cocoda-sdk 3.6.1 → 3.6.3

package/README.md

@@ -11,10 +11,10 @@
 - [Install](#install)
 - [Usage](#usage)
   - [Import](#import)
+  - [Multiple Instances](#multiple-instances)
   - [Configuration](#configuration)
-  - [Registries](#registries)
   - [Providers](#providers)
-  - [Multiple Instances](#multiple-instances)
+  - [Services](#services)
   - [Authenticated Requests](#authenticated-requests)
 - [API](#api)
   - [General](#general)
@@ -22,6 +22,7 @@
   - [Concepts](#concepts)
   - [Concordances](#concordances)
   - [Mappings](#mappings)
+  - [Registries](#registries)
   - [Annotations](#annotations)
   - [Occurrences](#occurrences)
   - [Types](#types)
@@ -60,6 +61,14 @@ cocoda-sdk also exports some other members:
 - `addAllProviders` - a method that adds all avaiable providers to an instance
   - Can be called without parameters to add to the default instance. Useful if you need all providers.
 
+### Multiple Instances
+
+The `createInstance` method can be used to create a new and independent instance with a separate configuration if needed:
+
+```js
+const newCdk = cdk.createInstance(config)
+```
+
 ### Configuration
 cocoda-sdk can be configured after import:
 
@@ -75,76 +84,9 @@ import { cdk } from "cocoda-sdk"
 await cdk.loadConfig("https://raw.githubusercontent.com/gbv/cocoda/dev/config/cocoda.default.json")
 ```
 
-The configuration is a JSON object corresponding the the [configuration format of Cocoda](https://github.com/gbv/cocoda#configuration). In particular, the configuration contains an array property [`registries`](#registries).
-
-If you only use cocoda-sdk with a single registry, configuration might not be necessary (see below).
-
-### Registries
-
-A registry is an individual source of data, for instance a set of concept schemes available from a specific terminology service. The simplest registry consists only of a unique identifier (`uri`) and the name of the access provider (`provider`):
-
-```json
-{
-  "uri": "http://coli-conc.gbv.de/registry/local-mappings",
-  "provider": "LocalMappings"
-}
-```
-
-For most providers the configuration should use the BARTOC vocabulary API type URI instead:
-
-```json
-{
-  "api": "http://bartoc.org/api-type/skosmos",
-  "endpoint": "https://www.loterre.fr/skosmos/905/"
-}
-```
-
-A list of available providers can be found [below](#providers). Most providers need additional properties to work correctly.
-
-#### Endpoint Determination
-For many providers, you need to specify one or more endpoints on the registry object for it to work. There are, however, three steps in which these endpoints are determined:
-
-1. By explicitly specifying an endpoint on the registry object.
-2. By performaning a request to the provider's `/status` endpoint and parsing its result (which is done in `registry.init()`).
-3. By implication using the `api` base URL.
-
-Values set earlier in these steps will never be overwritten by later steps. That means to disable an endpoint explicitly, you can set it to `null` when configuring the registry. Also, if step 2 is successful, it will be assumed that no further endpoints exist and all missing endpoints will be set to `null`, i.e. essentially skipping step 3.
-
-#### Using a Single Registry
-
-If you only have a single registry you want to access, you can initialize it as follows:
-
-```js
-import { cdk, LocalMappingsProvider } from "cocoda-sdk"
-// Local mappings are not included by default
-cdk.addProvider(LocalMappingsProvider)
-const registry = cdk.initializeRegistry({
-  uri: "http://coli-conc.gbv.de/registry/local-mappings",
-  provider: "LocalMappings"
-})
-// Now, access methods are available on the registry:
-registry.getMappings()
-```
-
-Most Providers can also be initialized with API Type URI from [BARTOC vocabulary API types list](https://bartoc.org/en/node/20002):
-
-```js
-const registry = cdk.initializeRegistry({
-  api: "http://bartoc.org/api-type/skosmos",
-  endpoint: "https://www.loterre.fr/skosmos/905/"
-})
-```
-
-It's also possible to directly use Registry classes.
-
-#### Using Registries From a Configuration
+The configuration is a JSON object corresponding the the [configuration format of Cocoda](https://github.com/gbv/cocoda#configuration). In particular, the configuration contains an array property `registries` holding a list of [services](#services).
 
-If you initialize cocoda-sdk with a [configuration](#configuration), it will initialize all included registries automatically. Those registries are then accessible via `cdk.config.registries`. Alternatively, you can retrieve registries by URI:
-
-```js
-// After setting up cdk
-const registry = cdk.getRegistryForUri("...")
-```
+If you use cocoda-sdk [with one single service](#using-a-single-service) only, configuration might not be necessary.
 
 ### Providers
 
@@ -166,10 +108,10 @@ The following providers are also exported, but have to be added via `cdk.addProv
 - `LobidApi` - access to GND via [lobid](https://lobid.org)
   - **This integration is currently experimental.**
 - `MyCoRe` - access to vocabularies via [MyCoRe](https://www.mycore.de/)
-  - **This integration is currently experimental. Only one vocabulary per registry is supported. Not recommended for large vocabularies as all of the vocabulary data is loaded and kept in memory.**
+  - **This integration is currently experimental. Only one vocabulary per service is supported. Not recommended for large vocabularies as all of the vocabulary data is loaded and kept in memory.**
 - `ReconciliationApi` - access to mapping suggestions via a [Reconciliation Service API](https://reconciliation-api.github.io/specs/draft/)
 - `OccurrencesApi` - access to concept occurrences via [occurrences-api](https://github.com/gbv/occurrences-api) (will be changed to [occurrences-server](https://github.com/gbv/occurrences-server) in the future)
-- `LabelSearchSuggestion` - access to mapping suggestions using other registries' search endpoints (using [jskos-server])
+- `LabelSearchSuggestion` - access to mapping suggestions using other services' search endpoints (using [jskos-server])
 - `ModApi` - (experimental) access to concept schemes and concepts via a [MOD](https://github.com/FAIR-IMPACT/MOD) API
 
 To add a provider, append `Provider` to its name and import it together with `cdk`:
@@ -206,12 +148,75 @@ cdk.addProvider(CustomProvider)
 
 See [`examples/custom-provider.js`](https://github.com/gbv/cocoda-sdk/blob/main/examples/custom-provider.js) for an extended example.
 
-### Multiple Instances
+### Services
 
-The `createInstance` method can be used to create a new and independent instance with a separate configuration if needed:
+*Services have also been called registries until cocoda-sdk 3.7.0 but the name was changed to not confuse with JSKOS Registries!*
+
+A service is an individual source of data, for instance a set of concept schemes available from a specific terminology web service.
+
+For most providers the service configuration must include an `api` URI from [BARTOC vocabulary API types](http://bartoc.org/en/node/20002):
+
+```json
+{
+  "api": "http://bartoc.org/api-type/skosmos",
+  "endpoint": "https://www.loterre.fr/skosmos/905/"
+}
+```
+
+Some services can also be configured with the name of the access provider (`provider`) instead:
+
+```json
+{
+  "provider": "LocalMappings"
+}
+```
+
+A list of available providers can be found [below](#providers). Most providers need additional properties to work correctly.
+
+#### Endpoint Determination
+
+For many providers, you need to specify one or more endpoints on the service object for it to work. There are, however, three steps in which these endpoints are determined:
+
+1. By explicitly specifying an endpoint on the service object.
+2. By performaning a request to the provider's `/status` endpoint and parsing its result (which is done in `service.init()`).
+3. By implication using the `api` base URL.
+
+Values set earlier in these steps will never be overwritten by later steps. That means to disable an endpoint explicitly, you can set it to `null` when configuring the service. Also, if step 2 is successful, it will be assumed that no further endpoints exist and all missing endpoints will be set to `null`, i.e. essentially skipping step 3.
+
+#### Using a Single Service
+
+If you only have a single service you want to access, you can initialize it as follows:
 
 ```js
-const newCdk = cdk.createInstance(config)
+import { cdk, LocalMappingsProvider } from "cocoda-sdk"
+// Local mappings are not included by default
+cdk.addProvider(LocalMappingsProvider)
+const service = cdk.initializeRegistry({
+  uri: "http://coli-conc.gbv.de/registry/local-mappings",
+  provider: "LocalMappings"
+})
+// Now, access methods are available on the service:
+service.getMappings()
+```
+
+Most Providers can also be initialized with API Type URI from [BARTOC vocabulary API types list](https://bartoc.org/en/node/20002):
+
+```js
+const service = cdk.initializeRegistry({
+  api: "http://bartoc.org/api-type/skosmos",
+  endpoint: "https://www.loterre.fr/skosmos/905/"
+})
+```
+
+It's also possible to directly use Provider classes.
+
+#### Using services from a configuration
+
+If you initialize cocoda-sdk with a [configuration](#configuration), it will initialize all included services automatically. Those services are then accessible via `cdk.config.registries`. Alternatively, you can retrieve services by URI:
+
+```js
+// After setting up cdk
+const service = cdk.getServiceForUri("...")
 ```
 
 ### Authenticated Requests
@@ -242,14 +247,14 @@ See also the code comments inside the example.
 <script src="https://cdn.jsdelivr.net/npm/gbv-login-client@0"></script>
 <script src="https://cdn.jsdelivr.net/npm/cocoda-sdk@2"></script>
 <script>
-// Initialize mapping registry at localhost:3000
-const registry = CDK.cdk.initializeRegistry({
+// Initialize mapping service at localhost:3000
+const service = CDK.cdk.initializeRegistry({
   provider: "MappingsApi",
   uri: "local:mappings",
   status: "http://localhost:3000/status",
 })
 // Note: This is an async function, so we might be dealing with race conditions here.
-registry.init()
+service.init()
 // Create client to connect to Login Server at localhost:3004
 let client = new LoginClient("localhost:3004", { ssl: false })
 let user
@@ -258,26 +263,26 @@ client.addEventListener(null, event => {
   switch (event.type) {
     case LoginClient.events.connect:
       // At this point, we don't know whether the user has logged in yet, but we can try
-      console.log(registry.isAuthorizedFor({ type: "mappings", action: "create", user }))
+      console.log(service.isAuthorizedFor({ type: "mappings", action: "create", user }))
       break
     case LoginClient.events.login:
       // Update user
       user = event.user
       // Now we know the user is logged in, so this should return true
       // Note that if the user is already logged in, this event will fire before connected
-      console.log(registry.isAuthorizedFor({ type: "mappings", action: "create", user }))
+      console.log(service.isAuthorizedFor({ type: "mappings", action: "create", user }))
       break
     case LoginClient.events.update:
       // Update user
       user = event.user
       break
     case LoginClient.events.about:
-      // Register the server's public key in the registry
-      registry.setAuth({ key: event.publicKey })
+      // Register the server's public key in the service
+      service.setAuth({ key: event.publicKey })
       break
     case LoginClient.events.token:
-      // On every token update, update the token in the registry
-      registry.setAuth({ bearerToken: event.token })
+      // On every token update, update the token in the service
+      service.setAuth({ bearerToken: event.token })
       break
   }
 })
@@ -291,7 +296,7 @@ client.connect()
 Note that for a real application, there are more things necessary:
 - Track whether the client is connected and whether the user is logged in
 - Tell the user to log in if necessary
-- Check if the `registry.init()` call finished before making requests (might not be necessary because requests will wait for initialization)
+- Check if the `init()` call finished before making requests (might not be necessary because requests will wait for initialization)
 - Error handling
 - etc.
 
@@ -303,7 +308,7 @@ You can find more in-depth examples here:
 
 ## API
 
-A cocoda-sdk instance itself offers only a handful of methods. The actual access to APIs happens through [registries](#registries). The following list of methods assume either an instance of cocoda-sdk (`cdk.someMethod`) or an initialized registry (`registry.someMethod`). Documentation for registry methods is on a per-provider basis. While the API should be the same for a particular methods across providers, the details on how to use it might differ.
+A cocoda-sdk instance itself offers only a handful of methods. The actual access to APIs happens through [services](#services). The following list of methods assume either an instance of cocoda-sdk (`cdk.someMethod`) or an initialized service (`service.someMethod`). Documentation for service methods is on a per-provider basis. While the API should be the same for a particular methods across providers, the details on how to use it might differ.
 
 Please refer to the [documentation](https://gbv.github.io/cocoda-sdk/CocodaSDK.html) for a list of methods of for cocoda-sdk instances.
 
@@ -429,6 +434,10 @@ Please refer to the [documentation](https://gbv.github.io/cocoda-sdk/CocodaSDK.h
 #### deleteMappings
 - [BaseProvider - deleteMappings](https://gbv.github.io/cocoda-sdk/BaseProvider.html#deleteMappings)
 
+### Registries
+
+- [getRegistries](https://gbv.github.io/cocoda-sdk/ConceptApiProvider.html#getRegistries)
+
 ### Annotations
 
 - [getAnnotations](https://gbv.github.io/cocoda-sdk/MappingsApiProvider.html#getAnnotations)

package/dist/cjs/index.cjs

@@ -291,6 +291,7 @@ function withCustomProps(arr, from) {
   return arr;
 }
 var listOfCapabilities = [
+  "registries",
   "schemes",
   "top",
   "data",
@@ -398,7 +399,8 @@ var BaseProvider = class {
       annotations: registry.annotations,
       occurrences: registry.occurrences,
       reconcile: registry.reconcile,
-      api: registry.endpoint || registry.api
+      api: registry.endpoint || registry.api,
+      registries: registry.registries
     };
     this._config = {};
     this.setRetryConfig();
@@ -436,7 +438,7 @@ var BaseProvider = class {
       }
       return data3;
     }, (error) => {
-      const count = error.config._retryCount ?? 0;
+      const count = error.config?._retryCount ?? 0;
       const method = error.config.method;
       const statusCode = error.response?.status;
       if (this._retryConfig.methods.includes(method) && this._retryConfig.statusCodes.includes(statusCode) && count < this._retryConfig.count) {
@@ -1942,7 +1944,8 @@ var ConceptApiProvider = class extends BaseProvider {
     types: true,
     suggest: true,
     search: true,
-    auth: true
+    auth: true,
+    registries: true
   };
   /**
    * @private
@@ -1966,7 +1969,8 @@ var ConceptApiProvider = class extends BaseProvider {
         ancestors: "/ancestors",
         types: "/types",
         suggest: "/suggest",
-        search: "/search"
+        search: "/search",
+        registries: "/registries"
       };
       for (let key of Object.keys(endpoints)) {
         if (this._api[key] === void 0) {
@@ -1974,6 +1978,7 @@ var ConceptApiProvider = class extends BaseProvider {
         }
       }
     }
+    this.has.registries = !!this._api.registries;
     this.has.schemes = !!this._api.schemes;
     if (!this.has.schemes && Array.isArray(this.schemes)) {
       this.has.schemes = true;
@@ -2041,6 +2046,32 @@ var ConceptApiProvider = class extends BaseProvider {
       return null;
     }
   }
+  /**
+   * Returns all concept registries.
+   *
+   * @param {Object} config
+   * @returns {Object[]} array of JSKOS concept registry objects
+   */
+  async getRegistries(config = {}) {
+    if (!this._api.registries) {
+      if (Array.isArray(this.registries)) {
+        return this.registries;
+      }
+      throw new MissingApiUrlError();
+    }
+    const registries = await this.axios({
+      ...config,
+      method: "get",
+      url: this._api.registries,
+      params: {
+        ...this._defaultParams,
+        // ? What should the default limit be?
+        limit: 500,
+        ...config.params || {}
+      }
+    });
+    return registries;
+  }
   /**
    * Returns all concept schemes.
    *
@@ -2117,13 +2148,10 @@ var ConceptApiProvider = class extends BaseProvider {
     if (!url) {
       throw new MissingApiUrlError();
     }
-    if (!concepts) {
-      throw new InvalidOrMissingParameterError({ parameter: "concepts" });
-    }
     if (!Array.isArray(concepts)) {
-      concepts = [concepts];
+      concepts = concepts ? [concepts] : [];
     }
-    let uris = concepts.map((concept) => concept.uri).filter((uri) => uri != null);
+    const uris = concepts.map((concept) => concept.uri).filter((uri) => uri != null);
     return this.axios({
       ...config,
       method: "get",
@@ -2131,7 +2159,7 @@ var ConceptApiProvider = class extends BaseProvider {
       params: {
         ...this._defaultParams,
         // ? What should the default limit be?
-        limit: 500,
+        limit: 100,
         ...config.params || {},
         uri: uris.join("|")
       }
@@ -2709,7 +2737,7 @@ var SkosmosApiProvider = class extends BaseProvider {
    * @private
    */
   _getApiUrl(scheme, endpoint, params) {
-    const VOCID = scheme && scheme.VOCID || this.schemes.find((s) => import_jskos_tools8.default.compare(s, scheme))?.VOCID;
+    const VOCID = scheme?.VOCID || this.schemes.find((s) => import_jskos_tools8.default.compare(s, scheme))?.VOCID;
     if (!VOCID) {
       throw new InvalidOrMissingParameterError({ parameter: "scheme", message: "Missing scheme or VOCID property on scheme" });
     }
@@ -2843,6 +2871,30 @@ var SkosmosApiProvider = class extends BaseProvider {
     if (!concept.type.length) {
       concept.type = ["http://www.w3.org/2004/02/skos/core#Concept"];
     }
+    const map = {
+      "skos:definition": "definition",
+      "skos:note": "note",
+      "skos:scopeNote": "scopeNote",
+      "skos:example": "example",
+      "skos:historyNote": "historyNote",
+      "skos:editorialNote": "editorialNote",
+      "skos:changeNote": "changeNote"
+    };
+    for (let key in map) {
+      let notes = skosmosConcept[key] || [];
+      if (!Array.isArray(notes)) {
+        notes = [notes];
+      }
+      if (notes.length) {
+        concept[map[key]] = {};
+        for (const { lang, value } of notes) {
+          if (lang && value) {
+            concept[map[key]][lang] ||= [];
+            concept[map[key]][lang].push(value);
+          }
+        }
+      }
+    }
     return concept;
   }
   /**
@@ -2922,20 +2974,20 @@ var SkosmosApiProvider = class extends BaseProvider {
     concepts = concepts.map((c) => ({ uri: c.uri, inScheme: c.inScheme }));
     const newConcepts = [];
     for (let concept of concepts) {
-      const url = this._getDataUrl(concept, { addFormatParameter: false });
+      if (!concept || !concept.uri) {
+        throw new InvalidOrMissingParameterError({ parameter: "concept", message: "Missing concept URI" });
+      }
+      const params = { uri: concept.uri, format: "application/json" };
+      const url = this._getApiUrl(concept?.inScheme?.[0], "/data", params);
       if (!url) {
         continue;
       }
       const result = await this.axios({
         ...config,
         method: "get",
-        url,
-        params: {
-          uri: concept.uri,
-          format: "application/json"
-        }
+        url
       });
-      const resultConcept = result && result.graph && result.graph.find((c) => import_jskos_tools8.default.compare(c, concept));
+      const resultConcept = result?.graph?.find((c) => import_jskos_tools8.default.compare(c, concept));
       if (resultConcept) {
         const newConcept = this._toJskosConcept(resultConcept, { concept, result });
         for (let type of ["broader", "narrower"]) {
@@ -3049,7 +3101,7 @@ var SkosmosApiProvider = class extends BaseProvider {
       method: "get",
       url
     });
-    for (let type of response && response.types || []) {
+    for (let type of response?.types || []) {
       if (type.uri == "http://www.w3.org/2004/02/skos/core#Concept") {
         continue;
       }
@@ -4382,7 +4434,7 @@ var OlsApiProvider = class extends BaseProvider {
   };
   constructor(config) {
     super(config);
-    this.endpoint = config.endpoint;
+    this.endpoint = config.endpoint || config.uri;
   }
   /**
    * Used by `registryForScheme` (see src/lib/CocodaSDK.js) to determine a provider config for a concept schceme.
@@ -4461,7 +4513,7 @@ var OlsApiProvider = class extends BaseProvider {
     }
     if (term["http://www.w3.org/2000/01/rdf-schema#label"]) {
       concept.prefLabel = {};
-      concept.prefLabel[lan] = term["http://www.w3.org/2000/01/rdf-schema#label"];
+      concept.prefLabel[lan] = term["http://www.w3.org/2000/01/rdf-schema#label"].value || term["http://www.w3.org/2000/01/rdf-schema#label"];
     }
     concept.type = [
       "http://www.w3.org/2004/02/skos/core#Concept",
@@ -4627,11 +4679,8 @@ var OlsApiProvider = class extends BaseProvider {
   async getTop({ scheme }) {
     const VOCID = await this._getSchemeVOCID(scheme);
     if (VOCID) {
-      let url = this._getApiUrl(["ontologies", VOCID, "classes"], { hasDirectParents: "false" });
-      let response = await this._request(url);
-      if (response?.elements) {
-        return Promise.all(response.elements.map((item) => this._termToJSKOS(item)));
-      }
+      let response = await this._paginate(["ontologies", VOCID, "classes"], { hasDirectParents: "false" }, null);
+      return Promise.all(response.map((item) => this._termToJSKOS(item)));
     }
     return [];
   }
@@ -4647,22 +4696,16 @@ var OlsApiProvider = class extends BaseProvider {
   async getNarrower({ concept }) {
     const { VOCID, iri } = await this._splitConcept(concept);
     if (VOCID && iri) {
-      let url = this._getApiUrl(["ontologies", VOCID, "classes", iri, "children"]);
-      let response = await this._request(url);
-      if (response?.elements) {
-        return Promise.all(response.elements.map((item) => this._termToJSKOS(item)));
-      }
+      const items = await this._paginate(["ontologies", VOCID, "classes", iri, "children"], {}, 0);
+      return Promise.all(items.map((item) => this._termToJSKOS(item)));
     }
     return [];
   }
   async getAncestors({ concept }) {
     const { VOCID, iri } = await this._splitConcept(concept);
     if (VOCID && iri) {
-      let url = this._getApiUrl(["ontologies", VOCID, "classes", iri, "ancestors"]);
-      let response = await this._request(url);
-      if (response?.elements) {
-        return Promise.all(response.elements.map((item) => this._termToJSKOS(item)));
-      }
+      let response = await this._paginate(["ontologies", VOCID, "classes", iri, "ancestors"], {}, null);
+      return Promise.all(response.map((item) => this._termToJSKOS(item)));
     }
     return [];
   }
@@ -5215,24 +5258,31 @@ var CocodaSDK = class _CocodaSDK {
     });
   }
   /**
-   * Method to get a registry by URI.
+   * Method to get a service by URI.
    *
-   * @param {string} uri URI of registry in config
-   * @returns {?Object} initialized registry from config if found
+   * @param {string} uri URI of service in config
+   * @returns {?Object} initialized service from config if found
    */
-  getRegistryForUri(uri) {
+  getServiceForUri(uri) {
     return this.config.registries.find((r) => r.uri == uri);
   }
+  // alias for backwards compatibility
+  getRegistryForUri(uri) {
+    return this.getRegistryForUri(uri);
+  }
   /**
-   * Method to initialize registry.
+   * Method to initialize service.
    *
-   * @param {Object} registry JSKOS registry object
-   * @returns {Object} initialized registry
+   * @param {Object} service JSKOS service object
+   * @returns {Object} initialized service
    */
-  initializeRegistry(registry) {
-    registry = providers.init(registry);
-    registry.cdk = this;
-    return registry;
+  initializeService(service) {
+    service = providers.init(service);
+    service.cdk = this;
+    return service;
+  }
+  initializeRegistry(service) {
+    return this.initializeService(service);
   }
   /**
    * Method to add custom provider.