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Merge pull request #15 from ag-computational-bio/json_config
Changed job_configurator.go to use a JSON string as jobconfig.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,107 +1 @@ | ||
| package scheduler | ||
|
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| import ( | ||
| "testing" | ||
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| 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" | ||
| ) | ||
|
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| func Test_species_should_be_quoted(t *testing.T) { | ||
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| job := db.Job{} | ||
| job.FastaKey = "irrelevant" | ||
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| config := api.JobConfig{} | ||
| config.Species = "test\"; rm -rf /" | ||
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| 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" | ||
|
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| config := api.JobConfig{} | ||
| config.Genus = "test\"; rm -rf /" | ||
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| 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" | ||
|
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| config := api.JobConfig{} | ||
| config.Strain = "test\"; rm -rf /" | ||
|
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| 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) | ||
| } | ||
| } | ||
|
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||
| func Test_locus_should_be_quoted(t *testing.T) { | ||
| job := db.Job{} | ||
| job.FastaKey = "irrelevant" | ||
|
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| config := api.JobConfig{} | ||
| config.Locus = "test\"; rm -rf /" | ||
|
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| 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" | ||
|
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| config := api.JobConfig{} | ||
| config.LocusTag = "test\"; rm -rf /" | ||
|
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| 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) | ||
| } | ||
| } | ||
|
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| func Test_plasmid_tag_should_be_quoted(t *testing.T) { | ||
| job := db.Job{} | ||
| job.FastaKey = "irrelevant" | ||
|
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| config := api.JobConfig{} | ||
| config.Plasmid = "test\"; rm -rf /" | ||
|
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| 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) | ||
| } | ||
| } | ||
|
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| 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) | ||
| } | ||
| } | ||
| } |
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