Pull test improvements from master

bitbucket-pipelines.yml

@@ -1,20 +1,11 @@
-image: atlassian/default-image:latest
+image: gavinband/ubuntu-14.04-build
 pipelines:
   default:
     - step:
         script:
-          - wget http://www.well.ox.ac.uk/~gav/resources/qctool_v2.0.1-Ubuntu14.04-x86_64.tgz
-          - tar -xzf qctool_v2.0.1-Ubuntu14.04-x86_64.tgz
-          - cp qctool_v2.0.1-Ubuntu14.04-x86_64/qctool /usr/bin/
-          - qctool
-          - apt-get install --assume-yes zlib1g-dev
-          - apt-get install --assume-yes python-pip
-          - python -m pip install robotframework
-          - qctool -g example/example.16bits.bgen -og /tmp/x.vcf
           - ./waf configure
           - ./waf
           - cd test/functional
-          - mkdir -p test-reports/-o
-
+          - mkdir -p test-reports/
           - pybot -o output.xml -l log.html -r report.html -d test-reports -x xunit.xml ./tests.txt
 

test/functional/run_tests.sh

@@ -2,4 +2,4 @@
 dir=$(dirname ${0})
 basedir=${dir}/../..
 echo ${dir}
-pybot -o NONE -l NONE -r NONE -d ${basedir}/build/test/functional/test-reports -x xunit.xml ${dir}/tests.txt
+pybot -o  output.html -l log.html -r NONE -d ${basedir}/build/test/functional/test-reports -x xunit.xml ${dir}/tests.txt

test/functional/test_rbgen.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+R="$1"
+RBGEN="${2}"
+if [[ ${R} == '' ]]; then
+  R='R'
+fi
+if [[ ${RBGEN} == '' ]]; then
+  RBGEN=build/R/rbgen
+fi
+
+${R} CMD INSTALL ${RBGEN}
+${R} --vanilla << HERE_DOC
+library( rbgen )
+
+## Test we can load data
+D = bgen.load( "example/example.16bits.bgen", ranges = data.frame( chromosome = '01', start = 0, end = 100000 ))
+str( D )
+head( D\$variants )
+D\$data[1,1:10,1:3]
+
+## Test we can load data on a subset of samples
+samples = c( "sample_001", "sample_102", "sample_050", "sample_499" )
+E = bgen.load( "example/example.16bits.bgen", ranges = data.frame( chromosome = '01', start = 0, end = 100000 ), samples = samples )
+stopifnot( length( which( E\$data != D\$data[,samples,] ) ) == 0 )
+stopifnot( length( which( D\$variants != E\$variants )) == 0 )
+
+## Test we can load data for some specific rsid
+rsids = c( "RSID_10", "RSID_20", "RSID_171", "RSID_9" )
+F = bgen.load( "example/example.16bits.bgen", rsids = rsids )
+str( F )
+head( F\$variants )
+F\$data
+
+## Check we can load complex data
+D = bgen.load(  "example/complex.bgen", data.frame( chromosome = '01', start = 0, end = 1000000 ), max_entries_per_sample = 50 )
+str(D)
+
+HERE_DOC

test/functional/tests.txt

@@ -4,6 +4,7 @@ ${HOME}	%{HOME}
 ${BUILDDIR}	${BASEDIR}/build
 ${TMPDIR}	${BUILDDIR}/test/functional/tmp
 ${BGENIX}	${BUILDDIR}/apps/bgenix
+${RBGEN}	${BUILDDIR}/R/rbgen
 ${QCTOOL}	qctool
 ${UNITTEST}	${BUILDDIR}/test/unit/test_bgen
 
@@ -39,6 +40,9 @@ Bgenix lists variants
 	${length}=	Get length	${lines}
 	Should be equal as integers	${length}	202
 
+Rbgen loads data
+	Run process	./test_rbgen.sh	R	${RBGEN}
+
 *** Keywords ***
 
 Create empty temp directory