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Additional user guide updates #283

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Nov 12, 2024
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5 changes: 2 additions & 3 deletions gen3/docs/blog/authors.yml
Original file line number Diff line number Diff line change
@@ -1,10 +1,9 @@
authors:
qureshi:
name: Jawad Qureshi
description: Lead Platform Engineer
description: Lead Platform Engineer, CTDS
avatar: https://github.com/jawadqur.png
elise:
name: Elise Castle
description: Platform Engineer - Gen3
url: https://github.com/EliseCastle23
description: Platform Engineer, CTDS
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I am curious why you are changing this from Gen3 to CTDS. Since this is all Gen3 documentation, and since I think the users will be more familiar with Gen3 than with CTDS (especially since we are inconsistent about CTDS vs CDIS) -- it feels like it would be better to use Gen3 . We can discuss more -- doesn't need to hold up merging this PR.

avatar: https://github.com/EliseCastle23.png
1 change: 1 addition & 0 deletions gen3/docs/blog/posts/gen3-laptop.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ date: 2023-09-13
slug: Gen3 on laptop
categories:
- Operator
- CTDS
tags:
- Kubernetes
- Minikube
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17 changes: 8 additions & 9 deletions gen3/docs/blog/posts/gen3-observability.md
Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
---
draft: false
slug: Observability
title: "Observability"
slug: observability
authors:
- elise
date: 2024-10-15
categories:
- Operator
- CTDS
tags:
- Observability
- Helm Chart
Expand All @@ -14,17 +18,14 @@ tags:
- Real User Monitoring (RUM)
- Metrics
- Log Aggregation
- Kubernetes
- Dashboards
- Kubernetes Monitoring
- Time-Series Database
- Alerting
- Frontend Monitoring
- Grafana Dashboards
- Open Source Monitoring
date: 2024-10-15
categories:
- Operator

---

# Deploying a Comprehensive Observability Stack with Helm
Expand All @@ -44,9 +45,7 @@ A log aggregation system designed to index and query logs with minimal resource

In this setup, Loki and Mimir are configured with internal ingress resources, enabling Alloy to send metrics and logs securely via VPC peering connections. Both Loki and Mimir write the ingested data to Amazon S3 for scalable and durable storage. This data can be queried and visualized through Grafana, which is hosted behind an internet-facing ingress. Access to Grafana can be restricted using CIDR ranges defined through the ALB ingress annotation: alb.ingress.kubernetes.io/inbound-cidrs: "cidrs". Additionally, the chart supports SAML authentication for Grafana, configured through the grafana.ini field, ensuring secure user access.

<p align="center">
<img src="Grafana.png" alt="Grafana Architecture" />
</p>
![Grafana architecutre](Grafana.png)


### Fips compliant images
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1 change: 1 addition & 0 deletions gen3/docs/blog/posts/k8s-for-dev.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ authors:
date: 2023-08-13
categories:
- Operator
- CTDS
slug: k8s for development
tags:
- Kubernetes
Expand Down
1 change: 1 addition & 0 deletions gen3/docs/blog/posts/k8s-productivity-tools.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ date: 2023-10-13
slug: k8s tools
categories:
- Operator
- CTDS
tags:
- Kubernetes
- Minikube
Expand Down
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23 changes: 19 additions & 4 deletions gen3/mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -104,12 +104,14 @@ nav:

theme:
favicon: img/Gen3-3.ico
logo: img/Gen3_Logo-01_blue_no_commons.png
logo: img/gen3_new_logo_white.svg
name: material
features:
- navigation.footer

custom_dir: overrides
palette:
- primary: black


# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
Expand All @@ -128,8 +130,6 @@ theme:
- navigation.indexes
- navigation.tracking
- navigation.path
extra_css:
- stylesheets/extra.css
use_directory_urls: true
markdown_extensions:
- admonition
Expand All @@ -145,8 +145,23 @@ plugins:
- tags
- blog:
enabled: true
authors: true
authors_file: blog/authors.yml
blog_dir: blog
blog_toc: true
- mkdocs-video:
is_video: True
extra:
social:
- icon: fontawesome/brands/linkedin
link: https://www.linkedin.com/company/center-for-translational-data-science/
- icon: fontawesome/brands/x-twitter
link: https://x.com/UChicagoCTDS
- icon: fontawesome/brands/x-twitter
link: https://x.com/gen3data
- icon: fontawesome/brands/slack
link: https://docs.google.com/forms/d/e/1FAIpQLSczyhhOXeCK9FdVtpQpelOHYnRj1EAq1rwwnm9q6cPAe5a7ug/viewform
- icon: fontawesome/brands/youtube
link: https://www.youtube.com/channel/UCMCwQy4EDd1BaskzZgIOsNQ/featured
- icon: fontawesome/brands/github
link: https://github.com/uc-cdis
106 changes: 106 additions & 0 deletions gen3/overrides/partials/footer.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
<!--
Copyright (c) 2016-2024 Martin Donath <[email protected]>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to
deal in the Software without restriction, including without limitation the
rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
sell copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
IN THE SOFTWARE.
-->

<!-- Footer -->
<footer class="md-footer">

<!-- Link to previous and/or next page -->
{% if "navigation.footer" in features %}
{% if page.previous_page or page.next_page %}
{% if page.meta and page.meta.hide %}
{% set hidden = "hidden" if "footer" in page.meta.hide %}
{% endif %}
<nav
class="md-footer__inner md-grid"
aria-label="{{ lang.t('footer') }}"
{{ hidden }}
>

<!-- Link to previous page -->
{% if page.previous_page %}
{% set direction = lang.t("footer.previous") %}
<a
href="{{ page.previous_page.url | url }}"
class="md-footer__link md-footer__link--prev"
aria-label="{{ direction }}: {{ page.previous_page.title | e }}"
>
<div class="md-footer__button md-icon">
{% set icon = config.theme.icon.previous or "material/arrow-left" %}
{% include ".icons/" ~ icon ~ ".svg" %}
</div>
<div class="md-footer__title">
<span class="md-footer__direction">
{{ direction }}
</span>
<div class="md-ellipsis">
{{ page.previous_page.title }}
</div>
</div>
</a>
{% endif %}

<!-- Link to next page -->
{% if page.next_page %}
{% set direction = lang.t("footer.next") %}
<a
href="{{ page.next_page.url | url }}"
class="md-footer__link md-footer__link--next"
aria-label="{{ direction }}: {{ page.next_page.title | e }}"
>
<div class="md-footer__title">
<span class="md-footer__direction">
{{ direction }}
</span>
<div class="md-ellipsis">
{{ page.next_page.title }}
</div>
</div>
<div class="md-footer__button md-icon">
{% set icon = config.theme.icon.next or "material/arrow-right" %}
{% include ".icons/" ~ icon ~ ".svg" %}
</div>
</a>
{% endif %}
</nav>
{% endif %}
{% endif %}

<!-- Further information -->
<div class="md-footer-meta md-typeset">
<div class="md-footer-meta__inner md-grid">
{% include "partials/copyright.html" %}

<!-- Custom link to Center for Translational Data Science -->
<div class="md-footer__link" style="vertical-align: middle; padding-bottom: 10px;">
<a href="https://ctds.uchicago.edu/" target="_blank" rel="noopener noreferrer">
Center for Translational Data Science
</a>
</div>
<!-- End of custom link -->

<!-- Social links -->
{% if config.extra.social %}
{% include "partials/social.html" %}
{% endif %}
</div>
</div>
</footer>
78 changes: 78 additions & 0 deletions gen3/overrides/partials/header.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
{#-
This file was automatically generated - do not edit
-#}
{% set class = "md-header" %}
{% if "navigation.tabs.sticky" in features %}
{% set class = class ~ " md-header--shadow md-header--lifted" %}
{% elif "navigation.tabs" not in features %}
{% set class = class ~ " md-header--shadow" %}
{% endif %}
<header class="{{ class }}" data-md-component="header">
<nav class="md-header__inner md-grid" aria-label="{{ lang.t('header') }}">
<a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}" class="md-header__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
{% include "partials/logo.html" %}
</a>
<label class="md-header__button md-icon" for="__drawer">
{% set icon = config.theme.icon.menu or "material/menu" %}
{% include ".icons/" ~ icon ~ ".svg" %}
</label>
<div class="md-header__title" data-md-component="header-title">
<div class="md-header__ellipsis">
<div class="md-header__topic">
<span class="md-ellipsis">
{{ config.site_name }}
</span>
</div>
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">
{% if page.meta and page.meta.title %}
{{ page.meta.title }}
{% else %}
{{ page.title }}
{% endif %}
</span>
</div>
</div>
</div>
{% if config.theme.palette %}
{% if not config.theme.palette is mapping %}
{% include "partials/palette.html" %}
{% endif %}
{% endif %}
{% if not config.theme.palette is mapping %}
{% include "partials/javascripts/palette.html" %}
{% endif %}
{% if config.extra.alternate %}
{% include "partials/alternate.html" %}
{% endif %}

<!-- Custom link to Gen3.org (with an external link icon) -->
<div style="margin-right: 10px; display: flex; align-items: center;">
<h1 href="https://gen3.org/" class="md-header__button" aria-label="Gen3.org" target="_blank" rel="noopener noreferrer" style="display: flex; align-items: center;">
Gen3.org
<!-- Insert your preferred external link icon here -->
<svg xmlns="http://www.w3.org/2000/svg" width="1em" height="1em" style="margin-left: 5px;" viewBox="0 0 16 16"><g fill="currentColor" fill-rule="evenodd"><path d="M8.636 3.5a.5.5 0 0 0-.5-.5H1.5A1.5 1.5 0 0 0 0 4.5v10A1.5 1.5 0 0 0 1.5 16h10a1.5 1.5 0 0 0 1.5-1.5V7.864a.5.5 0 0 0-1 0V14.5a.5.5 0 0 1-.5.5h-10a.5.5 0 0 1-.5-.5v-10a.5.5 0 0 1 .5-.5h6.636a.5.5 0 0 0 .5-.5"/><path d="M16 .5a.5.5 0 0 0-.5-.5h-5a.5.5 0 0 0 0 1h3.793L6.146 9.146a.5.5 0 1 0 .708.708L15 1.707V5.5a.5.5 0 0 0 1 0z"/></g></svg>
</h1>
</div>
<!-- End of custom link to Gen3.org with an external link icon -->


{% if "material/search" in config.plugins %}
<label class="md-header__button md-icon" for="__search">
{% set icon = config.theme.icon.search or "material/magnify" %}
{% include ".icons/" ~ icon ~ ".svg" %}
</label>
{% include "partials/search.html" %}
{% endif %}
{% if config.repo_url %}
<div class="md-header__source">
{% include "partials/source.html" %}
</div>
{% endif %}
</nav>
{% if "navigation.tabs.sticky" in features %}
{% if "navigation.tabs" in features %}
{% include "partials/tabs.html" %}
{% endif %}
{% endif %}
</header>
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