diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 6588e210aff0957a01ba66c4c436ae4dd9b7a163..f2587889371ac5ddd7f6bbad5b2f5574d303e07e 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -76,3 +76,9 @@ services:
keycloak:
keycloakUrl: {{ .Env.KEYCLOAK_URL }}
+
+pathologies:
+ pathologiesUrl: "file:/opt/portal/api/pathologies.json"
+
+algorithms:
+ disabledAlgorithmsUrl: "file:/opt/portal/api/disabledAlgorithms.json"
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index f9c84d85d6d01e7dd02f56fbf4c52db6d87b908f..b64596e794adb4c824a7a6a59d932cb6e6ebaddf 100644
--- a/pom.xml
+++ b/pom.xml
@@ -268,6 +268,14 @@
<include>**/*.yml</include> <!-- Only for development -->
</includes>
<filtering>true</filtering>
+
+ </resource>
+ <resource>
+ <directory>config</directory>
+ <includes>
+ <include>*.json</include>
+ </includes>
+ <filtering>true</filtering>
</resource>
</resources>
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
index ff28602a1b33e541fd89858d4a6f9d0bf9787605..81afa6418383a2a9817bdf0770f4a0b90a08af25 100644
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
@@ -6,6 +6,7 @@ import eu.hbp.mip.utils.CustomLoginUrlAuthenticationEntryPoint;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.security.oauth2.resource.AuthoritiesExtractor;
import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
@@ -70,6 +71,7 @@ public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
private static final Logger LOGGER = LoggerFactory.getLogger(SecurityConfiguration.class);
+ @Qualifier("oauth2ClientContext")
@Autowired
private OAuth2ClientContext oauth2ClientContext;
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index d5dca19ae3b3503876b884dabdf48e7a2d808898..07ab6ef291b4dcb32123e4c66f26a625e8b99261 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -17,6 +17,7 @@ import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
@@ -41,6 +42,7 @@ public class AlgorithmsApi {
private static final Gson gson = new Gson();
+ @Qualifier("userInfo")
@Autowired
private UserInfo userInfo;
@@ -53,6 +55,9 @@ public class AlgorithmsApi {
@Value("#{'${services.galaxy.galaxyApiKey}'}")
private String galaxyApiKey;
+ @Value("#{'${services.algorithms.disabledAlgorithmsUrl}'}")
+ private String disabledAlgorithmsUrl;
+
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
@@ -195,7 +200,7 @@ public class AlgorithmsApi {
*/
List<String> getDisabledAlgorithms() throws IOException {
- Resource resource = resourceLoader.getResource("file:/opt/portal/api/disabledAlgorithms.json");
+ Resource resource = resourceLoader.getResource(disabledAlgorithmsUrl);
List<String> response = gson.fromJson(convertInputStreamToString(
resource.getInputStream()),
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index 4ec7c8e36d421f0ead08e15bf05b13328f63d72c..a6979e70ccae284adeed66bdf125f83e256987e9 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -15,6 +15,7 @@ import eu.hbp.mip.utils.InputStreamConverter;
import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
@@ -35,6 +36,7 @@ public class PathologiesApi {
private static final Gson gson = new Gson();
+ @Qualifier("userInfo")
@Autowired
private UserInfo userInfo;
@@ -42,32 +44,37 @@ public class PathologiesApi {
@Value("#{'${hbp.authentication.enabled:1}'}")
private boolean authenticationIsEnabled;
+ @Value("#{'${services.pathologies.pathologiesUrl}'}")
+ private String pathologiesUrl;
+
@Autowired
private CustomResourceLoader resourceLoader;
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
+ String endpoint = "(GET) /pathologies";
+ String username = userInfo.getUser().getUsername();
+ Logging.LogUserAction(username, endpoint, "Loading pathologies ...");
// Load pathologies from file
- Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
+ Resource resource = resourceLoader.getResource(pathologiesUrl);
List<PathologyDTO> allPathologies;
try {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
}.getType());
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Unable to load pathologies");
+ Logging.LogUserAction(username, endpoint, "Unable to load pathologies");
throw new BadRequestException("The pathologies could not be loaded.");
}
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded " + allPathologies.size() + " pathologies");
+ Logging.LogUserAction(username, endpoint, "Successfully loaded " + allPathologies.size() + " pathologies");
return ResponseEntity.ok().body(gson.toJson(allPathologies));
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
+ Logging.LogUserAction(username, endpoint, "Successfully loaded all authorized pathologies");
return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
- userInfo.getUser().getUsername(), authentication.getAuthorities(), allPathologies));
+ username, authentication.getAuthorities(), allPathologies));
}
}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 825692ef70c731e54d1061293ec06d4dc8d1ab61..a4c205725b44f860118b7f8417fb14ef9f88f555 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -21,7 +21,7 @@ spring:
# HBP OAUTH2 LOGIN
hbp:
authentication:
- enabled: true
+ enabled: 0
client:
clientId: "MIP"
clientSecret: "dae83a6b-c769-4186-8383-f0984c6edf05"
@@ -71,5 +71,11 @@ services:
galaxyUsername: "admin"
galaxyPassword: "password"
- keycloak:
- keycloakUrl: 127.0.0.1
\ No newline at end of file
+ keycloak:
+ keycloakUrl: "127.0.0.1"
+
+ pathologies:
+ pathologiesUrl: "classPath:/pathologies.json"
+
+ algorithms:
+ disabledAlgorithmsUrl: "classPath:/disableAlgorithms.json"
\ No newline at end of file