init singlecell endpoint

dev/test.sql

@@ -0,0 +1,47 @@
+DROP TABLE IF EXISTS single_cell_expression;
+CREATE TABLE IF NOT EXISTS single_cell_expression (
+    GENETIC_PROFILE_ID int NOT NULL,
+    SAMPLE_ID int NOT NULL,
+    TISSUE varchar(255) NOT NULL,
+    CELL_TYPE varchar(255) NOT NULL,
+    ENTREZ_GENE_ID int NOT NULL,
+    EXPRESSION_VALUE float,
+    FOREIGN KEY(GENETIC_PROFILE_ID) REFERENCES genetic_profile(GENETIC_PROFILE_ID),
+    FOREIGN KEY(SAMPLE_ID) REFERENCES sample(INTERNAL_ID),
+    FOREIGN KEY(ENTREZ_GENE_ID) REFERENCES gene(ENTREZ_GENE_ID)
+);
+
+DELETE FROM genetic_profile WHERE STABLE_ID = "single_cell_expression";
+INSERT INTO genetic_profile (
+    GENETIC_PROFILE_ID, STABLE_ID, CANCER_STUDY_ID, GENETIC_ALTERATION_TYPE,
+    DATATYPE, NAME, DESCRIPTION, SHOW_PROFILE_IN_ANALYSIS_TAB
+) VALUES (
+    2, "SINGLE_CELL_EXPRESSION", 1, "single_cell_expression",
+    "single_cell_expression", "Single Cell Expression", "Test Single Cell Expression", 1
+);
+
+DELETE FROM gene WHERE ENTREZ_GENE_ID = 100;
+INSERT INTO gene (
+    ENTREZ_GENE_ID, HUGO_GENE_SYMBOL, GENETIC_ENTITY_ID
+) VALUES (
+    100, "TEST_GENE", 1
+);
+
+INSERT INTO single_cell_expression (
+    GENETIC_PROFILE_ID, SAMPLE_ID, TISSUE, CELL_TYPE, ENTREZ_GENE_ID, EXPRESSION_VALUE
+) VALUES (
+    2, 1, "omentum", "B cell", 7157, 1.34
+), (
+    2, 2, "omentum", "D cell", 7157, 4.24
+), (
+    2, 2, "omentum", "D cell", 100, -1.24
+), (
+    2, 2, "awesome tissue", "D cell", 7157, 8.24
+), (
+    2, 2, "awesome tissue", "D cell", 100, NULL
+);
+
+
+/* command:
+mysql -hlocalhost -P3306 --protocol=tcp --default-auth=mysql_native_password --get-server-public-key -ucbio -pP@ssword1 cbioportal < dev/test.sql 
+*/

src/main/java/org/cbioportal/model/MolecularProfile.java

@@ -25,7 +25,8 @@ public enum MolecularAlterationType {
         PROTEIN_ARRAY_PROTEIN_LEVEL,
         PROTEIN_ARRAY_PHOSPHORYLATION,
         GENESET_SCORE,
-        GENERIC_ASSAY
+        GENERIC_ASSAY,
+        SINGLE_CELL_EXPRESSION
     }
 
     public enum DataType {
@@ -165,4 +166,4 @@ public Boolean getPatientLevel() {
     public void setPatientLevel(Boolean patientLevel) {
         this.patientLevel = patientLevel;
     }
-}
+}

src/main/java/org/cbioportal/model/SingleCellExpression.java

@@ -0,0 +1,33 @@
+package org.cbioportal.model;
+
+import jakarta.validation.constraints.NotNull;
+
+public class SingleCellExpression extends Alteration {
+
+    @NotNull
+    private String tissue;
+    @NotNull
+    private String cellType;
+    @NotNull
+    private Float expressionValue;
+
+    public String getTissue() {
+        return tissue;
+    }
+    public void setTissue(String tissue) {
+        this.tissue = tissue;
+    }
+    public String getCellType() {
+        return cellType;
+    }
+    public void setCellType(String cellType) {
+        this.cellType = cellType;
+    }
+    public Float getExpressionValue() {
+        return expressionValue;
+    }
+    public void setExpressionValue(Float expressionValue) {
+        this.expressionValue = expressionValue;
+    }
+
+}

src/main/java/org/cbioportal/model/SingleCellExpressionGroupedBySample.java

@@ -0,0 +1,150 @@
+package org.cbioportal.model;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import jakarta.validation.constraints.NotNull;
+
+public class SingleCellExpressionGroupedBySample extends UniqueKeyBase {
+
+    @NotNull
+    private String molecularProfileId;
+    @NotNull
+    private String sampleId;
+    @NotNull
+    private String patientId;
+    @NotNull
+    private String studyId;
+    @NotNull
+    private List<SingleCellExpressionGroupedByTissue> singleCellExpressionGroupedByTissues;
+
+    public SingleCellExpressionGroupedBySample(String sampleId, List<SingleCellExpression> singleCellExpressions) {
+        // TODO: do a check if all are equal?
+        this.sampleId = sampleId;
+        this.molecularProfileId = singleCellExpressions.get(0).getMolecularProfileId();
+        this.patientId = singleCellExpressions.get(0).getPatientId();
+        this.studyId = singleCellExpressions.get(0).getStudyId();
+
+        Map<String, List<SingleCellExpression>> tissueMap = singleCellExpressions.stream()
+            .collect(Collectors.groupingBy(SingleCellExpression::getTissue));
+        this.singleCellExpressionGroupedByTissues = tissueMap.entrySet().stream()
+            .map(e -> new SingleCellExpressionGroupedByTissue(e.getKey(), e.getValue()))
+            .collect(Collectors.toList());
+    }
+
+    public String getMolecularProfileId() {
+        return molecularProfileId;
+    }
+    public void setMolecularProfileId(String molecularProfileId) {
+        this.molecularProfileId = molecularProfileId;
+    }
+    public String getSampleId() {
+        return sampleId;
+    }
+    public void setSampleId(String sampleId) {
+        this.sampleId = sampleId;
+    }
+    public String getPatientId() {
+        return patientId;
+    }
+    public void setPatientId(String patientId) {
+        this.patientId = patientId;
+    }
+    public String getStudyId() {
+        return studyId;
+    }
+    public void setStudyId(String studyId) {
+        this.studyId = studyId;
+    }
+    public List<SingleCellExpressionGroupedByTissue> getSingleCellExpressionGroupedByTissues() {
+        return singleCellExpressionGroupedByTissues;
+    }
+    public void setSingleCellExpressionGroupedByTissues(
+            List<SingleCellExpressionGroupedByTissue> singleCellExpressionGroupedByTissues) {
+        this.singleCellExpressionGroupedByTissues = singleCellExpressionGroupedByTissues;
+    }
+
+    class SingleCellExpressionGroupedByTissue {
+        @NotNull
+        private String tissue;
+        @NotNull
+        private List<SingleCellExpressionGroupedByCellType> singleCellExpressionGroupedByCellTypes;
+
+        public SingleCellExpressionGroupedByTissue(String tissue,
+                List<SingleCellExpression> singleCellExpressions) {
+            this.tissue = tissue;
+
+            Map<String, List<SingleCellExpression>> cellTypeMap = singleCellExpressions.stream()
+                .collect(Collectors.groupingBy(SingleCellExpression::getCellType));
+            this.singleCellExpressionGroupedByCellTypes = cellTypeMap.entrySet().stream()
+                .map(e -> new SingleCellExpressionGroupedByCellType(e.getKey(), e.getValue()))
+                .collect(Collectors.toList());
+        }
+        public String getTissue() {
+            return tissue;
+        }
+        public void setTissue(String tissue) {
+            this.tissue = tissue;
+        }
+        public List<SingleCellExpressionGroupedByCellType> getSingleCellExpressionGroupedByCellTypes() {
+            return singleCellExpressionGroupedByCellTypes;
+        }
+        public void setSingleCellExpressionGroupedByCellTypes(
+                List<SingleCellExpressionGroupedByCellType> singleCellExpressionGroupedByCellTypes) {
+            this.singleCellExpressionGroupedByCellTypes = singleCellExpressionGroupedByCellTypes;
+        }
+
+        class SingleCellExpressionGroupedByCellType {
+            @NotNull
+            private String cellType;
+            @NotNull
+            private List<geneExpression> geneExpressions;
+
+            public SingleCellExpressionGroupedByCellType(String cellType,
+                    List<SingleCellExpression> singleCellExpressions) {
+                this.cellType = cellType;
+
+                this.geneExpressions = singleCellExpressions.stream()
+                    .map(e -> new geneExpression(e.getEntrezGeneId(), e.getExpressionValue()))
+                    .collect(Collectors.toList());
+            }
+            public String getCellType() {
+                return cellType;
+            }
+            public void setCellType(String cellType) {
+                this.cellType = cellType;
+            }
+            public List<geneExpression> getGeneExpressions() {
+                return geneExpressions;
+            }
+            public void setGeneExpressions(List<geneExpression> geneExpressions) {
+                this.geneExpressions = geneExpressions;
+            }
+
+            class geneExpression {
+                @NotNull
+                private Integer entrezGeneId;
+                private Float expressionValue;
+
+                public geneExpression(Integer entrezGeneId, Float expressionValue) {
+                    this.entrezGeneId = entrezGeneId;
+                    this.expressionValue = expressionValue;
+                }
+
+                public Integer getEntrezGeneId() {
+                    return entrezGeneId;
+                }
+                public void setEntrezGeneId(Integer entrezGeneId) {
+                    this.entrezGeneId = entrezGeneId;
+                }
+                public Float getExpressionValue() {
+                    return expressionValue;
+                }
+                public void setExpressionValue(Float expressionValue) {
+                    this.expressionValue = expressionValue;
+                }
+            }
+        }
+    }
+}

src/main/java/org/cbioportal/persistence/SingleCellExpressionRepository.java

@@ -0,0 +1,15 @@
+package org.cbioportal.persistence;
+
+import java.util.List;
+
+import org.cbioportal.model.SingleCellExpression;
+import org.springframework.cache.annotation.Cacheable;
+
+public interface SingleCellExpressionRepository {
+
+    @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
+    public List<SingleCellExpression> fetchSingleCellExpressionInMolecularProfile(
+            String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds, Integer pageSize,
+            Integer pageNumber, String sortBy, String direction);
+
+}

src/main/java/org/cbioportal/persistence/mybatis/SingleCellExpressionMapper.java

@@ -0,0 +1,13 @@
+package org.cbioportal.persistence.mybatis;
+
+import org.cbioportal.model.SingleCellExpression;
+
+import java.util.List;
+
+public interface SingleCellExpressionMapper {
+
+    public List<SingleCellExpression> fetchSingleCellExpressionInMolecularProfile(
+            String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds, Integer limit, Integer offset,
+            String sortBy, String direction);
+
+}

src/main/java/org/cbioportal/persistence/mybatis/SingleCellExpressionMyBatisRepository.java

@@ -0,0 +1,27 @@
+package org.cbioportal.persistence.mybatis;
+
+import java.util.List;
+
+import org.cbioportal.model.SingleCellExpression;
+import org.cbioportal.persistence.SingleCellExpressionRepository;
+import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Repository;
+
+@Repository
+public class SingleCellExpressionMyBatisRepository implements SingleCellExpressionRepository {
+
+    @Autowired
+    private SingleCellExpressionMapper singleCellExpressionMapper;
+
+    @Override
+    public List<SingleCellExpression> fetchSingleCellExpressionInMolecularProfile(
+            String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds, Integer pageSize, Integer pageNumber,
+            String sortBy, String direction) {
+
+        List<SingleCellExpression> singleCellExpressions = singleCellExpressionMapper
+                .fetchSingleCellExpressionInMolecularProfile(molecularProfileId,
+                        sampleListId, entrezGeneIds, pageSize, PaginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
+        return singleCellExpressions;
+    }
+}

src/main/java/org/cbioportal/service/SingleCellExpressionService.java

@@ -0,0 +1,22 @@
+package org.cbioportal.service;
+
+import java.util.List;
+
+import org.cbioportal.service.exception.MolecularProfileNotFoundException;
+
+import org.cbioportal.model.SingleCellExpression;
+import org.cbioportal.model.SingleCellExpressionGroupedBySample;
+
+public interface SingleCellExpressionService {
+
+    List<SingleCellExpression> fetchSingleCellExpressionInMolecularProfile(
+            String molecularProfileId, String sampleListId,
+            List<Integer> entrezGeneIds, Integer pageSize, Integer pageNumber,
+            String sortBy, String direction)
+            throws MolecularProfileNotFoundException;
+
+    List<SingleCellExpressionGroupedBySample> fetchSingleCellExpressionInMolecularProfileGroupedBySample(
+            String molecularProfileId, String sampleListId,
+            List<Integer> entrezGeneIds, Integer pageSize, Integer pageNumber)
+            throws MolecularProfileNotFoundException;
+}

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

@@ -0,0 +1,50 @@
+package org.cbioportal.service.impl;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.cbioportal.service.SingleCellExpressionService;
+import org.cbioportal.service.exception.MolecularProfileNotFoundException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import org.cbioportal.model.SingleCellExpression;
+import org.cbioportal.model.SingleCellExpressionGroupedBySample;
+import org.cbioportal.persistence.SingleCellExpressionRepository;
+
+@Service
+public class SingleCellExpressionServiceImpl implements SingleCellExpressionService {
+
+    @Autowired
+    private SingleCellExpressionRepository singleCellExpressionRepository;
+
+    @Override
+    public List<SingleCellExpression> fetchSingleCellExpressionInMolecularProfile(
+            String molecularProfileId, String sampleListId,
+            List<Integer> entrezGeneIds, Integer pageSize, Integer pageNumber,
+            String sortBy, String direction)
+            throws MolecularProfileNotFoundException {
+
+        return singleCellExpressionRepository.fetchSingleCellExpressionInMolecularProfile(
+                molecularProfileId, sampleListId, entrezGeneIds, pageSize, pageNumber, sortBy, direction);
+    }
+
+    @Override
+    public List<SingleCellExpressionGroupedBySample> fetchSingleCellExpressionInMolecularProfileGroupedBySample(
+            String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds,
+            Integer pageSize, Integer pageNumber)
+            throws MolecularProfileNotFoundException {
+
+        List<SingleCellExpression> singleCellExpressionData = fetchSingleCellExpressionInMolecularProfile(
+                molecularProfileId, sampleListId, entrezGeneIds, pageSize, pageNumber, "sampleId", "ASC");
+
+        Map<String, List<SingleCellExpression>> singleCellExpressionGroupedBySamples = singleCellExpressionData.stream()
+                .collect(Collectors.groupingBy(SingleCellExpression::getSampleId));
+
+        return singleCellExpressionGroupedBySamples.entrySet().stream()
+                .map(e -> new SingleCellExpressionGroupedBySample(e.getKey(), e.getValue()))
+                .collect(Collectors.toList());
+    }
+
+}