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https://issues.apache.org/jira/browse/SPARK-46934?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Dongjoon Hyun updated SPARK-46934:
----------------------------------
Summary: Read/write roundtrip for struct type with special characters with
HMS (was: Unable to create Hive View from certain Spark Dataframe StructType)
> Read/write roundtrip for struct type with special characters with HMS
> ----------------------------------------------------------------------
>
> Key: SPARK-46934
> URL: https://issues.apache.org/jira/browse/SPARK-46934
> Project: Spark
> Issue Type: Improvement
> Components: SQL
> Affects Versions: 4.0.0
> Environment: Tested in Spark 3.3.0, 3.3.2.
> Reporter: Yu-Ting LIN
> Assignee: Kent Yao
> Priority: Major
> Labels: pull-request-available
> Fix For: 4.0.0
>
>
> We are trying to create a Hive View using following SQL command "CREATE OR
> REPLACE VIEW yuting AS SELECT INFO_ANN FROM table_2611810".
> Our table_2611810 has certain columns contain special characters such as "/".
> Here is the schema of this table.
> {code:java}
> contigName string
> start bigint
> end bigint
> names array<string>
> referenceAllele string
> alternateAlleles array<string>
> qual double
> filters array<string>
> splitFromMultiAllelic boolean
> INFO_NCAMP int
> INFO_ODDRATIO double
> INFO_NM double
> INFO_DBSNP_CAF array<string>
> INFO_SPANPAIR int
> INFO_TLAMP int
> INFO_PSTD double
> INFO_QSTD double
> INFO_SBF double
> INFO_AF array<double>
> INFO_QUAL double
> INFO_SHIFT3 int
> INFO_VARBIAS string
> INFO_HICOV int
> INFO_PMEAN double
> INFO_MSI double
> INFO_VD int
> INFO_DP int
> INFO_HICNT int
> INFO_ADJAF double
> INFO_SVLEN int
> INFO_RSEQ string
> INFO_MSigDb array<string>
> INFO_NMD array<string>
> INFO_ANN
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>
> INFO_BIAS string
> INFO_MQ double
> INFO_HIAF double
> INFO_END int
> INFO_SPLITREAD int
> INFO_GDAMP int
> INFO_LSEQ string
> INFO_LOF array<string>
> INFO_SAMPLE string
> INFO_AMPFLAG int
> INFO_SN double
> INFO_SVTYPE string
> INFO_TYPE string
> INFO_MSILEN double
> INFO_DUPRATE double
> INFO_DBSNP_COMMON int
> INFO_REFBIAS string
> genotypes
> array<struct<sampleId:string,alleleDepths:array<int>,ALD:array<int>,AF:array<double>,phased:boolean,calls:array<int>,VD:int,depth:int,RD:array<int>>>
> {code}
> You can see that column INFO_ANN is an array of struct and it contains column
> which has "/" inside such as "cDNA_pos/cDNA_length", etc.
> We believe that it is the root cause that cause the following SparkException:
> {code:java}
> scala> val schema = spark.sql("CREATE OR REPLACE VIEW yuting AS SELECT
> INFO_ANN FROM table_2611810")
> 24/01/31 07:50:02.658 [main] WARN o.a.spark.sql.catalyst.util.package -
> Truncated the string representation of a plan since it was too large. This
> behavior can be adjusted by setting 'spark.sql.debug.maxToStringFields'.
> org.apache.spark.SparkException: Cannot recognize hive type string:
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>,
> column: INFO_ANN
> at
> org.apache.spark.sql.errors.QueryExecutionErrors$.cannotRecognizeHiveTypeError(QueryExecutionErrors.scala:1455)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl$.getSparkSQLDataType(HiveClientImpl.scala:1022)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl$.$anonfun$verifyColumnDataType$1(HiveClientImpl.scala:1037)
> at scala.collection.Iterator.foreach(Iterator.scala:943)
> at scala.collection.Iterator.foreach$(Iterator.scala:943)
> at scala.collection.AbstractIterator.foreach(Iterator.scala:1431)
> at scala.collection.IterableLike.foreach(IterableLike.scala:74)
> at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
> at org.apache.spark.sql.types.StructType.foreach(StructType.scala:102)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl$.org$apache$spark$sql$hive$client$HiveClientImpl$$verifyColumnDataType(HiveClientImpl.scala:1037)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.$anonfun$createTable$1(HiveClientImpl.scala:553)
> at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.$anonfun$withHiveState$1(HiveClientImpl.scala:294)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.liftedTree1$1(HiveClientImpl.scala:225)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.retryLocked(HiveClientImpl.scala:224)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.withHiveState(HiveClientImpl.scala:274)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl.createTable(HiveClientImpl.scala:552)
> at
> org.apache.spark.sql.hive.HiveExternalCatalog.$anonfun$createTable$1(HiveExternalCatalog.scala:286)
> at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
> at
> org.apache.spark.sql.hive.HiveExternalCatalog.withClient(HiveExternalCatalog.scala:101)
> at
> org.apache.spark.sql.hive.HiveExternalCatalog.createTable(HiveExternalCatalog.scala:244)
> at
> org.apache.spark.sql.catalyst.catalog.ExternalCatalogWithListener.createTable(ExternalCatalogWithListener.scala:94)
> at
> org.apache.spark.sql.catalyst.catalog.SessionCatalog.createTable(SessionCatalog.scala:373)
> at
> org.apache.spark.sql.execution.command.CreateViewCommand.run(views.scala:166)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:75)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:73)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:84)
> at
> org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.$anonfun$applyOrElse$1(QueryExecution.scala:98)
> at
> org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$6(SQLExecution.scala:109)
> at
> org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:169)
> at
> org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:95)
> at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
> at
> org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
> at
> org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:98)
> at
> org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:94)
> at
> org.apache.spark.sql.catalyst.trees.TreeNode.$anonfun$transformDownWithPruning$1(TreeNode.scala:584)
> at
> org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:176)
> at
> org.apache.spark.sql.catalyst.trees.TreeNode.transformDownWithPruning(TreeNode.scala:584)
> at
> org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.org$apache$spark$sql$catalyst$plans$logical$AnalysisHelper$$super$transformDownWithPruning(LogicalPlan.scala:30)
> at
> org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning(AnalysisHelper.scala:267)
> at
> org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning$(AnalysisHelper.scala:263)
> at
> org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:30)
> at
> org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:30)
> at
> org.apache.spark.sql.catalyst.trees.TreeNode.transformDown(TreeNode.scala:560)
> at
> org.apache.spark.sql.execution.QueryExecution.eagerlyExecuteCommands(QueryExecution.scala:94)
> at
> org.apache.spark.sql.execution.QueryExecution.commandExecuted$lzycompute(QueryExecution.scala:81)
> at
> org.apache.spark.sql.execution.QueryExecution.commandExecuted(QueryExecution.scala:79)
> at org.apache.spark.sql.Dataset.<init>(Dataset.scala:220)
> at org.apache.spark.sql.Dataset$.$anonfun$ofRows$2(Dataset.scala:100)
> at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
> at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:97)
> at org.apache.spark.sql.SparkSession.$anonfun$sql$1(SparkSession.scala:622)
> at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
> at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:617)
> ... 49 elided
> Caused by: org.apache.spark.sql.catalyst.parser.ParseException:
> Syntax error at or near '/': extra input '/'(line 1, pos 247)== SQL ==
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------^^^
> at
> org.apache.spark.sql.catalyst.parser.ParseException.withCommand(ParseDriver.scala:306)
> at
> org.apache.spark.sql.catalyst.parser.AbstractSqlParser.parse(ParseDriver.scala:143)
> at
> org.apache.spark.sql.catalyst.parser.AbstractSqlParser.parseDataType(ParseDriver.scala:41)
> at
> org.apache.spark.sql.hive.client.HiveClientImpl$.getSparkSQLDataType(HiveClientImpl.scala:1019)
> ... 101 more {code}
> We have checked in the recent code
> [https://github.com/apache/spark/blob/88f121c47778f0755862046d09484a83932cb30b/sql/hive/src/main/scala/org/apache/spark/sql/hive/client/HiveClientImpl.scala#L1045],
> it seems that if we start from our StructType (INFO_ANN) and generates a
> Hive column with FieldSchema, we are still blocked in function
> getSparkSQLDataType in Line 1058.
> {code:java}
> scala> val c = schema.fields(33)
> c: org.apache.spark.sql.types.StructField =
> StructField(INFO_ANN,ArrayType(StructType(StructField(Allele,StringType,true),StructField(Annotation,ArrayType(StringType,true),true),StructField(Annotation_Impact,StringType,true),StructField(Gene_Name,StringType,true),StructField(Gene_ID,StringType,true),StructField(Feature_Type,StringType,true),StructField(Feature_ID,StringType,true),StructField(Transcript_BioType,StringType,true),StructField(Rank,StructType(StructField(rank,StringType,true),StructField(total,StringType,true)),true),StructField(HGVS_c,StringType,true),StructField(HGVS_p,StringType,true),StructField(cDNA_pos/cDNA_length,StructType(StructField(pos,StringType,true),StructField(length,StringType,true)),true),StructField(CDS_pos/CDS_length,StructType(St...
> scala> c.dataType.catalogString
> res9: String =
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>
> scala> val f = new FieldSchema(c.name, c.dataType.catalogString,
> c.getComment().orNull)
> f: org.apache.hadoop.hive.metastore.api.FieldSchema =
> FieldSchema(name:INFO_ANN,
> type:array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>,
> comment:null)
>
> scala> CatalystSqlParser.parseDataType(f.getType)
> org.apache.spark.sql.catalyst.parser.ParseException:
> Syntax error at or near '/': extra input '/'(line 1, pos 247)== SQL ==
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,cDNA_pos/cDNA_length:struct<pos:string,length:string>,CDS_pos/CDS_length:struct<pos:string,length:string>,AA_pos/AA_length:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------^^^
> at
> org.apache.spark.sql.catalyst.parser.ParseException.withCommand(ParseDriver.scala:306)
> at
> org.apache.spark.sql.catalyst.parser.AbstractSqlParser.parse(ParseDriver.scala:143)
> at
> org.apache.spark.sql.catalyst.parser.AbstractSqlParser.parseDataType(ParseDriver.scala:41)
> ... 49 elided{code}
> Possible Solution:
> Are we able to generate c.dataType.catalogString with `` such as
> {code:java}
> scala> c.dataType.catalogString res9: String =
> array<struct<Allele:string,Annotation:array<string>,Annotation_Impact:string,Gene_Name:string,Gene_ID:string,Feature_Type:string,Feature_ID:string,Transcript_BioType:string,Rank:struct<rank:string,total:string>,HGVS_c:string,HGVS_p:string,`cDNA_pos/cDNA_length`:struct<pos:string,length:string>,`CDS_pos/CDS_length`:struct<pos:string,length:string>,`AA_pos/AA_length`:struct<pos:string,length:string>,Distance:int,ERRORS/WARNINGS/INFO:string>>
> {code}
> Then there will not be any SparkException while calling
> CatalystSqlParser.parseDataType(f.getType)
>
> Thanks in advance for your helps.
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