Sample Retrieval

- Add versionRange to pom.xml to conform to specifications - Add ClickHouseDB query for retrieving sample_ids from sample table based on attribute
cBioPortal · May 17, 2023 · 5848c47 · 5848c47
1 parent f1efaf9
commit 5848c47
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diff --git a/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml b/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml
@@ -78,7 +78,7 @@
                     </trim>
                 </where>
             </if>
-            <if test="clinicalDataFilters != null and !clinicalDataFilters.isEmpty()">
+            <!-- <if test="clinicalDataFilters != null and !clinicalDataFilters.isEmpty()">
                 INTERSECT
                 SELECT sample_unique_id
                 FROM sample
@@ -103,6 +103,27 @@
                         </foreach>
                     </trim>
                  )
+            </if>  -->
+             <if test="clinicalDataFilters != null and !clinicalDataFilters.isEmpty()">
+                <foreach item="clinicalDataFilter" collection="clinicalDataFilters" open="INTERSECT" separator="INTERSECT">
+                    SELECT sample_unique_id
+                    FROM sample_clinical_attribute_numeric
+                    WHERE attribute_name = '${clinicalDataFilter.attributeId}'
+                    <foreach item="dataFilterValue" collection="clinicalDataFilter.values" open=" AND ((" separator=") OR (" close="))">
+                        <trim prefix="" prefixOverrides="AND">
+                            <if test="dataFilterValue.value eq 'NA'">
+                                AND attribute_value = -1000000
+                            </if>
+                            <if test="dataFilterValue.start != null">
+                                AND attribute_value &gt; ${dataFilterValue.start}
+                            </if>
+                            <if test="dataFilterValue.end != null">
+                                AND attribute_value &lt;= ${dataFilterValue.end}
+                            </if>
+                        </trim>
+                    </foreach>
+                </foreach>
+                )
             </if>
             <!-- ... extend for other elements of the StudyViewFilter object -->
         </trim>

diff --git a/pom.xml b/pom.xml
@@ -1203,6 +1203,7 @@
                     <goals>
                       <goal>execute</goal>
                     </goals>
+                    <versionRange></versionRange>
                   </pluginExecutionFilter>
                   <action>
                     <ignore/>