New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Visibility from Java, jrdd has private access in AvroGenomicRDD #1538

Closed
heuermh opened this Issue May 18, 2017 · 4 comments

Comments

Projects
2 participants
@heuermh
Member

heuermh commented May 18, 2017

SparkConf conf = new SparkConf()...
SparkContext sc = new SparkContext(conf);
JavaADAMContext jac = new JavaADAMContext(new ADAMContext(sc));
AlignmentRecordRDD alignments = jac.loadAlignments(args[0]);
JavaRDD<AlignmentRecord> rdd = alignments.jrdd;

I thought this worked before; perhaps we made a visibility change in GenomicRDD that prevents access from outside the org.bdgenomics.adam.rdd package

[ERROR] /adam-examples/src/main/java/com/github/heuermh/adam/examples/JavaCountAlignments.java:55: error: jrdd has private access in AvroGenomicRDD
[ERROR]         JavaRDD<AlignmentRecord> rdd = alignments.jrdd;
[ERROR]                                                  ^
[ERROR] 1 error
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft May 18, 2017

Member

It doesn't show as private, but it is a lazy val, which I'm guessing is the issue.

Member

fnothaft commented May 18, 2017

It doesn't show as private, but it is a lazy val, which I'm guessing is the issue.

@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh May 18, 2017

Member

Same happens with rrd, which isn't lazy

Member

heuermh commented May 18, 2017

Same happens with rrd, which isn't lazy

@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft May 18, 2017

Member

Add a paren:

fnothaft$ javap -cp adam-core/target/adam-core_2.10-0.23.0-SNAPSHOT.jar 

org.bdgenomics.adam.rdd.GenomicRDD
public interface org.bdgenomics.adam.rdd.GenomicRDD<T, U extends org.bdgenomics.adam.rdd.GenomicRDD<T, U>> {
  public abstract org.apache.spark.rdd.RDD<T> rdd();
  public abstract org.bdgenomics.adam.models.SequenceDictionary sequences();
  public abstract org.apache.spark.api.java.JavaRDD<T> jrdd();
Member

fnothaft commented May 18, 2017

Add a paren:

fnothaft$ javap -cp adam-core/target/adam-core_2.10-0.23.0-SNAPSHOT.jar 

org.bdgenomics.adam.rdd.GenomicRDD
public interface org.bdgenomics.adam.rdd.GenomicRDD<T, U extends org.bdgenomics.adam.rdd.GenomicRDD<T, U>> {
  public abstract org.apache.spark.rdd.RDD<T> rdd();
  public abstract org.bdgenomics.adam.models.SequenceDictionary sequences();
  public abstract org.apache.spark.api.java.JavaRDD<T> jrdd();
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh May 18, 2017

Member

Ah right, thanks

Member

heuermh commented May 18, 2017

Ah right, thanks

@heuermh heuermh closed this May 18, 2017

@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment