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>
This commit is contained in:
Adam Black
GitHub
parent
40e26982d4
commit
d84141b5d8
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@ -3,3 +3,13 @@
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.RData
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.RData
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.Ruserdata
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.Ruserdata
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extras/CodeToRun.R
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extras/CodeToRun.R
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# OS generated files #
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######################
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.DS_Store
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.DS_Store?
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._*
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.Spotlight-V100
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.Trashes
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ehthumbs.db
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Thumbs.db
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@ -139,3 +139,63 @@ createForeignKeys <- function(cdmVersion){
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}
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}
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return(paste0(sql_result, collapse = ""))
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return(paste0(sql_result, collapse = ""))
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}
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}
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# A helper function that will return a character string with the omop ascii art given a major and minor cdm version
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# example: cat(createAsciiHeader(5, 3))
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createAsciiHeader <- function(major, minor) {
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stopifnot(is.numeric(major), is.numeric(minor), length(major) == 1, length(minor) == 1)
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stopifnot(major %in% 0:99, minor %in% 0:99)
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# An inner function that returns an ascii art matrix for any number between 0 and 99
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numberMatrix <- function(num){
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stopifnot(is.numeric(num), num %in% 0:99)
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# An inner function that returns a 7x7 matrix of number ascii art for the number 0 through 9
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# for the number 1 a 7x5 matrix is returned because 1 is narrower than other numbers.
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singleDigit <- function(num) {
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nums <- c(' ### # ##### ##### # ####### ##### ####### ##### ##### # # ## # ## ## # # # ## # # ## ## # # # # ## # # # # # ## ## # # ##### ##### # # ###### ###### # ##### ####### # # # ######## ## # # # # # # # # # # # # # ## # # # ## # ### ##### ####### ##### # ##### ##### # ##### ##### ')
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numsMatrix <- matrix(data = strsplit(nums, character(0))[[1]], nrow = 7, byrow = T)
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cols <- seq(num*7+1, num*7+7, by = 1)
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out <- numsMatrix[1:7, cols]
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# the number 1 is narrower than the other numbers
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if(num == 1) out<- out[1:7, 2:6]
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out
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}
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if(num < 10){
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return(singleDigit(num))
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} else {
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space <- matrix(rep(" ", 7), nrow = 7)
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return(cbind(singleDigit(floor(num/10)), space, singleDigit(num %% 10)))
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}
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}
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omop <- c('.
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####### # # ####### ###### ##### ###### # # .
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# # ## ## # # # # # # # # ## ## # #.
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# # # # # # # # # # # # # # # # # # #.
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# # # # # # # ###### # # # # # # # #.
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# # # # # # # # # # # # # #.
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# # # # # # # # # # # # # # # .
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####### # # ####### # ##### ###### # # ## ')
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# convert to matrix and remove first column
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omop <- matrix(strsplit(omop, character(0))[[1]], nrow = 7, byrow = TRUE)
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omop <- omop[,c(-1, -2)]
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dot <- matrix(c(rep(" ", 3*4), rep("#", 3*3)), nrow = 7, byrow = TRUE)
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space <- matrix(rep(" ", 7), nrow = 7)
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newline <- matrix(rep("\n", 7, nrow = 7))
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header <- character(0)
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headerMatrix <- cbind(omop, space, numberMatrix(major), space, dot, space, numberMatrix(minor), newline)
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for(i in 1:7) {
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header <- c(header, as.character(headerMatrix[i,]))
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}
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header <- paste(header, collapse = "")
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return(header)
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}
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