working version

.editorconfig

@@ -0,0 +1,9 @@
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+[*.{java,py}]
+indent_style = space
+indent_size = 4

dev/data_single_cell_expression.txt

@@ -0,0 +1,4 @@
+Sample_Id	Entrez_Gene_Id	Hugo_Symbol	Cell_Type	Tissue	Expression_Value
+SHAH_H000004_T09_01_WG01		TP53	CELLTYPE	TISSUE	57.4
+SHAH_H000004_T09_01_WG01	7157		CELLTYPE2	TISSUE	57.4
+SAMPLE1	7157	TP53	CELLTYPE2	TISSUE	57.4

dev/meta_single_cell_expression.txt

@@ -0,0 +1,8 @@
+cancer_study_identifier: msk_spectrum_tme_2022
+genetic_alteration_type: SINGLE_CELL_EXPRESSION
+datatype: SINGLE_CELL_EXPRESSION
+stable_id: single_cell_expression
+show_profile_in_analysis_tab: false
+profile_name: single cell expression
+profile_description: single cell expression test
+data_filename: data_single_cell_expression.txt

scripts/importer/allowed_data_types.txt

@@ -68,3 +68,4 @@ GENERIC_ASSAY	LIMIT-VALUE	*
 GENERIC_ASSAY	BINARY	*
 GENERIC_ASSAY	CATEGORICAL	*
 STRUCTURAL_VARIANT	SV	structural_variants
+SINGLE_CELL_EXPRESSION	SINGLE_CELL_EXPRESSION	*

scripts/importer/cbioportal_common.py

@@ -66,6 +66,7 @@ class MetaFileTypes(object):
     CNA_CONTINUOUS = 'meta_contCNA'
     SEG = 'meta_segment'
     EXPRESSION = 'meta_expression'
+    SINGLE_CELL_EXPRESSION = 'meta_single_cell_expression'
     MUTATION = 'meta_mutations_extended'
     MUTATION_UNCALLED = 'meta_mutations_uncalled'
     METHYLATION = 'meta_methylation'
@@ -214,6 +215,18 @@ class MetaFileTypes(object):
         'data_filename': True,
         'gene_panel': False
     },
+    MetaFileTypes.SINGLE_CELL_EXPRESSION: {
+        'cancer_study_identifier': True,
+        'genetic_alteration_type': True,
+        'datatype': True,
+        'stable_id': True,
+        'source_stable_id': False,
+        'show_profile_in_analysis_tab': True,
+        'profile_name': True,
+        'profile_description': True,
+        'data_filename': True,
+        'gene_panel': False
+    },
     MetaFileTypes.METHYLATION: {
         'cancer_study_identifier': True,
         'genetic_alteration_type': True,
@@ -399,6 +412,7 @@ class MetaFileTypes(object):
     MetaFileTypes.CNA_CONTINUOUS: "org.mskcc.cbio.portal.scripts.ImportProfileData",
     MetaFileTypes.SEG: "org.mskcc.cbio.portal.scripts.ImportCopyNumberSegmentData",
     MetaFileTypes.EXPRESSION: "org.mskcc.cbio.portal.scripts.ImportProfileData",
+    MetaFileTypes.SINGLE_CELL_EXPRESSION: "org.mskcc.cbio.portal.scripts.ImportProfileData",
     MetaFileTypes.MUTATION: "org.mskcc.cbio.portal.scripts.ImportProfileData",
     MetaFileTypes.MUTATION_UNCALLED: "org.mskcc.cbio.portal.scripts.ImportProfileData",
     MetaFileTypes.METHYLATION: "org.mskcc.cbio.portal.scripts.ImportProfileData",
@@ -692,7 +706,8 @@ def get_meta_file_type(meta_dictionary, logger, filename):
         ("GENESET_SCORE", "P-VALUE"): MetaFileTypes.GSVA_PVALUES,
         ("GENERIC_ASSAY", "LIMIT-VALUE"): MetaFileTypes.GENERIC_ASSAY_CONTINUOUS,
         ("GENERIC_ASSAY", "BINARY"): MetaFileTypes.GENERIC_ASSAY_BINARY,
-        ("GENERIC_ASSAY", "CATEGORICAL"): MetaFileTypes.GENERIC_ASSAY_CATEGORICAL
+        ("GENERIC_ASSAY", "CATEGORICAL"): MetaFileTypes.GENERIC_ASSAY_CATEGORICAL,
+        ("SINGLE_CELL_EXPRESSION", "SINGLE_CELL_EXPRESSION"): MetaFileTypes.SINGLE_CELL_EXPRESSION
     }
     result = None
     if 'genetic_alteration_type' in meta_dictionary and 'datatype' in meta_dictionary:

src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java

@@ -570,6 +570,7 @@ public static void deleteCancerStudy(int internalCancerStudyId) throws DaoExcept
                 "DELETE FROM patient WHERE CANCER_STUDY_ID=?",
                 "DELETE FROM sample_list WHERE CANCER_STUDY_ID=?",
                 "DELETE FROM structural_variant WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
+                "DELETE FROM single_cell_expression WHERE GENETIC_PROFILE_ID IN (SELECT GENETIC_PROFILE_ID FROM genetic_profile WHERE CANCER_STUDY_ID=?)",
                 "DELETE FROM genetic_profile_link WHERE REFERRED_GENETIC_PROFILE_ID IN (select GENETIC_PROFILE_ID FROM genetic_profile where CANCER_STUDY_ID=?)",
                 "DELETE FROM genetic_profile WHERE CANCER_STUDY_ID=?",
                 "DELETE FROM gistic_to_gene WHERE GISTIC_ROI_ID IN (SELECT GISTIC_ROI_ID FROM gistic WHERE CANCER_STUDY_ID=?)",

src/main/java/org/mskcc/cbio/portal/dao/DaoSingleCellExpression.java

@@ -0,0 +1,66 @@
+/*
+ * Copyright (c) 2024 The Hyve B.V.
+ * This code is licensed under the GNU Affero General Public License (AGPL),
+ * version 3, or (at your option) any later version.
+ */
+
+/*
+ * This file is part of cBioPortal.
+ *
+ * cBioPortal is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+/*
+ * @author Matthijs Pon
+*/
+
+package org.mskcc.cbio.portal.dao;
+
+import java.sql.*;
+import org.mskcc.cbio.portal.model.*;
+
+public class DaoSingleCellExpression {
+
+	private DaoSingleCellExpression() {
+	}
+
+    public static void addSingleCellExpression(SingleCellExpression singleCellExpression) throws DaoException {
+        Connection connection = null;
+        PreparedStatement preparedStatement = null;
+        ResultSet resultSet = null;
+
+        try {
+        	// Open connection to database
+            connection = JdbcUtil.getDbConnection(DaoGeneticProfileLink.class);
+
+	        // Prepare SQL statement
+            preparedStatement = connection.prepareStatement("INSERT INTO single_cell_expression "
+                + "(GENETIC_PROFILE_ID, SAMPLE_ID, TISSUE, CELL_TYPE, ENTREZ_GENE_ID, EXPRESSION_VALUE) VALUES (?,?,?,?,?,?)");
+            // Fill in statement
+            preparedStatement.setInt(1, singleCellExpression.getGeneticProfileId());
+            preparedStatement.setInt(2, singleCellExpression.getSampleId());
+            preparedStatement.setString(3, singleCellExpression.getTissue());
+            preparedStatement.setString(4, singleCellExpression.getCellType());
+            preparedStatement.setLong(5, singleCellExpression.getGene().getEntrezGeneId());
+            preparedStatement.setString(6, singleCellExpression.getExpressionValue());
+
+            // Execute statement
+            preparedStatement.execute();
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoGeneticProfileLink.class, connection, preparedStatement, resultSet);
+        }
+    }
+}

src/main/java/org/mskcc/cbio/portal/model/GeneticAlterationType.java

@@ -52,5 +52,6 @@ public enum GeneticAlterationType {
     PROTEIN_ARRAY_PROTEIN_LEVEL,
     PROTEIN_ARRAY_PHOSPHORYLATION,
     GENESET_SCORE,
-    GENERIC_ASSAY
+    GENERIC_ASSAY,
+    SINGLE_CELL_EXPRESSION
 };

src/main/java/org/mskcc/cbio/portal/model/SingleCellExpression.java

@@ -0,0 +1,69 @@
+package org.mskcc.cbio.portal.model;
+
+public class SingleCellExpression {
+    private int sampleId;
+    private int geneticProfileId;
+    private CanonicalGene gene;
+    private String cellType;
+    private String tissue;
+    private String expressionValue;
+
+    public SingleCellExpression(int sampleId, int geneticProfileId, CanonicalGene gene, String cellType, String tissue,
+            String expressionValue) {
+        this.sampleId = sampleId;
+        this.geneticProfileId = geneticProfileId;
+        this.gene = gene;
+        this.cellType = cellType;
+        this.tissue = tissue;
+        this.expressionValue = expressionValue;
+    }
+
+    public int getSampleId() {
+        return sampleId;
+    }
+
+    public void setSampleId(int sampleId) {
+        this.sampleId = sampleId;
+    }
+
+    public int getGeneticProfileId() {
+        return geneticProfileId;
+    }
+
+    public void setGeneticProfileId(int geneticProfileId) {
+        this.geneticProfileId = geneticProfileId;
+    }
+
+    public CanonicalGene getGene() {
+        return gene;
+    }
+
+    public void setGene(CanonicalGene gene) {
+        this.gene = gene;
+    }
+
+    public String getCellType() {
+        return cellType;
+    }
+
+    public void setCellType(String cellType) {
+        this.cellType = cellType;
+    }
+
+    public String getTissue() {
+        return tissue;
+    }
+
+    public void setTissue(String tissue) {
+        this.tissue = tissue;
+    }
+
+    public String getExpressionValue() {
+        return expressionValue;
+    }
+
+    public void setExpressionValue(String expressionValue) {
+        this.expressionValue = expressionValue;
+    }
+
+}

src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java

@@ -136,7 +136,8 @@ public void run() {
                     );
                     genericAssayProfileImporter.importData();
                 }
-            } else if(
+            } 
+            else if(
                 geneticProfile.getGeneticAlterationType() == GeneticAlterationType.COPY_NUMBER_ALTERATION 
                 && DISCRETE_LONG.name().equals(geneticProfile.getOtherMetaDataField("datatype"))
             ) {
@@ -150,7 +151,15 @@ public void run() {
                     overwriteExisting
                 );
                 importer.importData();
+            } else if (geneticProfile.getGeneticAlterationType() == GeneticAlterationType.SINGLE_CELL_EXPRESSION) {
+                ImportSingleCellExpressionData importer = new ImportSingleCellExpressionData(
+                    dataFile,
+                    geneticProfile.getGeneticProfileId(),
+                    daoGene
+                );
+                importer.importData();
             } else {
+                // All other files go through this
                 ImportTabDelimData importer = new ImportTabDelimData(
                     dataFile, 
                     geneticProfile.getTargetLine(),