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wrapper tests #37

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merged 16 commits into from
Jul 19, 2017
Merged

wrapper tests #37

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edf608f
new files for wrapper tests
wk1993 Jul 14, 2017
7defa52
tests for caller wrapper
wk1993 Jul 15, 2017
06b9f60
Merge branch 'master' of https://github.com/ZSI-Bio/CNV-opt into cnvc…
wk1993 Jul 15, 2017
e591d5b
comment unproper test
wk1993 Jul 16, 2017
d789cf4
first try of removing bugfix in jenkins R tests
wk1993 Jul 16, 2017
0723b98
all uncommented tests
wk1993 Jul 16, 2017
7984521
2 bugfixes in tests
wk1993 Jul 17, 2017
5b4142a
Merge branch 'master' of https://github.com/ZSI-Bio/CNV-opt into cnvc…
wk1993 Jul 17, 2017
8e1c685
always install CNVCALLER.RUNNER package in tests
wk1993 Jul 17, 2017
0208b9d
proper path to CNVCALLER.RUNNER package
wk1993 Jul 17, 2017
5b82a73
removed unproper install
wk1993 Jul 17, 2017
c728ffa
install CNVCALLER.RUNNER package in tests
wk1993 Jul 18, 2017
ce95542
changes in R dirs in Jenkinsfile (not tested commit)
wk1993 Jul 18, 2017
6ebdd53
bugfix in R tests
wk1993 Jul 18, 2017
765f57f
bugfix in CODEX version
wk1993 Jul 18, 2017
8f7fa6e
proper structure of install and load packages in R tests
wk1993 Jul 18, 2017
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2 changes: 1 addition & 1 deletion Jenkinsfile
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Expand Up @@ -5,7 +5,7 @@ pipeline {
stage('Test R code') {
steps {
echo 'Testing R code....'
sh 'docker run -i --rm --network="host" -w="/tmp" -v $(pwd | sed "s|/var/jenkins_home|/data/home/jenkins|g")/R/tests:/tmp zsibio.ii.pw.edu.pl:50009/zsi-bio-toolset Rscript run_tests.R' }
sh 'docker run -i --rm --network="host" -w="/tmp" -v $(pwd | sed "s|/var/jenkins_home|/data/home/jenkins|g")/R:/tmp zsibio.ii.pw.edu.pl:50009/zsi-bio-toolset Rscript tests/run_tests.R' }
post {
always {
junit '**R/tests/*.xml'
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6 changes: 3 additions & 3 deletions R/CNVCALLER.RUNNER/inst/run_cnvcaller.R
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Expand Up @@ -45,11 +45,11 @@ read_parameters <- function(tabName, id, conn){
chr=chr))
}

save_calls <- function(calls, conn){
save_calls <- function(calls, table_name, parameters_id, conn){
if (nrow(calls) != 0) {
for(i in 1:nrow(calls)) {
call <- calls[i,]
query <- paste("INSERT INTO TEST_CALLS (parameters_id, sample_name, chr, cnv, st_bp, ed_bp, length_kb, st_exon, ed_exon, raw_cov, norm_cov, copy_no, lratio, mBIC) VALUES ('", opt$id, "','", call[1], "','", call[2], "','", call[3], "','", call[4], "','", call[5], "','", call[6], "','", call[7], "','", call[8], "','", call[9], "','", call[10], "','", call[11], "','", call[12], "','", call[13], "');", sep="")
query <- paste("INSERT INTO ", table_name, " (parameters_id, sample_name, chr, cnv, st_bp, ed_bp, length_kb, st_exon, ed_exon, raw_cov, norm_cov, copy_no, lratio, mBIC) VALUES ('", parameters_id, "','", call[1], "','", call[2], "','", call[3], "','", call[4], "','", call[5], "','", call[6], "','", call[7], "','", call[8], "','", call[9], "','", call[10], "','", call[11], "','", call[12], "','", call[13], "');", sep="")
dbSendUpdate(conn, query)
}
}
Expand Down Expand Up @@ -101,7 +101,7 @@ cov_table <- read_coverage_table(parameters$cov_table, conn_psql,parameters$chr)
#print(cov_table)
calls <- run_caller(parameters, cov_table)
#print(calls)
save_calls(calls, conn_psql)
save_calls(calls, "TEST_CALLS", opt$id, conn_psql)

dbDisconnect(conn_hive)
dbUnloadDriver(drv_hive)
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2 changes: 1 addition & 1 deletion R/CODEXCOV/DESCRIPTION
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Expand Up @@ -11,7 +11,7 @@ Description: An extended implementation of the CODEX package in R. It extends
parameters.
Depends:
R (>= 3.2.3),
CODEX (== 1.8.0),
CODEX (== 1.9.0),
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Why do we upgrade Codex version?

testthat (== 1.0.2.9000),
devtools (== 1.13.2),
DBI (== 0.7),
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7 changes: 4 additions & 3 deletions R/tests/run_tests.R
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Expand Up @@ -5,9 +5,10 @@ if (length(which(installed.packages()[,1] == "CODEX")) == 0){
biocLite("CODEX")
}

setwd('tests/')
devtools::install('../CNVCALLER.RUNNER')
devtools::install('../CODEXCOV')

library(testthat)
#source("test_functions_CODEX.R")
#source("test_functions_HMZDelFinder.R")
#capture.output(test_dir(".", reporter="junit"),file="results.xml")
out <- capture.output(test_dir(".", reporter="junit"))
writeLines(out[grep("<?xml version=", out):length(out)], "results.xml")
89 changes: 89 additions & 0 deletions R/tests/test_CODEXCOV_wrapper.R
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@@ -0,0 +1,89 @@
library(testthat)
library(CNVCALLER.RUNNER)

context("Testing run_wrapper_CODEXCOV function")

test_that("basic test for run_wrapper_CODEXCOV function, without calls",{
mapp_thresh <- "0.9"
cov_thresh_from <- "20"
cov_thresh_to <- "4000"
length_thresh_from <- "0"
length_thresh_to <- "200000"
gc_thresh_from <- "5"
gc_thresh_to <- "100"
K_from <- "1"
K_to <- "3"
lmax <- "200"
cov_table <- as.data.frame(matrix(data=c("NA12044",6,"2",17211,173310,151.636363636364,
"NA11829",4,"2",16712,167190,100,
"NA07051",7,"2",30275,304310,155.929936305732,
"NA07051",1,"2",14642,148820,160.3900414937759,
"NA12044",8,"2",69069,700290,581.723204994797,
"NA12044",9,"2",129133,1292530,30.4462809917355,
"NA12044",10,"2",228233,2283540,223.311475409836,
"NA11829",9,"2",129133,1292530,270.4462809917355,
"NA11829",10,"2",228233,2283540,223.311475409836,
"NA11994",9,"2",129133,1292530,180.4462809917355,
"NA11994",3,"2",15751,159900,500.29357798165138,
"NA11829",5,"2",16834,170740,400.19502074688797,
"NA07051",3,"2",15751,159900,900.75313807531381,
"NA18504",5,"2",16834,170740,110.46887966805,
"NA07051",4,"2",16599,167080,100.72815533980583,
"NA12044",4,"2",16599,166400,100.30952380952381,
"NA11994",2,"2",14943,150630,103.900826446281,
"NA18504",6,"2",17211,173310,81.801652892562,
"NA18504",10,"2",228233,2283540,223.311475409836,
"NA12044",2,"2",14943,150630,76.0661157024793,
"NA07051",8,"2",69069,700290,691.77627471384,
"NA07051",2,"2",14943,150630,170.0826446280992,
"NA18504",1,"2",14642,148820,35.8630705394191,
"NA18504",8,"2",69069,700290,240.60561914672,
"NA12044",3,"2",15751,159900,200.88202247191011,
"NA18504",9,"2",129133,1292530,200.4462809917355,
"NA11829",6,"2",17211,173310,148.95041322314,
"NA18504",2,"2",14943,150630,230.7603305785124,
"NA11829",8,"2",69069,700290,1022.60561914672,
"NA07051",5,"2",16834,170740,76.448132780083,
"NA12044",7,"2",30275,304310,126.821656050955,
"NA11994",4,"2",16599,167130,100.13913043478261,
"NA18504",3,"2",15751,159900,26.0833333333333,
"NA12044",5,"2",16834,170740,400.4070796460177,
"NA18504",7,"2",30275,304310,161.554140127389,
"NA11829",2,"2",14943,150630,22.289256198347,
"NA11994",10,"2",228233,2283540,200.17213114754098,
"NA07051",10,"2",228233,2283540,166.918032786885,
"NA11994",7,"2",30275,304310,172.980891719745,
"NA11994",6,"2",17211,173310,163.595041322314,
"NA11994",8,"2",69069,700290,88.76482830385,
"NA07051",9,"2",129133,1292530,320.4132231404959,
"NA11829",1,"2",14642,148820,51.244813278008,
"NA11829",7,"2",30275,304310,132.828025477707,
"NA11994",5,"2",16834,170740,600.70124481327801,
"NA11994",1,"2",14642,148820,146.879668049793,
"NA07051",6,"2",17211,173310,47.4876033057851,
"NA11829",3,"2",15751,159900,130.2958333333333,
"NA12044",1,"2",14642,148820,111.020746887967,
"NA18504",4,"2",16599,167170,300.58823529411765), nrow=50, ncol=6, byrow=TRUE))
colnames(cov_table) <- c("sample_name", "target_id", "chr", "pos_min", "pos_max", "cov_avg")
cov_table[,"sample_name"] <- sapply(cov_table[,"sample_name"], toString)
cov_table[,"target_id"] <- as.integer(cov_table[,"target_id"])
cov_table[,"chr"] <- sapply(cov_table[,"chr"], toString)
cov_table[,"pos_min"] <- as.integer(as.character(cov_table[,"pos_min"]))
cov_table[,"pos_max"] <- as.integer(as.character(cov_table[,"pos_max"]))
cov_table[,"cov_avg"] <- as.numeric(as.character(cov_table[,"cov_avg"]))
calls <- run_wrapper_CODEXCOV(mapp_thresh,
cov_thresh_from,
cov_thresh_to,
length_thresh_from,
length_thresh_to,
gc_thresh_from,
gc_thresh_to,
K_from,
K_to,
lmax,
cov_table)
expect_equal(length(calls), 0)
})



Empty file added R/tests/test_HMZDelFinder_wrapper.R
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2 changes: 0 additions & 2 deletions R/tests/test_functions_CODEX.R
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@@ -1,6 +1,4 @@
library(testthat)
if (length(which(installed.packages()[,1] == "devtools")) == 0){install.packages("devtools",repos="https://cloud.r-project.org/")}
if (length(which(installed.packages()[,1] == "CODEXCOV")) == 0){devtools::install("../CODEXCOV")}
library(CODEXCOV)

context("Testing gcmapp1 function")
Expand Down
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