JarCasting
JarCasting JarCasting

Shacli


License

License

MIT
Categories

Categories

CLI User Interface
GroupId

GroupId

org.shacli
ArtifactId

ArtifactId

shacli_2.12
Last Version

Last Version

0.1
Release Date

Release Date
Type

Type

jar
Description

Description

Shacli
Shacli
Project Organization

Project Organization

org.shacli
Source Code Management

Source Code Management

https://github.com/gaurav/shacli

Download shacli_2.12

Filename Size
shacli_2.12-0.1.pom
shacli_2.12-0.1.jar 67 KB
shacli_2.12-0.1-sources.jar 7 KB
shacli_2.12-0.1-javadoc.jar 1 MB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/org.shacli/shacli_2.12/ -->
<dependency>
    <groupId>org.shacli</groupId>
    <artifactId>shacli_2.12</artifactId>
    <version>0.1</version>
</dependency>
// https://jarcasting.com/artifacts/org.shacli/shacli_2.12/
implementation 'org.shacli:shacli_2.12:0.1'
// https://jarcasting.com/artifacts/org.shacli/shacli_2.12/
implementation ("org.shacli:shacli_2.12:0.1")
'org.shacli:shacli_2.12:jar:0.1'
<dependency org="org.shacli" name="shacli_2.12" rev="0.1">
  <artifact name="shacli_2.12" type="jar" />
</dependency>
@Grapes(
@Grab(group='org.shacli', module='shacli_2.12', version='0.1')
)
libraryDependencies += "org.shacli" % "shacli_2.12" % "0.1"
[org.shacli/shacli_2.12 "0.1"]

Dependencies

compile (8)

Group / Artifact Type Version
org.scala-lang : scala-library jar 2.12.10
com.typesafe.scala-logging : scala-logging_2.12 jar 3.9.2
ch.qos.logback : logback-classic jar 1.2.3
org.rogach : scallop_2.12 jar 3.3.2
org.apache.jena : jena-core jar 3.14.0
org.apache.jena : jena-arq jar 3.14.0
org.topbraid : shacl jar 1.3.1
com.github.tototoshi : scala-csv_2.12 jar 1.3.6

test (1)

Group / Artifact Type Version
com.lihaoyi : utest_2.12 jar 0.7.1

Project Modules

There are no modules declared in this project.

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

Versions

Version
0.1