+ cc_db_catalog()

Author: bbest

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: calcofi4r
 Title: CalCOFI R helper functions
-Version: 0.8.0
+Version: 0.8.1
 URL: https://calcofi.io/calcofi4r
 BugReports: https://github.com/calcofi/calcofi4r/issues
 Authors@R: c(
@@ -17,7 +17,7 @@ Description: The California Cooperative Oceanic Fisheries Investigations (CalCOF
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10)
 LazyData: true

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(cc_db_catalog)
 export(cc_db_connect)
 export(create_index)
 export(get_cruises)
@@ -22,20 +23,32 @@ import(leaflet)
 import(readr)
 import(sf)
 import(stringr)
+importFrom(DT,datatable)
 importFrom(RPostgres,Postgres)
 importFrom(classInt,classIntervals)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(dplyr,select)
 importFrom(glue,glue)
+importFrom(htmltools,HTML)
+importFrom(htmltools,div)
+importFrom(htmltools,em)
+importFrom(htmltools,span)
+importFrom(htmltools,strong)
 importFrom(isoband,iso_to_sfg)
 importFrom(isoband,isobands)
 importFrom(mapview,mapView)
+importFrom(markdown,mark)
 importFrom(mgcv,gam)
 importFrom(plotly,ggplotly)
 importFrom(plotly,highlight)
 importFrom(plotly,highlight_key)
+importFrom(purrr,pmap_chr)
 importFrom(raster,extent)
 importFrom(raster,projectExtent)
 importFrom(raster,raster)
 importFrom(raster,values)
+importFrom(readr,read_csv)
 importFrom(scales,extended_breaks)
 importFrom(sf,st_bbox)
 importFrom(sf,st_buffer)

NEWS.md

@@ -1,3 +1,7 @@
+# calcofi4r 0.8.1
+
+* Added `cc_db_catalog()` to list tables and columns in the database with descriptions (possibly formatted in markdown) by reading from new CalCOFI API endpoints: [api.calcofi.io/db_tables](https://api.calcofi.io/db_tables), [api.calcofi.io/db_columns](https://api.calcofi.io/db_columns).
+
 # calcofi4r 0.8.0
 
 * Removed non-ASCII characters to allow install of package on Windows.

R/database.R

@@ -41,6 +41,98 @@ cc_db_connect <- function(path_pw = "~/.calcofi_db_pass.txt"){
     password = readLines(path_pw))
 }
 
+#' Show CalCOFI database catalog as interactive table
+#'
+#' Read the tables and columns from the following [CalCOFI API](https://api.calcofi.io)
+#' and display as an interactive table (as `DT::datatable()`):
+#' - [api.calcofi.io/db_tables](https://api.calcofi.io/db_tables)
+#' - [api.calcofi.io/db_columns](https://api.calcofi.io/db_columns)
+#'
+#' @param tables optional character vector of table names to filter; default: `NULL`
+#'
+#' @return DT::datatable() of tables and columns
+#' @importFrom DT datatable
+#' @importFrom htmltools div em span strong HTML
+#' @importFrom markdown mark
+#' @importFrom purrr pmap_chr
+#' @importFrom readr read_csv
+#' @importFrom dplyr left_join filter select
+#' @importFrom glue glue
+#' @export
+#' @concept database
+#'
+#' @examples
+#' # full catalog
+#' cc_db_catalog()
+#' # only certain tables
+#' cc_db_catalog(tables = c("larvae_counts","nets","tows","stations","cruises"))
+cc_db_catalog <- function(tables = NULL){
+
+  d_tbls <- readr::read_csv(
+    "https://api.calcofi.io/db_tables", show_col_types = F)
+  d_cols <- readr::read_csv(
+    "https://api.calcofi.io/db_columns", show_col_types = F)
+
+  d <- d_tbls |>
+    dplyr::left_join(
+      d_cols,
+      by = c("schema","table_type","table"))
+
+  if (!is.null(tables))
+    d <- d |>
+      dplyr::filter(table %in% tables)
+
+  d |>
+    mutate(
+      Table = purrr::pmap_chr(
+        list(table_type, table, table_description),
+        function(table_type, table, table_description, ...){
+          ifelse(
+            is.na(table_description),
+            htmltools::div(
+              htmltools::span(style = "font-weight: 400;", htmltools::em(table_type), ":"), htmltools::strong(table)) |>
+              as.character(),
+            htmltools::div(
+              htmltools::span(style = "font-weight: 400;", htmltools::em(table_type), ":"), htmltools::strong(table),
+              htmltools::div(
+                style = "font-size: 0.75rem; font-weight: 400;",
+                htmltools::HTML(markdown::mark(table_description)))) |>
+              as.character() ) } ),
+      Column = purrr::pmap_chr(
+        list(column, column_type, column_description),
+        function(column, column_type, column_description, ...){
+          ifelse(
+            is.na(column_description),
+            htmltools::div(
+              htmltools::strong(column), htmltools::span(style = "font-weight: 400;", "(", htmltools::em(column_type), ")")) |>
+              as.character(),
+            htmltools::div(
+              htmltools::strong(column), htmltools::span(style = "font-weight: 400;", "(", htmltools::em(column_type), ")"),
+              htmltools::div(
+                style = "font-size: 0.75rem; font-weight: 400;",
+                htmltools::HTML(markdown::mark(column_description)))) |>
+              as.character() ) } ) ) |>
+    dplyr::select(Table, Column) |>
+    DT::datatable(
+      # extensions = c("RowGroup", "Buttons"),
+      extensions = c("RowGroup"),
+      options = list(
+        # dom      = "Blfrtip",
+        # buttons = c("copy", "csv", "excel", "pdf", "print"),
+        dom      = "lfrtip",
+        pageLength = 10,
+        lengthMenu = c(10, 100, 1000),
+        rowGroup = list(
+          dataSrc = c(0, 1) ),
+        columnDefs = list(
+          list(
+            visible = F,
+            targets = c(0,1) ) ) ),
+      escape   = F,
+      rownames = F)
+}
+
+
 #' Create index in database
 #'
 #' @param con database connection object from `DBI::dbConnect()`, e.g. from `cc_db_connect()`