Feature/storage provider architecture

.github/workflows/create-release.yml

@@ -42,7 +42,11 @@ jobs:
             ${{ runner.os }}-maven-
 
       - name: Set version in Maven project
-        run: mvn versions:set -DnewVersion="${{ github.event.inputs.versionTag }}" -DprocessAllModules -DgenerateBackupPoms=false
+        # Bump the centralized `revision` property in the root POM. With revision-based
+        # versioning (all modules inherit from ${revision}), the version lives in exactly
+        # one place. versions:set would overwrite the ${revision} expression, so use
+        # set-property to update the property value instead.
+        run: mvn org.codehaus.mojo:versions-maven-plugin:2.18.0:set-property -Dproperty=revision -DnewVersion="${{ github.event.inputs.versionTag }}" -DgenerateBackupPoms=false
 
       - name: Build with Maven
         run: mvn -B package --file pom.xml

README.md

@@ -1,2 +1,132 @@
-For the API documentation run the server and visit
-http://localhost:8080/swagger-ui/index.html
+# Data Download Server
+
+Spring Boot service for downloading (bio)measurement data via the QBiC download-API.
+
+## Configuration
+
+The service is configured via an external `application.properties` file. A commented,
+fully-documented template is available at
+[`rest-api/src/dist/application.properties`](rest-api/src/dist/application.properties).
+
+### Loading the external file (important)
+
+Spring Boot looks for `application.properties` relative to the **process working directory**
+(the directory you are *in* when you launch `java`), **not** relative to the JAR file's own
+location. If you just drop the file "next to the JAR" it is very easy for Spring to not find
+it — that happens whenever the JAR is launched from a different directory (or under systemd /
+a service manager that does not set the working directory).
+
+To make loading deterministic, always pass the file by absolute path on the command line:
+
+```
+java -jar /opt/app/rest-server-1.3.0.jar \
+  --spring.config.additional-location=/opt/app/application.properties
+```
+
+Use `--spring.config.additional-location` (not `--spring.config.location`) so the bundled
+defaults inside the JAR are still used for any key the external file does not set. The
+`file:` prefix is optional when the path is absolute.
+
+Alternatively, when running under systemd, set `WorkingDirectory` so the file is found
+relative to it:
+
+```ini
+[Service]
+WorkingDirectory=/opt/app
+ExecStart=/usr/bin/java -jar /opt/app/rest-server-1.3.0.jar
+```
+
+### Env vars still work (optional)
+
+Spring Boot's property precedence still applies, so specific values can be overridden without
+editing the file, e.g. `SERVER_PORT=9000 java -jar rest-server.jar`. The env var wins over
+the external file. The bundled `application.properties` inside the JAR also still supports the
+original environment-variable placeholders for backward compatibility.
+
+## Building for production
+
+### Prerequisites
+
+- JDK 21
+- Maven 3.x
+
+### Build everything
+
+The project is a multi-module Maven build:
+
+```
+data-download-server (POM parent)
+├── zip                        (library)
+├── measurement-provider       (library)
+├── storage-provider           (library)
+├── openbis-connector          (library)
+└── rest-api                   (Spring Boot application "rest-server")
+```
+
+The four library modules are **not** standalone services - they are dependencies of the
+Spring Boot application in `rest-api`. Building a package compiles every module and bundles
+all four libraries into a single executable JAR.
+
+From the project root:
+
+```bash
+# Build everything, including tests
+mvn package
+
+# Build everything, skip tests (faster, for a release artifact)
+mvn package -DskipTests
+```
+
+This produces one deployable artifact:
+
+```
+rest-api/target/rest-server-<version>.jar
+```
+
+### Build only the application (faster)
+
+The `-am` flag ("also make") builds `rest-api` together with all upstream modules it
+depends on - so this produces the same deployable JAR, but skips nothing it needs:
+
+```bash
+mvn -pl rest-api -am package
+```
+
+### Clean rebuild
+
+```bash
+mvn -pl rest-api -am clean package
+```
+
+### Deploy to Nexus (release)
+
+```bash
+mvn deploy
+```
+
+Publishes all modules to the QBiC Nexus repository configured in `distributionManagement`.
+
+## Versioning
+
+The whole project uses **one version, defined in one place**: the `<revision>` property in the
+root [`pom.xml`](pom.xml). All modules inherit this version and their build artifacts are named
+accordingly (e.g. `rest-server-1.3.0.jar`).
+
+To change the project version, edit the single property:
+
+```xml
+<properties>
+  <revision>1.3.0</revision>
+</properties>
+```
+
+There is no per-module `<version>` anywhere - child POMs reference the parent via
+`${revision}` and inter-module dependencies via `${project.version}`, so a bump is
+applied consistently to every module in one edit. The release workflow bumps this property
+automatically (`.github/workflows/create-release.yml`).
+
+## API documentation
+
+Run the server and visit
+[http://localhost:8090/swagger-ui.html](http://localhost:8090/swagger-ui.html)
+(port depends on your configuration; default `8090`).

measurement-provider/pom.xml

@@ -6,12 +6,11 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>data-download-server</artifactId>
-    <version>1.0.10</version>
+    <version>${revision}</version>
   </parent>
 
   <groupId>life.qbic.data-download</groupId>
   <artifactId>measurement-provider</artifactId>
-  <version>1.0.10</version>
   <packaging>jar</packaging>
   <dependencies>
     <dependency>

openbis-connector/pom.xml

@@ -7,13 +7,12 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>data-download-server</artifactId>
-    <version>1.0.10</version>
+    <version>${revision}</version>
   </parent>
 
   <groupId>life.qbic.data-download</groupId>
   <artifactId>openbis-connector</artifactId>
   <packaging>jar</packaging>
-  <version>1.0.10</version>
 
   <dependencyManagement>
     <dependencies>
@@ -66,7 +65,12 @@
     <dependency>
       <groupId>life.qbic.data-download</groupId>
       <artifactId>measurement-provider</artifactId>
-      <version>1.0.10</version>
+      <version>${project.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>life.qbic.data-download</groupId>
+      <artifactId>storage-provider</artifactId>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.junit.jupiter</groupId>

openbis-connector/src/main/java/life/qbic/data_download/openbis/OpenBisConnector.java

@@ -48,6 +48,11 @@ public class OpenBisConnector implements MeasurementFinder, MeasurementDataProvi
 
   private static final String UUID_REGEX = "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$";
 
+  /**
+   * Constructor for creating provider-specific instances with custom configuration.
+   * Used by ProviderRegistryConfig to create openBIS connectors with provider-specific settings.
+   * Also used as the Spring-injected constructor for the global openBIS connector bean.
+   */
   public OpenBisConnector(
       @Qualifier("openbisSessionFactory") SessionFactory sessionFactory,
       @Value("${openbis.server.application.url}") String applicationServerUrl,
@@ -147,13 +152,20 @@ private List<DataSetFile> searchFilesForMeasurement(OpenBisSession session,
         .toList();
   }
 
+  public List<DataSet> loadDataSetsForMeasurement(MeasurementId measurementId) {
+    try (var session = sessionFactory.getSession()) {
+      return loadDataSetsForMeasurement(session, measurementId);
+    }
+  }
+
   private List<DataSet> loadDataSetsForMeasurement(OpenBisSession session,
       MeasurementId measurementId) {
     DataSetSearchCriteria dataSetSearchCriteria = new DataSetSearchCriteria();
     dataSetSearchCriteria.withSample().withCode().thatEquals(measurementId.id());
 
     DataSetFetchOptions dataSetFetchOptions = new DataSetFetchOptions();
     dataSetFetchOptions.withChildrenUsing(dataSetFetchOptions);
+    dataSetFetchOptions.withPhysicalData();
 
     return applicationServer.searchDataSets(session.getToken(),
         dataSetSearchCriteria,