move and update docs

README.md

@@ -42,15 +42,15 @@ We use [pre-commit](https://pre-commit.com/) as a tool to maintain a unified doc
 
 Install
 
-  ```sh
-  brew install pre-commit
-  ```
+```sh
+brew install pre-commit
+```
 
 Run
 
-  ```sh
-  pre-commit run -a
-  ```
+```sh
+pre-commit run -a
+```
 
 ## Deployment
 

docs/deployment/helm/how-to-deploy.md → docs/home/helm/how-to-deploy.md

@@ -54,7 +54,7 @@ This tool ensures seamless access to ECR by handling credential rotation.
             access:
               secret:
                 name: ""
-   ```
+    ```
 
     b) Download Helm-chart:
 

docs/deployment/release-notes/v1.50-v1.59.md → docs/home/release-notes/v1.50-v1.59.md

@@ -10,76 +10,87 @@ We automated process of transferring data from the standalone version to the clu
 Things that you have keep in mind before upgrading process:
 
 - Migration time depends on resources(mostly on CPU and Disk IO) allocated for Clickhouse instances, during our tests we've mentioned average speed 50Gb per hour for instances with 4CPU/16Gb RAM
+
 - It's necessary **not to set** flags as `--wait` and `--timeout` during upgrading process because of migration time  
+
 - Optional: We've developed a tool that checks consistency of data, you could use it before and after the upgrading process and compare results of those checks just to be sure that everything went as expected
-  Description of using `clickhouse-helper sanity`:
-  1) Gather required variables.
 
-     ```shell
-      export ODM_URL=https://odm.localhost
-      export ODM_TOKEN=yourTokenFromRootUser
-      ```
+Description of using `clickhouse-helper sanity`:
+
+1. Gather required variables.
+
+    ```shell
+    export ODM_URL=https://odm.localhost
+    export ODM_TOKEN=yourTokenFromRootUser
+    ```
 
-  2) Run check over ODM instance before the upgrade.
+2. Run check over ODM instance before the upgrade.
 
-      ```shell
-      docker run \
-        --env ODM_URL=${ODM_URL} \
-        --env ODM_TOKEN=${ODM_TOKEN} \
-        oci://091468197733.dkr.ecr.us-east-1.amazonaws.com/genestack/clickhouse-helper \
-        odm sanity > sanity-result-before.jsonl
-      ```
+    ```shell
+    docker run \
+      --env ODM_URL=${ODM_URL} \
+      --env ODM_TOKEN=${ODM_TOKEN} \
+      oci://091468197733.dkr.ecr.us-east-1.amazonaws.com/genestack/clickhouse-helper \
+      odm sanity > sanity-result-before.jsonl
+    ```
 
-  3) Proceed with upgrading ODM instance
-  4) Run check over ODM instance after the upgrade
+3. Proceed with upgrading ODM instance
 
-      ```shell
-      docker run \
-        --env ODM_URL=${ODM_URL} \
-        --env ODM_TOKEN=${ODM_TOKEN} \
-        oci://091468197733.dkr.ecr.us-east-1.amazonaws.com/genestack/clickhouse-helper \
-        odm sanity > sanity-result-after.jsonl
-      ```
+4. Run check over ODM instance after the upgrade
 
-  5) Run a diff:
+    ```shell
+    docker run \
+      --env ODM_URL=${ODM_URL} \
+      --env ODM_TOKEN=${ODM_TOKEN} \
+      oci://091468197733.dkr.ecr.us-east-1.amazonaws.com/genestack/clickhouse-helper \
+      odm sanity > sanity-result-after.jsonl
+    ```
 
-      ```shell
-      diff sanity-result-before.jsonl sanity-result-after.jsonl
-      ```
+5. Run a diff:
 
-  Basically there should be no changes, except studies with already uploaded VCF files, they should be started to reimport.
+    ```shell
+    diff sanity-result-before.jsonl sanity-result-after.jsonl
+    ```
+
+Basically there should be no changes, except studies with already uploaded VCF files, they should be started to reimport.
 
 ## Version 1.57
 
+!!! tip ""
+    Helm chart version 1.57.0
+
 ### Helm configuration changes
 
 - Removed the link to the database for the service `func-file`. If you have it in your `values.yaml`, then you can safely remove the `spring` map completely.
 
-```yaml
-funcFile:
-  configurationFiles:
-    "application.yaml":
-      spring:
-        datasource:
-          # -- Mysql jdbc URL
-          url: "jdbc:mysql://..."
-```
+    ```yaml
+    funcFile:
+      configurationFiles:
+        "application.yaml":
+          spring:
+            datasource:
+              # -- Mysql jdbc URL
+              url: "jdbc:mysql://..."
+    ```
 
 - For the Clickhouse `busybox` image, the ability to set the repository and version has been added.
 
-```yaml
-clickhouse:
-  busyboxImage:
-    # -- Image registry
-    registry: docker.io
-    # -- Image repository
-    repository: busybox
-    # -- Image tag
-    tag: 1.36.1
-```
+    ```yaml
+    clickhouse:
+      busyboxImage:
+        # -- Image registry
+        registry: docker.io
+        # -- Image repository
+        repository: busybox
+        # -- Image tag
+        tag: 1.36.1
+    ```
 
 ## Version 1.56
 
+!!! tip ""
+    Helm chart version 1.56.1
+
 ### Export metrics to Genestack
 
 Fluent-bit was introduced as an extra service tasked with collecting and dispatching metrics in Prometheus format to a Genestack.
@@ -120,6 +131,9 @@ global:
 
 ## Version 1.55
 
+!!! tip ""
+    Helm chart version 1.55.4
+
 ### Configure ODM usage together with encrypted S3 bucket (SSE-KMS and SSE-S3 only)
 
 #### Introduction

docs/index.md

@@ -1,3 +1,3 @@
-# Welcome to Open Data Manager Documentation
+# Welcome to Open Data Manager Administrator Documentation
 
-This documentation contains information how to use ODM system.
+This documentation contains information how to deploy and support ODM system.

mkdocs.yml

@@ -1,35 +1,35 @@
-site_name: Open Data Manager Documentation
+site_name: Open Data Manager Administrator Documentation
 site_url: https://genestack.github.io/documentation
 
 nav:
-    - Home: index.md
-    - Deployment:
+    - Home:
+        - index.md
         - Requirements:
-            - Kubernetes: deployment/requirements/kubernetes.md
-            - Hardware: deployment/requirements/hardware.md
-            - External services: deployment/requirements/external-services.md
+            - Kubernetes: home/requirements/kubernetes.md
+            - Hardware: home/requirements/hardware.md
+            - External services: home/requirements/external-services.md
         - Clouds:
-            - Amazon Web Services (AWS): deployment/clouds/aws.md
-            - Microsoft Azure: deployment/clouds/azure.md
+            - Amazon Web Services (AWS): home/clouds/aws.md
+            - Microsoft Azure: home/clouds/azure.md
         - Single Sign-On:
-            - About SSO in ODM: deployment/single-sign-on/sso.md
+            - About SSO in ODM: home/single-sign-on/sso.md
             - OpenID:
-                - Microsoft Azure: deployment/single-sign-on/openid/azure.md
-                - Google Workspace: deployment/single-sign-on/openid/google.md
-                - Okta: deployment/single-sign-on/openid/okta.md
+                - Microsoft Azure: home/single-sign-on/openid/azure.md
+                - Google Workspace: home/single-sign-on/openid/google.md
+                - Okta: home/single-sign-on/openid/okta.md
             - SAML:
-                - Google Workspace: deployment/single-sign-on/saml/google.md
-                - Okta: deployment/single-sign-on/saml/okta.md
+                - Google Workspace: home/single-sign-on/saml/google.md
+                - Okta: home/single-sign-on/saml/okta.md
             - SCIM:
-                - Microsoft Azure: deployment/single-sign-on/scim/azure.md
+                - Microsoft Azure: home/single-sign-on/scim/azure.md
         - Helm:
-            - How to deploy: deployment/helm/how-to-deploy.md
+            - How to deploy: home/helm/how-to-deploy.md
         - Troubleshooting:
-            - AWS S3: deployment/troubleshooting/aws-s3.md
-            - Azure SSO: deployment/troubleshooting/azure-sso.md
-            - Azure SCIM: deployment/troubleshooting/azure-scim.md
+            - AWS S3: home/troubleshooting/aws-s3.md
+            - Azure SSO: home/troubleshooting/azure-sso.md
+            - Azure SCIM: home/troubleshooting/azure-scim.md
         - Release Notes:
-              - v1.50 - v1.59: deployment/release-notes/v1.50-v1.59.md
+              - v1.50 - v1.59: home/release-notes/v1.50-v1.59.md
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     name: material
     palette: