optimade 2.0.3 → 2.1.0

package/.eslintrc

@@ -0,0 +1,17 @@
+{
+    "extends": [
+        "eslint:recommended",
+        "plugin:@typescript-eslint/recommended"
+    ],
+    "plugins": [
+        "@typescript-eslint"
+    ],
+    "parser": "@typescript-eslint/parser",
+    "root": true,
+    "env": {
+        "node": true
+    },
+    "rules": {
+        "@typescript-eslint/no-explicit-any": "off"
+    }
+}

package/README.md

@@ -57,10 +57,10 @@ const providersMap = await optimadeClient.getProviders(); // { [id: string]: Pro
 
 const providerIds = Object.keys(providersMap); // string[]
 
-const results = await optimadeClient.getStructuresAll(
-  providerIds,
-  YOUR_OPTIMADE_QUERY,
-); // [StructuresResponse[], Provider][]
+const results = await optimadeClient.getStructuresAll({
+  providers: Provider[],
+  filter: YOUR_OPTIMADE_QUERY,
+}); // [StructuresResponse[], Provider][]
 ```
 
 Importing depends on your environment. See also the `examples` folder. The
@@ -79,12 +79,14 @@ const optimadeClient = new Optimade({
 optimadeClient.providers = prefetched.providers;
 optimadeClient.apis = prefetched.apis;
 
-const results = await optimadeClient.getStructuresAll(
-  providerIds,
-  YOUR_OPTIMADE_QUERY,
+const results = await optimadeClient.getStructuresAll({
+  providers: Provider[],
+  filter: YOUR_OPTIMADE_QUERY,
   page: number,
-  limit: number
-); // [StructuresResponse[], Provider][]
+  limit: number,
+  offset: number,
+  batch: true
+}); // [StructuresResponse[], Provider][]
 ```
 
 See also the `demo` folder.

package/dist/index.js

@@ -2,7 +2,7 @@
     typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('isomorphic-unfetch')) :
     typeof define === 'function' && define.amd ? define(['exports', 'isomorphic-unfetch'], factory) :
     (global = typeof globalThis !== 'undefined' ? globalThis : global || self, factory(global.optimade = {}));
-}(this, (function (exports) { 'use strict';
+})(this, (function (exports) { 'use strict';
 
     function allSettled(promises, catcher = () => null) {
         return Promise.all(promises.map(promise => promise.catch(catcher)));
@@ -25,34 +25,86 @@
         }
     }
 
+    var version = "2.1.0";
+
     class Optimade {
+        providersUrl = '';
+        corsProxyUrl = '';
+        providers = null;
+        apis = {};
+        reqStack = [];
         constructor({ providersUrl = '', corsProxyUrl = '' } = {}) {
-            this.providersUrl = '';
-            this.corsProxyUrl = '';
-            this.providers = null;
-            this.apis = {};
-            this.reqStack = [];
             this.corsProxyUrl = corsProxyUrl;
             this.providersUrl = this.wrapUrl(providersUrl);
         }
+        async addProvider(provider) {
+            if (!this.apis[provider.id]) {
+                this.apis[provider.id] = [];
+            }
+            try {
+                const ver = provider.attributes
+                    && provider.attributes.api_version ?
+                    provider.attributes.api_version.charAt(0) : '';
+                const api = await this.getApis(provider, ver ? `v${ver}` : '');
+                if (api.attributes.available_endpoints.includes('structures')) {
+                    this.apis[provider.id].push(api);
+                }
+            }
+            catch (ignore) {
+                console.log(ignore);
+            }
+            if (!provider.attributes.query_limits) {
+                const formula = `chemical_formula_anonymous="A2B"`;
+                const url = `${provider.attributes.base_url}/v1/structures?filter=${formula}&page_limit=1000`;
+                try {
+                    const res = await fetch(url).then(res => res.json());
+                    const version = res.meta && res.meta.api_version || this.apis[provider.id][0].attributes.api_version;
+                    const detail = (errors) => {
+                        return errors
+                            ? errors.length
+                                ? errors[0].detail
+                                : errors.detail
+                            : '10';
+                    };
+                    const limits = detail(res.errors)
+                        .match(/\d+/g)
+                        .filter((number) => +number < 1000)
+                        .map((number) => +number);
+                    provider.attributes = {
+                        ...provider.attributes,
+                        api_version: version,
+                        query_limits: limits
+                    };
+                }
+                catch (error) {
+                    console.log(error);
+                }
+            }
+            this.providers[provider.id] = provider;
+            return this.providers;
+        }
         async getProviders(api) {
             const providers = await (api ?
                 this.followLinks(api).catch(() => null) :
                 Optimade.getJSON(this.providersUrl).catch(() => null));
-            if (!providers)
+            if (!providers) {
                 return null;
-            if (!this.providers)
+            }
+            if (!this.providers) {
                 this.providers = {};
+            }
             const data = providers.data.filter(Optimade.isProviderValid);
             const ver = providers.meta && providers.meta.api_version ?
                 providers.meta.api_version.charAt(0) : '';
             for (const provider of data) {
-                if (!this.apis[provider.id])
+                if (!this.apis[provider.id]) {
                     this.apis[provider.id] = [];
+                }
                 try {
                     const api = await this.getApis(provider, ver ? `v${ver}` : '');
-                    if (!api)
+                    if (!api) {
                         continue;
+                    }
                     if (api.attributes.available_endpoints.includes('structures')) {
                         this.apis[provider.id].push(api);
                         if (!this.providers[provider.id]) {
@@ -63,7 +115,9 @@
                         await this.getProviders(api);
                     }
                 }
-                catch (ignore) { }
+                catch (ignore) {
+                    console.log(ignore);
+                }
             }
             return this.providers;
         }
@@ -71,25 +125,26 @@
             if (typeof provider === 'string') {
                 provider = this.providers[provider];
             }
-            if (!provider)
+            if (!provider) {
                 throw new Error('No provider found');
+            }
             const url = this.wrapUrl(`${provider.attributes.base_url}/${version}`, '/info');
-            if (this.isDuplicatedReq(url))
+            if (this.isDuplicatedReq(url)) {
                 return null;
+            }
             const apis = await Optimade.getJSON(url);
             return Optimade.apiVersion(apis);
         }
-        async getStructures(providerId, filter = '', page = 1, limit) {
-            if (!this.apis[providerId])
+        async getStructures({ providerId, filter, page, limit, offset }) {
+            if (!this.apis[providerId]) {
                 return null;
+            }
             const apis = this.apis[providerId].filter(api => api.attributes.available_endpoints.includes('structures'));
             const provider = this.providers[providerId];
             const structures = await allSettled(apis.map(async (api) => {
-                if (page <= 0)
-                    page = 1;
                 const pageLimit = limit ? `&page_limit=${limit}` : '';
-                const pageNumber = page ? `&page_number=${page - 1}` : '';
-                const pageOffset = limit && page ? `&page_offset=${limit * (page - 1)}` : '';
+                const pageNumber = page ? `&page_number=${page}` : '';
+                const pageOffset = offset ? `&page_offset=${offset}` : '';
                 const params = filter ? `${pageLimit + pageNumber + pageOffset}` : `?${pageLimit}`;
                 const url = this.wrapUrl(Optimade.apiVersionUrl(api), filter ? `/structures?filter=${filter + params}` : `/structures${params}`);
                 try {
@@ -106,17 +161,17 @@
                 }
                 else {
                     structure.meta.pages = Math.ceil(structure.meta.data_returned / (limit || structure.data.length));
-                    structure.meta.limits = provider.attributes.query_limits;
+                    structure.meta.limits = provider.attributes.query_limits || [10];
                     return structures.concat(structure);
                 }
             }, []);
         }
-        getStructuresAll(providerIds, filter = '', page = 0, limit, batch = true) {
-            const results = providerIds.reduce((structures, providerId) => {
+        getStructuresAll({ providers, filter, page, limit, offset, batch = true }) {
+            const results = providers.reduce((structures, providerId) => {
                 const provider = this.providers[providerId];
                 if (provider) {
                     structures.push(allSettled([
-                        this.getStructures(providerId, filter, page, limit),
+                        this.getStructures({ providerId, filter, page, limit, offset }),
                         Promise.resolve(provider)
                     ]));
                 }
@@ -125,8 +180,9 @@
             return batch ? Promise.all(results) : results;
         }
         async followLinks(api) {
-            if (!api.attributes.available_endpoints.includes('links'))
+            if (!api.attributes.available_endpoints.includes('links')) {
                 return null;
+            }
             const url = this.wrapUrl(Optimade.apiVersionUrl(api), '/links');
             return !this.isDuplicatedReq(url) ? Optimade.getJSON(url) : null;
         }
@@ -143,6 +199,7 @@
             if (params) {
                 Object.entries(params).forEach((param) => url.searchParams.append(...param));
             }
+            Object.assign(headers, { 'User-Agent': `tilde-lab-optimade-client/${version}` });
             const res = await fetchWithTimeout(url.toString(), { headers }, timeout);
             if (!res.ok) {
                 const err = await res.json();
@@ -176,4 +233,4 @@
 
     Object.defineProperty(exports, '__esModule', { value: true });
 
-})));
+}));

package/dist/index.mjs

@@ -21,34 +21,86 @@ async function fetchWithTimeout(url, options = {}, timeout = 5000) {
     }
 }
 
+var version = "2.1.0";
+
 class Optimade {
+    providersUrl = '';
+    corsProxyUrl = '';
+    providers = null;
+    apis = {};
+    reqStack = [];
     constructor({ providersUrl = '', corsProxyUrl = '' } = {}) {
-        this.providersUrl = '';
-        this.corsProxyUrl = '';
-        this.providers = null;
-        this.apis = {};
-        this.reqStack = [];
         this.corsProxyUrl = corsProxyUrl;
         this.providersUrl = this.wrapUrl(providersUrl);
     }
+    async addProvider(provider) {
+        if (!this.apis[provider.id]) {
+            this.apis[provider.id] = [];
+        }
+        try {
+            const ver = provider.attributes
+                && provider.attributes.api_version ?
+                provider.attributes.api_version.charAt(0) : '';
+            const api = await this.getApis(provider, ver ? `v${ver}` : '');
+            if (api.attributes.available_endpoints.includes('structures')) {
+                this.apis[provider.id].push(api);
+            }
+        }
+        catch (ignore) {
+            console.log(ignore);
+        }
+        if (!provider.attributes.query_limits) {
+            const formula = `chemical_formula_anonymous="A2B"`;
+            const url = `${provider.attributes.base_url}/v1/structures?filter=${formula}&page_limit=1000`;
+            try {
+                const res = await fetch(url).then(res => res.json());
+                const version = res.meta && res.meta.api_version || this.apis[provider.id][0].attributes.api_version;
+                const detail = (errors) => {
+                    return errors
+                        ? errors.length
+                            ? errors[0].detail
+                            : errors.detail
+                        : '10';
+                };
+                const limits = detail(res.errors)
+                    .match(/\d+/g)
+                    .filter((number) => +number < 1000)
+                    .map((number) => +number);
+                provider.attributes = {
+                    ...provider.attributes,
+                    api_version: version,
+                    query_limits: limits
+                };
+            }
+            catch (error) {
+                console.log(error);
+            }
+        }
+        this.providers[provider.id] = provider;
+        return this.providers;
+    }
     async getProviders(api) {
         const providers = await (api ?
             this.followLinks(api).catch(() => null) :
             Optimade.getJSON(this.providersUrl).catch(() => null));
-        if (!providers)
+        if (!providers) {
             return null;
-        if (!this.providers)
+        }
+        if (!this.providers) {
             this.providers = {};
+        }
         const data = providers.data.filter(Optimade.isProviderValid);
         const ver = providers.meta && providers.meta.api_version ?
             providers.meta.api_version.charAt(0) : '';
         for (const provider of data) {
-            if (!this.apis[provider.id])
+            if (!this.apis[provider.id]) {
                 this.apis[provider.id] = [];
+            }
             try {
                 const api = await this.getApis(provider, ver ? `v${ver}` : '');
-                if (!api)
+                if (!api) {
                     continue;
+                }
                 if (api.attributes.available_endpoints.includes('structures')) {
                     this.apis[provider.id].push(api);
                     if (!this.providers[provider.id]) {
@@ -59,7 +111,9 @@ class Optimade {
                     await this.getProviders(api);
                 }
             }
-            catch (ignore) { }
+            catch (ignore) {
+                console.log(ignore);
+            }
         }
         return this.providers;
     }
@@ -67,25 +121,26 @@ class Optimade {
         if (typeof provider === 'string') {
             provider = this.providers[provider];
         }
-        if (!provider)
+        if (!provider) {
             throw new Error('No provider found');
+        }
         const url = this.wrapUrl(`${provider.attributes.base_url}/${version}`, '/info');
-        if (this.isDuplicatedReq(url))
+        if (this.isDuplicatedReq(url)) {
             return null;
+        }
         const apis = await Optimade.getJSON(url);
         return Optimade.apiVersion(apis);
     }
-    async getStructures(providerId, filter = '', page = 1, limit) {
-        if (!this.apis[providerId])
+    async getStructures({ providerId, filter, page, limit, offset }) {
+        if (!this.apis[providerId]) {
             return null;
+        }
         const apis = this.apis[providerId].filter(api => api.attributes.available_endpoints.includes('structures'));
         const provider = this.providers[providerId];
         const structures = await allSettled(apis.map(async (api) => {
-            if (page <= 0)
-                page = 1;
             const pageLimit = limit ? `&page_limit=${limit}` : '';
-            const pageNumber = page ? `&page_number=${page - 1}` : '';
-            const pageOffset = limit && page ? `&page_offset=${limit * (page - 1)}` : '';
+            const pageNumber = page ? `&page_number=${page}` : '';
+            const pageOffset = offset ? `&page_offset=${offset}` : '';
             const params = filter ? `${pageLimit + pageNumber + pageOffset}` : `?${pageLimit}`;
             const url = this.wrapUrl(Optimade.apiVersionUrl(api), filter ? `/structures?filter=${filter + params}` : `/structures${params}`);
             try {
@@ -102,17 +157,17 @@ class Optimade {
             }
             else {
                 structure.meta.pages = Math.ceil(structure.meta.data_returned / (limit || structure.data.length));
-                structure.meta.limits = provider.attributes.query_limits;
+                structure.meta.limits = provider.attributes.query_limits || [10];
                 return structures.concat(structure);
             }
         }, []);
     }
-    getStructuresAll(providerIds, filter = '', page = 0, limit, batch = true) {
-        const results = providerIds.reduce((structures, providerId) => {
+    getStructuresAll({ providers, filter, page, limit, offset, batch = true }) {
+        const results = providers.reduce((structures, providerId) => {
             const provider = this.providers[providerId];
             if (provider) {
                 structures.push(allSettled([
-                    this.getStructures(providerId, filter, page, limit),
+                    this.getStructures({ providerId, filter, page, limit, offset }),
                     Promise.resolve(provider)
                 ]));
             }
@@ -121,8 +176,9 @@ class Optimade {
         return batch ? Promise.all(results) : results;
     }
     async followLinks(api) {
-        if (!api.attributes.available_endpoints.includes('links'))
+        if (!api.attributes.available_endpoints.includes('links')) {
             return null;
+        }
         const url = this.wrapUrl(Optimade.apiVersionUrl(api), '/links');
         return !this.isDuplicatedReq(url) ? Optimade.getJSON(url) : null;
     }
@@ -139,6 +195,7 @@ class Optimade {
         if (params) {
             Object.entries(params).forEach((param) => url.searchParams.append(...param));
         }
+        Object.assign(headers, { 'User-Agent': `tilde-lab-optimade-client/${version}` });
         const res = await fetchWithTimeout(url.toString(), { headers }, timeout);
         if (!res.ok) {
             const err = await res.json();

package/dist/prefetched.json

@@ -1 +1 @@
-{"providers":{"2dstructures":{"id":"2dstructures","type":"links","attributes":{"name":"2D Structures","description":"Two-dimensional (2D) materials from high-throughput computational exfoliation of experimentally known compounds.","base_url":"https://aiida.materialscloud.org/2dstructures/optimade","homepage":"https://materialscloud.org/explore/2dstructures","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"2dtopo":{"id":"2dtopo","type":"links","attributes":{"name":"2D topological insulators","description":"Quantum spin Hall insulator (QSHI) candidates through DFT band structure calculations of a database with 1825 compounds.","base_url":"https://aiida.materialscloud.org/2dtopo/optimade","homepage":"https://materialscloud.org/explore/2dtopo","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"cod":{"id":"cod","type":"links","attributes":{"name":"Crystallography Open Database","description":"Open-access collection of crystal structures of organic, inorganic, metal-organics compounds and minerals, excluding biopolymers","base_url":"https://www.crystallography.net/cod/optimade","homepage":"https://www.crystallography.net/cod","link_type":"child","query_limits":[10]}},"curated-cofs":{"id":"curated-cofs","type":"links","attributes":{"name":"CURATED covalent organic frameworks database","description":"Database of experimentally reported Covalent-Organic Frameworks (COFs), provided with DFT-optimized geometry and DDEC partial charges for molecular simulations.","base_url":"https://aiida.materialscloud.org/curated-cofs/optimade","homepage":"https://materialscloud.org/discover/curated-cofs","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"li-ion-conductors":{"id":"li-ion-conductors","type":"links","attributes":{"name":"Solid-state Li-ion conductors.","description":"High-throughput computational screening study for solid-state Li-ion conductors.","base_url":"https://aiida.materialscloud.org/li-ion-conductors/optimade","homepage":"https://materialscloud.org/explore/li-ion-conductors","link_type":"child","aggregate":"staging","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"mp":{"id":"mp","type":"links","attributes":{"name":"The Materials Project","description":"The Materials Project OPTIMADE endpoint","base_url":"https://optimade.materialsproject.org","homepage":"https://www.materialsproject.org","link_type":"child","api_version":"1.0.1","query_limits":[500]}},"mpds":{"id":"mpds","type":"links","attributes":{"name":"Materials Platform for Data Science","description":"A highly curated Pauling File dataset based on ~0.5M publications and backing up Springer Materials, ICDD PDF, ASM APD, MedeA, Pearson Crystal Data, AtomWork Advanced, etc.","base_url":"https://api.mpds.io","homepage":"https://mpds.io","link_type":"child","api_version":"1.0.0","query_limits":[10,100,750]}},"nmd":{"id":"nmd","type":"links","attributes":{"name":"novel materials discovery (NOMAD)","description":"A FAIR data sharing platform for materials science data","base_url":"https://nomad-lab.eu/prod/rae/optimade/","homepage":"https://nomad-lab.eu","link_type":"child","api_version":"1.0.1","query_limits":[500]}},"odbx":{"id":"odbx","type":"links","attributes":{"name":"odbx","description":"The Open Database of Xtals is run by the group of Dr Andrew Morris at the universities of Birmingham and Cambridge and is constructed using the matador library.","base_url":"https://optimade.odbx.science","homepage":"https://odbx.science","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[500]}},"optimade-sample":{"id":"optimade-sample","type":"links","attributes":{"name":"OPTIMADE Sample Database","description":"Database with example structures for OPTIMADE tests.","base_url":"https://aiida.materialscloud.org/optimade-sample/optimade","homepage":"https://materialscloud.org/explore/optimade-sample","link_type":"child","aggregate":"test","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"pyrene-mofs":{"id":"pyrene-mofs","type":"links","attributes":{"name":"Pyrene MOFs","description":"Pyrene Metal Organic Frameworks (MOFs).","base_url":"https://aiida.materialscloud.org/pyrene-mofs/optimade","homepage":"https://materialscloud.org/discover/pyrene-mofs","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"scdm":{"id":"scdm","type":"links","attributes":{"name":"Automated high-throughput Wannierisation","description":"Validation results of an automated protocol for generating maximally-localized Wannier functions in a high-throughput framework.","base_url":"https://aiida.materialscloud.org/autowannier/optimade","homepage":"https://materialscloud.org/explore/autowannier","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"sssp":{"id":"sssp","type":"links","attributes":{"name":"Standard solid-state pseudopotentials (SSSP)","description":"It contains data generated from the testing protocol of the standard solid-state pseudopotentials library.\n","base_url":"https://aiida.materialscloud.org/sssplibrary/optimade","homepage":"https://materialscloud.org/explore/sssplibrary","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"stoceriaitf":{"id":"stoceriaitf","type":"links","attributes":{"name":"SrTiO3-CeO2 interfaces","description":"Refining random structure searching results of SrTiO3-CeO2 interfaces, and exploring how it can affect ionic conduction. Candidate structures of the DFT validation calculations.","base_url":"https://aiida.materialscloud.org/stoceriaitf/optimade","homepage":"https://materialscloud.org/explore/stoceriaitf","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"tc-applicability":{"id":"tc-applicability","type":"links","attributes":{"name":"Applicability of tail-corrections in the molecular simulations of porous materials","description":"Tail-corrections in molecular simulations for adsorption of gasses in a diverse set of nanoporous crystalline materials (zeolites, Covalent Organic Framworks (COFs), and Metal Organic Frameworks (MOFs)).","base_url":"https://aiida.materialscloud.org/tc-applicability/optimade","homepage":"https://materialscloud.org/explore/tc-applicability","link_type":"child","aggregate":"ok","no_aggregate_reason":null,"api_version":"1.1.0","query_limits":[100]}},"tcod":{"id":"tcod","type":"links","attributes":{"name":"Theoretical 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package/dist/providers.json

@@ -1 +1 @@
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+{"2dstructures":{"id":"2dstructures","type":"links","attributes":{"name":"2D Structures","description":"Two-dimensional (2D) materials from high-throughput computational exfoliation of experimentally known compounds.","base_url":"https://aiida.materialscloud.org/2dstructures/optimade","homepage":"https://materialscloud.org/explore/2dstructures","link_type":"child","aggregate":"ok","no_aggregate_reason":null}},"2dtopo":{"id":"2dtopo","type":"links","attributes":{"name":"2D topological insulators","description":"Quantum spin Hall insulator (QSHI) candidates through DFT band structure calculations.","base_url":"https://aiida.materialscloud.org/2dtopo/optimade","homepage":"https://materialscloud.org/explore/2dtopo","link_type":"child","aggregate":"ok","no_aggregate_reason":null}},"aflow":{"id":"aflow","type":"links","attributes":{"name":"AFLOW","description":"The AFLOW OPTIMADE 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package/dist/{index.d.ts → src/index.d.ts}

@@ -10,14 +10,28 @@ export declare class Optimade {
         providersUrl?: string;
         corsProxyUrl?: string;
     });
+    addProvider(provider: Types.Provider): Promise<Types.ProvidersMap>;
     getProviders(api?: Types.Api): Promise<Types.ProvidersMap | null>;
     getApis(provider: Types.Provider | string, version?: string): Promise<Types.Api | null>;
-    getStructures(providerId: string, filter: string, page: number, limit: number): Promise<Types.StructuresResponse[] | Types.ResponseError>;
-    getStructuresAll(providerIds: string[], filter: string, page: number, limit: number, batch?: boolean): Promise<Promise<Types.StructuresResult>[]> | Promise<Types.StructuresResult>[];
+    getStructures({ providerId, filter, page, limit, offset }: {
+        providerId: string;
+        filter: string;
+        page: number;
+        limit: number;
+        offset: number;
+    }): Promise<Types.StructuresResponse[] | Types.ResponseError>;
+    getStructuresAll({ providers, filter, page, limit, offset, batch }: {
+        providers: string[];
+        filter: string;
+        page: number;
+        limit: number;
+        offset: number;
+        batch?: boolean;
+    }): Promise<Promise<Types.StructuresResult>[]> | Promise<Types.StructuresResult>[];
     private followLinks;
     private wrapUrl;
     private isDuplicatedReq;
-    static getJSON(uri: string, params?: {}, headers?: {}): Promise<any>;
+    static getJSON(uri: string, params?: any, headers?: {}): Promise<any>;
     static isProviderValid(provider: Types.Provider): boolean;
     static apiVersionUrl({ attributes: { api_version, available_api_versions } }: Types.Api): any;
     static apiVersion({ data, meta }: Types.InfoResponse): Types.Api;

package/dist/{types.d.ts → src/types.d.ts}

@@ -43,7 +43,7 @@ export interface Api {
         api_version: string;
         available_api_versions: ApiVer | ApiVer[];
         available_endpoints: string[];
-        entry_types_by_format: {};
+        entry_types_by_format: Record<string, unknown>;
         formats: string[];
     };
 }
@@ -57,6 +57,7 @@ export interface Provider {
         homepage?: string | null;
         link_type?: string;
         query_limits?: number[];
+        api_version?: string;
     };
 }
 export interface Structure {

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "optimade",
-  "version": "2.0.3",
+  "version": "2.1.0",
   "description": "Aggregating Optimade client for the online materials databases",
   "main": "dist/index.js",
   "module": "dist/index.mjs",
   "types": "dist/index.d.ts",
   "scripts": {
     "build": "npm run lint && rollup --config",
-    "lint": "tslint -c tslint.json \"src/**/*.ts\"",
-    "lint:fix": "tslint --fix -c tslint.json \"src/**/*.ts\"",
+    "lint": "eslint './src/**/*.ts'",
+    "lint:fix": "eslint --fix './src/**/*.ts'",
     "prepublishOnly": "npm run build && npm run prefetch",
     "test": "echo \"Error: no test specified\" && exit 1",
     "prefetch": "node prefetch.js"
@@ -16,17 +16,28 @@
   "author": "Pavel Malyshev",
   "license": "MIT",
   "devDependencies": {
+    "@types/eslint": "^8.4.2",
+    "@typescript-eslint/eslint-plugin": "^5.25.0",
+    "@typescript-eslint/parser": "^5.25.0",
+    "@rollup/plugin-json": "^4.1.0",
     "@types/jest": "^26.0.15",
     "jest": "^26.6.0",
     "rollup": "^2.47.0",
     "rollup-plugin-typescript2": "^0.28.0",
     "ts-jest": "^26.4.1",
-    "tslint": "^6.1.3",
-    "tslint-eslint-rules": "^5.4.0",
+    "eslint": "^8.16.0",
     "typescript": "^4.0.3"
   },
   "dependencies": {
     "isomorphic-unfetch": "^3.1.0",
     "node-abort-controller": "^3.0.1"
+  },
+  "keywords": [
+    "optimade",
+    "materials"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/tilde-lab/optimade-client"
   }
 }

package/prefetch.js

@@ -14,27 +14,39 @@ const optimade = new Optimade({
 	providersUrl: 'https://providers.optimade.org/providers.json'
 });
 
-optimade.getProviders().then(async () => {
+let time = performance.now(),
+	alltime = performance.now(),
+	skip = process.env.SKIP;
+//  || 'oqmd, jarvis';
+
+optimade.getProviders().then(async (providers) => {
+
+	console.warn('providers fetched from source', performance.now() - time);
+	time = performance.now();
 
 	const filteredApis = Object.entries(optimade.apis).filter(([k, v]) => v.length);
 	const apis = filteredApis.sort().reduce((acc, [k, v]) => {
 		return { ...acc, ...{ [k]: v } };
 	}, {});
 
-	const source = Object.keys(optimade.providers).sort().reduce(
+	const source = Object.keys(providers).sort().reduce(
 		(obj, key) => {
-			obj[key] = optimade.providers[key];
+			obj[key] = providers[key];
 			return obj;
 		}, {});
 
-	async function getQueryLimits(providers, max = 1000) {
+	console.warn('providers sorted', performance.now() - time);
+
+	async function getQueryLimits(providers, skip = '', max = 1000) {
+
+		providers = Object.fromEntries(Object.entries(providers).filter(([key]) => !skip.includes(key)));
 
 		const fetchLimits = async (k, v) => {
 			const formula = `chemical_formula_anonymous="A2B"`;
 			const url = `${v.attributes.base_url}/v1/structures?filter=${formula}&page_limit=${max}`;
 			try {
 				const res = await fetch(url).then(res => res.json());
-				const api = res.meta && res.meta.api_version;
+				const api = res.meta && res.meta.api_version || apis[k][0].attributes.api_version;
 				//console.dir(res);
 				const detail = (e) => {
 					return e
@@ -44,29 +56,33 @@ optimade.getProviders().then(async () => {
 						: '0';
 				};
 				const nums = detail(res.errors).match(/\d+/g).filter(n => +n < max).map(n => +n);
-				if (!nums.includes(0))
-					return {
-						[k]: { ...v, attributes: { ...v.attributes, api_version: api, ['query_limits']: nums } }
-					};
+				return {
+					[k]: { ...v, attributes: { ...v.attributes, api_version: api, ['query_limits']: !nums.includes(0) ? nums : [10] } }
+				};
 			} catch (error) {
 				console.log(error);
 			}
 		};
-
-		providers = await Object.entries(providers).reduce(async (promise, [k, v]) => {
+		time = performance.now();
+		return await Object.entries(providers).reduce(async (promise, [k, v], i) => {
 			const provider = await fetchLimits(k, v);
 			const acc = await promise;
+			console.log(i, provider);
 			return { ...acc, ...provider };
 		}, Promise.resolve({}));
-
-		//const log = { prefetched: Object.keys(providers).length, source: Object.keys(source).length };
-		//console.log(log);
-
-		return providers;
 	}
 
-	getQueryLimits(source).then(providers => {
+	getQueryLimits(source, skip).then(providers => {
 		const data = { providers, apis };
+
+		console.warn('limits fetched', performance.now() - time);
+
+		console.log({
+			prefetched: Object.keys(providers).length,
+			source: Object.keys(source).length,
+			alltime: performance.now() - alltime
+		});
+
 		fs.writeFile(path.join(__dirname, 'dist/prefetched.json'), JSON.stringify(data), (err) => {
 			if (err) throw err;
 			console.log('The prefetched.json file has been saved!');

package/rollup.config.js

@@ -1,4 +1,7 @@
+/* jshint esversion: 6 */
+
 import typescript from 'rollup-plugin-typescript2';
+import json from '@rollup/plugin-json';
 
 import pkg from './package.json';
 
@@ -14,5 +17,6 @@ export default {
     ],
     plugins: [
         typescript(),
+        json(),
     ],
 };

package/src/index.ts

@@ -1,11 +1,12 @@
 import { allSettled, fetchWithTimeout } from './utils';
+import { version } from '../package.json'
 
 import type * as Types from './types';
 export { Types };
 
 export class Optimade {
-    private providersUrl: string = '';
-    private corsProxyUrl: string = '';
+    private providersUrl = '';
+    private corsProxyUrl = '';
     providers: Types.ProvidersMap | null = null;
     apis: Types.ApisMap = {};
     private reqStack: string[] = [];
@@ -15,24 +16,74 @@ export class Optimade {
         this.providersUrl = this.wrapUrl(providersUrl);
     }
 
+    async addProvider(provider: Types.Provider) {
+        if (!this.apis[provider.id]) { this.apis[provider.id] = []; }
+
+        try {
+            const ver = provider.attributes
+                && provider.attributes.api_version ?
+                provider.attributes.api_version.charAt(0) : '';
+            const api = await this.getApis(provider, ver ? `v${ver}` : '');
+
+            if (api.attributes.available_endpoints.includes('structures')) {
+                this.apis[provider.id].push(api);
+            }
+
+        } catch (ignore) { console.log(ignore) }
+
+        if (!provider.attributes.query_limits) {
+            const formula = `chemical_formula_anonymous="A2B"`;
+            const url = `${provider.attributes.base_url}/v1/structures?filter=${formula}&page_limit=1000`;
+
+            try {
+                const res = await fetch(url).then(res => res.json());
+                const version = res.meta && res.meta.api_version || this.apis[provider.id][0].attributes.api_version;
+                const detail = (errors) => {
+                    return errors
+                        ? errors.length
+                            ? errors[0].detail
+                            : errors.detail
+                        : '10';
+                };
+                const limits = detail(res.errors)
+                    .match(/\d+/g)
+                    .filter((number: string) => +number < 1000)
+                    .map((number: string) => +number);
+
+                provider.attributes = {
+                    ...provider.attributes,
+                    api_version: version,
+                    query_limits: limits
+                }
+
+            } catch (error) {
+                console.log(error);
+            }
+        }
+
+        this.providers[provider.id] = provider
+
+        return this.providers;
+    }
+
     async getProviders(api?: Types.Api): Promise<Types.ProvidersMap | null> {
         const providers: Types.ProvidersResponse | null = await (api ?
             this.followLinks(api).catch(() => null) :
             Optimade.getJSON(this.providersUrl).catch(() => null)
         );
 
-        if (!providers) return null;
-        if (!this.providers) this.providers = {};
+        if (!providers) { return null; }
+        if (!this.providers) { this.providers = {}; }
 
         const data = providers.data.filter(Optimade.isProviderValid);
         const ver = providers.meta && providers.meta.api_version ?
             providers.meta.api_version.charAt(0) : '';
 
         for (const provider of data) {
-            if (!this.apis[provider.id]) this.apis[provider.id] = [];
+            if (!this.apis[provider.id]) { this.apis[provider.id] = []; }
             try {
                 const api = await this.getApis(provider, ver ? `v${ver}` : '');
-                if (!api) continue;
+                if (!api) { continue; }
 
                 if (api.attributes.available_endpoints.includes('structures')) {
                     this.apis[provider.id].push(api);
@@ -42,41 +93,40 @@ export class Optimade {
                 } else {
                     await this.getProviders(api);
                 }
-            } catch (ignore) { }
+            } catch (ignore) { console.log(ignore) }
         }
 
         return this.providers;
     }
 
-    async getApis(provider: Types.Provider | string, version: string = ''): Promise<Types.Api | null> {
+    async getApis(provider: Types.Provider | string, version = ''): Promise<Types.Api | null> {
         if (typeof provider === 'string') {
             provider = this.providers[provider];
         }
 
-        if (!provider) throw new Error('No provider found');
+        if (!provider) { throw new Error('No provider found'); }
 
         const url: string = this.wrapUrl(`${provider.attributes.base_url}/${version}`, '/info');
 
-        if (this.isDuplicatedReq(url)) return null;
+        if (this.isDuplicatedReq(url)) { return null; }
 
         const apis: Types.InfoResponse = await Optimade.getJSON(url);
         return Optimade.apiVersion(apis);
     }
 
-    async getStructures(providerId: string, filter: string = '', page: number = 1, limit: number): Promise<Types.StructuresResponse[] | Types.ResponseError> {
+    async getStructures({ providerId, filter, page, limit, offset }: { providerId: string; filter: string; page: number; limit: number; offset: number; }): Promise<Types.StructuresResponse[] | Types.ResponseError> {
 
-        if (!this.apis[providerId]) return null;
+        if (!this.apis[providerId]) { return null; }
 
         const apis = this.apis[providerId].filter(api => api.attributes.available_endpoints.includes('structures'));
         const provider = this.providers[providerId];
 
         const structures: Types.StructuresResponse[] = await allSettled(apis.map(async (api: Types.Api) => {
-            if (page <= 0) page = 1;
             const pageLimit = limit ? `&page_limit=${limit}` : '';
-            const pageNumber = page ? `&page_number=${page - 1}` : '';
-            const pageOffset = limit && page ? `&page_offset=${limit * (page - 1)}` : '';
+            const pageNumber = page ? `&page_number=${page}` : '';
+            const pageOffset = offset ? `&page_offset=${offset}` : '';
             const params = filter ? `${pageLimit + pageNumber + pageOffset}` : `?${pageLimit}`;
-            const url: string = this.wrapUrl(Optimade.apiVersionUrl(api), filter ? `/structures?filter=${filter + params}` : `/structures${params}`);
+            const url = this.wrapUrl(Optimade.apiVersionUrl(api), filter ? `/structures?filter=${filter + params}` : `/structures${params}`);
 
             try {
                 return await Optimade.getJSON(url, {}, { Origin: 'https://cors.optimade.science', 'X-Requested-With': 'XMLHttpRequest' });
@@ -98,13 +148,13 @@ export class Optimade {
         }, []);
     }
 
-    getStructuresAll(providerIds: string[], filter: string = '', page: number = 0, limit: number, batch: boolean = true): Promise<Promise<Types.StructuresResult>[]> | Promise<Types.StructuresResult>[] {
+    getStructuresAll({ providers, filter, page, limit, offset, batch = true }: { providers: string[]; filter: string; page: number; limit: number; offset: number; batch?: boolean; }): Promise<Promise<Types.StructuresResult>[]> | Promise<Types.StructuresResult>[] {
 
-        const results = providerIds.reduce((structures: Promise<any>[], providerId: string) => {
+        const results = providers.reduce((structures: Promise<any>[], providerId: string) => {
             const provider = this.providers[providerId];
             if (provider) {
                 structures.push(allSettled([
-                    this.getStructures(providerId, filter, page, limit),
+                    this.getStructures({ providerId, filter, page, limit, offset }),
                     Promise.resolve(provider)
                 ]));
             }
@@ -115,14 +165,14 @@ export class Optimade {
     }
 
     private async followLinks(api: Types.Api): Promise<Types.LinksResponse | null> {
-        if (!api.attributes.available_endpoints.includes('links')) return null;
+        if (!api.attributes.available_endpoints.includes('links')) { return null; }
 
         const url = this.wrapUrl(Optimade.apiVersionUrl(api), '/links');
 
         return !this.isDuplicatedReq(url) ? Optimade.getJSON(url) : null;
     }
 
-    private wrapUrl(url, tail = '') {
+    private wrapUrl(url: string, tail = ''): string {
         url = this.corsProxyUrl ? `${this.corsProxyUrl}/${url.replace('://', '/').replace('//', '/')}` : url;
         return tail ? url.replace(/\/$/, '') + tail : url;
     }
@@ -131,7 +181,7 @@ export class Optimade {
         return this.reqStack.includes(url) || !this.reqStack.unshift(url);
     }
 
-    static async getJSON(uri: string, params: {} = null, headers: {} = {}) {
+    static async getJSON(uri: string, params = null, headers = {}) {
 
         const url = new URL(uri);
         const timeout = 10000;
@@ -140,6 +190,8 @@ export class Optimade {
             Object.entries(params).forEach((param: [string, any]) => url.searchParams.append(...param));
         }
 
+        Object.assign(headers, { 'User-Agent': `tilde-lab-optimade-client/${version}` })
+
         const res = await fetchWithTimeout(url.toString(), { headers }, timeout);
 
         if (!res.ok) {

package/src/types.ts

@@ -46,7 +46,7 @@ export interface Api {
         api_version: string;
         available_api_versions: ApiVer | ApiVer[];
         available_endpoints: string[];
-        entry_types_by_format: {};
+        entry_types_by_format: Record<string, unknown>;
         formats: string[];
     };
 }
@@ -61,6 +61,7 @@ export interface Provider {
         homepage?: string | null;
         link_type?: string;
         query_limits?: number[];
+        api_version?: string;
     };
 }
 

package/tsconfig.json

@@ -11,6 +11,7 @@
         "noImplicitReturns": true,
         "noUnusedLocals": true,
         "noUnusedParameters": true,
+        "resolveJsonModule": true,
         "removeComments": true,
         "noLib": false,
         "moduleResolution": "node",

package/tslint.json

@@ -1,52 +0,0 @@
-{
-    "extends": [
-        "tslint:recommended",
-        "tslint-eslint-rules"
-    ],
-    "defaultSeverity": "warning",
-    "jsRules": {},
-    "rules": {
-        "curly": [
-            true,
-            "ignore-same-line"
-        ],
-        "interface-name": [
-            true,
-            "never-prefix"
-        ],
-        "max-line-length": [
-            true,
-            180
-        ],
-        "object-literal-sort-keys": false,
-        "trailing-comma": [
-            true,
-            {
-                "multiline": "never",
-                "singleline": "never"
-            }
-        ],
-        "arrow-parens": false,
-        "member-access": [
-            true,
-            "no-public"
-        ],
-        "eofline": false,
-        "whitespace": [
-            false,
-            "check-module"
-        ],
-        "no-angle-bracket-type-assertion": false,
-        "ordered-imports": false,
-        "quotemark": [
-            true,
-            "single",
-            "avoid-escape"
-        ],
-        "object-curly-spacing": [
-            true,
-            "always"
-        ]
-    },
-    "rulesDirectory": []
-}