validation error
SaibotMagd opened this issue · comments
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"
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).
That's no problem since I used the openly published dataset from Micha Wijesingha Ahchige published @ https://git.nfdi4plants.org/micwij/cmqtl_val1_arc
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>
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.
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.
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"