[ADAM-1889][ADAM-1884] updated ReferenceRegion in python #1892
Conversation
Test FAILed. Build result: ABORTED[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1892/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains ed66b35 # timeout=10Checking out Revision ed66b35 (origin/pr/1892/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ed66b35f1a212be8d41703f080721386a9ec0f51First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result ABORTEDNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
Jenkins, retest this please. |
Test FAILed. Build result: ABORTED[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1892/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains ed66b35 # timeout=10Checking out Revision ed66b35 (origin/pr/1892/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ed66b35f1a212be8d41703f080721386a9ec0f51First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result ABORTEDNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
Test FAILed. Build result: FAILURE[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1892/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 65c1794 # timeout=10Checking out Revision 65c1794 (origin/pr/1892/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 65c179418ba8f697b5a7965f19a9f5280c3f432dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
Test PASSed. |
Test PASSed. |
@@ -725,7 +725,7 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging { | |||
* @return Returns a new GenomicRDD containing only data that overlaps the | |||
* querys region. | |||
*/ | |||
def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): U = { | |||
def filterByOverlappingRegions(querys: java.lang.Iterable[ReferenceRegion]): U = { |
akmorrow13
Jan 29, 2018
Author
Contributor
@heuermh we needed to change this to be accessible to python (py4j takes a python iterator and converts it to java ArrayList > java.lang.Iterable). Is there a better way to do this?
@heuermh we needed to change this to be accessible to python (py4j takes a python iterator and converts it to java ArrayList > java.lang.Iterable). Is there a better way to do this?
heuermh
Jan 29, 2018
Member
The pattern we've been using so far is to have two methods, one marked as Java-friendly
. I'd recommend that here, unless the Scala or Java compiler isn't smart enough to distinguish the two different versions.
The pattern we've been using so far is to have two methods, one marked as Java-friendly
. I'd recommend that here, unless the Scala or Java compiler isn't smart enough to distinguish the two different versions.
akmorrow13
Jan 29, 2018
Author
Contributor
@heuermh can you give me an example of this so I can copy the style you have been using?
@heuermh can you give me an example of this so I can copy the style you have been using?
heuermh
Jan 29, 2018
Member
GenomicRDD has a Java friendly transmute method, https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala#L221 and others, just search for "friendly" ;)
GenomicRDD has a Java friendly transmute method, https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala#L221 and others, just search for "friendly" ;)
Test PASSed. |
* @param end end position | ||
* @return Reference Region for these genomic coordinates | ||
*/ | ||
def fromGenomicRange(referenceName: String, start: Long, end: Long): ReferenceRegion = { |
heuermh
Jan 29, 2018
Member
Is this method necessary? In other words, is it difficult to call ReferenceRegion(referenceName, start, end)
from Python?
Is this method necessary? In other words, is it difficult to call ReferenceRegion(referenceName, start, end)
from Python?
akmorrow13
Jan 29, 2018
Author
Contributor
you cannot call ReferenceRegion.apply(referenceName, start, end) from python.
you cannot call ReferenceRegion.apply(referenceName, start, end) from python.
heuermh
Jan 29, 2018
Member
ok
ok
@@ -725,7 +725,7 @@ trait GenomicRDD[T, U <: GenomicRDD[T, U]] extends Logging { | |||
* @return Returns a new GenomicRDD containing only data that overlaps the | |||
* querys region. | |||
*/ | |||
def filterByOverlappingRegions(querys: Iterable[ReferenceRegion]): U = { | |||
def filterByOverlappingRegions(querys: java.lang.Iterable[ReferenceRegion]): U = { |
heuermh
Jan 29, 2018
Member
The pattern we've been using so far is to have two methods, one marked as Java-friendly
. I'd recommend that here, unless the Scala or Java compiler isn't smart enough to distinguish the two different versions.
The pattern we've been using so far is to have two methods, one marked as Java-friendly
. I'd recommend that here, unless the Scala or Java compiler isn't smart enough to distinguish the two different versions.
package \ | ||
-DskipTests \ | ||
-P python \ | ||
test \ |
heuermh
Jan 29, 2018
Member
Don't we need package
for the line ./bin/pyadam < scripts/jenkins-test-pyadam.py
below (package
includes test
)?
Don't we need package
for the line ./bin/pyadam < scripts/jenkins-test-pyadam.py
below (package
includes test
)?
akmorrow13
Jan 30, 2018
Author
Contributor
Doesn't seem like it, the tests are passing currently.
Doesn't seem like it, the tests are passing currently.
fnothaft
Feb 2, 2018
Member
Yeah, we shouldn't need it.
Yeah, we shouldn't need it.
Test PASSed. |
Test PASSed. |
ping @fnothaft for review |
Merged! Thanks @akmorrow13! |
No description provided.