diff --git a/assembly/.gitignore b/assembly/.gitignore deleted file mode 100644 index faac96765..000000000 --- a/assembly/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -.DS_Store -*.class -*.log -.idea -.idea/* -*.iml -core/*.iml -.#* - -# sbt specific -dist/* -target/ -lib_managed/ -src_managed/ -project/boot/ -project/plugins/project/ - -# Scala-IDE specific -.scala_dependencies - -out/ diff --git a/assembly/.sbtopts b/assembly/.sbtopts deleted file mode 100644 index e4b7e3ada..000000000 --- a/assembly/.sbtopts +++ /dev/null @@ -1 +0,0 @@ --J-Xmx5G diff --git a/assembly/.travis.yml b/assembly/.travis.yml deleted file mode 100644 index a668ea2d9..000000000 --- a/assembly/.travis.yml +++ /dev/null @@ -1,9 +0,0 @@ -sudo: required -dist: trusty -language: scala -scala: - - 2.11.6 -branches: - only: - - master - - dev diff --git a/assembly/LICENSE b/assembly/LICENSE deleted file mode 100644 index 8dada3eda..000000000 --- a/assembly/LICENSE +++ /dev/null @@ -1,201 +0,0 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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Soon, we will split the code into multiple components, so licensing becomes less ambiguous. - # Changes + **0.0.1** - Assembly system from `reach` v1.3.2 + [more...](CHANGES.md) @@ -58,11 +52,11 @@ More publications from the Reach project are available [here](https://github.com This software requires Java 1.8. -The `jar` is available on Maven Central. To use, simply add the following dependency to your `build.sbt`: +The `jar` is available on Maven Central. To use, simply add the following dependency to your `build.sbt` (NOTE: replace yourVersion with the version you wish to use): ```scala libraryDependencies ++= Seq( - "org.clulab" %% "reach" % "1.3.2" + "org.clulab" %% "reach-assembly" % "yourVersion" ) ``` @@ -78,7 +72,7 @@ Add the generated jar files under `target/` to your `$CLASSPATH`, along with the You can run interactively explore assembly output for various snippets of text using the assembly shell: ```scala -sbt "runMain org.clulab.assembly.AssemblyShell" +sbt "runMain org.clulab.reach.assembly.AssemblyShell" ``` # Modifying the code diff --git a/assembly/build.sbt b/assembly/build.sbt index 9b52f73b7..4f5ad47e0 100644 --- a/assembly/build.sbt +++ b/assembly/build.sbt @@ -1,99 +1,16 @@ -import ReleaseTransformations._ - name := "reach-assembly" -organization := "org.clulab" - -scalaVersion := "2.11.8" - -scalacOptions ++= Seq("-feature", "-unchecked", "-deprecation") - -testOptions in Test += Tests.Argument("-oD") - -parallelExecution in Test := false - -// forward sbt's stdin to forked process -connectInput in run := true - -// don't show output prefix -outputStrategy := Some(StdoutOutput) - -// -// publishing settings -// - -// these are the steps to be performed during release -releaseProcess := Seq[ReleaseStep]( - checkSnapshotDependencies, - inquireVersions, - runClean, - runTest, - setReleaseVersion, - ReleaseStep(action = Command.process("publishSigned", _)), - ReleaseStep(action = Command.process("sonatypeReleaseAll", _)), - commitReleaseVersion, - tagRelease, - setNextVersion, - commitNextVersion, - pushChanges -) - -// publish to a maven repo -publishMavenStyle := true - -// the standard maven repository -publishTo := { - val nexus = "https://oss.sonatype.org/" - if (isSnapshot.value) - Some("snapshots" at nexus + "content/repositories/snapshots") - else - Some("releases" at nexus + "service/local/staging/deploy/maven2") -} - -// let’s remove any repositories for optional dependencies in our artifact -pomIncludeRepository := { _ => false } - -// mandatory stuff to add to the pom for publishing -pomExtra := ( - https://github.com/clulab/reach-assembly - - - Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html - repo - - - - https://github.com/clulab/reach-assembly - https://github.com/clulab/reach-assembly - - - - ghp - Gus Hahn-Powell - gushahnpowell@gmail.com - - ) - -// -// end publishing settings -// - //resolvers += "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots" libraryDependencies ++= { val akkaV = "2.4.3" Seq( "org.scalatest" %% "scalatest" % "2.2.4" % "test", - "org.clulab" %% "reach" % "1.3.2", - "org.clulab" %% "processors-main" % "6.0.0", - "org.clulab" %% "processors-corenlp" % "6.0.0", - "org.clulab" %% "processors-models" % "6.0.0", - "com.typesafe" % "config" % "1.2.1", - "commons-io" % "commons-io" % "2.4", + //"com.typesafe" % "config" % "1.2.1", + //"commons-io" % "commons-io" % "2.4", // logging - "ch.qos.logback" % "logback-classic" % "1.1.7", - "com.typesafe.scala-logging" %% "scala-logging" % "3.4.0", + //"ch.qos.logback" % "logback-classic" % "1.1.7", + //"com.typesafe.scala-logging" %% "scala-logging" % "3.4.0", // graph-based CSP "org.choco-solver" % "choco-graph" % "3.3.0", // Twirl @@ -109,14 +26,4 @@ libraryDependencies ++= { "com.typesafe.akka" %% "akka-slf4j" % akkaV, "com.typesafe.akka" %% "akka-http-xml-experimental" % akkaV ) -} - -// settings for building project website - -site.settings -// include documentation -site.includeScaladoc() - -ghpages.settings - -git.remoteRepo := "git@github.com:clulab/reach-assembly.git" +} \ No newline at end of file diff --git a/assembly/project/build.properties b/assembly/project/build.properties deleted file mode 100644 index d638b4f34..000000000 --- a/assembly/project/build.properties +++ /dev/null @@ -1 +0,0 @@ -sbt.version = 0.13.8 \ No newline at end of file diff --git a/assembly/project/plugins.sbt b/assembly/project/plugins.sbt deleted file mode 100644 index 07c111baa..000000000 --- a/assembly/project/plugins.sbt +++ /dev/null @@ -1,7 +0,0 @@ -// used for building project website -resolvers += "jgit-repo" at "http://download.eclipse.org/jgit/maven" -addSbtPlugin("com.typesafe.sbt" % "sbt-ghpages" % "0.5.4") - -addSbtPlugin("com.jsuereth" % "sbt-pgp" % "1.0.0") -addSbtPlugin("org.xerial.sbt" % "sbt-sonatype" % "1.1") -addSbtPlugin("com.github.gseitz" % "sbt-release" % "1.0.3") diff --git a/assembly/src/main/resources/logback.xml b/assembly/src/main/resources/logback.xml deleted file mode 100644 index 9127da939..000000000 --- a/assembly/src/main/resources/logback.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - - - logging.loglevel - - - - logging.logfile - - - - %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n - - - - - - ${logfile} - - %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n - - - - - - - - - diff --git a/assembly/src/main/resources/application.conf b/assembly/src/main/resources/reference.conf similarity index 72% rename from assembly/src/main/resources/application.conf rename to assembly/src/main/resources/reference.conf index 4468d2737..8aeeb0551 100644 --- a/assembly/src/main/resources/application.conf +++ b/assembly/src/main/resources/reference.conf @@ -2,43 +2,8 @@ # Configuration file for reach-assembly # -# the encoding of input and output files -encoding = "utf-8" - -# this is a list of sections that we should ignore -ignoreSections = ["references", "materials", "materials|methods", "methods", "supplementary-material"] - -# context engine config -contextEngine { - type = Policy4 - params = { - bound = 3 - } -} - -logging { - # defines project-wide logging level - loglevel = INFO - # this log file gets overwritten every time ReachCLI is executed - # so you should copy it if you want to keep it around - logfile = ${HOME}/reach-assembly.log -} - -# grounding configuration -grounding: { - # List of AdHoc grounding files to insert, in order, into the grounding search sequence. - # Each element of the list is a map of KB filename and optional meta info (not yet used): - # example: { kb: "adhoc.tsv", source: "NMZ at CMU" } - adHocFiles: [ - { kb: "NER-Grounding-Override.tsv.gz", source: "MITRE/NMZ/BG feedback overrides" } - ] - - # flag to turn off the influence of species on grounding - overrideSpecies = true -} - # number of simultaneous threads to use for parallelization -threadLimit = 2 +#threadLimit = 2 # settings for assembly assembly { diff --git a/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala b/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala index 0937ef848..f766ebfb9 100644 --- a/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala +++ b/assembly/src/main/scala/org/clulab/reach/assembly/AssemblyShell.scala @@ -8,7 +8,7 @@ import jline.console.ConsoleReader import jline.console.history.FileHistory import org.clulab.reach.display._ import org.clulab.reach.{context, ReachSystem} -import org.clulab.assembly.display._ +import org.clulab.reach.assembly.display._ object AssemblyShell extends App { diff --git a/assembly/version.sbt b/assembly/version.sbt deleted file mode 100644 index 7131d3537..000000000 --- a/assembly/version.sbt +++ /dev/null @@ -1 +0,0 @@ -version in ThisBuild := "0.0.2-SNAPSHOT" diff --git a/build.sbt b/build.sbt index c1fbf29ca..1c39f543b 100644 --- a/build.sbt +++ b/build.sbt @@ -68,16 +68,20 @@ lazy val root = (project in file(".")) (Keys.`package` in (main, Compile)).value } ) - .aggregate(main, export) - .dependsOn(main, export) // so that we can import from the console + .aggregate(main, assembly, export) + .dependsOn(main, assembly, export) // so that we can import from the console lazy val main = project .settings(commonSettings:_*) -lazy val export = project +lazy val assembly = project .settings(commonSettings:_*) .dependsOn(main) +lazy val export = project + .settings(commonSettings:_*) + .dependsOn(main, assembly) + // // publishing settings //