Validation error: 'dict' object has no attribute 'id'

[Raphael-Gazzotti]

After generating files with bids2openminds and attempting to validate them, the following error is returned:

'dict' object has no attribute 'id'

This issue may be related to embedded entities, but further investigation may be needed to confirm the cause.

We could coordinate with @renqingcm to investigate this further and give her the go-ahead to proceed with bids2ebrains once the issue is solved.

[renqingcm]

Here’s an example of the workflow and what the final, valid JSON-LD files look like after running conversion and applying all required metadata patches.

After running Step 1 (Convert) in the Streamlit interface using the ds001 BIDS example, I scanned the generated directory, the scan reported:

19 files have missing fields; 28 total gaps.

With missing keys aggregated by type:

SubjectState.ageCategory : 16  
Dataset.custodian : 1  
Dataset.description : 1  
DatasetVersion.accessibility : 1  
DatasetVersion.ethicsAssessment : 1  
DatasetVersion.keyword : 1  
DatasetVersion.license : 1  
DatasetVersion.preparationDesign : 1  
DatasetVersion.studyTarget : 1  
DatasetVersion.versionIdentifier : 1  
DatasetVersion.versionInnovation : 1  
FileRepository.hostedBy : 1  
FileRepository.label : 1

These fields were then filled in step 2 patch, where I selected valid openMINDS options (e.g., CC-BY license, agecategory, accessibility) and manually entered short text values for fields like Dataset.description and DatasetVersion.versionIdentifier, etc.

Here are how JSON-LD examples look after patching:
DatasetVersion jsonld:

{
  "@context": { "@vocab": "https://openminds.ebrains.eu/vocab/" },
  "@id": "https://kg.ebrains.eu/api/instances/87f13bd8-76da-4f35-9e29-0a25b8b2b1cc",
  "@type": "https://openminds.ebrains.eu/core/DatasetVersion",
  "behavioralProtocol": [ { "@id": "https://kg.ebrains.eu/api/instances/3b50b8d9-da3a-4f59-9812-4aa93f5882f8" } ],
  "dataType": [ { "@id": "https://openminds.ebrains.eu/instances/semanticDataType/rawData" } ],
  "digitalIdentifier": { "@id": "https://kg.ebrains.eu/api/instances/92ca155e-9648-47f1-9181-9026681c6a37" },
  "experimentalApproach": [ { "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/anatomy" }, { "@id": "https://openminds.ebrains.eu/instances/experimentalApproach/neuroimaging" } ],
  "fullName": "Balloon Analog Risk-taking Task",
  "repository": { "@id": "https://kg.ebrains.eu/api/instances/0712e83a-0d93-4104-a186-4f86bef38ef7" },
  "shortName": "Balloon Analog Risk-taking Task",
  "studiedSpecimen": [
    { "@id": "https://kg.ebrains.eu/api/instances/a21483ff-6a17-4e6c-8c0c-82106d0d8f37" },
    { "@id": "https://kg.ebrains.eu/api/instances/78a8f1e1-7aad-420a-8a2b-0ad1e5e6a6d3" },
    { "@id": "https://kg.ebrains.eu/api/instances/8590a186-a806-4211-815a-bffa470ed50a" },
    { "@id": "https://kg.ebrains.eu/api/instances/e76ada3d-2397-4abc-80b3-a68a2e90b0e1" },
    { "@id": "https://kg.ebrains.eu/api/instances/254aad88-93e2-4bfe-8aed-0d8de8b1ccfb" },
    { "@id": "https://kg.ebrains.eu/api/instances/618f37f8-6f25-4d14-aaac-84f71784eed2" },
    { "@id": "https://kg.ebrains.eu/api/instances/9b49fba7-38ce-4ad5-be29-2e2d65340909" },
    { "@id": "https://kg.ebrains.eu/api/instances/48f1d667-aec0-471c-af16-f9a443018ea9" },
    { "@id": "https://kg.ebrains.eu/api/instances/fc8bb114-31aa-454d-9cf9-8f75f06bdefe" },
    { "@id": "https://kg.ebrains.eu/api/instances/52eea4de-289a-484c-a9f2-546cb209461c" },
    { "@id": "https://kg.ebrains.eu/api/instances/6e868568-aed6-4540-81fd-666c0b8b026e" },
    { "@id": "https://kg.ebrains.eu/api/instances/af12aaab-7c0a-4ef8-9b34-3b76bf6fd00f" },
    { "@id": "https://kg.ebrains.eu/api/instances/908a316d-e788-4e1e-9c6f-f2c1483fcc03" },
    { "@id": "https://kg.ebrains.eu/api/instances/f44fae75-9ea7-4c66-80d9-330c742ecdc2" },
    { "@id": "https://kg.ebrains.eu/api/instances/d0c48c74-aaa4-4c92-91f4-badb555cc335" },
    { "@id": "https://kg.ebrains.eu/api/instances/0ddecbd1-f47f-4adf-80d9-4a2dc383b7d2" }
  ],
  "technique": [ { "@id": "https://openminds.ebrains.eu/instances/technique/structuralMagneticResonanceImaging" } ],
  "versionIdentifier": "v1.0.0",
  "accessibility": { "@id": "https://openminds.ebrains.eu/instances/productAccessibility/freeAccess" },
  "license": { "@id": "https://openminds.ebrains.eu/instances/licenses/CC-BY-4.0" },
  "preparationDesign": "Converted from BIDS using bids2openminds.",
  "ethicsAssessment": "All participants gave informed consent. Data were anonymized.",
  "studyTarget": "Risk-taking behavior in young adults.",
  "keyword": ["risk-taking", "behavior", "fMRI"],
}

SubjectState jsonld:

{
  "@context": { "@vocab": "https://openminds.ebrains.eu/vocab/" },
  "@id": "https://kg.ebrains.eu/api/instances/83e27d09-c3d0-4886-ba5d-26de66df32ac",
  "@type": "https://openminds.ebrains.eu/core/SubjectState",
  "age": { "@type": "https://openminds.ebrains.eu/core/QuantitativeValue", "unit": { "@id": "https://openminds.ebrains.eu/instances/unitOfMeasurement/year" }, "value": 26 },
  "internalIdentifier": "Studied state sub-09",
  "lookupLabel": "dsv_0a25b8b2b1cc_Studied state sub-09",
  "ageCategory": { "@id": "https://openminds.ebrains.eu/instances/ageCategory/adult" }
}

Dataset jsonld:

{
  "@context": { "@vocab": "https://openminds.ebrains.eu/vocab/" },
  "@id": "https://kg.ebrains.eu/api/instances/852dd116-d24c-4fab-bcbc-127e4ab4e75d",
  "@type": "https://openminds.ebrains.eu/core/Dataset",
  "digitalIdentifier": { "@id": "https://kg.ebrains.eu/api/instances/92ca155e-9648-47f1-9181-9026681c6a37" },
  "fullName": "Balloon Analog Risk-taking Task",
  "hasVersion": [ { "@id": "https://kg.ebrains.eu/api/instances/87f13bd8-76da-4f35-9e29-0a25b8b2b1cc" } ],
  "shortName": "Balloon Analog Risk-taking Task",
  "description": "Disease detection modeling",
  "custodian": [ { "@id": "https://kg.ebrains.eu/api/instances/c607bd54-0457-40bf-bede-4c4041caacdc" } ]
}

FileRepository.jsonld

{
  "@context": { "@vocab": "https://openminds.ebrains.eu/vocab/" },
  "@id": "https://kg.ebrains.eu/api/instances/ee8e5b5c-01b8-4d08-8ac7-156075497b1e",
  "@type": "https://openminds.ebrains.eu/core/FileRepository",
  "IRI": "unused://local-placeholder",
  "hostedBy": { "@id": "https://kg.ebrains.eu/instances/organizationalUnit/ebrains" },
  "label": "local-placeholder"
}

but the following error is returned when validating:
Unreadable JSON-LD: 'dict' object has no attribute 'id'