Merge branch 'master' into xy-plot-cachable

docs/deployment/customization/Caching.md

@@ -34,7 +34,7 @@ manager.createCache(appName + "ClinicalDataCache", config);
 ```
 
 You also need to create a new cache resolver
-in [RedisConfig.java](https://github.com/cBioPortal/cbioportal/blob/master/persistence/persistence-api/src/main/java/org/cbioportal/persistence/config/RedisConfig.java):
+in [RedisConfig.java](https://github.com/cBioPortal/cbioportal/blob/master/src/main/java/org/cbioportal/persistence/config/RedisConfig.java):
 
 ```
 @Bean

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

@@ -162,6 +162,18 @@ Prevent users from saving data by removing all Download tabs and download and co
 skin.hide_download_controls=
 ```
 
+### Quick select buttons
+
+This feature allows you to generate a Quick Select button on the top of your query page. The button, when clicked on, will automatically select the studies mentioned after the '#`.
+
+```
+skin.quick_select_buttons=
+```
+
+The format for the string should be ``<Button name>|<Mouse-over text>#study1a,study1b,....`` where:
+- `<Button name>` will be the label on the button (for e.g. TCGA PanCancer Atlas Studies, Curated set of non-redundant studies)
+- `<Mouse-over text>` will be the text that is displayed when you hover over the button (for e.g. 218 studies that are manually curated including TCGA and non-TCGA studies with no overlapping samples)
+- `study1a,study1b,....` are the study IDs of the loaded studies that should be selected when the button is clicked. (for e.g. acbc_mskcc_2015,acc_tcga_pan_can_atlas_2018)
 
 
 ### Control default setting for filtering of genes in mutation and CNA tables of patient view

docs/deployment/docker/import_data.md

@@ -16,13 +16,13 @@ These are the commands for importing `study_es_0` gene panels (`data_gene_panel_
 ```shell
 docker compose run \
     cbioportal \
-    bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt'
+    bash -c 'cd /core/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt'
 ```
 
 ```shell
 docker compose run \
     cbioportal \
-    bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt'
+    bash -c 'cd /core/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt'
 ```
 
 #### Step 2 - Import data

docs/development/cBioPortal-ER-Diagram.md

@@ -1,4 +1,6 @@
 # cBioPortal ER Diagram
 [cBioPortal ER Diagram - PDF Version](https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/db-scripts/cbioportal-er-diagram.pdf)
 
-![cBioPortal ER Diagram](https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/db-scripts/cbioportal-er-diagram.png)
+[cBioPortal ER Diagram - PNG File](https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/db-scripts/cbioportal-er-diagram.png)
+
+<img src="https://github.com/cBioPortal/cbioportal/raw/master/src/main/resources/db-scripts/cbioportal-er-diagram.png" alt="cBioPortal ER Diagram" style="max-width: 100%; height: auto;">

pom.xml

@@ -12,7 +12,7 @@
 
 	<groupId>org.cbioportal</groupId>
 	<artifactId>cbioportal</artifactId>
-	<version>6.0.23-SNAPSHOT</version>
+	<version>6.0.24-SNAPSHOT</version>
 
 	<description>cBioPortal for Cancer Genomics</description>
 
@@ -27,7 +27,7 @@
 		<!--        TODO replace with version of cbioportal frontend with compatible
         login url-->
 		<frontend.groupId>com.github.cbioportal</frontend.groupId>
-		<frontend.version>v6.0.22</frontend.version>
+		<frontend.version>v6.0.23</frontend.version>
 
         <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
 		<db.version>2.13.1</db.version>

src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java

@@ -168,7 +168,10 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
         List<String> involvedCancerStudies = context.involvedCancerStudies();
 
         var result = studyViewRepository.getClinicalDataCounts(context, filteredAttributes);
-
+
+        // normalize data counts so that values like TRUE, True, and true are all merged in one count
+        result.forEach(item -> item.setCounts(StudyViewColumnarServiceUtil.normalizeDataCounts(item.getCounts())));
+
         // attributes may be missing in result set because they have been filtered out
         // e.g. if the filtered samples happen to have no SEX data, they will not appear in the list
         // even though the inferred value of those attributes is NA

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -190,7 +190,7 @@
         WITH clinical_data_query AS (
         SELECT
         attribute_name AS attributeId,
-        upper(attribute_value) AS value,
+        attribute_value AS value,
         cast(count(*) AS INTEGER) as count
         FROM clinical_data_derived
         <where>

src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java

@@ -81,12 +81,12 @@ public void getCenterCounts() {
         var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts();
 
         assertEquals(7, categoricalClinicalDataCounts.size());
-        assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "MSK"));
-        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "DFCI"));
-        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "CHOP"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "MDA"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "OHSU"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UCSF"));
+        assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "msk"));
+        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "dfci"));
+        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "chop"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "mda"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ohsu"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ucsf"));
         // 1 empty string + 1 'NA' + 12 samples with no data
         assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
     }
@@ -108,12 +108,16 @@ public void getDeadCounts() {
         assertTrue(categoricalClinicalDataCountsOptional.isPresent());
         var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts();
 
-        assertEquals(6, categoricalClinicalDataCounts.size());
-        assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "TRUE"));
-        assertEquals(4, findClinicaDataCount(categoricalClinicalDataCounts, "FALSE"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT RELEASED"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT COLLECTED"));
-        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UNKNOWN"));
+        assertEquals(10, categoricalClinicalDataCounts.size());
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "True"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "TRUE"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "true"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "False"));
+        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "FALSE"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "false"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Released"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Not Collected"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "Unknown"));
         // 1 empty string + 1 'N/A' + 12 samples with no data
         assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
     }