JSKOS Server

Web service to access JSKOS data.

JSKOS Server implements the JSKOS API web service and storage for JSKOS data such as controlled vocabularies, concepts, and concept mappings.

Install

Docker

The easiest way to install and use JSKOS Server is with Docker and Docker Compose. Please refer to our Docker documentation for more information and instructions.

Dependencies

You need Node.js 18 or Node.js 20 (recommended) to run JSKOS Server. You need to have access to a MongoDB database (minimun v4; v6 or v7 recommended).

Clone and Install

git clone https://github.com/gbv/jskos-server.git
cd jskos-server
npm ci

Configuration

You can customize the application settings via a configuration file. By default, this configuration file resides in config/config.json. However, it is possible to adjust this path via the CONFIG_FILE environment variable. Note that the given path has to be either absolute (i.e. starting with /) or relative to the config/ folder (i.e. it defaults to ./config.json). Note that the path to the configuration file needs to be valid and writable because a namespace key will be generated and written to the file if it doesn't currently exist. Note that if the file exists and contains invalid JSON data, JSKOS Server will refuse to start.

Currently, there are only two environment variables:

NODE_ENV - either development (default) or production; currently, the only difference is that in production, HTTPS URIs are forced for entities created on POST requests.
CONFIG_FILE - alternate path to a configuration file, relative to the config/ folder; defaults to ./config.json.

You can either provide the environment variables during the command to start the server, or in a .env file in the root folder.

It is also possible to have more specific configuration based on the environment. These are set in config/config.development.json or config/config.production.json. Values from these files have precedent over the user configuration.

All missing keys will be defaulted from config/config.default.json:

{
  "verbosity": "warn",
  "baseUrl": null,
  "env": "development",
  "title": "JSKOS Server",
  "version": null,
  "closedWorldAssumption": true,
  "port": 3000,
  "proxies": [],
  "mongo": {
    "user": "",
    "pass": "",
    "host": "127.0.0.1",
    "port": 27017,
    "db": "jskos-server",
    "options": {
      "connectTimeoutMS": 360000,
      "socketTimeoutMS": 360000,
      "heartbeatFrequencyMS": 10000
    }
  },
  "auth": {
    "algorithm": "RS256",
    "key": null
  },
  "schemes": true,
  "concepts": true,
  "mappings": {
    "read": {
      "auth": false
    },
    "create": {
      "auth": true
    },
    "update": {
      "auth": true,
      "crossUser": false
    },
    "delete": {
      "auth": true,
      "crossUser": false
    },
    "fromSchemeWhitelist": null,
    "toSchemeWhitelist": null,
    "cardinality": "1-to-n"
  },
  "concordances": true,
  "annotations": {
    "read": {
      "auth": false
    },
    "create": {
      "auth": true
    },
    "update": {
      "auth": true,
      "crossUser": false
    },
    "delete": {
      "auth": true,
      "crossUser": false
    },
    "moderatingIdentities": [],
    "mismatchTagVocabulary": null
  },
  "anonymous": false,
  "identityProviders": null,
  "identities": null,
  "ips": null
}

The provided configuration files (user config and environment config) will be validated with the provided JSON Schema file under config/config.schema.json (public URI: https://gbv.github.io/jskos-server/status.schema.json). If validation fails, JSON Server will refuse to start! Please check whether your configuration is correct after each change. If there is something wrong, the console output will try to provide you with enough detail to fix the issue.

If you are running jskos-server behind a reverse proxy, it is necessary to provide the baseUrl key as well as the proxies key in your configuration (example for our production API):** See also:

{
  "baseUrl": "https://coli-conc.gbv.de/api/",
  "proxies": ["123.456.789.101", "234.567.891.011"]
}

With the keys schemes, concepts, mappings, concordances, and annotations, you can configure whether endpoints related to the specific functionality should be available. A minimal configuration file to just server read-only vocabulary and concept information could look like this:

{
  "mappings": false,
  "annotations": false,
  "concordances": false
}

Available actions for schemes, concepts, mappings, and annotations are read, create, update, and delete. By default, all types can be read, while mappings and annotations can be created, updated, and deleted with authentication. Explanantions for additional options:

auth: Boolean. Can be defined only on actions. Defines whether access will require authentication via JWT. By default false for read, and true for all other actions.
crossUser: Boolean or list of URI strings. Can be defined only on update and delete actions when auth is true. Defines whether it is possible to edit an entity from a different user than the authenticated one (true = allowed for all users, list = allowed for specified user URIs). false by default.
anonymous: Boolean. Can be defined on any level (deeper levels will take the values from higher levels if necessary*). If set, no creator and contributor is saved. false by default.
cardinality: String. Can be defined only on type mappings. Currently possible values: 1-to-n (default), 1-to-1. If 1-to-1 is configured, mappings with multiple concepts in to will be rejected.
identities: List of URI strings. Can be defined on any level (deeper levels will take the values from higher levels if necessary*). If set, an action with auth set to true can only be used by users with an URI given in the list. null by default (no restrictions).
identityProviders: List of strings. Can be defined on any level (deeper levels will take the values from higher levels if necessary*). If set, an action can only be used by users who have that identity associated with them. null by default (no restrictions).
ips: List of strings. Strings can be IPv4 addresses (e.g. 127.0.0.1, 123.234.123.234) or CIDR ranges (e.g. 192.168.0.1/24). Can be defined on any level (deeper levels will take the values from higher levels if necessary*). If set, an action can only be used by clients with a whitelisted IP address. null by default (no restrictions). Note: An empty array will allow all IPs. Note: This property will be removed for security reasons when accessing GET /status (meaning that clients will not be able to see the whitelisted IP addresses).
fromSchemeWhitelist/toSchemeWhitelist: Can be defined only on type mappings. List of scheme objects that are allowed for fromScheme/toScheme respectively. null allows all schemes.
mismatchTagVocabulary: Can be defined only on type annotations. A JSKOS Concept Schemes object with required property uri. When configured, concept URIs belonging to this vocabulary can be used to tag mapping mismatches in mapping annotations. See below for detailed information about configuration and usage of this feature.

* Only applies to actions create, update, and delete.

Note that any properties not mentioned here are not allowed!

Mapping Mismatch Tagging for Negative Assessment Annotations

To differentiate why a mapping was annotated with a negative assessment, a mismatch tagging vocabulary can now be configured under annotations.mismatchTagVocabulary. In theory, any vocabulary can be used, but our instance will use a very small "mismatch" vocabulary available in https://github.com/gbv/jskos-data/tree/master/mismatch.

To set up mapping mismatch tagging, add the vocabulary to the configuration:

{
  "annotations": {
    "mismatchTagVocabulary": {
      "uri": "https://uri.gbv.de/terminology/mismatch/"
    }
  }
}

Currently, the vocabulary and its concepts are required to be imported in the same JSKOS Server instance:

# Import vocabulary metadata
npm run import schemes https://raw.githubusercontent.com/gbv/jskos-data/master/mismatch/mismatch-scheme.json
# Reset existing concepts (e.g. if old version has been imported previously)
npm run reset -- -t concepts -s "https://uri.gbv.de/terminology/mismatch/"
# Import vocabulary concepts
npm run import concepts -- --set-api https://raw.githubusercontent.com/gbv/jskos-data/master/mismatch/mismatch-concepts.json

After restarting JSKOS Server, mapping mismatch tagging is available for annotations. To add such a tag to an annotation, add a body field like this:

{
  "motivation": "assessing",
  "bodyValue": "-1",
  "body": [
    {
      "type": "SpecificResource",
      "value": "https://uri.gbv.de/terminology/mismatch/scope",
      "purpose": "tagging"
    }
  ]
}

Currently, this is the only supported format, i.e. body as an array containing an object with type of "SpecificResource", purpose of "tagging", and the tag concept's URI as value.

To identify whether a JSKOS Server instance supports this kind of tagging, check the /status endpoint for the config.annotations.mismatchTagVocabulary key.

Access control

The rights to read, create, update and delete entities via API can be controlled via several configuration settings described above (data import is not limited by these restrictions):

Restricted access via ips is always applied in addition to other settings
Without authentication (auth set to false) the server does not know about user accounts. In this case the creator and contributor fields of an object can be set without limitations (default) or they are ignored when anonymous is set to true.
With authentication an action can be limited to accounts listed in identities (if set). Rights to create, update, and delete entities can further depend on two controls:
1. value of creator and contributor of a superordinated object. Concepts always belong to vocabularies via inScheme or topConceptOf and mappings can belong to concordances via partOf.
2. settings of crossUser together with value of creator and contributor of the object

The first control is only checked if it has a superordinated object with contributor and/or creator. This can only be the case for mappings and concepts. The connection to a superordinated object is checked on both the stored object and its modified value, so moving a mapping from one concordance to another is only allowed if access is granted for both. The authenticated user must be listed as creator or contributor of the superordinated object to pass this control.

The second control is only checked when the first control cannot be applied and only on authenticated actions update or delete where anonymous is set to false (this is the default). With crossUser set to false, the authenticated user must be listed as creator of the stored object. With crossUser set to true any authenticated user (optionally limited to those listed in identities) can update or delete the object.

For authenticated actions with anonymous being false creation of a new object will always set its initial creator to the autenticated user and update of an object will always add the user to contributor unless it is already included as creator or contributor. Further modification of creator and contributor (removal and addition of entries) is limited to vocabularies and concordance by authenticated users listed as creator of the object.

Here are some helpful example presets for configuration of "concordances, "mappings", or "annotations".

Read-only access (does not make sense for annotations):

{
  "read": {
    "auth": false
  }
}

Anyone can create, but only logged-in users can update and delete (and only their own items):

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": false
  },
  "update": {
    "auth": true,
    "crossUser": false
  },
  "delete": {
    "auth": true,
    "crossUser": false
  }
}

Anyone can create, logged-in users can update (independent of creator), logged-in users can delete their own items:

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": false
  },
  "update": {
    "auth": true,
    "crossUser": true
  },
  "delete": {
    "auth": true,
    "crossUser": false
  }
}

Anyone can create, as well as update and delete, independent of creator:

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": false
  },
  "update": {
    "auth": false,
    "crossUser": true
  },
  "delete": {
    "auth": false,
    "crossUser": true
  }
}

If write access for concept schemes and/or concepts is necessary, it is recommended that they are secured by only allowing certain users (via identities) or only allowing certain IP addresses (via ips):

Only user with URI https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619 can write:

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": true,
    "identities": ["https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619"]
  },
  "update": {
    "auth": true,
    "identities": ["https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619"]
  },
  "delete": {
    "auth": true,
    "identities": ["https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619"]
  }
}

Only localhost can write:

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": false,
    "ips": ["127.0.0.1"]
  },
  "update": {
    "auth": false,
    "ips": ["127.0.0.1"]
  },
  "delete": {
    "auth": false,
    "ips": ["127.0.0.1"]
  }
}

Note that auth is set to false because it refers to authentication via JWT. The IP filter is separate from that. An even more secure way would be to use both JWT authentication with an identities filter as well as an IP filter.

Only user with URI https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619 can create, but others can update/delete if they are creator/contributor of an entity:

{
  "read": {
    "auth": false
  },
  "create": {
    "auth": true,
    "identities": ["https://coli-conc.gbv.de/login/users/c0c1914a-f9d6-4b92-a624-bf44118b6619"]
  },
  "update": {
    "auth": true
  },
  "delete": {
    "auth": true
  }
}

A configuration like this will be used to handle concordances in Cocoda. Only selected accounts will be able to create new concordances, but they will be able to add other accounts as creator/contributor so that those accounts will be able to assign mappings to the concordance and edit mappings that belong to the concordance.

Authentication

It is possible to limit certain actions to authenticated users, indicated by the auth option (see example configurations above). Authorization is performed via JWTs (JSON Web Tokens). To configure authentication, you need to provide the JWT algorithm and the key/secret in the configuration file, like this:

"auth": {
  "algorithm": "RS256",
  "key": "-----BEGIN PUBLIC KEY-----\nMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA57ZWRoOjXYTQ9yujxAu7\ne3k4+JRBAqGdDVIRRq5vXB2D5nJBIhQjVjylumn+QnTX/MdZx8qn7X96npUwHwIh\nylCgUmsYXcjP08X/AXEcP5bPOkgBBCKjWmcm+p01RQSOM0nSptyxpyXzr2ppWe1b\nuYdRYDWj+JV7vm+jJA4NiFv4UnAhoG5lRATADzu0/6wpMK3dVMBL7L0jQoV5xBAb\nLADOy5hD9XEII3VPkUqDGIKM+Z24flkCIf0lQ7FjsoZ2mmM1SZJ5vPDcjMKreFkX\ncWlcwGHN0PUWZWLhb7c8yYa1rauMcwFwv0d2XyOEfgkqEJdCh8mVT/5jR48D2PNG\ncwIDAQAB\n-----END PUBLIC KEY-----\n"
}

The JWT has to be provided as a Bearer token in the authorization header, e.g. Authorization: Bearer <token>. Currently, all authorized endpoints will be accessible (although PUT/PATCH/DELETE are limited to the user who created the object by default), but later it will be possible to set scopes for certain users (see #47).

The authentication is designed to be used together with an instance of login-server, but it is also possible to use your own JWTs.

JWT Example

The recommended Node.js library for creating JWTs is jsonwebtoken. Note that for simplicity, we are using the HS256 algorithm which is symmetrical. In most cases, it would be better to use RS256 with a libarary like node-rsa instead.

Simple config, restricting the /mappings endpoint with authentication:

{
  "auth": {
    "algorithm": "HS256",
    "key": "yoursecret"
  },
  "mappings": {
    "read": {
      "auth": true
    }
  }
}

Creating a JWT:

const jwt = require("jsonwebtoken")
// Payload is an object containing the user object with an URI:
const data = {
  user: { uri: "urn:test:hallo" }
}
// Sign the token with our secret
const token = jwt.sign(data, "yoursecret", {
  algorithm: "HS256",
  expiresIn: "7d" // valid for 7 days
})

Using the token in a request (using curl):

# Request without header should return ForbiddenAccessError (code 403)
curl localhost:3000/mappings
# Request with header should return JSON data (insert your own token and jskos-server URL of course)
curl -H "Authorization: Bearer eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ1c2VyIjp7InVyaSI6InRlc3Q6aGFsbG8ifSwiaWF0IjoxNTg5NTMyNDU3LCJleHAiOjE1OTAxMzcyNTd9.fXIxgS0QyFk9Lvz7Z-fkb4tAueMTSNZ4zAuB6iwePq4" localhost:3000/mappings

If you are the only user that is supposed to be authenticated for your instance of jskos-server, you could in theory use something like this to create a token with a long lifetime and use it for all your requests. Please consider the security implications before doing this though.

Login Server Example

If you have multiple users using your instance of jskos-server, it is recommended to use login-server for authentication. login-server uses the asymmetrical RS256 algorithm by default and will create a public/private key pair on first launch. The public key will be in ./public.key and you will need that for the configuration:

{
  "auth": {
    "algorith": "RS256",
    "key": "-----BEGIN PUBLIC KEY-----\nMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA57ZWRoOjXYTQ9yujxAu7\ne3k4+JRBAqGdDVIRRq5vXB2D5nJBIhQjVjylumn+QnTX/MdZx8qn7X96npUwHwIh\nylCgUmsYXcjP08X/AXEcP5bPOkgBBCKjWmcm+p01RQSOM0nSptyxpyXzr2ppWe1b\nuYdRYDWj+JV7vm+jJA4NiFv4UnAhoG5lRATADzu0/6wpMK3dVMBL7L0jQoV5xBAb\nLADOy5hD9XEII3VPkUqDGIKM+Z24flkCIf0lQ7FjsoZ2mmM1SZJ5vPDcjMKreFkX\ncWlcwGHN0PUWZWLhb7c8yYa1rauMcwFwv0d2XyOEfgkqEJdCh8mVT/5jR48D2PNG\ncwIDAQAB\n-----END PUBLIC KEY-----\n"
  }
}

After that, you can use login-client to interact with your login-server instance and receive JWTs. When using WebSockets, login-server will periodically send a new JWT before the previous one expires. You can then use that to authenticate your requests to jskos-server. (An example on how to use login-client can be found in the source code of login-server.)

For testing your authentication without a full-fledged solution using login-client, you can use http://localhost:3004/token (where localhost:3004 is your instance of login-server) to request a JWT.

Note about previous additional options for auth:

postAuthRequired: now covered by mappings.create.auth
whitelist: now covered by identities
allowCrossUserEditing: now covered by mappings.update.crossUser and mappings.delete.crossUser

Data Import

JSKOS Server provides scripts to import JSKOS data into the database or delete data from the database. Right now, mappings, terminologies (concept schemes), concepts, concordances, and annotations, in JSON (object or array of objects) or NDJSON format are supported.

Import Notes

About hierarchies within concepts: Hierarchies are supported. However, only the broader field will be used during import. Both ancestors and narrower will be removed and the respective endpoints (GET /concepts/ancestors and GET /concepts/narrower) will dynamically rebuild these properties. That means that when converting your data, please normalize it so that the hierarchy is expressed via the broader field in JSKOS.

Example scheme (as JSON object) with concepts in a hierarchy (as NDJSON):

{
  "uri": "urn:test:scheme",
  "notation": [
    "TEST"
  ],
  "uriPattern": "^urn:test:concept-(.+)$"
}

{ "topConceptOf": [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-a" }
{ "inScheme":     [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-a.1",    "broader": [{ "uri": "urn:test:concept-a" }] }
{ "inScheme":     [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-a.2",    "broader": [{ "uri": "urn:test:concept-a" }] }
{ "topConceptOf": [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-b" }
{ "inScheme":     [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-b.1",    "broader": [{ "uri": "urn:test:concept-b" }] }
{ "inScheme":     [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-b.1.1",  "broader": [{ "uri": "urn:test:concept-b.1" }] }
{ "inScheme":     [{ "uri": "urn:test:scheme" }], "uri": "urn:test:concept-b.1.2",  "broader": [{ "uri": "urn:test:concept-b.1" }] }

(Note that a notation for the concepts can be omitted because we have defined uriPattern on the concept scheme. Also, we don't need to define inScheme for concepts with topConceptOf.)

About the created property for concept schemes: The import script uses the bulk write endpoints to import data. For concept schemes, this means that any existing data for imported schemes will be overwritten and replaced with the new data. This includes especially the created property which might not exist in your source data and will be set on import if necessary. If you need a consistent created date, make sure that your source data already includes this field.

Import Script

Examples of using the import script:

# Create indexes for all types
npm run import -- --indexes
# Import RVK scheme (from coli-conc API)
npm run import -- schemes https://coli-conc.gbv.de/rvk/api/voc
# Import RVK concepts (this will take a while)
npm run import -- concepts https://coli-conc.gbv.de/rvk/data/2019_1/rvko_2019_1.ndjson
# Import coli-conc concordances
npm run import -- concordances https://coli-conc.gbv.de/api/concordances

# Batch import multiple files or URLs
npm run import-batch -- mappings files.txt
# files.txt should contain one file or URL per line with the full path and no escaping.
# You can, for example, store these batch import files in folder `imports` which is ignored in git.

Note: If you have concepts in your database, make sure to run npm run import -- --indexes at least once. This will make sure all necessary indexes are created. Without this step, the /concepts/suggest and /concepts/search endpoints will not work.

For more information about the import script, run npm run import -- --help.

Reset Script

It is also possible to delete entities from the server via the command line. Running the command will first determine what exactly will be deleted and ask you for confirmation:

# Will delete everything from database
npm run reset
# Will delete mappings from database
npm run reset -- -t mappings
# Will delete all concepts that belong to a certain concept scheme URI
npm run reset -- -s http://uri.gbv.de/terminology/rvk/
# Will delete all mappings that belong to a certain concordance URI
npm run reset -- -c https://gbv.github.io/jskos/context.json
# Will delete entities with certain URIs
npm run reset -- http://rvk.uni-regensburg.de/nt/A http://rvk.uni-regensburg.de/nt/B
# Will show help for more information
npm run reset -- --help

For scripting, you can use the yes command to skip confirmation. Make sure you know what you're doing! Example: yes | npm run reset -- urn:test:uri.

Usage

Run Server

# Development server with hot reload and auto reconnect at localhost:3000 (default)
npm run start

# To run the server in production, run this:
NODE_ENV=production node ./server.js

Run Tests

Tests will use the real MongoDB with -test-${namespace} appended to the database name.

npm test

Run Supplemental Scripts

There are some supplemental scripts that were added to deal with specific sitatuations. These can be called with npm run extra name-of-script. The following scripts are available:

supplementNotationsInMappings: This will look for mappings where the field notation is missing for any of the concepts, and it will attempt to supplement those notations. This only works for vocabularies which are also imported into the same jskos-server instance and where either uriPattern or namespace are given.

API

General

All API methods stick to the following rules, unless otherwise specified.

Requests

All URL parameters are optional.
POST/PUT/PATCH requests require a JSON body.
Alternatively, POST can also receive the following inputs:
- any kind of JSON stream
- mutlipart/form-data with the file in data
- a URL with JSON data as url in the request params
- Note: The type request param might be required (either json, ndjson, or multipart)
All GET endpoints returning a certain type of JSKOS data offer the properties=[list] parameter, with [list] being a comma-separated list of properties.
- All JSKOS types allow removing properties by prefixing the property with -. All following properties in the list will also be removed.
- For concepts and mappings, the property annotations can be specified to add all annotations in the database for a certain item.
- For concepts, the properties narrower and ancestors can be specified to add narrower/ancestor concepts to a certain concept.
- Specifying a * adds all available properties.
- Example: properties=*,-narrower,notation will add properties annotations and ancestors, and remove the notation property from all return items.
- Properties can be explicitly re-added by prefixing them with +, e.g. properties=-from,to,+from will only remove the to property.
- Note that the + sign has to be properly encoded as %2B, otherwise it will be interpreted as a space.
All GET endpoints (except for /status and those with :_id) offer pagination via limit=[number] (default: 100) and offset=[number] (default: 0) parameters. In the response, there will be a Link header like described in the GitHub API documentation, as well as a X-Total-Count header containing the total number of results.

Write access

POST/PUT/PATCH/DELETE requests require authentication via a JWT from login-server in the header. Exception: Authentication for certain actions on certain endpoints can be disabled (see configuration).
PUT/PATCH/DELETE requests are required to come from the owner of the entity that is being modified.
POST/PUT/PATCH endpoints will override creator and contributor of submitted objects (see this comment for more details)
PATCH request bodies are merged on the top level, so it's enough to include object properties to be modified. To remove a top-level property, set it to null.

Responses

GET requests will return code 200 on success.
POST requests will return code 201 on success.
DELETE requests will return code 204 on success.
For possible error responses, see Errors.

GET /status

Returns a status object.

There is a JSON Schema for the format of this endpoint. It is available under /status.schema.json for every jskos-server installation (starting from version 1.0.0). The most recent schema can be accessed here: https://gbv.github.io/jskos-server/status.schema.json

Note that certain properties from the actual configuration will not be shown in the result for /status:

verbosity
port
mongo
namespace
proxies
ips (including inside of actions)
auth.key if a symmetrical algorithm is used (HS256, HS384, HS512)

Success Response

{
  "config": {
    "env": "development",
    "baseUrl": "http://localhost:3000/",
    "version": "1.1",
    "auth": {
      "algorithm": "RS256",
      "key": null
    },
    "schemes": {
      "read": {
        "auth": false
      }
    },
    "concepts": {
      "read": {
        "auth": false
      }
    },
    "mappings": {
      "read": {
        "auth": false
      },
      "create": {
        "auth": true
      },
      "update": {
        "auth": true,
        "crossUser": false
      },
      "delete": {
        "auth": true,
        "crossUser": false
      },
      "fromSchemeWhitelist": null,
      "toSchemeWhitelist": null,
      "anonymous": false,
      "cardinality": "1-to-n"
    },
    "concordances": {
      "read": {
        "auth": false
      }
    },
    "annotations": {
      "read": {
        "auth": false
      },
      "create": {
        "auth": true
      },
      "update": {
        "auth": true,
        "crossUser": false
      },
      "delete": {
        "auth": true,
        "crossUser": false
      },
      "mismatchTagVocabulary": {
        "uri": "https://uri.gbv.de/terminology/mismatch/",
        "API": [
          {
            "type": "http://bartoc.org/api-type/jskos",
            "url": "http://localhost:3000/"
          }
        ]
      }
    },
    "identityProviders": null,
    "identities": null
  },
  "data": "http://localhost:3000/data",
  "schemes": "http://localhost:3000/voc",
  "top": "http://localhost:3000/voc/top",
  "voc-search": "http://localhost:3000/voc/search",
  "voc-suggest": "http://localhost:3000/voc/suggest",
  "voc-concepts": "http://localhost:3000/voc/concepts",
  "concepts": "http://localhost:3000/concepts",
  "narrower": "http://localhost:3000/concepts/narrower",
  "ancestors": "http://localhost:3000/concepts/ancestors",
  "search": "http://localhost:3000/concepts/search",
  "suggest": "http://localhost:3000/concepts/suggest",
  "mappings": "http://localhost:3000/mappings",
  "concordances": "http://localhost:3000/concordances",
  "annotations": "http://localhost:3000/annotations",
  "types": null,
  "validate": "http://localhost:3000/validate",
  "ok": 1
}

Error Response

In case of an error, for instance a failed database connection, the value of response property ok is set to 0.

GET /checkAuth

Endpoint to check whether a user is authorized. If type or action are not set, it will use identities/identityProviders that are defined directly under config.

URL Params

type=[type] one of "schemes", "concepts", "mappings", "annotations" (optional)

action=[action] one of "read", "create", "update", "delete" (optional)

POST /validate

Endpoint to validate JSKOS objects via jskos-validate.

URL Params

type=[type] a JSKOS object type that all objects must have (optional)

unknownFields=[boolean] with 1 or true to allow unknown fields inside objects (by default, unknown fields do not pass validation)

knownSchemes=[boolean] with 1 or true to use concept schemes available in this jskos-server instance for validation of concepts. Implies type=concept and all concept must reference a known concept scheme via inScheme.

If neither type nor knownSchemes are specified, concept schemes in the data to be validated can be used to validate following concepts in the same request array (see last example below).

Success Response

Array with the JSON response provided by jskos-validate. The indices of the array correspond to the order of the given data. An element is true when the object passed validation, or an array of errors when the object failed validation. Data format of error objects may change in future versions but there is always at least field message.

Sample Call

In the following example, an empty object is validated. Since no type is specified, it is validated as a Resource which does not have required field names and therefore passes validation.

curl -X POST "https://coli-conc.gbv.de/dev-api/validate" -H 'Content-Type: application/json' -d '{}'

[
  true
]

In the following example, the same call is given, but the parameter type is set to mapping. Mappings require the fields from and to, therefore the empty object fails validation and errors are returned.

curl -X POST "https://coli-conc.gbv.de/dev-api/validate?type=mapping" -H 'Content-Type: application/json' -d '{}'

[
  [
    {
      "instancePath": "",
      "schemaPath": "#/required",
      "keyword": "required",
      "params": {
        "missingProperty": "from"
      },
      "message": "must have required property 'from'"
    },
    {
      "instancePath": "",
      "schemaPath": "#/required",
      "keyword": "required",
      "params": {
        "missingProperty": "to"
      },
      "message": "must have required property 'to'"
    }
  ]

]

In this example, an array of mixed typed objects is validated (given in file example.json):

[
  {
    "type": [ "http://www.w3.org/2004/02/skos/core#ConceptScheme" ],
    "uri": "http://example.org/voc",
    "notationPattern": "[a-z]+"
  },
  {
    "type": [ "http://www.w3.org/2004/02/skos/core#Concept" ],
    "uri": "http://example.org/1",
    "notation": [ "abc" ],
    "inScheme": [ { "uri": "http://example.org/voc" } ]
  },
  {
    "type": [ "http://www.w3.org/2004/02/skos/core#Concept" ],
    "uri": "http://example.org/2",
    "notation": [ "123" ],
    "inScheme": [ { "uri": "http://example.org/voc" } ]
  }
]

The first object is a concept scheme with notationPattern. Since the other two elements are concepts of that concept scheme (see inScheme), the concepts must additionally pass tests related to URI or notation patterns of the given schemes. Since the last concept has a notation that does not match the pattern, it fails the validation. Note that only object with appropriate type field are included in this additional part of validation.

curl -X POST "https://coli-conc.gbv.de/dev-api/validate" -H 'Content-Type: application/json' -d @example.json

[
  true,
  true,
  [
    {
      "message": "concept notation 123 does not match [a-z]+"
    }
  ]
]

GET /validate

Same as POST /validate but JSKOS data to be validated is passed via URL.

URL Params

url=[url] URL to load JSKOS data from

type=[type] see POST /validate

unknownFields=[boolean] see POST /validate

knownSchemes=[boolean] see POST /validate

GET /data

Returns data for a certain URI or URIs. Can return concept schemes, concepts, concordances, mappings, and annotations. This endpoint does not offer pagination via limit and offset. It will always return all results. Furthermore, there is no certain order to the result set (but it should be consistent across requests). If a certain type of data requires authentication and the user is not authenticated, that type of data will simply not be returned.

Note: As of version 2.0, this endpoint was adjusted to return all types of items that are available in the database, instead of just concepts and concept schemes. The additional parameters, apart from uri, were also removed. For the previous behavior (only without returning concept schemes), see GET /concepts.

URL Params

uri=[uri] URIs for JSKOS items separated by | (annotations, despite using id instead of uri, can also be queried here)

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors, narrower, and annotations)
Success Response

JSON array of JSKOS Items

GET /concordances

Lists all concordances for mappings.

URL Params

uri=[uri] URIs for concordances separated by |

fromScheme=[uri|notation] only show concordances from concept scheme (URI or notation) (separated by |)

toScheme=[uri|notation] only show concordances to concept scheme (URI or notation) (separated by |)

creator=[creator] only show concordances from creator (separated by |)

mode=[mode] specify the mode for the parameters above, one of and (default) and or

download=[type] returns the whole result as a download (available types are json and ndjson), ignores limit and offset
Success Response

JSON array of JSKOS Concordances

Sample Call

curl https://coli-conc.gbv.de/api/concordances?limit=1

[
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "creator": [
      {
        "prefLabel": {
          "de": "VZG"
        }
      }
    ],
    "distributions": [
      {
        "download": "https://coli-conc.gbv.de/api/mappings?partOf=http://coli-conc.gbv.de/concordances/ddc_rvk_recht&download=ndjson",
        "format": "http://format.gbv.de/jskos",
        "mimetype": "application/x-ndjson; charset=utf-8"
      }
    ],
    "extent": "2267",
    "fromScheme": {
      "notation": [
        "DDC"
      ],
      "uri": "http://bartoc.org/en/node/241"
    },
    "notation": [
      "ddc_rvk_recht"
    ],
    "scopeNote": {
      "de": [
        "Recht"
      ]
    },
    "toScheme": {
      "notation": [
        "RVK"
      ],
      "uri": "http://bartoc.org/en/node/533"
    },
    "type": [
      "http://rdfs.org/ns/void#Linkset"
    ],
    "uri": "http://coli-conc.gbv.de/concordances/ddc_rvk_recht"
  }
]

GET /concordances/:_id

Returns a specific concordance.

URL Params

None
Success Response

JSKOS object for concordance.
Error Response

If no concordance with _id could be found, it will return a 404 not found error.

POST /concordances

Saves one or more concordances in the database. Note that fromScheme and toScheme must be supported by the jskos-server instance.

URL Params

None
Success Reponse

JSKOS Concordance object(s) as were saved in the database.
Error Response

When a single concordance is provided, an error can be returned if there's something wrong with it (see errors). When multiple concordances are provided, the first error will be returned.

PUT /concordances/:_id

Overwrites a concordance in the database.

Success Reponse

JSKOS Concordance object as it was saved in the database.

Note that any changes to the uri, notation, fromScheme, toScheme, extent, distributions, and created properties will be ignored. (No error will be thrown in this case.)

PATCH /concordances/:_id

Adjusts a concordance in the database.

Success Reponse

JSKOS Concordance object as it was saved in the database.

Note that changes to the properties uri, notation, fromScheme, toScheme, created, extent, and distributions are currently not allowed and will result in an InvalidBodyError.

DELETE /concordances/:_id

Deletes a concordance from the database.

Success Reponse

Status 204, no content.

Note that only concordances which have no mappings associated can be deleted.

GET /mappings

Returns an array of mappings. Each mapping has a property uri under which the specific mapping can be accessed.

URL Params

identifier=[identifier1|identifier2|...] specify mapping identifiers separated by |

from=[uriOrNotation1|uriOrNotation2|...] specify the source URI or notation (truncated search possible by appending a *, multiple URIs/notations separated by |)

fromScheme=[uriOrNotation1|uriOrNotation2|...] only show mappings from concept scheme (URI or notation, multiple URIs/notations separated by |)

to=[uriOrNotation1|uriOrNotation2|...] specify the target URI or notation (truncated search possible by appending a *, multiple URIs/notations separated by |)

toScheme=[uriOrNotation1|uriOrNotation2|...] only show mappings to concept scheme (URI or notation, multiple URIs/notations separated by |)

mode=[mode] specify the mode for from/fromScheme, to/toScheme, and identifier, one of and (default) and or; note that 1) multiple values given for a single parameter are always connected via "or", and 2) from and fromScheme / to and toScheme are always connected via "and"

direction=[direction] specify the direction of the mapping. Available values are: forward (default), backward (essentially swaps from and to), both (combines forward and backward).

type=[uri1|uri2|...] only show mappings that conform to a certain type or types (see JSKOS Concept Mappings) (URIs separated by |)

partOf=[uri1|uri2|...] only show mappings that are part of certain concordances (URIs separated by |); value none returns mappings that are not part of a concordance, value any returns mappings that are part of any concordance

creator=[string1|string2|...] only show mappings that have a certain creator (separated by |)

annotatedBy=[uri1|uri2|...] has annotations by user with URI(s)

annotatedFor=[motivation] has annotations with a certain motivation (e.g. assessing); value none returns mappings that have no annotations at all, value any returns mappings that have any kind of annotation, values starting with ! (e.g. !assessing) filter out annotations with that motivation. Note that to mitigate performance issues with negative assertions (none or !xyz), jskos-server will return the number 9999999 in the X-Total-Count header (see this).

annotatedWith=[body] has annotations with a certain body value (e.g. +1) OR has a sum of assessment annotations that conforms to the given comparison operation; for the latter, either from or to must be given, annotatedFor must be either not set or set to assessing, and the value of this parameter needs to consist of a comparison operator (=, <, >, <=, or >=) followed by a number. Example: annotatedWith=>0 returns mappings with a positive assessment sum (equivalent to annotatedWith=>=1).

properties=[list] with [list] being a comma-separated list of properties (currently supporting only annotations for mappings)

download=[type] returns the whole result as a download (available types are json, ndjson, csv, and tsv), ignores limit and offset; note: csv and tsv are restricted (and fixed) to 5 target concepts, meaning that if the data set includes a mapping with more than 5 target concepts, only the first 5 will appear in the export

sort=[sort] sorts by a specific field. Available are created, modified, and mappingRelevance (default). Results will always be additionally sorted by from.memberSet.uri and _id in order to create a stable and sensible sort.

order=[order] order to use for sorting. Available are asc and desc (default).

cardinality=[cardinality] cardinality of the mapping. Available are 1-to-n (default) and 1-to-1.
Success Response

JSON array of JSKOS Concept Mappings

Sample Call

curl https://coli-conc.gbv.de/api/mappings?from=http://dewey.info/class/612.116/e23/

[
  {
    "from": {
      "memberSet": [
        {
          "uri": "http://dewey.info/class/612.116/e23/",
          "notation": [
            "612.116"
          ]
        }
      ]
    },
    "to": {
      "memberSet": [
        {
          "uri": "http://rvk.uni-regensburg.de/nt/WW_8800-WW_8839",
          "notation": [
            "WW 8800-WW 8839"
          ]
        }
      ]
    },
    "fromScheme": {
      "uri": "http://bartoc.org/en/node/241",
      "notation": [
        "DDC"
      ]
    },
    "toScheme": {
      "uri": "http://bartoc.org/en/node/533",
      "notation": [
        "RVK"
      ]
    },
    "identifier": [
      "urn:jskos:mapping:content:fb92cbed7466764dd2ca5fdf054bf55e65ec6b87",
      "urn:jskos:mapping:members:5aa92285bba839954baccdadc7df5ef4558860ed"
    ],
    "@context": "https://gbv.github.io/jskos/context.json"
  }
]

GET /mappings/suggest

Suggests notations used in mappings.

URL Params

search=[notation] specifies the notation (prefix) to search for
Success Response

JSON array of suggestions in OpenSearch Suggest Format.

Sample Call

curl https://coli-conc.gbv.de/api/mappings/suggest?search=A&limit=5

[
  "A",
  [
    "AN 74800",
    "AN 78950",
    "AN 70000",
    "AN 71000",
    "AN 96900"
  ],
  [
    42,
    25,
    19,
    18,
    17
  ],
  []
]

GET /mappings/voc

Lists all concept schemes used in mappings.

URL Params

from=[uri|notation] restrict mappings to those from a concept

to=[uri|notation] restrict mappings to those to a concept

mode=[mode] specify the mode for from and to, one of and and or (default)
Success Response

JSON array of JSKOS Concept Schemes

Sample Call

curl https://coli-conc.gbv.de/api/mappings/voc?from=612.112&to=612.112

[
  {
    "uri": "http://bartoc.org/en/node/430",
    "notation": [
      "GND"
    ],
    "fromCount": 2
  },
  {
    "uri": "http://bartoc.org/en/node/241",
    "notation": [
      "DDC"
    ],
    "fromCount": 2,
    "toCount": 2
  },
  {
    "uri": "http://bartoc.org/en/node/533",
    "notation": [
      "RVK"
    ],
    "toCount": 2
  }
]

GET /mappings/infer

Returns mappings based on stored mappings and mappings derived by inference. If a request to GET /mappings results in stored mappings, only those are returned. If no stored mappings match the request, the following algorithm is applied to infer virtual mappings (this is experimental and not all source schemes are supported):

Ancestors of the requested concept (from) are traversed from narrower to broader until matching mapping(s) from one of the ancestor concepts are found.
The resulting mappings are filtered and transformed based on their mapping type:
- exactMatch and narrowMatch result in narrowMatch (for instance Optics < Sciences when no mappings from Optics are stored but e.g. Physics is ancestor of Optics and mapped to Sciences)
- closeMatch results in narrowMatch unless query parameter strict is set to a true value. In this case mappings of this type are ignored (for instance Optics < Alchemy when Physics is ancestor of Optics and mapped to Alchemy but this may lead to doubtful mappings such as Computational Physics < Alchemy)
- relatedMatch and mappingRelation are not changed.

Inferred mappings don't have fields such as uri, identifier, creator, created... but uri of the mapping used for inference is included in source.

URL Params

This endpoint takes the same parameters as GET /mappings, except that to, download, and cardinality (fixed to "1-to-1") are not supported. Parameter direction only supports the default value "forward". Parameters from and fromScheme are mandatory to get a non-empty result.

strict=[boolean] values 1 or true disallow mapping type "closeMatch" for inferred mappings (default false)

depth=[number] a non-negative number of the depth used to infer mappings (not set by default); 0 means no inference, 1 means only the next ancestor concept (= broader) is used for inference, etc.
Success Response

JSON array of JSKOS Concept Mappings

Sample Call

curl https://coli-conc.gbv.de/api/mappings/infer?from=http%3A%2F%2Frvk.uni-regensburg.de%2Fnt%2FWI%25203130&fromScheme=http%3A%2F%2Fbartoc.org%2Fen%2Fnode%2F533&toScheme=http%3A%2F%2Fbartoc.org%2Fen%2Fnode%2F18785

[
  {
    "from": {
      "memberSet": [
        {
          "uri": "http://rvk.uni-regensburg.de/nt/WI%203130",
          "notation": [
            "WI 3130"
          ]
        }
      ]
    },
    "to": {
      "memberSet": [
        {
          "uri": "http://uri.gbv.de/terminology/bk/42.42",
          "notation": [
            "42.42"
          ]
        }
      ]
    },
    "fromScheme": {
      "uri": "http://bartoc.org/en/node/533",
      "notation": [
        "RVK"
      ]
    },
    "toScheme": {
      "uri": "http://bartoc.org/en/node/18785",
      "notation": [
        "BK"
      ]
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#narrowMatch"
    ],
    "source": [
      {
        "uri": "https://coli-conc.gbv.de/api/mappings/ef121206-a42d-4c3c-9ef3-b597c000acb4"
      }
    ],
    "identifier": [
      "urn:jskos:mapping:content:1b0fb2343795db4de7e1f8c7207b94a789614a15",
      "urn:jskos:mapping:members:2d22b62a0295959d587487d228d51836d05b1c50"
    ],
    "@context": "https://gbv.github.io/jskos/context.json"
  },
  {
    "from": {
      "memberSet": [
        {
          "uri": "http://rvk.uni-regensburg.de/nt/WI%203130",
          "notation": [
            "WI 3130"
          ]
        }
      ]
    },
    "to": {
      "memberSet": [
        {
          "uri": "http://uri.gbv.de/terminology/bk/42.44",
          "notation": [
            "42.44"
          ]
        }
      ]
    },
    "fromScheme": {
      "uri": "http://bartoc.org/en/node/533",
      "notation": [
        "RVK"
      ]
    },
    "toScheme": {
      "uri": "http://bartoc.org/en/node/18785",
      "notation": [
        "BK"
      ]
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#narrowMatch"
    ],
    "source": [
      {
        "uri": "https://coli-conc.gbv.de/api/mappings/6b920456-db5d-49b1-a197-b851df6f9dbd",
      }
    ],
    "identifier": [
      "urn:jskos:mapping:content:8bb72e1605f9c25b0c97889439e6dde952e0cbd0",
      "urn:jskos:mapping:members:5870d87ec08c9a9a5ccba182bd96b92ad2f9d688"
    ],
    "@context": "https://gbv.github.io/jskos/context.json"
  }
]

GET /mappings/:_id

Returns a specific mapping.

URL Params

properties=[list] with [list] being a comma-separated list of properties (currently supporting only annotations for mappings)
Success Response

JSKOS object for mapping.
Error Response

If no mapping with _id could be found, it will return a 404 not found error.

Sample Call

curl https://coli-conc.gbv.de/api/mappings/5c450ba1a32a4a82d0f3fbf3

{
  "from": {
    "memberSet": [
      {
        "uri": "http://rvk.uni-regensburg.de/nt/TA-TD",
        "notation": [
          "TA - TD"
        ]
      }
    ]
  },
  "toScheme": {
    "template": "http://dewey.info/class/(.+)/e23/",
    "pattern": "[0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+)?|[1-9][A-Z]?--[0-9]+|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+)?",
    "uri": "http://bartoc.org/en/node/241",
    "notation": [
      "DDC"
    ]
  },
  "fromScheme": {
    "notation": [
      "RVK"
    ],
    "uri": "http://bartoc.org/en/node/533"
  },
  "to": {
    "memberSet": [
      {
        "uri": "http://dewey.info/class/500/e23/",
        "notation": [
          "500"
        ]
      }
    ]
  },
  "identifier": [
    "urn:jskos:mapping:content:d37d117b5e3d811447bc332b184ac6e5ac4bde6b",
    "urn:jskos:mapping:members:4c480744ea32e7e71ba39fae6cc8d8e4e0382912"
  ],
  "partOf": [
    {
      "uri": "http://coli-conc.gbv.de/concordances/rvk_ddc_ta-td"
    }
  ],
  "creator": [
    {
      "prefLabel": {
        "de": "GESIS"
      }
    }
  ],
  "url": "https://coli-conc.gbv.de/api/mappings/5c450ba1a32a4a82d0f3fbf3",
  "@context": "https://gbv.github.io/jskos/context.json"
}

POST /mappings

Saves a mapping or multiple mappings in the database.

URL Params

bulk=[boolean] 1 or true enable bulk mode for importing multiple mappings into the database. Errors for individual mappings will be ignored and existing mappings will be overridden. The resulting set will only include the id for each mapping that was written into the database.
Success Reponse

JSKOS Mapping object as it was saved in the database, or array of mapping objects with only a uri if bulk mode was used..
Error Response

When a single mapping is provided, an error can be returned if there's something wrong with it (see errors). When multiple mappings are provided, the first error will be returned, except if bulk mode is enabled in which errors for individual mappings are ignored.

Note that the partOf property is currently not allowed. Associating a mapping with a concordances has to be done in a separate PUT or PATCH request.

PUT /mappings/:_id

Overwrites a mapping in the database.

Success Reponse

JSKOS Mapping object as it was saved in the database.

Note that any changes to the created property will be ignored. Note that changes to partOf (i.e. association with a concordance) are only possible if 1) fromScheme and toScheme are equal between the mapping and the concordance, 2) the authenticated user is creator of the mapping OR if the mapping is already part of a concordance, the user is creator/contributor of that concordance, and 3) the user is creator/contributor of the target concordance (if given).

PATCH /mappings/:_id

Adjusts a mapping in the database.

Success Reponse

JSKOS Mapping object as it was saved in the database.

Note that any changes to the created property will be ignored. Note that changes to partOf (i.e. association with a concordance) are only possible if 1) fromScheme and toScheme are equal between the mapping and the concordance, 2) the authenticated user is creator of the mapping OR if the mapping is already part of a concordance, the user is creator/contributor of that concordance, and 3) the user is creator/contributor of the target concordance (if given).

DELETE /mappings/:_id

Deletes a mapping from the database.

Success Reponse

Status 204, no content.

GET /voc

Lists supported terminologies (concept schemes).

URL Params

uri=[uri] URIs for concept schemes separated by |. If uri is not given, all supported concept schemes are returned.

type=URI type URI to filter schemes

languages=tag language codes to filter schemes, separated by , (exact values). Not to be confused with query parameter language at other endpoints!

// Note: The language parameter at other endpoints means "give me labels in these languages". That's why it should have a different name here. Until then, it is removed.

subject=URIs subject URI(s) to filter schemes, separated by |

license=URIs license URI(s) to filter schemes, separated by |

publisher=URI|label publisher URI or label to filter schemes (only exact matches)

partOf=URIs filter by registry URI that is listed in partOf field of the scheme, separated by |

sort=[property] sort the results by a certain property. Possible values: label (preferred or alternative label in English or other languages), notation (string), created (timestamp), modified (timestamp), counter (number after last / in URI)

order=[order] order to use for sorting. Available are asc (default) and desc.
Success Response

JSON array of JSKOS Concept Schemes

Sample Call

curl https://coli-conc.gbv.de/api/voc?limit=1

[
  {
    "uri": "http://dewey.info/scheme/edition/e23/",
    "prefLabel": {
      "de": "Dewey-Dezimalklassifikation",
      "en": "Dewey Decimal Classification"
    },
    "notation": [
      "DDC"
    ],
    "identifier": [
      "http://bartoc.org/en/node/241"
    ],
    "license": [
      {
        "uri": "http://creativecommons.org/licenses/by-nc-nd/3.0/"
      }
    ],
    "publisher": [
      {
        "uri": "http://d-nb.info/gnd/1086052218",
        "prefLabel": {
          "de": "OCLC"
        },
        "altLabel": {
          "de": [
            "OCLC Online Computer Library Center"
          ]
        },
        "url": "https://www.oclc.org/"
      }
    ],
    "@context": "https://gbv.github.io/jskos/context.json"
  }
]

POST /voc

Saves a concept scheme or multiple concept schemes in the database. Each concept scheme has to have a unique uri.

URL Params

bulk=[boolean] 1 or true enable bulk mode for importing multiple concept schemes into the database. Errors for individual concept schemes will be ignored and existing concept schemes will be overridden. The resulting set will only include the id for each concept scheme that was written into the database.
Success Reponse

JSKOS Concept Scheme object or array as was saved in the database, or array of concept scheme objects with only a uri if bulk mode was used.
Error Response

When a single concept scheme is provided, an error can be returned if there's something wrong with it (see errors). When multiple concept schemes are provided, the first error will be returned, except if bulk mode is enabled in which errors for individual concept schemes are ignored.

PUT /voc

Overwrites a concept scheme in the database. Is identified via its uri field.

Success Reponse

JSKOS Concept Scheme object as it was saved in the database.

Note that any changes to the created property will be ignored.

DELETE /voc

Deletes a concept scheme from the database.

URL Params

uri=URI URI for concept scheme to be deleted.
Success Reponse

Status 204, no content.

GET /voc/top

Lists top concepts for a concept scheme.

URL Params

uri=[uri] URI for a concept scheme

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors and narrower)
Success Response

JSON array of JSKOS Concepts

Sample Call

curl https://coli-conc.gbv.de/api/voc/top?uri=http://dewey.info/scheme/edition/e23/

GET /voc/concepts

Lists concepts for a concept scheme.

URL Params

uri=[uri] URI for a concept scheme (required)

near=[latitude,longitude] filters concepts by distance to a location (JSKOS field location), with latitude being a floating point value between -90 and 90 and longitude being a floating point value between -180 and 180

distance=[distance] value in kilometers which sets the radius for the near parameter if specified (default: 1)

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors, narrower, and annotations); not supported for download

download=[type] returns the whole result as a download (available types are json and ndjson), ignores limit and offset
Success Response

JSON array of JSKOS Concepts

Sample Call

curl https://coli-conc.gbv.de/api/voc/concepts?uri=http://dewey.info/scheme/edition/e23/

DELETE /voc/concepts

Deletes all concepts of a certain concept scheme from the database.

URL Params

uri=URI URI for a concept scheme
Success Reponse

Status 204, no content.

GET /voc/suggest

Returns concept scheme suggestions.

URL Params

search=[keyword|notation] specifies the keyword or notation (prefix) to search for

language=[string] comma-separated priority list of languages for labels in results

format=[string] return format for suggestions: jskos or opensearch (default)
Success Response

JSON array of suggestions.

GET /voc/search

Currently the same as /voc/suggest with parameter format=jskos.

GET /concepts

Returns detailed data for concepts. Note that there is no certain order to the result set (but it should be consistent across requests). Note that no data is returned if no filtering parameter is given (one of uri, notation, voc, or near).

URL Params

uri=[uri] URIs for concepts separated by |

notation=[notation] notations for concepts separated by |

voc=[uri] filter by concept scheme URI

near=[latitude,longitude] filters concepts by distance to a location (JSKOS field location), with latitude being a floating point value between -90 and 90 and longitude being a floating point value between -180 and 180

distance=[distance] value in kilometers which sets the radius for the near parameter if specified (default: 1)

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors, narrower, and annotations); not supported for download

download=[type] returns the whole result as a download (available types are json and ndjson), ignores limit and offset
Success Response

JSON array of JSKOS Concepts

Sample Call

curl https://coli-conc.gbv.de/api/concepts?uri=http://dewey.info/class/612.112/e23/

[
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/612.11/e23/"
      }
    ],
    "created": "2000-02-02",
    "identifier": [
      "16d595ff-ec01-3e55-b425-016cf92bb950"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2013-12-04",
    "notation": [
      "612.112"
    ],
    "prefLabel": {
      "de": "Leukozyten (Weiße Blutkörperchen)"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/612.112/e23/",
    "narrower": [
      null
    ]
  }
]

POST /concepts

Saves a concept or multiple concepts in the database. Each concept has to have a unique uri as well as a concept scheme that is available on the server in the inScheme or topConceptOf field.

URL Params

bulk=[boolean] 1 or true enable bulk mode for importing multiple concepts into the database. Errors for individual concepts will be ignored and existing concepts will be overridden. The resulting set will only include the URI for each concept that was written into the database.
Success Reponse

JSKOS Concept object or array as was saved in the database, or array of concept objects with only a URI if bulk mode was used.
Error Response

When a single concept is provided, an error can be returned if there's something wrong with it (see errors). When multiple concepts are provided, the first error will be returned, except if bulk mode is enabled in which errors for individual concepts are ignored.

PUT /concepts

Overwrites a concept in the database. Is identified via its uri field.

Success Reponse

JSKOS Concept object as it was saved in the database.

DELETE /concepts

Deletes a concept from the database.

URL Params

uri=URI URI for concept to be deleted.
Success Reponse

Status 204, no content.

GET /concepts/narrower

Returns narrower concepts for a concept.

Note: The old /narrower endpoint is deprecated as of version 2.0 and will be removed in version 3.0.

URL Params

uri=[uri] URI for a concept

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors and narrower)
Success Response

JSON array of JSKOS Concepts

Sample Call

curl https://coli-conc.gbv.de/api/concepts/narrower?uri=http://dewey.info/class/612.112/e23/

[
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/612.112/e23/"
      }
    ],
    "created": "2000-02-02",
    "identifier": [
      "cf6faa73-e5e7-3856-9429-611a8a39d253"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2005-11-02",
    "notation": [
      "612.1121"
    ],
    "prefLabel": {
      "de": "Biochemie"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/612.1121/e23/",
    "narrower": []
  },
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/612.112/e23/"
      }
    ],
    "created": "2000-02-02",
    "http://www.w3.org/2002/07/owl#deprecated": true,
    "identifier": [
      "23519115-b023-3812-a2c1-6fc99e169ae3"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2005-11-02",
    "notation": [
      "612.1122"
    ],
    "prefLabel": {
      "de": "Biophysik"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/612.1122/e23/",
    "narrower": []
  },
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/612.112/e23/"
      }
    ],
    "created": "2000-02-02",
    "identifier": [
      "4a070e77-094c-3638-9067-2b3625d612e9"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2005-11-02",
    "notation": [
      "612.1127"
    ],
    "prefLabel": {
      "de": "Anzahl und Auszählung"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/612.1127/e23/",
    "narrower": []
  }
]

GET /concepts/ancestors

Returns ancestor concepts for a concept.

Note: The old /ancestors endpoint is deprecated as of version 2.0 and will be removed in version 3.0.

URL Params

uri=[uri] URI for a concept

properties=[list] with [list] being a comma-separated list of properties (currently supporting ancestors and narrower)
Success Response

JSON array of JSKOS Concepts

Sample Call

curl https://coli-conc.gbv.de/api/concepts/ancestors?uri=http://dewey.info/class/61/e23/

[
  {
    "@context": "https://gbv.github.io/jskos/context.json",
    "created": "2000-02-02",
    "identifier": [
      "856c92e9-8b1f-3131-bfbe-f2d2266527d3"
    ],
    "modified": "2005-11-02",
    "notation": [
      "6"
    ],
    "prefLabel": {
      "de": "Technik, Medizin, angewandte Wissenschaften"
    },
    "topConceptOf": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/6/e23/",
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "narrower": [
      null
    ]
  }
]

GET /concepts/suggest

Returns concept suggestions.

Note: The old /suggest endpoint is deprecated as of version 2.0 and will be removed in version 3.0.

URL Params

search=[keyword|notation] specifies the keyword or notation (prefix) to search for

language=[string] comma-separated priority list of languages for labels in results

format=[string] return format for suggestions: jskos or opensearch (default)
Success Response

JSON array of suggestions.

Sample Calls

curl https://coli-conc.gbv.de/api/concepts/suggest?search=Krebs&limit=5

[
  "Krebs",
  [
    "133.5265 Krebs",
    "639.5 Krebstierfang",
    "639.6 Krebstierzucht",
    "616.994 Krebserkrankungen",
    "641.695 Krebstiere"
  ],
  [
    "",
    "",
    "",
    "",
    ""
  ],
  [
    "http://dewey.info/class/133.5265/e23/",
    "http://dewey.info/class/639.5/e23/",
    "http://dewey.info/class/639.6/e23/",
    "http://dewey.info/class/616.994/e23/",
    "http://dewey.info/class/641.695/e23/"
  ]
]

curl https://coli-conc.gbv.de/api/concepts/suggest?search=Krebs&limit=2&format=jskos

[
  {
    "_id": "http://dewey.info/class/133.5265/e23/",
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/133.526/e23/"
      }
    ],
    "created": "2000-02-02",
    "identifier": [
      "57e89e64-9de0-35c1-88da-856529d547c8"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2005-11-02",
    "notation": [
      "133.5265"
    ],
    "prefLabel": {
      "de": "Krebs"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/133.5265/e23/",
    "narrower": [],
    "priority": 292
  },
  {
    "_id": "http://dewey.info/class/639.5/e23/",
    "@context": "https://gbv.github.io/jskos/context.json",
    "broader": [
      {
        "uri": "http://dewey.info/class/639/e23/"
      }
    ],
    "created": "2000-02-02",
    "identifier": [
      "8b1dc20e-5d1e-34f4-8478-3fa022ba6fe0"
    ],
    "inScheme": [
      {
        "uri": "http://dewey.info/scheme/edition/e23/"
      }
    ],
    "modified": "2005-11-02",
    "notation": [
      "639.5"
    ],
    "prefLabel": {
      "de": "Krebstierfang"
    },
    "type": [
      "http://www.w3.org/2004/02/skos/core#Concept"
    ],
    "uri": "http://dewey.info/class/639.5/e23/",
    "narrower": [
      null
    ],
    "priority": 195
  }
]

GET /concepts/search

Currently the same as /concepts/suggest with parameter format=jskos. Additionally, search supports the parameter properties=[list] as in the other concept methods.

Note: The old /search endpoint is deprecated as of version 2.0 and will be removed in version 3.0.

GET /annotations

Returns an array of annotations. Each annotation has a property id under which the specific annotation can be accessed.

URL Params

id=[id] specify an annotation ID

creator=[uriOrName] only return annotations that have a certain creator (name or URI) (separated by |)

target=[target] only return annotations with a specific target URI (e.g. a mapping URI)

bodyValue=[bodyValue] only return annotations with a specific bodyValue (e.g. +1, -1)

motivation=[motivation] only return annotations with a specific motivation (e.g. assessing, moderating, tagging)
Success Response

Array of annotations in Web Annotation Data Model format

Sample Call

curl https://coli-conc.gbv.de/api/annotations?bodyValue=+1&limit=1

[
  {
    "target": {
      "id": "https://coli-conc.gbv.de/api/mappings/f8eff4e2-a6df-4d2c-8382-523072c59af7"
    },
    "motivation": "assessing",
    "bodyValue": "+1",
    "creator": "https://orcid.org/0000-0002-4087-8227",
    "created": "2019-01-31T09:44:12.699Z",
    "id": "https://coli-conc.gbv.de/api/annotations/2575e276-29c6-4d36-8477-b21be1790e64",
    "@context": "http://www.w3.org/ns/anno.jsonld",
    "type": "Annotation"
  }
]

GET /annotations/:_id

Returns a specific annotation.

Success Response

Object for annotation in Web Annotation Data Model format.
Error Response

If no annotation with _id could be found, it will return a 404 not found error.

Sample Call

curl https://coli-conc.gbv.de/api/annotations/5f23368f-a63b-4b69-acd6-b403110df97c

{
  "target": {
    "id": "https://coli-conc.gbv.de/api/mappings/f0cc5f65-5712-4820-9638-e662c0c4314e"
  },
  "motivation": "assessing",
  "bodyValue": "+1",
  "creator": {
    "id": "https://coli-conc.gbv.de/login/users/722cc9c5-2ce3-4ca0-b4fb-fef1f62236af",
    "name": "Jakob Voß"
  },
  "created": "2019-03-11T09:11:10.665Z",
  "id": "https://coli-conc.gbv.de/api/annotations/5f23368f-a63b-4b69-acd6-b403110df97c",
  "@context": "http://www.w3.org/ns/anno.jsonld",
  "type": "Annotation"
}

POST /annotations

Saves an annotation or multiple annotations in the database.

URL Params

bulk=[boolean] 1 or true enable bulk mode for importing multiple annotations into the database. Errors for individual annotations will be ignored and existing annotations will be overridden. The resulting set will only include the id for each annotation that was written into the database.
Success Reponse

Annotation object or array of object as was saved in the database in Web Annotation Data Model format, or array of annotation objects with only a id if bulk mode was used.
Error Response

When a single annotation is provided, an error can be returned if there's something wrong with it (see errors). When multiple annotations are provided, the first error will be returned, except if bulk mode is enabled in which errors for individual annotations are ignored.

PUT /annotations/:_id

Overwrites an annotation in the database.

Success Reponse

Annotation object as it was saved in the database in Web Annotation Data Model format.

Note that any changes to the created property will be ignored.

PATCH /annotations/:_id

Adjusts an annotation in the database.

Success Reponse

Annotation object as it was saved in the database in Web Annotation Data Model format.

Note that any changes to the created property will be ignored.

DELETE /annotations/:_id

Deletes an annotation from the database.

Success Reponse

Status 204, no content.

Errors

If possible, errors will be returned as a JSON object in the following format (example):

{
  error: "EntityNotFoundError",
  status: 404,
  message: "The requested entity ABC could not be found.",
}

The following errors are currently caught and returned as JSON:

EntityNotFoundError

Status code 404. Will be returned if GET /mappings/:_id or GET /annotations/:_id are requested with an unknown ID.

MalformedBodyError

Status code 400. Will be returned for POST/PUT/PATCH if the body was not JSON or missing.

MalformedRequestError

Status code 400. Will be returned if a required parameter is missing (currently implemented in GET /.../:_id endpoints, but should not be possible to reach).

DuplicateEntityError

Status code 422. Will be returned for POST if an entity with the same ID/URI already exists in the database.

InvalidBodyError

Status code 422. Will be returned for POST/PUT/PATCH if the body was valid JSON, but could not be validated (e.g. does not pass the JSKOS Schema).

CreatorDoesNotMatchError

Status code 403. Will be returned by PUT/PATCH/DELETE endpoints if the authenticated creator does not match the creator of the entity that is being edited.

BackendError

Status code 500. Will be returned if there's a backend error not related to the database or configuration.

DatabaseAccessError

Status code 500. Will be returned if the database is not available or if the current database request failed with an unknown error.

DatabaseInconsistencyError

Status code 500. Will be returned if there is an inconsistency issue with our database. Please contact us with the full error message if this occurs!

ConfigurationError

Status code 500. Will be returned if there is an error in the configuration that prevents the application from working correctly.

ForbiddenAccessError

Status code 403. Will be returned if the user is not allow access (i.e. when not on the whitelist or when an identity provider is missing).

Deployment

The application is currently deployed at http://coli-conc.gbv.de/api/. At the moment, there is no automatic deployment of new versions.

Notes about depolyment on Ubuntu

It is recommended to use a newer version of Node.js. Installing the dependencies might also require installing nodejs-legacy: sudo apt-get install nodejs-legacy (more info here). One possibility for running the application in production on Ubuntu 16.04 is described here. (Information about restarting pm2-based services on system reboot here.)

Update an instances deployed with PM2

# get updates from repository
git pull

# install dependencies
npm ci

# restart the process (adjust process name if needed)
pm2 restart jskos-server

Daily Import

If you'd like to run the import script daily to refresh current mappings, you can for example use a cronjob:

# Runs import script for jskos-server in /srv/cocoda/jskos-server at 1 AM each day.
00 01 * * * cd /srv/cocoda/jskos-server; ./scripts/import.sh

Running Behind a Reverse Proxy

There are certain things to consider when running jskos-server behind a reverse proxy:

Make sure the base URL is configured correctly in config.json so that correct URIs will be generated. Test this by creating a new mapping and making sure the URI of that mapping is correct and accessible.
Provide a list of trusted proxy IPs or ranges in the proxies key in config.json. E.g. "proxies": ["123.456.789.101", "234.567.891.011"]. See also: Express behind proxies.
The reverse proxy should be configured so that the base URL has a trailing slash: ~~https://example.com/api~~ ❌ - https://example.com/api/ ✅ (Note: Not implementing this has no further consequences except that /api will not be accessible.)
The reverse proxy should also be configured so that any URL except the base URL has no trailing slash: ~~https://example.com/api/status/~~ ❌ - https://example.com/api/status ✅
Make sure the target parameter (i.e. the actual IP and port where jskos-server is running) has a trailing slash.
Make sure the proxy is configured to correctly set the X-Forwarded-For header.

The following would be an example for 2./3./4. with an Apache reverse proxy:

<VirtualHost *:8099>
    Define API_PATH /api
    ServerName example.com

    RewriteEngine on
    # Remove trailing slash from everything EXCEPT the base URL
    RewriteCond %{REQUEST_URI} !^${API_PATH}/$
    RewriteRule ^(.*)/+$ $1 [R=301,L]
    # Force trailing slash for base URL only
    RewriteCond %{REQUEST_URI} ^${API_PATH}$
    RewriteRule ^(.+[^/])$ %{REQUEST_URI}/ [R=301,L]

    # Forward to jskos-server
    ProxyPass ${API_PATH}/ http://127.0.0.1:3000/
    ProxyPassReverse ${API_PATH}/ http://127.0.0.1:3000/

    # ...
</VirtualHost>

Related works

jskos-server is developed together with the cocoda mapping application.

Alternative open source applications for hosting concept schemes include:

See cocoda-sdk for efforts to provide uniform access to vocabulary information from different applications and sources.

Maintainers

Contribute

PRs accepted against the dev branch.

Small note: If editing the README, please conform to the standard-readme specification.

Publish

For maintainers only

Never work on the master branch directly. Always make changes on dev and then run the release script:

npm run release:patch # or minor or major

Name		Name	Last commit message	Last commit date
Latest commit History 880 Commits
.github/workflows		.github/workflows
bin		bin
config		config
docker		docker
errors		errors
models		models
routes		routes
services		services
test		test
utils		utils
views		views
.dockerignore		.dockerignore
.editorconfig		.editorconfig
.eslintrc.cjs		.eslintrc.cjs
.gitignore		.gitignore
.npmrc		.npmrc
LICENSE		LICENSE
README.md		README.md
ecosystem.example.json		ecosystem.example.json
package-lock.json		package-lock.json
package.json		package.json
server.js		server.js
status.schema.json		status.schema.json

License

gbv/jskos-server

Folders and files

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JSKOS Server

Table of Contents

Install

Docker

Dependencies

Clone and Install

Configuration

Mapping Mismatch Tagging for Negative Assessment Annotations

Access control

Authentication

JWT Example

Login Server Example

Data Import

Import Notes

Import Script

Reset Script

Usage

Run Server

Run Tests

Run Supplemental Scripts

API

General

Requests

Write access

Responses

GET /status

GET /checkAuth

POST /validate

GET /validate

GET /data

GET /concordances

GET /concordances/:_id

POST /concordances

PUT /concordances/:_id

PATCH /concordances/:_id

DELETE /concordances/:_id

GET /mappings

GET /mappings/suggest

GET /mappings/voc

GET /mappings/infer

GET /mappings/:_id

POST /mappings

PUT /mappings/:_id

PATCH /mappings/:_id

DELETE /mappings/:_id

GET /voc

POST /voc

PUT /voc

DELETE /voc

GET /voc/top

GET /voc/concepts

DELETE /voc/concepts

GET /voc/suggest

GET /voc/search

GET /concepts

POST /concepts

PUT /concepts

DELETE /concepts

GET /concepts/narrower

GET /concepts/ancestors

GET /concepts/suggest

GET /concepts/search

GET /annotations

GET /annotations/:_id

POST /annotations

PUT /annotations/:_id

PATCH /annotations/:_id

DELETE /annotations/:_id

Errors

EntityNotFoundError

MalformedBodyError

MalformedRequestError

DuplicateEntityError

InvalidBodyError