Merge branch 'develop' into examples

vip-api/pom.xml

@@ -111,18 +111,6 @@ knowledge of the CeCILL-B license and that you accept its terms.
             <version>${keycloak.version}</version>
         </dependency>
 
-        <!-- Json mapping library -->
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
-            <version>${jackson.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.datatype</groupId>
-            <artifactId>jackson-datatype-jsr310</artifactId>
-            <version>${jackson.version}</version>
-        </dependency>
-
         <!-- Validation implementation -->
         <dependency>
             <groupId>org.hibernate</groupId>

vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringWebConfig.java

@@ -108,15 +108,10 @@ public void addCorsMappings(CorsRegistry registry) {
     }
 
     /*
-     to verify that the proxy ist still valid each day
+     to verify that the proxy is still valid each day
      */
     @Override
     public void addInterceptors(InterceptorRegistry registry) {
         registry.addInterceptor(vipConfigurer);
     }
-
-    @Bean
-    public ObjectMapper objectMapper() {
-        return Jackson2ObjectMapperBuilder.json().build();
-    }
 }

vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ApiBusiness.java

@@ -11,6 +11,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
+import org.springframework.security.authentication.BadCredentialsException;
 import org.springframework.stereotype.Service;
 
 @Service
@@ -60,6 +61,9 @@ private User signin(String username, String password) throws ApiException {
             logger.info("Credentials OK for " + username);
             return user;
         } catch (BusinessException e) {
+            if (e.getMessage().startsWith("Authentication failed")) {
+                throw new ApiException(ApiException.ApiError.BAD_CREDENTIALS);
+            }
             throw new ApiException("Authentication Error", e);
         }
     }

vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ExecutionBusiness.java

@@ -298,8 +298,7 @@ public String initExecution(Execution execution)
         }
         String resultsLocation = execution.getResultsLocation();
         if (resultsLocation != null) {
-            inputMap.put(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME,
-                         resultsLocation);
+            inputMap.put(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME, resultsLocation);
         }
 
         checkInputExecNameIsValid(execution.getName());
@@ -368,39 +367,35 @@ private String initExecution(String pipelineId,
             // Check that all pipeline inputs are present
             Pipeline p = pipelineBusiness.getPipelineWithResultsDirectory(pipelineId);
             for (PipelineParameter pp : p.getParameters()) {
+                // always true on vip
                 if (pp.isReturnedValue()) {
                     continue;
                 }
-                // pp is an input
-                if (!(inputValues.get(pp.getName()) == null)) {
+                // ok if input is present
+                if ( inputValues.get(pp.getName()) != null) {
                     continue;
                 }
-                // pp is an empty input
+                // then ok if input has a default value (and we set it)
+                // beware : with gwendia, optional always have an defaultValue (either defined or No_Value_Provided)
                 if (pp.getDefaultValue() != null) {
                     inputValues.put(pp.getName(), pp.getDefaultValue().toString());
                     continue;
                 }
-                // pp is an empty input with no default value
+                // then ok if it is optional
+                // beware, with gwendia it should not be possible to enter this case (see previous condition)
                 if (pp.isOptional()) {
-                    inputValues.put("no", pp.getDefaultValue().toString());//that's how optional values are handled in VIP
                     continue;
                 }
-                // pp is an empty input with no default value and it is not optional
-                logger.error("Error initialising {}, missing {} parameter",
-                        pipelineId, pp.getName());
-                throw new ApiException("Parameter " + pp.getName() + " is empty while it is not optional and it has no default value.");
+                // error : pp is an empty input with no default value and it is not optional
+                logger.error("Error initialising {}, missing {} parameter", pipelineId, pp.getName());
+                throw new ApiException(ApiException.ApiError.INPUT_FIELD_MISSING, pp.getName());
             }
 
-            boolean hasInputResultsDirectory =
-                inputValues.containsKey(
-                    CoreConstants.RESULTS_DIRECTORY_PARAM_NAME);
-
-            boolean hasPipelineResultsDirectory =
-                p.getParameters().stream().anyMatch(
-                        param ->
+            boolean inputsContainsResultsDirectoryInput = inputValues.containsKey(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME);
+            boolean pipelineHasResultsDirectoryInput = p.getParameters().stream().anyMatch(param ->
                         param.getName().equals(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME));
 
-            if (hasInputResultsDirectory && !hasPipelineResultsDirectory) {
+            if (inputsContainsResultsDirectoryInput && ! pipelineHasResultsDirectoryInput) {
                 logger.error("Missing results-directory for {}", pipelineId);
                 throw new ApiException(
                     "Input has parameter results-directory but it is not defined in pipeline.");