Index

_

__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.Permission 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_dims() (in module mdvtools.conversions) _create_dt_heatmap() (in module mdvtools.conversions) _get_h5_handle() (mdvtools.mdvproject.MDVProject method) _initialize_oauth() (auth0_provider.Auth0Provider method) _lock (mdvtools.mdvproject.MDVProject attribute) _send_file() (in module mdvtools.server)

A

abundance_box_plot module abundance_box_plot_example module AbundanceBoxPlot (class in abundance_box_plot) access_level (mdvtools.dbutils.dbmodels.Project attribute) accessed_timestamp (mdvtools.dbutils.dbmodels.Project attribute) adata (in module pbmc3k_tutorial), [1], [2], [3] 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_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) add_viv_images() (mdvtools.mdvproject.MDVProject method) add_viv_viewer() (mdvtools.mdvproject.MDVProject method) administrator (mdvtools.dbutils.dbmodels.User attribute) app (in module mdvtools.dbutils.mdv_server_app) (in module mdvtools.mdv_desktop) (in module mdvtools.querytools.app) (mdvtools.project_router.SingleProjectShim attribute) args (in module mdvtools.csv_to_static) auth0_provider module Auth0Provider (class in auth0_provider) AUTH_ENABLED (mdvtools.project_router.ProjectBlueprint_v2 attribute) auth_provider module AuthProvider (class in auth_provider) Axes (class in chart_dicts) axis (chart_dicts.ScatterChart attribute) AxisProperties (class in chart_dicts)

B

backend_db (mdvtools.mdvproject.MDVProject attribute) base (in module pbmc3k_tutorial) (in module scanpy_pbmc3k) (in module scanpy_pbmc3k_tutorial) base_plot module BaseChart (class in chart_dicts) basename (in module mdvtools.csv_to_static)

BasePlot (class in base_plot) blueprints (mdvtools.project_router.ProjectBlueprint attribute) (mdvtools.project_router.ProjectBlueprint_v2 attribute) box_plot module box_plot_example module BoxPlot (class in box_plot)

C

can_read (mdvtools.dbutils.dbmodels.UserProject attribute) can_write (mdvtools.dbutils.dbmodels.UserProject attribute) cells_df (in module pbmc3k_tutorial) change_project_access() (mdvtools.dbutils.dbservice.ProjectService static method) chart_dicts module chart_prototypes (in module mdvtools.chart_prototypes) ChartKeys (in module mdvtools.chart_prototypes) check_columns_exist() (mdvtools.mdvproject.MDVProject method) check_htslib() (in module mdvtools.mdvproject) choices (in module dtypes_test) chrom_sizes (mdvtools.dbutils.dbmodels.Genome attribute) class_name (mdvtools.dbutils.dbmodels.Job attribute) col_types (in module mdvtools.csv_to_static) color_by (chart_dicts.ColorProperties attribute) color_legend (chart_dicts.ColorProperties attribute) ColorLegend (class in chart_dicts) ColorProperties (class in chart_dicts) Cols (in module mdvtools.mdvproject) column_metadata (in module dtypes_test) ColumnName (in module mdvtools.mdvproject) 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) contribution_heatmap_proto (in module mdvtools.chart_prototypes) convert_data_to_binary() (in module mdvtools.csv_to_static) (mdvtools.mdvproject.MDVProject method) convert_mudata_to_mdv() (in module mdvtools.conversions) convert_plot_to_json() (in module abundance_box_plot_example) (in module box_plot_example) (in module density_scatter_plot_example) (in module dot_plot_example) (in module heatmap_plot_example) (in module histogram_plot_example) (in module multiline_plot_example) (in module multiple_graphs_example) (in module pie_chart_example) (in module ring_chart_example) (in module row_chart_example) (in module scatter_plot_3D_example) (in module scatter_plot_example) (in module stacked_row_plot_example) (in module text_box_plot_example) (in module violin_plot_example) (in module wordcloud_plot_example) (mdvtools.mdvproject.MDVProject method)

convert_scanpy_to_mdv() (in module mdvtools.conversions) convert_to_static_page() (mdvtools.mdvproject.MDVProject method) convert_vcf_to_df() (in module mdvtools.conversions) convert_vcf_to_mdv() (in module mdvtools.conversions) copy_files_to_nfs() (in module scanpy_exp1) copy_images() (mdvtools.mdvproject.MDVProject method) counts (in module pbmc3k_tutorial) create_abundance_box_plot() (in module abundance_box_plot_example) create_app() (in module mdvtools.server) (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) create_base_directory() (in module mdvtools.dbutils.mdv_server_app) create_bed_gz_file() (in module mdvtools.mdvproject) create_box_plot() (in module box_plot_example) (in module multiple_graphs_example) create_datasource_template() (mdvtools.mdvproject.MDVProject method) create_dot_plot() (in module dot_plot_example) create_flask_app() (in module mdvtools.dbutils.mdv_server_app) create_heatmap_plot() (in module heatmap_plot_example) create_histogram_plot() (in module histogram_plot_example) create_image_view_prototype() (in module mdvtools.image_view_prototype) create_interaction_matrix_view() (in module mdvtools.spatial) create_multi_line_plot() (in module multiline_plot_example) create_pie_chart() (in module pie_chart_example) create_regulamentary_project() (in module mdvtools.conversions) create_ring_chart() (in module ring_chart_example) create_roi_interaction_view() (in module mdvtools.spatial) create_row_chart() (in module row_chart_example) create_scatter_plot() (in module density_scatter_plot_example) (in module scatter_plot_3D_example) (in module scatter_plot_example) create_stacked_row_plot() (in module stacked_row_plot_example) create_table_plot() (mdvtools.mdvproject.MDVProject method) create_text_box_plot() (in module text_box_plot_example) create_violin_plot() (in module violin_plot_example) create_wordcloud_plot() (in module wordcloud_plot_example) created_timestamp (mdvtools.dbutils.dbmodels.Project attribute)

D

data (in module scanpy_pbmc3k) (in module scanpy_pbmc3k_tutorial) (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 density_scatter_plot_example 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 dtypes_test) (in module genome_example) (in module mdvtools.csv_to_static) (in module mdvtools.tests.test_column_groups) dir (in module pbmc3k_tutorial) (mdvtools.mdvproject.MDVProject attribute) dispatch_request() (mdvtools.project_router.ProjectBlueprint method) (mdvtools.project_router.ProjectBlueprint_v2 method) display (chart_dicts.ColorLegend attribute) dot_chart_data (in module pbmc3k_tutorial) dot_plot module dot_plot (in module pbmc3k_tutorial) dot_plot_example module DotPlot (class in dot_plot) dtypes_test module

E

email (mdvtools.dbutils.dbmodels.User attribute) ENABLE_AUTH (in module mdvtools.dbutils.mdv_server_app)

ensure_regions_fields() (mdvtools.mdvproject.MDVProject method) execute_query() (in module mdvtools.querytools.app)

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_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)

G

gene_table (in module pbmc3k_tutorial) generate_id() (base_plot.BasePlot method) generate_versioned_filename() (in module scanpy_exp1) GeneSet (class in mdvtools.dbutils.dbmodels) Genome (class in mdvtools.dbutils.dbmodels) genome (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) genome_example module get_active_projects() (mdvtools.dbutils.dbservice.ProjectService static method) 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_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_files_by_project() (mdvtools.dbutils.dbservice.FileService static method) get_genome_browser() (mdvtools.mdvproject.MDVProject method) get_h5ad_files() (in module mdvtools.tests.test_anndata_conversion) 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_next_project_id() (mdvtools.dbutils.dbservice.ProjectService static method) get_project_by_id() (mdvtools.dbutils.dbservice.ProjectService static method) 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) get_selection_dialog() (mdvtools.mdvproject.MDVProject method) get_state() (in module mdvtools.csv_to_static) get_subgroup_bytes() (in module mdvtools.mdvproject) get_text_indices() (in module mdvtools.csv_to_static) get_token() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method) get_user() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method) get_view() (mdvtools.mdvproject.MDVProject method) get_views() (in module mdvtools.csv_to_static)

H

h5ad_file() (in module mdvtools.tests.test_anndata_conversion) h5file (mdvtools.mdvproject.MDVProject attribute) handle_callback() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method) has_images (in module mdvtools.csv_to_static) heatmap_plot module heatmap_plot_example module

HeatmapPlot (class in heatmap_plot) histogram_chart_data (in module pbmc3k_tutorial) histogram_chart_data_2 (in module pbmc3k_tutorial) histogram_plot module histogram_plot (in module pbmc3k_tutorial) histogram_plot_2 (in module pbmc3k_tutorial) histogram_plot_example module HistogramPlot (class in histogram_plot)

I

icon (mdvtools.dbutils.dbmodels.Genome attribute) id (chart_dicts.BaseChart attribute) (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Permission 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) image_table_plot module imagefolder (mdvtools.mdvproject.MDVProject attribute)

ImageTableChart (class in image_table_plot) index() (in module mdvtools.querytools.app) indir (in module mdvtools.csv_to_static) initialCharts (view.View attribute) 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_authenticated() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method) (mdvtools.project_router.ProjectBlueprint_v2 static method) is_deleted (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) is_public (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.Project attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) is_token_valid() (auth0_provider.Auth0Provider method)

J

Job (class in mdvtools.dbutils.dbmodels)

jobs (mdvtools.dbutils.dbmodels.User attribute) json_string (in module mdvtools.image_view_prototype)

L

label (chart_dicts.AxisProperties attribute) (mdvtools.dbutils.dbmodels.Genome attribute) last_name (mdvtools.dbutils.dbmodels.User attribute) layout (view.Panel attribute) legend (chart_dicts.BaseChart attribute) level (mdvtools.dbutils.dbmodels.SharedObject attribute) link (in module genome_example) links (view.View attribute) list_charts_cells (in module pbmc3k_tutorial) list_charts_genes (in module pbmc3k_tutorial) load_config() (in module mdvtools.dbutils.mdv_server_app) load_data() (in module abundance_box_plot_example) (in module box_plot_example) (in module density_scatter_plot_example) (in module dot_plot_example) (in module heatmap_plot_example) (in module histogram_plot_example) (in module multiline_plot_example) (in module multiple_graphs_example) (in module pie_chart_example) (in module ring_chart_example) (in module row_chart_example) (in module scatter_plot_3D_example) (in module scatter_plot_example) (in module stacked_row_plot_example) (in module text_box_plot_example) (in module violin_plot_example) (in module wordcloud_plot_example)

lock() (mdvtools.mdvproject.MDVProject method) log() (in module mdvtools.websocket) login() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method) logout() (auth0_provider.Auth0Provider method) (auth_provider.AuthProvider method)

M

main() (in module abundance_box_plot_example) (in module box_plot_example) (in module density_scatter_plot_example) (in module dot_plot_example) (in module heatmap_plot_example) (in module histogram_plot_example) (in module mdvtools.csv_to_static) (in module multiline_plot_example) (in module multiple_graphs_example) (in module pie_chart_example) (in module ring_chart_example) (in module row_chart_example) (in module scatter_plot_3D_example) (in module scatter_plot_example) (in module stacked_row_plot_example) (in module text_box_plot_example) (in module violin_plot_example) (in module wordcloud_plot_example) make_chart() (in module mdvtools.chart_prototypes) mdv_socketio() (in module mdvtools.websocket) MDVProject (class in mdvtools.mdvproject) mdvtools module mdvtools.chart_prototypes module mdvtools.conversions module mdvtools.csv_to_static module mdvtools.dbutils module mdvtools.dbutils.app module mdvtools.dbutils.dbmodels module mdvtools.dbutils.dbservice module mdvtools.dbutils.mdv_server_app module mdvtools.dbutils.routes module mdvtools.dbutils.test module mdvtools.dbutils.test.integration module mdvtools.dbutils.test.integration.test_dbservice_integration module mdvtools.dbutils.test.unit module mdvtools.dbutils.test.unit.test_dbservice module mdvtools.dbutils.test.unit.test_mdv_server_app module mdvtools.image_view_prototype module mdvtools.mdv_desktop module mdvtools.mdvproject module mdvtools.project_router module mdvtools.querytools module mdvtools.querytools.app module mdvtools.server module mdvtools.spatial module mdvtools.tests module mdvtools.tests.test_anndata_conversion module mdvtools.tests.test_bad_data module mdvtools.tests.test_column_groups module mdvtools.tests.test_multitext module mdvtools.websocket module module abundance_box_plot abundance_box_plot_example auth0_provider auth_provider base_plot box_plot box_plot_example chart_dicts density_scatter_plot density_scatter_plot_example dot_plot dot_plot_example dtypes_test genome_example heatmap_plot heatmap_plot_example histogram_plot histogram_plot_example image_table_plot mdvtools mdvtools.chart_prototypes mdvtools.conversions mdvtools.csv_to_static mdvtools.dbutils mdvtools.dbutils.app mdvtools.dbutils.dbmodels mdvtools.dbutils.dbservice mdvtools.dbutils.mdv_server_app mdvtools.dbutils.routes mdvtools.dbutils.test mdvtools.dbutils.test.integration mdvtools.dbutils.test.integration.test_dbservice_integration mdvtools.dbutils.test.unit mdvtools.dbutils.test.unit.test_dbservice mdvtools.dbutils.test.unit.test_mdv_server_app mdvtools.image_view_prototype mdvtools.mdv_desktop mdvtools.mdvproject mdvtools.project_router mdvtools.querytools mdvtools.querytools.app mdvtools.server mdvtools.spatial mdvtools.tests mdvtools.tests.test_anndata_conversion mdvtools.tests.test_bad_data mdvtools.tests.test_column_groups mdvtools.tests.test_multitext mdvtools.websocket multi_line_plot multiline_plot_example multiple_graphs_example pbmc3k_tutorial pie_chart pie_chart_example ring_chart ring_chart_example row_chart row_chart_example sankey_plot scanpy_exp1 scanpy_pbmc3k scanpy_pbmc3k_tutorial scatter_plot scatter_plot_3D scatter_plot_3D_example scatter_plot_example selection_dialog_plot stacked_row_plot stacked_row_plot_example table_plot text_box_plot text_box_plot_example view violin_plot violin_plot_example viv_chart wordcloud_plot wordcloud_plot_example

multi_line_plot module multi_line_proto (in module mdvtools.chart_prototypes) multiline_plot_example module MultiLinePlot (class in multi_line_plot) multiple_graphs_example module multitext (in module dtypes_test)

N

n (in module dtypes_test) 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) (mdvtools.project_router.ProjectBlueprint_v2 attribute)

nfs_dir (in module scanpy_exp1) nfs_server (in module scanpy_exp1) nrm (in module dtypes_test) numpy_dtypes (in module mdvtools.mdvproject)

O

oauth (in module mdvtools.dbutils.mdv_server_app) object_id (mdvtools.dbutils.dbmodels.SharedObject 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

p (in module dtypes_test) (in module genome_example) (in module mdvtools.tests.test_column_groups) (in module pbmc3k_tutorial) Panel (class in view) panelWidth (view.Panel attribute) param (chart_dicts.BaseChart attribute) parent (mdvtools.dbutils.dbmodels.Project attribute) parse_multitext (in module mdvtools.csv_to_static) parser (in module mdvtools.csv_to_static) password (mdvtools.dbutils.dbmodels.User attribute) path (in module dtypes_test) (in module mdvtools.mdvproject) (in module mdvtools.tests.test_column_groups) (mdvtools.dbutils.dbmodels.Project attribute) pbmc3k_tutorial module pca_np (in module pbmc3k_tutorial) Permission (class in mdvtools.dbutils.dbmodels) permission (mdvtools.dbutils.dbmodels.Permission attribute) permissions (mdvtools.dbutils.dbmodels.User attribute) pie_chart module

pie_chart_example module PieChart (class in pie_chart) plot_data (base_plot.BasePlot attribute) pos (chart_dicts.ColorLegend attribute) position (chart_dicts.BaseChart attribute) preference (mdvtools.dbutils.dbmodels.UserPreference attribute) preferences (mdvtools.dbutils.dbmodels.User attribute) Project (class in mdvtools.dbutils.dbmodels) project_dir (in module mdvtools.mdv_desktop) project_folder (in module genome_example) (in module scanpy_pbmc3k) (in module scanpy_pbmc3k_tutorial) project_id (mdvtools.dbutils.dbmodels.File attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) project_name (in module scanpy_exp1) project_path (in module pbmc3k_tutorial) ProjectBlueprint (class in mdvtools.project_router) ProjectBlueprint_v2 (class in mdvtools.project_router) projects (in module mdvtools.mdv_desktop) (mdvtools.dbutils.dbmodels.Genome attribute) (mdvtools.dbutils.dbmodels.User attribute) ProjectService (class in mdvtools.dbutils.dbservice)

R

r (in module pbmc3k_tutorial) register_app() (mdvtools.project_router.ProjectBlueprint static method) (mdvtools.project_router.ProjectBlueprint_v2 static method) register_auth0_routes() (in module mdvtools.dbutils.mdv_server_app) register_routes() (in module mdvtools.dbutils.mdv_server_app) remove_column() (mdvtools.mdvproject.MDVProject method) rename_columns() (in module mdvtools.csv_to_static) replace_text_values() (in module mdvtools.csv_to_static) restore_datasource() (mdvtools.mdvproject.MDVProject method) ring_chart module ring_chart_example module RingChart (class in ring_chart)

rng (in module dtypes_test) route() (mdvtools.project_router.ProjectBlueprint method) (mdvtools.project_router.ProjectBlueprint_v2 method) (mdvtools.project_router.SingleProjectShim method) routes (in module mdvtools.server) (mdvtools.project_router.ProjectBlueprint attribute) (mdvtools.project_router.ProjectBlueprint_v2 attribute) row_chart module row_chart (in module pbmc3k_tutorial) row_chart_data (in module pbmc3k_tutorial) row_chart_example module RowChart (class in row_chart) running (in module mdvtools.mdv_desktop)

S

sankey_plot module SankeyPlot (class in sankey_plot) save_json() (in module mdvtools.mdvproject) save_state() (mdvtools.mdvproject.MDVProject method) scanpy_exp1 module scanpy_pbmc3k module scanpy_pbmc3k_tutorial module scatter2D_chart (in module pbmc3k_tutorial) scatter2D_plot (in module pbmc3k_tutorial) scatter_chart (in module pbmc3k_tutorial) scatter_plot module scatter_plot (in module pbmc3k_tutorial) scatter_plot_3D module scatter_plot_3D_example module scatter_plot_example module ScatterChart (class in chart_dicts) 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) sent_on (mdvtools.dbutils.dbmodels.Job attribute) separator (in module mdvtools.csv_to_static) serve() (mdvtools.mdvproject.MDVProject method) serve_projects_from_db() (in module mdvtools.dbutils.mdv_server_app) serve_projects_from_filesystem() (in module mdvtools.dbutils.mdv_server_app) ServiceTestCase (class in mdvtools.dbutils.test.integration.test_dbservice_integration) 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) (viv_chart.VivChart 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_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) (viv_chart.VivChart 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_grid_position() (image_table_plot.ImageTableChart method) set_grid_size() (image_table_plot.ImageTableChart method) set_grouping() (abundance_box_plot.AbundanceBoxPlot method) set_image_label() (image_table_plot.ImageTableChart method) set_image_width() (image_table_plot.ImageTableChart method) set_images() (image_table_plot.ImageTableChart 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) (image_table_plot.ImageTableChart 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_margins() (image_table_plot.ImageTableChart 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() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) setup_views() (in module scanpy_pbmc3k) (in module scanpy_pbmc3k_tutorial) shared_with (mdvtools.dbutils.dbmodels.SharedObject attribute) SharedObject (class in mdvtools.dbutils.dbmodels) SingleProjectShim (class in mdvtools.project_router) size (chart_dicts.AxisProperties attribute) (chart_dicts.BaseChart attribute) skip_column_clean (mdvtools.mdvproject.MDVProject attribute) small_icon (mdvtools.dbutils.dbmodels.Genome attribute) soft_delete_project() (mdvtools.dbutils.dbservice.ProjectService static method) source_dir (in module scanpy_exp1) stacked_row_plot module stacked_row_plot_example module StackedRowChart (class in stacked_row_plot) StackedRowChart() (in module chart_dicts) 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)

T

table_chart (in module pbmc3k_tutorial) table_name (mdvtools.dbutils.dbmodels.GeneSet attribute) (mdvtools.dbutils.dbmodels.ViewSet attribute) table_plot module table_plot (in module pbmc3k_tutorial) TablePlot (class in table_plot) tables_exist() (in module mdvtools.dbutils.mdv_server_app) tar (in module pbmc3k_tutorial) tearDown() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_add_new_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_add_new_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_add_new_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_add_or_update_file_in_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_add_or_update_file_in_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_add_or_update_file_in_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_add_or_update_file_in_project_update_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_add_or_update_file_in_project_update_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_bad_data() (in module mdvtools.tests.test_bad_data) test_compliant_multitext() (in module mdvtools.tests.test_multitext) test_convert_scanpy_to_mdv() (in module mdvtools.tests.test_anndata_conversion) test_convert_scanpy_to_mdv_views() (in module mdvtools.tests.test_anndata_conversion) test_delete_files_by_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_delete_files_by_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_delete_files_by_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_file_exists_in_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_file_exists_in_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_file_exists_in_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_get_active_projects() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_get_active_projects_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_get_active_projects_success() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_get_file_by_path_and_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_get_file_by_path_and_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_get_file_by_path_and_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_get_files_by_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method)

test_get_files_by_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_get_files_by_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_get_next_project_id() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_get_next_project_id_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_get_next_project_id_success() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_get_project_by_id() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_get_project_by_id_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_get_project_by_id_success() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_project_dir() (in module mdvtools.tests.test_anndata_conversion) test_soft_delete_project() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_soft_delete_project_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_soft_delete_project_success() (mdvtools.dbutils.test.unit.test_dbservice.TestProjectService method) test_update_file_timestamp() (mdvtools.dbutils.test.integration.test_dbservice_integration.ServiceTestCase method) test_update_file_timestamp_failure() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) test_update_file_timestamp_success() (mdvtools.dbutils.test.unit.test_dbservice.TestFileService method) TestFileService (class in mdvtools.dbutils.test.unit.test_dbservice) TestProjectService (class in mdvtools.dbutils.test.unit.test_dbservice) text (in module dtypes_test) text16 (in module dtypes_test) text_box_plot module text_box_plot_example module TextBox (class in text_box_plot) textSize (chart_dicts.AxisProperties attribute) tickfont (chart_dicts.AxisProperties attribute) TIMESTAMP_UPDATE_INTERVAL (mdvtools.project_router.ProjectBlueprint_v2 attribute) title (chart_dicts.BaseChart attribute) to_json() (base_plot.BasePlot method) trackfolder (mdvtools.mdvproject.MDVProject attribute) translate_query_type_to_sql() (in module mdvtools.querytools.app) transpose_counts (in module pbmc3k_tutorial) type (chart_dicts.ScatterChart attribute) (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Project attribute) types (in module mdvtools.csv_to_static)

U

umap_np (in module pbmc3k_tutorial) unique (in module dtypes_test) 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 (in module pbmc3k_tutorial)

url_prefix (mdvtools.project_router.ProjectBlueprint attribute) (mdvtools.project_router.ProjectBlueprint_v2 attribute) User (class in mdvtools.dbutils.dbmodels) user_id (mdvtools.dbutils.dbmodels.Job attribute) (mdvtools.dbutils.dbmodels.Permission attribute) (mdvtools.dbutils.dbmodels.UserPreference attribute) (mdvtools.dbutils.dbmodels.UserProject attribute) UserPreference (class in mdvtools.dbutils.dbmodels) UserProject (class in mdvtools.dbutils.dbmodels) users (mdvtools.dbutils.dbmodels.Project attribute)

V

value (mdvtools.dbutils.dbmodels.Permission attribute) varm_np (in module pbmc3k_tutorial) vcf_filename (in module genome_example) view module View (class in view) view (in module dtypes_test) view_config (in module pbmc3k_tutorial) views (mdvtools.mdvproject.MDVProject property) ViewSet (class in mdvtools.dbutils.dbmodels)

viewsfile (mdvtools.mdvproject.MDVProject attribute) violin_plot module violin_plot_example module violin_proto (in module mdvtools.chart_prototypes) ViolinPlot (class in violin_plot) viv_chart module viv_proto (in module mdvtools.chart_prototypes) VivChart (class in viv_chart)

W

wait_for_database() (in module mdvtools.dbutils.mdv_server_app) watch_folder() (in module mdvtools.mdv_desktop) wordcloud_plot module

wordcloud_plot_example module WordcloudPlot (class in wordcloud_plot)

X

x (chart_dicts.Axes attribute) (in module dtypes_test)

Y

y (chart_dicts.Axes attribute) (in module dtypes_test)

Z

z (in module dtypes_test)