-
Notifications
You must be signed in to change notification settings - Fork 23
/
ds.matrixTranspose.R
187 lines (181 loc) · 8.05 KB
/
ds.matrixTranspose.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
#' @title Transposes a server-side matrix
#' @description Transposes a matrix and writes the output to the server-side
#' @details This operation converts matrix
#' \code{A} to matrix \code{C} where element \code{C[i,j]} of
#' matrix \code{C} equals element \code{A[j,i]} of matrix
#' \code{A}. Matrix \code{A}, therefore, has the same number
#' of rows as matrix \code{C} has columns and vice versa.
#'
#' Server function called: \code{matrixTransposeDS}
#'
#' @param M1 a character string specifying the name of the matrix.
#' @param newobj a character string that provides the name for the output
#' variable that is stored on the data servers.
#' Default \code{matrixtranspose.newobj}.
#' @param datasources a list of \code{\link{DSConnection-class}}
#' objects obtained after login. If the \code{datasources} argument is not specified
#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
#' @return \code{ds.matrixTranspose} returns to the server-side the transpose matrix.
#' Also, two validity messages are returned to the client-side
#' indicating whether the new object has been created in each data source and if so whether
#' it is in a valid form.
#' @author DataSHIELD Development Team
#' @examples
#' \dontrun{
#'
#' ## Version 6, for version 5 see the Wiki
#'
#' # connecting to the Opal servers
#'
#' require('DSI')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' builder <- DSI::newDSLoginBuilder()
#' builder$append(server = "study1",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM1", driver = "OpalDriver")
#' builder$append(server = "study2",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM2", driver = "OpalDriver")
#' builder$append(server = "study3",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM3", driver = "OpalDriver")
#' logindata <- builder$build()
#'
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#'
#' #Example 1: Transpose the server-side matrix
#'
#' #Create the server-side vector
#'
#' ds.rUnif(samp.size = 9,
#' min = -10.5,
#' max = 10.5,
#' newobj = "ss.vector.9",
#' seed.as.integer = 5575,
#' force.output.to.k.decimal.places = 0,
#' datasources = connections)
#'
#' #Create the server-side matrix
#'
#' ds.matrix(mdata = "ss.vector.9",
#' from = "serverside.vector",
#' nrows.scalar = 3,
#' ncols.scalar = 4,
#' byrow = TRUE,
#' newobj = "matrix",
#' datasources = connections)
#'
#' #Transpose the matrix
#'
#' ds.matrixTranspose(M1 = "matrix",
#' newobj = "matrix.transpose",
#' datasources = connections)
#'
#' # clear the Datashield R sessions and logout
#' datashield.logout(connections)
#' }
#' @export
#'
ds.matrixTranspose<-function(M1=NULL, newobj=NULL, datasources=NULL){
# look for DS connections
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
# check if user has provided the name of matrix representing M1
if(is.null(M1)){
return("Error: Please provide the name of the matrix representing M1")
}
# if no value spcified for output object, then specify a default
if(is.null(newobj)){
newobj <- "matrixtranspose.newobj"
}
# CALL THE MAIN SERVER SIDE FUNCTION
calltext <- call("matrixTransposeDS", M1)
DSI::datashield.assign(datasources, newobj, calltext)
#############################################################################################################
#DataSHIELD CLIENTSIDE MODULE: CHECK KEY DATA OBJECTS SUCCESSFULLY CREATED #
#
#SET APPROPRIATE PARAMETERS FOR THIS PARTICULAR FUNCTION #
test.obj.name<-newobj #
#
#TRACER #
#return(test.obj.name) #
#} #
#
#
# CALL SEVERSIDE FUNCTION #
calltext <- call("testObjExistsDS", test.obj.name) #
#
object.info<-DSI::datashield.aggregate(datasources, calltext) #
#
# CHECK IN EACH SOURCE WHETHER OBJECT NAME EXISTS #
# AND WHETHER OBJECT PHYSICALLY EXISTS WITH A NON-NULL CLASS #
num.datasources<-length(object.info) #
#
#
obj.name.exists.in.all.sources<-TRUE #
obj.non.null.in.all.sources<-TRUE #
#
for(j in 1:num.datasources){ #
if(!object.info[[j]]$test.obj.exists){ #
obj.name.exists.in.all.sources<-FALSE #
} #
if(is.null(object.info[[j]]$test.obj.class) || object.info[[j]]$test.obj.class=="ABSENT"){ #
obj.non.null.in.all.sources<-FALSE #
} #
} #
#
if(obj.name.exists.in.all.sources && obj.non.null.in.all.sources){ #
#
return.message<- #
paste0("A data object <", test.obj.name, "> has been created in all specified data sources") #
#
#
}else{ #
#
return.message.1<- #
paste0("Error: A valid data object <", test.obj.name, "> does NOT exist in ALL specified data sources") #
#
return.message.2<- #
paste0("It is either ABSENT and/or has no valid content/class,see return.info above") #
#
return.message.3<- #
paste0("Please use ds.ls() to identify where missing") #
#
#
return.message<-list(return.message.1,return.message.2,return.message.3) #
#
} #
#
calltext <- call("messageDS", test.obj.name) #
studyside.message<-DSI::datashield.aggregate(datasources, calltext) #
#
no.errors<-TRUE #
for(nd in 1:num.datasources){ #
if(studyside.message[[nd]]!="ALL OK: there are no studysideMessage(s) on this datasource"){ #
no.errors<-FALSE #
} #
} #
#
#
if(no.errors){ #
validity.check<-paste0("<",test.obj.name, "> appears valid in all sources") #
return(list(is.object.created=return.message,validity.check=validity.check)) #
} #
#
if(!no.errors){ #
validity.check<-paste0("<",test.obj.name,"> invalid in at least one source. See studyside.messages:") #
return(list(is.object.created=return.message,validity.check=validity.check, #
studyside.messages=studyside.message)) #
} #
#
#END OF CHECK OBJECT CREATED CORECTLY MODULE #
#############################################################################################################
}
#ds.matrixTranspose