update new resources section

gen3/docs/gen3-resources/developer-guide/gen3-architecture.md

@@ -0,0 +1,4 @@
+# Overview of Gen3 architecture
+
+we may need to break this into multiple pages later
+contains info from developer guide and more, with the goal to provide an Overview of Gen3 architecture to enable extending or modifying Gen3, and also about how to share your code (contributor guidelines)

gen3/docs/gen3-resources/developer-guide/index.md

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+# Gen3 Developer Guide - Extend Gen3
+
+home page for developer guide

gen3/docs/gen3-resources/operator-guide/index.md

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+# Gen3 Operator Guide - Deploy Gen3
+
+homepage for operator guide, describes contents and links to different sections

gen3/docs/gen3-resources/user-guide/download-data.md

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+# Download Data
+
+add section: Request access for Data (general info about controlled access data, how to request dbGaP access)
+How to download from the portal (exploration page or discovery page) - some of that info is scattered here: https://gen3.org/resources/user/access-data/
+Download with gen3-client: https://gen3.org/resources/user/gen3-client/ - only the download info, not upload
+also link to appropriate section in Use API (next section)

gen3/docs/gen3-resources/user-guide/gen3-sdk.md

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+# Analyze Data - Gen3 SDK
+
+https://gen3.org/resources/user/analyze-data/

gen3/docs/gen3-resources/user-guide/index.md

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+# Gen3 User Guide
+
+user guide home page, describing the contents of the user guide and linking to sections

gen3/docs/gen3-resources/user-guide/overview.md

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+# Overview of the portal
+
+this is different than the current overview. This should go through the different pages and features users would care about in the portal, and then link to the appropriate places elsewhere in docs.

gen3/docs/gen3-resources/user-guide/search.md

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+# Search for Data
+
+Search for data: https://gen3.org/resources/user/access-data/
+Query: https://gen3.org/resources/user/query-data/
+also link to appropriate section in Use API (last section)

gen3/docs/gen3-resources/user-guide/using-api.md

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+# Use the API
+
+https://gen3.org/resources/user/using-api/

gen3/docs/gen3-resources/user-guide/workspace.md

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+# Analyze Data - Workspace
+
+https://gen3.org/resources/user/analyze-data/

gen3/mkdocs.yml

@@ -7,22 +7,47 @@ nav:
   - Demo @ gen3.datacommons.io: https://gen3.datacommons.io/
   - New Resources Section:
     - gen3-resources/index.md # this is the "home page" for the New Resources page
-      # contains an outline for these 5 separate sections, and what they cover.
+      # contains an outline for these sections, and what they cover.
       # also some sort of figure
-    - Configure and Deploy Gen3:  gen3-resources/deploy-gen3.md
+    - Gen3 User Guide:
+      - gen3-resources/user-guide/index.md # user guide home page, describing the contents of the user guide and linking to sections
+      - Overview of the portal:  gen3-resources/user-guide/overview.md
+        # this is different than the current overview. This should go through the different pages and feeatures
+        # users would care about in the portal, and then link to the appropriate places elsewhere in docs.
+      - Search for Data: gen3-resources/user-guide/search.md
+        # Search for data: https://gen3.org/resources/user/access-data/
+        # Query: https://gen3.org/resources/user/query-data/
+        # also link to appropriate section in Use API (last section)
+      - Download Data: gen3-resources/user-guide/download-data.md
+        # add section: Request access for Data (general info about controlled access data, how to request dbGaP access)
+        # How to download from the portal (exploration page or discovery page) - some of that info is scattered here: https://gen3.org/resources/user/access-data/
+        # Download with gen3-client: https://gen3.org/resources/user/gen3-client/ - only the download info, not upload
+        # also link to appropriate section in Use API (next section)
+      - Analyze Data - Workspace: gen3-resources/user-guide/workspace.md
+        # https://gen3.org/resources/user/analyze-data/
+      - Analyze Data - Gen3 SDK: gen3-resources/user-guide/gen3-sdk.md
+        # also https://gen3.org/resources/user/analyze-data/
+      - Use the API: gen3-resources/user-guide/using-api.md
+        # https://gen3.org/resources/user/using-api/
+    - Gen3 Operator Guide - Deploy Gen3:
+      - gen3-resources/operator-guide/index.md
+      # homepage for operator guide, describes contents and links to different sections
+      - Configure and Deploy Gen3:  gen3-resources/operator-guide/deploy-gen3.md
       # contains content from the operator guide and also Helm docs
-    - Create Data Dictionary:  gen3-resources/create-data-dictionary.md
+      - Create Data Dictionary:  gen3-resources/operator-guide/create-data-dictionary.md
       # contains info about creating (and maintaining?) a data dictionary
-    - Submit Data:  gen3-resources/submit-data.md
+      - Submit Data:  gen3-resources/operator-guide/submit-data.md
       # contains info about submitting data (both for the first time and for updating content)
-    - Customize Gen3 Search Interface:  gen3-resources/customize-search.md
+      - Customize Gen3 Search Interface:  gen3-resources/operator-guide/customize-search.md
       # info from the current operator guide about configuring ETL and data explorer
-    - Find and Use Data:  gen3-resources/consume-data.md
-      # info from the current User Guide - except not the stuff about data submission/
-    - Extend your Gen3 Instance:  gen3-resources/developing-in-gen3.md
-      # contains info from developer guide and more, with the goal to provide information
-      # about how to create code to extend your Gen3 deployment, and also
-      # about how to share your code (contributor guidelines)
+    - Gen3 Developer Guide - Extend Gen3:
+      - gen3-resources/developer-guide/index.md
+      - Overview of Gen3 architecture:  gen3-resources/developer-guide/gen3-architecture.md
+      # we may need to break this into multiple pages later
+      # contains info from developer guide and more, with the goal to provide
+      # Overview of Gen3 architecture to enable extending or modifying Gen3,
+      # and also about how to share your code (contributor guidelines)
+      - Contribute Code to Gen3: gen3-resources/coming-soon.md
   - Get Started:
     - get-started/index.md
     - Set up gen3: get-started/coming-soon.md