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StuartWheaterStuartWheater
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Merge remote-tracking branch 'upstream/v6.1-dev' into v6.1-dev
2 parents c6df1f8 + a85fa0b commit 61c58e1

5 files changed

Lines changed: 116 additions & 114 deletions

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‎tests/testthat/definition_tests/def-assign-stats.R‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@ ds.test_env$MAX <- 5
1515
value[1] <- mean(some.local.values)
1616
value[2] <- var(some.local.values)
1717
value[3] <- length(some.local.values)
18-
value[4] <- min(some.local.values)
19-
value[5] <- max(some.local.values)
18+
#value[4] <- min(some.local.values)
19+
#value[5] <- max(some.local.values)
2020
return(value)
2121
}
2222

@@ -26,24 +26,24 @@ ds.test_env$MAX <- 5
2626
.calc.distribution.server <- function(name.variable)
2727
{
2828
#set an initial value
29-
value <- c(0.0,0.0,0.0,0.0,0.0)
29+
value <- c(0.0,0.0,0.0)
3030

3131
# compute dispersion and centrality
3232
mean.from.servers <- ds.mean(x=name.variable,type='combine', check=TRUE,save.mean.Nvalid=FALSE)
3333
var.from.servers <- ds.var(x=name.variable,type='combine')
3434

3535
# compute range
36-
levels <- ds.asFactor(name.variable, newobj.name = "factors")
37-
vector <- (as.numeric(unlist(levels[[1]])))
38-
server.min <- min(vector)
39-
server.max <- max(vector)
36+
#levels <- ds.asFactor(name.variable, newobj.name = "factors")
37+
#vector <- (as.numeric(unlist(levels[[1]])))
38+
#server.min <- min(vector)
39+
#server.max <- max(vector)
4040

4141
#values to return
4242
value[1] <- mean.from.servers[[1]][1]
4343
value[2] <- var.from.servers[[1]][1]
4444
value[3] <- mean.from.servers[[1]][3]
45-
value[4] <- min(vector)
46-
value[5] <- max(vector)
45+
#value[4] <- min(vector)
46+
#value[5] <- max(vector)
4747
return(value)
4848

4949
}

‎tests/testthat/definition_tests/def-ds.dataFrameSort.R‎

Lines changed: 62 additions & 90 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11

22
.test.function.parameters<-function(initial.df.name,key.name,sort.descending,sort.method,df.created)
3-
{
3+
{
44
if(class(initial.df.name)!="character" | class(key.name)!="character" | class(sort.method)!="character" | class(sort.descending) != "logical" | class(df.created)!="character")
5-
{
5+
{
66
expect_error(ds.dataFrameSort(df.name = initial.df.name,
77
sort.key.name = key.name,
88
sort.descending = sort.descending,
@@ -23,21 +23,21 @@
2323
}else{
2424
var.exist<-substr(key.name, 3, nchar(key.name))
2525
for(j in 1:length(ds.test_env$connections)){
26-
var.in.df<-var.exist %in% ds.colnames("D", datasources = ds.test_env$connections)[[j]]
27-
if(var.in.df==FALSE)
26+
var.in.df<-var.exist %in% ds.colnames("D", datasources = ds.test_env$connections)[[j]]
27+
if(var.in.df==FALSE)
28+
{
29+
results<-ds.dataFrameSort(df.name = initial.df.name,
30+
sort.key.name = key.name,
31+
sort.descending = sort.descending,
32+
sort.method = sort.method,
33+
newobj =df.created,
34+
datasources =test_env$connections)
35+
not.ok.message<-"NOT ALL OK: there are studysideMessage(s) on this datasource"
36+
for(j in 1:length(ds.test_env$connections))
2837
{
29-
results<-ds.dataFrameSort(df.name = initial.df.name,
30-
sort.key.name = key.name,
31-
sort.descending = sort.descending,
32-
sort.method = sort.method,
33-
newobj =df.created,
34-
datasources =test_env$connections)
35-
not.ok.message<-"NOT ALL OK: there are studysideMessage(s) on this datasource"
36-
for(j in 1:length(ds.test_env$connections))
37-
{
38-
expect_equal(results$studyside.messages[[j]],not.ok.message,ds.test_env$tolerance)
39-
}
38+
expect_equal(results$studyside.messages[[j]],not.ok.message,ds.test_env$tolerance)
4039
}
40+
}
4141

4242
}
4343
}
@@ -47,50 +47,51 @@
4747

4848

4949
.test.data.frame.creation<-function(initial.df.name,key.name,sort.descending,sort.method,df.created)
50-
{
51-
# Create a sort data frame
52-
sort.key.name<-paste(initial.df.name,key.name,sep="$")
53-
ds.dataFrameSort(df.name = initial.df.name,
50+
{
51+
# Create a sort data frame
52+
sort.key.name<-paste(initial.df.name,key.name,sep="$")
53+
ds.dataFrameSort(df.name = initial.df.name,
5454
sort.key.name = sort.key.name,
5555
sort.descending = sort.descending,
5656
sort.method = sort.method,
5757
newobj =df.created,
5858
datasources = ds.test_env$connections)
59-
type <- ds.class(df.created, datasources = ds.test_env$connections)
60-
exists <- ds.exists(df.created, datasources = ds.test_env$connections)
61-
cols.name <- ds.colnames(df.created,datasources = ds.test_env$connections)
62-
# Initial data frame column names
63-
initial.df.cols.name<-ds.colnames(initial.df.name, datasources = ds.test_env$connections)
64-
# Testing - testthat
65-
expect_true(type[[1]][1]=="data.frame")
59+
type <- ds.class(df.created, datasources = ds.test_env$connections)
60+
exists <- ds.exists(df.created, datasources = ds.test_env$connections)
61+
cols.name <- ds.colnames(df.created,datasources = ds.test_env$connections)
62+
# Initial data frame column names
63+
initial.df.cols.name<-ds.colnames(initial.df.name, datasources = ds.test_env$connections)
64+
# Testing - testthat
65+
expect_true(type[[1]][1]=="data.frame")
6666

67-
for(i in 1:length(exists))
68-
{
69-
expect_true(exists[[i]])
70-
}
71-
72-
for (i in 1:length(cols.name))
73-
{
74-
expect_equal(cols.name[[i]],
75-
initial.df.cols.name[[i]],
76-
ds.test_env$tolerance)
77-
}
67+
for(i in 1:length(exists))
68+
{
69+
expect_true(exists[[i]])
70+
}
7871

72+
for (i in 1:length(cols.name))
73+
{
74+
expect_equal(cols.name[[i]],
75+
initial.df.cols.name[[i]],
76+
ds.test_env$tolerance)
7977
}
78+
79+
}
8080

8181

8282

8383
.test.data.frame.sorting <-function(initial.df.name,key.name,sort.descending,sort.method,df.created,local.df.list)
84-
{
85-
84+
{
85+
library(dsDangerClient)
86+
8687
# Sort local dfs
8788
sort.local<-list()
8889
sort.local.dim<-list()
8990
sort.local.colnames<-list()
9091
for(i in 1:length(local.df.list))
91-
{
92+
{
9293
if (sort.method=="alphabetic")
93-
{
94+
{
9495
order.key<-order(as.character(local.df.list[[i]][,key.name]),
9596
decreasing = sort.descending,
9697
na.last = TRUE)
@@ -103,7 +104,8 @@
103104
}
104105
sort.local[[i]]<-local.df.list[[i]][order.key,]
105106
sort.local.dim[[i]]<-dim(local.df.list[[i]])
106-
}
107+
sort.local.colnames[[i]]<-colnames(local.df.list[[i]])
108+
}
107109
# Sort server dfs
108110
sort.key.name<-paste(initial.df.name,key.name,sep="$")
109111
ds.dataFrameSort(df.name = initial.df.name,
@@ -114,60 +116,30 @@
114116
datasources = ds.test_env$connections)
115117
sort.server.dim<-ds.dim(df.created,
116118
datasources = ds.test_env$connections)
117-
sort.key.name.class<-ds.class(sort.key.name, datasources = ds.test_env$connections)[[1]]
119+
sort.server.colnames<-ds.colnames(df.created,
120+
datasources = ds.test_env$connections)
121+
sorted.key.name<-paste(df.created,key.name,sep="$")
122+
ds.assign(toAssign = sorted.key.name,
123+
newobj = "server.key.variable",
124+
datasources = ds.test_env$connections)
118125

119126
for (i in 1:length(ds.test_env$connections))
120127
{
121128
expect_equal(sort.local.dim[[i]],
122129
sort.server.dim[[i]],
123130
ds.test_env$tolerance)
131+
expect_equal(sort.local.colnames[[i]],
132+
sort.server.colnames[[i]],
133+
ds.test_env$tolerance)
124134
}
135+
136+
server.data<-ds.DANGERdfEXTRACT(df.created,
137+
datasources = ds.test_env$connections)
138+
server.data<-server.data$study.specific.df
125139

126-
127-
128-
if(sort.key.name.class == "integer" | sort.key.name.class == "numeric" & sort.method == "numeric" )
129-
{
130-
sorted.key.name<-list()
131-
sort.server.mean<-list()
132-
sort.server.var<-list()
133-
len.key.server<-sort.server.dim[[1]][1]
134-
for(l in 1:3)
135-
{
136-
i<-c(1,(len.key.server/2)-2.5,len.key.server-5)
137-
j<-c(5,(len.key.server/2)+2.5,len.key.server)
138-
sorted.key.name<-paste(df.created,"$",key.name,"[",i[l],":",j[l],"]",sep="")
139-
140-
sort.server.mean[[l]]<-ds.mean(sorted.key.name, type = "c", datasources = ds.test_env$connections)[[1]][1]
141-
#sort.server.var[[l]]<-ds.var(sorted.key.name, type = "c", datasources = ds.test_env$connections)[[1]][1]
142-
}
143-
144-
145-
#expect_equal(sort.server.var[[1]],
146-
#sort.server.var[[2]],
147-
#ds.test_env$tolerance)
148-
#expect_equal(sort.server.var[[2]],
149-
#sort.server.var[[3]],
150-
#ds.test_env$tolerance)
151-
152-
if (sort.descending == TRUE & sort.method == "numeric")
153-
{
154-
expect_true(sort.server.mean[[1]] > sort.server.mean[[2]])
155-
expect_true(sort.server.mean[[2]] > sort.server.mean[[3]])
156-
}
157-
if (sort.descending == FALSE & sort.method == "numeric")
158-
{
159-
expect_true(sort.server.mean[[1]] < sort.server.mean[[2]])
160-
expect_true(sort.server.mean[[2]] < sort.server.mean[[3]])
161-
}
162-
163-
164-
165-
}
166-
167-
140+
for ( i in 1:length(server.data)){
141+
expect_equal(server.data[[i]][,key.name],
142+
sort.local[[i]][,key.name],
143+
ds.test_env$tolerance)
144+
}
168145
}
169-
170-
171-
172-
173-

‎tests/testthat/definition_tests/def-ds.dataFrameSubset.R‎

Lines changed: 23 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11

22
source("definition_tests/def-assign-stats.R")
3+
library(dsDangerClient)
34

45
.test.function.parameters<-function(initial.df.name,V1.name,V2.name,boole,keep.cols,rm.cols,keep.NAs,df.created)
56
{
@@ -137,6 +138,7 @@ subset.by.rows<-function(initial.df.name,V1.name,V2.name,boole,keep.NAs,df.creat
137138
newobj = df.created,
138139
datasources = ds.test_env$connections)
139140

141+
140142
#testing
141143
for (i in 1:length(df.subset.local))
142144
{
@@ -146,7 +148,7 @@ subset.by.rows<-function(initial.df.name,V1.name,V2.name,boole,keep.NAs,df.creat
146148
ds.test_env$tolerance)
147149
}
148150
#Calculate the mean, sd,length, min and max of the variable in the parameter 'V1.name'
149-
var1<-paste(df.created,V1.name,sep="$")
151+
subset.var<-paste(df.created,V1.name,sep="$")
150152
if(length(df.subset.local)==3)
151153
{
152154
local.rbind.df<-rbind(df.subset.local[[1]],df.subset.local[[2]],df.subset.local[[3]])
@@ -159,9 +161,9 @@ subset.by.rows<-function(initial.df.name,V1.name,V2.name,boole,keep.NAs,df.creat
159161
{
160162
local.rbind.df<-df.subset.local[[1]]
161163
}
162-
#dist.local <- .calc.distribution.locally(local.rbind.df[,V1.name])
163-
#dist.server <- .calc.distribution.server(var1)
164-
#expect_equal(dist.local,dist.server, tolerance = ds.test_env$tolerance)
164+
dist.local <- .calc.distribution.locally(local.rbind.df[,V1.name])
165+
dist.server <- .calc.distribution.server(subset.var)
166+
expect_equal(dist.local,dist.server, tolerance = ds.test_env$tolerance)
165167
}
166168

167169

@@ -201,7 +203,10 @@ subset.by.rows.cols<-function(initial.df.name,V1.name,V2.name,keep.cols,boole,ke
201203
}
202204

203205

204-
206+
# Upload server-side testing data frames in the client-side (danger function)
207+
server.data<-ds.DANGERdfEXTRACT(df.created,
208+
datasources = ds.test_env$connections)
209+
server.data<-server.data$study.specific.df
205210

206211
#testing- testthat
207212

@@ -246,6 +251,19 @@ subset.by.cols<-function(initial.df.name,V1.name,keep.cols,keep.NAs,df.created,l
246251
expect_equal(dim(df.subset.local[[i]]),ds.dim(df.created, datasources = ds.test_env$connections)[[i]],ds.test_env$tolerance)
247252
expect_equal(colnames(df.subset.local[[i]]),ds.colnames(df.created, datasources = ds.test_env$connections)[[i]],ds.test_env$tolerance)
248253
}
254+
# Upload server-side testing data frames in the client-side (danger function)
255+
server.data<-ds.DANGERdfEXTRACT(df.created,
256+
datasources = ds.test_env$connections)
257+
server.data<-server.data$study.specific.df
258+
259+
#testing- testthat
260+
261+
# for ( i in 1:length(server.data))
262+
# {
263+
# expect_equal(server.data[[i]][,1],
264+
# df.subset.local[[i]][,1],
265+
# ds.test_env$tolerance)
266+
# }
249267

250268
}
251269
# Clear the Datashield R sessions and logout

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