/
collection.go
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/
collection.go
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// Deals with parsing Collection responses from API Server.
package collection
import (
"flag"
"fmt"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
"git.curoverse.com/arvados.git/sdk/go/blockdigest"
"git.curoverse.com/arvados.git/sdk/go/logger"
"git.curoverse.com/arvados.git/sdk/go/manifest"
"git.curoverse.com/arvados.git/sdk/go/util"
"log"
"os"
"runtime/pprof"
"time"
)
var (
HeapProfileFilename string
)
// Collection representation
type Collection struct {
UUID string
OwnerUUID string
ReplicationLevel int
BlockDigestToSize map[blockdigest.BlockDigest]int
TotalSize int
}
// ReadCollections holds information about collections from API server
type ReadCollections struct {
ReadAllCollections bool
UUIDToCollection map[string]Collection
OwnerToCollectionSize map[string]int
BlockToDesiredReplication map[blockdigest.DigestWithSize]int
CollectionUUIDToIndex map[string]int
CollectionIndexToUUID []string
BlockToCollectionIndices map[blockdigest.DigestWithSize][]int
}
// GetCollectionsParams params
type GetCollectionsParams struct {
Client arvadosclient.ArvadosClient
Logger *logger.Logger
BatchSize int
}
// SdkCollectionInfo holds collection info from api
type SdkCollectionInfo struct {
UUID string `json:"uuid"`
OwnerUUID string `json:"owner_uuid"`
Redundancy int `json:"redundancy"`
ModifiedAt time.Time `json:"modified_at"`
ManifestText string `json:"manifest_text"`
}
// SdkCollectionList lists collections from api
type SdkCollectionList struct {
ItemsAvailable int `json:"items_available"`
Items []SdkCollectionInfo `json:"items"`
}
func init() {
flag.StringVar(&HeapProfileFilename,
"heap-profile",
"",
"File to write the heap profiles to. Leave blank to skip profiling.")
}
// WriteHeapProfile writes the heap profile to a file for later review.
// Since a file is expected to only contain a single heap profile this
// function overwrites the previously written profile, so it is safe
// to call multiple times in a single run.
// Otherwise we would see cumulative numbers as explained here:
// https://groups.google.com/d/msg/golang-nuts/ZyHciRglQYc/2nh4Ndu2fZcJ
func WriteHeapProfile() error {
if HeapProfileFilename != "" {
heapProfile, err := os.Create(HeapProfileFilename)
if err != nil {
return err
}
defer heapProfile.Close()
err = pprof.WriteHeapProfile(heapProfile)
return err
}
return nil
}
// GetCollectionsAndSummarize gets collections from api and summarizes
func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections, err error) {
results, err = GetCollections(params)
if err != nil {
return
}
results.Summarize(params.Logger)
log.Printf("Uuid to Size used: %v", results.OwnerToCollectionSize)
log.Printf("Read and processed %d collections",
len(results.UUIDToCollection))
// TODO(misha): Add a "readonly" flag. If we're in readonly mode,
// lots of behaviors can become warnings (and obviously we can't
// write anything).
// if !readCollections.ReadAllCollections {
// log.Fatalf("Did not read all collections")
// }
return
}
// GetCollections gets collections from api
func GetCollections(params GetCollectionsParams) (results ReadCollections, err error) {
if ¶ms.Client == nil {
err = fmt.Errorf("params.Client passed to GetCollections() should " +
"contain a valid ArvadosClient, but instead it is nil.")
return
}
fieldsWanted := []string{"manifest_text",
"owner_uuid",
"uuid",
"redundancy",
"modified_at"}
sdkParams := arvadosclient.Dict{
"select": fieldsWanted,
"order": []string{"modified_at ASC", "uuid ASC"},
"filters": [][]string{[]string{"modified_at", ">=", "1900-01-01T00:00:00Z"}},
"offset": 0}
if params.BatchSize > 0 {
sdkParams["limit"] = params.BatchSize
}
var defaultReplicationLevel int
{
var value interface{}
value, err = params.Client.Discovery("defaultCollectionReplication")
if err != nil {
return
}
defaultReplicationLevel = int(value.(float64))
if defaultReplicationLevel <= 0 {
err = fmt.Errorf("Default collection replication returned by arvados SDK "+
"should be a positive integer but instead it was %d.",
defaultReplicationLevel)
return
}
}
initialNumberOfCollectionsAvailable, err :=
util.NumberItemsAvailable(params.Client, "collections")
if err != nil {
return
}
// Include a 1% margin for collections added while we're reading so
// that we don't have to grow the map in most cases.
maxExpectedCollections := int(
float64(initialNumberOfCollectionsAvailable) * 1.01)
results.UUIDToCollection = make(map[string]Collection, maxExpectedCollections)
if params.Logger != nil {
params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
collectionInfo := logger.GetOrCreateMap(p, "collection_info")
collectionInfo["num_collections_at_start"] = initialNumberOfCollectionsAvailable
collectionInfo["batch_size"] = params.BatchSize
collectionInfo["default_replication_level"] = defaultReplicationLevel
})
}
// These values are just for getting the loop to run the first time,
// afterwards they'll be set to real values.
remainingCollections := 1
var totalCollections int
var previousTotalCollections int
for remainingCollections > 0 {
// We're still finding new collections
// Write the heap profile for examining memory usage
err = WriteHeapProfile()
if err != nil {
return
}
// Get next batch of collections.
var collections SdkCollectionList
err = params.Client.List("collections", sdkParams, &collections)
if err != nil {
return
}
batchCollections := len(collections.Items)
// We must always have at least one collection in the batch
if batchCollections < 1 {
err = fmt.Errorf("API query returned no collections for %+v", sdkParams)
return
}
// Update count of remaining collections
remainingCollections = collections.ItemsAvailable - sdkParams["offset"].(int) - batchCollections
// Process collection and update our date filter.
latestModificationDate, maxManifestSize, totalManifestSize, err := ProcessCollections(params.Logger,
collections.Items,
defaultReplicationLevel,
results.UUIDToCollection)
if err != nil {
return results, err
}
if sdkParams["filters"].([][]string)[0][2] != latestModificationDate.Format(time.RFC3339) {
sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339)
sdkParams["offset"] = 0
} else {
sdkParams["offset"] = sdkParams["offset"].(int) + batchCollections
}
// update counts
previousTotalCollections = totalCollections
totalCollections = len(results.UUIDToCollection)
log.Printf("%d collections read, %d (%d new) in last batch, "+
"%d remaining, "+
"%s latest modified date, %.0f %d %d avg,max,total manifest size",
totalCollections,
batchCollections,
totalCollections-previousTotalCollections,
remainingCollections,
sdkParams["filters"].([][]string)[0][2],
float32(totalManifestSize)/float32(totalCollections),
maxManifestSize, totalManifestSize)
if params.Logger != nil {
params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
collectionInfo := logger.GetOrCreateMap(p, "collection_info")
collectionInfo["collections_read"] = totalCollections
collectionInfo["latest_modified_date_seen"] = sdkParams["filters"].([][]string)[0][2]
collectionInfo["total_manifest_size"] = totalManifestSize
collectionInfo["max_manifest_size"] = maxManifestSize
})
}
}
// Make one final API request to verify that we have processed all collections available up to the latest modification date
var collections SdkCollectionList
sdkParams["filters"].([][]string)[0][1] = "<="
sdkParams["limit"] = 0
err = params.Client.List("collections", sdkParams, &collections)
if err != nil {
return
}
finalNumberOfCollectionsAvailable, err :=
util.NumberItemsAvailable(params.Client, "collections")
if err != nil {
return
}
if totalCollections < finalNumberOfCollectionsAvailable {
err = fmt.Errorf("API server indicates a total of %d collections "+
"available up to %v, but we only retrieved %d. "+
"Refusing to continue as this could indicate an "+
"otherwise undetected failure.",
finalNumberOfCollectionsAvailable,
sdkParams["filters"].([][]string)[0][2],
totalCollections)
return
}
// Write the heap profile for examining memory usage
err = WriteHeapProfile()
return
}
// StrCopy returns a newly allocated string.
// It is useful to copy slices so that the garbage collector can reuse
// the memory of the longer strings they came from.
func StrCopy(s string) string {
return string([]byte(s))
}
// ProcessCollections read from api server
func ProcessCollections(arvLogger *logger.Logger,
receivedCollections []SdkCollectionInfo,
defaultReplicationLevel int,
UUIDToCollection map[string]Collection,
) (
latestModificationDate time.Time,
maxManifestSize, totalManifestSize uint64,
err error,
) {
for _, sdkCollection := range receivedCollections {
collection := Collection{UUID: StrCopy(sdkCollection.UUID),
OwnerUUID: StrCopy(sdkCollection.OwnerUUID),
ReplicationLevel: sdkCollection.Redundancy,
BlockDigestToSize: make(map[blockdigest.BlockDigest]int)}
if sdkCollection.ModifiedAt.IsZero() {
err = fmt.Errorf(
"Arvados SDK collection returned with unexpected zero "+
"modification date. This probably means that either we failed to "+
"parse the modification date or the API server has changed how "+
"it returns modification dates: %+v",
collection)
return
}
if sdkCollection.ModifiedAt.After(latestModificationDate) {
latestModificationDate = sdkCollection.ModifiedAt
}
if collection.ReplicationLevel == 0 {
collection.ReplicationLevel = defaultReplicationLevel
}
manifest := manifest.Manifest{Text: sdkCollection.ManifestText}
manifestSize := uint64(len(sdkCollection.ManifestText))
if _, alreadySeen := UUIDToCollection[collection.UUID]; !alreadySeen {
totalManifestSize += manifestSize
}
if manifestSize > maxManifestSize {
maxManifestSize = manifestSize
}
blockChannel := manifest.BlockIterWithDuplicates()
for block := range blockChannel {
if storedSize, stored := collection.BlockDigestToSize[block.Digest]; stored && storedSize != block.Size {
log.Printf(
"Collection %s contains multiple sizes (%d and %d) for block %s",
collection.UUID,
storedSize,
block.Size,
block.Digest)
}
collection.BlockDigestToSize[block.Digest] = block.Size
}
if manifest.Err != nil {
err = manifest.Err
return
}
collection.TotalSize = 0
for _, size := range collection.BlockDigestToSize {
collection.TotalSize += size
}
UUIDToCollection[collection.UUID] = collection
// Clear out all the manifest strings that we don't need anymore.
// These hopefully form the bulk of our memory usage.
manifest.Text = ""
sdkCollection.ManifestText = ""
}
return
}
// Summarize the collections read
func (readCollections *ReadCollections) Summarize(arvLogger *logger.Logger) {
readCollections.OwnerToCollectionSize = make(map[string]int)
readCollections.BlockToDesiredReplication = make(map[blockdigest.DigestWithSize]int)
numCollections := len(readCollections.UUIDToCollection)
readCollections.CollectionUUIDToIndex = make(map[string]int, numCollections)
readCollections.CollectionIndexToUUID = make([]string, 0, numCollections)
readCollections.BlockToCollectionIndices = make(map[blockdigest.DigestWithSize][]int)
for _, coll := range readCollections.UUIDToCollection {
collectionIndex := len(readCollections.CollectionIndexToUUID)
readCollections.CollectionIndexToUUID =
append(readCollections.CollectionIndexToUUID, coll.UUID)
readCollections.CollectionUUIDToIndex[coll.UUID] = collectionIndex
readCollections.OwnerToCollectionSize[coll.OwnerUUID] =
readCollections.OwnerToCollectionSize[coll.OwnerUUID] + coll.TotalSize
for block, size := range coll.BlockDigestToSize {
locator := blockdigest.DigestWithSize{Digest: block, Size: uint32(size)}
readCollections.BlockToCollectionIndices[locator] =
append(readCollections.BlockToCollectionIndices[locator],
collectionIndex)
storedReplication := readCollections.BlockToDesiredReplication[locator]
if coll.ReplicationLevel > storedReplication {
readCollections.BlockToDesiredReplication[locator] =
coll.ReplicationLevel
}
}
}
if arvLogger != nil {
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
collectionInfo := logger.GetOrCreateMap(p, "collection_info")
// Since maps are shallow copied, we run a risk of concurrent
// updates here. By copying results.OwnerToCollectionSize into
// the log, we're assuming that it won't be updated.
collectionInfo["owner_to_collection_size"] =
readCollections.OwnerToCollectionSize
collectionInfo["distinct_blocks_named"] =
len(readCollections.BlockToDesiredReplication)
})
}
return
}