Merge branch 'dev' into release and bump version

gb-backend-e2e/src/test/groovy/tests/QuerySpec.groovy

@@ -149,7 +149,7 @@ class QuerySpec extends RESTSpec {
                 statusCode: 201,
                 body      : [
                         name             : 'test query',
-                        type             : 'patient',
+                        subjectDimension : 'patient',
                         queryConstraint  : [type: 'true'],// TODO replace with TrueConstraint representation from tm-core-api
                         bookmarked       : true,
                         subscribed       : false,

gb-backend/build.gradle

@@ -10,8 +10,8 @@ buildscript {
     }
 }
 
-version "0.1.0-RC1"
-group "nl.thehyve.gb.backend"
+version "0.2.0-RC1"
+group "nl.thehyve"
 
 apply plugin:"eclipse"
 apply plugin:"idea"

gb-backend/grails-app/domain/nl/thehyve/gb/backend/Query.groovy

@@ -9,7 +9,7 @@ package nl.thehyve.gb.backend
 class Query {
 
     String name
-    String type
+    String subjectDimension
     String username
     String queryConstraint
     Boolean bookmarked = false
@@ -31,7 +31,7 @@ class Query {
 
     static constraints = {
         name maxSize: 1000
-        type maxSize: 255, nullable: false
+        subjectDimension maxSize: 255, nullable: false
         username maxSize: 50
         queryConstraint type: 'text', nullable: false
         bookmarked nullable: true

gb-backend/grails-app/services/nl/thehyve/gb/backend/NotificationsMailService.groovy

@@ -70,11 +70,11 @@ class NotificationsMailService {
     /**
      * Fetches a list of sets for all queries user subscribed to with specific frequency
      * for which there were instances added or removed comparing to a previous query set
-     * and groups it by query type
+     * and groups it by query type (subject dimension).
      *
      * @param frequency
      * @param username
-     * @return A map of query type to list of sets with changes
+     * @return A map of query subject dimension to list of sets with changes
      */
     private Map<String, List<QuerySetChangesRepresentation>> getQueryTypeToQuerySetChangesRepresentations(
             SubscriptionFrequency frequency,

gb-backend/grails-app/services/nl/thehyve/gb/backend/QueryService.groovy

@@ -30,7 +30,7 @@ class QueryService {
         query.with {
             new QueryRepresentation(
                     id,
-                    type,
+                    subjectDimension,
                     username,
                     name,
                     queryConstraint ? BindingHelper.readFromString(queryConstraint, Object) : null,
@@ -97,7 +97,7 @@ class QueryService {
         }
         query.with {
             name = representation.name
-            type = representation.type // TODO TMT-741 - validate query type, currently it can be any string
+            subjectDimension = representation.subjectDimension // TODO TMT-741 - validate query subjectDimension, currently it can be any string
             queryConstraint = BindingHelper.writeAsString(representation.queryConstraint)
             bookmarked = representation.bookmarked ?: false
             subscribed = representation.subscribed ?: false

gb-backend/grails-app/services/nl/thehyve/gb/backend/QuerySetService.groovy

@@ -82,7 +82,7 @@ class QuerySetService {
     }
 
     void createQuerySetWithQueryInstances(QueryRepresentation queryRepresentation) {
-        log.info "Create set of type ${queryRepresentation.type} for query ${queryRepresentation.id}"
+        log.info "Create set of subjectDimension ${queryRepresentation.subjectDimension} for query ${queryRepresentation.id}"
         List<String> setInstances = getSetInstancesForQuery(queryRepresentation)
         Query query = queryService.getQueryById(queryRepresentation.id)
         QuerySet querySet = new QuerySet(
@@ -167,14 +167,14 @@ class QuerySetService {
 
     private List<String> getSetInstancesForQuery(QueryRepresentation query) {
         def newDimensionElements =
-                getDimensionElements(query.type, query.queryConstraint as Map)?.elements
-        listSetInstanceIds(query.type, newDimensionElements)
+                getDimensionElements(query.subjectDimension, query.queryConstraint as Map)?.elements
+        listSetInstanceIds(query.subjectDimension, newDimensionElements)
     }
 
     private List<String> getSetInstancesWithImpersonation(QueryRepresentation query) {
         def newDimensionElements =
-                getDimensionElementsForUser(query.type, query.queryConstraint as Map, query.username)?.elements
-        listSetInstanceIds(query.type, newDimensionElements)
+                getDimensionElementsForUser(query.subjectDimension, query.queryConstraint as Map, query.username)?.elements
+        listSetInstanceIds(query.subjectDimension, newDimensionElements)
     }
 
     private List<QuerySet> getQuerySets(Long queryId, User currentUser, Integer maxNumberOfSets) {
@@ -289,7 +289,7 @@ class QuerySetService {
                 set.createDate,
                 set.query.name,
                 set.query.id,
-                set.query.type,
+                set.query.subjectDimension,
                 objectsAdded,
                 objectsRemoved
         )

gb-backend/src/integration-test/groovy/nl/thehyve/gb/backend/QueryServiceSpec.groovy

@@ -46,7 +46,7 @@ class QueryServiceSpec extends Specification {
         def query1Representation = new QueryRepresentation()
         query1Representation.with {
             name = 'test query 1'
-            type = 'patient'
+            subjectDimension = 'patient'
             queryConstraint = [type: 'true']
             bookmarked = true
             subscribed = true
@@ -57,7 +57,7 @@ class QueryServiceSpec extends Specification {
         def query2Representation = new QueryRepresentation()
         query2Representation.with {
             name = 'test query 2'
-            type = 'diagnosis'
+            subjectDimension = 'diagnosis'
             queryConstraint = [type: 'true']
             bookmarked = true
             subscribed = false
@@ -67,7 +67,7 @@ class QueryServiceSpec extends Specification {
         def query3Representation = new QueryRepresentation()
         query3Representation.with {
             name = 'test query 3'
-            type = 'sample1'
+            subjectDimension = 'sample1'
             queryConstraint = [type: 'negation', arg: [type: 'true']]
             bookmarked = false
             subscribed = true

gb-backend/src/integration-test/groovy/nl/thehyve/gb/backend/QuerySetServiceSpec.groovy

@@ -161,7 +161,7 @@ class QuerySetServiceSpec extends Specification {
         def query1_invalid = new Query()
         query1_invalid.with {
             name = 'fail on scan query'
-            type = 'patient'
+            subjectDimension = 'patient'
             queryConstraint = '{"type": "concept", "conceptCode": "NON-EXISTENT"}'
             bookmarked = true
             subscribed = true
@@ -171,7 +171,7 @@ class QuerySetServiceSpec extends Specification {
         def query2 = new Query()
         query2.with {
             name = 'test query 1'
-            type = 'diagnosis'
+            subjectDimension = 'diagnosis'
             queryConstraint = '{"type": "true"}'
             bookmarked = true
             subscribed = true
@@ -181,7 +181,7 @@ class QuerySetServiceSpec extends Specification {
         def query3 = new Query()
         query3.with {
             name = 'test query 2'
-            type = 'patient'
+            subjectDimension = 'patient'
             queryConstraint = '{"type": "negation", "arg": {"type": "true"}}'
             bookmarked = false
             subscribed = true

gb-backend/src/main/groovy/nl/thehyve/gb/backend/EmailGenerator.groovy

@@ -62,25 +62,25 @@ class EmailGenerator {
         queryTypeToQuerySetsChanges.collect { type, querySetsChanges ->
             String table = updatesHtmlTablePerType(querySetsChanges)
             [
-                    "For subscription of type <b>${type}</b> there are the following updates:",
+                    "Cohort changes (type <b>${type}</b>):",
                     table
             ].join(BR)
         }.join(BR)
     }
 
     protected static String updatesHtmlTablePerType(List<QuerySetChangesRepresentation> querySetsChanges) {
-        String queryIdHeader = 'Your Query ID'
-        String queryNameHeader = 'Your Query Name'
+        String queryNameHeader = 'Your Cohort Name'
+        String queryIdHeader = 'Your Cohort ID'
         String addedSubjectHeader = 'Number of added instances'
         String removedSubjectHeader = 'Number of removed instances'
         String dateOfChangeHeader = 'Date of change'
 
         List<String> tableRows = querySetsChanges.collect { QuerySetChangesRepresentation change ->
-            "<tr><td>${change.queryId}</td><td>${change.queryName}</td><td>${change.objectsAdded.size()}</td><td>${change.objectsRemoved.size()}</td><td>${DATE_TIME_FORMAT.format(change.createDate)}</td></tr>".toString()
+            "<tr><td>${change.queryName}</td><td>${change.queryId}</td><td>${change.objectsAdded.size()}</td><td>${change.objectsRemoved.size()}</td><td>${DATE_TIME_FORMAT.format(change.createDate)}</td></tr>".toString()
         }
 
         '<table cellpadding="10">' +
-                '<tr>' + th(queryIdHeader) + th(queryNameHeader) + th(addedSubjectHeader) + th(removedSubjectHeader) + th(dateOfChangeHeader) + '</tr>' +
+                '<tr>' + th(queryNameHeader) + th(queryIdHeader) + th(addedSubjectHeader) + th(removedSubjectHeader) + th(dateOfChangeHeader) + '</tr>' +
                 tableRows.join('') +
                 '</table>'
     }

gb-backend/src/main/groovy/nl/thehyve/gb/backend/representation/QueryRepresentation.groovy

@@ -23,7 +23,7 @@ class QueryRepresentation {
     Long id
 
     @Size(min = 1)
-    String type
+    String subjectDimension
 
     @Size(min = 1)
     String username

gb-backend/src/test/groovy/nl/thehyve/gb/backend/user/EmailGeneratorSpec.groovy

@@ -27,22 +27,22 @@ class EmailGeneratorSpec extends Specification {
     def 'body of the query subscription updates'() {
         String clientAppName = 'ABC'
         Map<String, List<QuerySetChangesRepresentation>> querySetChanges = [
-                diagnosis: [
+                Diagnosis: [
                         new QuerySetChangesRepresentation(
                                 queryId: 36,
                                 queryName: 'test diagnosis query',
                                 createDate: DATE_TIME_FORMAT.parse('2019-02-07 09:59'),
-                                queryType: 'diagnosis',
+                                queryType: 'Diagnosis',
                                 objectsAdded: ['d1', 'd2', 'd3'],
                                 objectsRemoved: []
                         )
                 ],
-                patient  : [
+                Patient  : [
                         new QuerySetChangesRepresentation(
                                 queryId: 35,
                                 queryName: 'first saved query',
                                 createDate: DATE_TIME_FORMAT.parse('2017-05-03 13:30'),
-                                queryType: 'patient',
+                                queryType: 'Patient',
                                 objectsAdded: ['subj1', 'subj2', 'subj3'],
                                 objectsRemoved: ['subj10'],
 
@@ -51,7 +51,7 @@ class EmailGeneratorSpec extends Specification {
                                 queryId: 50,
                                 queryName: 'test query',
                                 createDate: DATE_TIME_FORMAT.parse('2017-08-16 8:45'),
-                                queryType: 'diagnosis',
+                                queryType: 'Diagnosis',
                                 objectsAdded: ['subj100', 'subj200', 'subj300', 'subj400', 'subj500', 'subj600'],
                                 objectsRemoved: ['subj101', 'subj201'],
                         ),
@@ -61,16 +61,16 @@ class EmailGeneratorSpec extends Specification {
         def expectedContent = 'Hello,<br /><br />' +
                 'You have subscribed to be notified to data updates for one or more queries that you have saved in the "ABC" application.' +
                 '<br />In this email you will find an overview of all data updates up until October 3 2018 15:25:' +
-                '<p />For subscription of type <b>diagnosis</b> there are the following updates:' +
+                '<p />Cohort changes (type <b>Diagnosis</b>):' +
                 '<br /><table cellpadding="10"><tr>' +
-                '<th align="left">Your Query ID</th><th align="left">Your Query Name</th><th align="left">Number of added instances</th><th align="left">Number of removed instances</th><th align="left">Date of change</th></tr>' +
-                '<tr><td>36</td><td>test diagnosis query</td><td>3</td><td>0</td><td>February 7 2019 9:59</td></tr>' +
+                '<th align="left">Your Cohort Name</th><th align="left">Your Cohort ID</th><th align="left">Number of added instances</th><th align="left">Number of removed instances</th><th align="left">Date of change</th></tr>' +
+                '<tr><td>test diagnosis query</td><td>36</td><td>3</td><td>0</td><td>February 7 2019 9:59</td></tr>' +
                 '</table>' +
-                '<br />For subscription of type <b>patient</b> there are the following updates:' +
+                '<br />Cohort changes (type <b>Patient</b>):' +
                 '<br /><table cellpadding="10">' +
-                '<tr><th align="left">Your Query ID</th><th align="left">Your Query Name</th><th align="left">Number of added instances</th><th align="left">Number of removed instances</th><th align="left">Date of change</th></tr>' +
-                '<tr><td>35</td><td>first saved query</td><td>3</td><td>1</td><td>May 3 2017 13:30</td></tr>' +
-                '<tr><td>50</td><td>test query</td><td>6</td><td>2</td><td>August 16 2017 8:45</td></tr>' +
+                '<tr><th align="left">Your Cohort Name</th><th align="left">Your Cohort ID</th><th align="left">Number of added instances</th><th align="left">Number of removed instances</th><th align="left">Date of change</th></tr>' +
+                '<tr><td>first saved query</td><td>35</td><td>3</td><td>1</td><td>May 3 2017 13:30</td></tr>' +
+                '<tr><td>test query</td><td>50</td><td>6</td><td>2</td><td>August 16 2017 8:45</td></tr>' +
                 '</table>' +
                 '<p />You can login to ABC to reload your queries and review the new data available.' +
                 '<br />Regards,<br /><br />ABC'