nextflow-io / nextflow-io/nextflow

Azure: Params File path cannot be a blob container 'az://'

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stale storage/azure
Dominant language
Groovy
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Merged PRs (30d)
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Description

Bug report

Expected behavior and actual behavior

Expecting that ability to reference a azure blob container for -params-file 'az://full/path/param.json'.

Actual behavior is a NextFlow error Missing Nextflow session which stop application from running. If -params-file file is on local file system, works as expected.

Steps to reproduce the problem
Program output

Top part of the stackTrace. Full nextflow.log attached.

Apr-11 10:33:09.445 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-azure@1.3.3
Apr-11 10:33:09.468 [main] DEBUG nextflow.file.FileHelper - > Added 'AzFileSystemProvider' to list of installed providers [az]
Apr-11 10:33:09.468 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-azure' required to handle file: az://root/params.json
Apr-11 10:33:09.472 [main] DEBUG n.cloud.azure.file.AzPathFactory - Creating Azure path factory
Apr-11 10:33:09.473 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.IllegalStateException: Missing Nextflow session
        at nextflow.cloud.azure.config.AzConfig.getConfig(AzConfig.groovy:66)
        at nextflow.cloud.azure.config.AzConfig.getConfig(AzConfig.groovy:72)
        at nextflow.cloud.azure.file.AzPathFactory.parseUri(AzPathFactory.groovy:51)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:567)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
        at nextflow.file.FileSystemPathFactory$_parse_closure1.doCall(FileSystemPathFactory.groovy:76)
        at nextflow.file.FileSystemPathFactory$_parse_closure1.call(FileSystemPathFactory.groovy)
        at nextflow.file.FileSystemPathFactory.lookup0(FileSystemPathFactory.groovy:104)
        at nextflow.file.FileSystemPathFactory.parse(FileSystemPathFactory.groovy:76)
        at nextflow.file.FileHelper.asPath0(FileHelper.groovy:309)
        at nextflow.file.FileHelper.asPath(FileHelper.groovy:297)
        at nextflow.cli.CmdRun.validateParamsFile(CmdRun.groovy:641)
        at nextflow.cli.CmdRun.memoizedMethodPriv$parsedParamsMap(CmdRun.groovy:574)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

nextflow.log

Environment
  • Nextflow version: 23.10.1.5891
  • Java version: [?]
  • Operating system: Ubuntu 20.04.6
  • Bash version: 5.0.17
Additional context

Command being executed : nextflow -log nextflow.log -c azure_batch.config run 'https://github.com/DarianHole/test-nextflow' -w 'az://root/workdir/' --outdir 'az://root/outputs/' -params-file 'az://root/params.json'

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with nextflow.cli.CmdRun.validateParamsFile and trace the failing path through nextflow.file.FileHelper, nextflow.cloud.azure.file.AzPathFactory, and nextflow.cloud.azure.config.AzConfig. Reproduce the command using the listed az:// params file and confirm that remote parameter loading no longer fails with Missing Nextflow session.

Written by the indexing model from the issue text.

Assessment

Tech stack
azure, groovy
Domain
cloud
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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