Merge pull request #45 from cBioPortal/inc-tab-delimited-uploader

(1/7) RFC 79: Implement incremental upload of tab delimited data.

README.md

@@ -9,6 +9,34 @@ This repo contains:
 ## Inclusion in main codebase
 The `cbioportal-core` code is currently included in the final Docker image during the Docker build process: https://github.com/cBioPortal/cbioportal/blob/master/docker/web-and-data/Dockerfile#L48
 
+## Running in docker
+
+Build docker image with:
+```bash
+docker build -t cbioportal-core .
+```
+
+Example of how to start loading of the whole study:
+```bash
+docker run -it -v $(pwd)/data/:/data/ -v $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -s /data/study_es_0 -p /data/api_json -o
+```
+
+### Incremental upload of data
+
+To add or update specific patient, sample, or molecular data in an already loaded study, you can perform an incremental upload. This process is quicker than reloading the entire study.
+
+To execute an incremental upload, use the -d (or --data_directory) option instead of -s (or --study_directory). Here is an example command:
+```bash
+docker run -it -v $(pwd)/data/:/data/ -v $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -d /data/study_es_0_inc -p /data/api_json -o
+```
+**Note:**
+While the directory should adhere to the standard cBioPortal file formats and study structure, please note the following specific guidelines for incremental uploads:
+
+- Incremental uploads are not supported for all data types. For instance, uploading study metadata, resources, or GSVA data incrementally is currently unsupported.
+- The data pertaining to patient or sample IDs should only include entries that are either new or need updates.
+
+This method ensures efficient updates without the need for complete study reuploads, saving time and computational resources.
+
 ## How to run integration tests
 
 This section guides you through the process of running integration tests by setting up a cBioPortal MySQL database environment using Docker. Please follow these steps carefully to ensure your testing environment is configured correctly.
@@ -119,15 +147,3 @@ The script will search for `core-*.jar` in the root of the project:
 python scripts/importer/metaImport.py -s tests/test_data/study_es_0 -p tests/test_data/api_json_unit_tests -o
 ```
 
-## Running in docker
-
-Build docker image with:
-```bash
-docker build -t cbioportal-core .
-```
-
-Example of how to start the loading:
-```bash
-docker run -it -v $(pwd)/data/:/data/ -v $(pwd)/application.properties:/application.properties cbioportal-core python importer/metaImport.py -s /data/study_es_0 -p /data/api_json -o
-```
-

pom.xml

@@ -252,6 +252,9 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<version>2.21.0</version>
+				<configuration>
+					<trimStackTrace>false</trimStackTrace>
+				</configuration>
 				<executions>
 					<execution>
 						<id>default-test</id>

scripts/importer/cbioportalImporter.py

@@ -464,6 +464,8 @@ def import_incremental_data(jvm_args, data_directory, update_generic_assay_entit
     Load all data types that are available and support incremental upload
     """
     for meta_file_type in INCREMENTAL_UPLOAD_SUPPORTED_META_TYPES:
+        if meta_file_type not in meta_file_type_to_meta_files:
+            continue
         meta_pairs = meta_file_type_to_meta_files[meta_file_type]
         for meta_pair in meta_pairs:
             meta_filename, meta_dictionary = meta_pair
@@ -651,5 +653,5 @@ def main(args):
 # ready to roll
 
 if __name__ == '__main__':
-    parsed_args = interface(args)
+    parsed_args = interface()
     main(parsed_args)

scripts/importer/cbioportal_common.py

@@ -370,7 +370,16 @@ class MetaFileTypes(object):
     MetaFileTypes.PATIENT_ATTRIBUTES,
     MetaFileTypes.SAMPLE_ATTRIBUTES,
     MetaFileTypes.MUTATION,
-    # TODO Add more types here as incremental upload is enabled
+    MetaFileTypes.MUTATION_UNCALLED,
+    MetaFileTypes.EXPRESSION,
+    MetaFileTypes.CNA_DISCRETE,
+    MetaFileTypes.CNA_CONTINUOUS,
+    MetaFileTypes.CNA_LOG2,
+    MetaFileTypes.METHYLATION,
+    MetaFileTypes.PROTEIN,
+    MetaFileTypes.GENERIC_ASSAY_CONTINUOUS,
+    MetaFileTypes.GENERIC_ASSAY_BINARY,
+    MetaFileTypes.GENERIC_ASSAY_CATEGORICAL,
 ]
 
 IMPORTER_CLASSNAME_BY_META_TYPE = {

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

@@ -119,7 +119,32 @@ private static long addCnaEventDirectly(CnaEvent cnaEvent) throws DaoException {
             JdbcUtil.closeAll(DaoCnaEvent.class, con, pstmt, rs);
         }
 	}
-
+
+    public static void removeSampleCnaEvents(int cnaProfileId, List<Integer> sampleIds) throws DaoException {
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoCnaEvent.class);
+            pstmt = con.prepareStatement
+                    ("DELETE sample_cna_event, alteration_driver_annotation" +
+                            " FROM sample_cna_event" +
+                            " LEFT JOIN alteration_driver_annotation ON alteration_driver_annotation.`ALTERATION_EVENT_ID` = sample_cna_event.`CNA_EVENT_ID`" +
+                            " WHERE sample_cna_event.`GENETIC_PROFILE_ID` = ? AND sample_cna_event.`SAMPLE_ID` IN (" +
+                            String.join(",", Collections.nCopies(sampleIds.size(), "?"))
+                            + ")");
+            pstmt.setInt(1, cnaProfileId);
+            for (int i = 0; i < sampleIds.size(); i++) {
+                pstmt.setInt(i + 2, sampleIds.get(i));
+            }
+            pstmt.executeUpdate();
+        } catch (SQLException e) {
+            throw new DaoException(e);
+        } finally {
+            JdbcUtil.closeAll(DaoCnaEvent.class, con, pstmt, rs);
+        }
+    }
+
     public static Map<Sample, Set<Long>> getSamplesWithAlterations(
             Collection<Long> eventIds) throws DaoException {
         return getSamplesWithAlterations(StringUtils.join(eventIds, ","));

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

@@ -46,6 +46,7 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.util.EntrezValidator;
 import org.mskcc.cbio.portal.util.ProgressMonitor;
 
 /**
@@ -322,7 +323,7 @@ public List<CanonicalGene> guessGene(String geneId, String chr) {
         }
 
         CanonicalGene gene;
-        if (geneId.matches("[0-9]+")) { // likely to be a entrez gene id
+        if (EntrezValidator.isaValidEntrezId(geneId)) { // likely to be a entrez gene id
             gene = getGene(Integer.parseInt(geneId));
             if (gene!=null) {
                 return Collections.singletonList(gene);

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

@@ -65,12 +65,10 @@ private DaoGeneticAlteration() {
      * Gets Instance of Dao Object. (Singleton pattern).
      *
      * @return DaoGeneticAlteration Object.
-     * @throws DaoException Dao Initialization Error.
      */
-    public static DaoGeneticAlteration getInstance() throws DaoException {
+    public static DaoGeneticAlteration getInstance() {
         if (daoGeneticAlteration == null) {
             daoGeneticAlteration = new DaoGeneticAlteration();
-
         }
 
         return daoGeneticAlteration;
@@ -96,7 +94,7 @@ public int addGeneticAlterations(int geneticProfileId, long entrezGeneId, String
             throws DaoException {
     	return addGeneticAlterationsForGeneticEntity(geneticProfileId, DaoGeneOptimized.getGeneticEntityId(entrezGeneId), values);
     }
-    
+
     public int addGeneticAlterationsForGeneticEntity(int geneticProfileId, int geneticEntityId, String[] values)
             throws DaoException {
 
@@ -239,8 +237,8 @@ public HashMap<Integer,HashMap<Integer, String>> getGeneticAlterationMapForEntit
                 int geneticEntityId = rs.getInt("GENETIC_ENTITY_ID");
                 String values = rs.getString("VALUES");
                 //hm.debug..
-                String valueParts[] = values.split(DELIM);
-                for (int i=0; i<valueParts.length; i++) {
+                String valueParts[] = values.split(DELIM, -1);
+                for (int i = 0; i < orderedSampleList.size(); i++) {
                     String value = valueParts[i];
                     Integer sampleId = orderedSampleList.get(i);
                     mapSampleValue.put(sampleId, value);
@@ -292,7 +290,11 @@ public static ArrayList<ObjectNode> getProcessedAlterationData(
             rs = pstmt.executeQuery();
             while (rs.next()) {
                 long entrezGeneId = DaoGeneOptimized.getEntrezGeneId(rs.getInt("GENETIC_ENTITY_ID"));
-                String[] values = rs.getString("VALUES").split(DELIM);
+                String valuesString = rs.getString("VALUES");
+                if (valuesString.endsWith(DELIM)) {
+                    valuesString = valuesString.substring(0, valuesString.length() - DELIM.length());
+                }
+                String[] values = valuesString.split(DELIM, -1);
                 ObjectNode datum = processor.process(
                         entrezGeneId,
                         values,
@@ -427,17 +429,19 @@ public int getCount() throws DaoException {
      * Deletes all Genetic Alteration Records associated with the specified Genetic Profile ID.
      *
      * @param geneticProfileId Genetic Profile ID.
+     * @param geneticEntityId Genetic Entity ID.
      * @throws DaoException Database Error.
      */
-    public void deleteAllRecordsInGeneticProfile(long geneticProfileId) throws DaoException {
+    public void deleteAllRecordsInGeneticProfile(long geneticProfileId, long geneticEntityId) throws DaoException {
         Connection con = null;
         PreparedStatement pstmt = null;
         ResultSet rs = null;
         try {
             con = JdbcUtil.getDbConnection(DaoGeneticAlteration.class);
             pstmt = con.prepareStatement("DELETE from " +
-                    "genetic_alteration WHERE GENETIC_PROFILE_ID=?");
+                    "genetic_alteration WHERE GENETIC_PROFILE_ID=? and GENETIC_ENTITY_ID=?");
             pstmt.setLong(1, geneticProfileId);
+            pstmt.setLong(2, geneticEntityId);
             pstmt.executeUpdate();
         } catch (SQLException e) {
             throw new DaoException(e);

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

@@ -35,10 +35,12 @@
 import java.sql.*;
 import java.util.*;
 import javax.sql.DataSource;
-import org.apache.commons.dbcp2.BasicDataSource;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.mskcc.cbio.portal.util.*;
+import org.springframework.jdbc.datasource.DataSourceTransactionManager;
+import org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy;
+import org.springframework.transaction.support.TransactionTemplate;
 
 /**
  * Connection Utility for JDBC.
@@ -50,24 +52,37 @@ public class JdbcUtil {
     private static DataSource dataSource;
     private static Map<String,Integer> activeConnectionCount = new HashMap<String,Integer>(); // keep track of the number of active connection per class/requester
     private static final Logger LOG = LoggerFactory.getLogger(JdbcUtil.class);
+    private static DataSourceTransactionManager transactionManager;
+    private static TransactionTemplate transactionTemplate;
 
     /**
      * Gets the data source
      * @return the data source
      */
     public static DataSource getDataSource() {
         if (dataSource == null) {
-            dataSource = new JdbcDataSource();
+            dataSource = new TransactionAwareDataSourceProxy(new JdbcDataSource());
+            initSpringTx();
         }
         return dataSource;
     }
 
+    private static void initSpringTx() {
+        transactionManager = new DataSourceTransactionManager(dataSource);
+        transactionTemplate = new TransactionTemplate(transactionManager);
+    }
+
     /**
      * Sets the data source
      * @param value the data source
      */
     public static void setDataSource(DataSource value) {
         dataSource = value;
+        initSpringTx();
+    }
+
+    public static TransactionTemplate getTransactionTemplate() {
+        return transactionTemplate;
     }
 
     /**

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

@@ -55,5 +55,9 @@ public boolean store(
         }
     }
 
+    public boolean isImportedAlready(CanonicalGene gene) {
+        return importSetOfGenes.contains(gene.getEntrezGeneId());
+    }
+
 
 }

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

@@ -188,7 +188,7 @@ public static void importHGNCData(File geneFile, String genomeBuild) throws IOEx
                 ProgressMonitor.incrementCurValue();
                 ConsoleUtil.showProgress();
                 String parts[] = line.split("\t", -1); // include trailing empty strings
-                if (!parts[0].matches("[0-9]+")) {
+                if (!EntrezValidator.isaValidEntrezId(parts[0])) {
                     ProgressMonitor.logWarning("Skipping gene with invalid entrez gene id '" + parts[1] + "'");
                     continue;
                 }

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

@@ -40,16 +40,19 @@
 import java.io.File;
 import java.io.FileReader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 import org.cbioportal.model.EntityType;
 import org.cbioportal.model.GenericEntityProperty;
 import org.cbioportal.model.GeneticEntity;
 import org.mskcc.cbio.portal.dao.DaoGenericAssay;
 import org.mskcc.cbio.portal.dao.DaoGeneticEntity;
 import org.mskcc.cbio.portal.model.GeneticAlterationType;
+import org.mskcc.cbio.portal.util.FileUtil;
 import org.mskcc.cbio.portal.util.ProgressMonitor;
 
 import joptsimple.OptionParser;
@@ -160,7 +163,6 @@ public static void startImport(OptionSet options, OptionSpec<String> data, Optio
     * @throws Exception
     */
     public static void importData(File dataFile, GeneticAlterationType geneticAlterationType, String additionalProperties, boolean updateInfo) throws Exception {
-
         ProgressMonitor.setCurrentMessage("Reading data from: " + dataFile.getCanonicalPath());
 
         // read generic assay data file
@@ -186,6 +188,10 @@ public static void importData(File dataFile, GeneticAlterationType geneticAltera
         currentLine = buf.readLine();
 
         while (currentLine != null) {
+            if (!FileUtil.isInfoLine(currentLine)) {
+                currentLine = buf.readLine();
+                continue;
+            }
 
             String[] parts = currentLine.split("\t");
 

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

@@ -79,7 +79,8 @@ public ImportGenericAssayPatientLevelData(File dataFile, String targetLine, int
      * @throws IOException  IO Error.
      * @throws DaoException Database Error.
      */
-    public void importData(int numLines) throws IOException, DaoException {
+    public void importData() throws IOException, DaoException {
+        int numLines = FileUtil.getNumLines(dataFile);
 
         geneticProfile = DaoGeneticProfile.getGeneticProfileById(geneticProfileId);