Initial implementation (GSI-1817) (#1)

* Adapt to actual package

* Commit in case computer spontaneously combusts

* Complete the outbox sub class

* Rename orchestrator methods for clarity

* Make UCSClient responsible for WOT generation

* Clean up the routes a little

* Update core, rest api, and UCS client code

* Implement Access API client

* Add event sub injection and realize main module

* Add UCS client unit tests + general test files

* Add access api client unit tests

* Add unit tests for core

* Add unit tests for the auditor

* Add unit tests for the rest api

* Add typical journey test and fix some minor problems

* Cover audit logging in integration test

* Remove audit recorder from unit test

* Add claim validity to grant access endpoint

* Log access granting

* Resolve mypy errors

* Set version to 1.0.0

* Add e2e ability to list and revoke upload access grants

* Add tests for the revoke and list endpoints

* Don't encrypt tokens for UCS

* Use outbox dao for research boxes

* Update config docs

* Add final missing endpoint to list all RDUBoxes with pagination

* Remove sort order, rename ucs stuff to be generic, various doc string and comment fixes

* Remove unused functions copied from the wps

* Prepend title and description with box_ for grants

* Remove unused module copied from wps

* Use StewardAuthContext on certain endpoints

* Return 404 in GET box endpoint if not authorized

* Fix straggler name referencing claims

* Further fix orchestrator doc strings

* Flatten validity

* Enable filtering boxes by locked status

* Don't call access API for single box retrieval if user is a steward

* Retrieve fewer results for fixed user in multi-box retrieval

* Make central 'is_data_steward' function

* Fix the way we check box access in get_upload_box_files

* Rename test module that references UCS and move silly import

* Add response metadata to endpoints and fix tags

* Remove extraneous 'default=...' kwarg

* Add 'state' field to FileUpload and fix test that was broken by recent change

* Switch config name back to ucs_url

* Apply mock dao changes from UCS to here

* Account for the fact that the access api returns dict of box IDs with expiration date

* Add an unhappy test case for box updates

* Rename user_id param to data_steward_id for clarity

* Sort boxes by locked, last changed, id

* Use populated boxes fixture in other orchestrator tests

* Remove unnecessary test user id and context

* Sort grants by validity, user id, iva id, box id, and grant id

* Grab new ghga event schemas version

* Remove certain local model definitions and import from lib instead

* Remove unused ignores to make mypy happy

* Update template files

* Apply fixes according to ruff

Author: TheByronHimes

.devcontainer/.dev_config.yaml

@@ -1,4 +1,13 @@
-# Please only mention the non-default settings here:
-
-language: Greek
 service_instance_id: "1"
+kafka_servers: ["kafka:9092"]
+mongo_dsn: mongodb://localhost:27017
+db_name: uos
+mongo_timeout: 300
+auth_key: "{}"
+ucs_url: http://127.0.0.1/upload
+access_url: http://127.0.0.1/access
+audit_record_topic: audit-records
+audit_record_type: audit_record_logged
+work_order_signing_key: "{}"
+file_upload_box_topic: file-upload-boxes
+research_data_upload_box_topic: research-data-upload-boxes

.devcontainer/Dockerfile

@@ -1,6 +1,6 @@
-FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
+FROM mcr.microsoft.com/devcontainers/python:2.0.2-3.13-trixie
 
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 
 # Update args in docker-compose.yaml to set the UID/GID of the "vscode" user.
 ARG USER_UID=1000

.devcontainer/dev_launcher

@@ -1,4 +1,3 @@
 #!/bin/bash
 
-# adapt to package name
-my-microservice
+uos run-rest

.devcontainer/devcontainer.json

@@ -70,6 +70,6 @@
 	},
 	"features": {
 		// details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker
-		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {"moby": false}
 	}
 }

.devcontainer/docker-compose.yml

@@ -7,8 +7,7 @@ services:
         # [Choice] Install Node.js
         INSTALL_NODE: "false"
         NODE_VERSION: "lts/*"
-        # Please adapt to package name:
-        PACKAGE_NAME: "my_microservice"
+        PACKAGE_NAME: "uos"
         # On Linux, you may need to update USER_UID and USER_GID below if not your local UID is not 1000.
         USER_UID: 1000
         USER_GID: 1000
@@ -30,8 +29,7 @@ services:
 
     # define environment variables
     environment:
-      # Please adapt to package name:
-      MY_MICROSERVICE_CONFIG_YAML: /workspace/.devcontainer/.dev_config.yaml
+      UOS_CONFIG_YAML: /workspace/.devcontainer/.dev_config.yaml
       # Used by db migration:
       DB_URL: postgresql://postgres:postgres@postgresql/postgres
     # Use "forwardPorts" in **devcontainer.json** to forward an app port locally.
@@ -45,25 +43,5 @@ services:
     volumes:
       - mongo_fs:/data/db
 
-  localstack:
-    image: localstack/localstack
-    environment:
-      SERVICES: s3
-      DEFAULT_REGION: eu-west-1
-      AWS_DEFAULT_REGION: eu-west-1
-      # accessible at localhost
-      HOSTNAME_EXTERNAL: localhost
-      USE_SSL: "false"
-      DATA_DIR: /var/lib/localstack/data
-      DEBUG: 1
-    volumes:
-      - type: volume
-        source: s3_fs
-        target: /var/lib/localstack
-        volume:
-          nocopy: true
-    # useful ports: 4566 - AWS API
-
 volumes:
-  s3_fs: {}
   mongo_fs: {}

.github/workflows/check_config_docs.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check config docs
         id: check-config-docs

.github/workflows/check_openapi_spec.yaml

@@ -12,11 +12,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check openapi.yaml
         id: check-openapi-docs

.github/workflows/check_pyproject.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check pyproject.toml
         id: check-pyproject

.github/workflows/check_readme.yaml

@@ -11,11 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Common steps
         id: common
         uses: ghga-de/gh-action-common@v6
+        with:
+          python-version: '3.13'
 
       - name: Check README
         id: check-readme

.github/workflows/check_template_files.yaml

@@ -11,13 +11,13 @@ jobs:
     steps:
       - name: Checkout repository
         id: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         id: setup-python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Check template files
         id: check-template-files