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>
biocompute-objects · Sep 26, 2024 · 2cc0198 · 2cc0198
1 parent a0962b8
commit 2cc0198
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Showing 14 changed files with 30 additions and 18 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/client/src/images/nextflow.png b/client/src/images/nextflow.png
diff --git 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
@@ -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
@@ -3,6 +3,8 @@
 """Authentication APIs
 """
 
+#test
+
 import jwt
 from bcodb.services import add_authentication, remove_authentication
 from bcodb.selectors import get_all_bcodbs