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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:

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

Type parameters (generics)

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


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