Changeset 13 for trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy

Timestamp:

Feb 10, 2011, 5:03:02 PM (11 years ago)

Author:

robert@…

Message:

Improved user interface and implemented basic export functionality

File:

• trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy (modified) (8 diffs)

trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy

@@ -12 +12 @@
  */
 class GscfService {
-
         def config = ConfigurationHolder.config
 
         static transactional = true
-
-
 
         /**
@@ -51 +48 @@
                 return "${config.gscf.baseURL}/study/showByToken/" + studyToken
         }
-        
-        /**
-        * Returns the url to add a new study in GSCF
-        *
-        * @return                       URL to redirect the user to
-        */
-   public String urlAddStudy( String studyToken ) {
-           return config.gscf.baseURL + config.gscf.addStudyPath
-   }
-
-   /**
-   * Retrieves the currently logged in user from GSCF
-   *
-   * @param sessionToken String
-   *
-   * @return Map
-   */
-  public Map getUser(String sessionToken) {
-          def user = [:]
-          this.callGSCF(sessionToken, "getUser").each {
-                  user[ it.key ] = it.value;
-          }
-          return user
-  }
-   
+
+        /**
+         * Returns the url to add a new study in GSCF
+         *
+         * @return                      URL to redirect the user to
+         */
+        public String urlAddStudy( String studyToken ) {
+                return config.gscf.baseURL + config.gscf.addStudyPath
+        }
+
+        /**
+         * Retrieves the currently logged in user from GSCF
+         *
+         * @param sessionToken String
+         *
+         * @return Map
+         */
+        public Map getUser(String sessionToken) {
+                def user = [:]
+                this.callGSCF(sessionToken, "getUser").each {
+                        user[ it.key ] = it.value;
+                }
+                return user
+        }
+
         /**
          * Retrieve a list of Studies from the GSCF
@@ -87 +84 @@
         }
 
-        
+
         /**
          * Retrieve a list of Studies from the GSCF
@@ -116 +113 @@
                 } catch( ResourceNotFoundException e ) {
                         throw new ResourceNotFoundException( "Study with token " + studyToken + " not found in GSCF" )
-                        throw e // Other exceptions are thrown as they appear
-                }
+                } // Other exceptions are thrown as they appear
 
                 // Return only the first element of the list, since we are only interested in one study
-                if( list.size() == 0 ) {
+                if( list?.size() ) {
+                        return list[0];
+                } else {
                         return []
-                } else {
-                        return list[0];
                 }
         }
@@ -172 +168 @@
         }
 
-        /** 
-         * Retrieve a list of Samples from the GSCF
-         * 
-         * @param sessionToken String
-         * @param assay Assay (parameter assay is optional, only used when you want to limit the list of samples of an Assay within a Study)
-         * 
-         * @return ArrayList 
-         */
-        public ArrayList getSamples(String sessionToken, String assayToken) throws NotAuthorizedException, ResourceNotFoundException {
-                // Samples of a Study limited to a single Assay
-                try {
-                        return this.callGSCF(sessionToken, "getSamples", ["assayToken":assayToken])
-                } catch( NotAuthorizedException e ) {
-                        throw new NotAuthorizedException( "User is not authorized to access study for assay with token " + assayToken )
-                } catch( ResourceNotFoundException e ) {1
-                        throw new ResourceNotFoundException( "Assay with token " + assayToken + " not found in GSCF" )
-                } // Other exceptions are thrown as they appear
-
-        }
-
+        
         /**
          * Retrieve a single Sample from the GSCF
-         * 
+         *
          * @param sessionToken String
          * @param assay Assay
-         * @param sample Sample  
-         * 
-         * @return ArrayList 
+         * @param sample Sample
+         *
+         * @return ArrayList
          */
         public def getSample(String sessionToken, String assayToken, String sampleToken) throws NotAuthorizedException, ResourceNotFoundException {
@@ -219 +196 @@
 
         }
+        
+        /** 
+         * Retrieve a list of Samples from the GSCF
+         * 
+         * @param sessionToken String
+         * @param assay Assay (parameter assay is optional, only used when you want to limit the list of samples of an Assay within a Study)
+         * 
+         * @return ArrayList 
+         */
+        public ArrayList getSamples(String sessionToken, String assayToken) throws NotAuthorizedException, ResourceNotFoundException {
+                // Samples of a Study limited to a single Assay
+                try {
+                        return this.callGSCF(sessionToken, "getSamples", ["assayToken":assayToken])
+                } catch( NotAuthorizedException e ) {
+                        throw new NotAuthorizedException( "User is not authorized to access study for assay with token " + assayToken )
+                } catch( ResourceNotFoundException e ) {1
+                        throw new ResourceNotFoundException( "Assay with token " + assayToken + " not found in GSCF" )
+                } // Other exceptions are thrown as they appear
+
+        }
+
+        /**
+         * Retrieve a list of samples from the GSCF
+         *
+         * @param sessionToken String
+         * @param sampleTokens List of sampleTokens
+         *
+         * @return ArrayList
+         */
+        public def getSamples(String sessionToken, List sampleTokens) throws NotAuthorizedException, ResourceNotFoundException {
+                def list
+
+                try {
+                        list = this.callGSCF(sessionToken, "getSamples", ["sampleToken": sampleTokens])
+                } catch( NotAuthorizedException e ) {
+                        throw new NotAuthorizedException( "User is not authorized to access samples" )
+                } catch( ResourceNotFoundException e ) {
+                        throw new ResourceNotFoundException( "Samples with token " + sampleTokens + " not found in GSCF" )
+                } // Other exceptions are thrown as they appear
+
+                // Return only the first element of the list, since we are only interested in one sample
+                return list
+        }
+
 
         /**
@@ -273 +294 @@
 
                 // concat all Rest Call specific arguments behind addr
-                restParams.each {parameter -> 
+                restParams.each {parameter ->
                         // If a list is given as value, the parameter should show up multiple times
                         if( parameter.value instanceof Collection ) {
@@ -281 +302 @@
                         } else {
                                 addr += "&${parameter.key}=" + parameter.value.toString().encodeAsURL()
-                        } 
+                        }
                 }