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nfdi4plants / arc-validate

Home of all the tools and libraries to create and run validation of ARCs
https://nfdi4plants.github.io/arc-validate/
MIT License
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validation error #36

Open SaibotMagd opened 11 months ago

SaibotMagd commented 11 months ago

the command: bash arc-validate.sh -p /arc/cmqtl_val1_arc -v inside the docker container gives me this error message

+ arc-validate -p /arc/cmqtl_val1_arc -v
Internal Error:                         
The option value was None (Parameter 'option')
"   at Microsoft.FSharp.Core.OptionModule.GetValue[T](FSharpOption`1 option) in D:\a\_work\1\s\src\FSharp.Core\option.fs:line 13
   at ArcValidation.CvTokenHelperFunctions.CvContainer.isPartOfInvestigation@79-2.Invoke(ICvBase x)
   at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
   at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
   at ArcValidation.InformationExtraction.Investigation.getContactsContainer@60.Invoke(CvContainer cv) in /opt/arc-validate/src/ArcValidation/InformationExtraction.fs:line 60
   at Microsoft.FSharp.Collections.Internal.IEnumerator.next@246[T](FSharpFunc`2 f, IEnumerator`1 e, FSharpRef`1 started, Unit unitVar0) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 248
   at Microsoft.FSharp.Collections.Internal.IEnumerator.filter@236.System.Collections.IEnumerator.MoveNext() in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 250
   at Microsoft.FSharp.Collections.SeqModule.ToList[T](IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 966
   at ArcValidation.TestGeneration.Critical.Arc.ISA.generateISATests(ArcConfig arcConfig) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcISA.fs:line 22
   at ARCValidate.main(String[] argv) in /opt/arc-validate/src/arc-validate/Program.fs:line 29"
omaus commented 11 months ago

Could you provide the Investigation file ("isa.investigation.xlsx") of this ARC here? If it contains sensible data which is not suited for publicity, you can also email me (maus@nfdi4plants.org).

SaibotMagd commented 11 months ago

That's no problem since I used the openly published dataset from Micha Wijesingha Ahchige published @ https://git.nfdi4plants.org/micwij/cmqtl_val1_arc

SaibotMagd commented 11 months ago

I also tried: https://git.nfdi4plants.org/x.zhou/sample_arc_model from Xiaoran Zhou (same error message). and: https://gitlab.nfdi4plants.de/martinkuhl/samplearc_proteomics which leads to this error message:

+ arc-validate -p /arc/SampleARC_Proteomics -v
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal1.mzLite failed in 00:00:00.0130000. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(MS) at Cell: W2
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal2.mzLite failed in 00:00:00.0130000. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(MS) at Cell: W3
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal3.mzLite failed in 00:00:00.0130000. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(MS) at Cell: W4
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal4.mzLite failed in 00:00:00.0130000. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(MS) at Cell: W5
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal1.prot failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(Computation analysis) at Cell: K2
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal2.prot failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(Computation analysis) at Cell: K3
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal3.prot failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(Computation analysis) at Cell: K4
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.Filesystem.DataPathNames.minimal4.prot failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/assays/assay1/isa.assay.xlsx in Worksheet Some(Computation analysis) at Cell: K5
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.FileSystem.generateArcFileSystemTests@73-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcFileSystem.fs:line 73
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.ISA.Semantic.Investigation.Person.Person1 [David Zimmer].Affiliation failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/isa.investigation.xlsx
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.ISA.generateISATests@45-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcISA.fs:line 45
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
[14:53:26 ERR] Critical.ISA.Semantic.Investigation.Person.Person2 [Martin Kuhl].Affiliation failed in 00:00:00. 
Actual entity is not present: /arc/SampleARC_Proteomics/isa.investigation.xlsx
   at ArcValidation.OntologyHelperFunctions.throwError@36.Invoke(String msg)
   at ArcValidation.OntologyHelperFunctions.throwError(FSharpFunc`2 failStringFunction, ValidationResult result) in /opt/arc-validate/src/ArcValidation/OntologyHelperFunctions.fs:line 36
   at ArcValidation.TestGeneration.Critical.Arc.ISA.generateISATests@45-16.Invoke(Unit unitVar0) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcISA.fs:line 45
   at Expecto.Impl.execTestAsync@569-1.Invoke(Unit unitVar)
   at Microsoft.FSharp.Control.AsyncPrimitives.CallThenInvoke[T,TResult](AsyncActivation`1 ctxt, TResult result1, FSharpFunc`2 part2) in D:\a\_work\1\s\src\FSharp.Core\async.fs:line 508 <Expecto>
SaibotMagd commented 11 months ago

And: https://git.nfdi4plants.org/brilator/samplearc_rnaseq


root@7d1289fefede:/opt/arc-validate# bash arc-validate.sh -p /arc/samplearc_rnaseq -v
+ arc-validate -p /arc/samplearc_rnaseq -v
Internal Error:                         
The option value was None (Parameter 'option')
"   at Microsoft.FSharp.Core.OptionModule.GetValue[T](FSharpOption`1 option) in D:\a\_work\1\s\src\FSharp.Core\option.fs:line 13
   at ArcValidation.CvTokenHelperFunctions.CvContainer.isPartOfInvestigation@79-2.Invoke(ICvBase x)
   at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
   at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
   at ArcValidation.InformationExtraction.Investigation.getContactsContainer@60.Invoke(CvContainer cv) in /opt/arc-validate/src/ArcValidation/InformationExtraction.fs:line 60
   at Microsoft.FSharp.Collections.Internal.IEnumerator.next@246[T](FSharpFunc`2 f, IEnumerator`1 e, FSharpRef`1 started, Unit unitVar0) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 248
   at Microsoft.FSharp.Collections.Internal.IEnumerator.filter@236.System.Collections.IEnumerator.MoveNext() in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 250
   at Microsoft.FSharp.Collections.SeqModule.ToList[T](IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 966
   at ArcValidation.TestGeneration.Critical.Arc.ISA.generateISATests(ArcConfig arcConfig) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcISA.fs:line 22
   at ARCValidate.main(String[] argv) in /opt/arc-validate/src/arc-validate/Program.fs:line 29"

So I started to try every dataset I could find in the plants-datahub, but couldn't find one working.

omaus commented 10 months ago

There was an error in handling filepaths in the current ARC Validation version which I fixed yesterday. Maybe this also fixed this issue...

Otherwise, we will launch the new version of the Validation soon™ which will have this bug fixed.

MicheleBortol commented 7 months ago

Hi, I am reviving this issue because I have encountered the same error as @SaibotMagd I have this issue both with the docker container and with the CI/CD pipeline on datahub. You can find the pipeline error here:https://git.nfdi4plants.org/michele.bortolomeazzi/mben_resolve/-/jobs/2532

This is the error I am getting from Docker:

root@d7ca40cef5e0:/arc# ls -alh
total 48K
drwxr-xr-x  8 root root 4.0K Nov 22 16:30 . 
drwxr-xr-x 22 root root 4.0K Nov 24 09:23 ..
drwxr-xr-x  2 root root 4.0K Nov 22 15:31 .arc
drwxr-xr-x  9 root root 4.0K Nov 22 16:30 .git
-rw-r-----  1 root root 1.8K Nov 22 15:31 .gitattributes
-rw-r--r--  1 root root  642 Nov 22 16:30 README.md
drwxr-xr-x  3 root root 4.0K Nov 22 15:31 assays
-rw-r--r--  1 root root 4.2K Nov 22 15:31 isa.investigation.xlsx
drwxr-xr-x  3 root root 4.0K Nov 22 15:31 runs
drwxr-xr-x  3 root root 4.0K Nov 22 15:32 studies
drwxr-xr-x  3 root root 4.0K Nov 22 15:32 workflows

root@d7ca40cef5e0:/arc# arc-validate -p .
Internal Error:
The option value was None (Parameter 'option')
"   at Microsoft.FSharp.Core.OptionModule.GetValue[T](FSharpOption`1 option) in D:\a\_work\1\s\src\FSharp.Core\option.fs:line 13
at ArcValidation.CvTokenHelperFunctions.CvContainer.isPartOfInvestigation@79-2.Invoke(ICvBase x)
at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
at Microsoft.FSharp.Collections.SeqModule.Exists[T](FSharpFunc`2 predicate, IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 641
at ArcValidation.InformationExtraction.Investigation.getContactsContainer@60.Invoke(CvContainer cv) in /opt/arc-validate/src/ArcValidation/InformationExtraction.fs:line 60
at Microsoft.FSharp.Collections.Internal.IEnumerator.next@246[T](FSharpFunc`2 f, IEnumerator`1 e, FSharpRef`1 started, Unit unitVar0) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 248
at Microsoft.FSharp.Collections.Internal.IEnumerator.filter@236.System.Collections.IEnumerator.MoveNext() in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 250
at Microsoft.FSharp.Collections.SeqModule.ToList[T](IEnumerable`1 source) in D:\a\_work\1\s\src\FSharp.Core\seq.fs:line 966
at ArcValidation.TestGeneration.Critical.Arc.ISA.generateISATests(ArcConfig arcConfig) in /opt/arc-validate/src/ArcValidation/TestGeneration/Critical/ArcISA.fs:line 22
at ARCValidate.main(String[] argv) in /opt/arc-validate/src/arc-validate/Program.fs:line 29"