docs: tag removal and side navigation

content/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md

@@ -8,9 +8,9 @@ Each data request includes a text file called `SAMPLE_INFO.txt` that provides a
 
 ### Definitions
 
-Below are the set of tags which may exist for any given file in St. Jude Cloud.
-Tags with `sj` prepended are required fields.
-Tags with `attr` prepended are information queried from the physician or research team’s records at the time of sample submission to St. Jude Cloud and are considered optional, as the level of information gathered for each sample varies.
+Below are the set of attributes which may exist for any given file in St. Jude Cloud.
+Properties with `sj` prepended are required fields.
+Properties with `attr` prepended are information queried from the physician or research team’s records at the time of sample submission to St. Jude Cloud and are considered optional, as the level of information gathered for each sample varies.
 
 | Property                          | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 |-----------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

content/4.pecan/1.overview/1.getting-started.md

@@ -4,40 +4,40 @@ navigation:
   title: Getting Started
 ---
 
-The PeCan platform presents curated pediatric cancer genomics data including variants, mutational signatures, and gene expression data in addition to histological slide images* from ~9000 hematological, CNS, and non-CNS solid tumor patient samples.
+The PeCan platform presents curated pediatric cancer genomics data including variants, mutational signatures, and gene expression data in addition to histological slide images from over 11,000 hematological, CNS, and non-CNS solid tumor patient samples.
 
 Data can be explored via a series of data facets containing both retrospective and prospective study cohorts from St. Jude Children's Research Hospital and other trusted institutions and research centers around the world such as [TARGET](https://ocg.cancer.gov/programs/target), [DKFZ](https://www.dkfz.de/en/index.html), and many others.
 Learn more about the data [here](/pecan/overview/methods-and-data).
-**Note that a number of histological slide images are currently embargoed until publication of the associated study.*
+
 
 ![logos](/img/pecan/overview/getting-started/logos.png)
 
 ## Home page
 
 The [PeCan home page](https://pecan.stjude.cloud/) showcases key components for each of the 4 data facets --Variants, Mutational Signatures, Expression, and Histology--, and the tool: PIE (Pediatric Cancer **P**athogenicity variant **I**nformation **E**xchange).
 
-To get started (**Figure 1**), click our navigational membrane which navigates the user to our sunburst and data facets or search a gene or variant.
+To get started (**Figure 1**), click our navigational membrane which navigates the user to our Diagnosis Search and data facets or search by a gene, variant or diagnosis in the search bar.
 
 ![PeCan Home](/img/pecan/overview/getting-started/home.png)
 
 **Figure 1: Home Page.**
 A user can become familiar by reading the key components that is offered in the PeCan Knowledge Base.
 Additionally, a user can navigate by using our navigational membrane or begin searching a gene or variant of interest.
 
-## Sunburst
+## Diagnosis Search
 
 The sunburst plot gives an at-a-glance disease distribution and disease hierarchy where all samples have been mapped to a custom ontology (**Figure 2**).
 This interactive interface updates as a user selects a diagnoses or subtype within in the sunburst.
 
 The diseases are categorized in three main root categories: **1)** HM -Hematopoietic Malignancies, **2)** BT -Brain Tumor, and **3)** ST -Solid Tumor.
-A user is encouraged to navigate via a subtype-centric experience by selecting a subtype and then navigate to each data facet for that available data.
+Users are encouraged to navigate via a subtype-centric experience by selecting a subtype and then navigate to each data facet for that available data.
 This will enable custom interface views per data facet based on the sunburst selection.
-Alternatively, a user can explore all of the available data within a data facet by clicking directly on the data facet icon instead of filtering by subtype on the sunburst.
+Alternatively, a user can explore all of the available data within a data facet by clicking directly on the data facet icon from the side navigation.
 
 ![PeCan Sunburst](/img/pecan/overview/getting-started/pecan.png)
 
-**Figure 2: Sunburst Interface.**
-A user is able to filter by diagnoses and/or subtype by selecting the interactive sunburst or by navigating directly into a data facet for the available data.
+**Figure 2: Diagnosis Search Interface and Facet Navigation**
+A user is able to filter by diagnoses and/or subtype by selecting the interactive sunburst or by navigating directly into a data facet for the available data by using the side navigation.
 
 ## Data Facets explained
 

deployment/preview/pr135/app.yaml

@@ -0,0 +1,87 @@
+apiVersion: helm.toolkit.fluxcd.io/v2beta1
+kind: HelmRelease
+metadata:
+  name: docs
+  namespace: docs-pr135
+spec:
+  interval: 30m
+  chart:
+    spec:
+      chart: generic
+      version: 1.1.x
+      sourceRef:
+        kind: HelmRepository
+        name: stjudecloud
+        namespace: flux-system
+      interval: 1h
+  values:
+    nameOverride: docs
+    extraDeploy:
+      - |
+        apiVersion: v1
+        kind: Service
+        metadata:
+          name: {{ template "common.names.fullname" . }}-oauth-bridge
+          labels: {{- include "common.labels.standard" . | nindent 4 }}
+            {{- if .Values.commonLabels }}
+            {{- include "common.tplvalues.render" ( dict "value" .Values.commonLabels "context" $ ) | nindent 4 }}
+            {{- end }}
+          {{- if .Values.commonAnnotations }}
+          annotations: {{- include "common.tplvalues.render" ( dict "value" .Values.commonAnnotations "context" $ ) | nindent 4 }}
+          {{- end }}
+        spec:
+          type: ExternalName
+          externalName: oauth2-proxy.oauth2-proxy
+      - |
+        ---
+        apiVersion: networking.k8s.io/v1
+        kind: Ingress
+        metadata:
+          name: {{ .Release.Name }}-oauth
+        spec:
+          ingressClassName: nginx
+          rules:
+          - host: {{ .Values.ingress.hostname }}
+            http:
+              paths:
+                - backend:
+                    service:
+                      name: {{ template "common.names.fullname" . }}-oauth-bridge
+                      port:
+                        number: 80
+                  path: /oauth2
+                  pathType: ImplementationSpecific
+          tls:
+          - hosts:
+            - {{ .Values.ingress.hostname }}
+            secretName: {{ .Values.ingress.hostname }}-tls
+    image:
+      repository: stjudecloud/docs
+      tag: pr135-62f5d9a-245 # {"$imagepolicy": "flux-system:docs-pr135:tag"}
+    podAnnotations:
+      linkerd.io/inject: enabled
+      config.linkerd.io/proxy-cpu-request: 20m
+    containerPorts:
+      http: 3000
+    service:
+      ports:
+        - name: http
+          protocol: TCP
+          port: 3000
+          targetPort: http
+    ingress:
+      enabled: true
+      hostname: docs-pr135.staging.stjude.cloud
+      path: /
+      annotations:
+        cert-manager.io/cluster-issuer: letsencrypt-prod
+        linkerd.io/inject: ingress
+        nginx.ingress.kubernetes.io/auth-signin: https://$host/oauth2/start?rd=$escaped_request_uri
+        nginx.ingress.kubernetes.io/auth-url: https://$host/oauth2/auth
+        nginx.ingress.kubernetes.io/service-upstream: "true"
+        nginx.ingress.kubernetes.io/enable-modsecurity: "true"
+        nginx.ingress.kubernetes.io/enable-owasp-core-rules: "true"
+      tls:
+        enabled: true
+    datadog:
+      enabled: false