refactoring of the file chunck writing

pkg/obiformats/file_chunk_write.go

@@ -0,0 +1,61 @@
+package obiformats
+
+import (
+	"io"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+
+	log "github.com/sirupsen/logrus"
+)
+
+func WriteFileChunk(
+	writer io.WriteCloser,
+	toBeClosed bool) ChannelFileChunk {
+
+	obiiter.RegisterAPipe()
+	chunk_channel := make(ChannelFileChunk)
+
+	go func() {
+		nextToPrint := 0
+		toBePrinted := make(map[int]FileChunk)
+		for chunk := range chunk_channel {
+			if chunk.Order == nextToPrint {
+				log.Debugf("Writing chunk: %d of length %d bytes",
+					chunk.Order,
+					len(chunk.Raw.Bytes()))
+
+				n, err := writer.Write(chunk.Raw.Bytes())
+
+				if err != nil {
+					log.Fatalf("Cannot write chunk %d only %d bytes written on %d sended : %v",
+						chunk.Order, n, len(chunk.Raw.Bytes()), err)
+				}
+				nextToPrint++
+
+				chunk, ok := toBePrinted[nextToPrint]
+				for ok {
+					log.Debug("Writing buffered chunk : ", chunk.Order)
+					_, _ = writer.Write(chunk.Raw.Bytes())
+					delete(toBePrinted, nextToPrint)
+					nextToPrint++
+					chunk, ok = toBePrinted[nextToPrint]
+				}
+			} else {
+				toBePrinted[chunk.Order] = chunk
+			}
+		}
+
+		log.Debugf("FIle have to be closed : %v", toBeClosed)
+		if toBeClosed {
+			err := writer.Close()
+			if err != nil {
+				log.Fatalf("Cannot close the writer : %v", err)
+			}
+		}
+
+		obiiter.UnregisterPipe()
+		log.Debugf("The writer has been closed")
+	}()
+
+	return chunk_channel
+}