Pathologies endpoint added.

config/pathologies.json

+[{
+		"code": "dementia",
+		"datasets": [{
+				"code": "adni"
+			}, {
+				"code": "ppmi"
+			}, {
+				"code": "edsd"
+			}
+
+		]
+	}, {
+		"code": "neuropathology",
+		"datasets": [{
+				"code": "neuro1"
+			}, {
+				"code": "neuro2"
+			}, {
+				"code": "neuro3"
+			}
+
+		]
+	}
+]

src/main/java/eu/hbp/mip/controllers/PathologiesApi.java

+/**
+ * Created by mirco on 04.12.15.
+ */
+
+package eu.hbp.mip.controllers;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import eu.hbp.mip.utils.CustomResourceLoader;
+import io.swagger.annotations.Api;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.ResourceLoader;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+
+@RestController
+@RequestMapping(value = "/pathologies", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/pathologies")
+public class PathologiesApi {
+
+    @RequestMapping(name = "/pathologies", method = RequestMethod.GET)
+    public String getPathologies() {
+        return loadPathologies();
+    }
+
+    @Autowired
+    private CustomResourceLoader resourceLoader;
+    private String loadPathologies() {
+
+        Resource resource  = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
+        String result;
+        try {
+            result = convertInputStreamToString(resource.getInputStream());
+        } catch (IOException e) {
+            result = "{\"error\" : \"The pathologies.json file could not be read.\"}";
+        }
+        return result;
+    }
+
+    // Pure Java
+    private static String convertInputStreamToString(InputStream inputStream) throws IOException {
+
+        ByteArrayOutputStream result = new ByteArrayOutputStream();
+        byte[] buffer = new byte[1024];
+        int length;
+        while ((length = inputStream.read(buffer)) != -1) {
+            result.write(buffer, 0, length);
+        }
+
+        return result.toString(StandardCharsets.UTF_8.name());
+
+    }
+}

src/main/java/eu/hbp/mip/utils/CustomResourceLoader.java

+package eu.hbp.mip.utils;
+
+import org.springframework.context.ResourceLoaderAware;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.ResourceLoader;
+import org.springframework.stereotype.Component;
+
+@Component
+public class CustomResourceLoader implements ResourceLoaderAware {
+
+    private ResourceLoader resourceLoader;
+
+    public void setResourceLoader(ResourceLoader resourceLoader) {
+        this.resourceLoader = resourceLoader;
+    }
+
+    public Resource getResource(String resourceLocation) {
+        return resourceLoader.getResource(resourceLocation);
+    }
+}
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