Merge pull request #5330 from ersinciftci/quick-search

Add API support for quick search
cBioPortal · Nov 27, 2018 · b234274 · b234274
2 parents 9e294f5 + fac4651
commit b234274
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Showing 32 changed files with 369 additions and 114 deletions.
diff --git a/persistence/persistence-api/src/main/java/org/cbioportal/persistence/GeneRepository.java b/persistence/persistence-api/src/main/java/org/cbioportal/persistence/GeneRepository.java
@@ -38,10 +38,10 @@
 
 public interface GeneRepository {
 
-    List<Gene> getAllGenes(String alias, String projection, Integer pageSize, Integer pageNumber, String sortBy, 
+    List<Gene> getAllGenes(String keyword, String alias, String projection, Integer pageSize, Integer pageNumber, String sortBy, 
                            String direction);
 
-    BaseMeta getMetaGenes(String alias);
+    BaseMeta getMetaGenes(String keyword, String alias);
 
     Gene getGeneByEntrezGeneId(Integer entrezGeneId);
 

diff --git a/persistence/persistence-api/src/main/java/org/cbioportal/persistence/PatientRepository.java b/persistence/persistence-api/src/main/java/org/cbioportal/persistence/PatientRepository.java
@@ -7,6 +7,11 @@
 
 public interface PatientRepository {
 
+    List<Patient> getAllPatients(String keyword, String projection, Integer pageSize, Integer pageNumber, String sortBy,
+        String direction);
+
+    BaseMeta getMetaPatients(String keyword);
+
     List<Patient> getAllPatientsInStudy(String studyId, String projection, Integer pageSize, Integer pageNumber, 
                                         String sortBy, String direction);
 

diff --git a/persistence/persistence-api/src/main/java/org/cbioportal/persistence/StudyRepository.java b/persistence/persistence-api/src/main/java/org/cbioportal/persistence/StudyRepository.java
@@ -8,10 +8,10 @@
 
 public interface StudyRepository {
 
-    List<CancerStudy> getAllStudies(String projection, Integer pageSize, Integer pageNumber,
+    List<CancerStudy> getAllStudies(String keyword, String projection, Integer pageSize, Integer pageNumber,
                                     String sortBy, String direction);
 
-    BaseMeta getMetaStudies();
+    BaseMeta getMetaStudies(String keyword);
 
     CancerStudy getStudy(String studyId, String projection);
 

diff --git a/...ence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java b/...ence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/GeneMapper.java
@@ -7,10 +7,10 @@
 
 public interface GeneMapper {
 
-    List<Gene> getGenes(String alias, String projection, Integer limit, Integer offset, String sortBy,
+    List<Gene> getGenes(String keyword, String alias, String projection, Integer limit, Integer offset, String sortBy,
                         String direction);
 
-    BaseMeta getMetaGenes(String alias);
+    BaseMeta getMetaGenes(String keyword, String alias);
 
     Gene getGeneByEntrezGeneId(Integer entrezGeneId, String projection);
 

diff --git a/...tence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java b/...tence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java
@@ -19,17 +19,17 @@ public class GeneMyBatisRepository implements GeneRepository {
     private OffsetCalculator offsetCalculator;
 
     @Override
-    public List<Gene> getAllGenes(String alias, String projection, Integer pageSize, Integer pageNumber, String sortBy,
+    public List<Gene> getAllGenes(String keyword, String alias, String projection, Integer pageSize, Integer pageNumber, String sortBy,
                                   String direction) {
 
-        return geneMapper.getGenes(alias, projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), 
+        return geneMapper.getGenes(keyword, alias, projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), 
             sortBy, direction);
     }
 
     @Override
-    public BaseMeta getMetaGenes(String alias) {
+    public BaseMeta getMetaGenes(String keyword, String alias) {
 
-        return geneMapper.getMetaGenes(alias);
+        return geneMapper.getMetaGenes(keyword, alias);
     }
 
     @Override

diff --git a/...e/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java b/...e/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/PatientMapper.java
@@ -7,10 +7,10 @@
 
 public interface PatientMapper {
 
-    List<Patient> getPatients(List<String> studyIds, List<String> patientIds, String projection, Integer limit, 
-                              Integer offset, String sortBy, String direction);
+    List<Patient> getPatients(List<String> studyIds, List<String> patientIds, String keyword, String projection, 
+        Integer limit, Integer offset, String sortBy, String direction);
 
-    BaseMeta getMetaPatients(List<String> studyIds, List<String> patientIds);
+    BaseMeta getMetaPatients(List<String> studyIds, List<String> patientIds, String keyword);
 
     Patient getPatient(String studyId, String patientId, String projection);
 

diff --git a/...ce-mybatis/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java b/...ce-mybatis/src/main/java/org/cbioportal/persistence/mybatis/PatientMyBatisRepository.java
@@ -7,7 +7,6 @@
 import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
-import org.springframework.web.accept.PathExtensionContentNegotiationStrategy;
 
 import java.util.Arrays;
 import java.util.List;
@@ -20,18 +19,31 @@ public class PatientMyBatisRepository implements PatientRepository {
     @Autowired
     private OffsetCalculator offsetCalculator;
 
+    @Override
+    public List<Patient> getAllPatients(String keyword, String projection, Integer pageSize, Integer pageNumber,
+            String sortBy, String direction) {
+        return patientMapper.getPatients(null, null, keyword, projection, pageSize,
+            offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
+    }
+
+    @Override
+    public BaseMeta getMetaPatients(String keyword) {
+
+        return patientMapper.getMetaPatients(null, null, keyword);
+    }
+
     @Override
     public List<Patient> getAllPatientsInStudy(String studyId, String projection, Integer pageSize, Integer pageNumber,
                                                String sortBy, String direction) {
 
-        return patientMapper.getPatients(Arrays.asList(studyId), null, projection, pageSize,
+        return patientMapper.getPatients(Arrays.asList(studyId), null, null, projection, pageSize,
             offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
     }
 
     @Override
     public BaseMeta getMetaPatientsInStudy(String studyId) {
 
-        return patientMapper.getMetaPatients(Arrays.asList(studyId), null);
+        return patientMapper.getMetaPatients(Arrays.asList(studyId), null, null);
     }
 
     @Override
@@ -43,13 +55,13 @@ public Patient getPatientInStudy(String studyId, String patientId) {
     @Override
     public List<Patient> fetchPatients(List<String> studyIds, List<String> patientIds, String projection) {
 
-        return patientMapper.getPatients(studyIds, patientIds, projection, 0, 0, null, null);
+        return patientMapper.getPatients(studyIds, patientIds, null, projection, 0, 0, null, null);
     }
 
     @Override
     public BaseMeta fetchMetaPatients(List<String> studyIds, List<String> patientIds) {
 
-        return patientMapper.getMetaPatients(studyIds, patientIds);
+        return patientMapper.getMetaPatients(studyIds, patientIds, null);
     }
 
 	@Override

diff --git a/...nce/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java b/...nce/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/StudyMapper.java
@@ -8,10 +8,10 @@
 
 public interface StudyMapper {
 
-    List<CancerStudy> getStudies(List<String> studyIds, String projection, Integer limit, Integer offset, String sortBy, 
+    List<CancerStudy> getStudies(List<String> studyIds, String keyword, String projection, Integer limit, Integer offset, String sortBy, 
         String direction);
 
-    BaseMeta getMetaStudies(List<String> studyIds);
+    BaseMeta getMetaStudies(List<String> studyIds, String keyword);
 
     CancerStudy getStudy(String studyId, String projection);
 

diff --git a/...ence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java b/...ence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/StudyMyBatisRepository.java
@@ -19,16 +19,16 @@ public class StudyMyBatisRepository implements StudyRepository {
     private OffsetCalculator offsetCalculator;
 
     @Override
-    public List<CancerStudy> getAllStudies(String projection, Integer pageSize, Integer pageNumber,
+    public List<CancerStudy> getAllStudies(String keyword, String projection, Integer pageSize, Integer pageNumber,
                                            String sortBy, String direction) {
 
-        return studyMapper.getStudies(null, projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), sortBy,
-                direction);
+        return studyMapper.getStudies(null, keyword, projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), 
+            sortBy, direction);
     }
 
     @Override
-    public BaseMeta getMetaStudies() {
-        return studyMapper.getMetaStudies(null);
+    public BaseMeta getMetaStudies(String keyword) {
+        return studyMapper.getMetaStudies(null, keyword);
     }
 
     @Override
@@ -39,13 +39,13 @@ public CancerStudy getStudy(String studyId, String projection) {
 	@Override
 	public List<CancerStudy> fetchStudies(List<String> studyIds, String projection) {
 
-        return studyMapper.getStudies(studyIds, projection, 0, 0, null, null);
+        return studyMapper.getStudies(studyIds, null, projection, 0, 0, null, null);
 	}
 
 	@Override
 	public BaseMeta fetchMetaStudies(List<String> studyIds) {
 
-        return studyMapper.getMetaStudies(studyIds);
+        return studyMapper.getMetaStudies(studyIds, null);
 	}
 
 	@Override

diff --git a/.../persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml b/.../persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/GeneMapper.xml
@@ -14,23 +14,43 @@
             gene.LENGTH AS "${prefix}length"
         </if>
     </sql>
+
+    <sql id="from">
+        FROM gene
+        <if test="alias != null">
+            INNER JOIN gene_alias ON gene.ENTREZ_GENE_ID = gene_alias.ENTREZ_GENE_ID
+        </if>
+    </sql>
+
+    <sql id="where">
+        <where>
+            <if test="alias != null">
+                gene_alias.GENE_ALIAS = #{alias}
+            </if>
+            <if test="keyword != null">
+                <bind name="searchKeyword" value="'%' + keyword.trim().toLowerCase() + '%'" />
+                LOWER(gene.HUGO_GENE_SYMBOL) like #{searchKeyword}
+            </if>
+        </where>
+    </sql>
 
     <select id="getGenes" resultType="org.cbioportal.model.Gene">
         SELECT
         <include refid="select">
             <property name="prefix" value=""/>
         </include>
-        FROM gene
-        <if test="alias != null">
-            INNER JOIN gene_alias ON gene.ENTREZ_GENE_ID = gene_alias.ENTREZ_GENE_ID
-            WHERE gene_alias.GENE_ALIAS = #{alias}
-        </if>
-        <if test="sortBy != null and projection != 'ID'">
+        <include refid="from"/>
+        <include refid="where"/>
+        <if test="sortBy != null and projection != 'ID' and keyword == null">
             ORDER BY ${sortBy} ${direction}
         </if>
-        <if test="projection == 'ID'">
+        <if test="projection == 'ID' and keyword == null">
             ORDER BY gene.ENTREZ_GENE_ID ASC
         </if>
+        <if test="keyword != null">
+            <bind name="orderKeyword" value="keyword.trim().toLowerCase() + '%'" />
+            ORDER BY CASE WHEN gene.HUGO_GENE_SYMBOL LIKE #{orderKeyword} THEN 0 ELSE 1 END, gene.HUGO_GENE_SYMBOL
+        </if>
         <if test="limit != null and limit != 0">
             LIMIT #{limit} OFFSET #{offset}
         </if>
@@ -39,11 +59,8 @@
     <select id="getMetaGenes" resultType="org.cbioportal.model.meta.BaseMeta">
         SELECT
         COUNT(*) AS totalCount
-        FROM gene
-        <if test="_parameter != null">
-            INNER JOIN gene_alias ON gene.ENTREZ_GENE_ID = gene_alias.ENTREZ_GENE_ID
-            WHERE gene_alias.GENE_ALIAS = #{alias}
-        </if>
+        <include refid="from"/>
+        <include refid="where"/>
     </select>
 
     <select id="getGeneByEntrezGeneId" resultType="org.cbioportal.model.Gene">

diff --git a/...rsistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml b/...rsistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/PatientMapper.xml
@@ -24,14 +24,20 @@
 
     <sql id="where">
         <where>
-            <if test="patientIds == null">
-                cancer_study.CANCER_STUDY_IDENTIFIER = #{studyIds[0]}
+            <if test="keyword == null">
+                <if test="patientIds == null and studyIds != null">
+                    cancer_study.CANCER_STUDY_IDENTIFIER = #{studyIds[0]}
+                </if>
+                <if test="patientIds != null">
+                    (cancer_study.CANCER_STUDY_IDENTIFIER, patient.STABLE_ID) IN
+                    <foreach index="i" collection="patientIds" open="(" separator="," close=")">
+                        (#{studyIds[${i}]}, #{patientIds[${i}]})
+                    </foreach>
+                </if>
             </if>
-            <if test="patientIds != null">
-                (cancer_study.CANCER_STUDY_IDENTIFIER, patient.STABLE_ID) IN
-                <foreach index="i" collection="patientIds" open="(" separator="," close=")">
-                    (#{studyIds[${i}]}, #{patientIds[${i}]})
-                </foreach>
+            <if test="keyword != null">
+                <bind name="searchKeyword" value="'%' + keyword.trim().toLowerCase() + '%'" />
+                LOWER(patient.STABLE_ID) like #{searchKeyword}
             </if>
         </where>
     </sql>
@@ -43,12 +49,16 @@
         </include>
         <include refid="from"/>
         <include refid="where"/>
-        <if test="sortBy != null and projection != 'ID'">
+        <if test="sortBy != null and projection != 'ID' and keyword == null">
             ORDER BY ${sortBy} ${direction}
         </if>
-        <if test="projection == 'ID'">
+        <if test="projection == 'ID' and keyword == null">
             ORDER BY patient.STABLE_ID ASC
         </if>
+        <if test="keyword != null">
+            <bind name="orderKeyword" value="keyword.trim().toLowerCase() + '%'" />
+            ORDER BY CASE WHEN patient.STABLE_ID LIKE #{orderKeyword} THEN 0 ELSE 1 END, patient.STABLE_ID
+        </if>
         <if test="limit != null and limit != 0">
             LIMIT #{limit} OFFSET #{offset}
         </if>

diff --git a/...persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml b/...persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml
@@ -42,11 +42,28 @@
         FROM cancer_study
         INNER JOIN sample_list ON cancer_study.CANCER_STUDY_ID = sample_list.CANCER_STUDY_ID
         INNER JOIN sample_list_list ON sample_list.LIST_ID = sample_list_list.LIST_ID
-        <if test="projection == 'DETAILED'">
+        <if test="projection == 'DETAILED' or keyword != null">
             INNER JOIN type_of_cancer ON cancer_study.TYPE_OF_CANCER_ID = type_of_cancer.TYPE_OF_CANCER_ID
         </if>
     </sql>
 
+    <sql id="where">
+        <where>
+            <if test="studyIds != null and !studyIds.isEmpty()">
+                cancer_study.CANCER_STUDY_IDENTIFIER IN
+                <foreach item="item" collection="studyIds" open="(" separator="," close=")">
+                    #{item}
+                </foreach>
+            </if>
+            <if test="keyword != null">
+                <bind name="searchKeyword" value="'%' + keyword.trim().toLowerCase() + '%'" />
+                LOWER(cancer_study.NAME) like #{searchKeyword} OR
+                LOWER(cancer_study.DESCRIPTION) like #{searchKeyword} OR
+                LOWER(type_of_cancer.NAME) like #{searchKeyword}
+            </if>
+        </where>
+    </sql>
+
     <select id="getStudies" resultType="org.cbioportal.model.CancerStudy">
         SELECT
         <include refid="select">
@@ -60,21 +77,19 @@
             <include refid="selectDetailed"/>
         </if>
         <include refid="from"/>
-        <where>
-            <if test="studyIds != null and !studyIds.isEmpty()">
-                cancer_study.CANCER_STUDY_IDENTIFIER IN
-                <foreach item="item" collection="studyIds" open="(" separator="," close=")">
-                    #{item}
-                </foreach>
-            </if>
-        </where>
+        <include refid="where"/>
         GROUP BY cancer_study.CANCER_STUDY_ID
-        <if test="sortBy != null and projection != 'ID'">
+        <if test="sortBy != null and projection != 'ID' and keyword == null">
             ORDER BY ${sortBy} ${direction}
         </if>
-        <if test="projection == 'ID'">
+        <if test="projection == 'ID' and keyword == null">
             ORDER BY cancer_study.CANCER_STUDY_IDENTIFIER ASC
         </if>
+        <if test="keyword != null">
+            <bind name="orderKeyword" value="keyword.trim().toLowerCase() + '%'" />
+            ORDER BY CASE WHEN cancer_study.NAME LIKE #{orderKeyword} THEN 0 ELSE 1 END,
+            CASE WHEN cancer_study.NAME LIKE '%tcga%' THEN 0 ELSE 1 END, cancer_study.NAME
+        </if>
         <if test="limit != null and limit != 0">
             LIMIT #{limit} OFFSET #{offset}
         </if>
@@ -84,14 +99,10 @@
         SELECT
         COUNT(*) AS totalCount
         FROM cancer_study
-        <where>
-            <if test="list != null and !list.isEmpty()">
-                cancer_study.CANCER_STUDY_IDENTIFIER IN
-                <foreach item="item" collection="list" open="(" separator="," close=")">
-                    #{item}
-                </foreach>
-            </if>
-        </where>
+        <if test="keyword != null">
+            INNER JOIN type_of_cancer ON cancer_study.TYPE_OF_CANCER_ID = type_of_cancer.TYPE_OF_CANCER_ID
+        </if>
+        <include refid="where"/>
     </select>
 
     <select id="getStudy" resultType="org.cbioportal.model.CancerStudy">