optimade 2.0.5 → 2.1.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "optimade",
-  "version": "2.0.5",
+  "version": "2.1.1",
   "description": "Aggregating Optimade client for the online materials databases",
   "main": "dist/index.js",
   "module": "dist/index.mjs",
@@ -23,14 +23,13 @@
     "@types/jest": "^26.0.15",
     "jest": "^26.6.0",
     "rollup": "^2.47.0",
-    "rollup-plugin-typescript2": "^0.28.0",
+    "rollup-plugin-typescript2": "^0.37.0",
     "ts-jest": "^26.4.1",
     "eslint": "^8.16.0",
     "typescript": "^4.0.3"
   },
   "dependencies": {
-    "isomorphic-unfetch": "^3.1.0",
-    "node-abort-controller": "^3.0.1"
+    "isomorphic-unfetch": "^3.1.0"
   },
   "keywords": [
     "optimade",
@@ -40,4 +39,4 @@
     "type": "git",
     "url": "git+https://github.com/tilde-lab/optimade-client"
   }
-}
+}

package/prefetch.js

@@ -6,10 +6,6 @@ const fs = require('fs');
 const path = require('path');
 const { Optimade } = require('./dist/index');
 
-const { AbortController } = require('node-abort-controller');
-
-global.AbortController = AbortController;
-
 const optimade = new Optimade({
 	providersUrl: 'https://providers.optimade.org/providers.json'
 });
@@ -55,19 +51,23 @@ optimade.getProviders().then(async (providers) => {
 							: e.detail
 						: '0';
 				};
+				// take care of the pagination for GUIs
 				const nums = detail(res.errors).match(/\d+/g).filter(n => +n < max).map(n => +n);
 				return {
 					[k]: { ...v, attributes: { ...v.attributes, api_version: api, ['query_limits']: !nums.includes(0) ? nums : [10] } }
 				};
 			} catch (error) {
-				console.log(error);
+				console.error(error);
 			}
 		};
 		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);
+
+			console.log(`Provider # ${i}:`);
+			console.log(JSON.stringify(provider, null, 4));
+
 			return { ...acc, ...provider };
 		}, Promise.resolve({}));
 	}
@@ -80,16 +80,16 @@ optimade.getProviders().then(async (providers) => {
 		console.log({
 			prefetched: Object.keys(providers).length,
 			source: Object.keys(source).length,
-			alltime: performance.now() - alltime
+			time: 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!');
 		});
-		fs.writeFile(path.join(__dirname, 'dist/providers.json'), JSON.stringify(source), (err) => {
+		fs.writeFile(path.join(__dirname, 'dist/providers.debug.json'), JSON.stringify(source), (err) => {
 			if (err) throw err;
-			console.log('The providers.json file has been saved!');
+			console.log('The providers.debug.json file has been saved!');
 		});
 	});
 

package/src/index.ts

@@ -114,7 +114,7 @@ export class Optimade {
         return Optimade.apiVersion(apis);
     }
 
-    async getStructures(providerId: string, filter = '', page = 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; }
 
@@ -122,12 +122,11 @@ export class Optimade {
         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' });
@@ -149,13 +148,13 @@ export class Optimade {
         }, []);
     }
 
-    getStructuresAll(providerIds: string[], filter = '', page = 1, limit: number, batch = 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)
                 ]));
             }
@@ -173,7 +172,7 @@ export class Optimade {
         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;
     }
@@ -191,7 +190,7 @@ export class Optimade {
             Object.entries(params).forEach((param: [string, any]) => url.searchParams.append(...param));
         }
 
-        Object.assign(headers, { 'User-Agent': `tilde-lab-optimade-client/${version}` })
+        Object.assign(headers, { 'User-Agent': `tilde-lab-optimade-client/${version}` });
 
         const res = await fetchWithTimeout(url.toString(), { headers }, timeout);
 
@@ -225,4 +224,4 @@ export class Optimade {
             data.find(({ attributes }) => attributes.api_version === meta.api_version) :
             data;
     }
-}
+}

package/dist/providers.json

@@ -1 +0,0 @@
-{"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 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}},"aflow":{"id":"aflow","type":"links","attributes":{"name":"AFLOW","description":"The AFLOW OPTIMADE endpoint","base_url":"http://aflow.org/API/optimade/","homepage":"http://aflow.org","link_type":"child"}},"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"}},"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}},"jarvis":{"id":"jarvis","type":"links","attributes":{"name":"JARVIS-DFT","description":"JARVIS-DFT is a materials property repository focused on density functional theory (DFT) predictions of material properties, especially for crystalline materials.","base_url":"https://jarvis.nist.gov/optimade/jarvisdft","homepage":"https://jarvis.nist.gov","link_type":"child"}},"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}},"mc3d-structures":{"id":"mc3d-structures","type":"links","attributes":{"name":"Materials Cloud three-dimensional crystals database","description":"Curated set of relaxed three-dimensional crystal structures based on raw CIF data from the experimantal databases MPDS, COD, and ICSD.","base_url":"https://aiida.materialscloud.org/mc3d-structures/optimade","homepage":"https://materialscloud.org/explore/mc3d-structures","link_type":"child","aggregate":"ok","no_aggregate_reason":null}},"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"}},"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"}},"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"}},"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}},"omdb_production":{"id":"omdb_production","type":"links","attributes":{"name":"Open Materials Database (omdb) production database","description":"This is the main production version of the Open Materials Database","base_url":"http://optimade.openmaterialsdb.se","homepage":"http://openmaterialsdb.se","link_type":"child"}},"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}},"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}},"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}},"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}},"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}},"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}},"tcod":{"id":"tcod","type":"links","attributes":{"name":"Theoretical Crystallography Open Database","description":"Open-access collection of theoretically calculated or refined crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers","base_url":"https://www.crystallography.net/tcod/optimade","homepage":"https://www.crystallography.net/tcod","link_type":"child"}},"tin-antimony-sulfoiodide":{"id":"tin-antimony-sulfoiodide","type":"links","attributes":{"name":"Hidden spontaneous polarisation in the chalcohalide photovoltaic Sn2SbS2I3","description":"Structural, dynamic and electronic characterisation of a novel mixed-metal chalcohalide revealing hidden symmetry breaking and spontaneous polarisation.","base_url":"https://aiida.materialscloud.org/tin-antimony-sulfoiodide/optimade","homepage":"https://materialscloud.org/explore/tin-antimony-sulfoiodide","link_type":"child","aggregate":"ok","no_aggregate_reason":null}},"twodmatpedia":{"id":"twodmatpedia","type":"links","attributes":{"name":"2DMatpedia","description":"2DMatpedia, an open computational database of two-dimensional materials from top-down and bottom-up approaches","base_url":"http://optimade.2dmatpedia.org","homepage":"http://2dmatpedia.org","link_type":"child"}}}