Make sure FASTA file is written only after the jobfolder is created for the last time

Author: milot-mirdita

backend/src/backend/jobsystem.go

@@ -58,6 +58,19 @@ func (m *JobRequest) UnmarshalJSON(b []byte) error {
 	return errors.New("Invalid Job Type")
 }
 
+func (m *JobRequest) WriteSupportFiles(base string) error {
+	switch m.Type {
+	case JobSearch:
+		if j, ok := m.Job.(SearchJob); ok {
+			return j.WriteFasta(filepath.Join(base, "job.fasta"))
+		}
+		return errors.New("Invalid Job Type")
+	case JobIndex:
+		return nil
+	}
+	return nil
+}
+
 type Job interface {
 	Hash() Id
 	Rank() float64
@@ -176,6 +189,11 @@ func (j *RedisJobSystem) NewJob(request JobRequest, jobsbase string, allowResubm
 
 	t := Ticket{id, StatusUnknown}
 	err = j.Client.Watch(func(tx *redis.Tx) error {
+		err := request.WriteSupportFiles(workdir)
+		if err != nil {
+			return err
+		}
+
 		file, err := os.Create(filepath.Join(workdir, "job.json"))
 		if err != nil {
 			return err
@@ -425,6 +443,11 @@ func (j *LocalJobSystem) NewJob(request JobRequest, jobsbase string, allowResubm
 		}
 	}
 
+	err = request.WriteSupportFiles(workdir)
+	if err != nil {
+		return Ticket{id, StatusError}, err
+	}
+
 	file, err := os.Create(filepath.Join(workdir, "job.json"))
 	if err != nil {
 		return Ticket{id, StatusError}, err

backend/src/backend/searchjob.go

@@ -5,8 +5,6 @@ import (
 	"encoding/base64"
 	"errors"
 	"io/ioutil"
-	"os"
-	"path/filepath"
 	"sort"
 	"strings"
 )
@@ -44,6 +42,14 @@ func (r SearchJob) Rank() float64 {
 	return float64(r.Size * max(len(r.Database), 1))
 }
 
+func (r SearchJob) WriteFasta(path string) error {
+	err := ioutil.WriteFile(path, []byte(r.query), 0644)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func isIn(num string, params []string) int {
 	for i, param := range params {
 		if num == param {
@@ -75,29 +81,12 @@ func NewSearchJobRequest(query string, dbs []string, validDbs []Params, mode str
 		ids[i] = item.Display.Path
 	}
 
-	paths := make([]string, len(job.Database))
-	for i, item := range job.Database {
+	for _, item := range job.Database {
 		idx := isIn(item, ids)
 		if idx == -1 {
 			return request, errors.New("Selected databases are not valid!")
-		} else {
-			paths[i] = validDbs[idx].Display.Path
-		}
-	}
-
-	id := request.Id
-	path := filepath.Join(resultPath, string(id))
-	if _, err := os.Stat(path); os.IsNotExist(err) {
-		err = os.Mkdir(path, 0755)
-		if err != nil {
-			return request, err
 		}
 	}
 
-	err := ioutil.WriteFile(filepath.Join(path, "job.fasta"), []byte(query), 0644)
-	if err != nil {
-		return request, err
-	}
-
 	return request, nil
 }