ArrayConstructor component output name

[Ville Rantanen]

Alejandra Cervera created an issue 2 days ago

The output of ArrayConstructor should be named out and not array to make it more consistent with other components.

what say we?

[Ville Rantanen]

i guess the output port name is not hardcoded in core/scala functions?

[Kristian Ovaska]

Renamed the port in ArrayConstructor and ArrayCombiner. It is hardcoded in a few places in the core. Also modified sequencing so it compiles after the change.

[Alejandra Cervera]

we are getting an error when using makeArray saying the output port name of ArrayConstructor is wrong. Can it be related to this? Same script was working yesterday and the script does not call ArrayConstructor explicitly, just makeArray

[Kristian Ovaska]

Yes, it can be related. Have you rebuilt bundles? What is the script and what is the error?

[Mikko Kivikoski]

[ERROR <run-workflow>] IllegalArgumentException: out port name array in component anduril.builtin.ArrayConstructor not found. [ERROR <run-workflow>] java.lang.IllegalArgumentException: out port name array in component anduril.builtin.ArrayConstructor not found. [ERROR <run-workflow>] at org.anduril.runtime.Component.apply(Component.scala:34) [ERROR <run-workflow>] at org.anduril.runtime.package$.makeArray(Tools.scala:168) [ERROR <run-workflow>] at network01$.<init>(pycloneAndurilTutorialTest.scala:19) [ERROR <run-workflow>] at network01$.<clinit>(pycloneAndurilTutorialTest.scala) [ERROR <run-workflow>] at java.lang.Class.forName0(Native Method) [ERROR <run-workflow>] at java.lang.Class.forName(Class.java:348) [ERROR <run-workflow>] at org.anduril.core.engine.NetworkEvaluator.loadWorkflowJAR(NetworkEvaluator.java:229) [ERROR <run-workflow>] at org.anduril.core.engine.NetworkEvaluator.evaluate(NetworkEvaluator.java:146)

#!/usr/bin/env anduril

import anduril.builtin. import anduril.tools. import anduril.microarray. import org.anduril.runtime.

object network01 {

val bashInput = INPUT("bashInput") val configFile = INPUT("config.fimplate") // config file's standard part, appended wiht sample specific sections later on val configSamples = INPUT("config.sample.fimplate") // Template for sample specific sections val tsvFiles = NamedMapCSV tsvFiles("SRR385938.tsv") = INPUT(path="tsv/SRR385938.tsv").out tsvFiles("SRR385939.tsv") = INPUT(path="tsv/SRR385939.tsv").out tsvFiles("SRR385940.tsv") = INPUT(path="tsv/SRR385940.tsv").out tsvFiles("SRR385941.tsv") = INPUT(path="tsv/SRR385941.tsv").out

val results=BashEvaluate(array1=makeArray(tsvFiles), //array2=INarray2, //array3=INarray3, command=bashInput, var1=configFile, var2=configSamples, //var6=INf, //vararray=INarray4, echoStdOut=true, failOnErr=true, param1="3", param2="", param3="", param4="", param5="", script="")

}

[Ville Rantanen]

there's something left over from earlier builds/commits. it works when you

cd $ANDURIL_HOME && hg pull && hg up -C && anduril build anduril -f

[Mikko Kivikoski]

Thanks Ville!