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Fix multimer not reading queries correctly
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@milot-mirdita
milot-mirdita committed Nov 27, 2024
1 parent 21ecbe4 commit f9bc266
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Showing 2 changed files with 87 additions and 22 deletions.
78 changes: 67 additions & 11 deletions backend/alignment.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ import (
"bytes"
"compress/gzip"
"encoding/json"
"fmt"
"io"
"os"
"path/filepath"
Expand Down Expand Up @@ -212,7 +213,7 @@ func ReadAlignment[T any](reader io.Reader) ([]T, error) {
return results, nil
}

func ReadQuery(id Id, entries []int64, jobsbase string) ([]FastaEntry, error) {
func ReadQueryByIds(id Id, ids []int64, jobsbase string) ([]FastaEntry, error) {
base := filepath.Join(jobsbase, string(id))
query := filepath.Join(base, "query")
seqReader := Reader[uint32]{}
Expand All @@ -228,22 +229,65 @@ func ReadQuery(id Id, entries []int64, jobsbase string) ([]FastaEntry, error) {
return fasta, err
}

for _, entry := range entries {
sequence := strings.TrimSpace(seqReader.Data(entry))
for _, id := range ids {
sequence := strings.TrimSpace(seqReader.Data(id))
header := strings.TrimSpace(hdrReader.Data(id))
fasta = append(fasta, FastaEntry{header, sequence})
}
seqReader.Delete()
hdrReader.Delete()
return fasta, nil
}

func ReadQueryByKeys(id Id, keys []uint32, jobsbase string) ([]FastaEntry, error) {
base := filepath.Join(jobsbase, string(id))
query := filepath.Join(base, "query")
seqReader := Reader[uint32]{}
err := seqReader.Make(dbpaths(query))
fasta := make([]FastaEntry, 0)
if err != nil {
return fasta, err
}
hdrReader := Reader[uint32]{}
err = hdrReader.Make(dbpaths(query + "_h"))
if err != nil {
seqReader.Delete()
header := strings.TrimSpace(hdrReader.Data(entry))
hdrReader.Delete()
return fasta, err
}

for _, key := range keys {
id, found := seqReader.Id(key)
sequence := ""
if found {
sequence = strings.TrimSpace(seqReader.Data(id))
}
id, found = hdrReader.Id(key)
header := ""
if found {
header = strings.TrimSpace(hdrReader.Data(id))
}
fasta = append(fasta, FastaEntry{header, sequence})
}
seqReader.Delete()
hdrReader.Delete()
return fasta, nil
}

func ReadAlignments[T any](id Id, entries []int64, databases []string, jobsbase string) ([]SearchResult, error) {
func ReadAlignments[T any, U interface{ ~uint32 | ~int64 }](id Id, entries []U, databases []string, jobsbase string) ([]SearchResult, error) {
base := filepath.Join(jobsbase, string(id))
reader := Reader[uint32]{}
res := make([]SearchResult, 0)

var lookupByKey bool
switch any(entries[0]).(type) {
case uint32:
lookupByKey = true
case int64:
lookupByKey = false
default:
return nil, fmt.Errorf("unsupported type: %T", entries[0])
}

for _, db := range databases {
name := filepath.Join(filepath.Clean(base), "alis_"+db)
err := reader.Make(dbpaths(name))
Expand All @@ -252,7 +296,19 @@ func ReadAlignments[T any](id Id, entries []int64, databases []string, jobsbase
}
all := make([][]T, 0)
for _, entry := range entries {
data := strings.NewReader(reader.Data(entry))
var body string
if lookupByKey {
alnKey := any(entry).(uint32)
alnId, found := reader.Id(alnKey)
if !found {
reader.Delete()
return nil, fmt.Errorf("missing key: %T", alnKey)
}
body = reader.Data(alnId)
} else {
body = reader.Data(any(entry).(int64))
}
data := strings.NewReader(body)
results, err := ReadAlignment[T](data)
if err != nil {
reader.Delete()
Expand All @@ -272,15 +328,15 @@ func ReadAlignments[T any](id Id, entries []int64, databases []string, jobsbase
}

func Alignments(id Id, entry []int64, databases []string, jobsbase string) ([]SearchResult, error) {
return ReadAlignments[AlignmentEntry](id, entry, databases, jobsbase)
return ReadAlignments[AlignmentEntry, int64](id, entry, databases, jobsbase)
}

func FSAlignments(id Id, entry []int64, databases []string, jobsbase string) ([]SearchResult, error) {
return ReadAlignments[FoldseekAlignmentEntry](id, entry, databases, jobsbase)
return ReadAlignments[FoldseekAlignmentEntry, int64](id, entry, databases, jobsbase)
}

func ComplexAlignments(id Id, entry []int64, databases []string, jobsbase string) ([]SearchResult, error) {
return ReadAlignments[ComplexAlignmentEntry](id, entry, databases, jobsbase)
func ComplexAlignments(id Id, entry []uint32, databases []string, jobsbase string) ([]SearchResult, error) {
return ReadAlignments[ComplexAlignmentEntry, uint32](id, entry, databases, jobsbase)
}

func addFile(tw *tar.Writer, path string) error {
Expand Down
31 changes: 20 additions & 11 deletions backend/server.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -770,12 +770,11 @@ func server(jobsystem JobSystem, config ConfigRoot) {
var fasta []FastaEntry
var results []SearchResult
var mode string
var ids []int64
isFoldseek := false
switch job := request.Job.(type) {
case SearchJob:
mode = job.Mode
ids = []int64{id}
ids := []int64{id}
databases := job.Database
if database != "" {
if isIn(database, job.Database) == -1 {
Expand All @@ -789,9 +788,14 @@ func server(jobsystem JobSystem, config ConfigRoot) {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
fasta, err = ReadQueryByIds(ticket.Id, ids, config.Paths.Results)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
case StructureSearchJob:
mode = job.Mode
ids = []int64{id}
ids := []int64{id}
isFoldseek = true
databases := job.Database
if database != "" {
Expand All @@ -806,17 +810,22 @@ func server(jobsystem JobSystem, config ConfigRoot) {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
fasta, err = ReadQueryByIds(ticket.Id, ids, config.Paths.Results)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
case ComplexSearchJob:
mode = job.Mode
result, err := Lookup(ticket.Id, 0, math.MaxInt32, config.Paths.Results, false)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
ids = make([]int64, 0)
keys := make([]uint32, 0)
for _, lookup := range result.Lookup {
if lookup.Set == uint32(id) {
ids = append(ids, int64(lookup.Id))
keys = append(keys, uint32(lookup.Id))
}
}
isFoldseek = true
Expand All @@ -828,7 +837,12 @@ func server(jobsystem JobSystem, config ConfigRoot) {
}
databases = []string{database}
}
results, err = ComplexAlignments(ticket.Id, ids, databases, config.Paths.Results)
results, err = ComplexAlignments(ticket.Id, keys, databases, config.Paths.Results)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
fasta, err = ReadQueryByKeys(ticket.Id, keys, config.Paths.Results)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
Expand Down Expand Up @@ -918,11 +932,6 @@ func server(jobsystem JobSystem, config ConfigRoot) {
}
}

fasta, err = ReadQuery(ticket.Id, ids, config.Paths.Results)
if err != nil {
http.Error(w, err.Error(), http.StatusBadRequest)
return
}
type AlignmentModeResponse struct {
Queries []FastaEntry `json:"queries"`
Mode string `json:"mode"`
Expand Down

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