject method) serve_project() (in module mdvtools.serverlite) serve_projects_from_db() (in module mdvtools.dbutils.mdv_server_app) serve_projects_from_filesystem() (in module mdvtools.dbutils.mdv_server_app) set_axis() (heatmap_plot.HeatmapPlot method) set_axis_properties() (base_plot.BasePlot method) (box_plot.BoxPlot method) (dot_plot.DotPlot method) (pie_chart.PieChart method) (ring_chart.RingChart method) (row_chart.RowChart method) (sankey_plot.SankeyPlot method) (stacked_row_plot.StackedRowChart method) (wordcloud_plot.WordcloudPlot method) set_axis_scales() (scatter_plot_3D.ScatterPlot3D method) set_axis_size() (pie_chart.PieChart method) (ring_chart.RingChart method) set_band_width() (box_plot.BoxPlot method) set_bandwidth() (multi_line_plot.MultiLinePlot method) (violin_plot.ViolinPlot method) set_box_color() (abundance_box_plot.AbundanceBoxPlot method) set_box_visible() (violin_plot.ViolinPlot method) set_brush() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (scatter_plot.ScatterPlot method) (scatter_plot_3D.ScatterPlot3D method) set_camera() (scatter_plot_3D.ScatterPlot3D method) set_category1() (density_scatter_plot.DensityScatterPlot method) set_category2() (density_scatter_plot.DensityScatterPlot method) set_center() (scatter_plot_3D.ScatterPlot3D method) set_chat_enabled() (mdvtools.mdvproject.MDVProject method) set_color_by() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (scatter_plot.ScatterPlot method) (scatter_plot_3D.ScatterPlot3D method) set_color_legend() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (dot_plot.DotPlot method) (multi_line_plot.MultiLinePlot method) (scatter_plot.ScatterPlot method) (stacked_row_plot.StackedRowChart method) set_color_range() (heatmap_plot.HeatmapPlot method) set_color_scale() (dot_plot.DotPlot method) (heatmap_plot.HeatmapPlot method) (violin_plot.ViolinPlot method) set_column() (mdvtools.mdvproject.MDVProject method) set_column_group() (mdvtools.mdvproject.MDVProject method) set_column_metadata() (mdvtools.mdvproject.MDVProject method) set_column_with_raw_data() (mdvtools.mdvproject.MDVProject method) set_datasource_metadata() (mdvtools.mdvproject.MDVProject method) set_default_color() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (scatter_plot.ScatterPlot method) (scatter_plot_3D.ScatterPlot3D method) set_editable() (mdvtools.mdvproject.MDVProject method) set_fill_color() (violin_plot.ViolinPlot method) set_filter() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (scatter_plot.ScatterPlot method) set_fraction_legend() (dot_plot.DotPlot method) set_grouping() (abundance_box_plot.AbundanceBoxPlot method) set_intensity_scale() (heatmap_plot.HeatmapPlot method) set_interactions() (mdvtools.mdvproject.MDVProject method) set_intervals() (box_plot.BoxPlot method) (multi_line_plot.MultiLinePlot method) set_label() (pie_chart.PieChart method) (ring_chart.RingChart method) set_legend() (base_plot.BasePlot method) (pie_chart.PieChart method) (ring_chart.RingChart method) set_line_color() (violin_plot.ViolinPlot method) set_log_transform() (abundance_box_plot.AbundanceBoxPlot method) set_meanline_visible() (violin_plot.ViolinPlot method) set_median_color() (abundance_box_plot.AbundanceBoxPlot method) set_method() (heatmap_plot.HeatmapPlot method) set_on_filter() (scatter_plot_3D.ScatterPlot3D method) set_opacity() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (heatmap_plot.HeatmapPlot method) (scatter_plot.ScatterPlot method) (scatter_plot_3D.ScatterPlot3D method) set_outlier_color() (abundance_box_plot.AbundanceBoxPlot method) set_param() (pie_chart.PieChart method) (ring_chart.RingChart method) set_points() (violin_plot.ViolinPlot method) set_position() (base_plot.BasePlot method) set_project_accessed_timestamp() (mdvtools.dbutils.dbservice.ProjectService static method) set_project_update_timestamp() (mdvtools.dbutils.dbservice.ProjectService static method) set_radius() (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (scatter_plot.ScatterPlot method) (scatter_plot_3D.ScatterPlot3D method) set_region_data() (mdvtools.mdvproject.MDVProject method) set_scaletrim() (multi_line_plot.MultiLinePlot method) set_text() (text_box_plot.TextBox method) set_text_size() (pie_chart.PieChart method) (ring_chart.RingChart method) set_tick_font() (pie_chart.PieChart method) (ring_chart.RingChart method) set_tooltip() (abundance_box_plot.AbundanceBoxPlot method) (box_plot.BoxPlot method) (density_scatter_plot.DensityScatterPlot method) (heatmap_plot.HeatmapPlot method) (scatter_plot.ScatterPlot method) (violin_plot.ViolinPlot method) set_view() (mdvtools.mdvproject.MDVProject method) set_whisker_color() (abundance_box_plot.AbundanceBoxPlot method) set_x_axis() (abundance_box_plot.AbundanceBoxPlot method) (heatmap_plot.HeatmapPlot method) (histogram_plot.HistogramPlot method) (multi_line_plot.MultiLinePlot method) set_y_axis() (abundance_box_plot.AbundanceBoxPlot method) (heatmap_plot.HeatmapPlot method) (histogram_plot.HistogramPlot method) (multi_line_plot.MultiLinePlot method) setup_logger() (in module mdvtools.logging_config) shared_with (mdvtools.dbutils.dbmodels.SharedObject attribute) SharedObject (class in mdvtools.dbutils.dbmodels) ShibbolethProvider (class in mdvtools.auth.shibboleth_provider) sid (mdvtools.websocket.SocketIOContextRequest attribute) SingleProjectShim (class in mdvtools.project_router) skip_column_clean (mdvtools.mdvproject.MDVProject attribute) small_icon (mdvtools.dbutils.dbmodels.Genome attribute) socketio (chatlog.ChatSocketAPI attribute) (chatlog.ChatSocketIOHandler attribute) (in module mdvtools.websocket) SocketIOContextRequest (class in mdvtools.websocket) soft_delete_project() (mdvtools.dbutils.dbservice.ProjectService static method) stacked_row_plot module StackedRowChart (class in stacked_row_plot) stat_chart_proto (in module mdvtools.chart_prototypes) stat_viv_proto (in module mdvtools.chart_prototypes) state (mdvtools.mdvproject.MDVProject property) statefile (mdvtools.mdvproject.MDVProject attribute) status (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) suppress_anndata_warnings() (in module mdvtools.tests.mock_anndata) sync_users_to_db() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) T table_name (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) table_plot module TablePlot (class in table_plot) tables_exist() (in module mdvtools.dbutils.mdv_server_app) temp_mdv_project() (in module mdvtools.tests.example_mock_usage) templates module text_box_plot module TextBox (class in text_box_plot) timestamp (chatlog.ChatLogItem attribute) TIMESTAMP_UPDATE_INTERVAL (in module mdvtools.auth.project_auth) to_dict() (chatlog.ChatLogItem method) to_json() (base_plot.BasePlot method) trackfolder (mdvtools.mdvproject.MDVProject attribute) translate_query_type_to_sql() (in module mdvtools.querytools.app) type (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) types (in module mdvtools.csv_to_static) U update_cache() (in module mdvtools.auth.authutils) update_chat_progress() (chatlog.ChatSocketAPI method) update_datasource_for_tiff() (mdvtools.mdvproject.MDVProject method) update_file_timestamp() (mdvtools.dbutils.dbservice.FileService static method) update_project_name() (mdvtools.dbutils.dbservice.ProjectService static method) update_timestamp (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.Project attribute) upload_image_file() (mdvtools.mdvproject.MDVProject method) upload_timestamp (mdvtools.dbutils.dbmodels.File attribute) url_prefix (mdvtools.project_router.ProjectBlueprint attribute) use_reloader (mdvtools.server_extension.MDVServerOptions attribute) User (class in mdvtools.dbutils.dbmodels) user_cache (in module mdvtools.auth.authutils) user_id (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.UserPreference attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) user_project_cache (in module mdvtools.auth.authutils) UserPreference (class in mdvtools.dbutils.dbmodels) UserProject (class in mdvtools.dbutils.dbmodels) UserProjectService (class in mdvtools.dbutils.dbservice) users (mdvtools.dbutils.dbmodels.Project attribute) UserService (class in mdvtools.dbutils.dbservice) V validate_anndata() (in module mdvtools.tests.mock_anndata) validate_user() (mdvtools.auth.auth0_provider.Auth0Provider method) (mdvtools.auth.auth_provider.AuthProvider method) (mdvtools.auth.dummy_provider.DummyAuthProvider method) (mdvtools.auth.shibboleth_provider.ShibbolethProvider method) view module View (class in view) view_name (chat_protocol.AskQuestionResult attribute) (chatlog.ChatLogItem attribute) views (mdvtools.mdvproject.MDVProject property) ViewSet (class in mdvtools.dbutils.dbmodels) viewsfile (mdvtools.mdvproject.MDVProject attribute) violin_plot module violin_proto (in module mdvtools.chart_prototypes) ViolinPlot (class in violin_plot) viv_proto (in module mdvtools.chart_prototypes) W wait_for_database() (in module mdvtools.dbutils.mdv_server_app) watch_folder() (in module mdvtools.mdv_desktop) websocket (mdvtools.server_extension.MDVServerOptions attribute) welcome (chat_protocol.ProjectChatProtocol attribute) wordcloud_plot module WordcloudPlot (class in wordcloud_plot) Z zip_and_remove() (in module mdvtools.cli)
