add bam header endpoint.

Co-authored-by: kostas-kou <[email protected]> Co-authored-by: pahatz <[email protected]>
neicnordic · Nov 1, 2023 · 4e683f6 · 4e683f6
1 parent c2c3332
commit 4e683f6
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Showing 5 changed files with 30 additions and 0 deletions.
diff --git a/api/api.go b/api/api.go
@@ -43,6 +43,7 @@ func Setup() *http.Server {
 	router.HEAD("/s3/*path", SelectedMiddleware(), s3.Download)
 	router.GET("/s3-encrypted/*path", SelectedMiddleware(), s3.Download)
 	router.GET("/health", healthResponse)
+	router.GET("/header/*path", SelectedMiddleware(), s3.Download)
 
 	// Configure TLS settings
 	log.Info("(3/5) Configuring TLS")

diff --git a/api/s3/s3.go b/api/s3/s3.go
@@ -222,6 +222,9 @@ func GetObject(c *gin.Context) {
 
 	// set the fileID so that download knows what file to download
 	c.Params = append(c.Params, gin.Param{Key: "fileid", Value: fileInfo.FileID})
+	if strings.Contains(c.Request.URL.String(), "header") {
+		c.Params = append(c.Params, gin.Param{Key: "type", Value: "header"})
+	}
 
 	// Download the file
 	sda.Download(c)

diff --git a/api/sda/sda.go b/api/sda/sda.go
@@ -11,6 +11,7 @@ import (
 	"strings"
 	"time"
 
+	"github.com/biogo/hts/bam"
 	"github.com/gin-gonic/gin"
 	"github.com/neicnordic/crypt4gh/model/headers"
 	"github.com/neicnordic/crypt4gh/streaming"
@@ -220,7 +221,23 @@ func Download(c *gin.Context) {
 			return
 		}
 	}
+	if c.Param("type") == "header" {
+		bamReader, err := bam.NewReader(fileStream, 0)
+		if err != nil {
+			log.Fatalln(err)
+		}
+		defer bamReader.Close()
+		reader := bamReader
+		h := reader.Header()
+		var r io.Reader
+		buf := new(bytes.Buffer)
+		fmt.Fprint(buf, h)
+		r = buf
+		sendStream(c.Writer, r)
 
+		return
+
+	}
 	sendStream(c.Writer, fileStream)
 }
 

diff --git a/go.mod b/go.mod
@@ -5,6 +5,7 @@ go 1.20
 require (
 	github.com/DATA-DOG/go-sqlmock v1.5.0
 	github.com/aws/aws-sdk-go v1.46.2
+	github.com/biogo/hts v1.4.4
 	github.com/dgraph-io/ristretto v0.1.1
 	github.com/gin-gonic/gin v1.9.1
 	github.com/google/uuid v1.3.1

diff --git a/go.sum b/go.sum
@@ -45,6 +45,10 @@ github.com/DATA-DOG/go-sqlmock v1.5.0/go.mod h1:f/Ixk793poVmq4qj/V1dPUg2JEAKC73Q
 github.com/aws/aws-sdk-go v1.33.0/go.mod h1:5zCpMtNQVjRREroY7sYe8lOMRSxkhG6MZveU8YkpAk0=
 github.com/aws/aws-sdk-go v1.46.2 h1:XZbOmjtN1VCfEtQq7QNFsbxIqO+bB+bRhiOBjp6AzWc=
 github.com/aws/aws-sdk-go v1.46.2/go.mod h1:aVsgQcEevwlmQ7qHE9I3h+dtQgpqhFB+i8Phjh7fkwI=
+github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1 h1:LAHY5JxqhOgJDeDBGKsQ4300qd3sG8C0j5CQS8gD+Kw=
+github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1/go.mod h1:fwtxkutinkQcME9Zlywh66T0jZLLjgrwSLY2WxH2N3U=
+github.com/biogo/hts v1.4.4 h1:Z+TminqAKRE/t6nyy5PwI/DL90kdew4GpghB+QdjjFk=
+github.com/biogo/hts v1.4.4/go.mod h1:AfPn4uJQ2zxi04Q/4vccdmCX16W+IsHXVguPsdh4HE4=
 github.com/bytedance/sonic v1.5.0/go.mod h1:ED5hyg4y6t3/9Ku1R6dU/4KyJ48DZ4jPhfY1O2AihPM=
 github.com/bytedance/sonic v1.10.0-rc/go.mod h1:ElCzW+ufi8qKqNW0FY314xriJhyJhuoJ3gFZdAHF7NM=
 github.com/bytedance/sonic v1.10.0 h1:qtNZduETEIWJVIyDl01BeNxur2rW9OwTQ/yBqFRkKEk=
@@ -194,8 +198,10 @@ github.com/klauspost/cpuid/v2 v2.0.9/go.mod h1:FInQzS24/EEf25PyTYn52gqo7WaD8xa02
 github.com/klauspost/cpuid/v2 v2.2.5 h1:0E5MSMDEoAulmXNFquVs//DdoomxaoTY1kUhbc/qbZg=
 github.com/klauspost/cpuid/v2 v2.2.5/go.mod h1:Lcz8mBdAVJIBVzewtcLocK12l3Y+JytZYpaMropDUws=
 github.com/knz/go-libedit v1.10.1/go.mod h1:MZTVkCWyz0oBc7JOWP3wNAzd002ZbM/5hgShxwh4x8M=
+github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
 github.com/kr/fs v0.1.0/go.mod h1:FFnZGqtBN9Gxj7eW1uZ42v5BccTP0vu6NEaFoC2HwRg=
 github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
+github.com/kr/pretty v0.2.0/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
 github.com/kr/pretty v0.3.1 h1:flRD4NNwYAUpkphVc1HcthR4KEIFJ65n8Mw5qdRn3LE=
 github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
 github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
@@ -284,6 +290,7 @@ github.com/twitchyliquid64/golang-asm v0.15.1 h1:SU5vSMR7hnwNxj24w34ZyCi/FmDZTkS
 github.com/twitchyliquid64/golang-asm v0.15.1/go.mod h1:a1lVb/DtPvCB8fslRZhAngC2+aY1QWCk3Cedj/Gdt08=
 github.com/ugorji/go/codec v1.2.11 h1:BMaWp1Bb6fHwEtbplGBGJ498wD+LKlNSl25MjdZY4dU=
 github.com/ugorji/go/codec v1.2.11/go.mod h1:UNopzCgEMSXjBc6AOMqYvWC1ktqTAfzJZUZgYf6w6lg=
+github.com/ulikunitz/xz v0.5.10/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
 github.com/yuin/goldmark v1.1.25/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.32/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
@@ -629,6 +636,7 @@ google.golang.org/protobuf v1.31.0/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqw
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
+gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
 gopkg.in/ini.v1 v1.67.0 h1:Dgnx+6+nfE+IfzjUEISNeydPJh9AXNNsWbGP9KzCsOA=
 gopkg.in/ini.v1 v1.67.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=