Add command to patch study meta data

README.md

@@ -62,6 +62,14 @@ For instance, uploading study metadata, resources, or GSVA data incrementally is
 
 This method ensures efficient updates without the need for complete study reuploads, saving time and computational resources.
 
+### Patching Study Metadata
+
+It is possible to update study name, description, citation or pmid without reloading the whole study. Below is an example of such command:
+
+```bash
+java -cp core-*.jar org.mskcc.cbio.portal.scripts.PatchCancerStudyMetadata meta_study.txt
+```
+
 ## 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.

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

@@ -0,0 +1,169 @@
+/*
+ * Copyright (c) 2016 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/>.
+*/
+
+package org.mskcc.cbio.portal.scripts;
+
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.JdbcUtil;
+import org.mskcc.cbio.portal.util.ProgressMonitor;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+
+/**
+ * Command Line Tool to update the metadata of a Single Cancer Study.
+ */
+public class PatchCancerStudyMetadata extends ConsoleRunnable {
+
+    public static final String CANCER_STUDY_IDENTIFIER_META_FIELD = "cancer_study_identifier";
+    public static final String NAME_META_FIELD = "name";
+    public static final String DESCRIPTION_META_FIELD = "description";
+    public static final String CITATION_META_FIELD = "citation";
+    public static final String PMID_META_FIELD = "pmid";
+    public static final Set<String> PATCH_SUPPORTED_META_FIELDS = Set.of(NAME_META_FIELD, DESCRIPTION_META_FIELD, CITATION_META_FIELD, PMID_META_FIELD);
+
+    public void run() {
+        run(args);
+    }
+
+    public static void run(String[] args) {
+        if (args.length < 1) {
+            throw new UsageException(
+                    PatchCancerStudyMetadata.class.getName(),
+                    null,
+                    "<cancer_study.txt>");
+        }
+        File file = new File(args[0]);
+        try {
+            run(file);
+        } catch (Exception e) {
+            throw new RuntimeException("File" + file, e);
+        }
+    }
+
+    public static void run(File file) throws IOException, SQLException, DaoException {
+        InputStream inputStream = new FileInputStream(file);
+        run(inputStream);
+    }
+
+    public static void run(InputStream inputStream) throws IOException, SQLException, DaoException {
+        TrimmedProperties properties = new TrimmedProperties();
+        properties.load(inputStream);
+        if (properties.isEmpty()) {
+            throw new IllegalStateException("No fields were found");
+        }
+        if (!properties.containsKey(CANCER_STUDY_IDENTIFIER_META_FIELD)) {
+            throw new IllegalStateException("No " + CANCER_STUDY_IDENTIFIER_META_FIELD + " field has been found");
+        }
+        if (properties.keySet().stream().noneMatch((PATCH_SUPPORTED_META_FIELDS::contains))) {
+            throw new IllegalStateException("No field to patch has been found. Supported fields: "
+                    + CANCER_STUDY_IDENTIFIER_META_FIELD);
+        }
+
+        Iterator<Map.Entry<Object, Object>> iterator = properties.entrySet().iterator();
+        while (iterator.hasNext()) {
+            Map.Entry<Object, Object> entry = iterator.next();
+            Object field = entry.getKey();
+            if (!CANCER_STUDY_IDENTIFIER_META_FIELD.equals(field) && !PATCH_SUPPORTED_META_FIELDS.contains(field)) {
+                ProgressMonitor.logWarning("Patch functionality is not supported for '" + field + "' field. Skipping it.");
+                iterator.remove();
+            }
+        }
+        if (!patchCancerStudy(properties)) {
+            throw new IllegalStateException("No study has been patched");
+        }
+        String message = "Patched cancer study:\n" +
+                properties.keySet().stream().sorted().map(
+                        (field) ->
+                                " --> " + field + ": " + properties.getProperty((String) field)).collect(Collectors.joining("\n"));
+
+        ProgressMonitor.setCurrentMessage(message);
+        ProgressMonitor.setCurrentMessage("Done");
+    }
+
+    /**
+     *
+     * @param cancerStudyMetadata - metadata to patch
+     * @return true - if record has been updated; false - otherwise
+     * @throws SQLException
+     */
+    public static boolean patchCancerStudy(Properties cancerStudyMetadata) throws SQLException {
+        Set<Object> orderedMetaFields = new TreeSet<>(cancerStudyMetadata.keySet());
+        if (!orderedMetaFields.remove(CANCER_STUDY_IDENTIFIER_META_FIELD)) {
+            throw new IllegalStateException("No " +  CANCER_STUDY_IDENTIFIER_META_FIELD + " field has found");
+        }
+        Connection con = null;
+        PreparedStatement pstmt = null;
+        try {
+            con = JdbcUtil.getDbConnection(PatchCancerStudyMetadata.class);
+            pstmt = con.prepareStatement("UPDATE cancer_study SET " +
+                    orderedMetaFields.stream().map((field) -> "`" + getDbField(field) + "` = ?").collect(Collectors.joining(",")) +
+                    "WHERE `CANCER_STUDY_IDENTIFIER` = ?");
+            int parameterIndex = 1;
+            for (Object field: orderedMetaFields) {
+                pstmt.setString(parameterIndex++, cancerStudyMetadata.getProperty((String) field));
+            }
+            pstmt.setString(parameterIndex, cancerStudyMetadata.getProperty(CANCER_STUDY_IDENTIFIER_META_FIELD));
+            return pstmt.executeUpdate() == 1;
+        } finally {
+            JdbcUtil.closeAll(PatchCancerStudyMetadata.class, con, pstmt, null);
+        }
+    }
+
+    /**
+     *
+     * @param field - meta data field
+     * @return corresponding database field
+     */
+    private static String getDbField(Object field) {
+        return field.toString().toUpperCase();
+    }
+
+    /**
+     * Makes an instance to run with the given command line arguments.
+     *
+     * @param args the command line arguments to be used
+     */
+    public PatchCancerStudyMetadata(String[] args) {
+        super(args);
+    }
+
+    /**
+     * Runs the command as a script and exits with an appropriate exit code.
+     *
+     * @param args the arguments given on the command line
+     */
+    public static void main(String[] args) {
+        ConsoleRunnable runner = new PatchCancerStudyMetadata(args);
+        runner.runInConsole();
+    }
+}