gaurav / shacli   0.1

MIT License Website GitHub

A CLI for SHACL

Scala versions: 2.12

Shacli: A SHACL CLI

Build Status Maven Central

Shacli is a command-line interface to the Shapes Constraint Language (SHACL). It was originally developed as part of the effort to convert the ClinGen Interpretation Model to SHACL, where we needed a tool that provided clear error messages to anyone using SHACL to validate incoming data.

It is implemented as a wrapper around TopQuadrant's SHACL library.

How to run Shacli

Shacli can be run directly by using Coursier. Coursier itself will need to be installed first, and is available on package managers such as Homebrew.

Once Coursier is installed, you can start Shacli. Note the use of -- to separate Coursier's arguments from Shacli's arguments.

$ coursier launch org.shacli:shacli_2.12:0.1 -- --help
SHACLI: A SHACLI CLI v0.1
  -h, --help      Show help message
  -v, --version   Show version of this program

Subcommand: validate
  -d, --display-nodes      Display all failing nodes as Turtle
  -i, --ignore  <arg>...   Don't display SourceConstraintComponent ending with
                           these strings
  -o, --only  <arg>...     Only display SourceConstraintComponent ending with
                           these strings
  -h, --help               Show help message

 trailing arguments:
  shapes (required)   Shapes file to validate (in Turtle)
  data (required)     Data file(s) to validate (in Turtle)
Subcommand: generate
  -b, --base-u-r-i  <arg>   Base URI of the shapes to generate
  -o, --output  <arg>       Output file where SHACL should be written
  -r, --reasoning  <arg>    Choose reasoning: none (default), rdfs or owl
  -h, --help                Show help message

 trailing arguments:
  data (required)   Data file(s) or directories to validate (in Turtle)

You can try validating the ClinGen examples files in the test/resources directory using the validate command.

$ ls
CHANGELOG.md LICENSE      README.md    build.sbt    docs         project      sonatype.sbt src          target
$ git branch
  master
* test-clingen-requirements
$ coursier launch org.shacli:shacli_2.12:0.1 -- validate src/test/resources/clingen_shapes.ttl src/test/resources/clingen_data.jsonld
10:55:08.015 [main] INFO  org.renci.shacli.ShacliApp$ - Starting validation of src/test/resources/clingen_data.jsonld against src/test/resources/clingen_shapes.ttl.
10:55:08.545 [main] WARN  org.apache.jena.riot - Bad IRI: <7/2/2012 8:45 AM> Spaces are not legal in URIs/IRIs.
10:55:08.629 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_CondMech165 (types: http://purl.obolibrary.org/obo/SEPIO_0000228; props: DC:source, http://purl.obolibrary.org/obo/SEPIO_0000278, http://purl.obolibrary.org/obo/SEPIO_0000276, http://purl.obolibrary.org/obo/SEPIO_0000197, http://purl.obolibrary.org/obo/SEPIO_0000167, rdf:type) was not checked.
10:55:08.629 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000174 (types: RDFS:Class; props: RDFS:subClassOf, rdf:type) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000265 (types: none; props: RDFS:label) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000154 (types: none; props: RDFS:label) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_Null406 (types: http://purl.obolibrary.org/obo/SEPIO_0000274; props: http://purl.obolibrary.org/obo/SEPIO_0000275, http://purl.obolibrary.org/obo/SEPIO_0000197, rdf:type) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_Contrib519 (types: http://purl.obolibrary.org/obo/SEPIO_0000158; props: http://purl.obolibrary.org/obo/SEPIO_0000160, http://purl.obolibrary.org/obo/SEPIO_0000017, http://purl.obolibrary.org/obo/BFO_0000055, rdf:type) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://reg.genome.network/allele/CA256496 (types: http://purl.obolibrary.org/obo/GENO_0000890; props: http://dataexchange.clinicalgenome.org/CG_0001, rdf:type) was not checked.
10:55:08.630 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_GenCond054 (types: http://purl.obolibrary.org/obo/SEPIO_0000219; props: http://purl.obolibrary.org/obo/SEPIO-CG_98901, rdf:type) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_EvLn132 (types: http://purl.obolibrary.org/obo/SEPIO_0000002; props: http://purl.obolibrary.org/obo/SEPIO_0000084, http://purl.obolibrary.org/obo/SEPIO_0000084, http://purl.obolibrary.org/obo/SEPIO_0000084, http://purl.obolibrary.org/obo/SEPIO_0000084, rdf:type) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000268 (types: none; props: RDFS:label) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_Agent010 (types: PROV:agent; props: RDFS:label, rdf:type) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/Orphanet_247 (types: none; props: RDFS:label) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_BMVR161 (types: http://purl.obolibrary.org/obo/SEPIO_0000246; props: DC:description, http://purl.obolibrary.org/obo/SEPIO_0000278, http://purl.obolibrary.org/obo/SEPIO_0000197, rdf:type) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_CtxAll099 (types: http://purl.obolibrary.org/obo/GENO_0000891; props: http://dataexchange.clinicalgenome.org/CG_0100, http://dataexchange.clinicalgenome.org/CG_0003, rdf:type) was not checked.
10:55:08.631 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000329 (types: none; props: RDFS:label) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO-CG_99034 (types: http://purl.obolibrary.org/obo/SEPIO_0000192; props: RDFS:label, DC:description, http://purl.obolibrary.org/obo/SEPIO_0000196, http://purl.obolibrary.org/obo/SEPIO_0000184, rdf:type) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO-CG_99015 (types: none; props: RDFS:label) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://www.genenames.org/12403 (types: none; props: RDFS:label) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_MolCon169 (types: http://purl.obolibrary.org/obo/SEPIO_0000229; props: http://purl.obolibrary.org/obo/SEPIO_0000275, http://purl.obolibrary.org/obo/SEPIO_0000197, rdf:type) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource SEPI:0000224 (types: none; props: RDFS:label) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://dataexchange.clinicalgenome.org/CGEX_CtxNm9099 (types: http://dataexchange.clinicalgenome.org/CG_0020; props: http://dataexchange.clinicalgenome.org/CG_0007, http://dataexchange.clinicalgenome.org/CG_0006, rdf:type) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SEPIO_0000191 (types: RDFS:Class; props: RDFS:subClassOf, rdf:type) was not checked.
10:55:08.632 [main] WARN  org.renci.shacli.ShacliApp$ - Resource http://purl.obolibrary.org/obo/SO_0001583 (types: none; props: RDFS:label) was not checked.
10:55:08.633 [main] WARN  org.renci.shacli.ShacliApp$ - 23 resources NOT checked.
10:55:08.633 [main] INFO  org.renci.shacli.ShacliApp$ - 1 resources checked.
CLASS <http://purl.obolibrary.org/obo/SEPIO_0000191> (2 errors)
Node http://dataexchange.clinicalgenome.org/CGEX_CritAssess156 (2 errors)
 - Path <http://www.w3.org/2000/01/rdf-schema#label> (1 errors)
   - [http://www.w3.org/ns/shacl#MinCountConstraintComponent] Property needs to have at least 1 values, but found 0

 - Path <http://purl.obolibrary.org/obo/SEPIO_0000197> (1 errors)
   - [http://www.w3.org/ns/shacl#NodeConstraintComponent] Value does not have shape cgshapes:CriterionAssessmentOutcomeValueSetShape (value: SEPI:0000224)



2 errors displayed
src/test/resources/clingen_data.jsonld FAILED VALIDATION

Statistics

5 Dependencies

No Dependent