func FatalWithMessage(arvLogger *logger.Logger, message string) {
if arvLogger != nil {
arvLogger.FinalUpdate(func(p map[string]interface{}, e map[string]interface{}) {
p["FATAL"] = message
runInfo := logger.GetOrCreateMap(p, "run_info")
runInfo["finished_at"] = time.Now()
})
}
log.Fatalf(message)
}
func GetServerStatus(arvLogger *logger.Logger,
keepServer ServerAddress,
client http.Client) {
url := fmt.Sprintf("http://%s:%d/status.json",
keepServer.Host,
keepServer.Port)
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := make(map[string]interface{})
serverInfo["status_request_sent_at"] = now
serverInfo["host"] = keepServer.Host
serverInfo["port"] = keepServer.Port
keepInfo[keepServer.Uuid] = serverInfo
})
}
resp, err := client.Get(url)
if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error getting keep status from %s: %v", url, err))
} else if resp.StatusCode != 200 {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Received error code %d in response to request "+
"for %s status: %s",
resp.StatusCode, url, resp.Status))
}
var keepStatus map[string]interface{}
decoder := json.NewDecoder(resp.Body)
decoder.UseNumber()
err = decoder.Decode(&keepStatus)
if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error decoding keep status from %s: %v", url, err))
}
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := keepInfo[keepServer.Uuid].(map[string]interface{})
serverInfo["status_response_processed_at"] = now
serverInfo["status"] = keepStatus
})
}
}
// Summarize results from keep server
func (readServers *ReadServers) Summarize(arvLogger *logger.Logger) {
readServers.BlockReplicationCounts = make(map[int]int)
for _, infos := range readServers.BlockToServers {
replication := len(infos)
readServers.BlockReplicationCounts[replication]++
}
if arvLogger != nil {
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
keepInfo["distinct_blocks_stored"] = len(readServers.BlockToServers)
})
}
}
// Useful to call at the begining of execution to log info about the
// current run.
func LogRunInfo(arvLogger *logger.Logger) {
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
runInfo := logger.GetOrCreateMap(p, "run_info")
runInfo["started_at"] = now
runInfo["args"] = os.Args
hostname, err := os.Hostname()
if err != nil {
runInfo["hostname_error"] = err.Error()
} else {
runInfo["hostname"] = hostname
}
runInfo["pid"] = os.Getpid()
})
}
}
// 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
}
// WritePullLists writes each pull list to a file.
// The filename is based on the hostname.
//
// This is just a hack for prototyping, it is not expected to be used
// in production.
func WritePullLists(arvLogger *logger.Logger,
pullLists map[string]PullList,
dryRun bool) error {
r := strings.NewReplacer(":", ".")
for host, list := range pullLists {
if arvLogger != nil {
// We need a local variable because Update doesn't call our mutator func until later,
// when our list variable might have been reused by the next loop iteration.
host := host
listLen := len(list)
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
pullListInfo := logger.GetOrCreateMap(p, "pull_list_len")
pullListInfo[host] = listLen
})
}
if dryRun {
log.Print("dry run, not sending pull list to service %s with %d blocks", host, len(list))
continue
}
filename := fmt.Sprintf("pull_list.%s", r.Replace(RemoveProtocolPrefix(host)))
pullListFile, err := os.Create(filename)
if err != nil {
return err
}
defer pullListFile.Close()
enc := json.NewEncoder(pullListFile)
err = enc.Encode(list)
if err != nil {
return err
}
log.Printf("Wrote pull list to %s.", filename)
}
return nil
}
// CreateIndexRequest to the keep server
func CreateIndexRequest(arvLogger *logger.Logger,
keepServer ServerAddress,
arv arvadosclient.ArvadosClient) (req *http.Request, err error) {
url := fmt.Sprintf("http://%s:%d/index", keepServer.Host, keepServer.Port)
log.Println("About to fetch keep server contents from " + url)
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := keepInfo[keepServer.UUID].(map[string]interface{})
serverInfo["index_request_sent_at"] = now
})
}
req, err = http.NewRequest("GET", url, nil)
if err != nil {
return req, fmt.Errorf("Error building http request for %s: %v", url, err)
}
req.Header.Add("Authorization", "OAuth2 "+arv.ApiToken)
return req, err
}
func CreateIndexRequest(arvLogger *logger.Logger,
keepServer ServerAddress) (req *http.Request) {
url := fmt.Sprintf("http://%s:%d/index", keepServer.Host, keepServer.Port)
log.Println("About to fetch keep server contents from " + url)
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := keepInfo[keepServer.Uuid].(map[string]interface{})
serverInfo["index_request_sent_at"] = now
})
}
req, err := http.NewRequest("GET", url, nil)
if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error building http request for %s: %v", url, err))
}
req.Header.Add("Authorization",
fmt.Sprintf("OAuth2 %s", GetDataManagerToken(arvLogger)))
return
}
func ReadServerResponse(arvLogger *logger.Logger,
keepServer ServerAddress,
resp *http.Response) (response ServerResponse) {
if resp.StatusCode != 200 {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Received error code %d in response to request "+
"for %s index: %s",
resp.StatusCode, keepServer.String(), resp.Status))
}
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := keepInfo[keepServer.Uuid].(map[string]interface{})
serverInfo["index_response_received_at"] = now
})
}
response.Address = keepServer
response.Contents.BlockDigestToInfo =
make(map[blockdigest.DigestWithSize]BlockInfo)
reader := bufio.NewReader(resp.Body)
numLines, numDuplicates, numSizeDisagreements := 0, 0, 0
for {
numLines++
line, err := reader.ReadString('\n')
if err == io.EOF {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Index from %s truncated at line %d",
keepServer.String(), numLines))
} else if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error reading index response from %s at line %d: %v",
keepServer.String(), numLines, err))
}
if line == "\n" {
if _, err := reader.Peek(1); err == nil {
extra, _ := reader.ReadString('\n')
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Index from %s had trailing data at line %d after EOF marker: %s",
keepServer.String(), numLines+1, extra))
} else if err != io.EOF {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Index from %s had read error after EOF marker at line %d: %v",
keepServer.String(), numLines, err))
}
numLines--
break
}
blockInfo, err := parseBlockInfoFromIndexLine(line)
if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error parsing BlockInfo from index line "+
"received from %s: %v",
keepServer.String(),
err))
}
if storedBlock, ok := response.Contents.BlockDigestToInfo[blockInfo.Digest]; ok {
// This server returned multiple lines containing the same block digest.
numDuplicates += 1
// Keep the block that's newer.
if storedBlock.Mtime < blockInfo.Mtime {
response.Contents.BlockDigestToInfo[blockInfo.Digest] = blockInfo
}
} else {
response.Contents.BlockDigestToInfo[blockInfo.Digest] = blockInfo
}
}
log.Printf("%s index contained %d lines with %d duplicates with "+
"%d size disagreements",
keepServer.String(),
numLines,
numDuplicates,
numSizeDisagreements)
if arvLogger != nil {
now := time.Now()
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
serverInfo := keepInfo[keepServer.Uuid].(map[string]interface{})
serverInfo["processing_finished_at"] = now
serverInfo["lines_received"] = numLines
serverInfo["duplicates_seen"] = numDuplicates
serverInfo["size_disagreements_seen"] = numSizeDisagreements
})
}
resp.Body.Close()
return
}
func singlerun() error {
arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Fatalf("Error setting up arvados client %s", err.Error())
}
if is_admin, err := util.UserIsAdmin(arv); err != nil {
log.Fatalf("Error querying current arvados user %s", err.Error())
} else if !is_admin {
log.Fatalf("Current user is not an admin. Datamanager can only be run by admins.")
}
var arvLogger *logger.Logger
if logEventTypePrefix != "" {
arvLogger = logger.NewLogger(logger.LoggerParams{
Client: arv,
EventTypePrefix: logEventTypePrefix,
WriteInterval: time.Second * time.Duration(logFrequencySeconds)})
}
loggerutil.LogRunInfo(arvLogger)
if arvLogger != nil {
arvLogger.AddWriteHook(loggerutil.LogMemoryAlloc)
}
var (
dataFetcher summary.DataFetcher
readCollections collection.ReadCollections
keepServerInfo keep.ReadServers
)
if summary.ShouldReadData() {
dataFetcher = summary.ReadData
} else {
dataFetcher = BuildDataFetcher(arv)
}
dataFetcher(arvLogger, &readCollections, &keepServerInfo)
summary.MaybeWriteData(arvLogger, readCollections, keepServerInfo)
buckets := summary.BucketReplication(readCollections, keepServerInfo)
bucketCounts := buckets.Counts()
replicationSummary := buckets.SummarizeBuckets(readCollections)
replicationCounts := replicationSummary.ComputeCounts()
log.Printf("Blocks In Collections: %d, "+
"\nBlocks In Keep: %d.",
len(readCollections.BlockToDesiredReplication),
len(keepServerInfo.BlockToServers))
log.Println(replicationCounts.PrettyPrint())
log.Printf("Blocks Histogram:")
for _, rlbss := range bucketCounts {
log.Printf("%+v: %10d",
rlbss.Levels,
rlbss.Count)
}
kc, err := keepclient.MakeKeepClient(&arv)
if err != nil {
loggerutil.FatalWithMessage(arvLogger,
fmt.Sprintf("Error setting up keep client %s", err.Error()))
}
// Log that we're finished. We force the recording, since go will
// not wait for the write timer before exiting.
if arvLogger != nil {
defer arvLogger.FinalUpdate(func(p map[string]interface{}, e map[string]interface{}) {
summaryInfo := logger.GetOrCreateMap(p, "summary_info")
summaryInfo["block_replication_counts"] = bucketCounts
summaryInfo["replication_summary"] = replicationCounts
p["summary_info"] = summaryInfo
p["run_info"].(map[string]interface{})["finished_at"] = time.Now()
})
}
pullServers := summary.ComputePullServers(kc,
&keepServerInfo,
readCollections.BlockToDesiredReplication,
replicationSummary.UnderReplicatedBlocks)
pullLists := summary.BuildPullLists(pullServers)
trashLists, trashErr := summary.BuildTrashLists(kc,
&keepServerInfo,
replicationSummary.KeepBlocksNotInCollections)
summary.WritePullLists(arvLogger, pullLists)
if trashErr != nil {
return err
} else {
keep.SendTrashLists(keep.GetDataManagerToken(arvLogger), kc, trashLists)
}
return nil
}
// SendTrashLists to trash queue
func SendTrashLists(arvLogger *logger.Logger, kc *keepclient.KeepClient, spl map[string]TrashList, dryRun bool) (errs []error) {
count := 0
barrier := make(chan error)
client := kc.Client
for url, v := range spl {
if arvLogger != nil {
// We need a local variable because Update doesn't call our mutator func until later,
// when our list variable might have been reused by the next loop iteration.
url := url
trashLen := len(v)
arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
trashListInfo := logger.GetOrCreateMap(p, "trash_list_len")
trashListInfo[url] = trashLen
})
}
if dryRun {
log.Printf("dry run, not sending trash list to service %s with %d blocks", url, len(v))
continue
}
count++
log.Printf("Sending trash list to %v", url)
go (func(url string, v TrashList) {
pipeReader, pipeWriter := io.Pipe()
go (func() {
enc := json.NewEncoder(pipeWriter)
enc.Encode(v)
pipeWriter.Close()
})()
req, err := http.NewRequest("PUT", fmt.Sprintf("%s/trash", url), pipeReader)
if err != nil {
log.Printf("Error creating trash list request for %v error: %v", url, err.Error())
barrier <- err
return
}
req.Header.Add("Authorization", "OAuth2 "+kc.Arvados.ApiToken)
// Make the request
var resp *http.Response
if resp, err = client.Do(req); err != nil {
log.Printf("Error sending trash list to %v error: %v", url, err.Error())
barrier <- err
return
}
log.Printf("Sent trash list to %v: response was HTTP %v", url, resp.Status)
io.Copy(ioutil.Discard, resp.Body)
resp.Body.Close()
if resp.StatusCode != 200 {
barrier <- errors.New(fmt.Sprintf("Got HTTP code %v", resp.StatusCode))
} else {
barrier <- nil
}
})(url, v)
}
for i := 0; i < count; i++ {
b := <-barrier
if b != nil {
errs = append(errs, b)
}
}
return errs
}