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Retrieving model with uuid and alias gives different results #339

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apdavison opened this issue Jun 6, 2023 · 1 comment
Open

Retrieving model with uuid and alias gives different results #339

apdavison opened this issue Jun 6, 2023 · 1 comment
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REST API v2

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@apdavison
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There are a few minor differences in "description" and "format" (null vs []). The main difference is that the parameters field of the model instance is empty when the model is retrieved via alias.

https://validation.brainsimulation.eu/models/32dc30ba-3de3-4c75-83f7-5c930de346d7

{
  "id": "32dc30ba-3de3-4c75-83f7-5c930de346d7",
  "uri": "https://kg.ebrains.eu/api/instances/32dc30ba-3de3-4c75-83f7-5c930de346d7",
  "name": "Reduced striatum microcircuit",
  "alias": "striatum_microcircuit_test",
  "author": [
     ...cut to save space...
  ],
  "owner": [
    {
      "given_name": "Andrew P.",
      "family_name": "Davison",
      "orcid": "https://orcid.org/0000-0002-4793-7541"
    }
  ],
  "project_id": "basal-ganglia-validation",
  "organization": null,
  "private": true,
  "cell_type": null,
  "model_scope": "network: microcircuit",
  "abstraction_level": "spiking neurons: biophysical",
  "brain_region": "striatum",
  "species": "Mus musculus",
  "description": "This is a small-scale model of the striatum microcircuit, used only for testing the EBRAINS Model Validation Framework",
  "date_created": "2023-06-06",
  "format": null,
  "images": null,
  "old_uuid": null,
  "instances": [
    {
      "id": "82f5a109-7fbc-4070-82b9-155d118ac462",
      "uri": "https://kg.ebrains.eu/api/instances/82f5a109-7fbc-4070-82b9-155d118ac462",
      "version": "20230606",
      "description": "",
      "parameters": "https://data-proxy.ebrains.eu/api/v1/buckets/basal-ganglia-validation/model_parameters/striatum_microcircuit_20230606.json",
      "code_format": null,
      "source": "https://github.com/apdavison/basalunit",
      "license": "The 3-Clause BSD License",
      "hash": null,
      "timestamp": "2023-06-06",
      "morphology": null,
      "model_id": "32dc30ba-3de3-4c75-83f7-5c930de346d7",
      "alternatives": []
    }
  ]
}

https://validation.brainsimulation.eu/models/striatum_microcircuit_test

{
  "id": "32dc30ba-3de3-4c75-83f7-5c930de346d7",
  "uri": "https://kg.ebrains.eu/api/instances/32dc30ba-3de3-4c75-83f7-5c930de346d7",
  "name": "Reduced striatum microcircuit",
  "alias": "striatum_microcircuit_test",
  "author": [
      ...cut to save space...
  ],
  "owner": [
    {
      "given_name": "Andrew P.",
      "family_name": "Davison",
      "orcid": "https://orcid.org/0000-0002-4793-7541"
    }
  ],
  "project_id": "basal-ganglia-validation",
  "organization": null,
  "private": true,
  "cell_type": null,
  "model_scope": "network: microcircuit",
  "abstraction_level": "spiking neurons: biophysical",
  "brain_region": "striatum",
  "species": "Mus musculus",
  "description": "This is a small-scale model of the striatum microcircuit, used only for testing the EBRAINS Model Validation Framework",
  "date_created": "2023-06-06",
  "format": [],
  "images": null,
  "old_uuid": null,
  "instances": [
    {
      "id": "82f5a109-7fbc-4070-82b9-155d118ac462",
      "uri": "https://kg.ebrains.eu/api/instances/82f5a109-7fbc-4070-82b9-155d118ac462",
      "version": "20230606",
      "description": null,
      "parameters": null,
      "code_format": null,
      "source": "https://github.com/apdavison/basalunit",
      "license": "The 3-Clause BSD License",
      "hash": null,
      "timestamp": "2023-06-06",
      "morphology": null,
      "model_id": "32dc30ba-3de3-4c75-83f7-5c930de346d7",
      "alternatives": []
    }
  ]
}

Context:

{
  "version": "3beta",
  "datastore": "core.kg.ebrains.eu",
  "build": {
    "git": "8d916b33",
    "target": "production",
    "date": "2023-05-12T11:22:56+02:00"
  }
}
@apdavison
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The missing parameters field was fixed by updating the stored query.

The current query is

{
  "@context": {
    "@vocab": "https://core.kg.ebrains.eu/vocab/query/",
    "query": "https://schema.hbp.eu/myQuery/",
    "propertyName": {
      "@id": "propertyName",
      "@type": "@id"
    },
    "path": {
      "@id": "path",
      "@type": "@id"
    }
  },
  "meta": {
    "name": "VF_ScientificModel",
    "responseVocab": "https://schema.hbp.eu/myQuery/",
    "type": "https://openminds.ebrains.eu/core/Model"
  },
  "structure": [
    {
      "propertyName": "query:uri",
      "path": "@id",
      "filter": {
        "op": "CONTAINS",
        "parameter": "id"
      }
    },
    {
      "propertyName": "query:name",
      "path": "https://openminds.ebrains.eu/vocab/fullName",
      "filter": {
        "op": "CONTAINS",
        "parameter": "name"
      }
    },
    {
      "propertyName": "query:alias",
      "path": "https://openminds.ebrains.eu/vocab/shortName",
      "filter": {
        "op": "EQUALS",
        "parameter": "alias"
      }
    },
    {
      "propertyName": "query:author",
      "path": {
        "@id": "https://openminds.ebrains.eu/vocab/developer",
        "typeFilter": {
          "@id": "https://openminds.ebrains.eu/core/Person"
        }
      },
      "required": true,
      "ensureOrder": true,
      "structure": [
        {
          "propertyName": "query:given_name",
          "path": "https://openminds.ebrains.eu/vocab/givenName"
        },
        {
          "propertyName": "query:family_name",
          "path": "https://openminds.ebrains.eu/vocab/familyName",
          "filter": {
            "op": "EQUALS",
            "parameter": "author"
          }
        },
        {
          "propertyName": "query:orcid",
          "singleValue": "FIRST",
          "path": [
            "https://openminds.ebrains.eu/vocab/digitalIdentifier",
            "https://openminds.ebrains.eu/vocab/identifier"
          ]
        }
      ]
    },
    {
      "propertyName": "query:owner",
      "path": {
        "@id": "https://openminds.ebrains.eu/vocab/custodian",
        "typeFilter": {
          "@id": "https://openminds.ebrains.eu/core/Person"
        }
      },
      "ensureOrder": true,
      "structure": [
        {
          "propertyName": "query:given_name",
          "path": "https://openminds.ebrains.eu/vocab/givenName"
        },
        {
          "propertyName": "query:family_name",
          "path": "https://openminds.ebrains.eu/vocab/familyName",
          "filter": {
            "op": "EQUALS",
            "parameter": "owner"
          }
        },
        {
          "propertyName": "query:orcid",
          "singleValue": "FIRST",
          "path": [
            "https://openminds.ebrains.eu/vocab/digitalIdentifier",
            "https://openminds.ebrains.eu/vocab/identifier"
          ]
        }
      ]
    },
    {
      "propertyName": "query:project_id",
      "path": "https://core.kg.ebrains.eu/vocab/meta/space"
    },
    {
      "propertyName": "query:organization",
      "ensureOrder": true,
      "singleValue": "FIRST",
      "filter": {
        "op": "EQUALS",
        "parameter": "organization"
      },
      "path": [
        {
          "@id": "https://openminds.ebrains.eu/vocab/custodian",
          "typeFilter": {
            "@id": "https://openminds.ebrains.eu/core/Organization"
          }
        },
        "https://openminds.ebrains.eu/vocab/fullName"
      ]
    },
    {
      "propertyName": "query:cell_type",
      "singleValue": "FIRST",
      "filter": {
        "op": "CONTAINS",
        "parameter": "cell_type"
      },
      "path": [
        {
          "@id": "https://openminds.ebrains.eu/vocab/studyTarget",
          "typeFilter": {
            "@id": "https://openminds.ebrains.eu/controlledTerms/CellType"
          }
        },
        "https://openminds.ebrains.eu/vocab/name"
      ]
    },
    {
      "propertyName": "query:model_scope",
      "singleValue": "FIRST",
      "filter": {
        "op": "CONTAINS",
        "parameter": "model_scope"
      },
      "path": [
        "https://openminds.ebrains.eu/vocab/scope",
        "https://openminds.ebrains.eu/vocab/name"
      ]
    },
    {
      "propertyName": "query:abstraction_level",
      "singleValue": "FIRST",
      "filter": {
        "op": "CONTAINS",
        "parameter": "abstraction_level"
      },
      "path": [
        "https://openminds.ebrains.eu/vocab/abstractionLevel",
        "https://openminds.ebrains.eu/vocab/name"
      ]
    },
    {
      "propertyName": "query:brain_region",
      "singleValue": "FIRST",
      "filter": {
        "op": "CONTAINS",
        "parameter": "brain_region"
      },
      "path": [
        {
          "@id": "https://openminds.ebrains.eu/vocab/studyTarget",
          "typeFilter": {
            "@id": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation"
          }
        },
        "https://openminds.ebrains.eu/vocab/name"
      ]
    },
    {
      "propertyName": "query:species",
      "singleValue": "FIRST",
      "filter": {
        "op": "CONTAINS",
        "parameter": "species"
      },
      "path": [
        {
          "@id": "https://openminds.ebrains.eu/vocab/studyTarget",
          "typeFilter": {
            "@id": "https://openminds.ebrains.eu/controlledTerms/Species"
          }
        },
        "https://openminds.ebrains.eu/vocab/name"
      ]
    },
    {
      "propertyName": "query:description",
      "path": "https://openminds.ebrains.eu/vocab/description"
    },
    {
      "propertyName": "query:instances",
      "path": "https://openminds.ebrains.eu/vocab/hasVersion",
      "required": true,
      "ensureOrder": true,
      "structure": [
        {
          "propertyName": "query:uri",
          "path": "@id"
        },
        {
          "propertyName": "query:version",
          "path": "https://openminds.ebrains.eu/vocab/versionIdentifier"
        },
        {
          "propertyName": "query:code_format",
          "ensureOrder": true,
          "singleValue": "FIRST",
          "filter": {
            "op": "CONTAINS",
            "parameter": "format"
          },
          "path": [
            "https://openminds.ebrains.eu/vocab/format",
            "https://openminds.ebrains.eu/vocab/name"
          ]
        },
        {
          "propertyName": "query:source",
          "singleValue": "FIRST",
          "path": [
            "https://openminds.ebrains.eu/vocab/repository",
            "https://openminds.ebrains.eu/vocab/IRI"
          ]
        },
        {
          "propertyName": "query:license",
          "singleValue": "FIRST",
          "path": [
            "https://openminds.ebrains.eu/vocab/license",
            "https://openminds.ebrains.eu/vocab/fullName"
          ]
        },
        {
          "propertyName": "query:repository",
          "singleValue": "FIRST",
          "path": [
            "https://openminds.ebrains.eu/vocab/repository",
            "https://openminds.ebrains.eu/vocab/hash",
            "https://openminds.ebrains.eu/vocab/digest"
          ]
        },
        {
          "propertyName": "query:timestamp",
          "path": "https://openminds.ebrains.eu/vocab/releaseDate"
        },
        {
          "propertyName": "query:model_id",
          "singleValue": "FIRST",
          "path": [
            {
              "@id": "https://openminds.ebrains.eu/vocab/hasVersion",
              "reverse": true
            },
            "@id"
          ]
        },
        {
          "propertyName": "query:alternatives",
          "ensureOrder": true,
          "path": [
            "https://openminds.ebrains.eu/vocab/isAlternativeVersionOf",
            "https://openminds.ebrains.eu/vocab/homepage"
          ],
          "structure": {
            "propertyName": "query:IRI",
            "path": "https://openminds.ebrains.eu/vocab/IRI"
          }
        },
        {
          "propertyName": "query:description",
          "path": "https://openminds.ebrains.eu/vocab/versionInnovation"
        },
        {
          "propertyName": "query:inputData",
          "path": [
            {
              "@id": "https://openminds.ebrains.eu/vocab/inputData",
              "typeFilter": [
                {
                  "@id": "https://openminds.ebrains.eu/core/File"
                },
                {
                  "@id": "https://openminds.ebrains.eu/core/WebResource"
                }
              ]
            },
            "https://openminds.ebrains.eu/vocab/IRI"
          ]
        },
        {
          "propertyName": "query:inputData",
          "path": [
            {
              "@id": "https://openminds.ebrains.eu/vocab/inputData",
              "typeFilter": [
                {
                  "@id": "https://openminds.ebrains.eu/core/WebResource"
                },
                {
                  "@id": "https://openminds.ebrains.eu/core/File"
                }
              ]
            },
            "https://openminds.ebrains.eu/vocab/IRI"
          ]
        }
      ]
    },
    {
      "propertyName": "query:format",
      "path": [
        "https://openminds.ebrains.eu/vocab/hasVersion",
        "https://openminds.ebrains.eu/vocab/format",
        "https://openminds.ebrains.eu/vocab/name"
      ]
    }
  ]
}

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