Create PDBe partial markup from web services

BioSchemas · Jun 16, 2018 · b141c46 · b141c46
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diff --git a/.babelrc b/.babelrc
@@ -0,0 +1,15 @@
+{
+    "presets": [
+        [
+            "env", {
+            "targets": {
+                "ie": 11
+            },
+            "modules": false
+        }
+        ]
+    ],
+    "plugins": [
+        "external-helpers"
+    ]
+}
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,24 @@
+.DS_Store
+
+npm-debug.log
+yarn.lock
+
+dist
+node_modules
+package-lock.json
+
+.idea
+*.log
+coverage
+.info
+.coveralls.yml
+.sass-cache
+.project
+.settings
+config.rb
+*.iml
+reports
+_includes
+_posts
+_sass
+_site
diff --git a/examples/index.html b/examples/index.html
@@ -0,0 +1,50 @@
+<!doctype html>
+<html class="no-js" lang="">
+<head>
+    <meta charset="utf-8">
+    <meta http-equiv="x-ua-compatible" content="ie=edge">
+    <title>bioschemas-pdbe-adapter-demo</title>
+
+</head>
+<body>
+<bioschemas-pdbe-adapter id="adapter1">
+    <data-loader id="loader1">
+        <source src="http://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/1BZG" />
+    </data-loader>
+</bioschemas-pdbe-adapter>
+
+<!-- Required for IE11 -->
+<script src="../node_modules/babel-polyfill/dist/polyfill.min.js"></script>
+<!-- Web component polyfill (only loads what it needs) -->
+<script src="../node_modules/@webcomponents/webcomponentsjs/webcomponents-lite.js" charset="utf-8"></script>
+<!-- Required to polyfill modern browsers as code is ES5 for IE... -->
+<script src="../node_modules/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js" charset="utf-8"></script>
+
+<script src="../node_modules/protvista-uniprot-entry-adapter/dist/ProtVistaUniProtEntryAdapter.js" charset="utf-8" defer></script>
+<script src="../node_modules/data-loader/dist/index.js" charset="utf-8" defer></script>
+<script src="../dist/BioschemasPDBeAdapter.js" charset="utf-8" defer></script>
+
+
+<script>
+    for (const adapter of document.querySelectorAll('bioschemas-pdbe-adapter')) {
+        adapter.addEventListener(
+            'load',
+            e => {
+                console.log('Data loaded');
+                console.log(e.target);
+                console.log(e.detail);
+            }
+        );
+        adapter.addEventListener(
+            'error',
+            e => {
+                console.log('error');
+                console.log(e.target);
+                console.log(e.detail);
+            }
+        );
+    }
+</script>
+
+</body>
+</html>
diff --git a/index.html b/index.html
@@ -0,0 +1,51 @@
+<!doctype html>
+<html class="no-js" lang="">
+<head>
+    <meta charset="utf-8">
+    <meta http-equiv="x-ua-compatible" content="ie=edge">
+    <title>bioschemas-pdbe-adapter-demo</title>
+
+</head>
+<body>
+<bioschemas-pdbe-adapter id="adapter1">
+    <data-loader id="loader1">
+        <source src="http://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/1BZG" />
+    </data-loader>
+</bioschemas-pdbe-adapter>
+
+
+<!-- Required for IE11 -->
+<script src="https://cdn.jsdelivr.net/npm/babel-polyfill/dist/polyfill.min.js"></script>
+<!-- Web component polyfill (only loads what it needs) -->
+<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/webcomponents-lite.js" charset="utf-8"></script>
+<!-- Required to polyfill modern browsers as code is ES5 for IE... -->
+<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js" charset="utf-8"></script>
+
+<script src="https://cdn.jsdelivr.net/npm/protvista-uniprot-entry-adapter/dist/ProtVistaUniProtEntryAdapter.js" charset="utf-8" defer></script>
+<script src="https://cdn.jsdelivr.net/npm/data-loader@latest/dist/index.js" charset="utf-8" defer></script>
+<script src="https://cdn.jsdelivr.net/npm/protvista-feature-adapter/dist/BioschemasPDBeAdapter.js" charset="utf-8" defer></script>
+
+
+<script>
+    for (const adapter of document.querySelectorAll('bioschemas-pdbe-adapter')) {
+        adapter.addEventListener(
+            'load',
+            e => {
+                console.log('Data loaded');
+                console.log(e.target);
+                console.log(e.detail);
+            }
+        );
+        adapter.addEventListener(
+            'error',
+            e => {
+                console.log('error');
+                console.log(e.target);
+                console.log(e.detail);
+            }
+        );
+    }
+</script>
+
+</body>
+</html>
diff --git a/package.json b/package.json
@@ -0,0 +1,45 @@
+{
+  "name": "bioschemas-pdbe-adapter",
+  "version": "0.0.1",
+  "description": "Adapter/Converter from PDBe services to Bioschemas JSON-LD ",
+  "main": "dist/BioschemasPDBeAdapter.js",
+  "module": "src/index.js",
+  "jsnext:main": "src/index.js",
+  "scripts": {
+    "build": "rimraf ./dist && mkdirp ./dist && rollup -c",
+    "rollup-watch": "rollup -cw",
+    "browser-sync": "browser-sync start --server -f dist/**/*.*",
+    "serve": "npm run rollup-watch & npm run browser-sync",
+    "npm-linkall": "npm link protvista-uniprot-entry-adapter data-loader"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/bioschemas/bioschemas-pdbe-adapter.git"
+  },
+  "keywords": [
+    "Bioschemas",
+    "dataloader",
+    "parser"
+  ],
+  "author": "ljgarcia",
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/bioschemas/bioschemas-pdbe-adapter/issues"
+  },
+  "homepage": "https://github.com/bioschemas/bioschemas-pdbe-adapter#readme",
+  "devDependencies": {
+    "@webcomponents/webcomponentsjs": "^1.0.19",
+    "babel-cli": "^6.24.1",
+    "babel-plugin-external-helpers": "^6.22.0",
+    "babel-preset-env": "^1.6.1",
+    "browser-sync": "^2.18.13",
+    "mkdirp": "^0.5.1",
+    "rimraf": "^2.6.1",
+    "rollup": "^0.49.3",
+    "rollup-plugin-babel": "^2.7.1",
+    "rollup-plugin-node-resolve": "^3.0.0"
+  },
+  "dependencies": {
+    "lodash-es": "^4.17.4"
+  }
+}
diff --git a/rollup.config.js b/rollup.config.js
@@ -0,0 +1,22 @@
+import babel from 'rollup-plugin-babel';
+import nodeResolve from 'rollup-plugin-node-resolve';
+
+export default {
+    input: 'src/index.js',
+    output: {
+        file: 'dist/BioschemasPDBeAdapter.js',
+        format: 'iife',
+        name: 'BioschemasPDBeAdapter',
+        sourcemap: true,
+        globals: {
+            'protvista-uniprot-entry-adapter': 'ProtVistaUniProtEntryAdapter'
+        }
+    },
+    external: ['protvista-uniprot-entry-adapter'],
+    plugins: [
+        nodeResolve({jsnext: true}),
+        babel({
+            exclude: 'node_modules/**'
+        })
+    ],
+};
diff --git a/src/BioschemasPDBeAdapter.js b/src/BioschemasPDBeAdapter.js
@@ -0,0 +1,25 @@
+/*jslint node: true */
+"use strict";
+
+import ProtVistaUniProtEntryAdapter from 'protvista-uniprot-entry-adapter';
+import ParserHelper from './ParserHelper';
+
+export default class BioschemasPDBeAdapter extends ProtVistaUniProtEntryAdapter {
+    constructor() {
+        super();
+        this._parser = new ParserHelper();
+    }
+
+    parseEntry(data) {
+        this._adaptedData = this._parser.adaptData(data);
+        this._renderEntry();
+        return this._adaptedData;
+    }
+
+    _renderEntry() {
+        const s = document.createElement('script');
+        s.type = 'application/ld+json';
+        s.innerHTML = JSON.stringify(this._adaptedData, null, 2);
+        document.body.appendChild(s);
+    }
+}
diff --git a/src/Context.js b/src/Context.js
@@ -0,0 +1,32 @@
+export const context = {
+    "@context": [
+        "http://schema.org",
+        {
+            "@base": "http://schema.org"
+        },
+        {
+            "ProteinStructure": {
+                "@id": "http://semanticscience.org/resource/SIO_011119"
+            },
+            "Protein": {
+                "@id": "http://purl.obolibrary.org/obo/PR_000000001"
+            },
+            "structureDeterminationMethod": {
+                "@id": "structureDeterminationMethod",
+                "@type": "@id"
+            },
+            "resolution": {
+                "@id": "resolution",
+                "@type": "@id"
+            },
+            "Domain": "http://semanticscience.org/resource/SIO_001379.rdf",
+            "boundMolecule": {
+                "@id": "boundMolecule",
+                "@type": "@id"
+            },
+            "Organism": {
+                "@id": "http://semanticscience.org/resource/SIO_010000"
+            }
+        }
+    ]
+};
diff --git a/src/ParserHelper.js b/src/ParserHelper.js
@@ -0,0 +1,51 @@
+/*jslint node: true */
+"use strict";
+
+import _filter from 'lodash-es/filter';
+import _assign from 'lodash-es/assign';
+import _map from 'lodash-es/map';
+import {context} from './Context';
+
+export default class ParserHelper {
+    constructor() {
+        this._accession = null;
+        this._adaptedData = _assign({}, context);
+        this._entry = {};
+    }
+
+    adaptData(entry) {
+        this._accession = Object.keys(entry)[0];
+        this._entry = entry[this._accession][0];
+        this._adaptRecord();
+        this._adaptMinimum();
+        return this._adaptedData;
+    }
+
+    _adaptRecord() {
+        this._adaptedData = _assign(this._adaptedData, {
+            "@type": "DataRecord",
+            "@id": `http://www.identifiers.org/pdbe:${this._accession}`,
+            "identifier": this._accession,
+            "url": `http://pdbe.org/${this._accession}`,
+            "datePublished": this._entry.revision_date,
+            "distribution": {
+                "@type": "DataDownload",
+                "url": `http://www.ebi.ac.uk/pdbe/entry-files/download/${this._accession}.cif`
+            }
+        });
+    }
+
+
+    _adaptMinimum() {
+        this._adaptedData.mainEntity = {
+            "@type": ["BioChemEntity", "ProteinStructure"],
+            "identifier": this._accession
+        };
+        try {
+            this._adaptedData.mainEntity.name = this._entry.title;
+            this._adaptedData.mainEntity.structureDeterminationMethod = this._entry.experimental_method;
+        } catch (e) {
+            this._adaptedData.mainEntity.name = this._accession;
+        }
+    }
+}
diff --git a/src/index.js b/src/index.js
@@ -0,0 +1,7 @@
+import BioschemasPDBeAdapter from './BioschemasPDBeAdapter';
+
+if (window.customElements) {
+    customElements.define('bioschemas-pdbe-adapter', BioschemasPDBeAdapter);
+}
+
+export default BioschemasPDBeAdapter;