JSON Context issue. Identify bad contexts #129
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Wait... this is a fragment from one original files: "@context": [
"https://schema.org/",
{
"gsqtime": "https://vocabs.gsq.digital/object?uri=http://linked.data.gov.au/def/trs",
"time": "http://www.w3.org/2006/time#",
"xsd": "https://www.w3.org/TR/2004/REC-xmlschema-2-20041028/datatypes.html"
}
],
"@type": "Dataset",
"identifier": "https://dx.doi.org/10.7288/V4/MAGIC/11131",
"sameAs": [
"https://earthref.org/MagIC/doi/10.1073/PNAS.1616976114"
], |
valentinedwv
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valentinedwv
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|
Failing tests on fix_129_context branch |
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WIfire, too. goes to: |
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similar to spec cases 20 and 22 But those are 'local' schemas. |
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branch fix_129 handles this. |
This was referenced Jan 10, 2023
valentinedwv
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Mar 6, 2023
* run configurations * adding a uuid command to get uuid for a file sent to stdin. updated cobra and viper package versions * Example JSON Paths and arrays of paths * glcon tool id --idtype indentifiersha --jsonld some file * test for #129. * Implemented changes to prevent context mangling * * Get things working and DRY code up a bit * Extract out a constant and a json processing function * Add test for json finding method * Test for the api config helper * Try to make this work for DataStream as well * Identifiers fix for @graph * fix wrap in quotes 'script[type="application/ld+json"]' * add an ideal example resource * IdentiferPath is a comma separated set of strings, or one string. * If you are trying not to recorder an array... and copy it, don't use the original later Clean up LdProc Normalize Tests. Empty triples will be empty triples * #150 #108 initialize gleaner and nabu configs idependently. * #145 * added test for a couple of problem children. * methods to allow dumping data before upload and glcon tools jsonld: jsonld > corrected jsonld rdf: jsonld > rdf * add a couple resources for cli testing * Headless rework to make more testable * Fix Minio connection check error, like was done on nabu * Implement headlessWait in the headless Javascript. Fixes #152 * Implement headlessWait in the headless Javascript. Fixes #152 add a test that is expected to fail, with 1 JSONld returned. * #155 enable --prefix flag for nabu * Using c.Page.LoadEventFired to wait for content. Works. leaving in the headlessWait incase another issue that requires its. * linux reading of config not working. Updating modules * Use the config class to read the gleanerConfig. * Use the config class to read the gleanerConfig. * Cleaned up tests. Files now used. (#161) Added ability to just generate a sha of the json. Was option, but not coded. * Fix 124 identifiers tests (#162) * Cleaned up tests. Files now used. Added ability to just generate a sha of the json. Was option, but not coded. * put in approvals into jsonutils * use log.info not println so this does not show up in console output. * test for #129. * Implemented changes to prevent context mangling * Example JSON Paths and arrays of paths * clean up some logging CLI. * glcon tool id --idtype indentifiersha --jsonld some file * If it's an array, we standardized. Tests to be sure arrays are not mangled by string and that strings are not mangled by array. * IdentiferPath is a comma separated set of strings, or one string. * methods to allow dumping data before upload glcon tools jsonld: jsonld > corrected jsonld rdf: jsonld > rdf Added ability to just generate a sha of the json. Was option, but not coded. * Fix 124 identifiers tests (#162) * put in approvals into jsonutils * add approval test .approved * Sort the jsonpath results because UUID generation depends on order of results. * One more fix for tool id. If no config is passed, just use a generic one. We need is the contexts, for the triples if it falls through to a normalizedsha makefile. copy binaries up to that assets are in correct location relative to binaries --------- Co-authored-by: melinda <melindaminch@oceannetworks.ca> Co-authored-by: Douglas Fils <drfils@gmail.com>
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Bad Context (string plus object) is getting mangled somewhere.
https://validator.schema.org/#url=https%3A%2F%2Fearthref.org%2FMagIC%2F11131
source:
{"@context": [ "https://schema.org/", { "gsqtime": "https://vocabs.gsq.digital/object?uri=http://linked.data.gov.au/def/trs", "time": "http://www.w3.org/2006/time#", "xsd": "https://www.w3.org/TR/2004/REC-xmlschema-2-20041028/datatypes.html" } ], "@type": "Dataset", "identifier": "https://dx.doi.org/10.7288/V4/MAGIC/11131", "sameAs": [ "https://earthref.org/MagIC/doi/10.1073/PNAS.1616976114" ], }getting uploaded as:
{ "@context": {"@vocab":"https:///"}, "@type": "Dataset", "identifier": "https://dx.doi.org/10.7288/V4/MAGIC/12004", "sameAs": [ "https://earthref.org/MagIC/doi/10.1016/0012-821X(78)90077-8" ], }Magic JSONLD, and the RDF seems a bit terse.
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Wait looking at this it is the same issue we have with wifire. bad context.
"@context": {"@vocab":"https:///"},{ "@context": {"@vocab":"https:///"}, "@type": "Dataset", "identifier": "https://dx.doi.org/10.7288/V4/MAGIC/12661", "sameAs": "https://earthref.org/MagIC/12661", "isAccessibleForFree": true, "license": "https://creativecommons.org/licenses/by/4.0/", "provider": { "@id": "https://earthref.org/MagIC", "@type": "Organization", "identifier": "https://www.re3data.org/repository/r3d100011910", "legalName": "Magnetics Information Consortium (MagIC) Data Repository", "name": "MagIC", "url": "https://earthref.org/MagIC" }, "publisher": { "@id": "https//earthref.org/MagIC" }, "sdPublisher": "EarthRef.org", "sdLicense": "https://creativecommons.org/licenses/by/4.0/", "sdDatePublished": "2022-10-14T21:01:51.447Z", "distribution": { "@type": "DataDownload", "contentUrl": "https://earthref.org/MagIC/download/12661/magic_contribution_12661.txt", "encodingFormat": [ "text/plain; application=earthref-tsv", "EarthRef-tsv-Multipart" ] }, "version": 2, "contributor": "MagIC Database Team", "dateModified": "2006-12-18T11:10:39.000Z", "citation": "<b>Facer, R.A. (1971).</b> Intrusion and magnetization of the Giles Complex, Central Australia.<i> Geophysical Journal of the Royal Astronomical Society 22: 517-520.</i>", "name": "<b>Facer, R.A. (1971).</b> Intrusion and magnetization of the Giles Complex, Central Australia.<i> Geophysical Journal of the Royal Astronomical Society 22: 517-520.</i> (Dataset)", "description": "Paleomagnetic, rock magnetic, or geomagnetic data found in the MagIC data repository from a paper titled: <b>Facer, R.A. (1971).</b> Intrusion and magnetization of the Giles Complex, Central Australia.<i> Geophysical Journal of the Royal Astronomical Society 22: 517-520.</i>", "datePublished": "2006-12-18T11:10:39.000Z", "temporalCoverage": { "@type": "time:ProperInterval", "time:hasBeginning": { "time:hasTRS": { "@id": "gsqtime:BeforePresent" }, "time:numericPosition": { "@value": 900000000, "@type": "xsd:decimal" }, "gstime:geologicTimeUnitAbbreviation": { "@type": "xsd:string", "value": "BP" } }, "time:hasEnd": { "time:hasTRS": { "@id": "gsqtime:BeforePresent" }, "time:numericPosition": { "@value": 1180000000, "@type": "xsd:decimal" }, "gstime:geologicTimeUnitAbbreviation": { "@type": "xsd:string", "value": "BP" } } }, "variableMeasured": [ { "@type": "PropertyValue", "name": "Direction K", "description": "Specimen direction in coordinates specified by tilt correction, Fisher's dispersion parameter Kappa", "minValue": 1.7, "maxValue": 3.2, "unitText": "Dimensionless" }, { "@type": "PropertyValue", "name": "Pole Longitude", "description": "Pole longitude, average of site VGP longitudes, north pole", "minValue": 307.1, "maxValue": 307.1, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Inclination", "description": "Directions in specimen coordinates, Inclination", "minValue": -86, "maxValue": -35, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Direction Alpha 95%", "description": "Specimen direction in coordinates specified by tilt correction, Fisher circle", "minValue": 12, "maxValue": 21, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Pole DM", "description": "Pole meridian uncertainty", "minValue": 24, "maxValue": 24, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Pole DP", "description": "Pole parallel latitude uncertainty", "minValue": 24, "maxValue": 24, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Percentage Reversed Sites", "description": "Percentage of sites that are reversed", "minValue": 200, "maxValue": 200, "unitText": "%" }, { "@type": "PropertyValue", "name": "Direction N Samples", "description": "Number of samples included in directional calculations.", "minValue": 39, "maxValue": 39 }, { "@type": "PropertyValue", "name": "Pole Latitude", "description": "Pole latitude, average of site VGP latitudes, north pole", "minValue": 18.4, "maxValue": 18.4, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Direction N Sites", "description": "Number of sites included in directional calculations", "minValue": 4, "maxValue": 39 }, { "@type": "PropertyValue", "name": "Direction Tilt K Ratio", "description": "Comparison of Fisher dispersion K after and before tilt correction", "minValue": 0.52, "maxValue": 0.52, "unitText": "Dimensionless" }, { "@type": "PropertyValue", "name": "Declination", "description": "Directions in specimen coordinates, Declination", "minValue": 169, "maxValue": 322, "unitText": "Degrees" }, { "@type": "PropertyValue", "name": "Direction Tilt Correction", "description": "Percentage tilt correction applied to the data", "minValue": 0, "maxValue": 100, "unitText": "%" } ] }Archive.zip
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