fix: GH-68 new "Data Depot" hierarchy (#76)

* fix: GH-68 new "Data Depot" hierarchy * fix: GH-68 split "Data Depot" overview
DesignSafe-CI · Aug 21, 2024 · f23c04b · f23c04b
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diff --git a/user-guide/docs/curating.md b/user-guide/docs/curating.md
diff --git a/user-guide/docs/curating/bestpractices.md b/user-guide/docs/curating/bestpractices.md
@@ -1,3 +1,5 @@
+## Best Practices
+
 ### Data Collections Development
 
 #### Accepted Data  { #accepteddata }

diff --git a/user-guide/docs/curating/faq.md b/user-guide/docs/curating/faq.md
@@ -1,3 +1,5 @@
+# Frequently Asked Questions
+
 ### Selecting Files & Data { #selecting }
 
 **Q: What are the best file formats for data publications?**  

diff --git a/user-guide/docs/curating/guides.md b/user-guide/docs/curating/guides.md
@@ -1,3 +1,5 @@
+## Guides
+
 Below are step-by-step guides on how to create projects in the Data Depot, and curate and publish work/data across DesignSafe. We offer the following project types when publishing: Experimental, Simulation, Hybrid Simulation, Field Research, and Other. More information on Data Depot policies, project types, and curation/publication can be found at:
 
 * <a href="#policies">Data Depot Repository (DDR) Policies</a></li>

diff --git a/user-guide/docs/curating/index.md b/user-guide/docs/curating/index.md
@@ -0,0 +1,11 @@
+# Curating & Publishing Projects
+
+{% include-markdown '../redirect.md' %}
+
+- [Curation & Publication Guides](guides.md)
+- [Best Practices](bestpractices.md)
+- [Data Depot/Curation Office Hours](https://www.designsafe-ci.org/facilities/virtual-office-hours/)
+- [Metrics Documentation](metrics.md)
+- [Curation & Publication FAQ](faq.md)
+- [Policies](policies.md)
+- [Metadata Dictionaries](../dictionary.md)
diff --git a/user-guide/docs/curating/metrics.md b/user-guide/docs/curating/metrics.md
@@ -1,3 +1,5 @@
+## Metrics
+
 ### Data Metrics { #data }
 
 Data metrics are research impact indicators complementary to other forms of evaluation such as number of paper citations, allowing researchers to assess the repercussions and influence of their work.  

diff --git a/user-guide/docs/curating/officehours.md b/user-guide/docs/curating/officehours.md
diff --git a/user-guide/docs/curating/policies.md b/user-guide/docs/curating/policies.md
@@ -1,3 +1,5 @@
+## Policies
+
 ### DesignSafe Data Depot Repository Mission and History
 
 #### Mission { #mission }

diff --git a/user-guide/docs/datadepot.md b/user-guide/docs/datadepot.md
@@ -0,0 +1,14 @@
+# DesignSafe Data Depot
+
+The <a href="https://www.designsafe-ci.org/data/browser/public/" target="_blank">Data Depot</a> is the data repository for DesignSafe. The web interface to the Data Depot allows you to browse, upload, download, share, curate and publish data stored within the repository. You are encouraged to use the Data Depot not only for curation and publication of research results, but as a working "scratch" area for any of your own data and work in progress. Scientific applications in the <a href="https://www.designsafe-ci.org/rw/workspace/" target="_blank">Tools & Applications</a> area can access your Data Depot files, enabling data analysis directly in the DesignSafe portal that minimizes the need to transfer data to your laptop. The Data Depot hosts both public and private data associated with a project, with the following directories:
+
+* **My Data**: Private directory for your data.
+* **HPC Work**: Work directory on TACC HPC machines for use with Jupyter.
+* **My Projects**: Data to be curated and published must be in this directory. Also has group access that you control.\
+* **Shared with Me**: DEPRECATED. Use My Projects. Legacy directory we are no longer utilizing, but some very early users may have data. 
+* **Box.com**: Access to your Box files for copying to DesignSafe.
+* **Dropbox.com**: Access to your Dropbox for copying to DesignSafe.
+* **Google Drive**: CURRENTLY NOT FUNCTIONAL. Google has made changes that we are working through to reenable.
+* **Published**: Curated data/projects with DOI's.
+* **Published (NEES)**: Curated data/projects from NEES program that ran from 1999 - 2015.
+* **Community Data**: Non-curated user-contributed data.
diff --git a/user-guide/docs/dictionary.md b/user-guide/docs/dictionary.md
@@ -1,3 +1,5 @@
+## Dictionaries
+
 ### Experimental
 
 {% include-markdown 'dictionary/experimental.md' %}

diff --git a/user-guide/docs/managingdata.md b/user-guide/docs/managingdata.md
diff --git a/user-guide/docs/managingdata/datadepot.md b/user-guide/docs/managingdata/datadepot.md
@@ -1,17 +1,5 @@
-The <a href="https://www.designsafe-ci.org/data/browser/public/" target="_blank">Data Depot</a> is the data repository for DesignSafe. The web interface to the Data Depot allows you to browse, upload, download, share, curate and publish data stored within the repository. You are encouraged to use the Data Depot not only for curation and publication of research results, but as a working "scratch" area for any of your own data and work in progress. Scientific applications in the <a href="https://www.designsafe-ci.org/rw/workspace/" target="_blank">Tools & Applications</a> area can access your Data Depot files, enabling data analysis directly in the DesignSafe portal that minimizes the need to transfer data to your laptop. The Data Depot hosts both public and private data associated with a project, with the following directories:
-
-
-* **My Data**: Private directory for your data.
-* **HPC Work**: Work directory on TACC HPC machines for use with Jupyter.
-* **My Projects**: Data to be curated and published must be in this directory. Also has group access that you control.\
-* **Shared with Me**: DEPRECATED. Use My Projects. Legacy directory we are no longer utilizing, but some very early users may have data. 
-* **Box.com**: Access to your Box files for copying to DesignSafe.
-* **Dropbox.com**: Access to your Dropbox for copying to DesignSafe.
-* **Google Drive**: CURRENTLY NOT FUNCTIONAL. Google has made changes that we are working through to reenable.
-* **Published**: Curated data/projects with DOI's.
-* **Published (NEES)**: Curated data/projects from NEES program that ran from 1999 - 2015.
-* **Community Data**: Non-curated user-contributed data.
-
+## DesignSafe Managing Data
+
 ### Browsing, Upload, and Download { #browsing } 
 
 ![Figure 1. Data Depot](./imgs/datadepotfigure.jpg)
@@ -31,5 +19,3 @@ A number of data transfer methods are supported for uploading and downloading fi
 ### Data Sharing, Collaboration, Curation & Publication { #sharing }
 
 My Projects is the simplest way to share data with your collaborators and to curate and ultimately publish your data and receive a Digital Object Identifier (DOI). Any team member in a project has both read and write access to the entire contents of the project. The Data Curation & Publication User Guide provides instructions for creating projects, managing team members, curating and publishing your data.
-
----
diff --git a/user-guide/docs/managingdata/datamanagementplan.md b/user-guide/docs/managingdata/datamanagementplan.md
@@ -1,3 +1,5 @@
+# Data Management Plan Guidance
+
 This document is intended as a Data Management Plan (DMP) guide that you can customize for the specific details of your research project that will use the NHERI DesignSafe cyberinfrastructure (CI). There is guidance on the five main DMP areas required by the National Science Foundation (NSF), along with information about the DesignSafe CI functionalities that can support your data management needs.
 
 [Data Management Plan](../documents/DesignSafe_Data_Management_Plan_Guidance.docx)
diff --git a/user-guide/docs/managingdata/datatransfer.md b/user-guide/docs/managingdata/datatransfer.md
@@ -1,3 +1,5 @@
+## Data Transfer
+
 DesignSafe supports multiple ways of moving data in and out of the Data Depot, the data transfer method that is best for you will depend on the quantity of data you wish to move. There are two broad categories of data transfer methods available; we will refer to these categories as large data transfer methods and normal data transfer methods. Large data transfer methods are for situations where you want to move a large amount of data (&gt; 2GB), a large numbers of files (&gt; 25), or folders. Whereas normal data transfer methods are for situations where you wish to move a small amount of data (&lt; 2GB) stored across a small number of files (&lt; 25).
 
 This document provides a brief description of the various methods available for moving data to DesignSafe to assist you in identifying the right data transfer method for your research needs. Once you have selected your data transfer method, each description concludes with a link to detailed instructions for initiating your transfer.

diff --git a/user-guide/docs/managingdata/experimentalfacilitychecklist.md b/user-guide/docs/managingdata/experimentalfacilitychecklist.md
@@ -1,3 +1,5 @@
+## Experimental Facility Checklist
+
 ### DesignSafe-EF Onboarding Checklist for Data Curation { #onboarding }
 
 DesignSafe has been developed as a comprehensive research environment supporting a range of activities from research planning to cloud-based data analysis to data curation/publication.  We encourage users to take full advantage of the DesignSafe capabilities associated with both the Data Depot data repository and the Tools and Apps.  To learn more about all of these capabilities, watch this <a href="https://www.youtube.com/watch?v=5Yus9MjtcTM&amp;feature=youtu.be" target="_blank">Introductory Webinar</a>.
@@ -60,5 +62,3 @@ DesignSafe has been developed as a comprehensive research environment supporting
 * DesignSafe provides the possibility to publish one experiment at a time, so you do not need to finish your entire research project to publish all the experiments.
 * You may version your data and thus you can publish the raw data and add later analysis or processed results as version 2.
 * The project PI and co PI should be involved in the process to make sure they agree with the data presentation. Clarify with the team the authorship and order of authors.
-
----
diff --git a/user-guide/docs/managingdata/index.md b/user-guide/docs/managingdata/index.md
@@ -0,0 +1,10 @@
+# Managing Data
+
+{% include-markdown '../redirect.md' %}
+
+- [Data Depot Overview](../datadepot.md)
+- [Managing Data](./datadepot.md)
+- [Setting Path to DS on Corral](./settingpathtodesignsafe.md)
+- [Data Transfer Guides](./datatransfer.md)
+- [Data Management Plan Guidance](./datamanagementplan.md)
+- [Experimental Facility Checklist](./experimentalfacilitychecklist.md)
diff --git a/user-guide/docs/managingdata/settingpathtodesignsafe.md b/user-guide/docs/managingdata/settingpathtodesignsafe.md
@@ -1,3 +1,4 @@
+## Setting Path to DesignSafe on Corral
 
 The data stored on DesignSafe resides on the large (40 PB), shared data resource Corral located at the Texas Advanced Computing Center. Importantly, Corral services many different projects, not only DesignSafe, and as such utilizes a complex file structure for organization. The purpose of this documentation is to explain how to navitage this complex file structure to locate the directories pertinent to your data transfer needs on DesignSafe.
 

diff --git a/user-guide/docs/recon.md b/user-guide/docs/recon.md
@@ -1,3 +1,5 @@
 # Recon Portal
 
-{% include-markdown 'tools/recon.md' %}
+{% include-markdown './redirect.md' %}
+
+- [Recon Portal User Guide](../tools/recon/)
diff --git a/user-guide/docs/redirect.md b/user-guide/docs/redirect.md
@@ -0,0 +1,5 @@
+!!! attention "This page has moved."
+    Please use navigation panel or links below to find the content.
+
+!!! caution "Update bookmarks and links."
+    This page is temporary, unmaintained, and will be deleted.
diff --git a/user-guide/mkdocs.yml b/user-guide/mkdocs.yml
@@ -15,9 +15,6 @@ theme:
     navigation_depth: 4
     features:
       - navigation.top
-    nav_redirects: # TACC Feature
-      - before: '#data-depotcuration-office-hours'
-        after: https://www.designsafe-ci.org/facilities/virtual-office-hours/
     analytics:
       gtag: G-D96RT1T24K
 
@@ -37,11 +34,24 @@ plugins:
 
 nav:
   - Data Depot:
-    - Managing Data: managingdata.md
-    - Curating &amp; Publishing Projects: curating.md
-      # NOTE: External link is achieved via `js/changeNavMarkup.js`, NOT here
-      # - Data Depot/Curation Office Hours: https://www.designsafe-ci.org/facilities/virtual-office-hours/
-    - Recon Portal: recon.md
+    - Overview: datadepot.md
+    - Managing Data:
+      - Overview: managingdata/datadepot.md
+      - Setting Path to DS on Corral: managingdata/settingpathtodesignsafe.md
+      - Data Transfer Guides: managingdata/datatransfer.md
+      - Data Management Plan: managingdata/datamanagementplan.md
+      - Experimental Facility Checklist: managingdata/experimentalfacilitychecklist.md
+    - Data Depot Repository:
+      - Office Hours: https://www.designsafe-ci.org/facilities/virtual-office-hours/
+      - Curating &amp; Publication:
+        - Guides: curating/guides.md
+        - Frequently Asked Questions: curating/faq.md
+      - Best Practices: curating/bestpractices.md
+      - Metrics Documentation: curating/metrics.md
+      - Policies: curating/policies.md
+      - Metadata Dictionaries: dictionary.md
+    - Recon Portal:
+      - Recon Portal User Guide: tools/recon.md
 
   - Tools and Apps:
     - Analysis Applications: analysis.md
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		@@ -1,3 +1,4 @@
		## Setting Path to DesignSafe on Corral

		The data stored on DesignSafe resides on the large (40 PB), shared data resource Corral located at the Texas Advanced Computing Center. Importantly, Corral services many different projects, not only DesignSafe, and as such utilizes a complex file structure for organization. The purpose of this documentation is to explain how to navitage this complex file structure to locate the directories pertinent to your data transfer needs on DesignSafe.

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