Adding an organism-hints model

src/model/hint.js

@@ -0,0 +1,66 @@
+import _ from 'lodash';
+
+//import { ENTITY_TYPE } from './entity-type.js';
+
+const HINT_TYPE = Object.freeze({
+    ORGANISM: 'organism'
+});
+const HINT_TYPES = _.flatMap(HINT_TYPE);
+
+
+const HINT_PASSAGE = Object.freeze({
+    TITLE: 'title',
+    ABSTRACT: 'abstract'
+});
+const HINT_PASSAGES = _.flatMap(HINT_PASSAGE);
+
+class Hint{
+
+    get text(){
+        return this._text;
+    }
+
+    set text(value){
+        this._text = value;
+    }
+
+    get type(){
+        return this._type;
+    }
+
+    set type(value){
+        if( value != HINT_TYPES.ORGANISM){
+            throw new Error('Invalid type' + value);
+        }
+        this._type = value;
+    }
+
+    get xref(){
+        return this._xref;
+    }
+
+    set xref(value){
+        if (!value.dbPrefix || !value.id){
+            throw new Error('Invalid xref' + JSON.stringify(value));
+        }
+        this._xref = value;
+    }
+
+    get section(){
+        return this._section;
+    }
+
+    set section(value){
+        if( value != HINT_PASSAGES.TITLE && value != HINT_PASSAGES.ABSTRACT){
+            throw new Error('Invalid section' + value);
+        }
+        this._section = value;
+    }
+
+
+}
+export { 
+    Hint, 
+    HINT_TYPES, 
+    HINT_PASSAGES 
+};

src/server/routes/api/document/hint/pubtator.js

@@ -0,0 +1,32 @@
+import _ from 'lodash';
+
+import {
+    Hint,
+    HINT_TYPES
+} from '../../../model/hint.js';
+
+function map (bioCDocument) {
+    let hints = [];
+
+    const byText = annotation => {
+        const sanitzed = text => text.toLowerCase();
+        const { text } = annotation;
+        return sanitzed(text);
+    };
+
+    const byAnnotation = annotation => {
+
+        const isValidType = annotation => {
+            const {infons: { type } } = annotation;
+            return type === HINT_TYPES.ORGANISM;
+        };
+
+        const hasXref = annotation => {
+            const { infons } = annotation;
+            return _.has(infons, 'identifier');
+        };
+
+        return isValidType(annotation) && hasXref(annotation);
+    };
+
+}