From c4e867a19a6fd0df6060e0e2b23f72aeb4aa3874 Mon Sep 17 00:00:00 2001
From: eecavanna <eecavanna@users.noreply.github.com>
Date: Tue, 19 Sep 2023 10:11:38 -0700
Subject: [PATCH 1/2] Start writing database migration how-to guide

---
 docs/howto-guides/database-migration.md | 57 +++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 docs/howto-guides/database-migration.md

diff --git a/docs/howto-guides/database-migration.md b/docs/howto-guides/database-migration.md
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@@ -0,0 +1,57 @@
+# How to migrate the database
+
+## Introduction
+
+In this [how-to guide](https://diataxis.fr/how-to-guides/), I'll tell you how you can migrate the Mongo database from one NMDC Schema version to another. Also, when telling you about a step that has a shortcoming I'm aware of, I'll point that out.
+
+## Glossary
+
+- **Mongo**: A nickname for MongoDB.
+- **Old schema**: The version of the NMDC Schema you will be migrating the database **from**.
+- **New schema**: The version of the NMDC Schema you will be migrating the database **to**.
+- **Origin database**: The database you want to migrate.
+- **Transformation database**: The database you will use to transform data.
+
+## Prerequisites
+
+1. You're running the latest version of [nmdc-runtime](https://github.com/microbiomedata/nmdc-runtime) on your computer—by that, I mean:
+    - Its [Docker-based development environment](https://github.com/microbiomedata/nmdc-runtime/blob/main/docker-compose.yml) is running on your computer (at least, the `fastapi` and `mongo` containers).
+    - The `main` branch in your clone matches the `main` branch on GitHub (run `$ git diff main origin/main` to check).
+    - The `main` branch is checked out and there are no uncommitted changes (run `$ git status` to check).
+    - The `nmdc-schema` Python package used by this version of `nmdc-runtime` contains the **old schema**.
+1. An `nmdc-schema` Python package containing the **new schema** is available on [PyPI](https://pypi.org/project/nmdc-schema/).
+    - The package version number is stored in [(nmdc-schema) `pyproject.toml`](https://github.com/microbiomedata/nmdc-schema/blob/main/pyproject.toml#L13)
+    - The schema version number is stored in [(nmdc-schema) `src/schema/nmdc.yaml`](https://github.com/microbiomedata/nmdc-schema/blob/main/src/schema/nmdc.yaml#L22)
+1. Root credentials for the **origin database**.
+1. Root credentials for the **transformation database**.
+
+## Procedure
+
+1. Make the **origin database** be **read-only** for all users except the `root` user.
+    1. Connect to the Mongo server containing the origin database.
+       ```shell
+       mongosh "mongodb://localhost:10000" --username root --authenticationDatabase admin
+       password: ********
+       ```
+    1. At the Mongo Shell, display the username and role of each user.
+       ```js
+       use admin;
+       db.getCollection("system.users").find({}, { _id: 0, user: 1, roles: 1 });
+       // --> [ { user: 'alice', roles: [ { role: 'readWrite', db: 'nmdc' } ] }, ... ]
+       ```
+       Copy/paste the output into a text file.
+    1. For every user that has the `readWrite` role on the `nmdc` database, change that role to `read`:
+       ```js
+       // TODO: Provide a mongosh command for this. Ensure it doesn't affect users' roles on other databases.
+       ```
+    > #### Shortcomings
+    > - This doesn't account for [user-defined roles](https://www.mongodb.com/docs/v6.0/core/security-user-defined-roles/), which could have a name other than `readWrite` while still providing write access to the `nmdc` database.
+    > - This doesn't account for the [built-in roles](https://www.mongodb.com/docs/v6.0/reference/built-in-roles/)—other than `root`—that provide modification access to the `nmdc` database (e.g. `dbAdmin`, `dbOwner`, etc.).
+
+## Appendix
+
+### Precursors to this how-to guide
+
+- The "Data Releases" section of [`docs/howto-buides/release-process.md`](./release-process.md)
+- The [Jupyter notebook](../../demo/metadata_migration/from_7_7_2_to_7_8_0/migrate_7_7_2_to_7_8_0.ipynb) used for the `nmdc-schema` version `7.7.2` -> `7.8.0` migration
+

From 83d94680b461faabc112ed9c1099667437dfcf50 Mon Sep 17 00:00:00 2001
From: eecavanna <eecavanna@users.noreply.github.com>
Date: Tue, 19 Sep 2023 10:12:27 -0700
Subject: [PATCH 2/2] Indicate contents of `docs/nb/` folder

---
 docs/contributing-docs.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/contributing-docs.md b/docs/contributing-docs.md
index 48eacb98..a0ae29a7 100644
--- a/docs/contributing-docs.md
+++ b/docs/contributing-docs.md
@@ -14,4 +14,5 @@ Reference for contributing to this documentation.
     mkdocs.yml    # The configuration file.
     docs/
         index.md  # The documentation homepage.
+        nb/       # Jupyter notebooks.
         ...       # Other markdown pages, images and other files.