refresh script updates

CHOP-CGTInformatics · Oct 16, 2024 · d395eae · d395eae
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diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -17,8 +17,10 @@ REDCapTidieR's
 RStudio
 Recode
 Recoding
+Stata
 Supertibble
 Supertibbles
+TRUEs
 Tibble
 Tibble's
 Tibbles
@@ -30,6 +32,7 @@ analytics
 api
 appendings
 cli
+de
 dplyr
 dropdown
 edu
@@ -38,6 +41,7 @@ ggplot
 gtsummary
 https
 httptest
+interpretable
 labelled
 multiselection
 nonrepeat
@@ -48,12 +52,15 @@ preprocess
 recode
 recoded
 recodes
+recoding
 skimr
 summarise
 supertbl
 supertibble
 supertibble's
+supertibbles
 tableStyleLight
+tbl
 tibble
 tibble's
 tibbles
@@ -62,7 +69,6 @@ tidyverse
 truefalse
 undirected
 unlabelled
-wb
 xlsx
 yesno
 ︎
diff --git a/man/convert_checkbox_vals.Rd b/man/convert_checkbox_vals.Rd
diff --git a/tests/testthat/test-read_redcap.R b/tests/testthat/test-read_redcap.R
@@ -680,5 +680,4 @@ test_that("get_repeat_event_types() works", {
   )
 
   expect_equal(out, expected_out)
-
 })
diff --git a/utility/cli_message_examples_reprex.md b/utility/cli_message_examples_reprex.md
@@ -34,13 +34,9 @@ read_redcap(letters[1:3], classic_token)
 read_redcap("https://www.google.com", classic_token)
 #> Error in `read_redcap()`:
 #> ✖ The REDCapR export operation was not successful.
-#> ! An unexpected error occured.
-#> ℹ This means that you probably discovered a bug!
-#> ℹ Please consider submitting a bug report here:
-#>   <https://github.com/CHOP-CGTInformatics/REDCapTidieR/issues>.
-#> Caused by error in `redcap_metadata_read()`:
-#> ! The REDCapR metadata export operation was not successful.  The error message was:
-#> <html><body><h1>404 Not Found</h1></body></html>
+#> ! The URL returned the HTTP error code 405 (POST Method not allowed).
+#> ℹ Are you sure the URI points to an active REDCap API endpoint?
+#> ℹ URI: `https://www.google.com`
 
 read_redcap("https://www.google.comm", classic_token)
 #> Error in `read_redcap()`:
@@ -63,13 +59,13 @@ read_redcap(redcap_uri, letters[1:3])
 
 read_redcap(redcap_uri, "")
 #> Error in `read_redcap()`:
-#> ✖ The token is an empty string, not a valid 32-character hexademical
-#>   value.
+#> ✖ The token is an empty string, which is not allowed.
 #> ℹ API token: ``
 
 read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7") # 31 hex characters
 #> Error in `read_redcap()`:
-#> ✖ The token is not a valid 32-character hexademical value.
+#> ✖ The token does not conform with the regex
+#>   `^([0-9A-Fa-f]{32})(?:\n)?$`.
 #> ℹ API token: `CC0CE44238EF65C5DA26A55DD749AF7`
 
 read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7A") # will be rejected by server
@@ -259,7 +255,7 @@ withr::with_tempdir({
 })
 #> Error:
 #> ✖ File
-#>   ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c744dd73619/temp.csv''
+#>   ''/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa7b9bea48/temp.csv''
 #>   already exists.
 #> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite
 #>   existing file.
@@ -300,25 +296,26 @@ withr::with_tempdir({
     write_redcap_xlsx(file = filepath)
 })
 #> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`:
-#>   '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c7456597c2b/temp'
+#>   '/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa11455c98/temp'
 #> ℹ The extension '.xlsx' will be appended to the file name.
 
 # Printed supertibble
 
 read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_CLASSIC_API")) %>%
   suppressWarnings()
-#> # A REDCapTidieR Supertibble with 9 instruments
-#>   redcap_form_name       redcap_form_label redcap_data redcap_metadata structure
-#>   <chr>                  <chr>             <list>      <list>          <chr>    
-#> 1 nonrepeated            Nonrepeated       <tibble>    <tibble>        nonrepea…
-#> 2 nonrepeated2           Nonrepeated2      <tibble>    <tibble>        nonrepea…
-#> 3 repeated               Repeated          <tibble>    <tibble>        repeating
-#> 4 data_field_types       Data Field Types  <tibble>    <tibble>        nonrepea…
-#> 5 text_input_validation… Text Input Valid… <tibble>    <tibble>        nonrepea…
-#> 6 api_no_access          API No Access     <tibble>    <tibble>        nonrepea…
-#> 7 api_no_access_2        API No Access 2   <tibble>    <tibble>        nonrepea…
-#> 8 survey                 Survey            <tibble>    <tibble>        nonrepea…
-#> 9 repeat_survey          Repeat Survey     <tibble>    <tibble>        repeating
+#> # A REDCapTidieR Supertibble with 10 instruments
+#>    redcap_form_name      redcap_form_label redcap_data redcap_metadata structure
+#>    <chr>                 <chr>             <list>      <list>          <chr>    
+#>  1 nonrepeated           Nonrepeated       <tibble>    <tibble>        nonrepea…
+#>  2 nonrepeated2          Nonrepeated2      <tibble>    <tibble>        nonrepea…
+#>  3 repeated              Repeated          <tibble>    <tibble>        repeating
+#>  4 data_field_types      Data Field Types  <tibble>    <tibble>        nonrepea…
+#>  5 text_input_validatio… Text Input Valid… <tibble>    <tibble>        nonrepea…
+#>  6 api_no_access         API No Access     <tibble>    <tibble>        nonrepea…
+#>  7 api_no_access_2       API No Access 2   <tibble>    <tibble>        nonrepea…
+#>  8 survey                Survey            <tibble>    <tibble>        nonrepea…
+#>  9 repeat_survey         Repeat Survey     <tibble>    <tibble>        repeating
+#> 10 labelled_vignette     Labelled Vignette <tibble>    <tibble>        nonrepea…
 #> # ℹ 5 more variables: data_rows <int>, data_cols <int>, data_size <lbstr_by>,
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
 
@@ -343,4 +340,4 @@ read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API"))
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
 ```
 
-<sup>Created on 2024-04-10 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
+<sup>Created on 2024-10-16 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
diff --git a/utility/microbenchmark_results.csv b/utility/microbenchmark_results.csv
@@ -1,42 +1,42 @@
 min,lq,mean,median,uq,max,neval,description,source
-1.15,1.15,1.15,1.15,1.15,1.15,1,simple static (read-only) test project,ouhsc
-1.7,1.7,1.7,1.7,1.7,1.7,1,longitudinal (read-only) ARM test project,ouhsc
-0.83,0.83,0.83,0.83,0.83,0.83,1,simple write data,ouhsc
-1.79,1.79,1.79,1.79,1.79,1.79,1,Russian Characters,ouhsc
-3.37,3.37,3.37,3.37,3.37,3.37,1,"super-wide --3,000 columns",ouhsc
-1,1,1,1,1,1,1,static (not longitudinal) survey test project,ouhsc
-0.82,0.82,0.82,0.82,0.82,0.82,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc
-0.77,0.77,0.77,0.77,0.77,0.77,1,nonnumeric record_id,ouhsc
-0.94,0.94,0.94,0.94,0.94,0.94,1,DAG Read,ouhsc
-0.82,0.82,0.82,0.82,0.82,0.82,1,potentially problematic values,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,Repeating Instruments,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,simple write metadata,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,DAG Write -admin,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,DAG Write -group A,ouhsc
-129.61,129.61,129.61,129.61,129.61,129.61,1,"super-wide #3--35,000 columns",ouhsc
-0.82,0.82,0.82,0.82,0.82,0.82,1,Repeating Instruments --Sparse,ouhsc
-0.8,0.8,0.8,0.8,0.8,0.8,1,Delete Single Arm,ouhsc
-1.29,1.29,1.29,1.29,1.29,1.29,1,Delete Multiple Arm,ouhsc
-1.55,1.55,1.55,1.55,1.55,1.55,1,longitudinal single arm,ouhsc
-0.78,0.78,0.78,0.78,0.78,0.78,1,decimal comma and dot,ouhsc
-0.82,0.82,0.82,0.82,0.82,0.82,1,decimal comma,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,decimal dot,ouhsc
-0.87,0.87,0.87,0.87,0.87,0.87,1,Validation Types,ouhsc
-0.81,0.81,0.81,0.81,0.81,0.81,1,Blank for Gray Status,ouhsc
-0.97,0.97,0.97,0.97,0.97,0.97,1,Checkboxes 1,ouhsc
-0.83,0.83,0.83,0.83,0.83,0.83,1,Vignette: Longitudinal & Repeating Measures,ouhsc
-1.11,1.11,1.11,1.11,1.11,1.11,1,classic,redcaptidier
-0.98,0.98,0.98,0.98,0.98,0.98,1,classic no repeat,redcaptidier
-1.7,1.7,1.7,1.7,1.7,1.7,1,longitudinal,redcaptidier
-1.67,1.67,1.67,1.67,1.67,1.67,1,longitudinal no arms,redcaptidier
-1.51,1.51,1.51,1.51,1.51,1.51,1,longitudinal no repeat,redcaptidier
-1.96,1.96,1.96,1.96,1.96,1.96,1,deep dive vignette,redcaptidier
-0.99,0.99,0.99,0.99,0.99,0.99,1,repeat first instrument,redcaptidier
-1.51,1.51,1.51,1.51,1.51,1.51,1,repeat event,redcaptidier
-1.04,1.04,1.04,1.04,1.04,1.04,1,restricted access,redcaptidier
-0.97,0.97,0.97,0.97,0.97,0.97,1,large sparse db,redcaptidier
-1.13,1.13,1.13,1.13,1.13,1.13,1,data access groups,redcaptidier
-1.78,1.78,1.78,1.78,1.78,1.78,1,longitudinal data access groups,redcaptidier
-2.06,2.06,2.06,2.06,2.06,2.06,1,mixed structure repeat no repeat,redcaptidier
-4.62,4.62,4.62,4.62,4.62,4.62,1,prodigy db,redcaptidier
-5.26,5.26,5.26,5.26,5.26,5.26,1,cart comprehensive db,redcaptidier
+0.96,0.96,0.96,0.96,0.96,0.96,1,simple static (read-only) test project,ouhsc
+2.35,2.35,2.35,2.35,2.35,2.35,1,longitudinal (read-only) ARM test project,ouhsc
+0.99,0.99,0.99,0.99,0.99,0.99,1,simple write data,ouhsc
+4.29,4.29,4.29,4.29,4.29,4.29,1,Russian Characters,ouhsc
+6.67,6.67,6.67,6.67,6.67,6.67,1,"super-wide --3,000 columns",ouhsc
+1.72,1.72,1.72,1.72,1.72,1.72,1,static (not longitudinal) survey test project,ouhsc
+1.43,1.43,1.43,1.43,1.43,1.43,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc
+1.12,1.12,1.12,1.12,1.12,1.12,1,nonnumeric record_id,ouhsc
+0.97,0.97,0.97,0.97,0.97,0.97,1,DAG Read,ouhsc
+0.9,0.9,0.9,0.9,0.9,0.9,1,potentially problematic values,ouhsc
+1.13,1.13,1.13,1.13,1.13,1.13,1,simple write metadata,ouhsc
+0.89,0.89,0.89,0.89,0.89,0.89,1,DAG Write -admin,ouhsc
+0.95,0.95,0.95,0.95,0.95,0.95,1,DAG Write -group A,ouhsc
+1278.89,1278.89,1278.89,1278.89,1278.89,1278.89,1,"super-wide #3--35,000 columns",ouhsc
+0.99,0.99,0.99,0.99,0.99,0.99,1,Repeating Instruments --Sparse,ouhsc
+1.1,1.1,1.1,1.1,1.1,1.1,1,Delete Single Arm,ouhsc
+2.35,2.35,2.35,2.35,2.35,2.35,1,Delete Multiple Arm,ouhsc
+2.13,2.13,2.13,2.13,2.13,2.13,1,longitudinal single arm,ouhsc
+1.25,1.25,1.25,1.25,1.25,1.25,1,decimal comma and dot,ouhsc
+1.32,1.32,1.32,1.32,1.32,1.32,1,decimal comma,ouhsc
+1.09,1.09,1.09,1.09,1.09,1.09,1,decimal dot,ouhsc
+1.21,1.21,1.21,1.21,1.21,1.21,1,Validation Types,ouhsc
+0.99,0.99,0.99,0.99,0.99,0.99,1,Blank for Gray Status,ouhsc
+1.32,1.32,1.32,1.32,1.32,1.32,1,Checkboxes 1,ouhsc
+1.13,1.13,1.13,1.13,1.13,1.13,1,Vignette: Longitudinal & Repeating Measures,ouhsc
+3.01,3.01,3.01,3.01,3.01,3.01,1,classic,redcaptidier
+3.34,3.34,3.34,3.34,3.34,3.34,1,classic no repeat,redcaptidier
+3.1,3.1,3.1,3.1,3.1,3.1,1,longitudinal,redcaptidier
+2.88,2.88,2.88,2.88,2.88,2.88,1,longitudinal no arms,redcaptidier
+3.5,3.5,3.5,3.5,3.5,3.5,1,longitudinal no repeat,redcaptidier
+5.16,5.16,5.16,5.16,5.16,5.16,1,deep dive vignette,redcaptidier
+2.8,2.8,2.8,2.8,2.8,2.8,1,repeat first instrument,redcaptidier
+4.69,4.69,4.69,4.69,4.69,4.69,1,repeat event,redcaptidier
+2.42,2.42,2.42,2.42,2.42,2.42,1,restricted access,redcaptidier
+1.99,1.99,1.99,1.99,1.99,1.99,1,large sparse db,redcaptidier
+1.63,1.63,1.63,1.63,1.63,1.63,1,data access groups,redcaptidier
+3.62,3.62,3.62,3.62,3.62,3.62,1,longitudinal data access groups,redcaptidier
+3.16,3.16,3.16,3.16,3.16,3.16,1,mixed structure repeat no repeat,redcaptidier
+11.29,11.29,11.29,11.29,11.29,11.29,1,prodigy db,redcaptidier
+15.8,15.8,15.8,15.8,15.8,15.8,1,cart comprehensive db,redcaptidier
+34.07,34.07,34.07,34.07,34.07,34.07,1,bmt outcomes db,redcaptidier
diff --git a/utility/test_creds.R b/utility/test_creds.R
@@ -9,12 +9,13 @@ ouhsc_creds <- readr::read_csv(file = "utility/redcapr.example.credentials", ski
   select(redcap_uri, token, comment)
 
 # Remove identified APIs that don't work
-ouhsc_creds <- ouhsc_creds[-c(5,6,10,15,19),]
+ouhsc_creds <- ouhsc_creds[-c(5,6,10,14,15,19),]
 # Empty rows (dataframe with 0 rows, 0 columns)
 # Single Column (dataframe with 0 rows, 0 columns)
 # Missing/invalid token, "---" (REDCapR errors as well)
 # Potentially problematic dictionary  (dataframe with 0 rows, 0 columns)
 # super-wide #2--5,785 columns (dataframe with 0 rows, 0 columns)
+# repeat instrument, no longer a working api key
 
 # Load REDCapTidieR and CGTI creds
 redcaptidier_creds <- tibble::tribble(
Original file line number	Diff line number	Diff line change
Expand Up		@@ -680,5 +680,4 @@ test_that("get_repeat_event_types() works", {
		)

		expect_equal(out, expected_out)

		})