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Project Details

Tech Stack

  • Java
  • SpringBoot 3
  • Angular
  • MongoDB
  • Maven

Note: frontend-maven-plugin is used to build and copy Angular project during the build process. Threfore, whole application is packaged in the final jar.

APIs

Action Endpoint Method Body
Get schema api/v2/schemas/ERC000022?id=<$id> GET
Get schema version api/v2/schemas/ERC000022/1.0.0 GET
Create schema api/v2/schemas POST [SCHEMA with metadata]
Update schema api/v2/schemas?id=<$id> PUT [SCHEMA with metdata]
Delete schema api/v2/schemas?id=<$id> DELETE
Get all schema /api/v2/schemas/search GET

Vanilla schema endpoints

Vanilla schema endpoints can be used to retrieve schema without wrappping metadata. These endpoints are useful when dealing with JSON Schema validators.

Action Endpoint
Get latest vanilla schema by id /registry/schemas/{$id}
Get latest vanilla schema by accession /registry/schemas/{accession}
Get versioned vanilla schema by accession /registry/schemas/{accession}/{version}

Submit schema

sequenceDiagram
    actor alice
    participant schema-store
    participant biovalidator
    participant MongoDB
    alice->>schema-store: submit schema
    schema-store->>biovalidator: validate against meta-schema
    biovalidator->>schema-store: valid
    schema-store->>MongoDB: accession and save
    schema-store->>alice: saved schema
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Example

curl -u <user>:<pass> 'http://localhost:8080/api/v2/schemas' -i -X POST -H "Content-Type: application/json;charset=UTF-8" -d '{
"id":"https://www.ebi.ac.uk/biosamples/schemas/biosamples-test/1.0.0",
"name":"biosamples-test","version":"1.0.0","title":"BioSamples test checklist",
"description":"Minimum required fields to submit a sample into EBI BioSamples database",
"domain":"https://www.ebi.ac.uk/biosamples/schemas",
"metaSchema":"https://schemablocks.org/metaschemas/json-schema-draft-07/1.0.1",
"schema":{"$schema":"http://json-schema.org/draft-07/schema#","$id":"https://www.ebi.ac.uk/biosamples/schemas/biosamples-test/1.0.0","additionalProperties":true,"definitions":{"nonEmptyString":{"type":"string","minLength":1}},"required":["name","characteristics"],"title":"sample","type":"object","properties":{"name":{"type":"string"},"accession":{"type":"string"},"characteristics":{"type":"object","anyOf":[{"required":["organism"]},{"required":["Organism"]},{"required":["species"]},{"required":["Species"]}],"properties":{"organism":{"type":"array","items":{"properties":{"text":{"$ref":"#/definitions/nonEmptyString"}},"required":["text"]}},"Organism":{"type":"array","items":{"properties":{"text":{"$ref":"#/definitions/nonEmptyString"}},"required":["text"]}},"Species":{"type":"array","items":{"properties":{"text":{"$ref":"#/definitions/nonEmptyString"}},"required":["text"]}},"species":{"type":"array","items":{"properties":{"text":{"$ref":"#/definitions/nonEmptyString"}},"required":["text"]}}}}}},
"authority":"BIOSAMPLES"
}'

DB Structure

schema-store has two collections: schema and metaschema. Both of these collections have similar document structure.

Document structure of schema collection

erDiagram
schema {
        string _id PK "$id field of the schema is copied to the top level _id field"
        string accession " [Auto-generated field. Starting from prefix 'BSDC'. ENA checklists are imported with 'ERC' prefix]"
        string title "Title of the schema"
        string description "Schema description"
        string metaSchema "Meta-schema to validate against"
        string schema "Schema to be stored. Schema is stored as a string field in the database"
        string version "version"
        string domain "Placeholder for AAP domain. But this field is no longer needed"
        string authority "Field to mark the origin of the schema. Current values 'BIOSAMPLES', 'ENA'"
    } 'ENA']
#### Example
```json
{
    "_id" : "https://www.ebi.ac.uk/biosamples/schemas/biosamples-minimal/1.0.0",
    "accession" : "BSDC00001",
    "title" : "BioSamples minimal checklist",
    "description" : "Minimum required fields to submit a sample into EBI BioSamples database",
    "metaSchema" : "https://schemablocks.org/metaschemas/json-schema-draft-07/1.0.1",
    "schema" : "{\"$schema\":\"http://json-schema.org/draft-07/schema#\",\"$id\":\"https://www.ebi.ac.uk/biosamples/schemas/biosamples-minimal/1.0.0\",\"additionalProperties\":true,\"definitions\":{\"nonEmptyString\":{\"type\":\"string\",\"minLength\":1}},\"required\":[\"name\",\"characteristics\"],\"title\":\"sample\",\"type\":\"object\",\"properties\":{\"name\":{\"type\":\"string\"},\"accession\":{\"type\":\"string\"},\"characteristics\":{\"type\":\"object\",\"anyOf\":[{\"required\":[\"organism\"]},{\"required\":[\"Organism\"]},{\"required\":[\"species\"]},{\"required\":[\"Species\"]}],\"properties\":{\"organism\":{\"type\":\"array\",\"items\":{\"properties\":{\"text\":{\"$ref\":\"#/definitions/nonEmptyString\"}},\"required\":[\"text\"]}},\"Organism\":{\"type\":\"array\",\"items\":{\"properties\":{\"text\":{\"$ref\":\"#/definitions/nonEmptyString\"}},\"required\":[\"text\"]}},\"Species\":{\"type\":\"array\",\"items\":{\"properties\":{\"text\":{\"$ref\":\"#/definitions/nonEmptyString\"}},\"required\":[\"text\"]}},\"species\":{\"type\":\"array\",\"items\":{\"properties\":{\"text\":{\"$ref\":\"#/definitions/nonEmptyString\"}},\"required\":[\"text\"]}}}}}}",
    "name" : "biosamples-minimal",
    "version" : "1.0.0",
    "domain" : "https://www.ebi.ac.uk/biosamples/schemas",
    "authority" : "BIOSAMPLES",
    "_class" : "uk.ac.ebi.biosamples.jsonschemastore.model.mongo.MongoJsonSchema"
}
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