TASK-5564 - Update data sources for CellBase 6.x

biodata-formats/pom.xml

@@ -42,6 +42,10 @@
             <groupId>org.opencb.commons</groupId>
             <artifactId>commons-lib</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>jakarta.xml.bind</groupId>
@@ -97,6 +101,16 @@
             <artifactId>jackson-mapper-asl</artifactId>
             <scope>test</scope>
         </dependency>-->
+        <!-- Apache POI for Excel files -->
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi-ooxml</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

biodata-formats/src/main/java/org/opencb/biodata/formats/feature/chimerdb/ChimerDbParserCallback.java

@@ -0,0 +1,25 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ Licensed under the Apache License, Version 2.0 (the "License");
+ *   ~ you may not use this file except in compliance with the License.
+ *   ~ You may obtain a copy of the License at
+ *   ~
+ *   ~     http://www.apache.org/licenses/LICENSE-2.0
+ *   ~
+ *   ~ Unless required by applicable law or agreed to in writing, software
+ *   ~ distributed under the License is distributed on an "AS IS" BASIS,
+ *   ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   ~ See the License for the specific language governing permissions and
+ *   ~ limitations under the License.
+ *   -->
+ *
+ */
+
+package org.opencb.biodata.formats.feature.chimerdb;
+
+
+public interface ChimerDbParserCallback<T> {
+    boolean processChimerDbObject(T object);
+}

biodata-formats/src/main/java/org/opencb/biodata/formats/feature/chimerdb/ChimerKbParser.java

@@ -0,0 +1,279 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ Licensed under the Apache License, Version 2.0 (the "License");
+ *   ~ you may not use this file except in compliance with the License.
+ *   ~ You may obtain a copy of the License at
+ *   ~
+ *   ~     http://www.apache.org/licenses/LICENSE-2.0
+ *   ~
+ *   ~ Unless required by applicable law or agreed to in writing, software
+ *   ~ distributed under the License is distributed on an "AS IS" BASIS,
+ *   ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   ~ See the License for the specific language governing permissions and
+ *   ~ limitations under the License.
+ *   -->
+ *
+ */
+
+package org.opencb.biodata.formats.feature.chimerdb;
+
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.opencb.biodata.models.core.chimerdb.ChimerKb;
+import org.opencb.biodata.models.core.chimerdb.ChimerKbGeneBreakpoint;
+import org.opencb.commons.utils.FileUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.stream.Collectors;
+
+import static org.opencb.biodata.formats.feature.chimerdb.ChimerPubParser.getIntCellValue;
+import static org.opencb.biodata.formats.feature.chimerdb.ChimerPubParser.getStringCellValue;
+
+public class ChimerKbParser {
+
+    private static Logger logger = LoggerFactory.getLogger(ChimerKbParser.class);
+
+    public static void parse(Path xlsxPath, ChimerDbParserCallback<ChimerKb> callback) throws IOException {
+        logger.info("Parsing ChimerKB file: {}", xlsxPath);
+        FileUtils.checkFile(xlsxPath);
+
+        try (FileInputStream excelFile = new FileInputStream(xlsxPath.toFile());
+             Workbook workbook = new XSSFWorkbook(excelFile)) {
+            // Get the first sheet from the workbook
+            Sheet sheet = workbook.getSheetAt(0);
+
+            // Iterate over rows
+            Iterator<Row> rowIterator = sheet.iterator();
+            while (rowIterator.hasNext()) {
+                Row row = rowIterator.next();
+
+                // Skip header row if needed (e.g., if first row is header)
+                if (row.getRowNum() == 0) {
+                    continue;
+                }
+
+                String strValue;
+                Integer intValue;
+
+                ChimerKb chimerKb = new ChimerKb();
+
+                // 0    1               2       3           4           5               6               7       8       9          10
+                // id	ChimerDB_Type	Source	webSource	Fusion_pair	5Gene_Junction	3Gene_Junction	H_gene	H_chr	H_position	H_strand
+                // 11       12      13          14          15                  16                  17              18
+                // T_gene	T_chr	T_position	T_strand	Genomic_breakpoint	Exonic_breakpoint	Breakpoint_Type	Genome_Build_Version
+                // 19   20      21          22      23          24      25          26                  27          28
+                // PMID	Disease	Validation	Frame	Chr_info	Kinase	Oncogene	Tumor_suppressor	Receptor	Transcription_Factor
+                // 29           30          31
+                // ChimerPub	ChimerSeq	ChimerSeq+
+
+                // ID
+                chimerKb.setId(String.valueOf((int) row.getCell(0).getNumericCellValue()));
+
+                // ChimerDB Type
+                strValue = getStringCellValue(row, 1);
+                if (strValue != null) {
+                    chimerKb.setChimerDbType(strValue);
+                }
+
+                // Source (different from source provided by user)
+                strValue = getStringCellValue(row, 2);
+                if (strValue != null) {
+                    chimerKb.setChimerSource(strValue);
+                }
+
+                // Web source
+                strValue = getStringCellValue(row, 3);
+                if (strValue != null) {
+                    chimerKb.setWebSource(strValue);
+                }
+
+                // Fusion pair
+                strValue = getStringCellValue(row, 4);
+                if (strValue != null) {
+                    chimerKb.setFusionPair(strValue);
+                }
+
+                // Gene junctions (5 and 3)
+                strValue = getStringCellValue(row, 5);
+                if (strValue != null) {
+                    chimerKb.setFiveGeneJunction(strValue);
+                }
+                strValue = getStringCellValue(row, 6);
+                if (strValue != null) {
+                    chimerKb.setThreeGeneJunction(strValue);
+                }
+
+                // Head gene breakpoint
+                ChimerKbGeneBreakpoint head = new ChimerKbGeneBreakpoint();
+                strValue = getStringCellValue(row, 7);
+                if (strValue != null) {
+                    head.setGeneName(strValue);
+                }
+                strValue = getStringCellValue(row, 8);
+                if (strValue != null) {
+                    if (strValue.startsWith("chr") || strValue.startsWith("Chr") || strValue.startsWith("CHR")) {
+                        // Remove 'chr' prefix if present
+                        strValue = strValue.substring(3);
+                    }
+                    head.setChromosome(strValue);
+                }
+                intValue = getIntCellValue(row, 9);
+                if (intValue != null) {
+                    head.setPosition(intValue);
+                }
+                strValue = getStringCellValue(row, 10);
+                if (strValue != null) {
+                    head.setStrand(strValue);
+                }
+                chimerKb.setHeadGene(head);
+
+                // Tail gene breakpoint
+                ChimerKbGeneBreakpoint tail = new ChimerKbGeneBreakpoint();
+                strValue = getStringCellValue(row, 11);
+                if (strValue != null) {
+                    tail.setGeneName(strValue);
+                }
+                strValue = getStringCellValue(row, 12);
+                if (strValue != null) {
+                    if (strValue.startsWith("chr") || strValue.startsWith("Chr") || strValue.startsWith("CHR")) {
+                        // Remove 'chr' prefix if present
+                        strValue = strValue.substring(3);
+                    }
+                    tail.setChromosome(strValue);
+                }
+                intValue = getIntCellValue(row, 13);
+                if (intValue != null) {
+                    tail.setPosition(intValue);
+                }
+                strValue = getStringCellValue(row, 14);
+                if (strValue != null) {
+                    tail.setStrand(strValue);
+                }
+                chimerKb.setTailGene(tail);
+
+                // Genomic breakpoint
+                intValue = getIntCellValue(row, 15);
+                if (intValue != null) {
+                    chimerKb.setGenomicBreakpoint(intValue == 1);
+                }
+
+                // Exonic breakpoint
+                intValue = getIntCellValue(row, 16);
+                if (intValue != null) {
+                    chimerKb.setExonicBreakpoint(intValue == 1);
+                }
+
+                // Breakpoint type
+                strValue = getStringCellValue(row, 17);
+                if (strValue != null) {
+                    chimerKb.setBreakpointType(strValue);
+                }
+
+                // Genome build version
+                strValue = getStringCellValue(row, 18);
+                if (strValue != null) {
+                    chimerKb.setGenomeBuildVersion(strValue);
+                }
+
+                // Publications
+                strValue = getStringCellValue(row, 19);
+                if (strValue != null) {
+                    chimerKb.setPmid(Arrays.stream(strValue.split(",")).map(String::trim).collect(Collectors.toList()));
+                } else {
+                    intValue = getIntCellValue(row, 19);
+                    if (intValue != null && intValue > 0) {
+                        chimerKb.setPmid(Arrays.asList(String.valueOf(intValue)));
+                    }
+                }
+
+                // Diseases
+                strValue = getStringCellValue(row, 20);
+                if (strValue != null) {
+                    chimerKb.setDiseases(Arrays.stream(strValue.split(",")).map(String::trim).collect(Collectors.toList()));
+                }
+
+                // Validations
+                strValue = getStringCellValue(row, 21);
+                if (strValue != null) {
+                    chimerKb.setValidations(Arrays.stream(strValue.split(",")).map(String::trim).collect(Collectors.toList()));
+                }
+
+                // Frame
+                strValue = getStringCellValue(row, 22);
+                if (strValue != null) {
+                    chimerKb.setFrame(strValue);
+                }
+
+                // Chromosome info
+                strValue = getStringCellValue(row, 23);
+                if (strValue != null) {
+                    chimerKb.setChrInfo(strValue);
+                }
+
+                // Kinase
+                strValue = getStringCellValue(row, 24);
+                if (strValue != null) {
+                    chimerKb.setKinase(strValue.equalsIgnoreCase("kinase"));
+                }
+
+                // Oncogene
+                strValue = getStringCellValue(row, 25);
+                if (strValue != null) {
+                    chimerKb.setOncogene(strValue.equalsIgnoreCase("oncogene"));
+                }
+
+                // Tumor suppressor
+                strValue = getStringCellValue(row, 26);
+                if (strValue != null) {
+                    chimerKb.setTumorSuppressor(strValue.equalsIgnoreCase("Tumor suppressor gene"));
+                }
+
+                // Receptor
+                strValue = getStringCellValue(row, 27);
+                if (strValue != null) {
+                    chimerKb.setReceptor(strValue.equalsIgnoreCase("Receptor"));
+                }
+
+                // Transcription factor
+                strValue = getStringCellValue(row, 28);
+                if (strValue != null) {
+                    chimerKb.setTranscriptionFactor(strValue.equalsIgnoreCase("Transcription factor"));
+                }
+
+                // ChimerPub
+                strValue = getStringCellValue(row, 29);
+                if (strValue != null) {
+                    chimerKb.setChimerPub(strValue.equalsIgnoreCase("Pub"));
+                }
+
+                // ChimerSeq
+                strValue = getStringCellValue(row, 30);
+                if (strValue != null) {
+                    chimerKb.setChimerSeq(strValue.equalsIgnoreCase("Seq"));
+                }
+
+                // ChimerSeq+
+                strValue = getStringCellValue(row, 31);
+                if (strValue != null) {
+                    chimerKb.setChimerSeqPlus(strValue.equalsIgnoreCase("Seq+"));
+                }
+
+                // Callback to process the gene fusion
+                callback.processChimerDbObject(chimerKb);
+            }
+        } catch (IOException e) {
+            throw new IOException("Error reading the ChimerKB file: " + e.getMessage(), e);
+        }
+        logger.info("ChimerKB file parsed successfully: {}", xlsxPath);
+    }
+}