Invalid JSON-LD syntax; an @context @type value must be an absolute IRI

samuel-kerrien commented 4 years ago

Hi guys,

I am playing with DATS and in the process I have tried to use several tools to expand/compact the json-ld representation:

pyld
json-ld playground (https://json-ld.org/playground/)

Both are failing with some of the example provided in this repository, for instance this file: https://github.com/datatagsuite/examples/blob/master/BDbag-AGR-example.json The error message they report is: Invalid JSON-LD syntax; an @context @type value must be an absolute IRI.

Now I can see that rdflib appears to be loading that data just fine in your notebook example: https://hub.gke.mybinder.org/user/datatagsuite-dats-tools-bxg5y72t/notebooks/notebooks/dats_agr.ipynb

Here is an example of the issue I seem to be facing with dataset_sdo_context.jsonld: https://github.com/datatagsuite/context/blob/master/sdo/dataset_sdo_context.jsonld both 'storedIn' and 'distribution' appear to have a @type that is not a valid IRI, respectively DataRepository and DatasetDistribution.

To give an example that would work in the json-ld playground, I have modified the file BDbag-AGR-example.json (see below) as follow:

I have inlined a modified version of the dataset context https://w3id.org/dats/context/sdo/dataset_sdo_context.jsonld. I have just prefixed the distributions and storedIn @type with sdo: to make it a valid IRI. Now I am unsure if this is the IRI you were intending to use of not.
I have removed the following data elements since their own context appear to suffer from the same issue: identifiers, creators, has_part, distributions. I assume I could identify the offending @type and modify them in a similar way to make them valid IRI.

{
    "@type": "Dataset",
    "@id": "http://identifiers.org/minid:b9j69h",
    "@context": {
            "sdo": "https://schema.org/",
            "Dataset": "sdo:Dataset",
            "identifier": {
              "@id": "sdo:identifier",
              "@type": "sdo:Text"
            },
            "alternateIdentifier": "sdo:alternateName",
            "relatedIdentifier": "sdo:mentions",
            "title": {
              "@id": "sdo:name",
              "@type": "sdo:Text"
            },
            "description": {
              "@id": "sdo:description",
              "@type": "sdo:Text"
            },
            "dates": "sdo:temporalCoverage",
            "spatialCoverage": "sdo:spatialCoverage",
            "storedIn": {
                "@id": "sdo:includedInDataCatalog",
                "@type": "sdo:DataRepository"
            },
            "distributions": {
              "@id": "sdo:distribution",
              "@type": "sdo:DatasetDistribution"
            },
            "primaryPublications": "sdo:citation",
            "citations": "sdo:citation",
            "producedBy": "sdo:producer",
            "creators": {
                "@id": "sdo:creator",
                "@type": "sdo:Thing"
            },
            "licenses": "sdo:license",
            "isAbout": "sdo:about",
            "hasPart": {
                "@id": "sdo:hasPart",
                "@type": "Dataset"
            },
            "acknowledges": "sdo:funder",
            "dimensions": "sdo:variableMeasured"
    },
    "title": "AGR Data set with identifier-based references to data in cloud storage",
    "description": "AGR Data set with identifier-based references to data in cloud storage",
    "dates": [{
        "date": "2018-03-19T17:43:57.073822",
        "type": {
            "value": "creation",
            "valueIRI": ""
        }
    }],
    "types": [{"information": {"value": "model organism data"}}],
    "extraProperties": [
        {
            "category": "checksum",
            "categoryIRI": "http://purl.obolibrary.org/obo/NCIT_C43522",
            "values": [{
                "value": "6484968f81afac84857d02b573b0d589fb2f9582a2b920572830dc5781e0a53c",
                "valueIRI": ""
            }]
        },
        {
            "category": "checksum algorithm",
            "categoryIRI": "http://purl.obolibrary.org/obo/NCIT_C16275",
            "values": [{
                "value": "MD5",
                "valueIRI": ""
            }]
        }
    ]
}

Any chance you could test this json-ld example on the json-ld playground (https://json-ld.org/playground/) and verify that your contexts are valid ?

proccaserra commented 4 years ago

Hi @samuel-kerrien (long time no see!)

Thanks for documenting the issue, I'll investigate further tomorrow but quickly I'll make to following points:

refactoring the @context information:

The correct Schemaorg element to use should be sod:DataCatalog (for DATS.DatasetRepository) and sdo:DataDownload (for DATS.DatasetDistribution)

"storedIn": { "@id": "sdo:includedInDataCatalog", "@type": "sdo:DataCatalog" }, "distributions": { "@id": "sdo:distribution", "@type": "sdo:DataDownload" }

In the DATS example: https://github.com/datatagsuite/examples/blob/master/BDbag-AGR-example.json

The JSON element @type point to the DATS objects hence no sdo prefixing is used.

"distributions": [{ "@type": "DatasetDistribution", "@context": "https://w3id.org/dats/context/sdo/dataset_distribution_sdo_context.jsonld",

this context matches to sdo:DataDownload https://github.com/datatagsuite/context/blob/master/sdo/dataset_distribution_sdo_context.jsonld

json-ld playground (https://json-ld.org/playground/) implementation behaves differently than rdflib (as you also noticed).

I ran into inconsistencies in a different context with triples returns varying greatly between the 2 libraries.

So more digging is required.

P

samuel-kerrien commented 4 years ago

Hi @proccaserra (indeed, a long time ;)),

Thanks a lot for your quick input on the issue I am raising, this is very helpful ! Quick comment on your 2 points:

Thanks for pointing out the correct @type for these 2 elements with invalid IRI, I can use that locally until you update your context hosted on GitHub. Do you have an ETA for when this might take ?

Looking further into the validation error of https://github.com/datatagsuite/examples/blob/master/BDbag-AGR-example.json I have found also an issue in the following context dataset_distribution_sdo_context.jsonld Here is the payload:

{
  "@context": {
    "sdo": "https://schema.org/",
    "DatasetDistribution": "sdo:DataDownload",
    "identifier": {
      "@id": "sdo:identifier",
      "@type": "sdo:Text"
    },
    "alternateIdentifiers": "sdo:identifier",
    "relatedIdentifiers": "sdo:identifier",
    "title": {
      "@id": "sdo:name",
      "@type": "sdo:Text"
    },
    "description": {
      "@id": "sdo:description",
      "@type": "sdo:Text"
    },
    "storedIn": {
      "@id": "sdo:includedInDataCatalog",
      "@type": "sdo:DataCatalog"
    },
    "version": "sdo:version",
    "licenses": "sdo:license",
    "access": {
      "@id": "sdo:accessMode",
      "@type": "Access"
    },
    "size": {
        "@id": "sdo:contentSize",
        "@type": "sdo:Text"
    }
  }
}

Please note the statement: "@type": "Access", it appears Access is not defined in that context, so as a result is not a valid IRI. The json-ld playground chokes on it.

As a demonstration, I have taken this file BDbag-AGR-example.json and inlined all the contexts and removed the has_part (because that's a lot more to inline and I expect the exact same errors will come up across the 6 sub-datasets), I have manually fixed the 3 @type issues I pointed out and the json-ld playground is happy with the syntax: http://tinyurl.com/wrdkldo (this will open my eample in json-ld playground).

So all in all, it seems to be there are 2 contexts to fix:

https://w3id.org/dats/context/sdo/dataset_sdo_context.jsonld (DataRepository and DatasetDistribution)
https://w3id.org/dats/context/sdo/dataset_distribution_sdo_context.jsonld (Access)

Actually, I took it one step further and inlined both my fixed dataset_sdo_context.jsonld and dataset_distribution_sdo_context.jsonld (I merely replaced Access by sdo:Access to make it a valid IRI, i am actually unsure if that's the vocabulary you intended to use) across all 6 sub-datasets in the has_part and it works in json-ld playground. Unfortunately I cannot share it since tinyurl fails to shorten such a long URL. I probably could remove the inline of all other contexts and that should work. I paste the content instead below.

{
    "@type": "Dataset",
    "@id": "http://identifiers.org/minid:b9j69h",
    "@context": {
        "sdo": "https://schema.org/",
        "Dataset": "sdo:Dataset",
        "identifier": {
          "@id": "sdo:identifier",
          "@type": "sdo:Text"
        },
        "alternateIdentifier": "sdo:alternateName",
        "relatedIdentifier": "sdo:mentions",
        "title": {
          "@id": "sdo:name",
          "@type": "sdo:Text"
        },
        "description": {
          "@id": "sdo:description",
          "@type": "sdo:Text"
        },
        "dates": "sdo:temporalCoverage",
        "spatialCoverage": "sdo:spatialCoverage",
        "storedIn": {
            "@id": "sdo:includedInDataCatalog",
            "@type": "sdo:DataCatalog"
        },
        "distributions": {
          "@id": "sdo:distribution",
          "@type": "sdo:DataDownload"
        },
        "primaryPublications": "sdo:citation",
        "citations": "sdo:citation",
        "producedBy": "sdo:producer",
        "creators": {
            "@id": "sdo:creator",
            "@type": "sdo:Thing"
        },
        "licenses": "sdo:license",
        "isAbout": "sdo:about",
        "hasPart": {
            "@id": "sdo:hasPart",
            "@type": "Dataset"
        },
        "acknowledges": "sdo:funder",
        "dimensions": "sdo:variableMeasured"
    },
    "identifier": {
        "@type": "Identifier",
        "@context": {
            "sdo": "https://schema.org/",
            "Identifier": "sdo:Thing",
            "identifier": "sdo:identifier",
            "identifierSource": {
               "@id": "sdo:Property",
               "@type": "sdo:Text"
            }
        },
        "identifier": "http://identifiers.org/minid:b9j69h",
        "identifierSource": "minid"
    },
    "title": "AGR Data set with identifier-based references to data in cloud storage",
    "description": "AGR Data set with identifier-based references to data in cloud storage",
    "dates": [{
        "date": "2018-03-19T17:43:57.073822",
        "type": {
            "value": "creation",
            "valueIRI": ""
        }
    }],
    "creators": [{
        "@type": "Person",
        "@context": {
            "sdo": "https://schema.org/",
            "Person": "sdo:Person",
            "identifier": "sdo:identifier",
            "firstName": "sdo:givenName",
            "lastName": "sdo:familyName",
            "fullName": "sdo:name",
            "email": "sdo:email",
            "affiliations": "sdo:affiliation",
            "roles": "sdo:roleName"
        },
        "@id": "http://orcid.org/0000-0003-2280-917X",
        "identifier": {
            "identifier": "http://orcid.org/0000-0003-2280-917X",
            "identifierSource": "orcid"
        },
        "affiliations": [{
            "@type": "Organization",

            "@context": {
              "sdo": "https://schema.org/",
              "Organization": "sdo:Organization",
              "identifier": {
                "@id": "sdo:identifier",
                "@type": "sdo:Text"
              },
              "name": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
              },
              "abbreviation": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
              },
              "location": {
                  "@id": "sdo:address",
                  "@type": "sdo:Text"
              },
              "roles": {
                  "@id": "sdo:roleName",
                  "@type": "sdo:Text"
              }
            },
            "name": "University of Southern California / Information Science"
        }],
        "firstName": "Michel",
        "fullName": "Mike d'Arcy",
        "lastName": "d'Arcy"
    }],
    "types": [{"information": {"value": "model organism data"}}],
    "hasPart": [
        {
            "@type": "Dataset",
            "@context": {
                "sdo": "https://schema.org/",
                "Dataset": "sdo:Dataset",
                "identifier": {
                  "@id": "sdo:identifier",
                  "@type": "sdo:Text"
                },
                "alternateIdentifier": "sdo:alternateName",
                "relatedIdentifier": "sdo:mentions",
                "title": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
                },
                "description": {
                  "@id": "sdo:description",
                  "@type": "sdo:Text"
                },
                "dates": "sdo:temporalCoverage",
                "spatialCoverage": "sdo:spatialCoverage",
                "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                },
                "distributions": {
                  "@id": "sdo:distribution",
                  "@type": "sdo:DataDownload"
                },
                "primaryPublications": "sdo:citation",
                "citations": "sdo:citation",
                "producedBy": "sdo:producer",
                "creators": {
                    "@id": "sdo:creator",
                    "@type": "sdo:Thing"
                },
                "licenses": "sdo:license",
                "isAbout": "sdo:about",
                "hasPart": {
                    "@id": "sdo:hasPart",
                    "@type": "Dataset"
                },
                "acknowledges": "sdo:funder",
                "dimensions": "sdo:variableMeasured"
            },
            "@id": "https://identifiers.org/minid:b9n39d",
            "identifier": {
                "identifier": "minid:b9n39d",
                "identifierSource": "minid"
            },
            "title": "A list of disease ontology terms obtained from the Disease Ontology website.",
            "types": [{"information": {"value": "ontology terms"}}],
            "creators": [ {} ],
            "distributions": [{
                "@type": "DatasetDistribution",
                "@context": {
                  "sdo": "https://schema.org/",
                  "DatasetDistribution": "sdo:DataDownload",
                  "identifier": {
                    "@id": "sdo:identifier",
                    "@type": "sdo:Text"
                  },
                  "alternateIdentifiers": "sdo:identifier",
                  "relatedIdentifiers": "sdo:identifier",
                  "title": {
                    "@id": "sdo:name",
                    "@type": "sdo:Text"
                  },
                  "description": {
                    "@id": "sdo:description",
                    "@type": "sdo:Text"
                  },
                  "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                  },
                  "version": "sdo:version",
                  "licenses": "sdo:license",
                  "access": {
                    "@id": "sdo:accessMode",
                    "@type": "sdo:Access"
                  },
                  "size": {
                      "@id": "sdo:contentSize",
                      "@type": "sdo:Text"
                  }
                },
                "identifier": {
                    "identifier": "minid:b9n39d",
                    "identifierSource": ""
                },
                "access": {
                    "@type": "Access",
                    "@context": "https://w3id.org/dats/context/sdo/access_sdo_context.jsonld",
                    "accessURL": "https://s3.amazonaws.com/mod-datadumps/DO/do_1.0.obo",
                    "landingPage": "https://identifiers.org/minid:b9n39d"
                },
                "conformsTo": [{
                    "name": "obo format",
                    "type": {
                        "value": "text/plain",
                        "valueIRI": ""
                    }
                }],
                "size": 4784295,
                "unit": {
                    "value": "byte",
                    "valueIRI": "http://purl.obolibrary.org/obo/UO_0000233"
                },
                "version": "Release 2.6.2018"
            }]
        },
        {
            "@type": "Dataset",
            "@id": "http://identifiers.org/minid:b9hd64",
            "@context": {
                "sdo": "https://schema.org/",
                "Dataset": "sdo:Dataset",
                "identifier": {
                  "@id": "sdo:identifier",
                  "@type": "sdo:Text"
                },
                "alternateIdentifier": "sdo:alternateName",
                "relatedIdentifier": "sdo:mentions",
                "title": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
                },
                "description": {
                  "@id": "sdo:description",
                  "@type": "sdo:Text"
                },
                "dates": "sdo:temporalCoverage",
                "spatialCoverage": "sdo:spatialCoverage",
                "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                },
                "distributions": {
                  "@id": "sdo:distribution",
                  "@type": "sdo:DataDownload"
                },
                "primaryPublications": "sdo:citation",
                "citations": "sdo:citation",
                "producedBy": "sdo:producer",
                "creators": {
                    "@id": "sdo:creator",
                    "@type": "sdo:Thing"
                },
                "licenses": "sdo:license",
                "isAbout": "sdo:about",
                "hasPart": {
                    "@id": "sdo:hasPart",
                    "@type": "Dataset"
                },
                "acknowledges": "sdo:funder",
                "dimensions": "sdo:variableMeasured"
            },
            "identifier": {
                "identifier": "minid:b9hd64",
                "identifierSource": "minid"
            },
            "title": "A list of gene ontology terms obtained from the Gene Ontology Consortium.",
            "types": [{"information": {"value": "ontology terms"}}],
            "creators": [ { } ],
            "distributions": [{
                "@type": "DatasetDistribution",
                "@context": {
                  "sdo": "https://schema.org/",
                  "DatasetDistribution": "sdo:DataDownload",
                  "identifier": {
                    "@id": "sdo:identifier",
                    "@type": "sdo:Text"
                  },
                  "alternateIdentifiers": "sdo:identifier",
                  "relatedIdentifiers": "sdo:identifier",
                  "title": {
                    "@id": "sdo:name",
                    "@type": "sdo:Text"
                  },
                  "description": {
                    "@id": "sdo:description",
                    "@type": "sdo:Text"
                  },
                  "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                  },
                  "version": "sdo:version",
                  "licenses": "sdo:license",
                  "access": {
                    "@id": "sdo:accessMode",
                    "@type": "sdo:Access"
                  },
                  "size": {
                      "@id": "sdo:contentSize",
                      "@type": "sdo:Text"
                  }
                },
                "identifier": {
                    "identifier": "minid:b9hd64",
                    "identifierSource": ""
                },
                "access": {
                    "@type": "Access",
                    "@context": "https://w3id.org/dats/context/sdo/access_sdo_context.jsonld",
                    "accessURL": "https://s3.amazonaws.com/mod-datadumps/GO/go_1.0.obo",
                    "landingPage": "http://identifiers.org/minid:b9hd64"
                },
                "conformsTo": [{
                    "name": "obo format",
                    "type": {
                        "value": "text/plain",
                        "valueIRI": ""
                    }
                }],
                "size": 36520029,
                "unit": {
                    "value": "byte",
                    "valueIRI": "http://purl.obolibrary.org/obo/UO_0000233"
                },
                "version": "Release 2.6.2018"
            }]
        },
        {
            "@type": "Dataset",
            "@id": "http://identifiers.org/minid:b9px1z",
            "@context": {
                "sdo": "https://schema.org/",
                "Dataset": "sdo:Dataset",
                "identifier": {
                  "@id": "sdo:identifier",
                  "@type": "sdo:Text"
                },
                "alternateIdentifier": "sdo:alternateName",
                "relatedIdentifier": "sdo:mentions",
                "title": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
                },
                "description": {
                  "@id": "sdo:description",
                  "@type": "sdo:Text"
                },
                "dates": "sdo:temporalCoverage",
                "spatialCoverage": "sdo:spatialCoverage",
                "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                },
                "distributions": {
                  "@id": "sdo:distribution",
                  "@type": "sdo:DataDownload"
                },
                "primaryPublications": "sdo:citation",
                "citations": "sdo:citation",
                "producedBy": "sdo:producer",
                "creators": {
                    "@id": "sdo:creator",
                    "@type": "sdo:Thing"
                },
                "licenses": "sdo:license",
                "isAbout": "sdo:about",
                "hasPart": {
                    "@id": "sdo:hasPart",
                    "@type": "Dataset"
                },
                "acknowledges": "sdo:funder",
                "dimensions": "sdo:variableMeasured"
            },
            "identifier": {
                "identifier": "minid:b9px1z",
                "identifierSource": "minid"
            },
            "title": "A list of sequence ontology terms obtained from the Sequence Ontology website.",
            "types": [{"information": {"value": "ontology terms"}}],
            "creators": [ {} ],
            "dates": [{
                "date": "2018-06-02T00:00:00.00Z",
                "type": {
                    "value": "creation",
                    "valueIRI": ""
                }
            }],
            "distributions": [{
                "@type": "DatasetDistribution",
                "@context": {
                  "sdo": "https://schema.org/",
                  "DatasetDistribution": "sdo:DataDownload",
                  "identifier": {
                    "@id": "sdo:identifier",
                    "@type": "sdo:Text"
                  },
                  "alternateIdentifiers": "sdo:identifier",
                  "relatedIdentifiers": "sdo:identifier",
                  "title": {
                    "@id": "sdo:name",
                    "@type": "sdo:Text"
                  },
                  "description": {
                    "@id": "sdo:description",
                    "@type": "sdo:Text"
                  },
                  "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                  },
                  "version": "sdo:version",
                  "licenses": "sdo:license",
                  "access": {
                    "@id": "sdo:accessMode",
                    "@type": "sdo:Access"
                  },
                  "size": {
                      "@id": "sdo:contentSize",
                      "@type": "sdo:Text"
                  }
                },
                "identifier": {
                    "identifier": "minid:b9px1z",
                    "identifierSource": ""
                },
                "access": {
                    "@type": "Access",
                    "@context": "https://w3id.org/dats/context/sdo/access_sdo_context.jsonld",
                    "accessURL": "https://s3.amazonaws.com/mod-datadumps/SO/so_1.0.obo",
                    "landingPage": "http://identifiers.org/minid:b9px1z"
                },
                "conformsTo": [{
                    "name": "obo format",
                    "type": {
                        "value": "text/plain",
                        "valueIRI": ""
                    }
                }],
                "size": 902733,
                "unit": {
                    "value": "byte",
                    "valueIRI": "http://purl.obolibrary.org/obo/UO_0000233"
                },
                "version": "Release 11.24.2015"
            }]
        },
        {
            "@type": "Dataset",
            "@id": "http://identifiers.org/minid:b9dm68",
            "@context": {
                "sdo": "https://schema.org/",
                "Dataset": "sdo:Dataset",
                "identifier": {
                  "@id": "sdo:identifier",
                  "@type": "sdo:Text"
                },
                "alternateIdentifier": "sdo:alternateName",
                "relatedIdentifier": "sdo:mentions",
                "title": {
                  "@id": "sdo:name",
                  "@type": "sdo:Text"
                },
                "description": {
                  "@id": "sdo:description",
                  "@type": "sdo:Text"
                },
                "dates": "sdo:temporalCoverage",
                "spatialCoverage": "sdo:spatialCoverage",
                "storedIn": {
                    "@id": "sdo:includedInDataCatalog",
                    "@type": "sdo:DataCatalog"
                },
                "distributions": {
                  "@id": "sdo:distribution",
                  "@type": "sdo:DataDownload"
                },
                "primaryPublications": "sdo:citation",
                "citations": "sdo:citation",
                "producedBy": "sdo:producer",
                "creators": {
                    "@id": "sdo:creator",
                    "@type": "sdo:Thing"
                },
                "licenses": "sdo:license",
                "isAbout": "sdo:about",
                "hasPart": {
                    "@id": "sdo:hasPart",
                    "@type": "Dataset"
                },
                "acknowledges": "sdo:funder",
                "dimensions": "sdo:variableMeasured"
            },
            "identifier": {
                "identifier": "minid:b9dm68",
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}

proccaserra commented 4 years ago

hi @samuel-kerrien , thx for investigating further. There were indeed problems in our sdo context file. I have pushed the fixes to 'dataset', dataset_distribution and access context file. with these, JS-playground no longer complains however, I am still getting errors with Google structured data testing tool so we are digging further. thx again. https://search.google.com/structured-data/testing-tool/u/0/

samuel-kerrien commented 4 years ago

Great, I can confirm it works smoother now in the json-ld playground. Thanks for the quick turn around.

I have had a quick look at the Google tool to validate structured data and it looks like all errors are related to contexts. Funnily enough, when I inline the context in the DATS file, the errors do not manifest. I am quite interested in your findings on the matter, would be great if you could post an update when you to crack this one ...

Cheers !

datatagsuite / examples

Invalid JSON-LD syntax; an @context @type value must be an absolute IRI #1