[WIP] Feature/db interface

.gitignore

@@ -29,3 +29,5 @@ coverage.*
 .vscode/
 
 site/
+
+drs-server

Makefile

@@ -5,23 +5,25 @@ MKDOCS_IMAGE ?= squidfunk/mkdocs-material:latest
 
 .PHONY: gen
 gen:
-	@mkdir -p .tmp internal/apigen
+	@mkdir -p .tmp apigen
 	# OpenAPI Generator (Go server stub)
 	# delete previous generated code
-	rm -rf internal/apigen
+	rm -rf apigen
 	# generate new code
 	docker run --rm \
+	  --user "$$(id -u):$$(id -g)" \
 	  -v "$(PWD):/local" \
 	  $(OAG_IMAGE) generate \
-	  -g go-gin-server \
+	  -g go-server \
 	  --skip-validate-spec \
 	  --git-repo-id drs-server \
 	  --git-user-id calypr \
 	  -i /local/$(OPENAPI) \
-	  -o /local/internal/apigen
-	# a bundle is created at internal/apigen/openapi.yaml, remove examples from it
+	  -o /local/apigen \
+	  --additional-properties outputAsLibrary=true,sourceFolder=drs,packageName=drs
+	# a bundle is created at apigen/openapi.yaml, remove examples from it
 	# as many are not compliant with the spec or seem to be randomly generated
-	go run ./cmd/openapi-remove-examples
+	# go run ./cmd/openapi-remove-examples
 
 .PHONY: test
 test:
@@ -36,6 +38,7 @@ serve:
 docs:
 	docker run --rm -it \
 	  -v "$(PWD):/docs" \
+	  --user "$$(id -u):$$(id -g)" \
 	  -p 8000:8000 \
 	  $(MKDOCS_IMAGE) \
 	  serve -a 0.0.0.0:8000

README.md

@@ -1,43 +1,68 @@
 # drs-server
 
-A lightweight reference implementation of a GA4GH Data Repository Service (DRS) server in Go.
+A lightweight, production-grade implementation of a GA4GH Data Repository Service (DRS) server in Go.
 
-## Table of Contents
-- [Overview](#overview)
-- [Quickstart](QUICKSTART.md)
-- [Contributing](CONTRIBUTING.md)
-- [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+## Purpose
 
+The `drs-server` provides a robust implementation of the [GA4GH DRS API](https://ga4gh.github.io/data-repository-service-schemas/). It is designed to manage metadata for data objects and provide secure access via signed URLs.
 
-## Overview
+### Key Features
+- **GA4GH DRS Compliance**: Implements the standard DRS API for describing and accessing data objects.
+- **Database Flexibility**: Supports both **SQLite** and **PostgreSQL** backends with a modular driver architecture.
+- **S3 Integration**: Native support for Amazon S3 (and compatible storage like MinIO) with signed URL generation for downloads and multipart uploads.
+- **Gen3 Compatibility Layers**:
+    - **Fence Compatibility**: Supports Fence-style `/data/download` and multipart upload endpoints.
+    - **Indexd Compatibility**: Provides Indexd-style metadata management for integration with `git-drs`.
 
-GA4GH DRS is a standard API for describing and accessing data objects in cloud or on‑premise repositories.  
-This project consumes the official GA4GH `data-repository-service-schemas` as a Git submodule and generates a Go HTTP server from the DRS OpenAPI spec.
+## Configuration
 
+The server is configured via a YAML or JSON file. Use the following structure to set up your environment:
 
-```mermaid
-graph TD
-  0[ga4gh/data-repository-service-schemas DRS OpenAPI spec submodule] --> B
-  A[Makefile] --> B[make gen]
-  A --> C2[cmd/server]
-  A --> D[make test]
-  A --> E[make docs/]
+```yaml
+port: 8080
 
-  B --> G[internal/apigen generated DRS server code]
-  B --> H[cmd/openapi-remove-examples clean OpenAPI helper] --> H2[internal/apigen/api/openapi.yaml]
+database:
+  sqlite:
+    file: "drs.db"
+  # Or use PostgreSQL:
+  # postgres:
+  #   host: "localhost"
+  #   port: 5432
+  #   user: "user"
+  #   password: "password"
+  #   database: "drs"
+  #   sslmode: "disable"
 
-  H2 --> C2
-  D --> C2
-  G --> C2
+s3_credentials:
+  - bucket: "my-test-bucket"
+    region: "us-east-1"
+    access_key: "AKIAXXXXXXXXXXXXXXXX"
+    secret_key: "wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY"
+    endpoint: "s3.amazonaws.com" # Optional: set for MinIO or custom backends
 ```
 
-* Makefile - targets for generation, tests, docs, and running the server.
-  * `make gen` - generates the DRS server code from the OpenAPI spec.
-    * ga4gh/data-repository-service-schemas - GA4GH DRS OpenAPI spec (Git submodule).
-    * internal/apigen - generated DRS server code.
-    * cmd/openapi-remove-examples - helper to clean the bundled OpenAPI.
-  * `make serve` - runs the DRS server.
-    * cmd/server - main HTTP server (uses gin-gonic/gin).
-  * `make test` - launches server, runs integration tests.
-  * `make docs` - serves documentation with MkDocs.
+## Running Integration Tests
+
+You can run integration tests using your own config file:
+
+```bash
+go test ./cmd/server -v -count=1 -testConfig=config.yaml
+```
+
+## Architecture
+
+The project follows a modular structure to ensure maintainability:
+- `db/core`: Core interfaces and models.
+- `db/sqlite`, `db/postgres`: Database implementation drivers.
+- `internal/api`: Subpackages for different API contexts (Admin, Fence, Gen3).
+- `service`: High-level business logic implementing the DRS service.
+- `urlmanager`: Logic for interacting with cloud storage providers.
+
+## Development
+
+The project uses a Makefile for common tasks:
+- `make gen`: Generates the DRS server code from the official GA4GH OpenAPI spec (Git submodule).
+- `make test`: Runs all unit and integration tests.
+- `make serve`: Starts the DRS server.
+
 

apigen/.openapi-generator/FILES

@@ -0,0 +1,58 @@
+.openapi-generator-ignore
+README.md
+api/openapi.yaml
+drs/api.go
+drs/api_objects.go
+drs/api_objects_service.go
+drs/api_service_info.go
+drs/api_service_info_service.go
+drs/api_upload_request.go
+drs/api_upload_request_service.go
+drs/error.go
+drs/helpers.go
+drs/impl.go
+drs/logger.go
+drs/model_access_method.go
+drs/model_access_method_access_url.go
+drs/model_access_method_authorizations.go
+drs/model_access_method_update_request.go
+drs/model_access_url.go
+drs/model_authorizations.go
+drs/model_bulk_access_method_update_request.go
+drs/model_bulk_access_method_update_request_updates_inner.go
+drs/model_bulk_access_url.go
+drs/model_bulk_delete_request.go
+drs/model_bulk_object_access_id.go
+drs/model_bulk_object_access_id_bulk_object_access_ids_inner.go
+drs/model_bulk_object_id_no_passport.go
+drs/model_bulk_update_access_methods_200_response.go
+drs/model_checksum.go
+drs/model_contents_object.go
+drs/model_delete_request.go
+drs/model_drs_object.go
+drs/model_drs_object_candidate.go
+drs/model_drs_service.go
+drs/model_drs_service_drs.go
+drs/model_drs_service_type.go
+drs/model_error.go
+drs/model_get_bulk_access_url_200_response.go
+drs/model_get_bulk_objects_200_response.go
+drs/model_get_bulk_objects_request.go
+drs/model_get_service_info_200_response.go
+drs/model_options_bulk_object_200_response.go
+drs/model_post_access_url_request.go
+drs/model_post_object_request.go
+drs/model_register_objects_201_response.go
+drs/model_register_objects_request.go
+drs/model_service.go
+drs/model_service_organization.go
+drs/model_service_type.go
+drs/model_summary.go
+drs/model_unresolved_inner.go
+drs/model_upload_method.go
+drs/model_upload_method_access_url.go
+drs/model_upload_request.go
+drs/model_upload_request_object.go
+drs/model_upload_response.go
+drs/model_upload_response_object.go
+drs/routers.go

apigen/.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.19.0-SNAPSHOT

apigen/README.md

@@ -0,0 +1,36 @@
+# Go API Server for drs
+
+No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
+
+## Overview
+This server was generated by the [openapi-generator]
+(https://openapi-generator.tech) project.
+By using the [OpenAPI-Spec](https://github.com/OAI/OpenAPI-Specification) from a remote server, you can easily generate a server stub.
+
+To see how to make this your own, look here:
+
+[README](https://openapi-generator.tech)
+
+- API version: 1.5.0
+- Build date: 2026-01-12T03:49:20.482821942Z[Etc/UTC]
+- Generator version: 7.19.0-SNAPSHOT
+
+
+### Running the server
+To run the server, follow these simple steps:
+
+```
+go run main.go
+```
+
+The server will be available on `http://localhost:8080`.
+
+To run the server in a docker container
+```
+docker build --network=host -t drs .
+```
+
+Once image is built use
+```
+docker run --rm -it drs
+```