diff options
| -rw-r--r-- | Makefile | 12 | ||||
| -rw-r--r-- | guix.scm | 6 | ||||
| -rwxr-xr-x | run_tests.sh | 6 | ||||
| -rw-r--r-- | test/dev_tests.rb | 25 | ||||
| -rw-r--r-- | test/lib/test-helpers.rb | 24 |
5 files changed, 60 insertions, 13 deletions
@@ -234,9 +234,13 @@ unittests: all ./bin/unittests-gemma ./bin/unittests-gemma fast-check: all unittests + rm -vf output/* + ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log + +old-check: all unittests rm -vf test/output/* - cd test && ./dev_test_suite.sh | tee ../dev_test.log - grep -q 'success rate: 100%' dev_test.log + cd test && ./dev_test_suite.sh | tee ../test.log + grep -q 'success rate: 100%' test.log slow-check: all rm -vf test/output/* @@ -248,9 +252,7 @@ lengthy-check: all cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log grep -q 'success rate: 100%' lengthy_test.log -check: fast-check slow-check - -check-all: check lengthy-check +check: fast-check clean: rm -vf $(SRC_DIR)/*.o @@ -24,7 +24,8 @@ (gnu packages ninja) (gnu packages parallel) (gnu packages perl) - (gnu packages perl6) + ;; (gnu packages perl6) + (gnu packages ruby) (gnu packages pkg-config) ;; (gnu packages shell) ;; for shunit2 (srfi srfi-1) @@ -50,11 +51,12 @@ ("gsl" ,gsl) ;; ("shunit2" ,shunit2) ;; comes with gemma ("openblas" ,openblas) + ("ruby" ,ruby) ;; for testing ("zlib:static" ,zlib "static") ("zlib" ,zlib) )) (native-inputs ; for running tests - `(("perl" ,perl) + `(("perl" ,perl) ("which" ,which) )) (home-page "https://github.com/genetics-statistics") diff --git a/run_tests.sh b/run_tests.sh deleted file mode 100755 index 1b220b0..0000000 --- a/run_tests.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env bash - -# The "tr" command fixes the ^M characters in the output. -cd test -./test_suite.sh 2>&1 | tr '\r' '\n' > test.log -cat test.log | grep -q 'success rate: 100%' diff --git a/test/dev_tests.rb b/test/dev_tests.rb new file mode 100644 index 0000000..8ce8dbc --- /dev/null +++ b/test/dev_tests.rb @@ -0,0 +1,25 @@ + +require 'minitest/autorun' +require 'lib/test-helpers' + +class TestQuick < MiniTest::Test + + include TestHelpers + + def setup + end + + def test_linear_model + assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + -p ./example/mouse_hs1940.pheno.txt \ + -n 1 \ + -a ./example/mouse_hs1940.anno.txt \ + -lm \ + -o mouse_hs1940_CD8_lm") + + expect('output/mouse_hs1940_CD8_lm.assoc.txt',[[2,1,"rs3707673"], + [2,10,"5.252187e-05"], + [3,9,"3.909916e-02"]]) + end + +end diff --git a/test/lib/test-helpers.rb b/test/lib/test-helpers.rb new file mode 100644 index 0000000..72b9cd9 --- /dev/null +++ b/test/lib/test-helpers.rb @@ -0,0 +1,24 @@ +module TestHelpers + + # Runs gemma and returns true if successful + def gemma(opts) + system("./bin/gemma #{opts}") + end + + def read(fn, line=0) + count = 0 + File.open(fn, "r:utf-8").each_line { |ln| + return ln.chomp.split("\t") if count == line + count += 1 + } + end + + def expect(fn, list) + lines = File.read(fn).split("\n") # avoid this for large files + list.each do | l | + line,colnum,value = l + cols = lines[line].chomp.split("\t") + assert_equal value,cols[colnum] + end + end +end |