From 06bc390ac15ee70cad02fe4aa68914ca08767174 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Tue, 27 Jan 2026 14:06:08 -0600 Subject: [PATCH 1/7] docs: EA-Updates-1-27-26 --- .../3.managing-data/5.renewing-your-daa.md | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md index 86a6bf9..7766db7 100644 --- a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md +++ b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md @@ -1,15 +1,23 @@ --- title: Filling Out The Extension Addendum -navigation: - title: Renewing Your DAA --- +## Renewing Your Data Access Agreement ### + The St. Jude Cloud [Data Access Agreement (DAA)](/genomics-platform/getting-started/glossary#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from [notifications@stjude.cloud](mailto:notifications@stjude.cloud) with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum. - In order to extend your DAA, you must fill out an Extension Addendum. The Extension Addendum will extend the previous agreement for an additional year. -Please note that if you do not fill out an Extension Addendum, you will be expected to delete all copies of the data subject to the expiring agreement. + +* If your insitution is within the United States, then you will have the option to complete the Extension Addendum vis DocuSign. +* If your instition is not within the United States, you will complete the Extension Addendum manually by downloading the form and following the steps outlined below. + +::callout{icon="i-heroicons-exclamation-circle" color="blue"} +**Note** +If you do not fill out an Extension Addendum, you will be expected to delete all copies of the data subject to the expiring agreement. +:: + +### Completing the Form Manually ### Follow the steps below to ensure that you have accurately filled out all sections of the Extension Addendum. From 5bdee59c2cf886475ef5289b7ef3ff976fff5d5d Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Tue, 27 Jan 2026 14:07:20 -0600 Subject: [PATCH 2/7] ci: :rocket: creates preview environment for pr132 [skip ci] --- deployment/preview/pr132/app.yaml | 88 +++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 deployment/preview/pr132/app.yaml diff --git a/deployment/preview/pr132/app.yaml b/deployment/preview/pr132/app.yaml new file mode 100644 index 0000000..3b18f83 --- /dev/null +++ b/deployment/preview/pr132/app.yaml @@ -0,0 +1,88 @@ +--- +apiVersion: helm.toolkit.fluxcd.io/v2beta1 +kind: HelmRelease +metadata: + name: docs + namespace: docs-pr132 +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: latest # {"$imagepolicy": "flux-system:docs-pr132:tag"} + podAnnotations: + linkerd.io/inject: enabled + config.linkerd.io/proxy-cpu-request: 20m + containerPorts: + http: 3000 + service: + ports: + - name: http + protocol: TCP + port: 3000 + targetPort: http + ingress: + enabled: true + hostname: docs-pr132.staging.stjude.cloud + path: / + annotations: + cert-manager.io/cluster-issuer: letsencrypt-prod + linkerd.io/inject: ingress + nginx.ingress.kubernetes.io/auth-signin: https://$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 From aca1c879e1652d5876c90fb2800b23d5708100ba Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Tue, 27 Jan 2026 20:14:20 +0000 Subject: [PATCH 3/7] chore: :rocket: released stjudecloud.azurecr.io/stjudecloud/docs:pr132-d7b3b39-238 to pr132 [skip ci] --- deployment/preview/pr132/app.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/deployment/preview/pr132/app.yaml b/deployment/preview/pr132/app.yaml index 3b18f83..0d1741b 100644 --- a/deployment/preview/pr132/app.yaml +++ b/deployment/preview/pr132/app.yaml @@ -1,4 +1,3 @@ ---- apiVersion: helm.toolkit.fluxcd.io/v2beta1 kind: HelmRelease metadata: @@ -58,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: latest # {"$imagepolicy": "flux-system:docs-pr132:tag"} + tag: pr132-d7b3b39-238 # {"$imagepolicy": "flux-system:docs-pr132:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From da73f66e10bbf3adaee8a385976f0e50738c68e5 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Wed, 28 Jan 2026 08:23:55 -0600 Subject: [PATCH 4/7] revise: updates from review and format --- .../3.managing-data/5.renewing-your-daa.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md index 7766db7..a33b892 100644 --- a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md +++ b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md @@ -1,8 +1,10 @@ --- title: Filling Out The Extension Addendum +navigation: + title: Renewing Your DAA --- -## Renewing Your Data Access Agreement ### +### Renewing Your Data Access Agreement ### The St. Jude Cloud [Data Access Agreement (DAA)](/genomics-platform/getting-started/glossary#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from [notifications@stjude.cloud](mailto:notifications@stjude.cloud) with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum. @@ -10,7 +12,7 @@ In order to extend your DAA, you must fill out an Extension Addendum. The Extension Addendum will extend the previous agreement for an additional year. * If your insitution is within the United States, then you will have the option to complete the Extension Addendum vis DocuSign. -* If your instition is not within the United States, you will complete the Extension Addendum manually by downloading the form and following the steps outlined below. +* If your instition is not within the United States, you will complete the Extension Addendum manually by downloading the form and following the steps outlined below. ::callout{icon="i-heroicons-exclamation-circle" color="blue"} **Note** @@ -50,7 +52,7 @@ Follow the steps below to ensure that you have accurately filled out all section ::callout{icon="i-heroicons-exclamation-circle" color="orange"} **St. Jude Employees**
-This section is not applicable for St. Jude employees. +The Information Security OFficer section is not applicable for St. Jude employees. :: * The bottom section of page 3 is for St. Jude to sign and date. From 79e876060ea62674184b128486b45329c326e1b8 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Wed, 28 Jan 2026 14:35:04 +0000 Subject: [PATCH 5/7] chore: :rocket: released stjudecloud.azurecr.io/stjudecloud/docs:pr132-94475bc-239 to pr132 [skip ci] --- deployment/preview/pr132/app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/preview/pr132/app.yaml b/deployment/preview/pr132/app.yaml index 0d1741b..4438887 100644 --- a/deployment/preview/pr132/app.yaml +++ b/deployment/preview/pr132/app.yaml @@ -57,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: pr132-d7b3b39-238 # {"$imagepolicy": "flux-system:docs-pr132:tag"} + tag: pr132-94475bc-239 # {"$imagepolicy": "flux-system:docs-pr132:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From 6c8d4e48c090815f8595e3c7ab5b056703bc626d Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Thu, 29 Jan 2026 15:57:53 -0600 Subject: [PATCH 6/7] docs: spelling revisions --- .../1.getting-started/2.accounts-and-billing.md | 4 ++-- .../3.managing-data/5.renewing-your-daa.md | 10 +++++----- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/content/3.genomics-platform/1.getting-started/2.accounts-and-billing.md b/content/3.genomics-platform/1.getting-started/2.accounts-and-billing.md index 505029c..3bf5ebb 100644 --- a/content/3.genomics-platform/1.getting-started/2.accounts-and-billing.md +++ b/content/3.genomics-platform/1.getting-started/2.accounts-and-billing.md @@ -5,7 +5,7 @@ description: Information on account creation and billing setup. St. Jude Cloud is built on top of [DNAnexus](https://www.dnanexus.com/), a data-analysis and management platform that specializes in the field of bioinformatics. All of our account management is shared between St. Jude Cloud and DNAnexus. -### Creating a St. Jude Cloud Account +## Creating a St. Jude Cloud Account To create an account, simply navigate to [Genomics Platform](https://platform.stjude.cloud) and then select “Log In.” @@ -23,7 +23,7 @@ Users who have an existing DNAnexus account must use the St. Jude Cloud account Once you have created an account through St. Jude Cloud your DNAnexus account and St. Jude Cloud account will be linked going forward. :: -### Billing Setup +## Billing Setup If you are a St. Jude employee, go to the [Bioinformatics Self Service page](https://sjcrh.sharepoint.com/sites/computational-biology/SitePages/Bioinformatics-Self-Service-on-St.-Jude-Cloud.aspx) on the Intranet for information on how to set up your billing account. diff --git a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md index a33b892..aa20109 100644 --- a/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md +++ b/content/3.genomics-platform/3.managing-data/5.renewing-your-daa.md @@ -4,22 +4,22 @@ navigation: title: Renewing Your DAA --- -### Renewing Your Data Access Agreement ### +## Renewing Your Data Access Agreement The St. Jude Cloud [Data Access Agreement (DAA)](/genomics-platform/getting-started/glossary#data-access-agreement) is only valid for one year after the date it was approved. When your DAA is about to expire, you will get an automated email from [notifications@stjude.cloud](mailto:notifications@stjude.cloud) with the name of the DAA that is expiring and a link to the St. Jude Cloud Extension Addendum. In order to extend your DAA, you must fill out an Extension Addendum. The Extension Addendum will extend the previous agreement for an additional year. -* If your insitution is within the United States, then you will have the option to complete the Extension Addendum vis DocuSign. -* If your instition is not within the United States, you will complete the Extension Addendum manually by downloading the form and following the steps outlined below. +* If your institution is within the United States, you will have the option to complete the Extension Addendum via DocuSign. +* If your institution is not within the United States, you will complete the Extension Addendum manually by downloading the form and following the steps outlined below. ::callout{icon="i-heroicons-exclamation-circle" color="blue"} **Note** If you do not fill out an Extension Addendum, you will be expected to delete all copies of the data subject to the expiring agreement. :: -### Completing the Form Manually ### +## Completing the Form Manually Follow the steps below to ensure that you have accurately filled out all sections of the Extension Addendum. @@ -52,7 +52,7 @@ Follow the steps below to ensure that you have accurately filled out all section ::callout{icon="i-heroicons-exclamation-circle" color="orange"} **St. Jude Employees**
-The Information Security OFficer section is not applicable for St. Jude employees. +The Information Security Officer section is not applicable for St. Jude employees. :: * The bottom section of page 3 is for St. Jude to sign and date. From c6663992bb82fb2971176e53804b4f31d2d117ff Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Thu, 29 Jan 2026 22:06:26 +0000 Subject: [PATCH 7/7] chore: :rocket: released stjudecloud.azurecr.io/stjudecloud/docs:pr132-ce80daf-243 to pr132 [skip ci] --- deployment/preview/pr132/app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/preview/pr132/app.yaml b/deployment/preview/pr132/app.yaml index 4438887..65126ca 100644 --- a/deployment/preview/pr132/app.yaml +++ b/deployment/preview/pr132/app.yaml @@ -57,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: pr132-94475bc-239 # {"$imagepolicy": "flux-system:docs-pr132:tag"} + tag: pr132-ce80daf-243 # {"$imagepolicy": "flux-system:docs-pr132:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m