add --launch-container option in launch command

[munishchouhan]

This PR will add --launch-container option in launch command

[pditommaso]

ok, let's sync with @tcrespog for the sdk

[munishchouhan]

PR to add in sdk
https://github.com/seqeralabs/tower-sdk-gencode/pull/8

[munishchouhan]

PR to add in sdk seqeralabs/tower-sdk-gencode#8

this SDK PR is not correct, checking with @JaimeSeqLabs to fix it

[munishchouhan]

SDK pr has been fixed

[munishchouhan]

@tcrespog is there recent chnages in GoogleBatchPlatform?

Tests are failing for it with new tower sdk

org.opentest4j.AssertionFailedError: expected: <> but was: <
 ERROR: The program tried to reflectively invoke method public java.lang.String io.seqera.tower.model.GoogleBatchConfig.getNextflowConfig() without it being registered for runtime reflection. Add it to the reflection metadata to solve this problem. See https://www.graalvm.org/latest/reference-manual/native-image/metadata/#reflection for help.


 ERROR: Connection error. Check the connection using the command 'tw info'.
>
	at app//org.junit.jupiter.api.AssertionUtils.fail(AssertionUtils.java:55)
	at app//org.junit.jupiter.api.AssertionUtils.failNotEqual(AssertionUtils.java:62)
	at app//org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:182)
	at app//org.junit.jupiter.api.AssertEquals.assertEquals(AssertEquals.java:177)
	at app//org.junit.jupiter.api.Assertions.assertEquals(Assertions.java:1141)
	at app//io.seqera.tower.cli.BaseCmdTest.assertOutput(BaseCmdTest.java:183)
	at app//io.seqera.tower.cli.computeenvs.platforms.GoogleBatchPlatformTest.testAdd(GoogleBatchPlatformTest.java:61)
	at [email protected]/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at [email protected]/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at [email protected]/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

[tcrespog]

is there recent chnages in GoogleBatchPlatform?

Yes, in In GoogleBatchConfig and others: https://github.com/seqeralabs/platform/pull/6691.

[JaimeSeqLabs]

Tests are failing for it with new tower sdk

The program tried to reflectively invoke method public java.lang.String io.seqera.tower.model.GoogleBatchConfig.getNextflowConfig() without it being registered for runtime reflection

I'm assuming the tests failing here are the native ones.
This is most likely because we need to manually add the new method signature to the reflect-config.json file.
(probably more methods that GraalVM missed in the last update)

[pditommaso]

Was the --launch-container option tested?

[munishchouhan]

Was the --launch-container option tested?

I am not sure, how to test it?

[JaimeSeqLabs]

1. Run a local instance of Seqera Platform
2. Point tw-cli to the local instance: export TOWER_API_ENDPOINT=http://localhost:8000/api
3. Do a launch using the new parameter: tw --insecure launch ... --launch-container ...

[pditommaso]

This option allows you to change the nextflow launcher used by Platform when running a workflow. Use for example quay.io/seqeralabs/nf-launcher:j17-24.07.0-edge.

You may want to use https://cloud.stage-seqera.io/ for sake of simplicity and run this "workflow" https://github.com/pditommaso/nf-sleep

When running it should show 24.07.0 as nextflow version.

(or use your local platform as Jaime is suggesting)

[munishchouhan]

Ok finally my pipeline runs and i can test it successfully
client:

% ./build/native/nativeCompile/tw  launch https://github.com/pditommaso/nf-sleep  \
--launch-container quay.io/seqeralabs/nf-launcher:j17-24.07.0-edge

[pditommaso]

Excellent.