added sequence count

DESCRIPTION

@@ -19,7 +19,6 @@ Imports:
     rentrez,
     MonetDBLite,
     DBI (>= 1.0.0),
-    R.utils,
     downloader,
     RCurl,
     cli,

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(count_db_ids)
 export(db_create)
 export(db_delete)
 export(db_download)

R/db-tools.R

@@ -219,13 +219,13 @@ demo_db_create <- function(db_type='nucleotide', n=100) {
 #' @name db_delete
 #' @title Delete database
 #' @family setup
-#' @description Delete the local SQL database and/or restez
-#' folder.
+#' @description Delete the local SQL database and/or restez folder.
 #' @param everything T/F, delete the whole restez folder as well?
+#' @details Any connected database will be automatically disconnected.
 #' @return NULL
 #' @export
 #' @example examples/db_delete.R
-db_delete <- function(everything = TRUE) {
+db_delete <- function(everything = FALSE) {
   restez_disconnect()
   if (length(sql_path_get()) > 0 && dir.exists(sql_path_get())) {
     unlink(sql_path_get(), recursive = TRUE)

R/general-get-tools.R

@@ -45,3 +45,27 @@ is_in_db <- function(id, db = 'nucleotide') {
   names(res) <- id
   res
 }
+
+#' @name count_db_ids
+#' @title Return the number of ids
+#' @description Return the number of ids in a user's restez database.
+#' @details Requires an open connection. If no connection or db 0 is returned.
+#' @param db character, database name
+#' @return integer
+#' @family get
+#' @export
+#' @example examples/count_db_ids.R
+count_db_ids <- function(db = 'nucleotide') {
+  if (!restez_ready()) {
+    warning('No database connection. Did you run `restez_connect`?')
+    return(0L)
+  }
+  connection <- connection_get()
+  qry <- "SELECT count(*) FROM nucleotide"
+  qry_res <- DBI::dbSendQuery(conn = connection, statement = qry)
+  on.exit(expr = {
+    DBI::dbClearResult(res = qry_res)
+  })
+  res <- DBI::dbFetch(res = qry_res)
+  as.integer(res[[1]])
+}

R/log-tools.R

@@ -214,24 +214,6 @@ last_add_get <- function() {
   last_entry_get(fp = fp)[[3]]
 }
 
-#' @name db_nrows_get
-#' @title Return the number of rows in a db
-#' @description Return the number of rows in the SQL database in the user's
-#' restez_path.
-#' @details Requires an open connection.
-#' @return integer
-#' @family private
-db_nrows_get <- function() {
-  qry <- "SELECT count(*) FROM nucleotide"
-  connection <- connection_get()
-  qry_res <- DBI::dbSendQuery(conn = connection, statement = qry)
-  on.exit(expr = {
-    DBI::dbClearResult(res = qry_res)
-  })
-  res <- DBI::dbFetch(res = qry_res)
-  res[[1]]
-}
-
 #' @name db_sqlngths_get
 #' @title Return the minimum and maximum sequence lengths in db
 #' @description Returns the maximum and minimum sequence lengths as set by the
@@ -242,10 +224,10 @@ db_nrows_get <- function() {
 db_sqlngths_get <- function() {
   fp <- file.path(restez_path_get(), 'seqlengths.tsv')
   if (!file.exists(fp)) {
-    return(c('min' = '', 'max' = 'max'))
+    return(c('min' = '0', 'max' = 'Inf'))
   }
   res <- utils::read.table(file = fp, header = TRUE, sep = '\t',
-                    stringsAsFactors = FALSE)[1, ]
+                           stringsAsFactors = FALSE)[1, ]
   res
 }
 

R/status-tools.R

@@ -65,10 +65,12 @@ status_class <- function() {
   # database
   flpth <- sql_path_get()
   sqlngths <- db_sqlngths_get()
+  nseqs <- suppressWarnings(count_db_ids())
   database_info <- list('Path' = flpth, 'Does path exist?' = dir.exists(flpth),
                         'N. GBs' = dir_size(flpth),
                         'Is database connected?' = connected(),
                         'Does the database have data?' = has_data(),
+                        'Number of sequences' = nseqs,
                         'Min. sequence length' = sqlngths[['min']],
                         'Max. sequence length' = sqlngths[['max']],
                         'Last_updated' = last_add_get())

examples/count_db_ids.R

@@ -0,0 +1,8 @@
+library(restez)
+restez_path_set(filepath = tempdir())
+restez_connect()
+demo_db_create()
+(count_db_ids())
+
+# delete demo after example
+db_delete(everything = TRUE)

examples/db_delete.R

@@ -6,7 +6,6 @@ demo_db_create(n = 10)
 db_delete(everything = FALSE)
 # Will not run: gb_sequence_get(id = 'demo_1')
 # only the SQL database is deleted
-restez_disconnect()
 db_delete(everything = TRUE)
 # Now returns NULL
 (restez_path_get())

examples/demo_db_create.R

@@ -8,5 +8,4 @@ demo_db_create(n = 100)
 (gb_sequence_get(id = 'demo_1'))
 
 # Delete a demo database after an example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/entrez_fetch.R

@@ -22,5 +22,4 @@ cat(gb_res)
 #                        rettype = 'gb')
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_definition_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_fasta_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_organism_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_record_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_sequence_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/gb_version_get.R

@@ -7,5 +7,4 @@ demo_db_create()
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/is_in_db.R

@@ -10,5 +10,4 @@ ids <- c('thisisnotanid', 'demo_1', 'demo_2')
 
 
 # delete demo after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/list_db_ids.R

@@ -18,5 +18,4 @@ cat(fasta_file)
 
 
 # delete after example
-restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)

examples/restez_connect.R

@@ -6,6 +6,6 @@ restez_connect()
 demo_db_create()
 restez_status()
 restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)
 # Errors
 # restez_status()

examples/restez_disconnect.R

@@ -6,6 +6,6 @@ demo_db_create()
 restez_status()
 # always remember to disconnect from a database when you've finished
 restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)
 # Errors
 # restez_status()

examples/restez_ready.R

@@ -5,5 +5,5 @@ restez_connect()
 demo_db_create()
 (restez_ready())
 restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)
 (restez_ready())

examples/restez_status.R

@@ -5,6 +5,6 @@ restez_connect()
 demo_db_create()
 restez_status()
 restez_disconnect()
-db_delete()
+db_delete(everything = TRUE)
 # Errors:
 # restez_status()