From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 9 Jul 2020 18:05:07 +0000 (-0400)
Subject: Add diff -timeout flag.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/701b1d8a25780ae77f6a4d05ef25103b7ea2cbd8?ds=sidebyside

Add diff -timeout flag.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---

diff --git a/diff.go b/diff.go
index 259c870e4b..2740104cf8 100644
--- a/diff.go
+++ b/diff.go
@@ -24,6 +24,7 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 	flags.SetOutput(stderr)
 	offset := flags.Int("offset", 0, "coordinate offset")
 	sequence := flags.String("sequence", "chr1", "sequence label")
+	timeout := flags.Duration("timeout", 0, "timeout (examples: \"1s\", \"1ms\")")
 	err = flags.Parse(args)
 	if err == flag.ErrHelp {
 		err = nil
@@ -63,7 +64,7 @@ func (cmd *diffFasta) RunCommand(prog string, args []string, stdin io.Reader, st
 		}
 	}
 
-	variants := hgvs.Diff(string(fasta[0]), string(fasta[1]))
+	variants := hgvs.Diff(string(fasta[0]), string(fasta[1]), *timeout)
 	if *offset != 0 {
 		for i := range variants {
 			variants[i].Position += *offset
diff --git a/hgvs/diff.go b/hgvs/diff.go
index e6e3b33647..7808259869 100644
--- a/hgvs/diff.go
+++ b/hgvs/diff.go
@@ -30,9 +30,13 @@ func (v *Variant) String() string {
 	}
 }
 
-func Diff(a, b string) []Variant {
+func Diff(a, b string, timeout time.Duration) []Variant {
 	dmp := diffmatchpatch.New()
-	diffs := cleanup(dmp.DiffCleanupEfficiency(dmp.DiffBisect(a, b, time.Time{})))
+	var deadline time.Time
+	if timeout > 0 {
+		deadline = time.Now().Add(timeout)
+	}
+	diffs := cleanup(dmp.DiffCleanupEfficiency(dmp.DiffBisect(a, b, deadline)))
 	pos := 1
 	var variants []Variant
 	for i := 0; i < len(diffs); i++ {
diff --git a/hgvs/diff_test.go b/hgvs/diff_test.go
index 6bad3116b2..9c04ea75b6 100644
--- a/hgvs/diff_test.go
+++ b/hgvs/diff_test.go
@@ -61,7 +61,7 @@ func (s *diffSuite) TestDiff(c *check.C) {
 	} {
 		c.Log(trial)
 		var vars []string
-		for _, v := range Diff(trial.a, trial.b) {
+		for _, v := range Diff(trial.a, trial.b, 0) {
 			vars = append(vars, v.String())
 		}
 		c.Check(vars, check.DeepEquals, trial.expect)