Tests: started to replace the test system - moving from shell scripts to Ruby tests

5 files changed, 60 insertions, 13 deletions

diff --git a/Makefile b/Makefile
index fd0e55b..a671e46 100644
--- a/Makefile
+++ b/Makefile
@@ -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
diff --git a/guix.scm b/guix.scm
index 2eea555..188c842 100644
--- a/guix.scm
+++ b/guix.scm
@@ -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