Merge pull request #1748 from sennetconsortium/tjmadonna/1731-collect…

…ions-section Tjmadonna/1731 collections section
sennetconsortium · Nov 21, 2024 · b7572e8 · b7572e8
2 parents fae2280 + d7dc4eb
commit b7572e8
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Showing 7 changed files with 81 additions and 28 deletions.
diff --git a/src/components/custom/entities/Collections.jsx b/src/components/custom/entities/Collections.jsx
@@ -0,0 +1,29 @@
+import SenNetAccordion from "@/components/custom/layout/SenNetAccordion";
+import Card from 'react-bootstrap/Card';
+import ClipboardCopy from "@/components//ClipboardCopy";
+import {getEntityViewUrl} from "@/components/custom/js/functions";
+
+function Collections({ entityType, data }) {
+    const titleType = data.length > 1 ? 'Collections' : 'Collection';
+
+    const collectionsView = data.map((collection) =>
+        <span key={collection.uuid}>
+            <a href={getEntityViewUrl('Collection', collection.uuid, {})}>{collection.sennet_id}</a><ClipboardCopy text={collection.sennet_id}/>
+            &nbsp;
+        </span>
+    );
+
+    return (
+        <SenNetAccordion title='Associated Collections'>
+            <Card border={'0'}>
+                <Card.Body>
+                    <p className='fw-light fs-6'>This <code>{entityType}</code> is contained in the <code>{titleType}</code>&nbsp;
+                        {collectionsView}
+                    </p>
+                </Card.Body>
+            </Card>
+        </SenNetAccordion>
+    )
+}
+
+export default Collections
diff --git a/src/components/custom/entities/dataset/Upload.jsx b/src/components/custom/entities/dataset/Upload.jsx
@@ -1,26 +1,19 @@
-import React, {useContext, useEffect, useState} from 'react'
-import PropTypes from 'prop-types'
-import SenNetAccordion from "../../layout/SenNetAccordion";
+import SenNetAccordion from "@/components/custom/layout/SenNetAccordion";
 import Card from 'react-bootstrap/Card';
-import ClipboardCopy from "../../../ClipboardCopy";
-import {getEntityViewUrl} from "../../js/functions";
+import ClipboardCopy from "@/components//ClipboardCopy";
+import {getEntityViewUrl} from "@/components/custom/js/functions";
 
 function Upload({ data }) {
-    useEffect(() => {
-    }, [])
-
     return (
-        <>
-            <SenNetAccordion title={'Associated Upload'}>
-                <Card border={'0'}>
-                    <Card.Body>
-                    <p className='fw-light fs-6'>This <code>Dataset</code> is contained in the data <code>Upload</code>
-                        &nbsp;<a href={getEntityViewUrl('Upload', data.uuid, {})}>{data.sennet_id}</a><ClipboardCopy text={data.sennet_id}/></p>
-                    </Card.Body>
-                </Card>
-            </SenNetAccordion>
-        </>
+        <SenNetAccordion title={'Associated Upload'}>
+            <Card border={'0'}>
+                <Card.Body>
+                <p className='fw-light fs-6'>This <code>Dataset</code> is contained in the data <code>Upload</code>
+                    &nbsp;<a href={getEntityViewUrl('Upload', data.uuid, {})}>{data.sennet_id}</a><ClipboardCopy text={data.sennet_id}/></p>
+                </Card.Body>
+            </Card>
+        </SenNetAccordion>
     )
 }
 
-export default Upload
+export default Upload
diff --git a/src/context/AppContext.jsx b/src/context/AppContext.jsx
@@ -145,7 +145,8 @@ export const AppProvider = ({ cache, banners, children }) => {
     const hasPublicAccess = (data) => {
         let publicAccess = false
         if (data) {
-            publicAccess =  (eq(data.data_access_level, 'public') || eq(data.status, 'published'))
+            publicAccess = (eq(data.data_access_level, 'public') || eq(data.status, 'published')
+                    || ((eq(data.entity_type, 'Collection') || eq(data.entity_type, 'Epicollection')) && data.doi_url))
                 && !router.pathname.contains('edit')
         }
         return publicAccess

diff --git a/src/pages/api/protocol.js b/src/pages/api/protocol.js
@@ -4,7 +4,7 @@ import log from "loglevel";
 
 export default async function handler(req, res) {
     let baseProtocolUrl = 'https://www.protocols.io/api/v4/protocols/'
-    let protocolId = getProtocolId(decodeURIComponent(req.query.uri))[0]
+    let protocolId = getProtocolId(decodeURIComponent(req.query.uri))
     log.info(protocolId)
 
     await fetch(baseProtocolUrl + protocolId, {

diff --git a/src/pages/dataset.jsx b/src/pages/dataset.jsx
@@ -24,6 +24,7 @@ import WarningIcon from '@mui/icons-material/Warning'
 const AppFooter = dynamic(() => import("@/components/custom/layout/AppFooter"))
 const AppNavbar = dynamic(() => import("@/components/custom/layout/AppNavbar"))
 const Attribution = dynamic(() => import("@/components/custom/entities/sample/Attribution"))
+const Collections = dynamic(() => import("@/components/custom/entities/Collections"))
 const ContributorsContacts = dynamic(() => import("@/components/custom/entities/ContributorsContacts"))
 const CreationActionRelationship = dynamic(() => import("@/components/custom/entities/dataset/CreationActionRelationship"))
 const DataProducts = dynamic(() => import("@/components/custom/entities/dataset/DataProducts"))
@@ -64,7 +65,7 @@ function ViewDataset() {
                     setPrimaryDatasetInfo(primary)
                     setDatasetCategories(getAssaySplitData(primary))
                 } else {
-                    console.error('fetchEntityForMultiAssayInfo', primary.error)
+                    log.error('fetchEntityForMultiAssayInfo', primary.error)
                 }
                 break;
             }
@@ -107,7 +108,7 @@ function ViewDataset() {
                 setCitationData(citation)
 
                 for (const ancestor of ancestry.ancestors) {
-                    console.log(ancestor)
+                    log.debug(ancestor)
                     if ((ancestor.metadata && Object.keys(ancestor.metadata).length) || (ancestor.ingest_metadata && Object.keys(ancestor.ingest_metadata) && 'metadata' in ancestor.ingest_metadata)) {
                         setAncestorHasMetadata(true)
                         break
@@ -181,6 +182,13 @@ function ViewDataset() {
                                                        data-bs-parent="#sidebar">Upload</a>
                                                 </li>
                                             }
+                                            {data.collections && data.collections.length > 0 &&
+                                                <li className="nav-item">
+                                                    <a href="#Associated Collections"
+                                                       className="nav-link"
+                                                       data-bs-parent="#sidebar">Collections</a>
+                                                </li>
+                                            }
                                             {showVitessce &&
                                                 <li className="nav-item">
                                                     <a href="#Vitessce"
@@ -254,6 +262,9 @@ function ViewDataset() {
                                             {/*Upload*/}
                                             {data.upload && data.upload.uuid && <Upload data={data.upload}/>}
 
+                                            {/*Collection*/}
+                                            {data.collections && data.collections.length > 0 && <Collections entityType='Dataset' data={data.collections}/>}
+
                                             {/* Vitessce */}
                                             <SennetVitessce data={data}/>
 
@@ -275,8 +286,6 @@ function ViewDataset() {
                                             {/*Files*/}
                                             <FileTreeView data={data}/>
 
-
-
                                             {/*Contributors*/}
                                             {!!(data.contributors && Object.keys(data.contributors).length) &&
                                                 <ContributorsContacts title={'Contributors'} data={data.contributors}/>

diff --git a/src/pages/sample.jsx b/src/pages/sample.jsx
@@ -2,7 +2,6 @@ import dynamic from "next/dynamic";
 import React, {useContext, useEffect, useState} from "react";
 import {useRouter} from 'next/router';
 import log from "loglevel";
-import {getRequestHeaders} from "@/components/custom/js/functions";
 import {get_write_privilege_for_group_uuid, getAncestryData, getEntityData} from "@/lib/services";
 import AppContext from "@/context/AppContext";
 import Alert from 'react-bootstrap/Alert';
@@ -12,6 +11,7 @@ import {APP_ROUTES} from "@/config/constants";
 const AppFooter = dynamic(() => import("@/components/custom/layout/AppFooter"))
 const AppNavbar = dynamic(() => import("@/components/custom/layout/AppNavbar"))
 const Attribution = dynamic(() => import("@/components/custom/entities/sample/Attribution"))
+const Collections = dynamic(() => import("@/components/custom/entities/Collections"))
 const Description = dynamic(() => import("@/components/custom/entities/sample/Description"))
 const Header = dynamic(() => import("@/components/custom/layout/Header"))
 const Metadata = dynamic(() => import("@/components/custom/entities/Metadata"))
@@ -107,6 +107,13 @@ function ViewSample() {
                                                    className="nav-link"
                                                    data-bs-parent="#sidebar">Tissue</a>
                                             </li>
+                                            {data.collections && data.collections.length > 0 &&
+                                                <li className="nav-item">
+                                                    <a href="#Associated Collections"
+                                                       className="nav-link"
+                                                       data-bs-parent="#sidebar">Collections</a>
+                                                </li>
+                                            }
                                             <li className="nav-item">
                                                 <a href="#Provenance"
                                                    className="nav-link"
@@ -157,6 +164,9 @@ function ViewSample() {
                                                 <Tissue data={data}/>
                                             }
 
+                                            {/*Collection*/}
+                                            {data.collections && data.collections.length > 0 && <Collections entityType='Sample' data={data.collections}/>}
+
                                             {/*Provenance*/}
                                             {data &&
                                                 <Provenance nodeData={data}/>
@@ -193,4 +203,4 @@ function ViewSample() {
 }
 
 
-export default ViewSample
+export default ViewSample
diff --git a/src/pages/source.jsx b/src/pages/source.jsx
@@ -2,7 +2,7 @@ import dynamic from "next/dynamic";
 import React, {useContext, useEffect, useState} from "react";
 import {useRouter} from 'next/router';
 import log from "loglevel";
-import {eq, extractSourceMappedMetadataInfo, getRequestHeaders} from "@/components/custom/js/functions";
+import {eq, extractSourceMappedMetadataInfo} from "@/components/custom/js/functions";
 import {get_write_privilege_for_group_uuid, getAncestryData, getEntityData} from "@/lib/services";
 import AppContext from "@/context/AppContext";
 import Alert from 'react-bootstrap/Alert';
@@ -11,6 +11,7 @@ import {EntityViewHeader} from "@/components/custom/layout/entity/ViewHeader";
 const AppFooter = dynamic(() => import("@/components/custom/layout/AppFooter"))
 const AppNavbar = dynamic(() => import("@/components/custom/layout/AppNavbar"))
 const Attribution = dynamic(() => import("@/components/custom/entities/sample/Attribution"))
+const Collections = dynamic(() => import("@/components/custom/entities/Collections"))
 const Description = dynamic(() => import("@/components/custom/entities/sample/Description"))
 const Header = dynamic(() => import("@/components/custom/layout/Header"))
 const Metadata = dynamic(() => import("@/components/custom/entities/Metadata"))
@@ -103,6 +104,13 @@ function ViewSource() {
                                                    className="nav-link "
                                                    data-bs-parent="#sidebar">Summary</a>
                                             </li>
+                                            {data.collections && data.collections.length > 0 &&
+                                                <li className="nav-item">
+                                                    <a href="#Associated Collections"
+                                                       className="nav-link"
+                                                       data-bs-parent="#sidebar">Collections</a>
+                                                </li>
+                                            }
                                             <li className="nav-item">
                                                 <a href="#Provenance"
                                                    className="nav-link"
@@ -146,6 +154,9 @@ function ViewSource() {
                                                          labId={data.lab_source_id}
                                             />
 
+                                            {/*Collection*/}
+                                            {data.collections && data.collections.length > 0 && <Collections entityType='Source' data={data.collections}/>}
+
                                             {/*Provenance*/}
                                             {data &&
                                                 <Provenance nodeData={data}/>