3408: Merge branch 'master' into 3408-production-datamanager

diff --git a/doc/_includes/_example_sdk_go.liquid b/doc/_includes/_example_sdk_go.liquid
index 08124e661066f43da6fb1637a55d2f73ecb4b4eb..e205c59670550edcbee4c64fa620248e9d390979 100644 (file)
--- a/doc/_includes/_example_sdk_go.liquid
+++ b/doc/_includes/_example_sdk_go.liquid
@@ -31,6 +31,9 @@ func main() {
        //
 
        type user struct {
+               // Remember to start each field name with a capital letter,
+               // otherwise it won't get populated by the arvados client because
+               // the field will be invisible to it.
                Uuid     string `json:"uuid"`
                FullName string `json:"full_name"`
        }

diff --git a/sdk/go/blockdigest/blockdigest.go b/sdk/go/blockdigest/blockdigest.go
new file mode 100644 (file)
index 0000000..9b818d3
--- /dev/null
+++ b/sdk/go/blockdigest/blockdigest.go
@@ -0,0 +1,49 @@
+/* Stores a Block Locator Digest compactly. Can be used as a map key. */
+
+package blockdigest
+
+import (
+       "fmt"
+       "log"
+       "strconv"
+)
+
+// Stores a Block Locator Digest compactly, up to 128 bits.
+// Can be used as a map key.
+type BlockDigest struct {
+       h uint64
+       l uint64
+}
+
+func (d BlockDigest) String() string {
+       return fmt.Sprintf("%016x%016x", d.h, d.l)
+}
+
+// Will create a new BlockDigest unless an error is encountered.
+func FromString(s string) (dig BlockDigest, err error) {
+       if len(s) != 32 {
+               err = fmt.Errorf("Block digest should be exactly 32 characters but this one is %d: %s", len(s), s)
+               return
+       }
+
+       var d BlockDigest
+       d.h, err = strconv.ParseUint(s[:16], 16, 64)
+       if err != nil {
+               return
+       }
+       d.l, err = strconv.ParseUint(s[16:], 16, 64)
+       if err != nil {
+               return
+       }
+       dig = d
+       return
+}
+
+// Will fatal with the error if an error is encountered
+func AssertFromString(s string) BlockDigest {
+       d, err := FromString(s)
+       if err != nil {
+               log.Fatalf("Error creating BlockDigest from %s: %v", s, err)
+       }
+       return d
+}

diff --git a/sdk/go/blockdigest/blockdigest_test.go b/sdk/go/blockdigest/blockdigest_test.go
new file mode 100644 (file)
index 0000000..068a138
--- /dev/null
+++ b/sdk/go/blockdigest/blockdigest_test.go
@@ -0,0 +1,79 @@
+package blockdigest
+
+import (
+       "fmt"
+       "strings"
+       "testing"
+)
+
+func expectValidDigestString(t *testing.T, s string) {
+       bd, err := FromString(s)
+       if err != nil {
+               t.Fatalf("Expected %s to produce a valid BlockDigest but instead got error: %v", s, err)
+       }
+
+       expected := strings.ToLower(s)
+               
+       if expected != bd.String() {
+               t.Fatalf("Expected %s to be returned by FromString(%s).String() but instead we received %s", expected, s, bd.String())
+       }
+}
+
+func expectInvalidDigestString(t *testing.T, s string) {
+       _, err := FromString(s)
+       if err == nil {
+               t.Fatalf("Expected %s to be an invalid BlockDigest, but did not receive an error", s)
+       }
+}
+
+func TestValidDigestStrings(t *testing.T) {
+       expectValidDigestString(t, "01234567890123456789abcdefabcdef")
+       expectValidDigestString(t, "01234567890123456789ABCDEFABCDEF")
+       expectValidDigestString(t, "01234567890123456789AbCdEfaBcDeF")
+}
+
+func TestInvalidDigestStrings(t *testing.T) {
+       expectInvalidDigestString(t, "01234567890123456789abcdefabcdeg")
+       expectInvalidDigestString(t, "01234567890123456789abcdefabcde")
+       expectInvalidDigestString(t, "01234567890123456789abcdefabcdefa")
+       expectInvalidDigestString(t, "g1234567890123456789abcdefabcdef")
+}
+
+func TestBlockDigestWorksAsMapKey(t *testing.T) {
+       m := make(map[BlockDigest]int)
+       bd := AssertFromString("01234567890123456789abcdefabcdef")
+       m[bd] = 5
+}
+
+func TestBlockDigestGetsPrettyPrintedByPrintf(t *testing.T) {
+       input := "01234567890123456789abcdefabcdef"
+       prettyPrinted := fmt.Sprintf("%v", AssertFromString(input))
+       if prettyPrinted != input {
+               t.Fatalf("Expected blockDigest produced from \"%s\" to be printed as " +
+                       "\"%s\", but instead it was printed as %s",
+                       input, input, prettyPrinted)
+       }
+}
+
+func TestBlockDigestGetsPrettyPrintedByPrintfInNestedStructs(t *testing.T) {
+       input := "01234567890123456789abcdefabcdef"
+       value := 42
+       nested := struct{
+               // Fun trivia fact: If this field was called "digest" instead of
+               // "Digest", then it would not be exported and String() would
+               // never get called on it and our output would look very
+               // different.
+               Digest BlockDigest
+               value int
+       }{
+               AssertFromString(input),
+               value,
+       }
+       prettyPrinted := fmt.Sprintf("%+v", nested)
+       expected := fmt.Sprintf("{Digest:%s value:%d}", input, value)
+       if prettyPrinted != expected {
+               t.Fatalf("Expected blockDigest produced from \"%s\" to be printed as " +
+                       "\"%s\", but instead it was printed as %s",
+                       input, expected, prettyPrinted)
+       }
+}

diff --git a/sdk/go/logger/logger.go b/sdk/go/logger/logger.go
new file mode 100644 (file)
index 0000000..e7bc8d1
--- /dev/null
+++ b/sdk/go/logger/logger.go
@@ -0,0 +1,194 @@
+// Logger periodically writes a log to the Arvados SDK.
+//
+// This package is useful for maintaining a log object that is updated
+// over time. This log object will be periodically written to the log,
+// as specified by WriteInterval in the Params.
+//
+// This package is safe for concurrent use as long as:
+// The maps passed to a LogMutator are not accessed outside of the
+// LogMutator
+//
+// Usage:
+// arvLogger := logger.NewLogger(params)
+// arvLogger.Update(func(properties map[string]interface{},
+//     entry map[string]interface{}) {
+//   // Modifiy properties and entry however you want
+//   // properties is a shortcut for entry["properties"].(map[string]interface{})
+//   // properties can take any values you want to give it,
+//   // entry will only take the fields listed at http://doc.arvados.org/api/schema/Log.html
+// })
+package logger
+
+import (
+       "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+       "log"
+       "time"
+)
+
+const (
+       startSuffix   = "-start"
+       partialSuffix = "-partial"
+       finalSuffix   = "-final"
+)
+
+type LoggerParams struct {
+       Client          arvadosclient.ArvadosClient // The client we use to write log entries
+       EventTypePrefix string                      // The prefix we use for the event type in the log entry
+       WriteInterval   time.Duration               // Wait at least this long between log writes
+}
+
+// A LogMutator is a function which modifies the log entry.
+// It takes two maps as arguments, properties is the first and entry
+// is the second
+// properties is a shortcut for entry["properties"].(map[string]interface{})
+// properties can take any values you want to give it.
+// entry will only take the fields listed at http://doc.arvados.org/api/schema/Log.html
+// properties and entry are only safe to access inside the LogMutator,
+// they should not be stored anywhere, otherwise you'll risk
+// concurrent access.
+type LogMutator func(map[string]interface{}, map[string]interface{})
+
+// A Logger is used to build up a log entry over time and write every
+// version of it.
+type Logger struct {
+       // The data we write
+       data       map[string]interface{} // The entire map that we give to the api
+       entry      map[string]interface{} // Convenience shortcut into data
+       properties map[string]interface{} // Convenience shortcut into data
+
+       params LoggerParams // Parameters we were given
+
+       // Variables to coordinate updating and writing.
+       modified    bool            // Has this data been modified since the last write?
+       workToDo    chan LogMutator // Work to do in the worker thread.
+       writeTicker *time.Ticker    // On each tick we write the log data to arvados, if it has been modified.
+       hasWritten  bool            // Whether we've written at all yet.
+
+       writeHooks []LogMutator // Mutators we call before each write.
+}
+
+// Create a new logger based on the specified parameters.
+func NewLogger(params LoggerParams) *Logger {
+       // sanity check parameters
+       if &params.Client == nil {
+               log.Fatal("Nil arvados client in LoggerParams passed in to NewLogger()")
+       }
+       if params.EventTypePrefix == "" {
+               log.Fatal("Empty event type prefix in LoggerParams passed in to NewLogger()")
+       }
+
+       l := &Logger{data: make(map[string]interface{}),
+               params: params}
+       l.entry = make(map[string]interface{})
+       l.data["log"] = l.entry
+       l.properties = make(map[string]interface{})
+       l.entry["properties"] = l.properties
+
+       l.workToDo = make(chan LogMutator, 10)
+       l.writeTicker = time.NewTicker(params.WriteInterval)
+
+       // Start the worker goroutine.
+       go l.work()
+
+       return l
+}
+
+// Exported functions will be called from other goroutines, therefore
+// all they are allowed to do is enqueue work to be done in the worker
+// goroutine.
+
+// Enqueues an update. This will happen in another goroutine after
+// this method returns.
+func (l *Logger) Update(mutator LogMutator) {
+       l.workToDo <- mutator
+}
+
+// Similar to Update(), but writes the log entry as soon as possible
+// (ignoring MinimumWriteInterval) and blocks until the entry has been
+// written. This is useful if you know that you're about to quit
+// (e.g. if you discovered a fatal error, or you're finished), since
+// go will not wait for timers (including the pending write timer) to
+// go off before exiting.
+func (l *Logger) FinalUpdate(mutator LogMutator) {
+       // Block on this channel until everything finishes
+       done := make(chan bool)
+
+       // TODO(misha): Consider not accepting any future updates somehow,
+       // since they won't get written if they come in after this.
+
+       // Stop the periodic write ticker. We'll perform the final write
+       // before returning from this function.
+       l.workToDo <- func(p map[string]interface{}, e map[string]interface{}) {
+               l.writeTicker.Stop()
+       }
+
+       // Apply the final update
+       l.workToDo <- mutator
+
+       // Perform the final write and signal that we can return.
+       l.workToDo <- func(p map[string]interface{}, e map[string]interface{}) {
+               l.write(true)
+               done <- true
+       }
+
+       // Wait until we've performed the write.
+       <-done
+}
+
+// Adds a hook which will be called every time this logger writes an entry.
+func (l *Logger) AddWriteHook(hook LogMutator) {
+       // We do the work in a LogMutator so that it happens in the worker
+       // goroutine.
+       l.workToDo <- func(p map[string]interface{}, e map[string]interface{}) {
+               l.writeHooks = append(l.writeHooks, hook)
+       }
+}
+
+// The worker loop
+func (l *Logger) work() {
+       for {
+               select {
+               case <-l.writeTicker.C:
+                       if l.modified {
+                               l.write(false)
+                               l.modified = false
+                       }
+               case mutator := <-l.workToDo:
+                       mutator(l.properties, l.entry)
+                       l.modified = true
+               }
+       }
+}
+
+// Actually writes the log entry.
+func (l *Logger) write(isFinal bool) {
+
+       // Run all our hooks
+       for _, hook := range l.writeHooks {
+               hook(l.properties, l.entry)
+       }
+
+       // Update the event type.
+       if isFinal {
+               l.entry["event_type"] = l.params.EventTypePrefix + finalSuffix
+       } else if l.hasWritten {
+               l.entry["event_type"] = l.params.EventTypePrefix + partialSuffix
+       } else {
+               l.entry["event_type"] = l.params.EventTypePrefix + startSuffix
+       }
+       l.hasWritten = true
+
+       // Write the log entry.
+       // This is a network write and will take a while, which is bad
+       // because we're blocking all the other work on this goroutine.
+       //
+       // TODO(misha): Consider rewriting this so that we can encode l.data
+       // into a string, and then perform the actual write in another
+       // routine. This will be tricky and will require support in the
+       // client.
+       err := l.params.Client.Create("logs", l.data, nil)
+       if err != nil {
+               log.Printf("Attempted to log: %v", l.data)
+               log.Fatalf("Received error writing log: %v", err)
+       }
+}

diff --git a/sdk/go/logger/main/testlogger.go b/sdk/go/logger/main/testlogger.go
new file mode 100644 (file)
index 0000000..6cd7dfb
--- /dev/null
+++ b/sdk/go/logger/main/testlogger.go
@@ -0,0 +1,29 @@
+// This binary tests the logger package.
+// It's not a standard unit test. Instead it writes to the actual log
+// and you have to clean up after it.
+
+package main
+
+import (
+       "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+       "git.curoverse.com/arvados.git/sdk/go/logger"
+       "log"
+)
+
+func main() {
+       arv, err := arvadosclient.MakeArvadosClient()
+       if err != nil {
+               log.Fatalf("Error setting up arvados client %v", err)
+       }
+
+       l := logger.NewLogger(logger.LoggerParams{Client: arv,
+               EventType: "experimental-logger-testing",
+               // No minimum write interval
+       })
+
+       {
+               properties, _ := l.Edit()
+               properties["Ninja"] = "Misha"
+       }
+       l.Record()
+}

diff --git a/sdk/go/manifest/manifest.go b/sdk/go/manifest/manifest.go
new file mode 100644 (file)
index 0000000..f6698c6
--- /dev/null
+++ b/sdk/go/manifest/manifest.go
@@ -0,0 +1,118 @@
+/* Deals with parsing Manifest Text. */
+
+// Inspired by the Manifest class in arvados/sdk/ruby/lib/arvados/keep.rb
+
+package manifest
+
+import (
+       "fmt"
+       "git.curoverse.com/arvados.git/sdk/go/blockdigest"
+       "log"
+       "regexp"
+       "strconv"
+       "strings"
+)
+
+var LocatorPattern = regexp.MustCompile(
+       "^[0-9a-fA-F]{32}\\+[0-9]+(\\+[A-Z][A-Za-z0-9@_-]+)*$")
+
+type Manifest struct {
+       Text string
+}
+
+type BlockLocator struct {
+       Digest blockdigest.BlockDigest
+       Size   int
+       Hints  []string
+}
+
+// Represents a single line from a manifest.
+type ManifestStream struct {
+       StreamName string
+       Blocks     []string
+       Files      []string
+}
+
+func ParseBlockLocator(s string) (b BlockLocator, err error) {
+       if !LocatorPattern.MatchString(s) {
+               err = fmt.Errorf("String \"%s\" does not match BlockLocator pattern "+
+                       "\"%s\".",
+                       s,
+                       LocatorPattern.String())
+       } else {
+               tokens := strings.Split(s, "+")
+               var blockSize int64
+               var blockDigest blockdigest.BlockDigest
+               // We expect both of the following to succeed since LocatorPattern
+               // restricts the strings appropriately.
+               blockDigest, err = blockdigest.FromString(tokens[0])
+               if err != nil {
+                       return
+               }
+               blockSize, err = strconv.ParseInt(tokens[1], 10, 0)
+               if err != nil {
+                       return
+               }
+               b.Digest = blockDigest
+               b.Size = int(blockSize)
+               b.Hints = tokens[2:]
+       }
+       return
+}
+
+func parseManifestStream(s string) (m ManifestStream) {
+       tokens := strings.Split(s, " ")
+       m.StreamName = tokens[0]
+       tokens = tokens[1:]
+       var i int
+       for i = range tokens {
+               if !LocatorPattern.MatchString(tokens[i]) {
+                       break
+               }
+       }
+       m.Blocks = tokens[:i]
+       m.Files = tokens[i:]
+       return
+}
+
+func (m *Manifest) StreamIter() <-chan ManifestStream {
+       ch := make(chan ManifestStream)
+       go func(input string) {
+               // This slice holds the current line and the remainder of the
+               // manifest.  We parse one line at a time, to save effort if we
+               // only need the first few lines.
+               lines := []string{"", input}
+               for {
+                       lines = strings.SplitN(lines[1], "\n", 2)
+                       if len(lines[0]) > 0 {
+                               // Only parse non-blank lines
+                               ch <- parseManifestStream(lines[0])
+                       }
+                       if len(lines) == 1 {
+                               break
+                       }
+               }
+               close(ch)
+       }(m.Text)
+       return ch
+}
+
+// Blocks may appear mulitple times within the same manifest if they
+// are used by multiple files. In that case this Iterator will output
+// the same block multiple times.
+func (m *Manifest) BlockIterWithDuplicates() <-chan BlockLocator {
+       blockChannel := make(chan BlockLocator)
+       go func(streamChannel <-chan ManifestStream) {
+               for m := range streamChannel {
+                       for _, block := range m.Blocks {
+                               if b, err := ParseBlockLocator(block); err == nil {
+                                       blockChannel <- b
+                               } else {
+                                       log.Printf("ERROR: Failed to parse block: %v", err)
+                               }
+                       }
+               }
+               close(blockChannel)
+       }(m.StreamIter())
+       return blockChannel
+}

diff --git a/sdk/go/manifest/manifest_test.go b/sdk/go/manifest/manifest_test.go
new file mode 100644 (file)
index 0000000..c1bfb14
--- /dev/null
+++ b/sdk/go/manifest/manifest_test.go
@@ -0,0 +1,178 @@
+package manifest
+
+import (
+       "git.curoverse.com/arvados.git/sdk/go/blockdigest"
+       "io/ioutil"
+       "runtime"
+       "testing"
+)
+
+func getStackTrace() (string) {
+       buf := make([]byte, 1000)
+       bytes_written := runtime.Stack(buf, false)
+       return "Stack Trace:\n" + string(buf[:bytes_written])
+}
+
+func expectFromChannel(t *testing.T, c <-chan string, expected string) {
+       actual, ok := <- c
+       if !ok {
+               t.Fatalf("Expected to receive %s but channel was closed. %s",
+                       expected,
+                       getStackTrace())
+       }
+       if actual != expected {
+               t.Fatalf("Expected %s but got %s instead. %s",
+                       expected,
+                       actual,
+                       getStackTrace())
+       }
+}
+
+func expectChannelClosed(t *testing.T, c <-chan interface{}) {
+       received, ok := <- c
+       if ok {
+               t.Fatalf("Expected channel to be closed, but received %v instead. %s",
+                       received,
+                       getStackTrace())
+       }
+}
+
+func expectEqual(t *testing.T, actual interface{}, expected interface{}) {
+       if actual != expected {
+               t.Fatalf("Expected %v but received %v instead. %s",
+                       expected,
+                       actual,
+                       getStackTrace())
+       }
+}
+
+func expectStringSlicesEqual(t *testing.T, actual []string, expected []string) {
+       if len(actual) != len(expected) {
+               t.Fatalf("Expected %v (length %d), but received %v (length %d) instead. %s", expected, len(expected), actual, len(actual), getStackTrace())
+       }
+       for i := range actual {
+               if actual[i] != expected[i] {
+                       t.Fatalf("Expected %v but received %v instead (first disagreement at position %d). %s", expected, actual, i, getStackTrace())
+               }
+       }
+}
+
+func expectManifestStream(t *testing.T, actual ManifestStream, expected ManifestStream) {
+       expectEqual(t, actual.StreamName, expected.StreamName)
+       expectStringSlicesEqual(t, actual.Blocks, expected.Blocks)
+       expectStringSlicesEqual(t, actual.Files, expected.Files)
+}
+
+func expectBlockLocator(t *testing.T, actual BlockLocator, expected BlockLocator) {
+       expectEqual(t, actual.Digest, expected.Digest)
+       expectEqual(t, actual.Size, expected.Size)
+       expectStringSlicesEqual(t, actual.Hints, expected.Hints)
+}
+
+func expectLocatorPatternMatch(t *testing.T, s string) {
+       if !LocatorPattern.MatchString(s) {
+               t.Fatalf("Expected \"%s\" to match locator pattern but it did not.",
+                       s)
+       }
+}
+
+func expectLocatorPatternFail(t *testing.T, s string) {
+       if LocatorPattern.MatchString(s) {
+               t.Fatalf("Expected \"%s\" to fail locator pattern but it passed.",
+                       s)
+       }
+}
+
+func TestLocatorPatternBasic(t *testing.T) {
+       expectLocatorPatternMatch(t, "12345678901234567890123456789012+12345")
+       expectLocatorPatternMatch(t, "A2345678901234abcdefababdeffdfdf+12345")
+       expectLocatorPatternMatch(t, "12345678901234567890123456789012+12345+A1")
+       expectLocatorPatternMatch(t,
+               "12345678901234567890123456789012+12345+A1+B123wxyz@_-")
+       expectLocatorPatternMatch(t,
+               "12345678901234567890123456789012+12345+A1+B123wxyz@_-+C@")
+
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+")
+       expectLocatorPatternFail(t,  "1234567890123456789012345678901+12345")
+       expectLocatorPatternFail(t,  "123456789012345678901234567890123+12345")
+       expectLocatorPatternFail(t,  "g2345678901234abcdefababdeffdfdf+12345")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345 ")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+1")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+1A")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+A")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+a1")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+A1+")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+A1+B")
+       expectLocatorPatternFail(t,  "12345678901234567890123456789012+12345+A+B2")
+}
+
+func TestParseManifestStreamSimple(t *testing.T) {
+       m := parseManifestStream(". 365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf 0:2310:qr1hi-8i9sb-ienvmpve1a0vpoi.log.txt")
+       expectManifestStream(t, m, ManifestStream{StreamName: ".",
+               Blocks: []string{"365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf"},
+               Files: []string{"0:2310:qr1hi-8i9sb-ienvmpve1a0vpoi.log.txt"}})
+}
+
+func TestParseBlockLocatorSimple(t *testing.T) {
+       b, err := ParseBlockLocator("365f83f5f808896ec834c8b595288735+2310+K@qr1hi+Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf")
+       if err != nil {
+               t.Fatalf("Unexpected error parsing block locator: %v", err)
+       }
+       expectBlockLocator(t, b, BlockLocator{Digest: blockdigest.AssertFromString("365f83f5f808896ec834c8b595288735"),
+               Size: 2310,
+               Hints: []string{"K@qr1hi",
+                       "Af0c9a66381f3b028677411926f0be1c6282fe67c@542b5ddf"}})
+}
+
+func TestStreamIterShortManifestWithBlankStreams(t *testing.T) {
+       content, err := ioutil.ReadFile("testdata/short_manifest")
+       if err != nil {
+               t.Fatalf("Unexpected error reading manifest from file: %v", err)
+       }
+       manifest := Manifest{string(content)}
+       streamIter := manifest.StreamIter()
+
+       firstStream := <-streamIter
+       expectManifestStream(t,
+               firstStream,
+               ManifestStream{StreamName: ".",
+                       Blocks: []string{"b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c"},
+                       Files: []string{"0:15893477:chr10_band0_s0_e3000000.fj"}})
+
+       received, ok := <- streamIter
+       if ok {
+               t.Fatalf("Expected streamIter to be closed, but received %v instead.",
+                       received)
+       }
+}
+
+func TestBlockIterLongManifest(t *testing.T) {
+       content, err := ioutil.ReadFile("testdata/long_manifest")
+       if err != nil {
+               t.Fatalf("Unexpected error reading manifest from file: %v", err)
+       }
+       manifest := Manifest{string(content)}
+       blockChannel := manifest.BlockIterWithDuplicates()
+
+       firstBlock := <-blockChannel
+       expectBlockLocator(t,
+               firstBlock,
+               BlockLocator{Digest: blockdigest.AssertFromString("b746e3d2104645f2f64cd3cc69dd895d"),
+                       Size: 15693477,
+                       Hints: []string{"E2866e643690156651c03d876e638e674dcd79475@5441920c"}})
+       blocksRead := 1
+       var lastBlock BlockLocator
+       for lastBlock = range blockChannel {
+               //log.Printf("Blocks Read: %d", blocksRead)
+               blocksRead++
+       }
+       expectEqual(t, blocksRead, 853)
+
+       expectBlockLocator(t,
+               lastBlock,
+               BlockLocator{Digest: blockdigest.AssertFromString("f9ce82f59e5908d2d70e18df9679b469"),
+                       Size: 31367794,
+                       Hints: []string{"E53f903684239bcc114f7bf8ff9bd6089f33058db@5441920c"}})
+}

diff --git a/sdk/go/manifest/testdata/long_manifest b/sdk/go/manifest/testdata/long_manifest
new file mode 100644 (file)
index 0000000..5f4a2b4
--- /dev/null
+++ b/sdk/go/manifest/testdata/long_manifest
@@ -0,0 +1,7 @@
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12005008464:52257569:chr6_band7_s15200000_e25200000.fj 12057266033:8929925:chr6_band8_s25200000_e27000000.fj 12066195958:17556391:chr6_band9_s27000000_e30400000.fj 12083752349:14247713:chr7_band0_s0_e2800000.fj 12098000062:11066306:chr7_band10_s35000000_e37200000.fj 12109066368:32087088:chr7_band11_s37200000_e43300000.fj 12141153456:10668222:chr7_band12_s43300000_e45400000.fj 12151821678:18626376:chr7_band13_s45400000_e49000000.fj 12170448054:7958919:chr7_band14_s49000000_e50500000.fj 12178406973:18713509:chr7_band15_s50500000_e54000000.fj 12197120482:18935900:chr7_band16_s54000000_e58000000.fj 12216056382:261032:chr7_band17_s58000000_e59900000.fj 12216317414:4289180:chr7_band18_s59900000_e61700000.fj 12220606594:22817045:chr7_band19_s61700000_e67000000.fj 12243423639:8953071:chr7_band1_s2800000_e4500000.fj 12252376710:26475183:chr7_band20_s67000000_e72200000.fj 12278851893:21260557:chr7_band21_s72200000_e77500000.fj 12300112450:47850592:chr7_band22_s77500000_e86400000.fj 12347963042:9284520:chr7_band23_s86400000_e88200000.fj 12357247562:15247848:chr7_band24_s88200000_e91100000.fj 12372495410:8580818:chr7_band25_s91100000_e92800000.fj 12381076228:26810427:chr7_band26_s92800000_e98000000.fj 12407886655:27671122:chr7_band27_s98000000_e103800000.fj 12435557777:3665630:chr7_band28_s103800000_e104500000.fj 12439223407:14940321:chr7_band29_s104500000_e107400000.fj 12454163728:12957633:chr7_band2_s4500000_e7300000.fj 12467121361:38098753:chr7_band30_s107400000_e114600000.fj 12505220114:14874016:chr7_band31_s114600000_e117400000.fj 12520094130:19901201:chr7_band32_s117400000_e121100000.fj 12539995331:14314479:chr7_band33_s121100000_e123800000.fj 12554309810:17691683:chr7_band34_s123800000_e127100000.fj 12572001493:10632852:chr7_band35_s127100000_e129200000.fj 12582634345:5806847:chr7_band36_s129200000_e130400000.fj 12588441192:11677084:chr7_band37_s130400000_e132600000.fj 12600118276:29615252:chr7_band38_s132600000_e138200000.fj 12629733528:24913008:chr7_band39_s138200000_e143100000.fj 12654646536:35077014:chr7_band3_s7300000_e13800000.fj 12689723550:23967238:chr7_band40_s143100000_e147900000.fj 12713690788:23454742:chr7_band41_s147900000_e152600000.fj 12737145530:12478502:chr7_band42_s152600000_e155100000.fj 12749624032:21624407:chr7_band43_s155100000_e159138663.fj 12771248439:14556948:chr7_band4_s13800000_e16500000.fj 12785805387:23503963:chr7_band5_s16500000_e20900000.fj 12809309350:23959972:chr7_band6_s20900000_e25500000.fj 12833269322:13023330:chr7_band7_s25500000_e28000000.fj 12846292652:4304022:chr7_band8_s28000000_e28800000.fj 12850596674:32133100:chr7_band9_s28800000_e35000000.fj 12882729774:11110146:chr8_band0_s0_e2200000.fj 12893839920:17322291:chr8_band10_s39700000_e43100000.fj 12911162211:3523440:chr8_band11_s43100000_e45600000.fj 12914685651:8688009:chr8_band12_s45600000_e48100000.fj 12923373660:21279449:chr8_band13_s48100000_e52200000.fj 12944653109:2084644:chr8_band14_s52200000_e52600000.fj 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+
+
+
+
+
+

diff --git a/sdk/go/manifest/testdata/short_manifest b/sdk/go/manifest/testdata/short_manifest
new file mode 100644 (file)
index 0000000..bb9336c
--- /dev/null
+++ b/sdk/go/manifest/testdata/short_manifest
@@ -0,0 +1,6 @@
+. b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c 0:15893477:chr10_band0_s0_e3000000.fj
+
+
+
+
+

diff --git a/sdk/go/util/util.go b/sdk/go/util/util.go
new file mode 100644 (file)
index 0000000..6bc8625
--- /dev/null
+++ b/sdk/go/util/util.go
@@ -0,0 +1,34 @@
+/* Helper methods for dealing with responses from API Server. */
+
+package util
+
+import (
+       "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+)
+
+func UserIsAdmin(arv arvadosclient.ArvadosClient) (is_admin bool, err error) {
+       type user struct {
+               IsAdmin bool `json:"is_admin"`
+       }
+       var u user
+       err = arv.Call("GET", "users", "", "current", nil, &u)
+       return u.IsAdmin, err
+}
+
+// Returns the total count of a particular type of resource
+//
+//   resource - the arvados resource to count
+// return
+//   count - the number of items of type resource the api server reports, if no error
+//   err - error accessing the resource, or nil if no error
+func NumberItemsAvailable(client arvadosclient.ArvadosClient, resource string) (count int, err error) {
+       var response struct {
+               ItemsAvailable int `json:"items_available"`
+       }
+       sdkParams := arvadosclient.Dict{"limit": 0}
+       err = client.List(resource, sdkParams, &response)
+       if err == nil {
+               count = response.ItemsAvailable
+       }
+       return
+}

diff --git a/services/datamanager/collection/collection.go b/services/datamanager/collection/collection.go
new file mode 100644 (file)
index 0000000..9a7a838
--- /dev/null
+++ b/services/datamanager/collection/collection.go
@@ -0,0 +1,293 @@
+/* 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"
+       "git.curoverse.com/arvados.git/services/datamanager/loggerutil"
+       "log"
+       "os"
+       "runtime"
+       "runtime/pprof"
+       "time"
+)
+
+var (
+       heap_profile_filename string
+       // globals for debugging
+       totalManifestSize uint64
+       maxManifestSize   uint64
+)
+
+type Collection struct {
+       Uuid              string
+       OwnerUuid         string
+       ReplicationLevel  int
+       BlockDigestToSize map[blockdigest.BlockDigest]int
+       TotalSize         int
+}
+
+type ReadCollections struct {
+       ReadAllCollections    bool
+       UuidToCollection      map[string]Collection
+       OwnerToCollectionSize map[string]int
+}
+
+type GetCollectionsParams struct {
+       Client    arvadosclient.ArvadosClient
+       Logger    *logger.Logger
+       BatchSize int
+}
+
+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"`
+}
+
+type SdkCollectionList struct {
+       ItemsAvailable int                 `json:"items_available"`
+       Items          []SdkCollectionInfo `json:"items"`
+}
+
+func init() {
+       flag.StringVar(&heap_profile_filename,
+               "heap-profile",
+               "",
+               "File to write the heap profiles to. Leave blank to skip profiling.")
+}
+
+// Write 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() {
+       if heap_profile_filename != "" {
+
+               heap_profile, err := os.Create(heap_profile_filename)
+               if err != nil {
+                       log.Fatal(err)
+               }
+
+               defer heap_profile.Close()
+
+               err = pprof.WriteHeapProfile(heap_profile)
+               if err != nil {
+                       log.Fatal(err)
+               }
+       }
+}
+
+func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections) {
+       results = GetCollections(params)
+       ComputeSizeOfOwnedCollections(&results)
+
+       if params.Logger != nil {
+               params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
+                       collectionInfo := p["collection_info"].(map[string]interface{})
+                       // 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"] = results.OwnerToCollectionSize
+               })
+       }
+
+       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
+}
+
+func GetCollections(params GetCollectionsParams) (results ReadCollections) {
+       if &params.Client == nil {
+               log.Fatalf("params.Client passed to GetCollections() should " +
+                       "contain a valid ArvadosClient, but instead it is nil.")
+       }
+
+       fieldsWanted := []string{"manifest_text",
+               "owner_uuid",
+               "uuid",
+               // TODO(misha): Start using the redundancy field.
+               "redundancy",
+               "modified_at"}
+
+       sdkParams := arvadosclient.Dict{
+               "select":  fieldsWanted,
+               "order":   []string{"modified_at ASC"},
+               "filters": [][]string{[]string{"modified_at", ">=", "1900-01-01T00:00:00Z"}}}
+
+       if params.BatchSize > 0 {
+               sdkParams["limit"] = params.BatchSize
+       }
+
+       initialNumberOfCollectionsAvailable, err :=
+               util.NumberItemsAvailable(params.Client, "collections")
+       if err != nil {
+               loggerutil.FatalWithMessage(params.Logger,
+                       fmt.Sprintf("Error querying collection count: %v", err))
+       }
+       // 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 := make(map[string]interface{})
+                       collectionInfo["num_collections_at_start"] = initialNumberOfCollectionsAvailable
+                       collectionInfo["batch_size"] = params.BatchSize
+                       p["collection_info"] = collectionInfo
+               })
+       }
+
+       // These values are just for getting the loop to run the first time,
+       // afterwards they'll be set to real values.
+       previousTotalCollections := -1
+       totalCollections := 0
+       for totalCollections > previousTotalCollections {
+               // We're still finding new collections
+
+               // Write the heap profile for examining memory usage
+               WriteHeapProfile()
+
+               // Get next batch of collections.
+               var collections SdkCollectionList
+               err := params.Client.List("collections", sdkParams, &collections)
+               if err != nil {
+                       loggerutil.FatalWithMessage(params.Logger,
+                               fmt.Sprintf("Error querying collections: %v", err))
+               }
+
+               // Process collection and update our date filter.
+               sdkParams["filters"].([][]string)[0][2] =
+                       ProcessCollections(params.Logger,
+                               collections.Items,
+                               results.UuidToCollection).Format(time.RFC3339)
+
+               // update counts
+               previousTotalCollections = totalCollections
+               totalCollections = len(results.UuidToCollection)
+
+               log.Printf("%d collections read, %d new in last batch, "+
+                       "%s latest modified date, %.0f %d %d avg,max,total manifest size",
+                       totalCollections,
+                       totalCollections-previousTotalCollections,
+                       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 := p["collection_info"].(map[string]interface{})
+                               collectionInfo["collections_read"] = totalCollections
+                               collectionInfo["latest_modified_date_seen"] = sdkParams["filters"].([][]string)[0][2]
+                               collectionInfo["total_manifest_size"] = totalManifestSize
+                               collectionInfo["max_manifest_size"] = maxManifestSize
+                       })
+               }
+       }
+
+       // Just in case this lowers the numbers reported in the heap profile.
+       runtime.GC()
+
+       // Write the heap profile for examining memory usage
+       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))
+}
+
+func ProcessCollections(arvLogger *logger.Logger,
+       receivedCollections []SdkCollectionInfo,
+       uuidToCollection map[string]Collection) (latestModificationDate time.Time) {
+       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() {
+                       loggerutil.FatalWithMessage(arvLogger,
+                               fmt.Sprintf(
+                                       "Arvados SDK collection returned with unexpected zero "+
+                                               "modifcation 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))
+               }
+
+               if sdkCollection.ModifiedAt.After(latestModificationDate) {
+                       latestModificationDate = sdkCollection.ModifiedAt
+               }
+               manifest := manifest.Manifest{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 stored_size, stored := collection.BlockDigestToSize[block.Digest]; stored && stored_size != block.Size {
+                               message := fmt.Sprintf(
+                                       "Collection %s contains multiple sizes (%d and %d) for block %s",
+                                       collection.Uuid,
+                                       stored_size,
+                                       block.Size,
+                                       block.Digest)
+                               loggerutil.FatalWithMessage(arvLogger, message)
+                       }
+                       collection.BlockDigestToSize[block.Digest] = block.Size
+               }
+               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
+}
+
+func ComputeSizeOfOwnedCollections(readCollections *ReadCollections) {
+       readCollections.OwnerToCollectionSize = make(map[string]int)
+       for _, coll := range readCollections.UuidToCollection {
+               readCollections.OwnerToCollectionSize[coll.OwnerUuid] =
+                       readCollections.OwnerToCollectionSize[coll.OwnerUuid] + coll.TotalSize
+       }
+
+       return
+}

diff --git a/services/datamanager/datamanager.go b/services/datamanager/datamanager.go
new file mode 100644 (file)
index 0000000..2c5c36d
--- /dev/null
+++ b/services/datamanager/datamanager.go
@@ -0,0 +1,83 @@
+/* Keep Datamanager. Responsible for checking on and reporting on Keep Storage */
+
+package main
+
+import (
+       "flag"
+       "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+       "git.curoverse.com/arvados.git/sdk/go/logger"
+       "git.curoverse.com/arvados.git/sdk/go/util"
+       "git.curoverse.com/arvados.git/services/datamanager/collection"
+       "git.curoverse.com/arvados.git/services/datamanager/keep"
+       "git.curoverse.com/arvados.git/services/datamanager/loggerutil"
+       "log"
+       "time"
+)
+
+var (
+       logEventTypePrefix        string
+       logFrequencySeconds int
+)
+
+func init() {
+       flag.StringVar(&logEventTypePrefix,
+               "log-event-type-prefix",
+               "experimental-data-manager",
+               "Prefix to use in the event_type of our arvados log entries. Set to empty to turn off logging")
+       flag.IntVar(&logFrequencySeconds,
+               "log-frequency-seconds",
+               20,
+               "How frequently we'll write log entries in seconds.")
+}
+
+func main() {
+       flag.Parse()
+
+       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)
+       }
+
+       collectionChannel := make(chan collection.ReadCollections)
+
+       go func() {
+               collectionChannel <- collection.GetCollectionsAndSummarize(
+                       collection.GetCollectionsParams{
+                               Client: arv, Logger: arvLogger, BatchSize: 50})
+       }()
+
+       keepServerInfo := keep.GetKeepServersAndSummarize(
+               keep.GetKeepServersParams{Client: arv, Logger: arvLogger, Limit: 1000})
+
+       readCollections := <-collectionChannel
+
+       // TODO(misha): Use these together to verify replication.
+       _ = readCollections
+       _ = keepServerInfo
+
+       // Log that we're finished. We force the recording, since go will
+       // not wait for the timer before exiting.
+       if arvLogger != nil {
+               arvLogger.FinalUpdate(func(p map[string]interface{}, e map[string]interface{}) {
+                       p["run_info"].(map[string]interface{})["time_finished"] = time.Now()
+               })
+       }
+}

diff --git a/services/datamanager/keep/keep.go b/services/datamanager/keep/keep.go
new file mode 100644 (file)
index 0000000..dcd6c49
--- /dev/null
+++ b/services/datamanager/keep/keep.go
@@ -0,0 +1,440 @@
+/* Deals with getting Keep Server blocks from API Server and Keep Servers. */
+
+package keep
+
+import (
+       "bufio"
+       "encoding/json"
+       "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/services/datamanager/loggerutil"
+       "io/ioutil"
+       "log"
+       "net/http"
+       "strconv"
+       "strings"
+       "sync"
+       "time"
+)
+
+type ServerAddress struct {
+       Host string `json:"service_host"`
+       Port int    `json:"service_port"`
+}
+
+// Info about a particular block returned by the server
+type BlockInfo struct {
+       Digest blockdigest.BlockDigest
+       Size   int
+       Mtime  int64 // TODO(misha): Replace this with a timestamp.
+}
+
+// Info about a specified block given by a server
+type BlockServerInfo struct {
+       ServerIndex int
+       Size        int
+       Mtime       int64 // TODO(misha): Replace this with a timestamp.
+}
+
+type ServerContents struct {
+       BlockDigestToInfo map[blockdigest.BlockDigest]BlockInfo
+}
+
+type ServerResponse struct {
+       Address  ServerAddress
+       Contents ServerContents
+}
+
+type ReadServers struct {
+       ReadAllServers           bool
+       KeepServerIndexToAddress []ServerAddress
+       KeepServerAddressToIndex map[ServerAddress]int
+       ServerToContents         map[ServerAddress]ServerContents
+       BlockToServers           map[blockdigest.BlockDigest][]BlockServerInfo
+       BlockReplicationCounts   map[int]int
+}
+
+type GetKeepServersParams struct {
+       Client arvadosclient.ArvadosClient
+       Logger *logger.Logger
+       Limit  int
+}
+
+type KeepServiceList struct {
+       ItemsAvailable int             `json:"items_available"`
+       KeepServers    []ServerAddress `json:"items"`
+}
+
+var (
+       // Don't access the token directly, use getDataManagerToken() to
+       // make sure it's been read.
+       dataManagerToken             string
+       dataManagerTokenFile         string
+       dataManagerTokenFileReadOnce sync.Once
+)
+
+func init() {
+       flag.StringVar(&dataManagerTokenFile,
+               "data-manager-token-file",
+               "",
+               "File with the API token we should use to contact keep servers.")
+}
+
+func (s ServerAddress) String() string {
+       return fmt.Sprintf("%s:%d", s.Host, s.Port)
+}
+
+func getDataManagerToken(arvLogger *logger.Logger) string {
+       readDataManagerToken := func() {
+               if dataManagerTokenFile == "" {
+                       flag.Usage()
+                       loggerutil.FatalWithMessage(arvLogger,
+                               "Data Manager Token needed, but data manager token file not specified.")
+               } else {
+                       rawRead, err := ioutil.ReadFile(dataManagerTokenFile)
+                       if err != nil {
+                               loggerutil.FatalWithMessage(arvLogger,
+                                       fmt.Sprintf("Unexpected error reading token file %s: %v",
+                                               dataManagerTokenFile,
+                                               err))
+                       }
+                       dataManagerToken = strings.TrimSpace(string(rawRead))
+               }
+       }
+
+       dataManagerTokenFileReadOnce.Do(readDataManagerToken)
+       return dataManagerToken
+}
+
+func GetKeepServersAndSummarize(params GetKeepServersParams) (results ReadServers) {
+       results = GetKeepServers(params)
+       log.Printf("Returned %d keep disks", len(results.ServerToContents))
+
+       ComputeBlockReplicationCounts(&results)
+       log.Printf("Replication level distribution: %v",
+               results.BlockReplicationCounts)
+
+       return
+}
+
+func GetKeepServers(params GetKeepServersParams) (results ReadServers) {
+       if &params.Client == nil {
+               log.Fatalf("params.Client passed to GetKeepServers() should " +
+                       "contain a valid ArvadosClient, but instead it is nil.")
+       }
+
+       sdkParams := arvadosclient.Dict{
+               "filters": [][]string{[]string{"service_type", "=", "disk"}},
+       }
+       if params.Limit > 0 {
+               sdkParams["limit"] = params.Limit
+       }
+
+       var sdkResponse KeepServiceList
+       err := params.Client.List("keep_services", sdkParams, &sdkResponse)
+
+       if err != nil {
+               loggerutil.FatalWithMessage(params.Logger,
+                       fmt.Sprintf("Error requesting keep disks from API server: %v", err))
+       }
+
+       if params.Logger != nil {
+               params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
+                       keepInfo := make(map[string]interface{})
+
+                       keepInfo["num_keep_servers_available"] = sdkResponse.ItemsAvailable
+                       keepInfo["num_keep_servers_received"] = len(sdkResponse.KeepServers)
+                       keepInfo["keep_servers"] = sdkResponse.KeepServers
+
+                       p["keep_info"] = keepInfo
+               })
+       }
+
+       log.Printf("Received keep services list: %+v", sdkResponse)
+
+       if len(sdkResponse.KeepServers) < sdkResponse.ItemsAvailable {
+               loggerutil.FatalWithMessage(params.Logger,
+                       fmt.Sprintf("Did not receive all available keep servers: %+v", sdkResponse))
+       }
+
+       results.KeepServerIndexToAddress = sdkResponse.KeepServers
+       results.KeepServerAddressToIndex = make(map[ServerAddress]int)
+       for i, address := range results.KeepServerIndexToAddress {
+               results.KeepServerAddressToIndex[address] = i
+       }
+
+       log.Printf("Got Server Addresses: %v", results)
+
+       // This is safe for concurrent use
+       client := http.Client{}
+
+       // Send off all the index requests concurrently
+       responseChan := make(chan ServerResponse)
+       for _, keepServer := range sdkResponse.KeepServers {
+               // The above keepsServer variable is reused for each iteration, so
+               // it would be shared across all goroutines. This would result in
+               // us querying one server n times instead of n different servers
+               // as we intended. To avoid this we add it as an explicit
+               // parameter which gets copied. This bug and solution is described
+               // in https://golang.org/doc/effective_go.html#channels
+               go func(keepServer ServerAddress) {
+                       responseChan <- GetServerContents(params.Logger,
+                               keepServer,
+                               client)
+               }(keepServer)
+       }
+
+       results.ServerToContents = make(map[ServerAddress]ServerContents)
+       results.BlockToServers = make(map[blockdigest.BlockDigest][]BlockServerInfo)
+
+       // Read all the responses
+       for i := range sdkResponse.KeepServers {
+               _ = i // Here to prevent go from complaining.
+               response := <-responseChan
+               log.Printf("Received channel response from %v containing %d files",
+                       response.Address,
+                       len(response.Contents.BlockDigestToInfo))
+               results.ServerToContents[response.Address] = response.Contents
+               serverIndex := results.KeepServerAddressToIndex[response.Address]
+               for _, blockInfo := range response.Contents.BlockDigestToInfo {
+                       results.BlockToServers[blockInfo.Digest] = append(
+                               results.BlockToServers[blockInfo.Digest],
+                               BlockServerInfo{ServerIndex: serverIndex,
+                                       Size:  blockInfo.Size,
+                                       Mtime: blockInfo.Mtime})
+               }
+       }
+       return
+}
+
+func GetServerContents(arvLogger *logger.Logger,
+       keepServer ServerAddress,
+       client http.Client) (response ServerResponse) {
+
+       GetServerStatus(arvLogger, keepServer, client)
+
+       req := CreateIndexRequest(arvLogger, keepServer)
+       resp, err := client.Do(req)
+       if err != nil {
+               loggerutil.FatalWithMessage(arvLogger,
+                       fmt.Sprintf("Error fetching %s: %v", req.URL.String(), err))
+       }
+
+       return ReadServerResponse(arvLogger, keepServer, resp)
+}
+
+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 := p["keep_info"].(map[string]interface{})
+                       serverInfo := make(map[string]interface{})
+                       serverInfo["time_status_request_sent"] = now
+
+                       keepInfo[keepServer.String()] = 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 := p["keep_info"].(map[string]interface{})
+                       serverInfo := keepInfo[keepServer.String()].(map[string]interface{})
+                       serverInfo["time_status_response_processed"] = now
+                       serverInfo["status"] = keepStatus
+               })
+       }
+}
+
+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 := p["keep_info"].(map[string]interface{})
+                       serverInfo := keepInfo[keepServer.String()].(map[string]interface{})
+                       serverInfo["time_index_request_sent"] = 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 := p["keep_info"].(map[string]interface{})
+                       serverInfo := keepInfo[keepServer.String()].(map[string]interface{})
+                       serverInfo["time_index_response_received"] = now
+               })
+       }
+
+       response.Address = keepServer
+       response.Contents.BlockDigestToInfo =
+               make(map[blockdigest.BlockDigest]BlockInfo)
+       scanner := bufio.NewScanner(resp.Body)
+       numLines, numDuplicates, numSizeDisagreements := 0, 0, 0
+       for scanner.Scan() {
+               numLines++
+               blockInfo, err := parseBlockInfoFromIndexLine(scanner.Text())
+               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
+                       if storedBlock.Size != blockInfo.Size {
+                               numSizeDisagreements += 1
+                               // TODO(misha): Consider failing here.
+                               message := fmt.Sprintf("Saw different sizes for the same block "+
+                                       "on %s: %+v %+v",
+                                       keepServer.String(),
+                                       storedBlock,
+                                       blockInfo)
+                               log.Println(message)
+                               if arvLogger != nil {
+                                       arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
+                                               keepInfo := p["keep_info"].(map[string]interface{})
+                                               serverInfo := keepInfo[keepServer.String()].(map[string]interface{})
+                                               var error_list []string
+                                               read_error_list, has_list := serverInfo["error_list"]
+                                               if has_list {
+                                                       error_list = read_error_list.([]string)
+                                               } // If we didn't have the list, error_list is already an empty list
+                                               serverInfo["error_list"] = append(error_list, message)
+                                       })
+                               }
+                       }
+                       // Keep the block that is bigger, or the block that's newer in
+                       // the case of a size tie.
+                       if storedBlock.Size < blockInfo.Size ||
+                               (storedBlock.Size == blockInfo.Size &&
+                                       storedBlock.Mtime < blockInfo.Mtime) {
+                               response.Contents.BlockDigestToInfo[blockInfo.Digest] = blockInfo
+                       }
+               } else {
+                       response.Contents.BlockDigestToInfo[blockInfo.Digest] = blockInfo
+               }
+       }
+       if err := scanner.Err(); err != nil {
+               loggerutil.FatalWithMessage(arvLogger,
+                       fmt.Sprintf("Received error scanning index response from %s: %v",
+                               keepServer.String(),
+                               err))
+       } else {
+               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 := p["keep_info"].(map[string]interface{})
+                               serverInfo := keepInfo[keepServer.String()].(map[string]interface{})
+
+                               serverInfo["time_processing_finished"] = now
+                               serverInfo["lines_received"] = numLines
+                               serverInfo["duplicates_seen"] = numDuplicates
+                               serverInfo["size_disagreements_seen"] = numSizeDisagreements
+                       })
+               }
+       }
+       resp.Body.Close()
+       return
+}
+
+func parseBlockInfoFromIndexLine(indexLine string) (blockInfo BlockInfo, err error) {
+       tokens := strings.Fields(indexLine)
+       if len(tokens) != 2 {
+               err = fmt.Errorf("Expected 2 tokens per line but received a "+
+                       "line containing %v instead.",
+                       tokens)
+       }
+
+       var locator manifest.BlockLocator
+       if locator, err = manifest.ParseBlockLocator(tokens[0]); err != nil {
+               return
+       }
+       if len(locator.Hints) > 0 {
+               err = fmt.Errorf("Block locator in index line should not contain hints "+
+                       "but it does: %v",
+                       locator)
+               return
+       }
+
+       blockInfo.Mtime, err = strconv.ParseInt(tokens[1], 10, 64)
+       if err != nil {
+               return
+       }
+       blockInfo.Digest = locator.Digest
+       blockInfo.Size = locator.Size
+       return
+}
+
+func ComputeBlockReplicationCounts(readServers *ReadServers) {
+       readServers.BlockReplicationCounts = make(map[int]int)
+       for _, infos := range readServers.BlockToServers {
+               replication := len(infos)
+               readServers.BlockReplicationCounts[replication] += 1
+       }
+}

diff --git a/services/datamanager/loggerutil/loggerutil.go b/services/datamanager/loggerutil/loggerutil.go
new file mode 100644 (file)
index 0000000..1514922
--- /dev/null
+++ b/services/datamanager/loggerutil/loggerutil.go
@@ -0,0 +1,53 @@
+/* Datamanager-specific logging methods. */
+
+package loggerutil
+
+import (
+       "git.curoverse.com/arvados.git/sdk/go/logger"
+       "log"
+       "os"
+       "runtime"
+       "time"
+)
+
+// 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 := make(map[string]interface{})
+                       runInfo["time_started"] = 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()
+                       p["run_info"] = runInfo
+               })
+       }
+}
+
+// A LogMutator that records the current memory usage. This is most useful as a logger write hook.
+//
+// Assumes we already have a map named "run_info" in properties. LogRunInfo() can create such a map for you if you call it.
+func LogMemoryAlloc(p map[string]interface{}, e map[string]interface{}) {
+       runInfo := p["run_info"].(map[string]interface{})
+       var memStats runtime.MemStats
+       runtime.ReadMemStats(&memStats)
+       runInfo["alloc_bytes_in_use"] = memStats.Alloc
+}
+
+func FatalWithMessage(arvLogger *logger.Logger, message string) {
+       if arvLogger != nil {
+               arvLogger.FinalUpdate(func(p map[string]interface{}, e map[string]interface{}) {
+                       p["FATAL"] = message
+                       p["run_info"].(map[string]interface{})["time_finished"] = time.Now()
+               })
+       }
+
+       log.Fatalf(message)
+}