add changes to v5.4 (#433)

* Add github actions workflow to build package and run tests. * update Description file * rename .Rproj file. * Consolidate 'create' functions into one file. * Add tests for create functions. * update description * removed spaces in file and folder names. Regenerated ddl output. Tried to fix Field_Level.csv file. * consolidate write functions into one file. Add execute function. * update docs * add tests for write and execute functions * update documentation * Add windows and linux runners in github actions. * update github actions * download drivers before running tests * fix small error in setup test file. * debug github actions * debug github actions * debug github actions * debug github actions * fix tiny bug * comment out execute ddl test * fix bug in test * Add execute test back in * revert accidental change in description * add print statement for debugging schema error on github actions. * Fix schema environment variable name * Add comment to github actions workflow file. * remove placeholder text in function documentation. * Rename createdDdl.R to createDdl.R * Hack-a-thon updates Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264 * Changed bigint to integer for consistency * Updated DDLs * Add tests for redshift. Clean up test setup file. * Foreign key fixes * Add imports and update docs. * Fix bug in setup test script. * update setup file * Add tests for oracle and sql server. Move setup.R file. * fix bug in setup * debug tests on github * debug github actions * debug actions. * debug actions * debug actions. * Add missing secrets to yaml!! * debug actions * test connection on all platforms * add ddl execution * add windows and linux runners * Resolving conflicts * Removing unnecessary file * Trying again to remove .DS_Store, adding to gitignore * Allow user to specify output location in buildRelease * replace outputpath with outputfolder for consitent argument names in the package. * Add test for buildRelease. * replace outputpath with outputfolder for consistency. update documentation. * move ddl folder to inst so it is accessible from tests * update documentation * Add OMOP header genearator function Co-authored-by: Adam Black <adam.black@odysseusinc.com> Co-authored-by: Clair Blacketer <mblacke@its.jnj.com> Co-authored-by: clairblacketer <clairblacketer@users.noreply.github.com>
2021-08-20 13:00:03 -04:00 · 2021-08-20 13:00:03 -04:00 · d84141b5d8
parent 40e26982d4
commit d84141b5d8
2 changed files with 70 additions and 0 deletions
--- a/.gitignore
+++ b/.gitignore
@ -3,3 +3,13 @@
 .RData
 .Ruserdata
 extras/CodeToRun.R
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/R/createDdl.R
+++ b/R/createDdl.R
@ -139,3 +139,63 @@ createForeignKeys <- function(cdmVersion){
  }
  return(paste0(sql_result, collapse = ""))
 }
+
+
+
+# A helper function that will return a character string with the omop ascii art given a major and minor cdm version
+# example: cat(createAsciiHeader(5, 3))
+createAsciiHeader <- function(major, minor) {
+
+  stopifnot(is.numeric(major), is.numeric(minor), length(major) == 1, length(minor) == 1)
+  stopifnot(major %in% 0:99, minor %in% 0:99)
+
+  # An inner function that returns an ascii art matrix for any number between 0 and 99
+  numberMatrix <- function(num){
+    stopifnot(is.numeric(num), num %in% 0:99)
+
+    # An inner function that returns a 7x7 matrix of number ascii art for the number 0 through 9
+    # for the number 1 a 7x5 matrix is returned because 1 is narrower than other numbers.
+    singleDigit <- function(num) {
+      nums <- c('  ###     #    #####  ##### #      ####### ##### ####### #####  #####  #   #   ##   #     ##     ##    # #      #     ##    # #     ##     ##     # # #         #      ##    # #      #          #  #     ##     ##     #   #    #####  ##### #    # ###### ######    #    #####  #######     #   #   #            ########      ##     #  #    #     #      # #   #    #   #      #     #     # #     ##     #  #    #     ##     #  ###   ##### ####### #####      #  #####  #####   #     #####  ##### ')
+      numsMatrix <- matrix(data = strsplit(nums, character(0))[[1]], nrow = 7, byrow = T)
+      cols <- seq(num*7+1, num*7+7, by = 1)
+      out <- numsMatrix[1:7, cols]
+      # the number 1 is narrower than the other numbers
+      if(num == 1) out<- out[1:7, 2:6]
+      out
+    }
+
+    if(num < 10){
+      return(singleDigit(num))
+    } else {
+      space <- matrix(rep(" ", 7), nrow = 7)
+      return(cbind(singleDigit(floor(num/10)), space, singleDigit(num %% 10)))
+    }
+  }
+
+  omop <- c('.
+  ####### #     # ####### ######      #####  ######  #     #          .
+  #     # ##   ## #     # #     #    #     # #     # ##   ##    #    #.
+  #     # # # # # #     # #     #    #       #     # # # # #    #    #.
+  #     # #  #  # #     # ######     #       #     # #  #  #    #    #.
+  #     # #     # #     # #          #       #     # #     #    #    #.
+  #     # #     # #     # #          #     # #     # #     #     #  # .
+  ####### #     # ####### #           #####  ######  #     #      ##  ')
+
+  # convert to matrix and remove first column
+  omop <- matrix(strsplit(omop, character(0))[[1]], nrow = 7, byrow = TRUE)
+  omop <- omop[,c(-1, -2)]
+
+  dot <- matrix(c(rep(" ", 3*4), rep("#", 3*3)), nrow = 7, byrow = TRUE)
+  space <- matrix(rep(" ", 7), nrow = 7)
+  newline <- matrix(rep("\n", 7, nrow = 7))
+
+
+  header <- character(0)
+  headerMatrix <- cbind(omop, space, numberMatrix(major), space, dot, space, numberMatrix(minor), newline)
+  for(i in 1:7) {
+    header <- c(header, as.character(headerMatrix[i,]))
+  }
+  header <- paste(header, collapse = "")
+  return(header)
+}