Merge pull request #15 from umccr/hm_testing

add labmetadata table query function

.Rbuildignore

@@ -17,4 +17,5 @@
 ^nogit$
 ^vignettes$
 inst/reports/datashare/nogit
+inst/reports/seqrunsum/.quarto
 inst/reports/seqrunsum/nogit

.github/workflows/R-CMD-check.yaml

@@ -46,7 +46,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            any::roxytest
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pr-commands.yaml

@@ -34,7 +34,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::roxygen2
+          extra-packages: |
+            any::roxygen2
+            any::roxytest
           needs: pr-document
 
       - name: Document
@@ -78,7 +80,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Style
-        run: styler::style_pkg()
+        run: styler::style_pkg(exclude_dirs = c("tests"))
         shell: Rscript {0}
 
       - name: commit

NAMESPACE

@@ -16,6 +16,7 @@ export(meta_wts_alignment_qc)
 export(meta_wts_tumor_only)
 export(portaldb_query)
 export(portaldb_query_fastqlistrow)
+export(portaldb_query_labmetadata)
 export(portaldb_query_limsrow)
 export(portaldb_query_table)
 export(portaldb_query_workflow)

R/query.R

@@ -129,3 +129,25 @@ portaldb_query_limsrow <- function(query = NULL) {
 portaldb_query_fastqlistrow <- function(query = NULL) {
   portaldb_query_table(query = query, table = "data_portal_fastqlistrow")
 }
+
+#' PortalDB Query labmetadata Table
+#'
+#' Queries the `data_portal_labmetadata` table with the given query.
+#' Note this is simply a convenience function that prepends
+#' `SELECT * FROM "data_portal"."data_portal"."data_portal_labmetadata" ` to any
+#' `query` you provide.
+#' See examples.
+#'
+#' @param query SQL query string.
+#' @return Tibble with results from query.
+#'
+#' @examples
+#' \dontrun{
+#' libids <- shQuote(paste(c("L2400340", "L2400256"), collapse = "|"))
+#' query <- glue("WHERE REGEXP_LIKE(\"library_id\", {libids});")
+#' portaldb_query_labmetadata(query)
+#' }
+#' @export
+portaldb_query_labmetadata <- function(query = NULL) {
+  portaldb_query_table(query = query, table = "data_portal_labmetadata")
+}

inst/reports/seqrunsum/report.qmd

@@ -27,8 +27,8 @@ format:
       body-width: 1300px
 params:
   title: "UMCCR PortalDB Workflow Summary"
-  date_start: "2024-05-30"
-  date_end: "2024-06-03"
+  date_start: "2024-06-15"
+  date_end: "2024-06-17"
 ---
 
 ```{r}
@@ -59,14 +59,6 @@ set.seed(42)
 source(here("inst/reports/seqrunsum/funcs.R"))
 ```
 
-```{r eval=interactive()}
-params <- list(
-  date_start = "2024-05-31",
-  date_end = "2024-06-03"
-)
-```
-
-
 ```{r}
 #| label: vars
 fmt1 <- "%Y-%m-%dT%H:%M:%S"