/
build.sbt
405 lines (357 loc) · 20 KB
/
build.sbt
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
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
import scala.sys.process._
name := "Mimir-Core"
version := "0.3.2"
organization := "info.mimirdb"
scalaVersion := "2.12.10"
dependencyOverrides += "org.scala-lang" % "scala-library" % scalaVersion.value
// Needed to avoid cryptic EOFException crashes in forked tests
// in Travis with `sudo: false`.
// See https://github.com/sbt/sbt/issues/653
// and https://github.com/travis-ci/travis-ci/issues/3775
javaOptions ++= Seq("-Xmx8G" )
scalacOptions ++= Seq(
"-feature"
)
unmanagedResourceDirectories in Compile += baseDirectory.value / "lib_extra"
includeFilter in (Compile, unmanagedResourceDirectories):= ".dylib,.dll,.so"
unmanagedClasspath in Runtime += baseDirectory.value / "conf"
unmanagedResourceDirectories in Compile += baseDirectory.value / "conf"
fork := true
outputStrategy in run := Some(StdoutOutput)
connectInput in run := true
cancelable in Global := true
javaOptions ++= Seq(
"-Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS",
"-Dcom.github.fommil.netlib.LAPACK=com.github.fommil.netlib.F2jLAPACK",
"-Dcom.github.fommil.netlib.ARPACK=com.github.fommil.netlib.F2jARPACK"
// ,"-agentlib:jdwp=transport=dt_shmem,address=jdbconn,server=y,suspend=n"
)
scalacOptions in Test ++= Seq("-Yrangepos")
parallelExecution in Test := false
testOptions in Test ++= Seq( Tests.Argument("junitxml"), Tests.Argument("console") )
mainClass in Compile := Some("mimir.Mimir")
//if you want to debug tests uncomment this
//javaOptions += "-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"
lazy val runMimirVizier = inputKey[Unit]("run MimirVizier")
runMimirVizier := {
val args = sbt.complete.Parsers.spaceDelimited("[main args]").parsed
val classpath = (fullClasspath in Compile).value
val classpathString = Path.makeString(classpath map { _.data })
val debugTestJVMArgs = Seq()//Seq("-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005")
val jvmArgs = debugTestJVMArgs ++ Seq("-Xmx4g", "-Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS", "-Dcom.github.fommil.netlib.LAPACK=com.github.fommil.netlib.F2jLAPACK", "-Dcom.github.fommil.netlib.ARPACK=com.github.fommil.netlib.F2jARPACK")
val (jh, os, bj, bd, jo, ci, ev) = (javaHome.value, outputStrategy.value, Vector[java.io.File](),
Some(baseDirectory.value), (jvmArgs ++ Seq("-classpath", classpathString)).toVector, connectInput.value, sys.props.get("os.name") match {
//case Some(osname) if osname.startsWith("Mac OS X") => Map(("DYLD_INSERT_LIBRARIES",System.getProperty("java.home")+"/lib/libjsig.dylib"))
case Some(osname) if osname.startsWith("Mac OS X") => sys.props.get("os.arch") match {
case Some(osarch) if osarch.endsWith("64") => Map(("LD_PRELOAD_64",System.getProperty("java.home")+"/lib/libjsig.dylib"))
case Some(osarch) => Map(("LD_PRELOAD",System.getProperty("java.home")+"/lib/libjsig.dylib"))
case None => envVars.value
}
case Some(otherosname) => sys.props.get("os.arch") match {
case Some(osarch) if osarch.endsWith("64") => Map(("LD_PRELOAD_64",System.getProperty("java.home")+"/lib/"+System.getProperty("os.arch")+"/libjsig.so"))
case Some(osarch) => Map(("LD_PRELOAD",System.getProperty("java.home")+"/lib/"+System.getProperty("os.arch")+"/libjsig.so"))
case None => envVars.value
}
case None => envVars.value
})
Fork.java(
ForkOptions(jh, os, bj, bd, jo, ci, ev),
"mimir.MimirVizier" +: args
)
}
lazy val runTestResults = inputKey[Unit]("run runTestResults")
runTestResults := {
val args = sbt.complete.Parsers.spaceDelimited("[main args]").parsed
val classpath = (fullClasspath in Compile).value
val classpathString = Path.makeString(classpath map { _.data })
val debugTestJVMArgs = Seq()//Seq("-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005")
val jvmArgs = debugTestJVMArgs ++ Seq("-Xmx4g", "-Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS", "-Dcom.github.fommil.netlib.LAPACK=com.github.fommil.netlib.F2jLAPACK", "-Dcom.github.fommil.netlib.ARPACK=com.github.fommil.netlib.F2jARPACK")
val (jh, os, bj, bd, jo, ci, ev) = (javaHome.value, outputStrategy.value, Vector[java.io.File](),
Some(baseDirectory.value), (jvmArgs ++ Seq("-classpath", classpathString)).toVector,
connectInput.value, envVars.value)
Fork.java(
ForkOptions(jh, os, bj, bd, jo, ci, ev),
"mimir.util.TestResults" +: args
)
}
lazy val runBackup = inputKey[Unit]("run runBackup")
runBackup := {
val args = sbt.complete.Parsers.spaceDelimited("[main args]").parsed
val classpath = (fullClasspath in Compile).value
val classpathString = Path.makeString(classpath map { _.data })
val debugTestJVMArgs = Seq()//Seq("-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005")
val jvmArgs = debugTestJVMArgs ++ Seq("-Xmx4g", "-Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS", "-Dcom.github.fommil.netlib.LAPACK=com.github.fommil.netlib.F2jLAPACK", "-Dcom.github.fommil.netlib.ARPACK=com.github.fommil.netlib.F2jARPACK")
val (jh, os, bj, bd, jo, ci, ev) = (javaHome.value, outputStrategy.value, Vector[java.io.File](),
Some(baseDirectory.value), (jvmArgs ++ Seq("-classpath", classpathString)).toVector,
connectInput.value, envVars.value)
Fork.java(
ForkOptions(jh, os, bj, bd, jo, ci, ev),
"mimir.util.BackupUtils" +: args
)
}
//for tests that need to run in their own jvm because they need specific envArgs or otherwise
testGrouping in Test := {
val (jh, os, bj, bd, jo, ci, ev) = (javaHome.value, outputStrategy.value, Vector[java.io.File](),
baseDirectory.value, javaOptions.value.toVector, connectInput.value, envVars.value)
val testsToForkSeperately = Seq("mimir.algebra.gprom.OperatorTranslationSpec","mimir.demo.MimirGProMDemo")
val gpromTestsForkEnvArgs = sys.props.get("os.name") match {
case Some(osname) if osname.startsWith("Mac OS X") => Map(("DYLD_INSERT_LIBRARIES",System.getProperty("java.home")+"/lib/libjsig.dylib"))
case Some(otherosname) => Map(("LD_PRELOAD",System.getProperty("java.home")+"/lib/"+System.getProperty("os.arch")+"/libjsig.so"))
case None => envVars.value
}
val seperateForkedEnvArgs = Map(("mimir.algebra.gprom.OperatorTranslationSpec", gpromTestsForkEnvArgs), ("mimir.demo.MimirGProMDemo", gpromTestsForkEnvArgs))
val (forkedTests, otherTests) = (definedTests in Test).value.partition { test => testsToForkSeperately.contains(test.name) }
Seq(Tests.Group(name = "Single JVM tests", tests = otherTests, runPolicy = Tests.SubProcess(
ForkOptions( jh, os, bj, Some(bd), jo, ci, ev)
))) ++ forkedTests.map { test =>
Tests.Group(name = test.name, tests = Seq(test), runPolicy = Tests.SubProcess(
ForkOptions( jh, os, bj, Some(bd), jo, ci, seperateForkedEnvArgs.getOrElse(test.name, ev))
))
}
}
resolvers += "MimirDB" at "https://maven.mimirdb.info/"
resolvers += "MVNRepository" at "https://mvnrepository.com/artifact/"
resolvers ++= Seq("snapshots", "releases").map(Resolver.sonatypeRepo)
resolvers += Resolver.mavenLocal
updateOptions := updateOptions.value.withGigahorse(false)
dependencyOverrides += "com.fasterxml.jackson.core" % "jackson-core" % "2.9.10"
dependencyOverrides += "com.fasterxml.jackson.core" % "jackson-databind" % "2.9.10"
dependencyOverrides += "com.fasterxml.jackson.module" % "jackson-module-scala_2.12" % "2.9.10"
libraryDependencies ++= Seq(
////////////////////// Command-Line Interface Utilities //////////////////////
"org.rogach" %% "scallop" % "3.1.3",
"org.jline" % "jline" % "3.2.0",
"info.mimirdb" %% "sparsity" % "1.7.0",
"com.lihaoyi" %% "fastparse" % "2.1.0",
"org.apache.commons" % "commons-text" % "1.8",
////////////////////// Dev Tools -- Logging, Testing, etc... //////////////////////
"com.typesafe.scala-logging" %% "scala-logging" % "3.9.2",
"ch.qos.logback" % "logback-classic" % "1.2.3",
"org.specs2" %% "specs2-core" % "4.6.0" % "test",
"org.specs2" %% "specs2-matcher-extra" % "4.6.0" % "test",
"org.specs2" %% "specs2-junit" % "4.6.0" % "test",
"org.clapper" %% "classutil" % "1.1.2",
"com.amazonaws" % "aws-java-sdk-core" % "1.11.234",
"com.amazonaws" % "aws-java-sdk-s3" % "1.11.234",
//"ch.cern.sparkmeasure" %% "spark-measure" % "0.13",
"org.scala-lang" % "scala-compiler" % "2.12.7",
"org.ddahl" %% "rscala" % "3.2.15",
//////////////////////// Data Munging Tools //////////////////////
"com.github.nscala-time" %% "nscala-time" % "2.20.0",
"org.apache.lucene" % "lucene-spellchecker" % "3.6.2",
"org.apache.servicemix.bundles" % "org.apache.servicemix.bundles.collections-generic"
% "4.01_1",
"org.scala-lang.modules" %% "scala-parser-combinators" % "1.0.6",
"org.apache.commons" % "commons-csv" % "1.4",
"commons-io" % "commons-io" % "2.5",
"com.github.wnameless" % "json-flattener" % "0.2.2",
"com.typesafe.play" %% "play-json" % "2.7.0-M1" excludeAll( ExclusionRule("com.fasterxml.jackson.core")),
"technology.tabula" % "tabula" % "1.0.3",
"org.apache.commons" % "commons-compress" % "1.19",
//////////////////////// Lens Libraries //////////////////////
// WEKA - General-purpose Classifier Training/Deployment Library
// Used by the imputation lens
// ("nz.ac.waikato.cms.weka" % "weka-stable" % "3.8.1").
// exclude("nz.ac.waikato.cms.weka", "weka-dev").
// exclude("nz.ac.waikato.cms.weka.thirdparty", "java-cup-11b-runtime"),
// ("nz.ac.waikato.cms.moa" % "moa" % "2014.11").
// exclude("nz.ac.waikato.cms.weka", "weka-dev").
// exclude("nz.ac.waikato.cms.weka.thirdparty", "java-cup-11b-runtime"),
//spark ml
"org.apache.spark" % "spark-sql_2.12" % "2.4.4",// excludeAll(ExclusionRule(organization = "org.slf4j", name = "slf4j-log4j12"), ExclusionRule("org.apache.hadoop")),
"org.apache.spark" % "spark-mllib_2.12" % "2.4.4",// excludeAll(ExclusionRule(organization = "org.slf4j", name = "slf4j-log4j12"), ExclusionRule("org.apache.hadoop")),
"org.apache.spark" % "spark-hive_2.12" % "2.4.4",// excludeAll(ExclusionRule(organization = "org.slf4j", name = "slf4j-log4j12"), ExclusionRule("org.apache.hadoop")),
"com.databricks" % "spark-xml_2.12" % "0.9.0",// excludeAll(ExclusionRule(organization = "org.slf4j", name = "slf4j-log4j12"), ExclusionRule("org.apache.hadoop")),
"com.sun.xml.txw2" % "txw2" % "20110809",
"com.crealytics" %% "spark-excel" % "0.12.0",// excludeAll(ExclusionRule(organization = "org.slf4j", name = "slf4j-log4j12"), ExclusionRule("org.apache.hadoop")),
//"com.google.api.client" % "google-api-client-json" % "1.2.2-alpha",
"org.apache.hadoop" % "hadoop-client" % "2.8.2" exclude("org.slf4j", "slf4j-log4j12"),
"org.apache.hadoop" % "hadoop-aws" % "2.8.2" exclude("org.slf4j", "slf4j-log4j12"),
"net.java.dev.jets3t" % "jets3t" % "0.9.4",
("com.google.api-client" % "google-api-client" % "1.30.9").exclude("com.google.guava", "guava-jdk5"),
"com.google.oauth-client" % "google-oauth-client-jetty" % "1.30.6",
"com.google.apis" % "google-api-services-sheets" % "v4-rev610-1.25.0",
"org.datasyslab" % "geospark" % "1.2.0",
"org.datasyslab" % "geospark-sql_2.3" % "1.2.0",
"com.fasterxml.jackson.core" % "jackson-core" % "2.10.0",
//////////////////////// Jung ////////////////////////
// General purpose graph manipulation library
// Used to detect and analyze Functional Dependencies
"net.sf.jung" % "jung-graph-impl" % "2.0.1",
"net.sf.jung" % "jung-algorithms" % "2.0.1",
"net.sf.jung" % "jung-visualization" % "2.0.1",
"jgraph" % "jgraph" % "5.13.0.0",
"javax.measure" % "jsr-275" % "0.9.1",
//////////////////////// JDBC Backends //////////////////////
"org.xerial" % "sqlite-jdbc" % "3.16.1",
"org.postgresql" % "postgresql" % "9.4-1201-jdbc41",
/// Explicitly not including MySQL, since it's GPL-licensed. If you want
/// to use MySQL, you're free to compile your own version of Mimir.
///////////////////// Viztrails Integration ///////////////////
"org.eclipse.jetty" % "jetty-http" % "9.4.10.v20180503",
"org.eclipse.jetty" % "jetty-io" % "9.4.10.v20180503",
"org.eclipse.jetty" % "jetty-security" % "9.4.10.v20180503",
"org.eclipse.jetty" % "jetty-server" % "9.4.10.v20180503",
"org.eclipse.jetty" % "jetty-servlet" % "9.4.10.v20180503" ,
"org.eclipse.jetty" % "jetty-servlets" % "9.4.10.v20180503" ,
"org.eclipse.jetty" % "jetty-util" % "9.4.10.v20180503" ,
"org.eclipse.jetty" % "jetty-webapp" % "9.4.10.v20180503" ,
//////////////////////// Visualization //////////////////////
// For now, all of this happens in python with matplotlib
// and so we don't need any external dependencies.
//"org.vegas-viz" %% "vegas" % "0.3.9",
//"org.sameersingh.scalaplot" % "scalaplot" % "0.0.4",
//////////////////////// Linear Solver /////////////////////////
"com.github.vagmcs" %% "optimus" % "3.1.0",
"com.github.vagmcs" %% "optimus-solver-oj" % "3.1.0"
)
////// Generate a Coursier Bootstrap Jar
// See https://get-coursier.io/docs
//
lazy val bootstrap = taskKey[Unit]("Generate Bootstrap Jar")
bootstrap := {
val logger = ProcessLogger(println(_), println(_))
val coursier_bin = "bin/coursier"
val coursier_url = "https://git.io/coursier-cli"
val mimir_bin = "bin/mimir"
if(!java.nio.file.Files.exists(java.nio.file.Paths.get("bin/coursier"))){
println("Downloading Coursier...")
Process(List(
"curl", "-L",
"-o", coursier_bin,
coursier_url
)) ! logger match {
case 0 =>
case n => sys.error(s"Could not download Coursier")
}
Process(List(
"chmod", "+x", coursier_bin
)) ! logger
println("... done")
}
println("Coursier available. Generating Repository List")
val resolverArgs = resolvers.value.map {
case r: MavenRepository => Seq("-r", r.root)
}.flatten
val (art, file) = packagedArtifact.in(Compile, packageBin).value
val qualified_artifact_name = file.name.replace(".jar", "").replaceFirst("-([0-9.]+)$", "")
val full_artifact_name = s"${organization.value}:${qualified_artifact_name}:${version.value}"
println("Rendering bootstraps for "+full_artifact_name)
for(resolver <- resolverArgs){
println(" "+resolver)
}
println
println("Generating Mimir binary")
Process(List(
coursier_bin,
"bootstrap",
full_artifact_name,
"-f",
"-o", "bin/mimir",
"-r", "central"
)++resolverArgs) ! logger match {
case 0 =>
case n => sys.error(s"Bootstrap failed")
}
println("Generating Mimir-API Server binary")
Process(List(
coursier_bin,
"bootstrap",
full_artifact_name,
"-f",
"-o", "bin/mimir-api",
"-r", "central",
"-M", "mimir.MimirVizier"
)++resolverArgs) ! logger match {
case 0 =>
case n => sys.error(s"Bootstrap failed")
}
}
////// Assembly Plugin //////
// We use the assembly plugin to create self-contained jar files
// https://github.com/sbt/sbt-assembly
test in assembly := {}
assemblyJarName in assembly := "Mimir.jar"
mainClass in assembly := Some("mimir.Mimir")
val nettyMeta = ".*META-INF\\/io\\.netty.*".r
assemblyMergeStrategy in assembly := {
case PathList("org","aopalliance", xs @ _*) => MergeStrategy.last
case PathList("javax", "inject", xs @ _*) => MergeStrategy.last
case PathList("javax", "servlet", xs @ _*) => MergeStrategy.last
case PathList("javax", "activation", xs @ _*) => MergeStrategy.last
case PathList("org", "apache", xs @ _*) => MergeStrategy.last
case PathList("io", "netty", xs @ _*) => MergeStrategy.last
case PathList("com", "google", xs @ _*) => MergeStrategy.last
case PathList("com", "esotericsoftware", xs @ _*) => MergeStrategy.last
case PathList("com", "codahale", xs @ _*) => MergeStrategy.last
case PathList("com", "yammer", xs @ _*) => MergeStrategy.last
case PathList("ch", "qos", xs @ _*) => MergeStrategy.first
case PathList("org", "slf4j", xs @ _*) => MergeStrategy.first
case PathList("org", "codehaus", xs @ _*) => MergeStrategy.last
case PathList("com", "googlecode", xs @ _*) => MergeStrategy.last
case "overview.html" => MergeStrategy.rename
case "about.html" => MergeStrategy.rename
case "META-INF/ECLIPSEF.RSA" => MergeStrategy.last
case "META-INF/mailcap" => MergeStrategy.last
case "META-INF/mimetypes.default" => MergeStrategy.last
case nettyMeta() => MergeStrategy.last
case "plugin.properties" => MergeStrategy.last
case "log4j.properties" => MergeStrategy.last
case x =>
val oldStrategy = (assemblyMergeStrategy in assembly).value
oldStrategy(x)
}
////// Publishing Metadata //////
// use `sbt publish make-pom` to generate
// a publishable jar artifact and its POM metadata
publishMavenStyle := true
pomExtra := <url>http://mimirdb.info</url>
<licenses>
<license>
<name>Apache License 2.0</name>
<url>http://www.apache.org/licenses/</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<url>git@github.com:ubodin/mimir.git</url>
<connection>scm:git:git@github.com:ubodin/mimir.git</connection>
</scm>
/////// Publishing Options ////////
// use `sbt publish` to update the package in
// your own local ivy cache
publishTo := Some(Resolver.file("file", new File(Path.userHome.absolutePath+"/.m2/repository")))
/*/////// Docker Image Creation Options ////////
// use `sbt docker` to generate docker image
import sbtdocker._
enablePlugins(DockerPlugin)
dockerfile in docker := {
val userDataVolMountPoint = "/usr/local/source/"
val sbtPath = s"${userDataVolMountPoint}sbt/bin/sbt"
val initContainer = Seq(
s"if [ -e ${userDataVolMountPoint}initComplete ]",
"then",
"echo 'already initialized...'",
s"(cd ${userDataVolMountPoint}mimir; git pull; ${sbtPath} run)",
"else",
s"""curl -sL "https://github.com/sbt/sbt/releases/download/v0.13.15/sbt-0.13.15.tgz" | gunzip | tar -x -C ${userDataVolMountPoint}""",
s"chmod 0755 ${sbtPath}",
s"git clone https://github.com/UBOdin/mimir.git ${userDataVolMountPoint}mimir",
s"(cd ${userDataVolMountPoint}mimir; ${sbtPath} compile; ${sbtPath} compile)",
s"touch ${userDataVolMountPoint}initComplete",
"echo 'initialization complete...'",
s"(cd ${userDataVolMountPoint}mimir; git pull; ${sbtPath} run)",
"fi"
)
val instructions = Seq(
sbtdocker.Instructions.From("frolvlad/alpine-oraclejdk8"),
sbtdocker.Instructions.Volume(Seq(s"type=volume,source=mimir-vol,target=${userDataVolMountPoint}")),
sbtdocker.Instructions.Run.exec(Seq("apk", "add", "--no-cache", "bash")),
sbtdocker.Instructions.Run.exec(Seq("apk", "add", "--no-cache", "curl")),
sbtdocker.Instructions.Run.exec(Seq("apk", "add", "--no-cache", "git")),
sbtdocker.Instructions.Run.exec(Seq("mkdir", s"${userDataVolMountPoint}")),
sbtdocker.Instructions.Run(s"""( ${initContainer.map(el => s"""echo "$el" >> ${userDataVolMountPoint}initContainer.sh; """).mkString("") } chmod 0755 ${userDataVolMountPoint}initContainer.sh)"""),
sbtdocker.Instructions.EntryPoint.exec(Seq("/bin/bash", "-c", s"${userDataVolMountPoint}initContainer.sh"))
)
Dockerfile(instructions)
}*/