-
Notifications
You must be signed in to change notification settings - Fork 0
/
migrate.sc
186 lines (147 loc) · 6.34 KB
/
migrate.sc
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
interp.configureCompiler(_.settings.YpartialUnification.value = true)
interp.repositories() ++= Seq(coursier.maven.MavenRepository(
"https://oss.sonatype.org/content/repositories/releases"))
@
import $plugin.$ivy.`org.spire-math::kind-projector:0.9.7`
import scala.concurrent.duration._
/*
Migration of (Meta)Data from Cromwell's SQL datastore to Google Datastore
Algorithm:
every N seconds,
lastRowPulled <- query datastore by auto Id desc to get last row pushed to the Datastore
newData <- query Cromwell metadata from lastRow until end of all metadata
entities <- convert data into Datastore objects known as "Entities"
push the entites into Datastore
possible optimizations to be made:
Only pull data from datastore if we see there is no more data to be pulled from MySQL
pull data from mysql and load to DS in separate threads
*/
import $ivy.`org.tpolecat::doobie-core:0.5.3`
import $ivy.`org.tpolecat::doobie-hikari:0.5.3`
import $ivy.`com.google.cloud:google-cloud-datastore:1.35.0`
import $ivy.`mysql:mysql-connector-java:8.0.11`
import $ivy.`com.chuusai::shapeless:2.3.3`
import $ivy.`org.hsqldb:hsqldb:2.4.1`
import shapeless.syntax.std.tuple._
import $file.simple_rpc_server
import simple_rpc_server._
import doobie._
import doobie.implicits._
import cats.effect.IO
import java.util.concurrent.Executors
import java.time.Instant
import scala.{Stream => _}
import java.math.BigInteger
import scodec._
import scodec.codecs._
import _root_.scodec.codecs.implicits._
import fs2.{Pure, Stream, Sink, Pipe, Scheduler, Segment, Pull}
import fs2.Stream._
import cats.effect.Effect
import cats.instances.long._
import cats.instances.vector._
import cats.data.State
import com.google.cloud.datastore.{Query => DSQuery, _}
//import com.google.cloud.datastore.Query._
import com.google.cloud.datastore.StructuredQuery.OrderBy;
import collection.JavaConverters._
import com.google.cloud.datastore.ReadOption
import cats.Monad
import cats.syntax.monad._
import cats.syntax.traverse._
import cats.instances.list._
def datastore[F[_]: Effect]: Stream[F, Datastore] =
Stream emit DatastoreOptions.getDefaultInstance().getService()
def queryLatest[F[_]](implicit eff : Effect[F], m: Monad[Stream[F, ?]]): Pipe[F, Datastore, List[Entity]] =
_.flatMap{
datastore =>
val query = DSQuery.newEntityQueryBuilder()
.setKind("metadata")
.setOrderBy(OrderBy.desc("autoId"))
.setLimit(1)
.build();
Stream.eval(eff.delay {datastore.run(query, Seq.empty[ReadOption]:_*).asScala.toList})
}
def emitList[F[_]: Effect, A]: Pipe[F, Seq[A], A] = _.flatMap(Stream.emits(_))
def pullEveryMinute = {
def fullLatestFromDatastore: Stream[IO, Long] =
datastore[IO].through(queryLatest).through(emitList).map(_.getLong("autoId"))
val timer =
Scheduler.
fromScheduledExecutorService(Executors.newScheduledThreadPool(1)).
awakeEvery[IO](5.seconds)
def onlyEmitIfNew: Pipe[IO, Int, Option[Int]] =
scanState(0)({
n =>
State{old =>
if (old == n)
(n, None)
else
(n, Some(old))
}})
fullLatestFromDatastore.zipWith(timer){ case (ds, _) => ds }
}
type MetadataColumns = (Int, String, String, Option[String], Option[Int], Option[Int], Option[String], Instant, Option[String])
def find(offset: Int): doobie.Query0[MetadataColumns] =
sql"select * from METADATA_ENTRY order by METADATA_JOURNAL_ID limit 500 offset $offset".
query[(Int, String, String, Option[String], Option[Int], Option[Int], Option[String], Instant, Option[String])]
case class DoobieConfig(driver: String, connectionString: String, user: String, pass: String)
implicit val c = Codec[DoobieConfig]
val counter: fs2.Stream[Pure, Int] = fs2.Stream.unfold(0){s => val n = s + 500
Some((n,n))
}
@main
def server(args: String*) = {
val datastore = DatastoreOptions.getDefaultInstance().getService();
val tcpServer: fs2.Stream[IO, DoobieConfig] = simple_rpc_server.server[DoobieConfig](args.head)
tcpServer.
flatMap{
case DoobieConfig(driver, connectionString, user, pass) =>
val xa = Transactor.fromDriverManager[IO](driver, connectionString, user, pass)
val finder = find(0).stream
xa.transP.apply(finder)
}.map{
case tuple@(autoId, wfId, metadataKey, optCallFQN, optJobScatterIndex, optJobRetryAttempt, optMetadataValue, timestamp, optValueType) =>
val key = tuple.hashCode.toString
val taskKey = datastore.newKeyFactory().setKind("metadata").newKey(key)
import com.google.cloud.Timestamp
val ts = Timestamp.ofTimeSecondsAndNanos(timestamp.getEpochSecond, timestamp.getNano)
val builder = Entity.newBuilder(taskKey)
.set("autoId", autoId)
.set("wfId", wfId)
.set("metadataKey", metadataKey)
.set("timestamp", ts)
optCallFQN.foreach(builder.set("callFQN", _))
optJobScatterIndex.foreach(builder.set("jobScatterIndex", _))
optJobRetryAttempt.foreach(builder.set("jobRetryAttempt", _))
optMetadataValue.foreach(builder.set("metadataValue", _))
optValueType.foreach(builder.set("valueType", _))
builder.build()
}
.chunkLimit(500)
.flatMap{
entities =>
Stream.eval(IO {datastore.put(entities.toList:_*) })
}.compile.drain.unsafeRunSync()
}
@main def client(args: String*) = simple_rpc_server.client(DoobieConfig("com.mysql.cj.jdbc.Driver","jdbc:mysql://localhost/DatabaseName?useSSL=false","ChooseAName","YourOtherPassword"), args:_*)
def scanState[F[_], S, A, B](init: S)(f: A => State[S, B]): Pipe[F, A, B] =
_.pull.scanSegments(init){
case (previousState, segment: Segment[A, Unit]) =>
segment.mapAccumulate(previousState)({
case (state, o1) =>
val stateFunc = f(o1)
(stateFunc run state).value
}).mapResult(_._2)
}.stream
/*
driver = "org.hsqldb.jdbcDriver"
url = "jdbc:hsqldb:file:metadata;shutdown=false;hsqldb.tx=mvcc"
connectionTimeout = 20000
*/
def allWorkflows: doobie.Query0[String] =
sql"select WORKFLOW_EXECUTION_UUID from WORKFLOW_STORE_ENTRY".
query[String]
val xa = Transactor.fromDriverManager[IO]("org.hsqldb.jdbcDriver", "jdbc:hsqldb:file:metadata", "ChooseAName","YourOtherPassword")
val finder = allWorkflows.stream
xa.transP.apply(finder).evalMap(res => IO(println(res))).compile.drain.unsafeRunSync