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Propagate request trace through logs #123

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13 changes: 7 additions & 6 deletions backend/complexsearchjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ func (r ComplexSearchJob) WritePDB(path string) error {
return nil
}

func NewComplexSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string) (JobRequest, error) {
func NewComplexSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string, otelTrace OtelTraceContext) (JobRequest, error) {
job := ComplexSearchJob{
max(strings.Count(query, "HEADER"), 1),
dbs,
Expand All @@ -58,11 +58,12 @@ func NewComplexSearchJobRequest(query string, dbs []string, validDbs []Params, m
}

request := JobRequest{
job.Hash(),
StatusPending,
JobComplexSearch,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobComplexSearch,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

ids := make([]string, 0)
Expand Down
13 changes: 7 additions & 6 deletions backend/folddiscojob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ func (r FoldDiscoJob) WritePDB(path string) error {
return nil
}

func NewFoldDiscoJobRequest(query string, motif string, dbs []string, validDbs []Params, resultPath string, email string) (JobRequest, error) {
func NewFoldDiscoJobRequest(query string, motif string, dbs []string, validDbs []Params, resultPath string, email string, otelTrace OtelTraceContext) (JobRequest, error) {
job := FoldDiscoJob{
max(strings.Count(query, "HEADER"), 1),
dbs,
Expand All @@ -64,11 +64,12 @@ func NewFoldDiscoJobRequest(query string, motif string, dbs []string, validDbs [
}

request := JobRequest{
job.Hash(),
StatusPending,
JobFoldDisco,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobFoldDisco,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

ids := make([]string, 0)
Expand Down
12 changes: 7 additions & 5 deletions backend/foldmasonmsa.go
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Original file line number Diff line number Diff line change
Expand Up @@ -77,17 +77,19 @@ func NewFoldMasonMSAJobRequest(
fileNames []string,
gapOpen int64,
gapExtend int64,
otelTrace OtelTraceContext,
) (JobRequest, error) {
job := FoldMasonMSAJob{
queries,
fileNames,
}
request := JobRequest{
job.Hash(),
StatusPending,
JobFoldMasonMSA,
job,
"",
Id: job.Hash(),
Status: StatusPending,
Type: JobFoldMasonMSA,
Job: job,
Email: "",
OtelTrace: otelTrace.Ptr(),
}
return request, nil
}
13 changes: 7 additions & 6 deletions backend/indexjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -22,17 +22,18 @@ func (r IndexJob) Rank() float64 {
return float64(0)
}

func NewIndexJobRequest(path string, email string) (JobRequest, error) {
func NewIndexJobRequest(path string, email string, otelTrace OtelTraceContext) (JobRequest, error) {
job := IndexJob{
path,
}

request := JobRequest{
job.Hash(),
StatusPending,
JobIndex,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobIndex,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

return request, nil
Expand Down
13 changes: 7 additions & 6 deletions backend/interfacesearchjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ func (r InterfaceSearchJob) WritePDB(path string) error {
return nil
}

func NewInterfaceSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string) (JobRequest, error) {
func NewInterfaceSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string, otelTrace OtelTraceContext) (JobRequest, error) {
job := InterfaceSearchJob{
max(strings.Count(query, "HEADER"), 1),
dbs,
Expand All @@ -58,11 +58,12 @@ func NewInterfaceSearchJobRequest(query string, dbs []string, validDbs []Params,
}

request := JobRequest{
job.Hash(),
StatusPending,
JobInterfaceSearch,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobInterfaceSearch,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

ids := make([]string, 0)
Expand Down
18 changes: 13 additions & 5 deletions backend/jobsystem.go
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Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,19 @@ const (
)

type JobRequest struct {
Id Id `json:"id" validate:"required"`
Status Status `json:"status" validate:"required"`
Type JobType `json:"type" validate:"required"`
Job interface{} `json:"job" validate:"required"`
Email string `json:"email" validate:"omitempty,email"`
Id Id `json:"id" validate:"required"`
Status Status `json:"status" validate:"required"`
Type JobType `json:"type" validate:"required"`
Job interface{} `json:"job" validate:"required"`
Email string `json:"email" validate:"omitempty,email"`
OtelTrace *OtelTraceContext `json:"otelTrace,omitempty"`
}

func (r JobRequest) String() string {
if r.OtelTrace == nil {
return fmt.Sprintf("ticket=%s type=%s status=%s", r.Id, r.Type, r.Status)
}
return fmt.Sprintf("ticket=%s type=%s status=%s%s", r.Id, r.Type, r.Status, *r.OtelTrace)
}

type jobRequest JobRequest
Expand Down
13 changes: 7 additions & 6 deletions backend/msajob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ func (r MsaJob) WriteFasta(path string) error {
return nil
}

func NewMsaJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string) (JobRequest, error) {
func NewMsaJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, otelTrace OtelTraceContext) (JobRequest, error) {
job := MsaJob{
max(strings.Count(query, ">"), 1),
dbs,
Expand All @@ -52,11 +52,12 @@ func NewMsaJobRequest(query string, dbs []string, validDbs []Params, mode string
}

request := JobRequest{
job.Hash(),
StatusPending,
JobMsa,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobMsa,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

ids := make([]string, len(validDbs))
Expand Down
13 changes: 7 additions & 6 deletions backend/pairjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -34,19 +34,20 @@ func (r PairJob) WriteFasta(path string) error {
return nil
}

func NewPairJobRequest(query string, mode string, mail string) (JobRequest, error) {
func NewPairJobRequest(query string, mode string, mail string, otelTrace OtelTraceContext) (JobRequest, error) {
job := PairJob{
max(strings.Count(query, ">"), 1),
mode,
query,
}

request := JobRequest{
job.Hash(),
StatusPending,
JobPair,
job,
mail,
Id: job.Hash(),
Status: StatusPending,
Type: JobPair,
Job: job,
Email: mail,
OtelTrace: otelTrace.Ptr(),
}

return request, nil
Expand Down
13 changes: 7 additions & 6 deletions backend/searchjob.go
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ func isIn(num string, params []string) int {

var validTaxonFilter = regexp.MustCompile(`^[0-9]+(,!?[0-9]+)*$|^$`).MatchString

func NewSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string) (JobRequest, error) {
func NewSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string, otelTrace OtelTraceContext) (JobRequest, error) {
job := SearchJob{
max(strings.Count(query, ">"), 1),
dbs,
Expand All @@ -78,11 +78,12 @@ func NewSearchJobRequest(query string, dbs []string, validDbs []Params, mode str
}

request := JobRequest{
job.Hash(),
StatusPending,
JobSearch,
job,
email,
Id: job.Hash(),
Status: StatusPending,
Type: JobSearch,
Job: job,
Email: email,
OtelTrace: otelTrace.Ptr(),
}

ids := make([]string, len(validDbs))
Expand Down
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