diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..49359aa --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,72 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +repos: +- repo: https://github.com/lorenzwalthert/precommit + rev: v0.3.2.9019 + hooks: + - id: style-files + args: [--style_pkg=styler, --style_fun=tidyverse_style] + # codemeta must be above use-tidy-description when both are used + # - id: codemeta-description-updated + - id: use-tidy-description + - id: lintr + - id: readme-rmd-rendered + - id: parsable-R + - id: no-browser-statement + - id: no-debug-statement + - id: deps-in-desc + - id: spell-check + exclude: > + (?x)^( + .*\.[rR]| + .*\.feather| + .*\.jpeg| + .*\.pdf| + .*\.png| + .*\.py| + .*\.RData| + .*\.rds| + .*\.Rds| + .*\.Rproj| + .*\.sh| + (.*/|)\.gitignore| + (.*/|)\.gitlab-ci\.yml| + (.*/|)\.lintr| + (.*/|)\.pre-commit-.*| + (.*/|)\.Rbuildignore| + (.*/|)\.Renviron| + (.*/|)\.Rprofile| + (.*/|)\.travis\.yml| + (.*/|)appveyor\.yml| + (.*/|)NAMESPACE| + (.*/|)renv/settings\.dcf| + (.*/|)renv\.lock| + (.*/|)WORDLIST| + \.github/workflows/.*| + data/.*| + )$ +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-added-large-files + args: ['--maxkb=200'] + - id: file-contents-sorter + files: '^\.Rbuildignore$' + - id: end-of-file-fixer + exclude: '\.Rd' + - id: check-merge-conflict +- repo: https://github.com/pre-commit-ci/pre-commit-ci-config + rev: v1.5.1 + hooks: + # Only reuiqred when https://pre-commit.ci is used for config validation + - id: check-pre-commit-ci-config +- repo: local + hooks: + - id: forbid-to-commit + name: Don't commit common R artifacts + entry: Cannot commit .Rhistory, .RData, .Rds or .rds. + language: fail + files: '\.(Rhistory|RData|Rds|rds)$' + # `exclude: ` to allow committing specific files +ci: + autoupdate_schedule: monthly diff --git a/DESCRIPTION b/DESCRIPTION index 3c1feac..0e401d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dataflow Title: Data Flow App Demo -Version: 23.06.1 +Version: 23.10.1 Authors@R: person('L', 'Wolfe', email = 'loren.wolfe@sagebase.org', role = c('cre', 'aut')) Description: A data flow package. License: MIT + file LICENSE diff --git a/R/app_server.R b/R/app_server.R index 70a9b5d..6a6e04a 100644 --- a/R/app_server.R +++ b/R/app_server.R @@ -7,9 +7,10 @@ #' app_server <- function( input, output, session ) { + # Your application server logic options(shiny.reactlog = TRUE) - + # AUTHENTICATION params <- parseQueryString(isolate(session$clientData$url_search)) if (!has_auth_code(params)) { @@ -35,287 +36,216 @@ app_server <- function( input, output, session ) { session$userData$access_token <- access_token - # generate dashboard configuration from dataFlow schema - dash_config <- dfamodules::generate_dashboard_config(schema_url = global_config$schema_url, - display_names = list(contributor = "Contributor", - entityId = "Synapse ID", - dataset = "Data Type", - dataset_name = "Dataset Folder Name", - num_items = "Number of Items in Manifest", - release_scheduled = "Release Date", - embargo = "Embargo", - standard_compliance = "QC Checks", - released = "Released", - data_portal = "Data Portal", - Component = NA), - icon = TRUE, - na_replace = list(num_items = "No Manifest", - release_scheduled = "Not Scheduled", - embargo = "No Embargo", - dataset = "No Manifest"), - base_url = schematic_api_url) - - # download data flow status manifest - manifest_obj <- dfamodules::dataset_manifest_download(asset_view = global_config$asset_view, - dataset_id = global_config$manifest_dataset_id, - access_token = access_token, - base_url = schematic_api_url) + # SET UP REACTIVE VALUES ################################################### - manifest_dfa <- dfamodules::prep_manifest_dfa(manifest = manifest_obj$content, - config = dash_config) + # reactive dash config + dash_config_react <- reactiveVal(NULL) - # PREPARE MANIFEST FOR DASH ########################################################### + # reactive data flow manifest + original_manifest <- reactiveVal(NULL) + admin_manifest <- reactiveVal(NULL) + + # reactive filtered manifest + filtered_manifest_react <- reactiveVal(NULL) + + # capture selected dcc configuration in a list + selected_dcc_config_list <- list( + project_name = reactiveVal(NULL), + synapse_asset_view = reactiveVal(NULL), + manifest_dataset_id = reactiveVal(NULL), + schema_url = reactiveVal(NULL), + icon = reactiveVal(NULL) + ) - # add status to manifest - manifest_w_status <- shiny::reactive({ + + # SELECT A DCC ############################################################# + mod_select_dcc_out <- dfamodules::mod_select_dcc_server("select_dcc", + dcc_config, + access_token) + + # CONFIGURE APP ############################################################ + observeEvent(mod_select_dcc_out()$btn_click, { + + # move to dashboard page + shinydashboard::updateTabItems(session = session, + inputId = "tabs", + selected = "tab_dashboard") + + # show waiter on button click + waiter::waiter_show( + html = shiny::tagList( + shiny::img(src = "www/loading.gif"), + shiny::h3("Getting data. This may take a moment.", style = "color:white;")), + color="#424874" + ) + + # update reactiveVals + selected_dcc_config_list$synapse_asset_view(mod_select_dcc_out()$selected_dcc_config$synapse_asset_view) + selected_dcc_config_list$manifest_dataset_id(mod_select_dcc_out()$selected_dcc_config$manifest_dataset_id) + selected_dcc_config_list$project_name(mod_select_dcc_out()$selected_dcc_config$project_name) + selected_dcc_config_list$schema_url(mod_select_dcc_out()$selected_dcc_config$schema_url) + selected_dcc_config_list$icon(mod_select_dcc_out()$selected_dcc_config$icon) + + dash_config <- dfamodules::generate_dashboard_config( + schema_url = selected_dcc_config_list$schema_url(), + icon = selected_dcc_config_list$icon(), + base_url = schematic_api_url) + + # download manifest + manifest_obj <- dfamodules::dataset_manifest_download( + asset_view = selected_dcc_config_list$synapse_asset_view(), + dataset_id = selected_dcc_config_list$manifest_dataset_id(), + access_token = access_token, + base_url = schematic_api_url + ) + + # prep manifest for app + prepped_manifest <- dfamodules::prep_manifest_dfa( + manifest = manifest_obj$content, + config = dash_config + ) - # add some columns to manifest to make logic easier - manifest <- manifest_dfa %>% - dplyr::mutate(scheduled = !is.na(release_scheduled), - no_embargo = is.na(embargo) || embargo < Sys.Date(), - past_due = !is.na(release_scheduled) && release_scheduled < Sys.Date()) + # update reactiveVals + original_manifest(prepped_manifest) + admin_manifest(prepped_manifest) - # generate status variable based on some logic that defines various data flow statuses - status <- sapply(1:nrow(manifest), function(i) { - row <- manifest[i, ] - - if (row$scheduled == FALSE) { - status <- "not scheduled" - } else if (row$no_embargo == FALSE || row$standard_compliance == FALSE) { - status <- "quarantine" - } else if (row$no_embargo == TRUE & row$standard_compliance == TRUE & row$released == FALSE) { - status <- "quarantine (ready for release)" - } else if (row$released == TRUE) { - status <- "released" - } else { - NA - } - - status - }) + dash_config_react(dash_config) - # add status to manifest - manifest$data_flow_status <- status + # FILTER MANIFEST FOR DASH ############################################### + + filtered_manifest <- dfamodules::mod_datatable_filters_server( + "datatable_filters_1", + original_manifest + ) - manifest + # DATASET DASH ########################################################### + + dfamodules::mod_datatable_dashboard_server( + "dashboard_1", + filtered_manifest, + dash_config_react + ) + + # DATASET DASH VIZ : DISTRIBUTIONS ######################################## + + dfamodules::mod_distribution_server( + id = "distribution_contributor", + df = filtered_manifest, + group_by_var = "contributor", + title = NULL, + x_lab = "Contributor", + y_lab = "Number of Datasets", + fill = "#0d1c38" + ) + + dfamodules::mod_distribution_server( + id = "distribution_datatype", + df = filtered_manifest, + group_by_var = "dataset_type", + title = NULL, + x_lab = "Type of dataset", + y_lab = "Number of Datasets", + fill = "#0d1c38" + ) + + # hide waiter + waiter::waiter_hide() + }) - # FILTER MANIFEST FOR DASH UI ########################################################### + # ADMINISTRATOR ############################################################# + # SELECT STORAGE PROJECT ##################################################### - # prepare inputs for filter module - filter_inputs <- shiny::reactive({ - - contributor_choices <- unique(manifest_w_status()$contributor) - dataset_choices <- unique(manifest_w_status()$dataset) - release_daterange_start <- min(manifest_w_status()$release_scheduled, na.rm = TRUE) - release_daterange_end <- max(manifest_w_status()$release_scheduled, na.rm = TRUE) - status_choices <- unique(manifest_w_status()$data_flow_status) - - list(contributor_choices, - dataset_choices, - release_daterange_start, - release_daterange_end, - status_choices) - }) + selected_project_id <- reactiveVal(NULL) + + observe({ - output$filter_module <- shiny::renderUI({ - filters <- filter_inputs() - dfamodules::mod_datatable_filters_ui("datatable_filters_1", - contributor_choices = filters[[1]], - dataset_choices = filters[[2]], - release_daterange = c(filters[[3]], filters[[4]]), - status_choices = filters[[5]]) + if (input$tabs == "tab_administrator") { + + mod_select_storage_project_out <- dfamodules::mod_select_storage_project_server( + id = "select_storage_project_1", + asset_view = selected_dcc_config_list$synapse_asset_view, + access_token = access_token, + base_url = schematic_api_url) + + selected_project_id(mod_select_storage_project_out()) + } }) - # FILTER MANIFEST FOR DASH SERVER #################################################### - filtered_manifest <- dfamodules::mod_datatable_filters_server("datatable_filters_1", - manifest_w_status) - - - # DATASET DASH ####################################################################### - - dfamodules::mod_datatable_dashboard_server("dashboard_1", - filtered_manifest, - dash_config) - - # DATASET DASH VIZ : DISTRIBUTIONS #################################################### + # SELECT DATASETS ########################################################## - dfamodules::mod_distribution_server(id = "distribution_contributor", - df = filtered_manifest, - group_by_var = "contributor", - title = NULL, - x_lab = "Contributor", - y_lab = "Number of Datasets", - fill = "#0d1c38") + mod_dataset_selection_out <- dfamodules::mod_dataset_selection_server( + id = "dataset_selection_1", + storage_project_id = selected_project_id, + asset_view = selected_dcc_config_list$synapse_asset_view, + access_token = access_token, + base_url = schematic_api_url + ) + + # COLLECT WIDGET SELECTIONS ################################################ - dfamodules::mod_distribution_server(id = "distribution_datatype", - df = filtered_manifest, - group_by_var = "dataset", - title = NULL, - x_lab = "Type of dataset", - y_lab = "Number of Datasets", - fill = "#0d1c38") + mod_administrator_widgets_out <- dfamodules::mod_administrator_widgets_server("update_data_flow_status_1") - # PREPARE DATA FOR STACKED BAR PLOTS ################################################## - # specifically stacked bar plots that show data flow status grouped by contributor + # MAKE UPDATES TO MANIFEST ################################################# - stacked_bar_data <- shiny::reactive({ - - release_status_data <- filtered_manifest() %>% - dplyr::group_by(contributor) %>% - dplyr::group_by(dataset, .add = TRUE) %>% - dplyr::group_by(data_flow_status, .add = TRUE) %>% - dplyr::tally() - - # reorder factors - release_status_data$data_flow_status <- factor(release_status_data$data_flow_status, - levels = c("released", "quarantine (ready for release)", "quarantine", "not scheduled")) - - release_status_data + updated_manifest <- reactive({ + dfamodules::apply_administrator_selections( + dataflow_manifest = admin_manifest(), + administrator_widget_output = mod_administrator_widgets_out(), + dataset_selection_module_output = mod_dataset_selection_out() + ) }) - dfamodules::mod_stacked_bar_server(id = "stacked_bar_release_status", - df = stacked_bar_data, - x_var = "contributor", - y_var = "n", - fill_var = "data_flow_status", - title = NULL, - x_lab = "Contributors", - y_lab = NULL, - colors = c("#085631", "#ffa500", "#a72a1e", "#3d3d3d"), - coord_flip = TRUE) + # SHOW MANIFEST PREVIEW #################################################### + # # get names of selected datasets - # drop down for runners plot - output$select_project_ui <- shiny::renderUI({ - - contributors <- unique(filtered_manifest()$contributor) - - shiny::selectInput(inputId = "select_project_input", - label = NULL, - choices = contributors, - selectize = FALSE) + selected_rows <- shiny::reactive({ + mod_dataset_selection_out()$id }) - # wrangle data for stacked bar plot (runners) - - release_data_runners <- shiny::reactive({ - - shiny::req(input$select_project_input) - - release_status_data <- filtered_manifest() %>% - dplyr::filter(!is.na(release_scheduled)) %>% - dplyr::filter(contributor == input$select_project_input) %>% - dplyr::group_by(contributor) %>% - dplyr::group_by(release_scheduled, .add = TRUE) %>% - dplyr::group_by(data_flow_status, .add = TRUE) %>% - dplyr::tally() - - release_status_data$data_flow_status <- factor(release_status_data$data_flow_status, - levels = c("released", "quarantine (ready for release)", "quarantine")) - - release_status_data - }) - - - dfamodules::mod_stacked_bar_server(id = "stacked_runners", - df = release_data_runners, - x_var = "release_scheduled", - y_var = "n", - fill_var = "data_flow_status", - title = NULL, - x_lab = "Release Dates", - y_lab = NULL, - x_line = Sys.Date(), - colors = c("#085631", "#ffa500", "#a72a1e"), - width = 10, - date_breaks = "1 month", - coord_flip = FALSE) - - # ADMINISTRATOR ####################################################################### - - # reactive value that holds manifest_dfa - rv_manifest <- shiny::reactiveVal(manifest_dfa) - - # STORAGE PROJECT SELECTION - - select_storage_project_out <- dfamodules::mod_select_storage_project_server(id = "select_storage_project_1", - asset_view = global_config$asset_view, - access_token = access_token, - base_url = schematic_api_url) - - # DATASET SELECTION - - dataset_selection <- dfamodules::mod_dataset_selection_server(id = "dataset_selection_1", - storage_project_df = select_storage_project_out, - asset_view = global_config$asset_view, - access_token = access_token, - base_url = schematic_api_url) - - # UPDATE DATA FLOW STATUS SELECTIONS - updated_data_flow_status <- dfamodules::mod_update_data_flow_status_server("update_data_flow_status_1") - - - # MODIFY MANIFEST - modified_manifest <- shiny::reactive({ - shiny::req(updated_data_flow_status()) - - dfamodules::update_dfs_manifest(dfs_manifest = rv_manifest(), - dfs_updates = updated_data_flow_status(), - selected_datasets_df = dataset_selection()) - }) + dfamodules::mod_manifest_preview_server( + "highlight_datatable_1", + updated_manifest, + selected_rows, + "dataset_id" + ) - # BUTTON CLICK UPDATE MANIFEST + # BUTTON CLICK ACTIONS ##################################################### + + # save updates for submission to a submission manifest reactiveVal + # prevents user from having to fully submit a manifest to make new selections shiny::observeEvent(input$save_update, { - rv_manifest(modified_manifest()) + admin_manifest(updated_manifest()) }) + # clear updates + # also clears the submission manifest of any cached updates shiny::observeEvent(input$clear_update, { - rv_manifest(manifest_dfa) + admin_manifest(original_manifest()) }) + + # SUBMIT MODEL TO SYNAPSE ################################################# - # PREP MANIFEST FOR SYNAPSE SUBMISSION - + # prep manifest for submission manifest_submit <- shiny::reactive({ - dfamodules::prep_manifest_submit(modified_manifest(), - dash_config) - }) - - # DISPLAY MANIFEST - admin_display_manifest <- shiny::reactive({ + req(dash_config_react()) + req(updated_manifest()) - # rearrange manifest so it's more readable - manifest <- dfamodules::rearrange_dataframe(manifest_submit(), - names(dash_config)) - - # make columns factors - factor_cols <- dfamodules::get_colname_by_type(dash_config, type = "drop_down_filter") - manifest[factor_cols] <- lapply(manifest[,factor_cols], factor) - - # return - manifest + dfamodules::prep_manifest_submit( + updated_manifest(), + dash_config_react() + ) }) - # get names of selected datasets - selected_row_names <- shiny::reactive({ - dataset_selection()$id - - }) - - dfamodules::mod_highlight_datatable_server("highlight_datatable_1", - admin_display_manifest, - selected_row_names, - "entityId") - - # SUBMIT MODEL TO SYNAPSE - # make sure to submit using a manifest that has been run through date to string - dfamodules::mod_submit_model_server(id = "submit_model_1", - dfs_manifest = manifest_submit, - data_type = NULL, - asset_view = global_config$asset_view, - dataset_id = global_config$manifest_dataset_id, - manifest_dir = "./manifest", - access_token = access_token, - base_url = schematic_api_url, - schema_url = global_config$schema_url) - + dfamodules::mod_submit_model_server( + id = "submit_model_1", + dfs_manifest = manifest_submit, + data_type = NULL, + asset_view = selected_dcc_config_list$synapse_asset_view, + dataset_id = selected_dcc_config_list$manifest_dataset_id, + manifest_dir = "./manifest", + access_token = access_token, + base_url = schematic_api_url, + schema_url = selected_dcc_config_list$schema_url + ) } diff --git a/R/app_ui.R b/R/app_ui.R index 5ed3ee8..5bcedc8 100644 --- a/R/app_ui.R +++ b/R/app_ui.R @@ -1,146 +1,133 @@ #' The application User-Interface -#' -#' @param request Internal parameter for `{shiny}`. +#' +#' @param request Internal parameter for `{shiny}`. #' DO NOT REMOVE. #' @import shiny #' @noRd -#' +#' app_ui <- function() { - shiny::tagList( # Leave this function for adding external resources golem_add_external_resources(), - - # initialize waiter + use preloader - waiter::useWaiter(), - waiter::waiterPreloader( - - html = shiny::tagList( - shiny::img(src = "www/loading.gif"), - shiny::h4("Retrieving Synapse information...", style = "color:white;")), - color="#424874"), - + + # initialize shinyjs + shinyjs::useShinyjs(), + # define colors for icons in datatable # green check shiny::tags$style(".fa-check {color:#58A158}"), # red x shiny::tags$style(".fa-xmark {color:#B2242A}"), - + # Your application UI logic - + # dashboardPage shinydashboard::dashboardPage( - + # dashboardHeader shinydashboard::dashboardHeader( - title = "Data Flow" + title = "Data Flow" ), - + # dashboardSidebar shinydashboard::dashboardSidebar( - - #sidebarMenu + # sidebarMenu shinydashboard::sidebarMenu( - shinydashboard::menuItem("Dashboard", - tabName = "dataset-dashboard", - icon = icon("dashboard")), - shinydashboard::menuItem("Administrator", - tabName = "administrator", - icon = icon("cog")) - + id = "tabs", + shinydashboard::menuItem("Select a DCC", + tabName = "tab_select_dcc", + icon = icon("rocket") + ), + shinydashboard::menuItem("Dashboard", + tabName = "tab_dashboard", + icon = icon("dashboard") + ), + shinydashboard::menuItem("Administrator", + tabName = "tab_administrator", + icon = icon("pencil") + ) ) ), - - #dashboardBody + + # dashboardBody shinydashboard::dashboardBody( - + + # initialize waiter + use preloader + waiter::use_waiter(), + waiter::waiter_preloader( + html = shiny::tagList( + shiny::img(src = "www/loading.gif"), + shiny::h4("Retrieving Synapse information...", style = "color:white;") + ), + color = "#424874" + ), + # implement dca theme module dcamodules::use_dca(theme = "sage"), - - # initialize shinyjs - shinyjs::useShinyjs(), - + # dashboardTabItems shinydashboard::tabItems( - + shinydashboard::tabItem( + tabName = "tab_select_dcc", + shiny::fluidRow( + dfamodules::mod_select_dcc_ui( + "select_dcc", + dcc_config + ) + ) + ), + # dataset view dashboard tab - shinydashboard::tabItem(tabName = "dataset-dashboard", - - shiny::fluidRow( - shiny::uiOutput("filter_module")), - - - shiny::fluidRow( - shinydashboard::box( - width = NULL, - title = "Dashboard", - status = "primary", - collapsible = TRUE, - dfamodules::mod_datatable_dashboard_ui("dashboard_1") - )), - - shiny::fluidRow( - shinydashboard::box( - title = "Distribution of datasets by contributor", - status = "primary", - collapsible = TRUE, - dfamodules::mod_distribution_ui("distribution_contributor")), - shinydashboard::box( - title = "Distribution of datasets by data type", - status = "primary", - collapsible = TRUE, - dfamodules::mod_distribution_ui("distribution_datatype") - )), - - shiny::fluidRow( - shinydashboard::box( - title = "Release status of all datasets by contributor", - status = "primary", - collapsible = TRUE, - dfamodules::mod_stacked_bar_ui("stacked_bar_release_status")), - shinydashboard::box( - title = "Data flow status by release date", - status = "primary", - collapsible = TRUE, - - shiny::uiOutput("select_project_ui"), - - dfamodules::mod_stacked_bar_ui("stacked_runners"))) + shinydashboard::tabItem( + tabName = "tab_dashboard", + shiny::fluidRow( + dfamodules::mod_datatable_filters_ui("datatable_filters_1") + ), + shiny::fluidRow( + shinydashboard::box( + width = NULL, + title = "Dashboard", + status = "primary", + collapsible = TRUE, + dfamodules::mod_datatable_dashboard_ui("dashboard_1") + ) + ), + shiny::fluidRow( + shinydashboard::box( + title = "Distribution of datasets by contributor", + status = "primary", + collapsible = TRUE, + dfamodules::mod_distribution_ui("distribution_contributor") + ), + shinydashboard::box( + title = "Distribution of datasets by data type", + status = "primary", + collapsible = TRUE, + dfamodules::mod_distribution_ui("distribution_datatype") + ) + ) ), - + # Administrator tab - shinydashboard::tabItem(tabName = "administrator", - - shiny::fluidPage( - - dfamodules::mod_select_storage_project_ui("select_storage_project_1"), - - dfamodules::mod_dataset_selection_ui("dataset_selection_1"), - - br(), - - dfamodules::mod_update_data_flow_status_ui("update_data_flow_status_1"), - - shinydashboard::box( - - width = NULL, - - dfamodules::mod_highlight_datatable_ui("highlight_datatable_1"), - - br(), - - shiny::actionButton("save_update", "Save Updates"), - shiny::actionButton("clear_update", "Clear Updates") - - ), - - shiny::br(), - - dfamodules::mod_submit_model_ui("submit_model_1")) - + shinydashboard::tabItem( + tabName = "tab_administrator", + shiny::fluidPage( + dfamodules::mod_select_storage_project_ui("select_storage_project_1"), + dfamodules::mod_dataset_selection_ui("dataset_selection_1"), + br(), + dfamodules::mod_administrator_widgets_ui("update_data_flow_status_1"), + shinydashboard::box( + width = NULL, + dfamodules::mod_manifest_preview_ui("highlight_datatable_1"), + br(), + shiny::actionButton("save_update", "Save Updates"), + shiny::actionButton("clear_update", "Clear Updates") + ), + shiny::br(), + dfamodules::mod_submit_model_ui("submit_model_1") + ) ) - ) ) ) @@ -148,27 +135,26 @@ app_ui <- function() { } #' Add external Resources to the Application -#' -#' This function is internally used to add external -#' resources inside the Shiny application. -#' +#' +#' This function is internally used to add external +#' resources inside the Shiny application. +#' #' @import shiny #' @importFrom golem add_resource_path activate_js favicon bundle_resources #' @noRd -golem_add_external_resources <- function(){ - +golem_add_external_resources <- function() { add_resource_path( - 'www', app_sys('app/www') + "www", app_sys("app/www") ) - + tags$head( favicon(), bundle_resources( - path = app_sys('app/www'), - app_title = 'Data Flow' + path = app_sys("app/www"), + app_title = "Data Flow" ) # Add here other external resources - # for example, you can add shinyalert::useShinyalert() + # for example, you can add shinyalert::useShinyalert() ) } @@ -182,4 +168,4 @@ uiFunc <- function(req) { } else { app_ui() } -} \ No newline at end of file +} diff --git a/R/global.R b/R/global.R index fb751e9..029ee44 100644 --- a/R/global.R +++ b/R/global.R @@ -1,21 +1,9 @@ # READ IN CONFIG -global_config <- jsonlite::read_json("inst/global.json") +dcc_config <- readr::read_csv("https://raw.githubusercontent.com/Sage-Bionetworks/data_flow_config/main/dcc_config.csv", + show_col_types = FALSE) # GET SCHEMATIC API URL -# If there is a config file, use that -# Else use environment variables -if ("schematic_api_url" %in% names(global_config)) { - schematic_api_url <- global_config$schematic_api_url -} else { - schematic_api_url <- Sys.getenv("DFA_SCHEMATIC_API_URL") -} - -# check that all variables are present -if (is.null(schematic_api_url) || nchar(schematic_api_url) == 0) stop("missing DFA_SCHEMATIC_API_URL environmental variable") -if (is.null(global_config$asset_view) || nchar(global_config$asset_view) == 0) stop("asset_view is missing from global.json") -if (is.null(global_config$manifest_dataset_id) || nchar(global_config$manifest_dataset_id) == 0) stop("manifest_dataset_id is missing from global.json") -if (is.null(global_config$schema_url) || nchar(global_config$schema_url) == 0) stop("schema_url is missing from global.json") - +schematic_api_url <- Sys.getenv("DFA_SCHEMATIC_API_URL") message("DFA is using ", schematic_api_url) # SET UP OAUTH @@ -78,3 +66,4 @@ api <- httr::oauth_endpoint( # The 'openid' scope is required by the protocol for retrieving user information. scope <- "openid view download modify" + diff --git a/inst/data_model/dataflow_component.csv b/inst/data_model/dataflow_component.csv index a2b5e60..6ee39e5 100644 --- a/inst/data_model/dataflow_component.csv +++ b/inst/data_model/dataflow_component.csv @@ -1,14 +1,17 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -dataFlow,Describes data flow status,,"Component, contributor, entityId, dataset_name, dataset, num_items, release_scheduled, embargo, standard_compliance, data_portal, released",,TRUE,DataType,,, -contributor,Storage project that dataset is contained in,,,,TRUE,DataProperty,,,str -entityId,Synapse unique ID,,,,TRUE,DataProperty,,,str -dataset_name,Unique dataset name,,,,TRUE,DataProperty,,,str -dataset,Type of dataset,,,,TRUE,DataProperty,,,str +dataFlow,Describes data flow status,,"Component, contributor, dataset_id, dataset_name, dataset_type, upload_date, num_items, dataset_size, scheduled_release_date, release_date, status, released_destinations, released, metadata_check, governance_compliance",,TRUE,DataType,,, +contributor,"The team of a contributing user. The team reflects the contributing institution in standard DCC setups).  Note that for DCCs picking option 1 in the standard DCC setup, the Synapse project name also reflects the contributing institutions and can be used instead of the team name.",,,,TRUE,DataProperty,,,str +dataset_id,Synapse ID of manifest folder,,,,TRUE,DataProperty,,,str +dataset_name,Name of dataset,,,,TRUE,DataProperty,,,str +dataset_type,Type of dataset,,,,TRUE,DataProperty,,,str +upload_date,Date when both data records and data files (if applicable) have been uploaded,,,,TRUE,DataProperty,,,date num_items,Number of files contained in a manifest,,,,TRUE,DataProperty,,,int -release_scheduled,Date that a dataset is scheduled for release,,,,TRUE,DataProperty,,,date -embargo,Date that indicates when a dataset is released from embargo,,,,TRUE,DataProperty,,,date -standard_compliance,Has dataset passed standard validation checks,"TRUE, FALSE",,,TRUE,DataProperty,,,str -data_portal,"Has dataset been published to data portal +dataset_size,GB of data in a dataset,,,,TRUE,DataProperty,,,int +scheduled_release_date,Date that a dataset is scheduled for release,,,,TRUE,DataProperty,,,date +release_date,Date when a given dataset has actually been released,,,,TRUE,DataProperty,,,date +status,Data flow status of a dataset,"Not uploaded, uploaded, curated, quarantine, preprocessing, scheduled for release, ready for release, released",,,TRUE,DataProperty,,,str +released_destinations,Location that a dataset has been released to,"Not applicable, data portal, dbGaP",,,TRUE,DataProperty,,,str +released,"Whether or not a dataset has been released ","TRUE, FALSE",,,TRUE,DataProperty,,,str -released,"Has this dataset been released -","TRUE, FALSE",,,TRUE,DataProperty,,,str \ No newline at end of file +metadata_check,Whether or not a dataset has passed DCA/Schematic metadata checks,"TRUE, FALSE",,,TRUE,DataProperty,,,str +governance_compliance,Whether or not all files in a manifest have passed governance requirements,"TRUE, FALSE",,,TRUE,DataProperty,,,str \ No newline at end of file diff --git a/inst/data_model/dataflow_component.jsonld b/inst/data_model/dataflow_component.jsonld index 9126097..1c32498 100644 --- a/inst/data_model/dataflow_component.jsonld +++ b/inst/data_model/dataflow_component.jsonld @@ -1995,31 +1995,43 @@ "@id": "bts:Contributor" }, { - "@id": "bts:EntityId" + "@id": "bts:DatasetId" }, { "@id": "bts:DatasetName" }, { - "@id": "bts:Dataset" + "@id": "bts:DatasetType" + }, + { + "@id": "bts:UploadDate" }, { "@id": "bts:NumItems" }, { - "@id": "bts:ReleaseScheduled" + "@id": "bts:DatasetSize" + }, + { + "@id": "bts:ScheduledReleaseDate" }, { - "@id": "bts:Embargo" + "@id": "bts:ReleaseDate" }, { - "@id": "bts:StandardCompliance" + "@id": "bts:Status" }, { - "@id": "bts:DataPortal" + "@id": "bts:ReleasedDestinations" }, { "@id": "bts:Released" + }, + { + "@id": "bts:MetadataCheck" + }, + { + "@id": "bts:GovernanceCompliance" } ], "sms:validationRules": [] @@ -2027,7 +2039,7 @@ { "@id": "bts:Contributor", "@type": "rdfs:Class", - "rdfs:comment": "Storage project that dataset is contained in", + "rdfs:comment": "The team of a contributing user. The team reflects the contributing institution in standard DCC setups).  Note that for DCCs picking option 1 in the standard DCC setup, the Synapse project name also reflects the contributing institutions and can be used instead of the team name.", "rdfs:label": "Contributor", "rdfs:subClassOf": [ { @@ -2044,10 +2056,10 @@ ] }, { - "@id": "bts:EntityId", + "@id": "bts:DatasetId", "@type": "rdfs:Class", - "rdfs:comment": "Synapse unique ID", - "rdfs:label": "EntityId", + "rdfs:comment": "Synapse ID of manifest folder", + "rdfs:label": "DatasetId", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2056,7 +2068,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "entityId", + "sms:displayName": "dataset_id", "sms:required": "sms:true", "sms:validationRules": [ "str" @@ -2065,7 +2077,7 @@ { "@id": "bts:DatasetName", "@type": "rdfs:Class", - "rdfs:comment": "Unique dataset name", + "rdfs:comment": "Name of dataset", "rdfs:label": "DatasetName", "rdfs:subClassOf": [ { @@ -2082,10 +2094,10 @@ ] }, { - "@id": "bts:Dataset", + "@id": "bts:DatasetType", "@type": "rdfs:Class", "rdfs:comment": "Type of dataset", - "rdfs:label": "Dataset", + "rdfs:label": "DatasetType", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2094,12 +2106,31 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "dataset", + "sms:displayName": "dataset_type", "sms:required": "sms:true", "sms:validationRules": [ "str" ] }, + { + "@id": "bts:UploadDate", + "@type": "rdfs:Class", + "rdfs:comment": "Date when both data records and data files (if applicable) have been uploaded", + "rdfs:label": "UploadDate", + "rdfs:subClassOf": [ + { + "@id": "bts:DataProperty" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "upload_date", + "sms:required": "sms:true", + "sms:validationRules": [ + "date" + ] + }, { "@id": "bts:NumItems", "@type": "rdfs:Class", @@ -2120,10 +2151,29 @@ ] }, { - "@id": "bts:ReleaseScheduled", + "@id": "bts:DatasetSize", + "@type": "rdfs:Class", + "rdfs:comment": "GB of data in a dataset", + "rdfs:label": "DatasetSize", + "rdfs:subClassOf": [ + { + "@id": "bts:DataProperty" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "dataset_size", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:ScheduledReleaseDate", "@type": "rdfs:Class", "rdfs:comment": "Date that a dataset is scheduled for release", - "rdfs:label": "ReleaseScheduled", + "rdfs:label": "ScheduledReleaseDate", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2132,17 +2182,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "release_scheduled", + "sms:displayName": "scheduled_release_date", "sms:required": "sms:true", "sms:validationRules": [ "date" ] }, { - "@id": "bts:Embargo", + "@id": "bts:ReleaseDate", "@type": "rdfs:Class", - "rdfs:comment": "Date that indicates when a dataset is released from embargo", - "rdfs:label": "Embargo", + "rdfs:comment": "Date when a given dataset has actually been released", + "rdfs:label": "ReleaseDate", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2151,17 +2201,92 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "embargo", + "sms:displayName": "release_date", "sms:required": "sms:true", "sms:validationRules": [ "date" ] }, { - "@id": "bts:StandardCompliance", + "@id": "bts:Status", "@type": "rdfs:Class", - "rdfs:comment": "Has dataset passed standard validation checks", - "rdfs:label": "StandardCompliance", + "rdfs:comment": "Data flow status of a dataset", + "rdfs:label": "Status", + "rdfs:subClassOf": [ + { + "@id": "bts:DataProperty" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Notuploaded" + }, + { + "@id": "bts:Uploaded" + }, + { + "@id": "bts:Curated" + }, + { + "@id": "bts:Quarantine" + }, + { + "@id": "bts:Preprocessing" + }, + { + "@id": "bts:Scheduledforrelease" + }, + { + "@id": "bts:Readyforrelease" + }, + { + "@id": "bts:Released" + } + ], + "sms:displayName": "status", + "sms:required": "sms:true", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:ReleasedDestinations", + "@type": "rdfs:Class", + "rdfs:comment": "Location that a dataset has been released to", + "rdfs:label": "ReleasedDestinations", + "rdfs:subClassOf": [ + { + "@id": "bts:DataProperty" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Notapplicable" + }, + { + "@id": "bts:Dataportal" + }, + { + "@id": "bts:DbGaP" + } + ], + "sms:displayName": "released_destinations", + "sms:required": "sms:true", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:Released", + "@type": "rdfs:Class", + "rdfs:comment": "Whether or not a dataset has been released\n", + "rdfs:label": "Released", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2178,17 +2303,17 @@ "@id": "bts:FALSE" } ], - "sms:displayName": "standard_compliance", + "sms:displayName": "released", "sms:required": "sms:true", "sms:validationRules": [ "str" ] }, { - "@id": "bts:DataPortal", + "@id": "bts:MetadataCheck", "@type": "rdfs:Class", - "rdfs:comment": "Has dataset been published to data portal\n", - "rdfs:label": "DataPortal", + "rdfs:comment": "Whether or not a dataset has passed DCA/Schematic metadata checks", + "rdfs:label": "MetadataCheck", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2205,17 +2330,17 @@ "@id": "bts:FALSE" } ], - "sms:displayName": "data_portal", + "sms:displayName": "metadata_check", "sms:required": "sms:true", "sms:validationRules": [ "str" ] }, { - "@id": "bts:Released", + "@id": "bts:GovernanceCompliance", "@type": "rdfs:Class", - "rdfs:comment": "Has this dataset been released\n", - "rdfs:label": "Released", + "rdfs:comment": "Whether or not all files in a manifest have passed governance requirements", + "rdfs:label": "GovernanceCompliance", "rdfs:subClassOf": [ { "@id": "bts:DataProperty" @@ -2232,7 +2357,7 @@ "@id": "bts:FALSE" } ], - "sms:displayName": "released", + "sms:displayName": "governance_compliance", "sms:required": "sms:true", "sms:validationRules": [ "str" @@ -2255,6 +2380,176 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Notuploaded", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Notuploaded", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not uploaded", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Uploaded", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Uploaded", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "uploaded", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Curated", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Curated", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "curated", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Quarantine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Quarantine", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "quarantine", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Preprocessing", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Preprocessing", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "preprocessing", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Scheduledforrelease", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Scheduledforrelease", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scheduled for release", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Readyforrelease", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Readyforrelease", + "rdfs:subClassOf": [ + { + "@id": "bts:Status" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ready for release", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Notapplicable", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Notapplicable", + "rdfs:subClassOf": [ + { + "@id": "bts:ReleasedDestinations" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Not applicable", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Dataportal", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Dataportal", + "rdfs:subClassOf": [ + { + "@id": "bts:ReleasedDestinations" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "data portal", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DbGaP", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "DbGaP", + "rdfs:subClassOf": [ + { + "@id": "bts:ReleasedDestinations" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "dbGaP", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:TRUE", "@type": "rdfs:Class", @@ -2262,7 +2557,7 @@ "rdfs:label": "TRUE", "rdfs:subClassOf": [ { - "@id": "bts:StandardCompliance" + "@id": "bts:Released" } ], "schema:isPartOf": { @@ -2279,7 +2574,7 @@ "rdfs:label": "FALSE", "rdfs:subClassOf": [ { - "@id": "bts:StandardCompliance" + "@id": "bts:Released" } ], "schema:isPartOf": { diff --git a/inst/ex_synapse_storage_manifest_dataflow.csv b/inst/ex_synapse_storage_manifest_dataflow.csv deleted file mode 100644 index 0da1e2e..0000000 --- a/inst/ex_synapse_storage_manifest_dataflow.csv +++ /dev/null @@ -1,44 +0,0 @@ -"Component","Uuid","contributor","data_portal","dataset","dataset_name","embargo","entityId","num_items","release_scheduled","released","standard_compliance" -"DataFlow","1fe0b597-f1d2-4998-8221-e720a1aaf6f8","FAIR demo data",FALSE,"Biospecimen","biospecimen","Not Applicable","syn35294937","1","Not Applicable",FALSE,"FALSE" -"DataFlow","bccb2827-0a1c-4b0d-b555-75bf6e2d2ba7","FAIR demo data",TRUE,"Patient","patient","Not Applicable","syn36003517","3","2022-10-01",FALSE,"TRUE" -"DataFlow","b12f7681-d8be-41ef-9d9b-5cbe1e519da8","FAIR demo data",FALSE,"BulkRNA-seqAssay","bulk RNA seq","2023-05-01","syn36003526","2","2023-06-01",FALSE,"TRUE" -"DataFlow","dd560889-1d54-4e5f-a030-99c505e801d1","FAIR demo data",TRUE,"Patient","MockComponent","Not Applicable","syn44539618","4","2022-10-01",TRUE,"TRUE" -"DataFlow","50be3874-cfb8-433f-ae9d-03af3e55c532","FAIR demo data",FALSE,"OtherAssay","other assay","Not Applicable","syn51118988","1","Not Applicable",FALSE,"FALSE" -"DataFlow","731858c8-87ba-497e-9c88-ca6814922a35","FAIR demo data",FALSE,"Not Applicable","multi-user test","Not Applicable","syn51339739","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","3cd328e6-e2a5-44db-9a36-5459009b8095","FAIR demo data",FALSE,"Not Applicable","patient-test","Not Applicable","syn51340084","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","e13bedf6-f580-4785-a6f4-51305b614d49","FAIR demo data",FALSE,"Not Applicable","Amy","Not Applicable","syn51358894","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","2a22fd57-e73f-49b8-bf4a-de70051f2a90","FAIR demo data",FALSE,"Biospecimen","Abby VL","Not Applicable","syn51358897","1","Not Applicable",FALSE,"FALSE" -"DataFlow","15cb737c-5ee9-46c2-89b6-35add1369ed1","FAIR demo data",FALSE,"Not Applicable","Mieko","Not Applicable","syn51358898","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","5d83aa64-cc41-403b-b3e8-8af6a75d5d0b","FAIR demo data",FALSE,"Not Applicable","Rixing","Not Applicable","syn51358903","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","ec91c232-7f05-402a-9d5d-bf6b61b3fecc","FAIR demo data",FALSE,"Not Applicable","Milen","Not Applicable","syn51358905","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","facec835-c7fe-4c5f-9dce-9647e4c061fe","FAIR demo data",FALSE,"Not Applicable","Abby W","Not Applicable","syn51358910","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","efc58382-158d-47db-9c70-47aa83e10a2b","FAIR demo data",FALSE,"Not Applicable","Amelia","Not Applicable","syn51358911","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","d30c7893-741d-44f6-ad5f-a6473a0c5b5f","FAIR demo data",FALSE,"Not Applicable","Andrew","Not Applicable","syn51358912","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","d1376b05-39fd-476b-9cec-4d314d480548","FAIR demo data",FALSE,"Not Applicable","Anthony","Not Applicable","syn51358914","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","e50cb768-87f8-48b3-995b-5cd61d7ff80b","FAIR demo data",FALSE,"Not Applicable","Brad","Not Applicable","syn51358916","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","96ef2e9e-8ba1-47be-9a0e-8d6830f4b2e5","FAIR demo data",FALSE,"Not Applicable","Bruce","Not Applicable","syn51358920","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","1e3818c1-6e9d-44ed-a92a-9801060fcf44","FAIR demo data",FALSE,"Not Applicable","Loren","Not Applicable","syn51358924","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","d6005116-a8b8-48af-9aa3-191ef099114c","FAIR demo data",FALSE,"Not Applicable","Lingling","Not Applicable","syn51358925","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","9fbade39-22ec-4530-a38f-dfcca277cd9e","FAIR demo data",FALSE,"Not Applicable","Mialy","Not Applicable","syn51358929","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","a6e9e4af-8327-4e56-be6d-ba575aa5294e","FAIR demo data",FALSE,"Not Applicable","Milan","Not Applicable","syn51358931","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","69f9bfc8-3020-4dfb-a8d1-6c5be718bd61","FAIR demo data",FALSE,"Not Applicable","Nick","Not Applicable","syn51358937","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","6cc4a4ba-1de9-4576-9c3e-d6225dd4804a","FAIR demo data",FALSE,"Not Applicable","ex_extra_folder","Not Applicable","syn51362652","Not Applicable","Not Applicable",FALSE,"FALSE" -"DataFlow","0e8a636c-09ad-42dc-91ee-2f52728c49a1","FAIR Demo Project A",TRUE,"Biospecimen","Biospecimen","2023-05-01","syn50896963","14","2022-06-01",TRUE,"TRUE" 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Assay,2022-08-08,75,15,2022-09-01,2022-09-02,released,dbGaP,TRUE,TRUE,TRUE +DataFlow,Demo 3,syn321,patient,Patient,2022-08-09,5,2,2022-09-01,2022-09-02,released,dbGaP,TRUE,TRUE,TRUE \ No newline at end of file diff --git a/inst/manifests/demo_manifests/htan/synapse_storage_manifest_dataflow.csv b/inst/manifests/demo_manifests/htan/synapse_storage_manifest_dataflow.csv new file mode 100644 index 0000000..88ce328 --- /dev/null +++ b/inst/manifests/demo_manifests/htan/synapse_storage_manifest_dataflow.csv @@ -0,0 +1,17 @@ +Component,contributor,dataset_id,dataset_name,dataset_type,upload_date,num_items,dataset_size,scheduled_release_date,release_date,status,released_destinations,released,metadata_check,governance_compliance +DataFlow,HTAN A,syn120,biospecimen,Biospecimen,2023-10-20,30,5,2024-03-20,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,HTAN A,syn123,patient,Patient,2023-10-20,10,1,2024-03-20,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,HTAN A,syn125,demo_data,Demographic,2023-10-15,10,1,2024-03-20,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,HTAN A,syn128,biospecimen_2,Biospecimen,2023-10-15,10,1,2024-03-20,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,HTAN A,syn122,other_assay,Other Assay,2023-10-15,20,1.5,2024-03-20,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,HTAN B,syn234,patient,Not applicable,Not applicable,5,2,Not applicable,Not applicable,Not uploaded,Not applicable,FALSE,FALSE,FALSE +DataFlow,HTAN B,syn203,biospecimen,Not applicable,Not applicable,5,2,Not applicable,Not applicable,Not uploaded,Not applicable,FALSE,FALSE,FALSE +DataFlow,HTAN B,syn222,other_assay,Not applicable,Not applicable,15,4,Not applicable,Not applicable,Not uploaded,Not applicable,FALSE,FALSE,FALSE +DataFlow,HTAN C,syn300,biospecimen,Biospecimen,2022-08-29,50,10,2022-09-01,Not applicable,ready for release,dbGaP,FALSE,TRUE,TRUE +DataFlow,HTAN C,syn302,patient,Patient,2022-08-15,25,5,2022-09-01,Not applicable,ready for release,dbGaP,FALSE,TRUE,TRUE +DataFlow,HTAN C,syn345,demo_data,Demographic,2022-08-15,25,5,2022-09-01,Not applicable,ready for release,dbGaP,FALSE,TRUE,TRUE +DataFlow,HTAN C,syn340,biospecimen_2,Biospecimen,2022-08-15,3,1,2022-09-01,Not applicable,preprocessing,dbGaP,FALSE,FALSE,TRUE +DataFlow,HTAN C,syn355,other_assay,Other Assay,2022-08-15,75,15,2022-09-01,Not applicable,preprocessing,dbGaP,FALSE,FALSE,TRUE +DataFlow,HTAN C,syn321,patient,Patient,2022-08-15,5,2,2022-09-01,Not applicable,preprocessing,dbGaP,FALSE,TRUE,FALSE +DataFlow,HTAN C,syn340,other_assay,Other Assay_2,2022-08-15,5,2,2022-09-01,Not applicable,quarantine,dbGaP,FALSE,FALSE,FALSE +DataFlow,HTAN C,syn355,other_assay,Other Assay_3,Not applicable,5,2,2022-09-01,Not applicable,Not uploaded,dbGaP,FALSE,FALSE,FALSE \ No newline at end of file diff --git a/inst/manifests/demo_manifests/include/synapse_storage_manifest_dataflow.csv b/inst/manifests/demo_manifests/include/synapse_storage_manifest_dataflow.csv new file mode 100644 index 0000000..da99ab1 --- /dev/null +++ b/inst/manifests/demo_manifests/include/synapse_storage_manifest_dataflow.csv @@ -0,0 +1,19 @@ +Component,contributor,dataset_id,dataset_name,dataset_type,upload_date,num_items,dataset_size,scheduled_release_date,release_date,status,released_destinations,released,metadata_check,governance_compliance +DataFlow,INCLUDE 1,syn120,biospecimen,Biospecimen,Not applicable,30,5,2024-06-01,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,INCLUDE 1,syn123,patient,Patient,Not applicable,10,1,2024-06-01,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,INCLUDE 1,syn125,demo_data,Demographic,Not applicable,10,1,2024-06-01,Not applicable,scheduled for release,data portal,FALSE,FALSE,FALSE +DataFlow,INCLUDE 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"706740d3af9ba03aa4eb637cf9252622e3e87729", + "RemoteRef": "main", + "RemoteSha": "186060a0107db12255b1c65275e9dfc3e77be53e", "Requirements": [ "DT", "dplyr", @@ -431,15 +432,17 @@ "htmltools", "httr", "jsonlite", + "lubridate", "magrittr", "purrr", + "readr", "rlang", "shiny", "shinydashboard", "shinyjs", "waiter" ], - "Hash": "2cb0f0df8bae10acb9664a576f2cbb88" + "Hash": "05924f504f548e7b17adb4bb6fce1c37" }, "diffobj": { "Package": "diffobj", @@ -489,7 +492,7 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.1.2", + "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -508,7 +511,7 @@ "utils", "vctrs" ], - "Hash": "dea6970ff715ca541c387de363ff405e" + "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949" }, "ellipsis": { "Package": "ellipsis", @@ -764,7 +767,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.5", + "Version": "0.5.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -777,7 +780,7 @@ "rlang", "utils" ], - "Hash": 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"api.github.com", + "RemoteUsername": "rstudio", + "RemoteRepo": "renv", + "RemoteRef": "0.17.3", + "RemoteSha": "f13c47646a298fca7af0fcbfa3a97e485c8ede3b", "Requirements": [ "utils" ], - "Hash": "4543b8cd233ae25c6aba8548be9e747e" + "Hash": "ff201994e417dd8be999691f6f556701" }, "rlang": { "Package": "rlang", @@ -1538,7 +1559,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1568,7 +1589,7 @@ "withr", "xtable" ], - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5" + "Hash": "438b99792adbe82a8329ad8697d45afe" }, "shinydashboard": { "Package": "shinydashboard", @@ -1745,6 +1766,17 @@ ], "Hash": "79540e5fcd9e0435af547d885f184fd5" }, + "timechange": { + "Package": "timechange", + "Version": "0.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11" + ], + "Hash": "8548b44f79a35ba1791308b61e6012d7" + }, "tinytex": { "Package": "tinytex", "Version": "0.45",