diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 3b93114541d3ac242b051e71f5f38bf2923e68f9..d685d2f2f6e3d11c509d72e774789fa2532649b4 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -82,3 +82,8 @@ keycloak:
# cors-exposed-headers: "*"
# logoutUrl: {{ .Env.LOGOUT_URL }}
+
+# Files are imported when building the docker image
+files:
+ pathologies_json: "file:/opt/portal/api/pathologies.json"
+ disabledAlgorithms_json: "file:/opt/portal/api/disabledAlgorithms.json"
diff --git a/pom.xml b/pom.xml
index 5292dffd056dbb97d42ea3f766101386b0c9149f..a21e63e379243642933f3042bd6700734633b1a2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -278,6 +278,15 @@
</includes>
<filtering>true</filtering>
</resource>
+
+ <!-- Used for development. Docker/config folder files added as resources -->
+ <resource>
+ <directory>config</directory>
+ <includes>
+ <include>*.json</include>
+ </includes>
+ <filtering>true</filtering>
+ </resource>
</resources>
<plugins>
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index bca25598a6e59827a6a938e30fc9db1b9b5d5614..909d2c1c81dc040c78bba7c29d4f43bcb1e925ca 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -29,7 +29,6 @@ public class PersistenceConfiguration {
return DataSourceBuilder.create().build();
}
-
@Bean(name = "entityManagerFactory")
@DependsOn("flyway")
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
index 22f904af5f97e70d45925434940e594f772df498..8617e2270a5903a872c4ec432fb5016b71cb9b14 100644
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
@@ -1,21 +1,16 @@
package eu.hbp.mip.configuration;
import eu.hbp.mip.configuration.SecurityUtils.CORSFilter;
-import eu.hbp.mip.configuration.SecurityUtils.CustomAccessDeniedHandler;
-import eu.hbp.mip.configuration.SecurityUtils.CustomLoginUrlAuthenticationEntryPoint;
import org.keycloak.adapters.KeycloakConfigResolver;
import org.keycloak.adapters.springboot.KeycloakSpringBootConfigResolver;
import org.keycloak.adapters.springsecurity.KeycloakConfiguration;
import org.keycloak.adapters.springsecurity.authentication.KeycloakAuthenticationProvider;
import org.keycloak.adapters.springsecurity.authentication.KeycloakLogoutHandler;
import org.keycloak.adapters.springsecurity.config.KeycloakWebSecurityConfigurerAdapter;
-import org.keycloak.adapters.springsecurity.filter.KeycloakAuthenticationProcessingFilter;
-import org.keycloak.adapters.springsecurity.filter.KeycloakPreAuthActionsFilter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.web.servlet.FilterRegistrationBean;
import org.springframework.context.annotation.Bean;
import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
import org.springframework.security.config.annotation.web.builders.HttpSecurity;
@@ -24,25 +19,18 @@ import org.springframework.security.core.session.SessionRegistryImpl;
import org.springframework.security.web.access.channel.ChannelProcessingFilter;
import org.springframework.security.web.authentication.session.RegisterSessionAuthenticationStrategy;
import org.springframework.security.web.authentication.session.SessionAuthenticationStrategy;
-import org.springframework.security.web.csrf.CsrfFilter;
import org.springframework.security.web.csrf.CsrfToken;
import org.springframework.security.web.csrf.CsrfTokenRepository;
import org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository;
-import org.springframework.web.cors.CorsConfiguration;
-import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
-import org.springframework.web.filter.CorsFilter;
import org.springframework.web.filter.OncePerRequestFilter;
import org.springframework.web.util.WebUtils;
-import javax.net.ssl.*;
import javax.servlet.FilterChain;
import javax.servlet.ServletException;
import javax.servlet.http.Cookie;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
-import java.security.SecureRandom;
-import java.security.cert.X509Certificate;
// Reference for OAuth2 login: https://spring.io/guides/tutorials/spring-boot-oauth2/
@@ -132,8 +120,8 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
// ).permitAll()
// .antMatchers("/galaxy*", "/galaxy/*").hasRole("DATA MANAGER")
// .anyRequest().hasRole("RESEARCHER")
- // .and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint(loginUrl))
- // .accessDeniedHandler(new CustomAccessDeniedHandler())
+ // .and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint(loginUrl))
+ // .accessDeniedHandler(new CustomAccessDeniedHandler())
// .and().csrf().ignoringAntMatchers("/logout").csrfTokenRepository(csrfTokenRepository())
// .and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class).csrf();
// .and().logout().logoutSuccessUrl("/logout");
@@ -141,7 +129,7 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
//
// // TODO .and().logout().addLogoutHandler(authLogoutHandler()).logoutSuccessUrl(redirectAfterLogoutUrl)
// .and().logout().permitAll()
- // TODO ?? .addFilterBefore(ssoFilter(), BasicAuthenticationFilter.class);
+ // TODO ?? .addFilterBefore(ssoFilter(), BasicAuthenticationFilter.class);
} else {
http.antMatcher("/**")
.authorizeRequests()
@@ -150,7 +138,6 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
}
}
-
// @Bean
// public FilterRegistrationBean corsFilter() {
// UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
@@ -223,7 +210,6 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
return repository;
}
-
// @Bean
// public AuthoritiesExtractor keycloakAuthoritiesExtractor() {
// return new KeycloakAuthoritiesExtractor();
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index 51fc1b4857ad777bcfb7461e0314b09537e37559..72dff716a5fb388806e50282df756039d3058458 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;
@@ -53,6 +54,9 @@ public class AlgorithmsApi {
@Value("#{'${services.galaxy.galaxyApiKey}'}")
private String galaxyApiKey;
+ @Value("#{'${files.disabledAlgorithms_json}'}")
+ private String disabledAlgorithmsFilePath;
+
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
@@ -195,7 +199,7 @@ public class AlgorithmsApi {
*/
List<String> getDisabledAlgorithms() throws IOException {
- Resource resource = resourceLoader.getResource("file:/opt/portal/api/disabledAlgorithms.json");
+ Resource resource = resourceLoader.getResource(disabledAlgorithmsFilePath);
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 055b04b2363e5522f244d5319197275993b79643..0f3f3c2bb5f4216e92f4863a93c1999d02c0d469 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -1,7 +1,3 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
package eu.hbp.mip.controllers;
import com.google.gson.Gson;
@@ -42,32 +38,37 @@ public class PathologiesApi {
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
+ @Value("#{'${files.pathologies_json}'}")
+ private String pathologiesFilePath;
+
@Autowired
private CustomResourceLoader resourceLoader;
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- Logging.LogUserAction(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
+ String endpoint = "(GET) /pathologies";
+ String username = activeUserService.getActiveUser().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(pathologiesFilePath);
List<PathologyDTO> allPathologies;
try {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
}.getType());
} catch (IOException e) {
- Logging.LogUserAction(activeUserService.getActiveUser().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(activeUserService.getActiveUser().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(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
+ Logging.LogUserAction(username, endpoint, "Successfully loaded all authorized pathologies");
return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
- activeUserService.getActiveUser().getUsername(), authentication.getAuthorities(), allPathologies));
+ username, authentication.getAuthorities(), allPathologies));
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
index 696fac039275ae760711ac6d9ee7350c15691f47..7bc4fb7b7a82c385d62f4a56428b13a61a575753 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -31,13 +31,11 @@ public class SecurityApi {
@Autowired
private SecurityConfiguration securityConfiguration;
-
// TODO How to redirect? keycloak off?
@RequestMapping(path = "/login/hbp", method = RequestMethod.GET)
@ConditionalOnExpression("${authentication.enabled:0}")
public void noLogin(HttpServletResponse httpServletResponse) throws IOException {
Logging.LogUserAction(activeUserService.getActiveUser().getUsername(), "(GET) /user/login/hbp", "Unauthorized login.");
-
httpServletResponse.sendRedirect(securityConfiguration.getFrontendRedirectAfterLogin());
}
@@ -47,7 +45,7 @@ public class SecurityApi {
@Value("#{'${services.galaxy.galaxyPassword:password}'}")
private String galaxyPassword;
- @Value("#{'${services.galaxy.galaxyContext:nativeGalaxy}'}")
+ @Value("#{'${services.galaxy.galaxpathoyContext:nativeGalaxy}'}")
private String galaxyContext;
/**
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 7ffffc7ebfca5f53cbd840cf259b8643667fa335..3f6bb87b00683c13ea8684c4464a135c337f7ff6 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -474,8 +474,8 @@ public class ExperimentService {
* @return the experiment information that was retrieved from exareme
*/
public ExperimentDTO createExaremeExperiment(ExperimentDTO experimentDTO, String endpoint) {
-
UserDAO user = activeUserService.getActiveUser();
+
Logging.LogUserAction(user.getUsername(), endpoint, "Running the algorithm...");
ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, endpoint);
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 65ab563a91ca742cb81d154592a5e2f8bf81e26e..fb4e06de77f68567e992054cc6ea66a447d673f7 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -82,3 +82,8 @@ keycloak:
# cors-exposed-headers: "*"
# logoutUrl: {{ .Env.LOGOUT_URL }}
+
+# Files are loaded from the resources
+files:
+ pathologies_json: "classPath:/pathologies.json"
+ disabledAlgorithms_json: "classPath:/disabledAlgorithms.json"