Merge pull request #74 from gf-dcc/updates

random updates

blog/2024-02-20.md

@@ -0,0 +1,13 @@
+---
+slug: gray-foundation-summit
+title: Gray Foundation hosts researchers and DCC in NYC Summit
+
+authors: [Christina]
+tags: [summit, events]
+---
+
+In an inspiring gathering of minds and missions, researchers from approximately 14 institutions recently came together to discuss their advancements and plan for the year ahead in the battle to prevent ovarian and breast cancer linked to BRCA mutations.
+Thanks to Jon and Mindy Gray along with the Gray Foundation team who put together a fantastic event. 
+
+![Alt text](<IMG_6555 (1).JPEG>) 
+![Alt text](<IMG_5047 (2).jpg>)

docs/data annotation support/_category_.json

@@ -1,5 +1,5 @@
 {
-  "label": "Data Annotation Support",
+  "label": "Data Standards",
   "position": 4,
   "collapsible": true,
   "collapsed": true,

docs/data sharing and access policies/overview.md

@@ -2,7 +2,7 @@
 sidebar_position: 1
 ---
 
-# Understanding Governance
+# Governance Policies
 
 Data governance involves managing data access and availability effectively.
 

docs/faq.md

@@ -11,7 +11,7 @@ sidebar_position: 5
 - [Data Storage](#data-storage)
 - [Data Sharing](#data-sharing)
 - [About cBioportal](#about-cbioportal)
-- [Using Synapse/Sage Bionetworks Resources](#using-synapse-sage-bionetworks-resources)
+- [Using Synapse/Sage Bionetworks Resources](#using-synapsesage-bionetworks-resources)
 
 </details>
 

docs/intro.mdx

@@ -61,6 +61,3 @@ end
     P3 ==> L;
         ```
 </center>
-
-Typical NF projects often follow a similar timeline, starting with data sharing plans and progressing through phases of data validation, documentation, and a dedicated data portal. These projects ultimately reach Phase 3, where their data becomes accessible to the public, facilitating collaboration and research.
-

docs/onboarding/_category_.json

@@ -1,5 +1,5 @@
 {
-  "label": "Introduction - Basics",
+  "label": "Introduction to Synapse",
   "position": 2,
   "collapsible": true,
   "collapsed": false,

docs/onboarding/annotate.md

@@ -20,31 +20,16 @@ Here's are examples of the google sheets that are generated for common assays:
 
 These templates ensure that your data is well-documented and organized, making it easier for you to manage and share your research.
 
-### 🛠️ Troubleshooting 
+## 🛠️ Troubleshooting Tips
 
-<details>
-<summary> I cannot see my project or folder  </summary>
+### Can't Find Your Project or Folder?
+This issue often arises from permission settings. Reach out to us for assistance in getting your account properly set up.
 
-This is usually a permissions issue. Please contact us to get your account added.
+### Missing a Suitable Template for Your Data?
+Typically, an appropriate template should be available. If not, let us know so we can provide a suitable template for you.
 
-</details>
-<details>
-<summary> I do not see a template that is a good fit for my data </summary>
+### Experiencing App Freezes or Crashes?
+Please inform the DCC about this issue. We will coordinate with our technical team to resolve it as soon as possible.
 
-Usually the right template should already exist. Contact us and we'll add the right template.
-
-</details>
-
-<details>
-<summary> The app hangs or crashes </summary>
-
-Contact the DCC and we'll contact the tooling team for troubleshooting.
-
-</details>
-
-<details>
-<summary> I have a validation issue </summary>
-
-Check the validation error messages, and if it is confusing or you disagree, please contact the DCC.
-
-</details>
+### Encountering Validation Errors?
+First, review the validation error messages carefully. If anything is unclear or you believe there's a mistake, please get in touch with the DCC for further assistance.

docs/working group meetings/clinical-data-standards.mdx

@@ -3,11 +3,7 @@ import TabItem from '@theme/TabItem';
 
 # Portal Design Working Group
 
+[November 2023 - Current] 
 The focus of the Portal Design Working Group is to collaboratively brainstorm strategies for enhancing data discoverability, accessibility, interoperability, and reusability. Within this working group, our objectives include improving our existing portal and sharing valuable insights on how data can be effectively repurposed. This may include demonstrating methods for seamlessly transferring data to external analysis tools.
 All persons affiliated the Gray Foundation atlas are encouraged to attend. 
-
-#### Meeting Notes:
-
-- [Nov 2, 2023 Summary](https://docs.google.com/document/d/1KpUYz-yOqJ3Zrr6ZZSvg_HXsIL3oeV3_VwNeUUkzN78/edit#heading=h.wdrdbgqvrne)
-- Dec 7, 2023 Summary
-- Jan 4, 2024 Summary
+This working group meets on the first Thursday of the month at 3pm EST. For more information, please email [email protected] 

docusaurus.config.js

@@ -138,6 +138,12 @@ const config = {
         ],
         copyright: `Copyright © ${new Date().getFullYear()} Sage Bionetworks, Built with Docusaurus.`,
       },
+      algolia: {
+        appId: '8KBY934MOI',
+        apiKey: 'd1fdceacdb284264b8094eb1f9bfedcd',
+        indexName: 'graybrcaatlas',
+        contextualSearch: true, // Optional, but useful for versioned docs
+      },
       prism: {
         theme: lightCodeTheme,
         additionalLanguages: ['bash', 'diff', 'json'],

package.json

@@ -14,9 +14,11 @@
     "write-heading-ids": "docusaurus write-heading-ids"
   },
   "dependencies": {
-    "@docusaurus/core": "^3.0.0",
-    "@docusaurus/preset-classic": "^3.0.0",
-    "@docusaurus/theme-mermaid": "^3.0.0",
+    "@docsearch/js": "3",
+    "@docsearch/react": "3",
+    "@docusaurus/core": "^3.1.1",
+    "@docusaurus/preset-classic": "^3.1.1",
+    "@docusaurus/theme-mermaid": "^3.1.1",
     "@mdx-js/react": "^3.0.0",
     "clsx": "^1.2.1",
     "mermaid": "^10.6.1",
@@ -27,8 +29,8 @@
     "react-dom": "^18.2.0"
   },
   "devDependencies": {
-    "@docusaurus/module-type-aliases": "^3.0.0-beta.0",
-    "@docusaurus/tsconfig": "3.0.0-beta.0",
+    "@docusaurus/module-type-aliases": "^3.1.1",
+    "@docusaurus/tsconfig": "^3.1.1",
     "@types/react": "^18.2.29",
     "typescript": "~5.2.2"
   },