ScalaEvaluate

Executes a Scala script. The script is executed in an environment where relevant imports and variable definitions have been made. See Anduril Scala API for available utility classes. The Table class in that API provides I/O support for BED, CSV, FASTA, FASTQ, gzip and VCF formats.

The following variables are visible during execution. Here, X{1-3} refers to variables X1, X2 and X3.

Variable	Kind	Class	Description
table{1-5}	val	org.anduril.runtime.table.Table	Input tables; null if not provided
table1.*	def	Members	Members of table1 are imported into main name space
table{1-5}File	val	java.io.File	Input files; null if not provided
var{1-3}File	val	java.io.File	Generic inputs; null if not provided
param{1-5}	val	java.lang.String	Value of extra parameter
tableOut	var	org.anduril.runtime.table.Table	If assigned, this table is written to tableOutFile; initially null
tableOutFile	val	java.io.File	Output table file
optOut{1-3}File	val	java.io.File	Generic outputs

Members of table1 (if defined) can be accessed without "table1." qualifier. If any table object is assigned to tableOut, it is written to tableOutFile. All outputs are empty if not explictly written to.

Automatically imported classes include:

java.io.File
scala.collection.immutable.SortedMap
scala.collection.immutable.TreeMap
scala.collection.mutable.ArrayBuffer
org.anduril.runtime.table._
org.anduril.runtime.table.processor.ColumnStatistics

Version	1.0
Bundle	tools
Categories	External
Specialties	generic
Authors	Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker	View/Report issues
Requires	commons-primitives-1.0.jar (jar) ; commons-math3-3.2.jar (jar)
Source files	component.xml ScalaEvaluate.sh
Usage	Example with default values ScalaEvaluate( //scriptFile = ScalaSource, //table1 = CSV, //table2 = CSV, //table3 = CSV, //table4 = CSV, //table5 = CSV, //var1 = IN1, //var2 = IN2, //var3 = IN3, defaultOutput = "", format = "csv", param1 = "", param2 = "", param3 = "", param4 = "", param5 = "", scalaFlags = "", scriptStr = "" )

Type parameters (generics)

IN1
IN2
IN3
OUT1
OUT2
OUT3

Inputs

Name	Type	Mandatory	Description
scriptFile	ScalaSource	Optional	Scala source file. Either this or the parameter must be given.
table1	CSV	Optional	Data table 1, visible as table1 (Table).
table2	CSV	Optional	Data table 2, visible as table2 (Table).
table3	CSV	Optional	Data table 3, visible as table3 (Table).
table4	CSV	Optional	Data table 4, visible as table4 (Table).
table5	CSV	Optional	Data table 5, visible as table5 (Table).
var1	IN1 or Array<IN1> (generic)	Optional	Generic input that may be used for folders, arrays and binaries. Visible as var1 (File).
var2	IN2 or Array<IN2> (generic)	Optional	Generic input that may be used for folders, arrays and binaries. Visible as var2 (File).
var3	IN3 or Array<IN3> (generic)	Optional	Generic input that may be used for folders, arrays and binaries. Visible as var3 (File).

Outputs

Name	Type	Description
table	CSV	Result table.
optOut1	OUT1 or Array<OUT1> (generic)	An optional output that can be used for custom data types.
optOut2	OUT2 or Array<OUT2> (generic)	An optional output that can be used for custom data types.
optOut3	OUT3 or Array<OUT3> (generic)	An optional output that can be used for custom data types.
scriptOut	ScalaSource	Final Scala script that was executed. Used for debugging.

Parameters

Name	Type	Default	Description
defaultOutput	string	""	Name of an input port that is written to the output by default. Example: table1. If empty, no table is written to output by default.
format	string	"csv"	Override input table file formats. The default format for all tables is csv. To override the formats of all tables, set the parameter to one of bed, csv, fasta, fastq or vcf. To override formats for individual tables, use the syntax TABLE=FORMAT,TABLE=FORMAT, where TABLE is one of table1 to table5 and FORMAT is as above.
param1	string	""	Extra parameter, visible as param1 (String).
param2	string	""	Extra parameter, visible as param2 (String).
param3	string	""	Extra parameter, visible as param3 (String).
param4	string	""	Extra parameter, visible as param4 (String).
param5	string	""	Extra parameter, visible as param5 (String).
scalaFlags	string	""	Extra command line flags for the Scala compiler. If multiple flags are given, they are separated by space. Flags to the underlying JVM need to be prefixed with -J, e.g., -J-Xprof.
scriptStr	string	""	Scala source string. Either this or the input must be given. If both are given, this parameter is appended to the input.

Test cases

Test case	Parameters▼	IN scriptFile	IN table1	IN table2	IN table3	IN table4	IN table5	IN var1	IN var2	IN var3	OUT table	OUT optOut1	OUT optOut2	OUT optOut3	OUT scriptOut
case1	properties	scriptFile	table1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	table	(missing)	(missing)	(missing)	(missing)
	parameter.defaultOutput = table1
case2_modify	(missing)	scriptFile	table1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	table	(missing)	(missing)	(missing)	(missing)
case3_join	properties	scriptFile	table1	table2	table3	(missing)	(missing)	(missing)	(missing)	(missing)	table	(missing)	(missing)	(missing)	(missing)
	metadata.timeout=0
case4_join2	(missing)	scriptFile	table1	table2	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	table	(missing)	(missing)	(missing)	(missing)
case5_stats	properties	scriptFile	table1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)
	metadata.timeout=0
case6_collect	(missing)	scriptFile	table1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)
case7_join3	(missing)	scriptFile	table1	table2	table3	(missing)	(missing)	(missing)	(missing)	(missing)	table	(missing)	(missing)	(missing)	(missing)
case8_small	properties	scriptFile	table1	table2	table3	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)
	scalaFlags=-optimize -deprecation

Generated 2019-02-08 07:42:19 by Anduril 2.0.0