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/
importer.go
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/
importer.go
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// Copyright 2018 Mark Wardle / Eldrix Ltd
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package terminology
import (
"context"
"fmt"
"runtime"
"sync"
"sync/atomic"
"time"
"github.com/wardle/go-terminology/snomed"
)
// Importer manages the import of SNOMED CT components from the filesystem
type Importer struct {
storer Storer
snomed.ImportChannels
batchSize int // size of each batch.
threads int // number of threads importing a type of component
verbose bool
nconcepts, ndescriptions, nrelationships, nrefsets int32
}
// Storer defines the behaviour of a service that can accept a batch of SNOMED components for storage.
type Storer interface {
Put(context context.Context, components interface{}) error
}
// NoopStorer is a no-op storer, which does nothing with the results. Useful for profiling.
type NoopStorer struct{}
// Put a batch of SNOMED components, which is a no-op.
func (ns *NoopStorer) Put(context context.Context, components interface{}) error {
return nil
}
// NewImporter creates a new Importer
func NewImporter(storer Storer, batchSize int, threads int, verbose bool) *Importer {
if batchSize == 0 {
batchSize = 500
}
if threads == 0 {
threads = runtime.NumCPU() / 4
if threads == 0 {
threads = 1
}
}
importer := &Importer{
storer: storer,
verbose: verbose,
batchSize: batchSize,
threads: threads,
}
return importer
}
// Import starts the import process
func (im *Importer) Import(ctx context.Context, root string) {
start := time.Now()
im.ImportChannels = *snomed.Import(ctx, root, im.batchSize)
var conceptsWg, descriptionsWg, relationshipsWg, refsetsWg sync.WaitGroup
done := make(chan struct{})
if im.verbose {
go func() {
for {
for _, r := range `-\|/` {
select {
case <-ctx.Done():
return
case <-done:
return
default:
im.progress(start, string(r)+" importing")
time.Sleep(1 * time.Second)
}
}
}
}()
}
for i := 0; i < im.threads; i++ {
conceptsWg.Add(1)
go func() {
defer conceptsWg.Done()
im.importConcepts(ctx, im.Concepts)
}()
}
for i := 0; i < im.threads; i++ {
descriptionsWg.Add(1)
go func() {
defer descriptionsWg.Done()
im.importDescriptions(ctx, im.Descriptions)
}()
}
for i := 0; i < im.threads; i++ {
relationshipsWg.Add(1)
go func() {
defer relationshipsWg.Done()
im.importRelationships(ctx, im.Relationships)
}()
}
for i := 0; i < im.threads; i++ {
refsetsWg.Add(1)
go func() {
defer refsetsWg.Done()
im.importRefsets(ctx, im.Refsets)
}()
}
conceptsWg.Wait()
descriptionsWg.Wait()
relationshipsWg.Wait()
refsetsWg.Wait()
close(done)
im.progress(start, "Import complete. Processed: ")
}
func (im *Importer) progress(start time.Time, prefix string) {
fmt.Printf("\r%s: %s: %d concepts, %d descriptions, %d relationships and %d refset items...",
prefix,
time.Since(start),
atomic.LoadInt32(&im.nconcepts),
atomic.LoadInt32(&im.ndescriptions),
atomic.LoadInt32(&im.nrelationships),
atomic.LoadInt32(&im.nrefsets))
}
func (im *Importer) importConcepts(ctx context.Context, cc <-chan []*snomed.Concept) {
for {
select {
case <-ctx.Done():
return
case batch := <-cc:
if batch == nil {
return
}
err := im.storer.Put(ctx, batch)
if err != nil {
panic(err)
}
atomic.AddInt32(&im.nconcepts, int32(len(batch)))
}
}
}
func (im *Importer) importDescriptions(ctx context.Context, dd <-chan []*snomed.Description) {
for {
select {
case <-ctx.Done():
return
case batch := <-dd:
if batch == nil {
return
}
err := im.storer.Put(ctx, batch)
if err != nil {
panic(err)
}
atomic.AddInt32(&im.ndescriptions, int32(len(batch)))
}
}
}
func (im *Importer) importRelationships(ctx context.Context, rels <-chan []*snomed.Relationship) {
for {
select {
case <-ctx.Done():
return
case batch := <-rels:
if batch == nil {
return
}
err := im.storer.Put(ctx, batch)
if err != nil {
panic(err)
}
atomic.AddInt32(&im.nrelationships, int32(len(batch)))
}
}
}
func (im *Importer) importRefsets(ctx context.Context, refsets <-chan []*snomed.ReferenceSetItem) {
for {
select {
case <-ctx.Done():
return
case batch := <-refsets:
if batch == nil {
return
}
err := im.storer.Put(ctx, batch)
if err != nil {
panic(err)
}
atomic.AddInt32(&im.nrefsets, int32(len(batch)))
}
}
}