From 2cc019842d0921a48a4aef55df8fde5a3ff11aa6 Mon Sep 17 00:00:00 2001
From: Tianyi Wang <90009613+tiwa1154@users.noreply.github.com>
Date: Thu, 26 Sep 2024 10:51:21 -0400
Subject: [PATCH] 24.09.26 PRD push (#459) (#460)

* Static page update (#447)

* updated static page

* Updated CSS

---------



* Homepageedits (#458)

* Removed workshop from homepage, added pilot project instead

* Modified homepage and help buttons on Builder Page to open a new tab

---------



* test

---------

Co-authored-by: tianywan819 <57418894+tianywan819@users.noreply.github.com>
Co-authored-by: hadleyking <hadley_king@gwu.edu>
---
 client/src/App.css                               |   1 -
 .../src/components/builder/descriptionDomain.js  |   2 +-
 client/src/components/builder/errorDomain.js     |   2 +-
 client/src/components/builder/executionDomain.js |   2 +-
 client/src/components/builder/extensionDomain.js |   2 +-
 client/src/components/builder/ioDomain.js        |   2 +-
 .../src/components/builder/parametricDomain.js   |   2 +-
 .../src/components/builder/provenanceDomain.js   |   2 +-
 client/src/components/builder/usabilityDomain.js |   2 +-
 client/src/images/Builder_edit.png               | Bin 0 -> 2722 bytes
 client/src/images/nextflow.png                   | Bin 0 -> 4300 bytes
 client/src/pages/Home.js                         |  15 ++++++++-------
 client/src/pages/Resources.js                    |  14 ++++++++++++--
 server/authentication/apis.py                    |   2 ++
 14 files changed, 30 insertions(+), 18 deletions(-)
 create mode 100644 client/src/images/Builder_edit.png
 create mode 100644 client/src/images/nextflow.png

diff --git a/client/src/App.css b/client/src/App.css
index fa4a729d..6df3d1d5 100644
--- a/client/src/App.css
+++ b/client/src/App.css
@@ -113,7 +113,6 @@
 /* ---------------------------------------------------------------------------------------------------- */
 /* Page box components */
 .About-half-width-box{
-  min-height: 650px; /* Ensure both boxes have a minimum height */
   min-width: 350px;/* min-width: 275px; Ensure both boxes have a minimum width */
   width: 90%; /* Half the width of the container minus spacing */
   margin: 0 auto; /* Add spacing between the boxes */
diff --git a/client/src/components/builder/descriptionDomain.js b/client/src/components/builder/descriptionDomain.js
index 73ceab04..6c09efcd 100644
--- a/client/src/components/builder/descriptionDomain.js
+++ b/client/src/components/builder/descriptionDomain.js
@@ -53,7 +53,7 @@ export const  DescriptionDomain = ({onSave}) => {
                   <span className="bold-title">
                                     Description Domain
                     <Tooltip title="Explanation of Description Domain">
-                      <Button size="xs" href='https://wiki.biocomputeobject.org/index.php?title=Description-domain'>
+                      <Button size="xs" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Description-domain'>
                         <HelpOutlineIcon />
                       </Button>
                     </Tooltip>
diff --git a/client/src/components/builder/errorDomain.js b/client/src/components/builder/errorDomain.js
index 3deee765..a8ded540 100644
--- a/client/src/components/builder/errorDomain.js
+++ b/client/src/components/builder/errorDomain.js
@@ -67,7 +67,7 @@ export const ErrorDomain = ({onSave}) => {
                 <span className="bold-title">
                   Error Domain
                   <Tooltip title="Explanation of Error Domain">
-                    <Button size="small" href='https://github.com/biocompute-objects/BCO_Specification/blob/main/content/error-domain.md'>
+                    <Button size="small" target="_blank" href='https://github.com/biocompute-objects/BCO_Specification/blob/main/content/error-domain.md'>
                       <HelpOutlineIcon />
                     </Button>
                   </Tooltip>
diff --git a/client/src/components/builder/executionDomain.js b/client/src/components/builder/executionDomain.js
index f6feadbd..d833e5e2 100644
--- a/client/src/components/builder/executionDomain.js
+++ b/client/src/components/builder/executionDomain.js
@@ -66,7 +66,7 @@ export const ExecutionDomain = ({onSave}) => {
                   <span className="bold-title">
                       Execution Domain
                     <Tooltip title="Explanation of Execution Domain">
-                      <Button size="xs" href='https://wiki.biocomputeobject.org/index.php?title=Execution-domain'>
+                      <Button size="xs" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Execution-domain'>
                         <HelpOutlineIcon />
                       </Button>
                     </Tooltip>
diff --git a/client/src/components/builder/extensionDomain.js b/client/src/components/builder/extensionDomain.js
index 653f214d..adf50d43 100644
--- a/client/src/components/builder/extensionDomain.js
+++ b/client/src/components/builder/extensionDomain.js
@@ -39,7 +39,7 @@ export const  ExtensionDomain = ({onSave}) => {
           <span className="bold-title">
             Extension Domain
             <Tooltip title="Explanation of Extension Domain">
-              <Button size="small" href='https://wiki.biocomputeobject.org/index.php?title=Extension-domain'>
+              <Button size="small" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Extension-domain'>
                 <HelpOutlineIcon />
               </Button>
             </Tooltip>
diff --git a/client/src/components/builder/ioDomain.js b/client/src/components/builder/ioDomain.js
index ecb3bdf1..e9d4c803 100644
--- a/client/src/components/builder/ioDomain.js
+++ b/client/src/components/builder/ioDomain.js
@@ -43,7 +43,7 @@ export const  IODomain = ({onSave}) => {
                     <span className="bold-title">
                       I/O Domain
                       <Tooltip title="Explanation of IO Domain">
-                        <Button size="xs" href='https://wiki.biocomputeobject.org/index.php?title=Iodomain'>
+                        <Button size="xs" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Iodomain'>
                           <HelpOutlineIcon />
                         </Button>
                       </Tooltip>
diff --git a/client/src/components/builder/parametricDomain.js b/client/src/components/builder/parametricDomain.js
index da2578e3..cb301b39 100644
--- a/client/src/components/builder/parametricDomain.js
+++ b/client/src/components/builder/parametricDomain.js
@@ -38,7 +38,7 @@ export const  ParametricDomain = ({onSave}) => {
                   <span className="bold-title">
                     Parametric Domain
                     <Tooltip title="Explanation of Parametric Domain">
-                      <Button size="xs" href='https://wiki.biocomputeobject.org/index.php?title=Parametric-domain'>
+                      <Button size="xs" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Parametric-domain'>
                         <HelpOutlineIcon />
                       </Button>
                     </Tooltip>
diff --git a/client/src/components/builder/provenanceDomain.js b/client/src/components/builder/provenanceDomain.js
index b1d3f0ef..a86ad71e 100644
--- a/client/src/components/builder/provenanceDomain.js
+++ b/client/src/components/builder/provenanceDomain.js
@@ -98,7 +98,7 @@ export const  ProvenanceDomain = ({onSave} ) => {
                     <span className="bold-title">
                       Provenance Domain
                       <Tooltip title="Explanation of Provenance Domain">
-                        <Button size="small" href='https://wiki.biocomputeobject.org/index.php?title=Provenance-domain'>
+                        <Button size="small" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Provenance-domain'>
                           <HelpOutlineIcon />
                         </Button>
                       </Tooltip>
diff --git a/client/src/components/builder/usabilityDomain.js b/client/src/components/builder/usabilityDomain.js
index c1cb86c1..bf71ddd6 100644
--- a/client/src/components/builder/usabilityDomain.js
+++ b/client/src/components/builder/usabilityDomain.js
@@ -53,7 +53,7 @@ export const  UsabilityDomain = ({onSave}) => {
                   <span className="bold-title">
                                     Usability Domain
                     <Tooltip title="Explanation of Usability Domain">
-                      <Button size="xs" href='https://wiki.biocomputeobject.org/index.php?title=Usability-domain'>
+                      <Button size="xs" target="_blank" href='https://wiki.biocomputeobject.org/index.php?title=Usability-domain'>
                         <HelpOutlineIcon />
                       </Button>
                     </Tooltip>
diff --git a/client/src/images/Builder_edit.png b/client/src/images/Builder_edit.png
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diff --git a/client/src/pages/Home.js b/client/src/pages/Home.js
index b3ad8d35..2094f881 100644
--- a/client/src/pages/Home.js
+++ b/client/src/pages/Home.js
@@ -9,6 +9,7 @@ import ieee from "../images/ieee.jpg";
 import workshoppic from "../images/workshop.jpg"
 import mediaWiki from "../images/mediawikiwiki.svg";
 import cloudlogo from "../images/cloud.png"
+import builderlogo from "../images/Builder_edit.png"
 
 const HomePage = () => {
   return (
@@ -28,7 +29,7 @@ const HomePage = () => {
               <FullWidthBox
                 link=""
                 title="BioCompute: A platform for bioinformatics analysis workflow documentation"
-                content="BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers (CBER, CDER and CFSAN). The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format."
+                content="BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Computational Analyses to facilitate communication between researchers, federal agencies and industires. This pipeline documentation approach has been adopted by a three FDA centers (CBER, CDER and CFSAN). Through this web portal, users can create BioCompute Objects (BCOs) in JSON format using the Builder and search for existing BCOs."
                 cssClass="home-colorBackground"
               />
               <br/>
@@ -50,7 +51,7 @@ const HomePage = () => {
                   <ThirdBox
                     link="/builder"
                     title="BioCompute Builder"
-                    image={logo}
+                    image={builderlogo}
                     content="Use the BioCompute Builder or view objects in the database.
                     The BioCompute Builder is a platform-free, form-based editor."
                   />
@@ -71,11 +72,11 @@ const HomePage = () => {
               <Grid container justifyContent="center" spacing={3}>
                 <Grid item xs={12} sm={12} lg={12} xl={12} >
                   <FullWidthBox
-                    link="https://wiki.biocomputeobject.org/index.php?title=BioCompute_Spring_Workshop_2024"
-                    title="2024 BioCompute Conference & Workshop"
-                    content="This workshop provides an opportunity to learn about interoperability between platforms that host BioCompute Objects (BCOs), the FDA’s 'Portal' for reading, writing and sharing BCOs, real world applications including intended use in regulatory submissions, and potential implementations, including the use of AI/ML. "
+                    link="https://wiki.biocomputeobject.org/BCO_Pilot_Project"
+                    title="BioCompute Pilot Project"
+                    content="The purpose of the pilot is to bring both the sponsors and FDA to agreement around BCO usage to streamline and standardize computational workflow submissions and reviews. Expected to obtain first-hand knowledge of submitting computational analyses to the FDA and how to efficiently and effectively ease communication barrier between sponsors and government agency.  "
                     cssClass=""
-                    image={workshoppic}
+                    
                   />
                 </Grid>
                 <Grid item xs={12} sm={6} lg={4} xl={4}>
@@ -92,7 +93,7 @@ const HomePage = () => {
                   <ThirdBox
                     link="https://hivelab.biochemistry.gwu.edu/publications#Multimedia"
                     title="Previous workshop material"
-                    content="Collection of posters, presentation slides, and other materials from previous BioCompute workshops or conferences."
+                    content="Collection of posters, presentation slides, recordings, and other materials from previous BioCompute workshops or conferences."
                     cssClass=""
                     image={workshoppic}
                   />
diff --git a/client/src/pages/Resources.js b/client/src/pages/Resources.js
index 476c08f4..6a663eaa 100644
--- a/client/src/pages/Resources.js
+++ b/client/src/pages/Resources.js
@@ -9,6 +9,7 @@ import {
 
 import ThirdBox from "../components/ThirdBox.js";
 import FullWidthBox from "../components/FullWidthBox.js";
+import HalfWidthBox from "../components/HalfWidthBox.js"
 import logo from "../images/logo.png"
 import hive from "../images/hive.png"
 import gitLogo from "../images/Octocat.png";
@@ -17,6 +18,7 @@ import dnaNexus from "../images/dnanexus.png"
 import galaxy from "../images/galaxy.png"
 import cgc from "../images/cgc2.png"
 import swagger from "../images/swagger.png"
+import nextflow from "../images/nextflow.png"
 
 export default function Resources() {
   const bcodbUrl = process.env.REACT_APP_BCOAPI_URL
@@ -25,14 +27,22 @@ export default function Resources() {
     <Paper>
       <Container maxWidth={false}>
         <Grid container justifyContent="center" spacing={3}>
-          <Grid item xs={12} sm={12} lg={12} xl={12}>
-            <FullWidthBox
+          <Grid item xs={4} sm={4} lg={6} xl={6}>
+            <HalfWidthBox
               title="BCODB API"
               image={swagger}
               content="Explore the BioCompute data base RESTful APIs, generated by Swagger"
               link={`${bcodbUrl}docs/`}
             />
           </Grid>
+          <Grid item xs={4} sm={4} lg={6} xl={6}>
+            <HalfWidthBox
+              title="Nextflow"
+              image={nextflow}
+              content="Automatically generate BCO from Nextflow pipelines with provenance information "
+              link="https://github.com/nextflow-io/nf-prov"
+            />
+          </Grid>
           <Grid item xs={12} sm={6} lg={4} xl={4}>
             <ThirdBox
               link="https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main"
diff --git a/server/authentication/apis.py b/server/authentication/apis.py
index 6bfe5262..1aab85ea 100644
--- a/server/authentication/apis.py
+++ b/server/authentication/apis.py
@@ -3,6 +3,8 @@
 """Authentication APIs
 """
 
+#test
+
 import jwt
 from bcodb.services import add_authentication, remove_authentication
 from bcodb.selectors import get_all_bcodbs