Merge pull request #365 from MoTrPAC/364_JZ_Public_Accessible_Bucket

Connects to #364. Migrate static resources from publicly accessible GCP bucket to AWS CDN.

src/AnnouncementsPage/announcements.json

@@ -53,13 +53,13 @@
             },
             {
                 "label": "Webinar presentation slides",
-                "url": "http://study-docs.motrpac-data.org/MoTrPAC_BIC_Data_hub_webinar_slides.pdf",
+                "url": "https://d1yw74buhe0ts0.cloudfront.net/docs/MoTrPAC_BIC_Data_hub_webinar_slides.pdf",
                 "gaEventCategory": "NIH Funding Opportunity Webinar",
                 "gaEventAction": "Webinar Presentation Slides"
             },
             {
                 "label": "Recorded webinar",
-                "url": "http://study-docs.motrpac-data.org/MoTrPAC_BIC_Data_hub_recorded_webinar.mp4",
+                "url": "https://youtu.be/JT2Gr_tnJr4",
                 "gaEventCategory": "NIH Funding Opportunity Webinar",
                 "gaEventAction": "Webinar Recorded Video"
             }

src/App/App.jsx

@@ -30,7 +30,6 @@ import Tutorials from '../Tutorials/tutorials';
 import Publications from '../Publications/publications';
 import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups';
 import FullTableEnduranceTraining from '../Publications/Data/Animal/Phenotype/fullTableEnduranceTraining';
-import ClinicalStudyProtocols from '../Publications/Docs/Protocol/Clinical/clinicalStudyProtocols';
 import Pass1b06PhenotypeAnimalConnected from '../AnalysisPage/pass1b06PhenotypeAnimal';
 import CallbackConnected from '../Auth/callback';
 import { withTracker } from '../GoogleAnalytics/googleAnalytics';
@@ -148,11 +147,6 @@ function App({ history = History }) {
                 exact
                 component={withTracker(FullTableEnduranceTraining)}
               />
-              <Route
-                path="/publications/docs/protocol/clinical/study-protocols"
-                exact
-                component={withTracker(ClinicalStudyProtocols)}
-              />
               <PrivateRoute
                 path="/analysis-phenotype"
                 component={withTracker(Pass1b06PhenotypeAnimalConnected)}

src/App/__test__/App.test.jsx

@@ -23,7 +23,7 @@ describe('<App />', () => {
   });
 
   test('It should contain fifteen <Route /> children', () => {
-    expect(component.find('Route').length).toBe(22);
+    expect(component.find('Route').length).toBe(21);
   });
 
   test('It should contain four <PrivateRoute /> children', () => {

src/DataAccess/studyDocuments.js

@@ -1,6 +1,6 @@
-const baseUrl = 'http://study-docs.motrpac-data.org';
+const baseUrl = 'https://d1yw74buhe0ts0.cloudfront.net/docs';
 
-const StudyDocuments = [
+export const AnimalStudyDocuments = [
   {
     title: 'Animal protocol',
     location: `${baseUrl}/Animal_Protocol.pdf`,
@@ -63,4 +63,29 @@ const StudyDocuments = [
   },
 ];
 
-export default StudyDocuments;
+export const HumanStudyDocuments = [
+  {
+    title: 'MoTrPAC Adult Study - Protocol',
+    location: `${baseUrl}/MoTrPAC_Adult_Study_Protocol.pdf`,
+    description: 'Describes the MoTrPAC research study for the Adult humans including design, rationale, objectives, methodologies, and how data is managed and analyzed.',
+    filetype: 'pdf',
+  },
+  {
+    title: 'MoTrPAC Adult Study - Manual of Procedures chapters',
+    location: `${baseUrl}/MoTrPAC_Adult_Study_Manual_of_Procedures_chapters.pdf`,
+    description: 'Details the conduct of the MoTrPAC study operations for standardized implementation of the Adult human protocol.',
+    filetype: 'pdf',
+  },
+  {
+    title: 'MoTrPAC Pediatric Study - Protocol',
+    location: `${baseUrl}/MoTrPAC_Pediatric_Study_Protocol.pdf`,
+    description: 'Describes the MoTrPAC research study for the Pediatric humans including design, rationale, objectives, methodologies, and how data is managed and analyzed.',
+    filetype: 'pdf',
+  },
+  {
+    title: 'MoTrPAC Pediatric Study - Manual of Procedures chapters',
+    location: `${baseUrl}/MoTrPAC_Pediatric_Study_Manual_of_Procedures_chapters.pdf`,
+    description: 'Details the conduct of the MoTrPAC study operations for standardized implementation of the Pediatric human protocol.',
+    filetype: 'pdf',
+  },
+];

src/MethodsPage/methods.jsx

@@ -4,6 +4,7 @@ import { connect } from 'react-redux';
 import { Helmet } from 'react-helmet';
 import PageTitle from '../lib/ui/pageTitle';
 import StudyDocumentsTable from '../lib/studyDocumentsTable';
+import HumanStudyDocumentsTable from '../lib/humanStudyDocumentsTable';
 import ExternalLink from '../lib/ui/externalLink';
 
 /**
@@ -16,6 +17,8 @@ import ExternalLink from '../lib/ui/externalLink';
 export function Methods({ profile }) {
   const userType = profile.user_metadata && profile.user_metadata.userType;
 
+  const baseUrl = 'https://d1yw74buhe0ts0.cloudfront.net/docs';
+
   return (
     <div className="methodsPage px-3 px-md-4 mb-3 container">
       <Helmet>
@@ -26,35 +29,22 @@ export function Methods({ profile }) {
       <div className="methods-content-container">
         <div className="methods-summary-container row mb-4">
           <div className="lead col-12">
-            The MoTrPAC study is divided into two main parts; human and animal
-            (rats). Preclinical Animal Study Sites (PASSs) conduct the endurance
-            exercise and training intervention in rats (see{' '}
-            <ExternalLink
-              to="https://motrpac.org/actDocumentDownload.cfm?docGUID=A31CDD1F-8A59-41D9-BABA-125B37A39BF5"
-              label="animal protocol"
-            />
-            ), and Human Clinical Exercise Sites conduct the human endurance and
-            resistance training interventions (see{' '}
-            <ExternalLink
-              to="https://motrpac.org/actDocumentDownload.cfm?docGUID=8120CEC8-5761-4C74-9EB3-4544EEC99FA4"
-              label="adult protocol"
-            />{' '}
-            and{' '}
-            <ExternalLink
-              to="https://motrpac.org/actDocumentDownload.cfm?docGUID=67F818DF-22CC-4C56-88F4-B07FDA8BA6EE"
-              label="pediatric protocol"
-            />
-            ). Multiple biospecimen samples are collected at different time
-            points after acute and chronic exercise. Please see the Animal
-            protocol below for details on the animal training intervention and
-            sample collection. The biospecimen samples are distributed from a
-            central biorepository to various Chemical Analysis Sites (CASs) for
-            molecular ‘omics analysis. Specific methods for the different
-            molecular assays are described in the Manual Of Procedures (MOPs).
-            There is one for the genomic, transcriptomic and epigenomic data
-            (GET), one for proteomics and one for metabolomics. In addition, the
-            assay-specific quality control (QC) procedures are described in the
-            QC Standard Operating Procedures (SOPs) documents.
+            The MoTrPAC study is divided into two main parts; human and animal (rats).
+            Preclinical Animal Study Sites (PASSs) conduct the endurance exercise and
+            training intervention in rats, and Human Clinical Exercise Sites conduct
+            the human endurance and resistance training interventions. Multiple
+            biospecimen samples are collected at different time points after acute
+            and chronic exercise. Please see the Animal protocol below for details
+            on the animal training intervention and sample collection, and the Adult
+            and Pediatric protocols for the human interventions and sample collection.
+            The biospecimen samples are distributed from a central biorepository to
+            various Chemical Analysis Sites (CASs) for molecular 'omics analysis.
+            Specific methods for the different molecular assays and specific
+            operational details are described in the Manual Of Procedures (MOPs).
+            There is one for the genomic, transcriptomic and epigenomic data (GET),
+            one for proteomics and one for metabolomics. In addition, the
+            assay-specific quality control (QC) procedures are described in the QC
+            Standard Operating Procedures (SOPs) documents.
           </div>
         </div>
         {userType && userType === 'internal' ? (
@@ -69,9 +59,14 @@ export function Methods({ profile }) {
             </div>
           </section>
         ) : (
-          <section className="study-docs-container">
-            <StudyDocumentsTable currentView={userType} />
-          </section>
+          <>
+            <section className="study-docs-container">
+              <StudyDocumentsTable currentView={userType} />
+            </section>
+            <section className="study-docs-container pt-4">
+              <HumanStudyDocumentsTable />
+            </section>
+          </>
         )}
       </div>
     </div>

src/ReleasePage/releases.json

@@ -227,7 +227,7 @@
     "date": "October 15, 2019",
     "target": "external",
     "description": "This release contains data from 6-month old rats that performed an acute bout of endurance exercise. There is data from 5 different tissues collected at multiple different time points after exercise. Untrained control animals from 2 time points are also included. The data includes phenotypic and -omic data from multiple assays, including RNA sequencing, Reduced Representation Bisulfite Sequencing (RRBS), proteomics, phosphoproteomics, acetylproteomics, and targeted and untargeted metabolomics. You may choose to download different bundled assay quantitative results and the phenotypic data separately, or all of them together.",
-    "readme_file_location": "http://study-docs.motrpac-data.org/MoTrPAC_External_Data_Release_ReadMe.pdf",
+    "readme_file_location": "https://d1yw74buhe0ts0.cloudfront.net/docs/MoTrPAC_External_Data_Release_ReadMe.pdf",
     "result_files": {
       "bucket_name": "motrpac-external-release1-results",
       "data_types": [