Merge pull request #52 from atorus-research/dev

Dev

.gitignore

@@ -22,6 +22,9 @@
 vignettes/*.html
 vignettes/*.pdf
 
+# Files to draft tests
+*/define_examples/*
+
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
@@ -42,3 +45,5 @@ tests/testthat/temp_data/*
 docs
 doc
 Meta
+.DS_Store?
+.DS_Store

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metacore
 Title: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows
-Version: 0.0.4
+Version: 0.1.0
 Authors@R: 
     c(person(given = "Christina",
              family = "Fillmore",
@@ -27,7 +27,7 @@ Description: Create an immutable container holding metadata for the purpose of b
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = FALSE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Suggests: 
     testthat,
     knitr,
@@ -39,7 +39,7 @@ Imports:
     dplyr,
     stringr,
     magrittr,
-    XML,
+    xml2,
     purrr,
     readxl,
     rlang,

NAMESPACE

@@ -25,13 +25,6 @@ export(xml_to_ds_vars)
 export(xml_to_value_spec)
 export(xml_to_var_spec)
 import(R6)
-importFrom(XML,getNodeSet)
-importFrom(XML,xmlElementsByTagName)
-importFrom(XML,xmlGetAttr)
-importFrom(XML,xmlNamespaceDefinitions)
-importFrom(XML,xmlToDataFrame)
-importFrom(XML,xmlTreeParse)
-importFrom(XML,xmlValue)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
@@ -67,7 +60,9 @@ importFrom(purrr,map_dfr)
 importFrom(purrr,map_int)
 importFrom(purrr,map_lgl)
 importFrom(purrr,pmap_chr)
+importFrom(purrr,quietly)
 importFrom(purrr,reduce)
+importFrom(purrr,safely)
 importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
 importFrom(rlang,"!!")
@@ -80,6 +75,7 @@ importFrom(rlang,prim_name)
 importFrom(rlang,sym)
 importFrom(stats,na.omit)
 importFrom(stats,var)
+importFrom(stringr,regex)
 importFrom(stringr,str_c)
 importFrom(stringr,str_count)
 importFrom(stringr,str_detect)
@@ -93,6 +89,7 @@ importFrom(stringr,str_replace_na)
 importFrom(stringr,str_split)
 importFrom(stringr,str_starts)
 importFrom(stringr,str_subset)
+importFrom(stringr,str_to_lower)
 importFrom(stringr,str_trim)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
@@ -101,3 +98,11 @@ importFrom(tidyr,nest)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,everything)
+importFrom(tidyselect,matches)
+importFrom(xml2,read_xml)
+importFrom(xml2,xml_attr)
+importFrom(xml2,xml_find_all)
+importFrom(xml2,xml_find_first)
+importFrom(xml2,xml_ns_strip)
+importFrom(xml2,xml_parent)
+importFrom(xml2,xml_text)

NEWS.md

@@ -1,3 +1,15 @@
+# Metacore 0.1.0
+- Updates for latest version of {tidyselect}
+- Move from XML to xml2 for define.xml processing
+- Correct issue with warning on ds_var$core 
+- Correct bug with not reading the derivation of predecessor and assigned variables correctly
+
+# Metacore 0.0.6 
+- Correct typos
+- Limits origin value/make all origins lower case 
+
+# Metacore 0.0.5
+- [#47](https://github.com/atorus-research/metacore/issues/47) Improve `yn_to_tf()` to be more robust in parsing yes/no columns
 
 # Metacore 0.0.4
 - Adds a supp table to store the `idvar` and `qeval` information 

R/metacore.R

@@ -15,7 +15,7 @@
 #' @family Metacore
 #' @noRd
 #'
-#'
+#' @importFrom stringr str_to_lower
 MetaCore_initialize <- function(ds_spec, ds_vars, var_spec, value_spec, derivations, codelist, supp){
 
    private$.ds_spec <- ds_spec %>%
@@ -47,7 +47,9 @@ MetaCore_initialize <- function(ds_spec, ds_vars, var_spec, value_spec, derivati
                  dataset = "Dataset Name",
                  variable = "Variable Name",
                  where = "Value of the Variable",
-                 derivation_id = "ID of Derivation")
+                 derivation_id = "ID of Derivation") %>%
+      mutate(origin = str_to_lower(.data$origin))
+
 
    private$.derivations <- derivations %>%
       add_labs(derivation_id = "ID of Derivation",