From c5c02c6732bac0283039ca85fef5096f86863877 Mon Sep 17 00:00:00 2001 From: SemanticBeeng Date: Sun, 9 Feb 2020 09:14:33 -0800 Subject: [PATCH] `#todo` fix [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala:102:16: not found: value spark_bam [error] import spark_bam._, hammerlab.path._ [error] ^ [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala:102:29: not found: value hammerlab [error] import spark_bam._, hammerlab.path._ [error] ^ [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala:103:23: not found: value Path [error] val bamPath = Path(resolvedPath) [error] ^ [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala:106:12: value loadReads is not a member of org.apache.spark.SparkContext [error] possible cause: maybe a semicolon is missing before `value loadReads'? [error] .loadReads(bamPath) [error] ^ [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/VCF/VCFRelation.scala:3:11: object projectglow is not a member of package io [error] import io.projectglow.Glow [error] ^ [error] /development/projects/05_ds/spark/bdg-sequila/src/main/scala/org/biodatageeks/sequila/datasources/VCF/VCFRelation.scala:35:7: not found: value Glow [error] Glow.transform(m.toLowerCase(), inputDf, Map("reference_genome_path" -> ref_genome_path.get)) [error] ^ [error] 6 errors found See fix for `AliasViewChild` as per https://github.com/apache/spark/pull/22713 --- .../scala/org/biodatageeks/sequila/utvf/SeQuiLaAnalyzer.scala | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/main/scala/org/biodatageeks/sequila/utvf/SeQuiLaAnalyzer.scala b/src/main/scala/org/biodatageeks/sequila/utvf/SeQuiLaAnalyzer.scala index 52de1f49..f159afc0 100644 --- a/src/main/scala/org/biodatageeks/sequila/utvf/SeQuiLaAnalyzer.scala +++ b/src/main/scala/org/biodatageeks/sequila/utvf/SeQuiLaAnalyzer.scala @@ -66,7 +66,9 @@ class SeQuiLaAnalyzer(catalog: SessionCatalog, conf: SQLConf) extends Analyzer(c Batch("Post-Hoc Resolution", Once, postHocResolutionRules: _*), Batch("SeQuiLa", Once,sequilaOptmazationRules: _*), //SeQuilaOptimization rules Batch("View", Once, - /*#todo AliasViewChild*/EliminateView), + /*#todo AliasViewChild + * https://github.com/mgaido91/spark/blob/0d334e33dcbbfbbf3c69cd0c26b5ce497a77675c/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/analysis/view.scala#L31-L50 + * */EliminateView), Batch("Nondeterministic", Once, PullOutNondeterministic), Batch("UDF", Once,