improve numerical clinical data filter

cBioPortal · Aug 20, 2024 · 24253fb · 24253fb
1 parent 776fbae
commit 24253fb
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Showing 3 changed files with 84 additions and 13 deletions.
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -244,18 +244,39 @@
                         <property name="attribute_value" value="attribute_value"/>
                     </include>
                 </if>
-                <if test="dataFilterValue.start != null || dataFilterValue.end != null">
-                    AND match(attribute_value, '^[\d\.]+$')
+                <if test="dataFilterValue.start != null and dataFilterValue.end == null">
+                    AND match(attribute_value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$')
+                </if>
+                <if test="dataFilterValue.start == null and dataFilterValue.end != null">
+                    AND match(attribute_value, '^&lt;?=?[-+]?[0-9]*[.,]?[0-9]+$')
+                </if>
+                <if test="dataFilterValue.start != null and dataFilterValue.end != null">
+                    AND match(attribute_value, '^[-+]?[0-9]*[.,]?[0-9]+$')
+                </if>
+                <if test="dataFilterValue.start != null or dataFilterValue.end != null">   
                     <choose>
                         <when test="dataFilterValue.start == dataFilterValue.end">
-                            AND abs(minus(cast(attribute_value as float), ${dataFilterValue.start})) &lt; exp(-11)
+                            AND abs(
+                                minus(
+                                    <include refid="castStringValueToFloat">
+                                        <property name="attribute_value" value="attribute_value"/>
+                                    </include>,
+                                    ${dataFilterValue.start}
+                                )
+                            ) &lt; exp(-11)
                         </when>
                         <otherwise>
                             <if test="dataFilterValue.start != null">
-                                AND cast(attribute_value as float) &gt; ${dataFilterValue.start}
+                                AND
+                                <include refid="castStringValueToFloat">
+                                    <property name="attribute_value" value="attribute_value"/>
+                                </include> &gt; ${dataFilterValue.start}
                             </if>
                             <if test="dataFilterValue.end != null">
-                                AND cast(attribute_value as float) &lt;= ${dataFilterValue.end}
+                                AND
+                                <include refid="castStringValueToFloat">
+                                    <property name="attribute_value" value="attribute_value"/>
+                                </include> &lt;= ${dataFilterValue.end}
                             </if>
                         </otherwise>
                     </choose>

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -620,6 +620,29 @@
         </where>
     </sql>
 
+    <!--
+        Convert string values to a single numerical value for filtering purposes only.
+        Not designed as a general purpose decimal number parser.
+        
+        Examples conversions:
+        '6' to 6
+        '>=6' to 6
+        '<=6' to 6
+        '>6' to 6.00..1...
+        '<6' to 5.99..9...
+    -->
+    <sql id="castStringValueToFloat">
+        multiIf(
+            (startsWith(${attribute_value}, '&lt;=') OR startsWith(${attribute_value}, '>=')),
+            cast(substr(${attribute_value}, 3) as float),
+            startsWith(${attribute_value}, '&lt;'),
+            cast(substr(${attribute_value}, 2) as float) - exp(-10),
+            startsWith(${attribute_value}, '>'),
+            cast(substr(${attribute_value}, 2) as float) + exp(-10),
+            cast(${attribute_value} as float)
+        )
+    </sql>
+
     <!-- This is to match actual NA values ('NA', 'NAN', and 'N/A') in addition to the empty string -->
     <sql id="isAttributeValueNA">
         ${attribute_value}=''

diff --git a/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java
@@ -187,12 +187,12 @@ public void getMutationCountsFilteredByAge() {
     }
 
     @Test
-    public void getMutationCountsFilteredByAgeWithSpecialValues() {
+    public void getMutationCountsFilteredByAgeWithOpenStartValues() {
         StudyViewFilter studyViewFilter = new StudyViewFilter();
         studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
 
         // filter patients with age less than 20
-        // (there are 4 patients within this range, which are 301,302,303, and 306)
+        // (there are 4 patients within this range, which are 301, 302, 303, and 306)
         ClinicalDataFilter filter = buildClinicalDataFilter("age", null, 20);
         studyViewFilter.setClinicalDataFilters(List.of(filter));
 
@@ -207,17 +207,44 @@ public void getMutationCountsFilteredByAgeWithSpecialValues() {
             Collections.emptyList()
         );
 
-        // TODO commented out tests below are failing due to a known issue 
-        //  (https://github.com/cBioPortal/rfc80-team/issues/32)
-        // assertEquals(4, mutationCountsFiltered.size());
-        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
-        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
-        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
+        assertEquals(4, mutationCountsFiltered.size());
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
         assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306
 
         // no patients/samples with NA
         assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA")); 
     }
+
+    @Test
+    public void getMutationCountsFilteredByAgeWithOpenEndValues() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        // filter patients with age greater than 80
+        // (there are 4 patients within this range, which are 317, 318, 319, 304, and 305)
+        ClinicalDataFilter filter = buildClinicalDataFilter("age", 80, null);
+        studyViewFilter.setClinicalDataFilters(List.of(filter));
+
+        var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter
+                .getBuilder()
+                .setPatientNumericalClinicalDataFilters(List.of(filter))
+                .build(),
+            true,
+            List.of("mutation_count"),
+            Collections.emptyList()
+        );
+
+        assertEquals(3, mutationCountsFiltered.size());
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 304
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 305
+
+        // patients/samples with NA data: 317, 318, and 319
+        assertEquals(3, findClinicaDataCount(mutationCountsFiltered, "NA"));
+    }
 
     private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) {
         DataFilterValue value = new DataFilterValue();