Changeset 1233 for trunk/grails-app/domain

Timestamp:

Dec 2, 2010, 6:03:36 PM (11 years ago)

Author:

work@…

Message:

• introduced deleteSample method to be sure a sample -and it's relations- are correctly deleted.
• hopefully this resolves #223

File:

• trunk/grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (22 diffs)

trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

@@ -12 +12 @@
  */
 class Study extends TemplateEntity {
-        static searchable = true
+        static searchable = true
 
         SecUser owner           // The owner of the study. A new study is automatically owned by its creator.
-        String title        // The title of the study
-        String code             // currently used as the external study ID, e.g. to reference a study in a SAM module
+        String title            // The title of the study
+        String code              // currently used as the external study ID, e.g. to reference a study in a SAM module
         Date dateCreated
         Date lastUpdated
@@ -27 +27 @@
         List assays
         boolean published = false // Determines whether a study is private (only accessable by the owner and writers) or published (also visible to readers)
-    boolean publicstudy = false  // Determines whether anonymous users are allowed to see this study. This has only effect when published = true
-        
-        static hasMany = [              
+        boolean publicstudy = false  // Determines whether anonymous users are allowed to see this study. This has only effect when published = true
+
+        static hasMany = [
                 subjects: Subject,
                 samplingEvents: SamplingEvent,
@@ -38 +38 @@
                 persons: StudyPerson,
                 publications: Publication,
-                readers: SecUser,
-                writers: SecUser
+                readers: SecUser,
+                writers: SecUser
         ]
 
         static constraints = {
                 owner(nullable: true, blank: true)
-                code(nullable:false, blank:true,unique:true)
+                code(nullable: false, blank: true, unique: true)
 
                 // TODO: add custom validator for 'published' to assess whether the study meets all quality criteria for publication
@@ -60 +60 @@
         // The external identifier (studyToken) is currently the code of the study.
         // It is used from within dbNP submodules to refer to particular study in this GSCF instance.
+
         def getToken() { code }
 
@@ -76 +77 @@
                         name: 'code',
                         type: TemplateFieldType.STRING,
-                        preferredIdentifier:true,
+                        preferredIdentifier: true,
                         comment: 'Fill out the code by which many people will recognize your study',
                         required: true),
@@ -102 +103 @@
          */
         def List<Event> getOrphanEvents() {
-                def orphans =   events.findAll { event -> !event.belongsToGroup(eventGroups) } +
-                                                samplingEvents.findAll { event -> !event.belongsToGroup(eventGroups) }
+                def orphans = events.findAll { event -> !event.belongsToGroup(eventGroups) } +
+                        samplingEvents.findAll { event -> !event.belongsToGroup(eventGroups) }
 
                 return orphans
@@ -129 +130 @@
          */
         List<Template> giveAllAssayTemplates() {
-                TemplateEntity.giveTemplates(( (assays) ? assays : [] ))
+                TemplateEntity.giveTemplates(((assays) ? assays : []))
         }
 
@@ -147 +148 @@
                 // gives trouble when asking .size() to the result
                 // So we also use giveTemplates here
-                TemplateEntity.giveTemplates( ((events) ? events : []) + ((samplingEvents) ? samplingEvents : []) )
-        }
-
+                TemplateEntity.giveTemplates(((events) ? events : []) + ((samplingEvents) ? samplingEvents : []))
+        }
 
         /**
@@ -200 +200 @@
         }
 
-
         /**
          * Delete a specific subject from this study, including all its relations
          * @param subject The subject to be deleted
-         * @return A String which contains a (user-readable) message describing the changes to the database
-         */
-        String deleteSubject(Subject subject) {
-                String msg = "Subject ${subject.name} was deleted"
-
+         * @void
+         */
+        void deleteSubject(Subject subject) {
                 // Delete the subject from the event groups it was referenced in
                 this.eventGroups.each {
                         if (it.subjects.contains(subject)) {
                                 it.removeFromSubjects(subject)
-                                msg += ", deleted from event group '${it.name}'"
                         }
                 }
@@ -219 +215 @@
                 // Delete the samples that have this subject as parent
                 this.samples.findAll { it.parentSubject.equals(subject) }.each {
-                        // This should remove the sample itself too, because of the cascading belongsTo relation
-                        this.removeFromSamples(it)
-                        // But apparently it needs an explicit delete() too
-                        it.delete()
-                        msg += ", sample '${it.name}' was deleted"
+                        this.deleteSample(it)
                 }
 
                 // This should remove the subject itself too, because of the cascading belongsTo relation
                 this.removeFromSubjects(subject)
+
                 // But apparently it needs an explicit delete() too
                 subject.delete()
-
-                return msg
         }
 
@@ -257 +248 @@
          * Delete an event from the study, including all its relations
          * @param Event
-         * @return String
-         */
-        String deleteEvent(Event event) {
-                String msg = "Event ${event} was deleted"
-
+         * @void
+         */
+        void deleteEvent(Event event) {
                 // remove event from the study
                 this.removeFromEvents(event)
@@ -269 +258 @@
                         eventGroup.removeFromEvents(event)
                 }
-
-                return msg
+        }
+
+        /**
+         * Delete a sample from the study, including all its relations
+         * @param Event
+         * @void
+         */
+        void deleteSample(Sample sample) {
+                // remove the sample from the study
+                this.removeFromSamples(sample)
+
+                // remove the sample from any sampling events it belongs to
+                this.samplingEvents.findAll { it.samples.any { it == sample }}.each {
+                        it.removeFromSamples(sample)
+                }
+
+                // remove the sample from any assays it belongs to
+                this.assays.findAll { it.samples.any { it == sample }}.each {
+                        it.removeFromSamples(sample)
+                }
+
+                // Also here, contrary to documentation, an extra delete() is needed
+                // otherwise date is not properly deleted!
+                sample.delete()
         }
 
@@ -276 +287 @@
          * Delete a samplingEvent from the study, including all its relations
          * @param SamplingEvent
-         * @return String
-         */
-        String deleteSamplingEvent(SamplingEvent samplingEvent) {
-                String msg = "SamplingEvent ${samplingEvent} was deleted"
-
+         * @void
+         */
+        void deleteSamplingEvent(SamplingEvent samplingEvent) {
                 // remove event from eventGroups
                 this.eventGroups.each() { eventGroup ->
@@ -289 +298 @@
                 this.samples.findAll { it.parentEvent.equals(samplingEvent) }.each {
                         // This should remove the sample itself too, because of the cascading belongsTo relation
-                        this.removeFromSamples(it)
-                        // But apparently it needs an explicit delete() too
-                        it.delete()
-                        msg += ", sample '${it.name}' was deleted"
+                        this.deleteSample(it)
                 }
 
@@ -302 +308 @@
                 // (Which can be verified by outcommenting this line, then SampleTests.testDeleteViaParentSamplingEvent fails
                 samplingEvent.delete()
-
-                return msg
-        }
-        
+        }
+
         /**
          * Delete an eventGroup from the study, including all its relations
          * @param EventGroup
-         * @return String
-         */
-        String deleteEventGroup(EventGroup eventGroup) {
-                String msg = "EventGroup ${eventGroup} was deleted"
-
+         * @void
+         */
+        void deleteEventGroup(EventGroup eventGroup) {
                 // If the event group contains sampling events
                 if (eventGroup.samplingEvents) {
@@ -328 +330 @@
                                 this.samples.findAll { sample ->
                                         (
-                                                (eventGroup.subjects.findAll {
-                                                        it.equals(sample.parentSubject)
-                                                })
+                                        (eventGroup.subjects.findAll {
+                                                it.equals(sample.parentSubject)
+                                        })
                                                 &&
                                                 (eventGroup.samplingEvents.findAll {
                                                         (
-                                                                (it.id && sample.parentEvent.id && it.id==sample.parentEvent.id)
+                                                        (it.id && sample.parentEvent.id && it.id == sample.parentEvent.id)
                                                                 ||
                                                                 (it.getIdentifier() == sample.parentEvent.getIdentifier())
@@ -344 +346 @@
                                 }.each() { sample ->
                                         // remove sample from study
-
-                                        // -------
-                                        // NOTE, the right samples are found, but the don't
-                                        // get deleted from the database!
-                                        // -------
-
-                                        println ".removing sample '${sample.name}' from study '${this.title}'"
-                                        msg += ", sample '${sample.name}' was deleted"
-                                        this.removeFromSamples( sample )
-
-                                        // remove the sample from any sampling events it belongs to
-                                        this.samplingEvents.findAll { it.samples.any { it == sample }} .each {
-                                                println ".removed sample ${sample.name} from sampling event ${it} at ${it.getStartTimeString()}"
-                                                it.removeFromSamples(sample)
-                                        }
-
-                                        // remove the sample from any assays it belongs to
-                                        this.assays.findAll { it.samples.any { it == sample }} .each {
-                                                println ".removed sample ${sample.name} from assay ${it.name}"
-                                                it.removeFromSamples(sample)
-                                        }
-
-                                        // Also here, contrary to documentation, an extra delete() is needed
-                                        // otherwise date is not properly deleted!
-                                        sample.delete()
+                                        this.deleteSample(sample)
                                 }
                         }
 
                         // remove all samplingEvents from this eventGroup
-                        eventGroup.samplingEvents.findAll{}.each() {
+                        eventGroup.samplingEvents.findAll {}.each() {
                                 eventGroup.removeFromSamplingEvents(it)
-                                println ".removed samplingEvent '${it.name}' from eventGroup '${eventGroup.name}'"
-                                msg += ", samplingEvent '${it.name}' was removed from eventGroup '${eventGroup.name}'"
                         }
                 }
@@ -383 +359 @@
                 if (eventGroup.subjects) {
                         // remove all subject from this eventGroup
-                        eventGroup.subjects.findAll{}.each() {
+                        eventGroup.subjects.findAll {}.each() {
                                 eventGroup.removeFromSubjects(it)
-                                println ".removed subject '${it.name}' from eventGroup '${eventGroup.name}'"
-                                msg += ", subject '${it.name}' was removed from eventGroup '${eventGroup.name}'"
                         }
                 }
 
                 // remove the eventGroup from the study
-                println ".remove eventGroup '${eventGroup.name}' from study '${this.title}'"
                 this.removeFromEventGroups(eventGroup)
 
@@ -397 +370 @@
                 // otherwise cascaded deletes are not properly performed
                 eventGroup.delete()
-
-                return msg
-        }
-
-    /**
-     * Returns true if the given user is allowed to read this study
-     */
-    public boolean canRead(SecUser loggedInUser) {
-        // Anonymous readers are only given access when published and public
-        if( loggedInUser == null ) {
-            return this.publicstudy && this.published;
-        }
+        }
+
+        /**
+         * Returns true if the given user is allowed to read this study
+         */
+        public boolean canRead(SecUser loggedInUser) {
+                // Anonymous readers are only given access when published and public
+                if (loggedInUser == null) {
+                        return this.publicstudy && this.published;
+                }
 
                 // Administrators are allowed to read every study
-                if( loggedInUser.hasAdminRights() ) {
+                if (loggedInUser.hasAdminRights()) {
                         return true;
                 }
 
-        // Owners and writers are allowed to read this study
-        if( this.owner == loggedInUser || this.writers.contains(loggedInUser) ) {
-            return true
-        }
-            
-        // Readers are allowed to read this study when it is published
-        if( this.readers.contains(loggedInUser) && this.published ) {
-            return true
-        }
-        
-        return false
-    }
-
-    /**
-     * Returns true if the given user is allowed to write this study
-     */
-    public boolean canWrite(SecUser loggedInUser) {
-        if( loggedInUser == null ) {
-            return false;
-        }
+                // Owners and writers are allowed to read this study
+                if (this.owner == loggedInUser || this.writers.contains(loggedInUser)) {
+                        return true
+                }
+
+                // Readers are allowed to read this study when it is published
+                if (this.readers.contains(loggedInUser) && this.published) {
+                        return true
+                }
+
+                return false
+        }
+
+        /**
+         * Returns true if the given user is allowed to write this study
+         */
+        public boolean canWrite(SecUser loggedInUser) {
+                if (loggedInUser == null) {
+                        return false;
+                }
 
                 // Administrators are allowed to write every study
-                if( loggedInUser.hasAdminRights() ) {
+                if (loggedInUser.hasAdminRights()) {
                         return true;
                 }
 
-        return this.owner == loggedInUser || this.writers.contains(loggedInUser)
-    }
-
-    /**
-     * Returns true if the given user is the owner of this study
-     */
-    public boolean isOwner(SecUser loggedInUser) {
-        if( loggedInUser == null ) {
-            return false;
-        }
-        return this.owner == loggedInUser
-    }
+                return this.owner == loggedInUser || this.writers.contains(loggedInUser)
+        }
+
+        /**
+         * Returns true if the given user is the owner of this study
+         */
+        public boolean isOwner(SecUser loggedInUser) {
+                if (loggedInUser == null) {
+                        return false;
+                }
+                return this.owner == loggedInUser
+        }
 
         /**
@@ -459 +430 @@
         public static giveWritableStudies(SecUser user, int max) {
                 // User that are not logged in, are not allowed to write to a study
-                if( user == null )
-                        return [];
-                        
+                if (user == null)
+                return [];
+
                 def c = Study.createCriteria()
 
                 // Administrators are allowed to read everything
-                if( user.hasAdminRights() ) {
+                if (user.hasAdminRights()) {
                         return c.list {
                                 maxResults(max)
@@ -474 +445 @@
                         maxResults(max)
                         or {
-                                eq( "owner", user )
+                                eq("owner", user)
                                 writers {
-                                        eq( "id", user.id )
+                                        eq("id", user.id)
                                 }
                         }
@@ -488 +459 @@
                 def c = Study.createCriteria()
 
-        // Administrators are allowed to read everything
-                if( user == null ) {
-            return c.list {
+                // Administrators are allowed to read everything
+                if (user == null) {
+                        return c.list {
                                 maxResults(max)
-                and {
-                    eq( "published", true )
-                    eq( "publicstudy", true )
-                }
-            }
-        } else if( user.hasAdminRights() ) {
-            return c.list {
+                                and {
+                                        eq("published", true)
+                                        eq("publicstudy", true)
+                                }
+                        }
+                } else if (user.hasAdminRights()) {
+                        return c.list {
                                 maxResults(max)
                         }
-                } else  {
-            return c.list {
+                } else {
+                        return c.list {
                                 maxResults(max)
-                or {
-                    eq( "owner", user )
-                    writers {
-                        eq( "id", user.id )
-                    }
-                    and {
-                        readers {
-                            eq( "id", user.id )
-                        }
-                        eq( "published", true )
-                    }
-                }
-            }
-        }
+                                or {
+                                        eq("owner", user)
+                                        writers {
+                                                eq("id", user.id)
+                                        }
+                                        and {
+                                                readers {
+                                                        eq("id", user.id)
+                                                }
+                                                eq("published", true)
+                                        }
+                                }
+                        }
+                }
         }
 }