chore(docs): rewrite installation page; set mermaid and markdown_extensions plugins

Author: alexhambley

docs/installation.md

@@ -1,106 +1,97 @@
-# Installation
+# Installation & Setup
 
-## Service Snapshot
+The service runs with Docker Compose. The default setup validates metadata documents only; enabling object storage adds validation of complete stored crates. If you are upgrading from a 1.\* release, see the [upgrade guide](upgrading.md) first.
 
-Cratey Validator is a web service that checks whether RO-Crates follow the 
-expected structure and metadata rules. It can validate a complete RO-Crate 
-stored in MinIO-compatible object storage, or it can validate the contents 
-of an `ro-crate-metadata.json` file directly.
+## Quick start
 
-At a high level, a client sends a validation request, the service runs the 
-RO-Crate validation checks, and the result is either returned directly or 
-saved so it can be retrieved later.
+You will need Docker with Docker Compose. 
 
-## What You Can Validate
+First, clone the repository, copy the example environment file, and start the stack:
 
-### Stored RO-Crates
-
-Use this option when the RO-Crate already exists in MinIO-compatible object 
-storage. The service reads the crate from the configured bucket, runs the 
-validation checks, and saves the validation result back to object storage.
-
-This is useful for validating complete crates as part of an upload, review, 
-or publication workflow.
+```bash
+git clone https://github.com/eScienceLab/RO-Crate-Validation-Service.git
+cd RO-Crate-Validation-Service
+cp example.env .env
+docker compose up --build
+```
 
+!!! warning
+    You should update the default `.env` values when running the object store in production.
 
-### Metadata Files
+The API is served at `http://localhost:5001`. Redis and a Celery worker are also started, but are only used once storage is enabled. To check the service is up:
 
-Use this option when you only need to check the contents of 
-`ro-crate-metadata.json`. Instead of asking the service to download a full 
-crate, you submit the metadata JSON directly and receive the validation result 
-in the response.
+```bash
+curl http://localhost:5001/healthz
+```
 
-This is useful for quick checks while editing metadata or before a complete 
-crate has been assembled.
+This returns `{"status": "ok"}`.
 
+To validate some metadata, post the contents of an `ro-crate-metadata.json` file to the metadata endpoint. The [running example](https://www.researchobject.org/ro-crate/specification/1.2/introduction.html#running-example) from the RO-Crate specification is a good test document. The file needs to be sent as an escaped JSON string, which `jq` can do:
 
-### Saved Validation Results
+```bash
+jq -Rs '{crate_json: .}' ro-crate-metadata.json | curl -X POST http://localhost:5001/v1/ro_crates/validate_metadata -H 'Content-Type: application/json' -d @-
+```
 
-After a stored RO-Crate has been validated, the saved validation result can be 
-retrieved later. This lets another application or user interface show the most 
-recent validation status without rerunning the checks.
+The response contains a `status` of `valid`, `invalid` or `error`, along with the detailed findings. The [API reference](api.md) describes the endpoints and result format in full.
 
+## Enabling object storage
 
-## Before You Start
+To validate a complete RO-Crate (zip or directory) held in an object store, set `STORAGE_ENABLED=true` in `.env`. Storage mode requires six settings, [described below](#configuration-reference): `S3_ENDPOINT`, `S3_ACCESS_KEY`, `S3_SECRET_KEY`, `S3_BUCKET`, `CELERY_BROKER_URL` and `CELERY_RESULT_BACKEND`. The service will fail at startup if any are missing. The Compose stack already sets the Celery variables to the bundled Redis, so in practice only the S3 settings in `.env` matter here.
 
-For stored RO-Crate validation, you need:
+Then start the stack with the bundled development object store (RustFS):
 
-- A MinIO-compatible object store.
-- A bucket containing the RO-Crate.
-- Access credentials for that bucket.
-- The crate identifier used by the object store.
+```bash
+docker compose --profile objectstore up --build
+```
 
-For metadata-only validation, you only need the contents of 
-`ro-crate-metadata.json`.
+RustFS serves the S3 API on port 9000 and a web console at `http://localhost:9001`. Development credentials are set in `example.env`. 
 
+!!! warning
+    The service does not create the bucket itself. Create the bucket in the console or with any S3 client. The bucket name needs to match `S3_BUCKET` (`ro-crates` by default). 
 
-## Running The Service
+Upload an RO-Crate under the crate prefix: `crates/<id>.zip` for a zipped RO-Crate, or `crates/<id>/` for a directory. Note that for a zipped RO-Crate, `ro-crate-metadata.json` must be at the root of the archive.
 
-The service can be started with Docker Compose:
+The readiness endpoint checks the object store and broker connections:
 
 ```bash
-docker compose up --build
+curl http://localhost:5001/readyz
 ```
 
-For local container development, use:
-
-```bash
-docker compose --file docker-compose-develop.yml up --build
-```
+## Using your own object store
 
-Expected local services:
+Any S3-compatible store can be used in place of RustFS, including AWS S3, MinIO and Ceph: set `S3_ENDPOINT`, the credentials and `S3_BUCKET` for your store, and skip the `objectstore` profile. If you already run a 1.\* release against MinIO, the [upgrade guide](upgrading.md) maps the old settings to the new ones.
 
-- Flask API: `http://localhost:5001`
-- MinIO API: `http://localhost:9000`
-- MinIO console: `http://localhost:9001`
-- Redis: `localhost:6379`
+## Configuration reference
 
-MinIO needs a bucket for RO-Crates, normally `ro-crates`. Bucket versioning 
-should be enabled so uploaded crate objects can be tracked reliably.
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `STORAGE_ENABLED` | `false` | Enable the stored-crate endpoints and storage checks |
+| `S3_ENDPOINT` | — | Object store endpoint, e.g. `objectstore:9000` (required in storage mode) |
+| `S3_ACCESS_KEY` | — | Object store access key (required in storage mode) |
+| `S3_SECRET_KEY` | — | Object store secret key (required in storage mode) |
+| `S3_BUCKET` | — | Bucket holding crates and results (required in storage mode) |
+| `S3_USE_SSL` | `false` | Use HTTPS to the object store |
+| `S3_REGION` | — | Region; needed for AWS S3 |
+| `S3_CRATE_PREFIX` | `crates` | Key prefix crates are read from |
+| `S3_RESULTS_PREFIX` | `validation-results` | Key prefix results are written to |
+| `CELERY_BROKER_URL` | — | Redis broker URL (required in storage mode; preset in the Compose stack) |
+| `CELERY_RESULT_BACKEND` | — | Celery result backend URL (required in storage mode; preset in the Compose stack) |
+| `PROFILES_PATH` | — | Profiles directory that replaces the bundled profiles |
+| `EXTRA_PROFILES_PATH` | — | Profiles directory added to the bundled profiles |
+| `CACHE_PATH` | `/app/.rocrate-cache` in the published image | Validator HTTP cache location |
+| `VALIDATION_OFFLINE` | `false` | Validate using only the cache, with no network access |
+| `FLASK_ENV` | `development` | Set to `production` to disable debug behaviour |
 
+## Custom profiles
 
-## Configuration
+The validator comes with the base RO-Crate profiles. For Five Safes validation, the prebuilt `ghcr.io/esciencelab/ro-crate-validation-service-fivesafes-profile` image has the `five-safes-crate` profile already included; see [Five Safes validation](five-safes.md).
 
-The main environment variables are:
+Adding other profiles works by mounting a directory of profile definitions into both the `flask` and `celery_worker` containers. You set `EXTRA_PROFILES_PATH` to the mounted path. Both containers need the mount as metadata-only validation runs in the API process and stored-crate validation runs in the worker. There is a working example in `docker-compose-develop.yml`. 
 
-- `FLASK_APP`: Flask entrypoint, normally `cratey.py`.
-- `FLASK_ENV`: selects development or production config.
-- `CELERY_BROKER_URL`: Redis broker URL.
-- `CELERY_RESULT_BACKEND`: Redis result backend URL.
-- `PROFILES_PATH`: optional path to custom RO-Crate validator profile 
-definitions.
-- `MINIO_ENDPOINT`: default MinIO endpoint used by Docker examples.
-- `MINIO_ROOT_USER`: MinIO root username for local development.
-- `MINIO_ROOT_PASSWORD`: MinIO root password.
-- `MINIO_BUCKET_NAME`: default bucket name used by local setup.
+`EXTRA_PROFILES_PATH` adds the directory to the bundled profiles, whereas `PROFILES_PATH` replaces them entirely.
 
-API calls also pass MinIO access details in `minio_config`, so the service can validate crates in a specified object store and bucket.
+## Offline validation
 
-## More Information
+The validator fetches profile and context resources over HTTP and caches them. The published images pre-populate this cache at build time, so setting `VALIDATION_OFFLINE=true` runs validation entirely from the cache, with no network access at runtime. This is useful inside TREs and other restricted networks. 
 
-- For endpoint paths, request bodies, response codes, validation profiles, and 
-result storage paths, see the [REST API documentation](./rest_api).
-- For implementation details, service components, runtime flow, and test 
-coverage, see the [Architecture documentation](./architecture).
-- For deployment context and the architecture diagram, see 
-[Deployment](./deployment).
+Online validation (the default) also uses and refreshes the same cache. Offline validation requires `rocrate-validator` at 0.10.0 or later, which the published images include.

mkdocs.yml

@@ -6,3 +6,8 @@ nav:
   - ENTRUST: entrust.md
   - Contributions: contribution.md
 theme: readthedocs
+plugins:
+  - search
+  - mermaid2
+markdown_extensions:
+  - admonition