[BEAM-646] Explicitly pass Pipeline in AppliedPTransform

[tgroh]

Be sure to do all of the following to help us incorporate your contribution
quickly and easily:

• Make sure the PR title is formatted like:
  [BEAM-<Jira issue #>] Description of pull request
• Make sure tests pass via mvn clean verify. (Even better, enable
  Travis-CI on your fork and ensure the whole test matrix passes).
• Replace <Jira issue #> in the title with the actual Jira issue
  number, if there is one.
• If this contribution is large, please file an Apache
  Individual Contributor License Agreement.

---

This changes the signature to only use expanded PInputs and POutputs.
This also requires passing the Pipeline object directly, as a root input
(PBegin) expands to no PValues, so the Pipeline cannot be reobtained
from the expansion.

[tgroh]

R: @kennknowles

[kennknowles]

Yup, since an expanded PInput might not actually have anything in it, you can't use that to grab the pipeline.

[kennknowles]

(LGTM)

[asfbot]

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/beam_PreCommit_Java_MavenInstall/7254/

Build result: ABORTED

[...truncated 8506 lines...] ... 31 moreCaused by: java.lang.RuntimeException: The forked VM terminated without properly saying goodbye. VM crash or System.exit called?Command was /bin/sh -c cd /home/jenkins/jenkins-slave/workspace/beam_PreCommit_Java_MavenInstall@2/sdks/java/harness && /usr/local/asfpackages/java/jdk1.8.0_102/jre/bin/java org.apache.maven.surefire.booter.ForkedBooter /home/jenkins/jenkins-slave/workspace/beam_PreCommit_Java_MavenInstall@2/sdks/java/harness/target/surefire/surefire7206054842057175277tmp /home/jenkins/jenkins-slave/workspace/beam_PreCommit_Java_MavenInstall@2/sdks/java/harness/target/surefire/surefire_164820059904913692047tmp at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:590) at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:460) at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:229) at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:201) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:1026) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:862) at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:755) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134) ... 32 more2017-02-09T20:38:45.552 [ERROR] 2017-02-09T20:38:45.552 [ERROR] Re-run Maven using the -X switch to enable full debug logging.2017-02-09T20:38:45.552 [ERROR] 2017-02-09T20:38:45.552 [ERROR] For more information about the errors and possible solutions, please read the following articles:2017-02-09T20:38:45.552 [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException2017-02-09T20:38:45.552 [ERROR] 2017-02-09T20:38:45.552 [ERROR] After correcting the problems, you can resume the build with the command2017-02-09T20:38:45.552 [ERROR] mvn -rf :beam-sdks-java-harnessBuild was abortedchannel stoppedSetting status of 3c6bea0 to FAILURE with url https://builds.apache.org/job/beam_PreCommit_Java_MavenInstall/7254/ and message: 'Build finished. 'Using context: Jenkins: Maven clean install
--none--

[tgroh]

retest this please

[coveralls]

Coverage increased (+0.01%) to 69.728% when pulling 3c6bea0 on tgroh:explicit_applied_transform_pipeline into 2eeeaa2 on apache:master.

[asfbot]

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/beam_PreCommit_Java_MavenInstall/7262/
--none--