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Chore/update brhstaging #2247
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Chore/update brhstaging #2247
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a0f8dbc
switch frontend config
mfshao 0fe0c8b
update helm chart branch
mfshao dc850d5
test on branch
mfshao 5b111c4
add frontendroot
mfshao 7da7e2f
put gen3-helm back
mfshao 0e9c638
Merge branch 'master' into chore/update-brhstaging
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9 changes: 9 additions & 0 deletions
9
brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/403.json
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| @@ -0,0 +1,9 @@ | ||
| { | ||
| "content": [ | ||
| { | ||
| "type": "markdown", | ||
| "text": "# 403: Not Authorized \n You are not authorized to access this page. If you believe this is an error, contact your administrator or support.", | ||
| "className": "text-center" | ||
| } | ||
| ] | ||
| } |
9 changes: 9 additions & 0 deletions
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brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/404.json
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| @@ -0,0 +1,9 @@ | ||
| { | ||
| "content": [ | ||
| { | ||
| "type": "markdown", | ||
| "text": "# 404: Page Not Found \n Sorry, we couldn't find the page you were looking for.", | ||
| "className": "text-center" | ||
| } | ||
| ] | ||
| } |
115 changes: 115 additions & 0 deletions
115
brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/analysisTools.json
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|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| { | ||
| "type": "breadcrumb", | ||
| "label": "Example Analysis", | ||
| "description": "The Jupyter notebooks contained in this notebook viewer pull data from various sources to generate and output useful tables, charts, graphs, and models. Each notebook is static, meaning the data being used by the notebooks is not updated in real time. Executable versions of these notebooks are also available in the 'Tutorials' Gen3 Workspace Image.", | ||
| "tools": [ | ||
| { | ||
| "title": "Multi-Container Nextflow Tutorial", | ||
| "description": "In this notebook, we will set up and explain each file in a Nextflow workflow which uses Python scripts. Our workflow consists of two Python scripts that are each executed in a different Conda environment.", | ||
| "image": "/dashboard/Public/notebooks/nextflow_logo.png", | ||
| "href": "/dashboard/Public/notebooks/multi_container_nextflow.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Nextflow Proteome Data Commons (PDC) Clustergram", | ||
| "description": "In this notebook, we demonstrate how to retrieve, process, and visualize protein relative expression data from the PDC API with Nextflow. We illustrate use of Nextflow features such as channels, parameters, and environment and configuration files", | ||
| "image": "/dashboard/Public/notebooks/nextflow_logo.png", | ||
| "href": "/dashboard/Public/notebooks/PDC_clustergram_nextflow.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "JCOIN MOUD Accessibility Analysis", | ||
| "description": "In this Jupyter notebook, we used the data from the OEPS database to analyze the Medication for Opioid Use Disorder (MOUD) providers accessibility at state and county level across the United States.", | ||
| "image": "/dashboard/Public/notebooks/JCOIN_MOUD_accessibility_jupyter_notebook_BRH.png", | ||
| "href": "/dashboard/Public/notebooks/JCOIN_MOUD_accessibility_jupyter_notebook_BRH.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Graphing the Pandemic Era: Unraveling Opioid Treatment Policy Shifts Amidst COVID-19", | ||
| "description": "In this notebook we use data from NIDA-PDAPS, hosted on the JCOIN Data Commons, to visualize three pandemic-era changes in opioid treatment policy at state levels across the US.", | ||
| "image": "/dashboard/Public/notebooks/JCOIN_PDAPS_Public_Policy_Changes.png", | ||
| "href": "/dashboard/Public/notebooks/JCOIN_PDAPS_Public_Policy_Changes_v2.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Proteome Data Commons (PDC) Clustergram", | ||
| "description": "This notebook attempts to demonstrate the use the PDC API to retrieve the associated clinical metadata for all samples, format the data for analysis using pandas and cluster and visualize the data using the Seaborn clustermap package.", | ||
| "image": "/dashboard/Public/notebooks/PDC_clustergram.png", | ||
| "href": "/dashboard/Public/notebooks/PDC_clustergram.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "MIDRC CT Scan", | ||
| "description": "In this notebook we demonstrate how to pull in MIDRC CT scan data, how to view the CT scan images, how to convert the image file format, and how to extract clinical data and file metadata from the DICOM file headers.", | ||
| "image": "/dashboard/Public/notebooks/MIDRC_CT_Scan_Demo.png", | ||
| "href": "/dashboard/Public/notebooks/MIDRC_CT_Scan_Demo.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Data Exploration using Python of Framingham Heart Study Teaching Dataset", | ||
| "description": "In this Python tutorial, we demonstrate how to pull the Framingham teaching dataset from the BioData Catalyst data commons into a BRH workspace, and perform data exploration and visualization using Python packages.", | ||
| "image": "/dashboard/Public/notebooks/BDC_Biolincc_Framingham_study_exploration.png", | ||
| "href": "/dashboard/Public/notebooks/BDC_Biolincc_Framingham_study_exploration.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Data Exploration using R of Framingham Heart Study Teaching Dataset", | ||
| "description": "In this tutorial, using R code, we will demonstrate how to pull the object file of the Framingham teaching dataset from the BioData Catalyst data commons into a BRH workspace and perform data exploration and visualization using R packages.", | ||
| "href": "/dashboard/Public/notebooks/BDC_Framingham_study_exploration_R.html", | ||
| "image": "/dashboard/Public/notebooks/BDC_Framingham_study_exploration_R.png", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Data Exploration of CAMP Study Teaching Dataset", | ||
| "description": "In this tutorial, we demonstrate how to pull the object file of CAMP study from BioData Catalyst data commons into a BRH workspace, and perform data exploration and visualization using Python packages.", | ||
| "image": "/dashboard/Public/notebooks/BDC_CAMP_study_exploration_notebook.png", | ||
| "href": "/dashboard/Public/notebooks/BDC_CAMP_study_exploration_notebook.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "MIDRC Open-R1 Clinical Data Analysis", | ||
| "description": "In this notebook we will visualize the distribution of subjects accross a variety demographics and their COVID-19 status in the Open-R1 dataset from The Medical Imaging and Data Resource Center.", | ||
| "image": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.png", | ||
| "href": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.html", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Identification of Potential Drug Targets of Inflammatory Bowel Disease", | ||
| "description": "This notebook demonstrates an approach to query data in EpiGraphDB to prioritize potential alternative drug targets in the same protein-protein interaction network for Inflammatory Bowel Disease", | ||
| "href": "/dashboard/Public/notebooks/IBD_notebook.html", | ||
| "image": "/dashboard/Public/notebooks/IBD_notebook.png", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| }, | ||
| { | ||
| "title": "Predictive Insights into Heart Health: Investigating the Framingham Heart Study Dataset", | ||
| "description": "In this Jupyter notebook, we'll delve into the Framingham dataset, analyzing its contents, performing exploratory data analysis, and leveraging linear and logistic regression.", | ||
| "href": "/dashboard/Public/notebooks/BDC_Framingham_predictive_insights.html", | ||
| "image": "/dashboard/Public/notebooks/BDC_Framingham_predictive_insights.png", | ||
| "type": "notebook", | ||
| "icon": "/images/apps/icons/jupyter.svg", | ||
| "btnText": "View" | ||
| } | ||
| ] | ||
| } |
14 changes: 14 additions & 0 deletions
14
brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/authz.json
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| @@ -0,0 +1,14 @@ | ||
| { | ||
| "routes": { | ||
| "/Workspace": { | ||
| "loginRequired": true, | ||
| "authz": ["/workspace"] | ||
| }, | ||
| "/Profile": { | ||
| "loginRequired": true | ||
| }, | ||
| "*": { | ||
| "loginRequired": false | ||
| } | ||
| } | ||
| } |
10 changes: 10 additions & 0 deletions
10
brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/colors.json
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|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| { | ||
| "primary": "#3283C8", | ||
| "secondary": "#3283C8", | ||
| "accent": "#b75113", | ||
| "base": "#c0c0c0", | ||
| "accentWarm": "#25869b", | ||
| "accentCool": "#1f839b", | ||
| "chart": "#0d95A1", | ||
| "table": "#c0c0c0" | ||
| } |
32 changes: 32 additions & 0 deletions
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brhprod/brhstaging.data-commons.org/values/frontend/config/gen3/dataLibrary.json
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| { | ||
| "useAPI": true, | ||
| "actions": [ | ||
| { | ||
| "id": "exportTerra", | ||
| "label": "Export to Terra", | ||
| "rules": [ | ||
| { | ||
| "field": "type", | ||
| "operator": "equals", | ||
| "value": "terraform" | ||
| }, | ||
| { | ||
| "field": "type", | ||
| "operator": "count", | ||
| "value": 1 | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "id": "exportZip", | ||
| "label": "Export to ZIP", | ||
| "rules": [ | ||
| { | ||
| "field": "type", | ||
| "operator": "equals", | ||
| "value": "csv" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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👍 did this manually already.
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I'm actually not sure brh staging is on
feat/deployment-canary. Does that still mean anything?I'm tempting to switch it back to just
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no longer seeing that branch in gen3-helm, will put it back to master