feat: add support for PMCID resolution

This adds support for automatic resolution for PMCID identifiers. Now PMCID will be able to be cited automatically, along with PMID and DOI. Closes #240
dsifford · Nov 22, 2016 · a1e9d95 · a1e9d95
1 parent 5c3a65f
commit a1e9d95
Show file tree

Hide file tree

Showing 18 changed files with 221 additions and 195 deletions.
diff --git a/src/lib/js/__tests__/Frontend-test.ts b/src/lib/js/__tests__/Frontend-test.ts
@@ -22,7 +22,7 @@ describe('Frontend', () => {
         it('should render appropriately', () => {
             const citation1 = document.getElementById('citation-1');
             expect(citation1.getAttribute('data-citations')).toBe(
-                `<div id="aaaaaaaa">Test reference 1</div><div id="cccccccc">Test reference 3</div>`
+                `<div id="aaaaaaaa">Test reference 1</div><div id="cccccccc">Test reference 3</div>`,
             );
         });
         it('should create a tooltip on click', () => {

diff --git a/src/lib/js/components/__tests__/Spinner-test.tsx b/src/lib/js/components/__tests__/Spinner-test.tsx
@@ -15,7 +15,7 @@ interface SpinnerProps {
 
 const setup = (props: SpinnerProps) => {
     const component = mount(
-        <Spinner {...props} />
+        <Spinner {...props} />,
     );
     return {
         component,

diff --git a/src/lib/js/components/__tests__/ToggleSwitch-test.tsx b/src/lib/js/components/__tests__/ToggleSwitch-test.tsx
@@ -9,7 +9,7 @@ const setup = (checked = false) => {
             checked={checked}
             label="Test Label"
             onChange={spy}
-        />
+        />,
     );
     return {
         component,

diff --git a/src/lib/js/reference-list/API.ts b/src/lib/js/reference-list/API.ts
@@ -1,9 +1,10 @@
-import { getFromDOI, getFromPMID } from '../utils/resolvers/';
+import { getFromDOI, getFromPubmed } from '../utils/resolvers/';
 import { generateID, processCSLDate } from '../utils/HelperFunctions';
 
 export function getRemoteData(identifierList: string, mce: TinyMCE.WindowManager): Promise<CSL.Data[]> {
     return new Promise(resolve => {
         const pmidList: string[] = [];
+        const pmcidList: string[] = [];
         const doiList: string[] = [];
         const errList: string[] = [];
         const identifiers = identifierList.replace(/\s/g, '');
@@ -18,10 +19,15 @@ export function getRemoteData(identifierList: string, mce: TinyMCE.WindowManager
                 pmidList.push(id);
                 return;
             }
+            if (/^PMC\d+$/.test(id)) {
+                pmcidList.push(id.substring(3));
+                return;
+            }
             errList.push(id);
         });
 
-        if (pmidList.length > 0) promises.push(getFromPMID(pmidList.join(',')));
+        if (pmidList.length > 0) promises.push(getFromPubmed('PMID', pmidList.join(',')));
+        if (pmcidList.length > 0) promises.push(getFromPubmed('PMCID', pmcidList.join(',')));
         if (doiList.length > 0) promises.push(getFromDOI(doiList));
 
         if (promises.length === 0) {

diff --git a/src/lib/js/reference-list/components/ReferenceList.tsx b/src/lib/js/reference-list/components/ReferenceList.tsx
@@ -218,20 +218,24 @@ export class ReferenceList extends React.Component<{store: Store}, {}> {
         });
     }
 
-    insertInlineCitation = (e?: React.MouseEvent<HTMLAnchorElement>, data: CSL.Data[] = []) => {
-
+    /* FIXME: Fix when PR closes in the react repo */
+    insertInlineCitation = (e?: React.MouseEvent<HTMLAnchorElement>, d: CSL.Data[]|Event = []) => {
+        let data: CSL.Data[] = [];
         if (e) e.preventDefault();
         this.editor.setProgressState(true);
 
         /**
          * If no data, then this must be a case where we're inserting from the
          *   list selection.
          */
-        if (data.length === 0) {
+        if (d instanceof Event || d.length === 0) {
             this.selected.forEach(id => {
                 data.push(this.props.store.citations.CSL.get(id));
             });
         }
+        else {
+            data = d;
+        }
 
         /**
          * Checks to see if there is a inline citation selected. If so, extract the ids
@@ -415,15 +419,16 @@ export class ReferenceList extends React.Component<{store: Store}, {}> {
 
         /**
          * Vertical space that is already allocated.
-         * 200 = all static, non-participating sections of the list + padding
+         * 180 = all static, non-participating sections of the list + padding
+         * 84 = vertical height of menu when open
          */
-        const listOffset = 200 + topOffset + (this.menuOpen ? 91 : 0);
+        const listOffset = 180 + topOffset + (this.menuOpen ? 84 : 0);
         const remainingHeight = window.innerHeight - listOffset;
 
         list.style.top = `${topOffset}px`;
         if (!bothOpen) {
-            this.citedListUI.maxHeight = `calc(100vh - ${listOffset}px + 38px)`;
-            this.uncitedListUI.maxHeight = `calc(100vh - ${listOffset}px + 38px)`;
+            this.citedListUI.maxHeight = `calc(100vh - ${listOffset}px)`;
+            this.uncitedListUI.maxHeight = `calc(100vh - ${listOffset}px)`;
             return;
         }
 
@@ -432,16 +437,16 @@ export class ReferenceList extends React.Component<{store: Store}, {}> {
         let citedHeight = 0;
         let uncitedHeight = 0;
 
-        for (let i = 0; i < cited.children.length; i++) {
-            citedHeight += cited.children[i].clientHeight + 1;
+        for (const child of Array.from(cited.children)) {
+            citedHeight += child.clientHeight + 1;
             if (citedHeight > (remainingHeight / 2)) {
                 citedHeight = remainingHeight / 2;
                 break;
             }
         }
 
-        for (let i = 0; i < uncited.children.length; i++) {
-            uncitedHeight += uncited.children[i].clientHeight + 1;
+        for (const child of Array.from(uncited.children)) {
+            uncitedHeight += child.clientHeight + 1;
             if (uncitedHeight > (remainingHeight / 2)) {
                 uncitedHeight = remainingHeight / 2;
                 break;

diff --git a/src/lib/js/reference-list/components/__tests__/ReferenceList-test.tsx b/src/lib/js/reference-list/components/__tests__/ReferenceList-test.tsx
@@ -1,5 +1,4 @@
 jest.mock('../../../utils/CSLProcessor');
-// jest.mock('../../../utils/TinymceFunctions');
 
 import * as React from 'react';
 import { mount } from 'enzyme';
@@ -333,23 +332,23 @@ describe('<ReferenceList />', () => {
 
             // Toggle pinned state
             instance.togglePinned();
-            expect(instance.citedListUI.maxHeight).toBe('372px');
+            expect(instance.citedListUI.maxHeight).toBe('392px');
             expect(instance.uncitedListUI.maxHeight).toBe('101px');
 
             // New dimentions
             setupDimentions(100, [200, 250, 500]);
             instance.togglePinned();
             instance.togglePinned();
-            expect(instance.citedListUI.maxHeight).toBe('253.16666666666666px');
-            expect(instance.uncitedListUI.maxHeight).toBe('253.16666666666666px');
+            expect(instance.citedListUI.maxHeight).toBe('263.1666666666667px');
+            expect(instance.uncitedListUI.maxHeight).toBe('263.1666666666667px');
 
             // New dimentions
             setupDimentions(150, [50, 50, 650]);
             instance.toggleMenu();
             instance.togglePinned();
             instance.togglePinned();
             expect(instance.citedListUI.maxHeight).toBe('102px');
-            expect(instance.uncitedListUI.maxHeight).toBe('320px');
+            expect(instance.uncitedListUI.maxHeight).toBe('347px');
         });
     });
 });
diff --git a/src/lib/js/tinymce/components/import-window/__tests__/ImportWindow-test.tsx b/src/lib/js/tinymce/components/import-window/__tests__/ImportWindow-test.tsx
@@ -39,13 +39,6 @@ describe('<ImportWindow />', () => {
         setup();
         expect(ImportWindow.prototype.componentDidMount).toHaveBeenCalledTimes(1);
     });
-    it('should trigger handleFileUpload when upload field changed', () => {
-        const { upload, component, instance } = setup();
-        const handleFileUpload = spyOn(instance, 'handleFileUpload');
-        component.update();
-        upload.simulate('change', { target: { files: [new File(['testdata'], 'test')], value: 'test.ris' } });
-        expect(handleFileUpload).toHaveBeenCalledTimes(1);
-    });
     it('should set filename', () => {
         spyOn(window, 'FileReader').and.returnValue({
             addEventListener: () => null,

diff --git a/src/lib/js/tinymce/components/pubmed-window/PubmedWindow.tsx b/src/lib/js/tinymce/components/pubmed-window/PubmedWindow.tsx
@@ -48,7 +48,7 @@ export class PubmedWindow extends React.Component<{}, {}> {
     }
 
     @action
-    consumeQueryData = (data: PubMed.SingleReference[]) => {
+    consumeQueryData = (data: PubMed.DataPMID[]) => {
         if (data.length === 0) {
             top.tinyMCE.activeEditor.windowManager.alert(this.errors.noResults);
         }
@@ -74,7 +74,7 @@ export class PubmedWindow extends React.Component<{}, {}> {
     sendQuery = (e) => {
         this.toggleLoadState();
         e.preventDefault();
-        pubmedQuery(this.query, true)
+        pubmedQuery(this.query)
         .then(this.consumeQueryData)
         .catch(err => top.tinyMCE.activeEditor.windowManager.alert(err.message));
     }

diff --git a/src/lib/js/tinymce/components/pubmed-window/ResultList.tsx b/src/lib/js/tinymce/components/pubmed-window/ResultList.tsx
@@ -3,7 +3,7 @@ import { observer } from 'mobx-react';
 import { preventScrollPropagation } from '../../../utils/HelperFunctions';
 
 interface ResultListProps {
-    results: PubMed.SingleReference[];
+    results: PubMed.DataPMID[];
     select(pmid: string): void;
 }
 

diff --git a/src/lib/js/tinymce/components/pubmed-window/__tests__/ResultList-test.tsx b/src/lib/js/tinymce/components/pubmed-window/__tests__/ResultList-test.tsx
@@ -2,13 +2,13 @@ import * as React from 'react';
 import { mount } from 'enzyme';
 import { ResultList } from '../ResultList';
 
-const testData: PubMed.SingleReference[] = [
+const testData: PubMed.DataPMID[] = [
     {
         authors: [
-            { name: 'Author 1' },
-            { name: 'Author 2' },
-            { name: 'Author 3' },
-            { name: 'NOT VISIBLE' },
+            { authtype: 'Author', name: 'Author 1' },
+            { authtype: 'Author', name: 'Author 2' },
+            { authtype: 'Author', name: 'Author 3' },
+            { authtype: 'Author', name: 'NOT VISIBLE' },
         ],
         pubdate: '2016 May 1',
         source: 'J Test 1',
@@ -17,10 +17,10 @@ const testData: PubMed.SingleReference[] = [
     },
     {
         authors: [
-            { name: 'First A' },
-            { name: 'Second A' },
-            { name: 'Third A' },
-            { name: 'NOT VISIBLE' },
+            { authtype: 'Author', name: 'First A' },
+            { authtype: 'Author', name: 'Second A' },
+            { authtype: 'Author', name: 'Third A' },
+            { authtype: 'Author', name: 'NOT VISIBLE' },
         ],
         pubdate: '2016 May 2',
         source: 'J Test 2',
@@ -59,9 +59,9 @@ describe('<ResultList />', () => {
         expect(spy.mock.calls[0]).toEqual(['11111']);
     });
     it('should scroll to the top on update', () => {
-        const { component, instance } = setup();
+        const { instance } = setup();
         instance.element.scrollTop = 150;
-        component.update();
+        instance.componentDidUpdate();
         expect(instance.element.scrollTop).toBe(0);
     });
     it('should handle scroll', () => {

diff --git a/src/lib/js/tinymce/components/reference-window/components/ReferenceWindow.tsx b/src/lib/js/tinymce/components/reference-window/components/ReferenceWindow.tsx
@@ -89,8 +89,8 @@ export class ReferenceWindow extends React.Component<{}, {}> {
                 const titleKey = kind === 'chapter' ? 'container-title' : 'title';
                 this.manualData.merge({
                     accessed: new Date(Date.now()).toISOString().split('T')[0].split('-').join('/'),
-                    'number-of-pages': meta.book['number-of-pages'],
                     issued: meta.book.issued,
+                    'number-of-pages': meta.book['number-of-pages'],
                     publisher: meta.book.publisher,
                     [titleKey]: meta.book.title,
                 });