cBioPortal · forus · Jul 17, 2024 · May 29, 2024
diff --git a/scripts/importer/cbioportalImporter.py b/scripts/importer/cbioportalImporter.py
@@ -36,6 +36,8 @@
 from .cbioportal_common import IMPORT_STUDY_CLASS
 from .cbioportal_common import UPDATE_STUDY_STATUS_CLASS
 from .cbioportal_common import REMOVE_STUDY_CLASS
+from .cbioportal_common import REMOVE_SAMPLES_CLASS
+from .cbioportal_common import REMOVE_PATIENTS_CLASS
 from .cbioportal_common import IMPORT_CASE_LIST_CLASS
 from .cbioportal_common import ADD_CASE_LIST_CLASS
 from .cbioportal_common import VERSION_UTIL_CLASS
@@ -53,10 +55,12 @@
 IMPORT_CANCER_TYPE = "import-cancer-type"
 IMPORT_STUDY = "import-study"
 REMOVE_STUDY = "remove-study"
+REMOVE_SAMPLES = "remove-samples"
+REMOVE_PATIENTS = "remove-patients"
 IMPORT_STUDY_DATA = "import-study-data"
 IMPORT_CASE_LIST = "import-case-list"
 
-COMMANDS = [IMPORT_CANCER_TYPE, IMPORT_STUDY, REMOVE_STUDY, IMPORT_STUDY_DATA, IMPORT_CASE_LIST]
+COMMANDS = [IMPORT_CANCER_TYPE, IMPORT_STUDY, IMPORT_STUDY_DATA, IMPORT_CASE_LIST, REMOVE_STUDY, REMOVE_SAMPLES, REMOVE_PATIENTS]
 
 # ------------------------------------------------------------------------------
 # sub-routines
@@ -104,6 +108,24 @@ def remove_study_id(jvm_args, study_id):
     args.append("--noprogress") # don't report memory usage and % progress
     run_java(*args)
 
+def remove_samples(jvm_args, study_ids, sample_ids):
+    args = jvm_args.split(' ')
+    args.append(REMOVE_SAMPLES_CLASS)
+    args.append("--study_ids")
+    args.append(study_ids)
+    args.append("--sample_ids")
+    args.append(sample_ids)
+    run_java(*args)
+
+def remove_patients(jvm_args, study_ids, patient_ids):
+    args = jvm_args.split(' ')
+    args.append(REMOVE_PATIENTS_CLASS)
+    args.append("--study_ids")
+    args.append(study_ids)
+    args.append("--patient_ids")
+    args.append(patient_ids)
+    run_java(*args)
+
 def update_case_lists(jvm_args, meta_filename, case_lists_file_or_dir = None):
     args = jvm_args.split(' ')
     args.append(UPDATE_CASE_LIST_CLASS)
@@ -213,7 +235,7 @@ def process_case_lists(jvm_args, case_list_dir):
         if not (case_list.startswith('.') or case_list.endswith('~')):
             import_case_list(jvm_args, os.path.join(case_list_dir, case_list))
 
-def process_command(jvm_args, command, meta_filename, data_filename, study_ids, update_generic_assay_entity = None):
+def process_command(jvm_args, command, meta_filename, data_filename, study_ids, patient_ids, sample_ids, update_generic_assay_entity = None):
     if command == IMPORT_CANCER_TYPE:
         import_cancer_type(jvm_args, data_filename)
     elif command == IMPORT_STUDY:
@@ -227,6 +249,10 @@ def process_command(jvm_args, command, meta_filename, data_filename, study_ids,
                 remove_study_id(jvm_args, study_id)
         else:
             raise RuntimeError('Your command uses both -id and -meta. Please, use only one of the two parameters.')
+    elif command == REMOVE_SAMPLES:
+        remove_samples(jvm_args, study_ids, sample_ids)
+    elif command == REMOVE_PATIENTS:
+        remove_patients(jvm_args, study_ids, patient_ids)
     elif command == IMPORT_STUDY_DATA:
         import_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity)
     elif command == IMPORT_CASE_LIST:
@@ -505,7 +531,7 @@ def usage():
                            '--command [%s] --study_directory <path to directory> '
                            '--meta_filename <path to metafile>'
                            '--data_filename <path to datafile>'
-                           '--study_ids <cancer study ids for remove-study command, comma separated>' % (COMMANDS)), file=OUTPUT_FILE)
+                           '--study_ids <cancer study ids for remove-study or remove-samples command, comma separated>' % (COMMANDS)), file=OUTPUT_FILE)
 
 def check_args(command):
     if command not in COMMANDS:
@@ -545,23 +571,32 @@ def interface(args=None):
     parent_parser = argparse.ArgumentParser(description='cBioPortal meta Importer')
     add_parser_args(parent_parser)
     parser = argparse.ArgumentParser()
+    allowed_commands_csv = ', '.join(COMMANDS)
     subparsers = parser.add_subparsers(title='subcommands', dest='subcommand',
-                          help='Command for import. Allowed commands: import-cancer-type, '
-                          'import-study, import-study-data, import-case-list or '
-                          'remove-study')
+                          help='Command for import. Allowed commands: ' + allowed_commands_csv)
     import_cancer_type = subparsers.add_parser('import-cancer-type', parents=[parent_parser], add_help=False)
     import_study = subparsers.add_parser('import-study', parents=[parent_parser], add_help=False)
     import_study_data = subparsers.add_parser('import-study-data', parents=[parent_parser], add_help=False)
     import_case_list = subparsers.add_parser('import-case-list', parents=[parent_parser], add_help=False)
     remove_study = subparsers.add_parser('remove-study', parents=[parent_parser], add_help=False)
-
     remove_study.add_argument('-id', '--study_ids', type=str, required=False,
                         help='Cancer Study IDs for `remove-study` command, comma separated')
-    parser.add_argument('-c', '--command', type=str, required=False, 
+
+    remove_samples = subparsers.add_parser('remove-samples', parents=[], add_help=True)
+    remove_samples.add_argument('--study_ids', type=str, required=True,
+                        help='Cancer Study ID(s) that contains sample(s). Comma separated, if multiple.')
+    remove_samples.add_argument('--sample_ids', type=str, required=True,
+                        help='Sample ID(s). Comma separated, if multiple.')
+
+    remove_patients = subparsers.add_parser('remove-patients', parents=[], add_help=True)
+    remove_patients.add_argument('--study_ids', type=str, required=True,
+                        help='Cancer Study ID(s) that contains sample(s). Comma separated, if multiple.')
+    remove_patients.add_argument('--patient_ids', type=str, required=True,
+                        help='Patient ID(s). Comma separated, if multiple.')
+
+    parser.add_argument('-c', '--command', type=str, required=False,
                         help='This argument is outdated. Please use the listed subcommands, without the -c flag. '
-                        'Command for import. Allowed commands: import-cancer-type, '
-                        'import-study, import-study-data, import-case-list or '
-                        'remove-study')
+                        'Command for import. Allowed commands: ' + allowed_commands_csv)
     add_parser_args(parser)
     parser.add_argument('-id', '--study_ids', type=str, required=False,
                         help='Cancer Study IDs for `remove-study` command, comma separated')
@@ -647,7 +682,15 @@ def main(args):
     else:
         check_args(args.command)
         check_files(args.meta_filename, args.data_filename)
-        process_command(jvm_args, args.command, args.meta_filename, args.data_filename, args.study_ids, args.update_generic_assay_entity)
+        process_command(
+            jvm_args,
+            args.command,
+            args.meta_filename,
+            args.data_filename,
+            args.study_ids,
+            args.patient_ids if hasattr(args, 'patient_ids') else None,
+            args.sample_ids if hasattr(args, 'sample_ids') else None,
+            args.update_generic_assay_entity)
 
 # ------------------------------------------------------------------------------
 # ready to roll

diff --git a/scripts/importer/cbioportal_common.py b/scripts/importer/cbioportal_common.py
@@ -34,6 +34,8 @@
 IMPORT_STUDY_CLASS = "org.mskcc.cbio.portal.scripts.ImportCancerStudy"
 UPDATE_STUDY_STATUS_CLASS = "org.mskcc.cbio.portal.scripts.UpdateCancerStudy"
 REMOVE_STUDY_CLASS = "org.mskcc.cbio.portal.scripts.RemoveCancerStudy"
+REMOVE_SAMPLES_CLASS = "org.mskcc.cbio.portal.scripts.RemoveSamples"
+REMOVE_PATIENTS_CLASS = "org.mskcc.cbio.portal.scripts.RemovePatients"
 IMPORT_CANCER_TYPE_CLASS = "org.mskcc.cbio.portal.scripts.ImportTypesOfCancers"
 IMPORT_CASE_LIST_CLASS = "org.mskcc.cbio.portal.scripts.ImportSampleList"
 ADD_CASE_LIST_CLASS = "org.mskcc.cbio.portal.scripts.AddCaseList"

diff --git a/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticAlteration.java b/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticAlteration.java
@@ -32,25 +32,30 @@
 
 package org.mskcc.cbio.portal.dao;
 
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import org.apache.commons.lang3.StringUtils;
 import org.mskcc.cbio.portal.model.CanonicalGene;
 
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
 import java.util.Map.Entry;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-import org.apache.commons.lang3.StringUtils;
+import java.util.Set;
 
 /**
  * Data Access Object for the Genetic Alteration Table.
  *
  * @author Ethan Cerami.
  */
 public class DaoGeneticAlteration {
+
     private static final String DELIM = ",";
     public static final String NAN = "NaN";
     private static DaoGeneticAlteration daoGeneticAlteration = null;

diff --git a/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java b/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticProfileSamples.java
@@ -64,7 +64,7 @@ public static int addGeneticProfileSamples(int geneticProfileId, List<Integer> o
         StringBuffer orderedSampleListBuf = new StringBuffer();
         //  Created Joined String, based on DELIM token
         for (Integer sampleId :  orderedSampleList) {
-            orderedSampleListBuf.append(Integer.toString(sampleId)).append(DELIM);
+            orderedSampleListBuf.append(sampleId).append(DELIM);
         }
         try {
             con = JdbcUtil.getDbConnection(DaoGeneticProfileSamples.class);
@@ -126,7 +126,11 @@ public static ArrayList <Integer> getOrderedSampleList(int geneticProfileId) thr
                 String orderedSampleList = rs.getString("ORDERED_SAMPLE_LIST");
 
                 //  Split, based on DELIM token
-                String parts[] = orderedSampleList.split(DELIM);
+                String[] parts = orderedSampleList.split(DELIM);
+                if (parts.length == 1 && parts[0].isBlank()) {
+                    throw new IllegalStateException("genetic_profile_samples row for geneticProfileId="
+                            + geneticProfileId + " has blank ORDERED_SAMPLE_LIST. Consider removing it.");
+                }
                 ArrayList <Integer> sampleList = new ArrayList <Integer>();
                 for (String internalSampleId : parts) {
                     sampleList.add(Integer.parseInt(internalSampleId));

diff --git a/src/main/java/org/mskcc/cbio/portal/dao/DaoPatient.java b/src/main/java/org/mskcc/cbio/portal/dao/DaoPatient.java
@@ -35,9 +35,12 @@
 import org.mskcc.cbio.portal.model.*;
 
 import org.apache.commons.collections4.map.MultiKeyMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.sql.*;
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * DAO to `patient`.
@@ -46,6 +49,8 @@
  */
 public class DaoPatient {
 
+    private static final Logger log = LoggerFactory.getLogger(DaoPatient.class);
+
     private static final String SAMPLE_COUNT_ATTR_ID = "SAMPLE_COUNT";
 
     private static final Map<Integer, Patient> byInternalId = new HashMap<Integer, Patient>();
@@ -215,4 +220,58 @@ private static Patient extractPatient(ResultSet rs) throws SQLException
 			throw new SQLException(e);
 		}
     }
+
+    /**
+     * Removes patients information from the study
+     * @param internalStudyId - id of the study that contains the patients
+     * @param patientStableIds - patient stable ids to remove
+     * @throws DaoException
+     */
+    public static void deletePatients(int internalStudyId, Set<String> patientStableIds) throws DaoException
+    {
+        if (patientStableIds == null || patientStableIds.isEmpty()) {
+            log.info("No patients specified to remove for study with internal id={}. Skipping.", internalStudyId);
+            return;
+        }
+        log.info("Removing {} patients from study with internal id={} ...", patientStableIds, internalStudyId);
+
+        Set<Integer> internalPatientIds = findInternalPatientIdsInStudy(internalStudyId, patientStableIds);
+        Set<String> patientsSampleStableIds = internalPatientIds.stream().flatMap(internalPatientId ->
+                DaoSample.getSamplesByPatientId(internalPatientId).stream().map(Sample::getStableId))
+                .collect(Collectors.toSet());
+        DaoSample.deleteSamples(internalStudyId, patientsSampleStableIds);
+
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        try {
+            con = JdbcUtil.getDbConnection(DaoPatient.class);
+            pstmt = con.prepareStatement("DELETE FROM `patient` WHERE `INTERNAL_ID` IN ("
+                    + String.join(",", Collections.nCopies(internalPatientIds.size(), "?"))
+                    + ")");
+            int parameterIndex = 1;
+            for (Integer internalPatientId : internalPatientIds) {
+                pstmt.setInt(parameterIndex++, internalPatientId);
+            };
+            pstmt.executeUpdate();
+        }
+        catch (SQLException e) {
+            throw new DaoException(e);
+        }
+        finally {
+            JdbcUtil.closeAll(DaoPatient.class, con, pstmt, null);
+        }
+        log.info("Removing {} patients from study with internal id={} done.", patientStableIds, internalStudyId);
+    }
+
+    public static Set<Integer> findInternalPatientIdsInStudy(Integer internalStudyId, Set<String> patientStableIds) {
+        HashSet<Integer> internalPatientIds = new HashSet<>();
+        for (String patientId : patientStableIds) {
+            Patient patientByCancerStudyAndPatientId = DaoPatient.getPatientByCancerStudyAndPatientId(internalStudyId, patientId);
+            if (patientByCancerStudyAndPatientId == null) {
+                throw new NoSuchElementException("Patient with stable id=" + patientId + " not found in study with internal id=" + internalStudyId + ".");
+            }
+            internalPatientIds.add(patientByCancerStudyAndPatientId.getInternalId());
+        }
+        return internalPatientIds;
+    }
 }