removing back, AGDR spelling and look at nav ordering

natnesi · natnesi · commit e446d7b15ca5 · 2024-04-16T02:46:49.000Z
diff --git a/docs/index.md b/docs/index.md
@@ -17,5 +17,5 @@ layout: default
 
 ## Support
 
-[Submit a request](mailto:gasupport@nesi.org.nz?Request_from_Support_Pages)
+[Submit a request](mailto:gasupport@nesi.org.nz?Request_from_Support_Pages){:target="_blank"}
 
diff --git a/docs/releases/08Aug2023.md b/docs/releases/08Aug2023.md
@@ -60,5 +60,3 @@ Note: JupyterHub, Kibana are not used and not updated
 Removing the starting G in "GKakapo125+ genome sequencing"
  
 (Note: Repo.data.nesi.org.nz was updated on the 3rd of August with the following version differences: indexd 2022.05 and peregrine: 2022.05)
-
-[back](index.md)
diff --git a/docs/releases/16Jan2024.md b/docs/releases/16Jan2024.md
@@ -51,5 +51,3 @@ Note: JupyterHub, Kibana are not used and not updated
 - The content policy was invalid creating some errors when the data.agdr.org.nz was loaded
  
 (Note: Repo.data.nesi.org.nz is not updated. We will start deprecating this deployment soon. Please use data.agdr.org.nz)
-
-[back](index.md)
diff --git a/docs/releases/16Oct2023.md b/docs/releases/16Oct2023.md
@@ -5,5 +5,3 @@
 - Updated text on the landing page
  
 Note: no change of versions https://gadr.zendesk.com/hc/en-gb/articles/7512059827087-data-agdr-org-nz-08-August-2023
-
-[back](index.md)
diff --git a/docs/releases/22June2023.md b/docs/releases/22June2023.md
@@ -15,5 +15,3 @@ Santure, A. (2023). Assembly of female and male hihi genomes (stitchbird; Notiom
 
 - NZ Bats, AGDR00036
 Jemma Geoghegan. Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae [Data set]. Genomic Sequence published 2023 via Aotearoa Genomic Data Repository. https://doi.org/10.57748/CYHD-AD62
-
-[back](index.md)
diff --git a/docs/releases/deficiencies.md b/docs/releases/deficiencies.md
@@ -5,5 +5,3 @@
 - Also message": "'unaligned reads' is not one of ['Unaligned Reads']" - must be capital case
 
 - TSV cannot have any empty columns
-
-[back](index.md)
diff --git a/docs/releases/index.md b/docs/releases/index.md
@@ -7,5 +7,3 @@ data.agdr.org.nz web application release notes
 - [data.agdr.org.nz 16 October 2023](16Oct2023.md)
 - [data.agdr.org.nz 08 August 2023](08Aug2023.md)
 - [data.agdr.org.nz 22 June 2023](22June2023.md)
-
-[back](../index.md)
diff --git a/docs/releases/summary.md b/docs/releases/summary.md
diff --git a/docs/user-guides/globus.md b/docs/user-guides/globus.md
@@ -48,4 +48,3 @@ Recommendations: please use standard conventions for file and folder naming (wit
 
 ![Alt text](../assets/images/globus3.png)
 
-[back](index.md)
diff --git a/docs/user-guides/index.md b/docs/user-guides/index.md
@@ -4,5 +4,3 @@
 - [Requesting access to data](requesting.md)
 - [Accessing data hosted on NeSI Globus endpoint](globus.md)
 - [Submission Process](submission.md)
-
-[back](../index.md)
diff --git a/docs/user-guides/navigating.md b/docs/user-guides/navigating.md
@@ -52,5 +52,3 @@ Relationships between nodes are represented by arrows from one node to another.
 - View the Data Dictionary as a table to see the name and a brief description of each node, organised by node category. Click on the name of a node to display more information about its properties.
 
 The metadata dictionary is under review and we would appreciate feedback.
-
-[back](index.md)
diff --git a/docs/user-guides/requesting.md b/docs/user-guides/requesting.md
@@ -21,5 +21,3 @@ After submitting the form, you will receive an e-mail confirmation. Please answe
 ![Alt text](../assets/images/request3.png)
 
 Once the form is submitted, NeSI’s support team is notified of a new request and a ticket is created. The request will be reviewed by the AGDR team and passed on to the appropriate kaitiaki. After approval access will be granted to the data, alternatively we will reach out for more information in order to support your application and move towards approval. This process usually takes about 1 month, but feel free to reach out to gasupport@gmail.com if you have any concerns.
-
-[back](index.md)
diff --git a/docs/user-guides/submission.md b/docs/user-guides/submission.md
@@ -22,5 +22,3 @@ The metadata Template spreadsheet is available as a [google sheet](https://docs.
 Once you have made a copy of this document, please fill in all the fields as much as you can under 'Your input'. Please note that there are multiple tabs which you can access via the buttons at the bottom.
 The required fields are highlighted in green, though we recommend you provide as much metadata as possible. This spreadsheet is based on the AGDR data dictionary - https://data.agdr.org.nz/DD although some of the more obscure fields are not included in the template. If you have additional metadata, please let us know and we will see how best we can accommodate it. 
 If you have any questions throughout the process, please feel free to reach out to gasupport@nesi.org.nz.
-
-[back](index.md)
diff --git a/docs/user-guides/summary.md b/docs/user-guides/summary.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -39,9 +39,9 @@ plugins:
 repo_name: GitHub
 repo_url: https://github.com/nesi/agdr-docs-concept
 edit_uri: edit/main/docs/
-site_description: AgDR
+site_description: AGDR
 site_dir: public
-site_name: AgDR
+site_name: AGDR
 site_url: https://github.com/nesi/agdr-docs-concept
 extra_css:
   - assets/stylesheets/neoteroi-mkdocs.css
@@ -75,3 +75,19 @@ theme:
       toggle:
         icon: material/lightbulb-outline
         name: Switch to light mode
+# Page tree
+nav:
+  - Home: index.md
+  - User Guides:
+    - user-guides/index.md
+    - Navigating the data repository: navigating.md
+    - Requesting access to data: requesting.md
+    - Accessing data hosted on NeSI Globus endpoint: globus.md
+    - Submission Process: submission.md
+  - Releases:
+    - releases/index.md
+    - Known Deficiencies: releases/deficiencies.md
+    - data.agdr.org.nz 16 January 2024: releases/16Jan2024.md
+    - data.agdr.org.nz 16 October 2023: releases/16Oct2023.md
+    - data.agdr.org.nz 08 August 2023: releases/08Aug2023.md
+    - data.agdr.org.nz 22 June 2023: releases/22June2023.md

Original file line number	Diff line number	Diff line change
`@@ -17,5 +17,5 @@ layout: default`
`17`	`17`
`18`	`18`	`## Support`
`19`	`19`
`20`		`-[Submit a request](mailto:[email protected]?Request_from_Support_Pages)`
	`20`	`+[Submit a request](mailto:[email protected]?Request_from_Support_Pages){:target="_blank"}`
`21`	`21`
Original file line number	Diff line number	Diff line change
`@@ -48,4 +48,3 @@ Recommendations: please use standard conventions for file and folder naming (wit`
`48`	`48`
`49`	`49`	`![Alt text](../assets/images/globus3.png)`
`50`	`50`
`51`		`-[back](index.md)`
-Original file line number
+Diff line change
 ![Alt text](../assets/images/request3.png)
 Once the form is submitted, NeSI’s support team is notified of a new request and a ticket is created. The request will be reviewed by the AGDR team and passed on to the appropriate kaitiaki. After approval access will be granted to the data, alternatively we will reach out for more information in order to support your application and move towards approval. This process usually takes about 1 month, but feel free to reach out to [email protected] if you have any concerns.
+-
 -[back](index.md)