Adds the ability to read gzip-tar file for the taxonomy dump

pkg/obiutils/xopen_test.go

@@ -0,0 +1,148 @@
+package obiutils
+
+import (
+	"bufio"
+	"bytes"
+	"compress/gzip"
+	"fmt"
+	"io"
+	"os"
+	"strings"
+	"testing"
+
+	. "gopkg.in/check.v1"
+)
+
+func Test(t *testing.T) { TestingT(t) }
+
+type XopenTest struct{}
+
+var _ = Suite(&XopenTest{})
+
+func gzFromString(s string) string {
+	var c bytes.Buffer
+	gz := gzip.NewWriter(&c)
+	gz.Write([]byte(s))
+	return c.String()
+}
+
+var gzTests = []struct {
+	isGz bool
+	data string
+}{
+	{false, "asdf"},
+	{true, gzFromString("asdf")},
+}
+
+func (s *XopenTest) TestIsGzip(c *C) {
+	for _, t := range gzTests {
+		isGz, err := IsGzip(bufio.NewReader(strings.NewReader(t.data)))
+		c.Assert(err, IsNil)
+		c.Assert(t.isGz, Equals, isGz)
+	}
+}
+
+func (s *XopenTest) TestIsStdin(c *C) {
+	r := IsStdin()
+	c.Assert(r, Equals, false)
+}
+
+func (s *XopenTest) TestRopen(c *C) {
+	rdr, err := Ropen("-")
+	c.Assert(err, ErrorMatches, "stdin not detected")
+	c.Assert(rdr, IsNil)
+}
+
+func (s *XopenTest) TestWopen(c *C) {
+	for _, f := range []string{"t.gz", "t"} {
+		testString := "ASDF1234"
+		wtr, err := Wopen(f)
+		c.Assert(err, IsNil)
+		_, err = os.Stat(f)
+		c.Assert(err, IsNil)
+		c.Assert(wtr.wtr, NotNil)
+		fmt.Fprint(wtr, testString)
+		wtr.Close()
+
+		rdr, err := Ropen(f)
+		c.Assert(err, IsNil)
+
+		str, err := rdr.ReadString(99)
+		c.Assert(str, Equals, testString)
+		c.Assert(err, Equals, io.EOF)
+		str, _ = rdr.ReadString(99)
+		c.Assert(str, Equals, "")
+
+		rdr.Close()
+		os.Remove(f)
+	}
+}
+
+var httpTests = []struct {
+	url         string
+	expectError bool
+}{
+	{"https://raw.githubusercontent.com/brentp/xopen/master/README.md", false},
+	{"http://raw.githubusercontent.com/brentp/xopen/master/README.md", false},
+	{"http://raw.githubusercontent.com/brentp/xopen/master/BAD.md", true},
+}
+
+func (s *XopenTest) TestReadHttp(c *C) {
+	for _, t := range httpTests {
+		rdr, err := Ropen(t.url)
+		if !t.expectError {
+			c.Assert(err, IsNil)
+			v, err := rdr.ReadString(byte('\n'))
+			c.Assert(err, IsNil)
+			c.Assert(len(v), Not(Equals), 0)
+		} else {
+			c.Assert(err, ErrorMatches, ".* 404 Not Found")
+		}
+	}
+}
+
+// func (s *XopenTest) TestReadProcess(c *C) {
+// 	for _, cmd := range []string{"|ls -lh", "|ls", "|ls -lh xopen_test.go"} {
+// 		rdr, err := Ropen(cmd)
+// 		c.Assert(err, IsNil)
+// 		b := make([]byte, 1000)
+// 		_, err = rdr.Read(b)
+// 		if err != io.EOF {
+// 			c.Assert(err, IsNil)
+// 		}
+// 		lines := strings.Split(string(b), "\n")
+// 		has := false
+// 		for _, line := range lines {
+// 			if strings.Contains(line, "xopen_test.go") {
+// 				has = true
+// 			}
+// 		}
+// 		c.Assert(has, Equals, true)
+// 	}
+// }
+
+func (s *XopenTest) TestOpenStdout(c *C) {
+	w, err := Wopen("-")
+	c.Assert(err, IsNil)
+	c.Assert(w.wtr, Equals, os.Stdout)
+}
+
+func (s *XopenTest) TestOpenBadFile(c *C) {
+	r, err := Ropen("XXXXXXXXXXXXXXXXXXXXXXX")
+	c.Assert(r, IsNil)
+	c.Assert(err, ErrorMatches, ".*no such file.*")
+}
+
+func (s *XopenTest) TestExists(c *C) {
+	c.Assert(Exists("xopen.go"), Equals, true)
+	c.Assert(Exists("____xx"), Equals, false)
+}
+
+func (s *XopenTest) TestUser(c *C) {
+	c.Assert(Exists("~"), Equals, true)
+}
+
+func (s *XopenTest) TestExpand(c *C) {
+	_, err := ExpandUser("~baduser66")
+	c.Assert(err, Not(IsNil))
+}