-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #15 from ag-computational-bio/json_config
Changed job_configurator.go to use a JSON string as jobconfig.
- Loading branch information
Showing
3 changed files
with
25 additions
and
132 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,107 +1 @@ | ||
package scheduler | ||
|
||
import ( | ||
"testing" | ||
|
||
api "github.com/ag-computational-bio/bakta-web-api-go/bakta/web/api/proto/v1" | ||
db "github.com/ag-computational-bio/bakta-web-backend/database" | ||
) | ||
|
||
func Test_species_should_be_quoted(t *testing.T) { | ||
|
||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.Species = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --species \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
func Test_genus_should_be_quoted(t *testing.T) { | ||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.Genus = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --genus \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
func Test_strain_should_be_quoted(t *testing.T) { | ||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.Strain = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --strain \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
|
||
func Test_locus_should_be_quoted(t *testing.T) { | ||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.Locus = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --locus \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
func Test_locus_tag_should_be_quoted(t *testing.T) { | ||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.LocusTag = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --locus-tag \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
|
||
func Test_plasmid_tag_should_be_quoted(t *testing.T) { | ||
job := db.Job{} | ||
job.FastaKey = "irrelevant" | ||
|
||
config := api.JobConfig{} | ||
config.Plasmid = "test\"; rm -rf /" | ||
|
||
jobstring, _ := createBaktaConf(&job, &config) | ||
expected := "--tmp-dir /cache --threads 12 --prefix result -o /output --db /db/db --plasmid \"test\\\"; rm -rf /\" --gram ? /data/irrelevant" | ||
if jobstring != expected { | ||
t.Errorf("Expected '%v', Got '%v'", expected, jobstring) | ||
} | ||
} | ||
|
||
func TestQuote(t *testing.T) { | ||
testData := []struct { | ||
input string | ||
expected string | ||
}{ | ||
{"", "\"\""}, | ||
{"test", "\"test\""}, | ||
{"test\" rm -rf /", "\"test\\\" rm -rf /\""}, | ||
} | ||
for _, data := range testData { | ||
quoted := quote(data.input) | ||
if quoted != data.expected { | ||
t.Errorf("Expected '%v', Got '%v'", data.expected, quoted) | ||
} | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters