Does not validate Azure or Google blob storage #171

adamrtalbot · 2024-07-05T10:53:16Z

Azure and Google blob storage failed to validate if it was a directory or path. This PR skips validating directories so it does raise an inappropriate error.

nvnieuwk

LGTM!

nvnieuwk · 2024-07-05T10:54:46Z

(waiting for the tests, then I'll merge and release)

adamrtalbot · 2024-07-05T10:54:47Z

Before we merge - is there a way of checking my regex? I couldn't see a good test to add it to.

nvnieuwk · 2024-07-05T10:55:47Z

Before we merge - is there a way of checking my regex? I couldn't see a good test to add it to.

You could add a dummy az:// and gs:// path as an input to a test where existence is checked. It doesn't matter if it exists, because it will be skipped

adamrtalbot · 2024-07-05T10:59:37Z

Before we merge - is there a way of checking my regex? I couldn't see a good test to add it to.

You could add a dummy az:// and gs:// path as an input to a test where existence is checked. It doesn't matter if it exists, because it will be skipped

yeah but, how do I test it? I've never used a custom plugin before 😅

nvnieuwk · 2024-07-05T11:03:55Z

Ah hahahah you can copy paste a test in this file. Feel free to ask me if something is not clear in it :)

adamrtalbot · 2024-07-05T11:04:03Z

OK first attempt here: f70cecc

nvnieuwk · 2024-07-05T11:05:50Z

The schema you used doesn't actually check for file existence :p can you use or create another one?

adamrtalbot · 2024-07-05T11:09:14Z

Corrected? 38b48b7

ewels · 2024-07-05T11:19:46Z

Should we also do this whilst we're here? nextflow-io#37

nvnieuwk · 2024-07-05T11:22:22Z

There's also no exists in that schema: https://github.com/nextflow-io/nf-validation/blob/master/plugins/nf-validation/src/testResources/nextflow_schema_with_samplesheet.json

Also better to not use a schema that has the schema keyword in it, because it will try and read the file.

It does look like no exists tests were in nf-validation. Can you write a small new schema yourself? It needs to contain these keywords at least:

"type": "string",
"format": "file-path",
"exists": true

nvnieuwk · 2024-07-05T11:22:57Z

Should we also do this whilst we're here? nextflow-io#37

Good idea!

nvnieuwk · 2024-07-05T11:25:45Z

@adamrtalbot can you add this line to this file?

nf-validation/plugins/nf-validation/build.gradle

Line 58 in 35fa8d6

implementation 'org.json:json:20240303'

adamrtalbot · 2024-07-05T11:29:26Z

implementation 'org.json:json:20240303'

get yer own PR: #172

adamrtalbot · 2024-07-05T11:32:46Z

@nvnieuwk looks good now! can you give it a final check for me?

CHANGELOG.md

nvnieuwk

Awesome looks good!

nvnieuwk · 2024-07-05T11:44:15Z

Can I merge this?

adamrtalbot · 2024-07-05T12:39:29Z

Can I merge this?

I think so! I haven't been able to test for real yet 😬

nvnieuwk · 2024-07-05T12:54:44Z

Eh it should be fine :)

ewels · 2024-07-05T20:49:14Z

Eh it should be fine :)

Given the history of this plugin, please test it 🙈 😆

nvnieuwk · 2024-07-09T08:18:52Z

@adamrtalbot can you run a test? I don't have access to azure or google blob :)

adamrtalbot · 2024-07-09T10:04:31Z

@adamrtalbot can you run a test? I don't have access to azure or google blob :)

I'll give it a try but I've never done plugin development so might take me some time. Of course you don't actually need a file, you just need a parameter of type file = az:// or gs://.

adamrtalbot · 2024-07-09T10:12:02Z

~~@nvnieuwk are there any existing template repos or anything I can grab and modify instead of starting from scratch?~~

Dur, in ./examples: https://github.com/nextflow-io/nf-validation/tree/0edaedfd172d8d26f539b0f33a4443d3c0ac789c/examples/fromSamplesheetBasic

adamrtalbot · 2024-07-09T10:15:04Z

> ./gradlew check

FAILURE: Build failed with an exception.

* What went wrong:
Could not determine the dependencies of task ':plugins:nf-validation:test'.
> Could not resolve all task dependencies for configuration ':plugins:nf-validation:testRuntimeClasspath'.
   > Could not resolve org.codehaus.groovy:groovy:3.0.14.
     Required by:
         project :plugins:nf-validation
         project :plugins:nf-validation > org.codehaus.groovy:groovy-nio:3.0.14
      > Module 'org.codehaus.groovy:groovy' has been rejected:
           Cannot select module with conflict on capability 'org.codehaus.groovy:groovy:3.0.14' also provided by [org.apache.groovy:groovy:4.0.22(groovyRuntimeElements)]
   > Could not resolve org.codehaus.groovy:groovy-nio:3.0.14.
     Required by:
         project :plugins:nf-validation
      > Module 'org.codehaus.groovy:groovy-nio' has been rejected:
           Cannot select module with conflict on capability 'org.codehaus.groovy:groovy-nio:3.0.14' also provided by [org.apache.groovy:groovy-nio:4.0.22(groovyRuntimeElements)]
   > Could not resolve io.nextflow:nextflow:22.10.0.
     Required by:
         project :plugins:nf-validation
      > No matching variant of project :nextflow:nextflow was found. The consumer was configured to find a runtime of a library compatible with Java 17, packaged as a jar, preferably optimized for standard JVMs, and its dependencies declared externally but:
          - Variant 'apiElements' capability io.nextflow:nextflow:24.06.0-edge declares a library compatible with Java 11, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares an API of a component and the consumer needed a runtime of a component
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'coverageDataElementsForTest' capability io.nextflow:nextflow:24.06.0-edge:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about how its dependencies are found (required its dependencies declared externally)
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
          - Variant 'mainSourceElements' capability io.nextflow:nextflow:24.06.0-edge declares a component, and its dependencies declared externally:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
          - Variant 'runtimeElements' capability io.nextflow:nextflow:24.06.0-edge declares a runtime of a library compatible with Java 11, packaged as a jar, and its dependencies declared externally:
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testFixturesApiElements' capability io.nextflow:nextflow-test-fixtures:24.06.0-edge declares a library, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares an API of a component compatible with Java 21 and the consumer needed a runtime of a component compatible with Java 17
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testFixturesRuntimeElements' capability io.nextflow:nextflow-test-fixtures:24.06.0-edge declares a runtime of a library, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares a component compatible with Java 21 and the consumer needed a component compatible with Java 17
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testResultsElementsForTest' capability io.nextflow:nextflow:24.06.0-edge:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about how its dependencies are found (required its dependencies declared externally)
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
   > Could not resolve io.nextflow:nf-commons:22.10.0.
     Required by:
         project :plugins:nf-validation
      > No matching variant of project :nextflow:nf-commons was found. The consumer was configured to find a runtime of a library compatible with Java 17, packaged as a jar, preferably optimized for standard JVMs, and its dependencies declared externally but:
          - Variant 'apiElements' capability io.nextflow:nf-commons:24.06.0-edge declares a library compatible with Java 11, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares an API of a component and the consumer needed a runtime of a component
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'coverageDataElementsForTest' capability io.nextflow:nf-commons:24.06.0-edge:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about how its dependencies are found (required its dependencies declared externally)
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
          - Variant 'mainSourceElements' capability io.nextflow:nf-commons:24.06.0-edge declares a component, and its dependencies declared externally:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
          - Variant 'runtimeElements' capability io.nextflow:nf-commons:24.06.0-edge declares a runtime of a library compatible with Java 11, packaged as a jar, and its dependencies declared externally:
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testFixturesApiElements' capability io.nextflow:nf-commons-test-fixtures:24.06.0-edge declares a library, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares an API of a component compatible with Java 21 and the consumer needed a runtime of a component compatible with Java 17
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testFixturesRuntimeElements' capability io.nextflow:nf-commons-test-fixtures:24.06.0-edge declares a runtime of a library, packaged as a jar, and its dependencies declared externally:
              - Incompatible because this component declares a component compatible with Java 21 and the consumer needed a component compatible with Java 17
              - Other compatible attribute:
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
          - Variant 'testResultsElementsForTest' capability io.nextflow:nf-commons:24.06.0-edge:
              - Incompatible because this component declares a component of category 'verification' and the consumer needed a library
              - Other compatible attributes:
                  - Doesn't say anything about how its dependencies are found (required its dependencies declared externally)
                  - Doesn't say anything about its target Java environment (preferred optimized for standard JVMs)
                  - Doesn't say anything about its target Java version (required compatibility with Java 17)
                  - Doesn't say anything about its elements (required them packaged as a jar)
                  - Doesn't say anything about its usage (required a runtime)
   > Could not resolve org.apache.groovy:groovy:4.0.22.
     Required by:
         project :plugins:nf-validation > project :nextflow:nextflow
         project :plugins:nf-validation > project :nextflow:nextflow > project :nextflow:nf-commons
         project :plugins:nf-validation > project :nextflow:nextflow > project :nextflow:nf-httpfs
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-nio:4.0.22
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-xml:4.0.22
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-json:4.0.22
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-templates:4.0.22
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-yaml:4.0.22
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-xml:4.0.22 > org.apache.groovy:groovy-bom:4.0.22
      > Module 'org.apache.groovy:groovy' has been rejected:
           Cannot select module with conflict on capability 'org.codehaus.groovy:groovy:4.0.22' also provided by [org.codehaus.groovy:groovy:3.0.14(runtime)]
   > Could not resolve org.apache.groovy:groovy-nio:4.0.22.
     Required by:
         project :plugins:nf-validation > project :nextflow:nextflow
         project :plugins:nf-validation > project :nextflow:nextflow > project :nextflow:nf-commons
         project :plugins:nf-validation > project :nextflow:nextflow > project :nextflow:nf-httpfs
         project :plugins:nf-validation > project :nextflow:nextflow > org.apache.groovy:groovy-xml:4.0.22 > org.apache.groovy:groovy-bom:4.0.22
      > Module 'org.apache.groovy:groovy-nio' has been rejected:
           Cannot select module with conflict on capability 'org.codehaus.groovy:groovy-nio:4.0.22' also provided by [org.codehaus.groovy:groovy-nio:3.0.14(runtime)]

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 2s
18 actionable tasks: 9 executed, 9 up-to-date

adamrtalbot · 2024-07-09T10:18:11Z

> ./gradlew compileGroovy

> Task :nextflow:nextflow:compileGroovy
Note: /Users/adam.talbot/nextflow/modules/nextflow/src/main/groovy/nextflow/sort/BigSort.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :plugins:nf-validation:compileGroovy FAILED
startup failed:
/Users/adam.talbot/nf-validation/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy: 157: [Static type checking] - Cannot call <K,V> org.codehaus.groovy.runtime.DefaultGroovyMethods#subMap(java.util.Map<K, V>, java.util.Collection<K>) with arguments [java.util.Map<java.lang.String, java.lang.String>, java.util.List<java.lang.Object>]
 @ line 157, column 59.
   String,String> newMap = (Map) row.subMap
                                 ^

/Users/adam.talbot/nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy: 867: [Static type checking] - Cannot call <K,V> org.codehaus.groovy.runtime.DefaultGroovyMethods#leftShift(java.util.Map<K, V>, java.util.Map<K, V>) with arguments [java.util.LinkedHashMap<java.lang.String, java.util.LinkedHashMap<java.lang.Object, java.lang.Object>>, java.util.LinkedHashMap<java.lang.Object, java.lang.Object>]
 @ line 867, column 16.
           return [ 'Core Nextflow options' : workflow_summary ] << params_summary as LinkedHashMap
                  ^

2 errors


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':plugins:nf-validation:compileGroovy'.
> Compilation failed; see the compiler error output for details.

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 16s
28 actionable tasks: 10 executed, 18 up-to-date

nvnieuwk · 2024-07-09T10:48:25Z

What is your java version?

adamrtalbot · 2024-07-09T11:09:38Z

What is your java version?

java 17.0.10-tem
groovy 4.0.22

Both installed with sdkman

nvnieuwk · 2024-07-09T11:11:53Z

Can you try again with an older version (the plugin has been developed in java 11). Not sure that this will fix it but I've no idea at the moment why it would be failing

adamrtalbot · 2024-07-09T11:36:27Z

No dice! This is on a Mac using Sonoma 14.5 btw.

> sdk use java 11.0.21-tem

Using java version 11.0.21-tem in this shell.
> ./gradlew compileGroovy
Starting a Gradle Daemon, 3 incompatible Daemons could not be reused, use --status for details

> Task :nextflow:nextflow:compileGroovy
Note: /Users/adam.talbot/nextflow/modules/nextflow/src/main/groovy/nextflow/sort/BigSort.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :plugins:nf-validation:compileGroovy FAILED
startup failed:
/Users/adam.talbot/nf-validation/plugins/nf-validation/src/main/nextflow/validation/SamplesheetConverter.groovy: 157: [Static type checking] - Cannot call <K,V> org.codehaus.groovy.runtime.DefaultGroovyMethods#subMap(java.util.Map<K, V>, java.util.Collection<K>) with arguments [java.util.Map<java.lang.String, java.lang.String>, java.util.List<java.lang.Object>]
 @ line 157, column 40.
                       def newMap = (Map) row.subMap((List) [key] + (List) unique)
                                          ^

/Users/adam.talbot/nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy: 867: [Static type checking] - Cannot call <K,V> org.codehaus.groovy.runtime.DefaultGroovyMethods#leftShift(java.util.Map<K, V>, java.util.Map<K, V>) with arguments [java.util.LinkedHashMap<java.lang.String, java.util.LinkedHashMap<java.lang.Object, java.lang.Object>>, java.util.LinkedHashMap<java.lang.Object, java.lang.Object>]
 @ line 867, column 16.
           return [ 'Core Nextflow options' : workflow_summary ] << params_summary as LinkedHashMap
                  ^

2 errors


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':plugins:nf-validation:compileGroovy'.
> Compilation failed; see the compiler error output for details.

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 25s
28 actionable tasks: 24 executed, 4 up-to-date

nvnieuwk · 2024-07-09T12:40:17Z

Yeah I've no idea if it's because of some Mac issue or something else :/. It's weird because the tests are running

nvnieuwk

Some logging adjustments

...ns/nf-validation/src/main/nextflow/validation/FormatValidators/DirectoryPathValidator.groovy

.../nf-validation/src/main/nextflow/validation/FormatValidators/FilePathPatternValidator.groovy

plugins/nf-validation/src/main/nextflow/validation/FormatValidators/FilePathValidator.groovy

plugins/nf-validation/src/main/nextflow/validation/FormatValidators/PathValidator.groovy

plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

…ators/DirectoryPathValidator.groovy Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

…ators/FilePathPatternValidator.groovy Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

adamrtalbot · 2024-08-07T15:22:31Z

Demonstrated to work:

main.nf:

include { validateParameters } from 'plugin/nf-validation'

workflow {
    validateParameters()
    println("Hi ${params.input}")
}

nextflow_schema.json:

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/nf-core/testpipeline/master/nextflow_schema.json",
  "title": "nf-core/testpipeline pipeline parameters",
  "description": "this is a test",
  "type": "object",
  "definitions": {
    "file_patterns": {
      "title": "Input/output options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "properties": {
        "input": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "default": "az://igenomes/"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/file_patterns"
    }
  ]
}

nextflow.config:

params.input = 'az://igenomes/'

plugins {
    id '[email protected]' // Or 1.1.3 to demonstrate the fix!
}

With [email protected]:

> nextflow run .
Nextflow 24.04.4 is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.04.2
Launching `./main.nf` [shrivelled_morse] DSL2 - revision: a2030e4699
ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: 'az://igenomes/' is not a file, but a directory (az://igenomes/)

 -- Check script 'main.nf' at line: 5 or see '.nextflow.log' file for more details

With [email protected]:

> nextflow run .
Nextflow 24.04.4 is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.04.2
Launching `./main.nf` [admiring_hoover] DSL2 - revision: a2030e4699
Hi az://igenomes/

Does not validate Azure or Google blob storage

e50417e

Azure and Google blob storage failed to validate if it was a directory or path. This PR skips validating directories so it does raise an inappropriate error.

nvnieuwk approved these changes Jul 5, 2024

View reviewed changes

Add tests ignoring for az/s3/gs paths

f70cecc

Correct tests

38b48b7

Correct tests AGAIN

de1fcda

adamrtalbot added 2 commits July 5, 2024 12:30

CHANGELOG

8ab7282

Actually add path

7e47cf2

adamrtalbot commented Jul 5, 2024

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

a22b3f0

nvnieuwk approved these changes Jul 5, 2024

View reviewed changes

Bump nf-validation version

9c9a1fe

mirpedrol approved these changes Jul 5, 2024

View reviewed changes

Merge branch 'master' into do_not_validate_az_and_gcp_paths

5ff250f

adamrtalbot mentioned this pull request Jul 10, 2024

Params outdir should *not* end with a trailing slash seqeralabs/showcase-automation#27

Open

nvnieuwk reviewed Aug 1, 2024

View reviewed changes

adamrtalbot and others added 3 commits August 1, 2024 12:56

Update plugins/nf-validation/src/main/nextflow/validation/FormatValid…

85057af

…ators/DirectoryPathValidator.groovy Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Apply suggestions from code review

5a99d96

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

Update plugins/nf-validation/src/main/nextflow/validation/FormatValid…

1a93ea9

…ators/FilePathPatternValidator.groovy Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

adamrtalbot merged commit 750a56d into nextflow-io:master Aug 7, 2024
3 checks passed

adamrtalbot deleted the do_not_validate_az_and_gcp_paths branch August 7, 2024 15:23

adamrtalbot mentioned this pull request Aug 8, 2024

Update nf-validation to v1.1.4 nextflow-io/plugins#86

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Does not validate Azure or Google blob storage #171

Does not validate Azure or Google blob storage #171

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Does not validate Azure or Google blob storage #171

Does not validate Azure or Google blob storage #171

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adamrtalbot commented Jul 9, 2024 •

edited

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