Update documentation for new wildcards with the latest SewerRat API.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SewerRat
-Version: 0.2.12
-Date: 2024-10-31
+Version: 0.3.0
+Date: 2024-11-05
 Title: Client for the SewerRat API
 Description: 
     Search metadata files across a shared filesystem via the SewerRat API.

R/query.R

@@ -44,14 +44,15 @@
 #' If there are no parentheses, any \code{NOT} will take precedence over the other boolean operations,
 #' i.e., the above query is the same as \code{NOT a b AND c d}.
 #'
-#' Even more advanced users can prefix any sequence of search terms with the name of a metadata field, 
+#' Users can prefix any sequence of search terms with the name of a metadata field, 
 #' to only search for matches within that field of the metadata file, e.g.,
 #' \code{(title: prostate cancer) AND (genome: GRCh38 OR genome: GRCm38)}.
 #' Note that this does not extend to the \code{AND}, \code{OR} and \code{NOT} keywords,
 #' e.g., \code{title:foo OR bar} will not limit the search for \code{bar} to the \code{title} field.
 #'
-#' Extremely advanced users can attach a \code{\%} wildcard to any term to enable a partial search,
-#' e.g., \code{neur\%} will match files with \code{neuron}, \code{neural}, \code{neurological}, etc.
+#' Users can attach the usual \code{*} or \code{?} wildcards to any term to enable pattern matching.
+#' For example, \code{neur*} will match files with \code{neuron}, \code{neural}, \code{neurological}, etc.,
+#' while \code{cd?} will match files with \code{cd4}, \code{cd8}, \code{cd9}, etc.
 #' 
 #' @author Aaron Lun
 #' @examples
@@ -70,15 +71,15 @@
 #' register(mydir, "metadata.json", url=info$url)
 #'
 #' query("aaron", url=info$url)
-#' query("lun%", url=info$url) 
-#' query("lun% AND aaron", url=info$url)
+#' query("lun*", url=info$url) 
+#' query("lun* AND aaron", url=info$url)
 #' query("meal:bar%", url=info$url)
 #'
 #' query(path="diet/", url=info$url) # has 'diet/' in the path
 #' query(user=Sys.info()["user"], url=info$url) # created by the current user
 #' query(from=Sys.time() - 60, url=info$url) # no more than 1 minute old
 #'
-#' q <- query("lun%", url=info$url)
+#' q <- query("lun*", url=info$url)
 #' formatQueryResults(q)
 #' @export
 #' @import httr2

R/startSewerRat.R

@@ -25,7 +25,7 @@
 #' startSewerRat() # initialize a new instance.
 #' 
 #' @export
-startSewerRat <- function(db=tempfile(fileext=".sqlite3"), port=NULL, wait = 1, version = "1.0.13", overwrite = FALSE) {
+startSewerRat <- function(db=tempfile(fileext=".sqlite3"), port=NULL, wait = 1, version = "1.1.0", overwrite = FALSE) {
     if (!is.null(running$active)) {
         return(list(new=FALSE, port=running$port, url=assemble_url(running$port)))
     }

tests/testthat/test-query.R

@@ -15,10 +15,10 @@ write(file=file.path(mydir, "diet", "metadata.json"),
 register(mydir, "metadata.json", url=info$url)
 
 test_that("formatQueryResults works properly", {
-    q <- query("lun%", url=info$url)
+    q <- query("lun*", url=info$url)
     res <- formatQueryResults(q)
 
-    expect_gt(nrow(res), 0L)
+    expect_gte(nrow(res), 2L)
     expect_identical(nrow(res), length(q))
     expect_equal(as.double(res$time), vapply(q, function(y) y$time, 0))
     expect_identical(res$metadata[[1]], q[[1]]$metadata)

vignettes/userguide.Rmd

@@ -66,9 +66,9 @@ This function does not require filesystem access and can be executed remotely.
 
 ```{r}
 lapply(query("foo", url=info$url), function(x) x$path)
-lapply(query("bar%", url=info$url), function(x) x$path) # partial match to 'bar...'
-lapply(query("bar% AND foo", url=info$url), function(x) x$path) # boolean operations
-lapply(query("food:bar%", url=info$url), function(x) x$path) # match in the 'food' field
+lapply(query("bar*", url=info$url), function(x) x$path) # partial match to 'bar...'
+lapply(query("bar* AND foo", url=info$url), function(x) x$path) # boolean operations
+lapply(query("food:bar*", url=info$url), function(x) x$path) # match in the 'food' field
 ```
 
 We can also search on the user, path components, and time of creation: