diff --git a/.env.development b/.env.development
index 52a3fdf..41384b0 100644
--- a/.env.development
+++ b/.env.development
@@ -1,6 +1,6 @@
GEN3_COMMONS_NAME=gen3
-NEXT_PUBLIC_GEN3_API=https://localhost:3010
-NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010
+NEXT_PUBLIC_GEN3_API=https://qa-mickey.planx-pla.net/
+NEXT_PUBLIC_GEN3_DOMAIN=https://qa-mickey.planx-pla.net/
# set these if you want to use different endpoints
#NEXT_PUBLIC_GEN3_GUPPY_API=
diff --git a/config/gen3/landingPage.json b/config/gen3/landingPage.json
index 9f1d633..389fe06 100644
--- a/config/gen3/landingPage.json
+++ b/config/gen3/landingPage.json
@@ -2,31 +2,15 @@
"body": [
{
"title": {
- "text": "Gen3 Data Platform",
- "level": 2
+ "text": "VA Data Commons",
+ "level": 1
}
},
{
"splitarea": {
"left": [
{
- "text": "The Gen3 Data Platform is a single web interface which allows visitors to discover, access and analyze data. Making data easily findable enables secondary, cross-study analyses, promotes dissemination of research and accelerates new discoveries."
- },
- {
- "link": {
- "href": "/discovery",
- "linkType": "portal",
- "text": "Explore Gen3 Data"
- }
- },
- {
- "text": "The Gen3 platform consists of open-source software services that support the emergence of healthy data ecosystems by enabling the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 aims to accelerate and democratize the process of scientific discovery by making it easy to manage, analyze, harmonize, and share large and complex datasets in the cloud."
- },
- {
- "link": {
- "href": "https://gen3.datacommons.io",
- "text": "Learn More"
- }
+ "text": "The VA Data Commons supports the research and analysis of US military Veteran medical and genomic data and aims to accelerate scientific discovery and development of therapies, diagnostic tests, and other technologies for improving the lives of Veterans and beyond. The data commons features GWAS analyses on harmonized data."
}
],
"right": [
@@ -38,35 +22,6 @@
}
]
}
- },
- {
- "break": "standard"
- },
- {
- "cardsArea": {
- "title": "",
- "cards": [
- {
- "icon": "MdOutlineSearch",
- "bodyText": "Search studies and related datasets for download or analysis in a workspace.",
- "btnText": "Discover",
- "href": "/Discovery",
- "linkType": "portal"
- },
- {
- "icon": "MdOutlineBarChart",
- "bodyText": "Explore Tutorials and Example Analysis.",
- "btnText": "Analyze",
- "href": "/resource-browser",
- "linkType": "portal"
- }
- ]
- }
- },
- {
- "quoteArea": {
- "quote": "Our vision is a world in which researchers have ready access to the data needed and the tools required to make data-driven discoveries that increase our scientific knowledge and improve the quality of life."
- }
}
]
}
diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json
index d04260e..eb78261 100644
--- a/config/gen3/navigation.json
+++ b/config/gen3/navigation.json
@@ -6,72 +6,41 @@
"navigationPanel": "bg-base-max text-primary"
},
"logo": {
- "src": "/icons/gen3-dark.svg",
- "width": 120,
+ "src": "/images/logo.png",
+ "width": 300,
"height": 60,
"href": "/"
},
"items": [
{
- "icon": "gen3:query",
- "href": "/Discovery",
- "name": "Discovery",
- "tooltip": "Use free-text search and tags to rapidly find relevant studies."
- },
- {
- "icon": "gen3:dictionary",
- "href": "/DataDictionary",
- "name": "Dictionary",
- "tooltip": "The Data Dictionary serves to inform the data model and is updated as new data is ingested."
- },
- {
- "icon": "gen3:exploration",
- "href": "/Explorer",
- "name": "Exploration",
- "tooltip": "The Exploration Page enables discovery of the data at the subject level and features a cohort builder."
- },
- {
- "icon": "gen3:query",
- "href": "/Query",
- "name": "Query",
- "tooltip": "Query the databases using GraphiQL."
+ "icon": "gen3:workspace",
+ "href": "/#hostname#workspace/",
+ "name": "Workspace",
+ "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources."
},
{
"icon": "gen3:analysis",
"href": "/resource-browser",
- "name": "Analysis",
+ "name": "Apps",
"tooltip": "Learn how to use Jupyter Notebooks to explore and visualize data available by running a tutorial notebook, or use one of these examples as a launching point for your own custom analysis."
},
- {
- "icon": "gen3:workspace",
- "href": "/#hostname#workspace/",
- "name": "Workspace",
- "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources."
- },
{
"icon": "gen3:profile",
"href": "/Profile",
"name": "Profile",
"tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services."
- },
- {
- "icon": "gen3:profile",
- "href": "/DataLibrary",
- "name": "Data Library",
- "tooltip": "library of data"
}
]
},
"topBar": {
"items": [
{
- "rightIcon": "gen3:upload",
- "href": "/submission",
- "name": "Browse Data"
+ "href": "https://uc-cdis.github.io/vadc-mkdocs/",
+ "name": "Help and Guidance"
},
{
- "href": "https://gen3.org/resources/user/",
- "name": "Documentation"
+ "href": "mailto:vadc@lists.uchicago.edu",
+ "name": "Email Support"
}
],
"loginButtonVisibility": "visible"
diff --git a/config/icons/gen3.json b/config/icons/gen3.json
index 26d4c6a..a3366da 100644
--- a/config/icons/gen3.json
+++ b/config/icons/gen3.json
@@ -1,6 +1,6 @@
{
"prefix": "gen3",
- "lastModified": 1730144270,
+ "lastModified": 1734543795,
"icons": {
"aisearch": {
"body": "",
@@ -31,13 +31,11 @@
},
"chevron-expand": {
"body": "",
- "width": 512,
- "height": 512
+ "width": 512
},
"comparison": {
"body": "",
- "width": 512,
- "height": 512
+ "width": 512
},
"datafile": {
"body": "",
@@ -49,70 +47,13 @@
"width": 489.709,
"height": 489.709
},
- "dictionary-icon-administrative": {
- "body": ""
- },
- "dictionary-icon-analysis": {
- "body": "",
- "height": 21
- },
- "dictionary-icon-biospecimen": {
- "body": ""
- },
- "dictionary-icon-clinical": {
- "body": ""
- },
- "dictionary-icon-clinical-assessment": {
- "body": ""
- },
- "dictionary-icon-data-file": {
- "body": ""
- },
- "dictionary-icon-data-observations": {
- "body": ""
- },
- "dictionary-icon-default": {
- "body": "",
- "height": 21
- },
- "dictionary-icon-experimental-methods": {
- "body": ""
- },
- "dictionary-icon-imaging": {
- "body": ""
- },
- "dictionary-icon-index-file": {
- "body": ""
- },
- "dictionary-icon-medical-history": {
- "body": ""
- },
- "dictionary-icon-metadata": {
- "body": ""
- },
- "dictionary-icon-notation": {
- "body": ""
- },
- "dictionary-icon-study-administration": {
- "body": ""
- },
- "dictionary-icon-subject-characteristics": {
- "body": ""
- },
- "dot": {
- "body": "",
- "width": 256,
- "height": 256
- },
"download": {
"body": "",
- "width": 24,
"height": 24
},
"exploration": {
"body": "",
- "width": 512,
- "height": 512
+ "width": 512
},
"gen3": {
"body": "",
@@ -136,19 +77,22 @@
},
"logincircle": {
"body": "",
- "width": 24,
"height": 24
},
- "open-in-modal": {
- "body": "",
- "width": 24,
- "height": 24
+ "not-found": {
+ "body": "",
+ "width": 302,
+ "height": 203
},
"notebook": {
"body": "",
"width": 682.667,
"height": 682.667
},
+ "open-in-modal": {
+ "body": "",
+ "height": 24
+ },
"profile": {
"body": "",
"width": 512.001,
@@ -161,20 +105,17 @@
},
"upload": {
"body": "",
- "width": 24,
"height": 24
},
"user": {
"body": "",
- "width": 448,
- "height": 512
+ "width": 448
},
"workspace": {
"body": "",
- "width": 512,
- "height": 512
+ "width": 512
}
},
- "width": 20,
- "height": 20
+ "width": 24,
+ "height": 512
}
diff --git a/public/icons/gitops-favicon.ico b/public/icons/gitops-favicon.ico
new file mode 100644
index 0000000..62922b7
Binary files /dev/null and b/public/icons/gitops-favicon.ico differ
diff --git a/public/images/logo.png b/public/images/logo.png
new file mode 100644
index 0000000..14d4004
Binary files /dev/null and b/public/images/logo.png differ