Core JSON returned by API doesn't validate against JSON schema

[smrgeoinfo]

Using JSON schema iSamples (github-- isamplesorg/metadata/src/schemas/iSamplesSchemaCore1.0.json

get metadata records in core schema via the API, e.g. https://central.isample.xyz/isamples_central/thing/ark%3A%2F65665%2F309fc4ed5-cbc9-4821-918a-1ff0aa92d0dd?format=core

Load the JSON in Oxygen, and run validator against JSON schema (I tried on records from all 4 authorities). Errors reported:

• Description: #/curation/access_constraints: expected type: JSONArray, found: String -- fix: "access_constraints": "", should be "access_constraints": [] or "access_constraints": [""] or "access_constraints": ["constraint text 1", "constraint text 2"]

• Description: #/keywords/0: expected type: JSONObject, found: String -- fix: "keywords": ["Individual Sample"], should be "keywords": [{"keyword":"Individual Sample"}],

• Description: #/produced_by/@id: extraneous key [@id] is not permitted -- fix: current schema has an identifier property on the sampling event, this is where the id should go.

               "produced_by": {
                        "@id": "SamplingEventID",
  
    should be:
  
                    "produced_by": {
                        "label": "....",
                        "description": ".....",
                        "has_feature_of_interest": ".....",
                        "identifier":"SamplingEventID", ....
  
        to validate. Perhaps we need to modify the schema to use the JSON-LD @ids?

• Description: #/produced_by/responsibility/0: expected type: JSONObject, found: String -- fix: value should be an agent object. "responsibility": ["Carl Francis,,Sample Owner"], should be "responsibility": [{"name":"Carl Francis","role":"Sample Owner"}],

• Description: #/produced_by/result_time: [2007-02-03 12:00:00] is not a valid date. Expected [yyyy-MM-dd] -- fix: data type is JSON schema date, this requires yyyy-MM-dd format, so value should be "2007-02-03". If we want to allow timestamps, we'd need to revise JSON schema; could allow either date or dateTime format for the date string

• Description: #/produced_by/sampling_site/sample_location/latitude: expected type: Number, found: Null

• Description: #/produced_by/sampling_site/sample_location/longitude: expected type: Number, found: Null -- fix: 'null' is not recognized by the validator as a number. I'd suggest just leaving "latitude" and "longitude" keys out if there are no values. In fact, if there are no coordinates, an empty object might be the best solution-- it indicates an explicit null. "sample_location": {},

[smrgeoinfo]

generalize dates to allow YYYY, YYYY-MM, YYYY-MM-DD, YYYY-MM-DDThh-mm etc.... Update schema. Generate issue

[dannymandel]

This is done. Will be fixed next time we push to central. The change we made to the schema (which we now validate against our unit tests) was this:

                "result_time": {
                    "description": "Date on which the sample was collected.",
                    "anyOf": [
                        {
                            "format": "date"
                        },
                        {
                            "format": "date-time"
                        }
                    ],

                    "type": "string"
                },

[smrgeoinfo]

Have to update the LinkML/YAML schema as well to keep in sync with the JSON. I was going to allow all the various formats (YYYY, YYYY-MM, YYYY-MM-DD, YYYY-MM-DDThh-mm), but then went out of town before I could figure out how to do it in the LinkML

[smrgeoinfo]

I'd suggest adding some regex patterns to allow YYYY and YYYY-MM: "anyOf": [ { "format": "date", "description": "YYYY-MM-DD" }, { "format": "date-time", "description": "YYYY:MM::DDThh:mm:ss.sTZD" }, { "pattern": "^(?:[1]?[0-9]{3}|20[0-2][0-9])$", "description": "gets YYYY" }, { "pattern": "^(?:[1]?[0-9]{3}|20[0-2][0-9])-(?:0[1-9]|1[0-2])$", "description": "gets YYYY-MM" } ],

see https://github.com/isamplesorg/isamples_inabox/issues/389