Merge remote-tracking branch 'origin/master' into bugfix/ch/Fix-incom…

…patible-with-sqlmodeOnlyFullGroupBy

core/src/main/scripts/importer/validateData.py

@@ -2941,7 +2941,6 @@ def checkLine(self, data):
                     self.logger.error(
                             'Value in DFS_STATUS column is not 0:DiseaseFree, '
                             '1:Recurred/Progressed, 1:Recurred, 1:Progressed',
-                            'DiseaseFree, Recurred/Progressed, Recurred or Progressed',
                             extra={'line_number': self.line_number,
                                    'column_number': col_index + 1,
                                    'cause': value})

docs/deployment/customization/portal.properties-Reference.md

@@ -627,6 +627,30 @@ By default, the tree is expanded (property value is `false`).
 skin.geneset_hierarchy.collapse_by_default = true
 ```
 
+## Cross study expression and protein data
+
+
+By default we hide expression data for multi-study queries as they are 
+usually not normalized across studies. For the public cBioPortal for instance, only TCGA Pancan Atlas studies expression data has been normalized.  
+
+If you know the expression data in your instance is comparable, or is comparable for a subset of
+studies, you can configure a rule as follows. 
+
+The value of this property can be boolean (true|false) or a javascript function
+which executes at runtime and is passed the list of study objects being queried
+by the user and evaluates whether expression data can be safely displayed.
+
+```
+// a function that accepts the users's selected studies and
+// returns whether or not to allow expression data from the involved studies to be mixed
+enable_cross_study_expression = (selectedStudies)=>{ [your logic] return true|false }
+```
+
+```
+// boolean
+enable_cross_study_expression = true|false
+```
+
 ## Request Body Compression
 
 ### Background

pom.xml

@@ -276,7 +276,7 @@
   </profiles>
 
   <properties>
-    <frontend.version>v5.2.10</frontend.version>
+    <frontend.version>v5.2.11</frontend.version>
     <frontend.groupId>com.github.cbioportal</frontend.groupId>
     <spring.version>5.2.20.RELEASE</spring.version>
     <spring.integration.version>5.3.0.RELEASE</spring.integration.version>

portal/src/main/webapp/config_service.jsp

@@ -113,6 +113,7 @@
             "skin.home_page.unauthorized_studies_global_message",
             "skin.show_settings_menu",
             "skin.hide_logout_button",
+            "enable_cross_study_expression",
             "quick_search.enabled",
             "default_cross_cancer_study_session_id",
             "default_cross_cancer_study_list",

src/main/resources/portal.properties.EXAMPLE

@@ -114,6 +114,11 @@ setting controlling which name should be used to display the authenticated user
 ## enable and set this property to specify a study group to be used to identify public studies for which no specific authorization entries are needed in the `authorities` table
 # always_show_study_group=
 
+## enable expression data in multi-study queries (oncoprint and plots tab)
+# true | false | (studies)=>{ return true } 
+# enable_cross_study_expression=
+
+
 ## change the `-Dauthenticate=` JVM argument to configure
 ## which method of authentication to use (false, googleplus, social_auth_google, social_auth_microsoft, saml, openid, noauthsessionservice)