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Merged
OllyButters merged 3 commits into from
Aug 15, 2019
Merged

Update 'ds.listClientsideFunctions' value checked, plus tidyup and version update #41

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ac19c84
Update 'ds.listClientsideFunctions', plus tidyup
StuartWheater Aug 15, 2019
e5cd6a0
Updated version
StuartWheater Aug 15, 2019
6691646
Updated "nfilter.glm" value checked
StuartWheater Aug 15, 2019
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: dsBaseClient
Title: DataSHIELD Client Functions
Version: 5.0.0-01
Version: 5.0.0-02
Author: DataSHIELD Developers <datashield@newcastle.ac.uk>
Maintainer: DataSHIELD Developers <datashield@newcastle.ac.uk>
Description: DataSHIELD client functions for the client site.
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137 changes: 75 additions & 62 deletions R/ds.listClientsideFunctions.R
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Expand Up @@ -6,75 +6,88 @@
#' dsStatsClient, or userDefinedClient. Operates by directly interrogating
#' the R objects stored in the input client packages and objects with name
#' "ds. ....." in .GlobalEnv
#' @param all.functions logical, if TRUE will list all client-side functions
#' in the input client-side packages and/or in .GlobalEnv. Default = TRUE
#' @param dsBaseClient logical, if TRUE will selectively list client-side functions
#' in "package:dsBaseClient". Default = FALSE.
#' @param dsGraphicsClient logical, if TRUE will selectively list client-side functions
#' in "package:dsGraphicsClient". Default = FALSE.
#' @param dsModellingClient logical, if TRUE will selectively list client-side functions
#' in "package:dsModellingClient". Default = FALSE.
#' @param dsStatsClient logical, if TRUE will selectively list client-side functions
#' in "package:dsStatsClient". Default = FALSE.
#' @param dsBetaTestClient logical, if TRUE will selectively list client-side functions
#' in "package:dsBetaTestClient". Default = FALSE.
#' @param userDefinedClient logical, if TRUE will selectively list user defined
#' client-side functions held as R objects with name "ds. ..." in .Global.env". Default = FALSE.
#' @return list containing all functions in each or all of these five classes
#' @author Paul Burton for DataSHIELD Development Team
#' @export
ds.listClientsideFunctions <-function(all.functions=TRUE,
dsBaseClient=FALSE,
dsGraphicsClient=FALSE,
dsModellingClient=FALSE,
dsStatsClient=FALSE,
dsBetaTestClient=FALSE,
userDefinedClient=FALSE
){
#THIS IS UNDERLYING SEARCH FUNCTION IN R IF NEEDED: search()
if(all.functions==TRUE&&dsBaseClient==FALSE&&dsGraphicsClient==FALSE&&
dsModellingClient==FALSE&&dsStatsClient==FALSE&&dsBetaTestClient==FALSE&&
userDefinedClient==FALSE){
cat("\n### dsBaseClient functions \n")
print(ls(pos="package:dsBaseClient"))
cat("\n\n### dsGraphicsClient functions \n")
print(ls(pos="package:dsGraphicsClient"))
cat("\n\n### dsModellingClient functions \n")
print(ls(pos="package:dsModellingClient"))
cat("\n\n### dsStatsClient functions \n")
print(ls(pos="package:dsStatsClient"))
cat("\n\n### dsBetaTestClient functions \n")
print(ls(pos="package:dsBetaTestClient"))
cat("\n\n### userDefinedClient functions \n")
print(ls(pos=".GlobalEnv",pattern="ds.*"))
ds.listClientsideFunctions <-function(){

}else{
if(dsBaseClient==TRUE){
cat("\n### dsBaseClient functions \n")
print(ls(pos="package:dsBaseClient"))}
if(dsGraphicsClient==TRUE){
cat("\n### dsBaseGraphics functions \n")
print(ls(pos="package:dsGraphicsClient"))}
if(dsModellingClient==TRUE){
cat("\n### dsModellingClient functions \n")
print(ls(pos="package:dsModellingClient"))}
if(dsStatsClient==TRUE){
cat("\n### dsStatsClient functions \n")
print(ls(pos="package:dsStatsClient"))}
if(dsBetaTestClient==TRUE){
cat("\n### dsBetaTestClient functions \n")
print(ls(pos="package:dsBetaTestClient"))}
if(userDefinedClient==TRUE){
cat("\n### userDefinedClient functions \n")
print(ls(pos=".GlobalEnv",pattern="ds.*"))}
search.path<-search()

print.text.full<-NULL

test.dsBaseClient<-FALSE
test.dsBetaTestClient<-FALSE
test.userDefinedClient<-FALSE
test.no.functions<-TRUE
potential.clientside.repositories<-NULL

if(dsBaseClient==FALSE&&dsGraphicsClient==FALSE&&dsModellingClient==FALSE&&
dsStatsClient==FALSE&&dsStatsClient==FALSE&&dsBetaTestClient==FALSE&&userDefinedClient==FALSE){
for(j in 1:length(search.path))
{

print("ALL OPTIONS DECLARED FALSE SO NO OUTPUT")
if(search.path[j]=="package:dsBaseClient")
{
test.dsBaseClient<-TRUE
test.no.functions<-FALSE
}

if(search.path[j]=="package:dsBetaTestClient")
{
test.dsBetaTestClient<-TRUE
test.no.functions<-FALSE
}

if(search.path[j]==".GlobalEnv")
{
test.userDefinedClient<-TRUE
test.no.functions<-FALSE
}
}
}


cat("\n### Full search path \n")
print.search.list<-search()
print(print.search.list)


if(test.userDefinedClient==TRUE)
{
cat("\n### userDefinedClient functions \n")
print.text<-ls(pos=".GlobalEnv",pattern="ds.*")
if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository"
print(print.text)
print.text.full<-c(print.text.full,print.text)
}

if(test.dsBetaTestClient==TRUE)
{
cat("\n### dsBetaTestClient functions \n")
print.text<-ls(pos="package:dsBetaTestClient")
if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository"
print(print.text)
print.text.full<-c(print.text.full,print.text)
}

if(test.dsBaseClient==TRUE)
{
cat("\n### dsBaseClient functions \n")
print.text<-ls(pos="package:dsBaseClient")
if(identical(print.text,character(0)))print.text<-"No clientside functions in this repository"
print(print.text)
print.text.full<-c(print.text.full,print.text)
}

if(test.no.functions==TRUE)
{
cat("\n### No standard clientside functions identified \n")
}

cat("\nIf you cannot see one or more of the clientside functions you expected to find",
"please see above for the full search path. If one of the paths is a possible clientside repository",
"issue the R command ls(pos='package:dsPackageName')",
"where 'package:dsPackageName' is the full name stated in the search path\n\n")

return(print.text.full)
}
#ds.listClientsideFunctions
# ds.listClientsideFunctions()


27 changes: 1 addition & 26 deletions man/ds.listClientsideFunctions.Rd
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154 changes: 154 additions & 0 deletions tests/testthat/atest-smk-ds.listClientsideFunctions.R
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#-------------------------------------------------------------------------------
# Copyright (c) 2019 University of Newcastle upon Tyne. All rights reserved.
#
# This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#-------------------------------------------------------------------------------

#
# Set up
#

connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_HDL"))

#
# Tests
#

context("ds.listClientsideFunctions::smk::check results")
test_that("check results", {
output <- paste(
[1] "ds.test_env"
[2] "checkClass"
[3] "colPercent"
[4] "ds.asCharacter"
[5] "ds.asDataMatrix"
[6] "ds.asFactor"
[7] "ds.asInteger"
[8] "ds.asList"
[9] "ds.asLogical"
[10] "ds.asMatrix"
[11] "ds.asNumeric"
[12] "ds.assign"
[13] "ds.Boole"
[14] "ds.c"
[15] "ds.cbind"
[16] "ds.changeRefGroup"
[17] "ds.class"
[18] "ds.colnames"
[19] "ds.contourPlot"
[20] "ds.cor"
[21] "ds.corTest"
[22] "ds.cov"
[23] "ds.dataFrame"
[24] "ds.dataFrameSort"
[25] "ds.dataFrameSubset"
[26] "ds.densityGrid"
[27] "ds.dim"
[28] "ds.exists"
[29] "ds.exp"
[30] "ds.gee"
[31] "ds.glm"
[32] "ds.glmSLMA"
[33] "ds.heatmapPlot"
[34] "ds.histogram"
[35] "ds.isNA"
[36] "ds.isValid"
[37] "ds.length"
[38] "ds.levels"
[39] "ds.lexis"
[40] "ds.list"
[41] "ds.listClientsideFunctions"
[42] "ds.listDisclosureSettings"
[43] "ds.listOpals"
[44] "ds.listServersideFunctions"
[45] "ds.log"
[46] "ds.look"
[47] "ds.ls"
[48] "ds.make"
[49] "ds.matrix"
[50] "ds.matrixDet"
[51] "ds.matrixDet.report"
[52] "ds.matrixDiag"
[53] "ds.matrixDimnames"
[54] "ds.matrixInvert"
[55] "ds.matrixMult"
[56] "ds.matrixTranspose"
[57] "ds.mean"
[58] "ds.meanByClass"
[59] "ds.meanSdGp"
[60] "ds.merge"
[61] "ds.message"
[62] "ds.names"
[63] "ds.numNA"
[64] "ds.quantileMean"
[65] "ds.rbind"
[66] "ds.rBinom"
[67] "ds.recodeLevels"
[68] "ds.recodeValues"
[69] "ds.replaceNA"
[70] "ds.reShape"
[71] "ds.rm"
[72] "ds.rNorm"
[73] "ds.rowColCalc"
[74] "ds.rPois"
[75] "ds.rUnif"
[76] "ds.scatterPlot"
[77] "ds.seq"
[78] "ds.setDefaultOpals"
[79] "ds.setSeed"
[80] "ds.subset"
[81] "ds.subsetByClass"
[82] "ds.summary"
[83] "ds.table1D"
[84] "ds.table2D"
[85] "ds.tapply"
[86] "ds.tapply.assign"
[87] "ds.testObjExists"
[88] "ds.unList"
[89] "ds.var"
[90] "ds.vectorCalc"
[91] "extract"
[92] "findLoginObjects"
[93] "geeChecks"
[94] "geehelper1"
[95] "geehelper2"
[96] "getOpals"
[97] "getPooledMean"
[98] "getPooledVar"
[99] "glmChecks"
[100] "init.object.list.global.environment"
[101] "init.object.list.testing.environment"
[102] "init.opal.list"
[103] "isAssigned"
[104] "isDefined"
[105] "library.dynam.unload"
[106] "logical2int"
[107] "meanByClassHelper0a"
[108] "meanByClassHelper0b"
[109] "meanByClassHelper1"
[110] "meanByClassHelper2"
[111] "meanByClassHelper3"
[112] "meanByClassHelper4"
[113] "rowPercent"
[114] "subsetHelper"
[115] "system.file"
)

res <- ds.listClientsideFunctions()

print("======")
print(res)
print("======")

expect_equal(res, output)
})

#
# Done
#

disconnect.studies.dataset.cnsim()
5 changes: 0 additions & 5 deletions tests/testthat/libraries/load_libraries.R
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4 changes: 1 addition & 3 deletions tests/testthat/setup.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ source("connection_to_datasets/login_details.R")
source("connection_to_datasets/init_all_datasets.R")
source("connection_to_datasets/init_studies_datasets.R")
source("connection_to_datasets/init_discordant_datasets.R")
#source("libraries/load_libraries.R")


init.all.datasets()
Expand All @@ -37,7 +36,6 @@ test_that("The virtual machine is loaded. ",
#define test_environment variables - connection to data shield and read from local files


#load.libraries()
#load the packages required for datashield to work
#test_that(" The packages dsBase, dsModelling, dsGraphics, dsStats are installed and loaded.",
#{
Expand All @@ -48,7 +46,7 @@ test_that("The virtual machine is loaded. ",
#})


print ("connect to server")
#print ("connect to server")
if (ds.test_env$context == ds.test_env$contexts[1])
{
#ds.test_env$connection.opal <- datashield.login(logins=ds.test_env$login.data, assign=TRUE,variables=ds.test_env$stats.var)
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