Merge branch 'develop' into PEPPER-947

pepper-apis/ddp-common/pom.xml

@@ -15,6 +15,7 @@
         <logback.version>1.4.5</logback.version>
         <sonar.sources>src/main/java</sonar.sources>
         <sonar.java.binaries>target/classes</sonar.java.binaries>
+        <liquibase.version>4.8.0</liquibase.version>
     </properties>
 
     <dependencies>
@@ -64,6 +65,7 @@
         <dependency>
             <groupId>org.liquibase</groupId>
             <artifactId>liquibase-core</artifactId>
+            <version>${liquibase.version}</version>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>

pepper-apis/dsm-core/pom.xml

@@ -262,7 +262,7 @@
         <dependency>
             <groupId>net.minidev</groupId>
             <artifactId>json-smart</artifactId>
-            <version>2.3.1</version>
+            <version>2.4.11</version>
             <scope>compile</scope>
         </dependency>
     </dependencies>

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/DSMServer.java

@@ -111,6 +111,7 @@
 import org.broadinstitute.dsm.route.MailingListRoute;
 import org.broadinstitute.dsm.route.MedicalRecordLogRoute;
 import org.broadinstitute.dsm.route.NDIRoute;
+import org.broadinstitute.dsm.route.OncHistoryTemplateRoute;
 import org.broadinstitute.dsm.route.OncHistoryUploadRoute;
 import org.broadinstitute.dsm.route.ParticipantEventRoute;
 import org.broadinstitute.dsm.route.ParticipantExitRoute;
@@ -120,6 +121,9 @@
 import org.broadinstitute.dsm.route.TriggerSurveyRoute;
 import org.broadinstitute.dsm.route.UserSettingRoute;
 import org.broadinstitute.dsm.route.ViewFilterRoute;
+import org.broadinstitute.dsm.route.admin.StudyRoleRoute;
+import org.broadinstitute.dsm.route.admin.UserRoleRoute;
+import org.broadinstitute.dsm.route.admin.UserRoute;
 import org.broadinstitute.dsm.route.dashboard.NewDashboardRoute;
 import org.broadinstitute.dsm.route.familymember.AddFamilyMemberRoute;
 import org.broadinstitute.dsm.route.kit.KitFinalScanRoute;
@@ -583,6 +587,7 @@ protected void setupCustomRouting(@NonNull Config cfg) {
         if (!cfg.getBoolean("ui.production")) {
             get(apiRoot + RoutePath.CREATE_CLINICAL_KIT_ENDPOINT, new CreateClinicalDummyKitRoute(new OncHistoryDetailDaoImpl()),
                     new JsonTransformer());
+
             get(apiRoot + RoutePath.CREATE_CLINICAL_KIT_ENDPOINT_WITH_PARTICIPANT, new CreateClinicalDummyKitRoute(
                     new OncHistoryDetailDaoImpl()), new JsonTransformer());
             get(apiRoot + RoutePath.DUMMY_ENDPOINT, new CreateBSPDummyKitRoute(), new JsonTransformer());
@@ -666,6 +671,8 @@ protected void setupCustomRouting(@NonNull Config cfg) {
 
         setupMiscellaneousRoutes();
 
+        setupAdminRoutes();
+
         setupSharedRoutes(kitUtil, notificationUtil, patchUtil);
 
         setupCohortTagRoutes();
@@ -868,6 +875,8 @@ private void setupMedicalRecordRoutes(@NonNull Config cfg, @NonNull Notification
         post(uiRoot + RoutePath.DOWNLOAD_PARTICIPANT_LIST_ROUTE, new DownloadParticipantListRoute());
 
         post(uiRoot + RoutePath.ONC_HISTORY_ROUTE, new OncHistoryUploadRoute(), new JsonTransformer());
+
+        get(uiRoot + RoutePath.ONC_HISTORY_TEMPLATE_ROUTE, new OncHistoryTemplateRoute());
     }
 
     private void setupMRAbstractionRoutes() {
@@ -912,9 +921,23 @@ private void setupMiscellaneousRoutes() {
 
         GetParticipantDataRoute getParticipantDataRoute = new GetParticipantDataRoute();
         get(uiRoot + RoutePath.GET_PARTICIPANT_DATA, getParticipantDataRoute, new JsonTransformer());
+    }
 
+    private void setupAdminRoutes() {
+        StudyRoleRoute studyRoleRoute = new StudyRoleRoute();
+        get(uiRoot + RoutePath.STUDY_ROLE, studyRoleRoute, new JsonTransformer());
+
+        UserRoleRoute userRoleRoute = new UserRoleRoute();
+        get(uiRoot + RoutePath.USER_ROLE, userRoleRoute, new JsonTransformer());
+        post(uiRoot + RoutePath.USER_ROLE, userRoleRoute, new JsonTransformer());
+        delete(uiRoot + RoutePath.USER_ROLE, userRoleRoute, new JsonTransformer());
+
+        UserRoute userRoute = new UserRoute();
+        post(uiRoot + RoutePath.USER, userRoute, new JsonTransformer());
+        delete(uiRoot + RoutePath.USER, userRoute, new JsonTransformer());
     }
 
+
     private void setupSomaticUploadRoutes(@NonNull Config cfg) {
         SomaticResultUploadService somaticResultUploadService = SomaticResultUploadService.fromConfig(cfg);
         post(uiRoot + RoutePath.SOMATIC_DOCUMENT_ROUTE,

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/UserSettings.java

@@ -6,9 +6,11 @@
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.sql.Statement;
 
 import lombok.Data;
 import lombok.NonNull;
+import org.broadinstitute.dsm.exception.DsmInternalError;
 import org.broadinstitute.dsm.statics.DBConstants;
 import org.broadinstitute.dsm.statics.QueryExtension;
 import org.broadinstitute.lddp.db.SimpleResult;
@@ -27,6 +29,8 @@ public class UserSettings {
                     + "WHERE user.user_id = settings.user_id AND user.is_active = 1";
     private static final String SQL_INSERT_USER_SETTINGS = "INSERT INTO user_settings SET user_id = ?";
 
+    private static final String SQL_DELETE_USER_SETTINGS = "DELETE FROM user_settings WHERE user_id = ?";
+
     private static final String USER_ID = "userId";
 
     private int rowsOnPage;
@@ -104,12 +108,38 @@ public static UserSettings getUserSettings(@NonNull String email) {
         return us;
     }
 
-    public static void insertUserSetting(Connection conn, int userId) {
-        try (PreparedStatement insertKit = conn.prepareStatement(SQL_INSERT_USER_SETTINGS)) {
-            insertKit.setInt(1, userId);
-            insertKit.executeUpdate();
-        } catch (SQLException e) {
-            throw new RuntimeException("Error inserting new user_settings ", e);
+    public static int createUserSettings(int userId) {
+        return inTransaction(conn -> insertUserSetting(conn, userId));
+    }
+
+    public static int insertUserSetting(Connection conn, int userId) {
+        int id = -1;
+        try (PreparedStatement stmt = conn.prepareStatement(SQL_INSERT_USER_SETTINGS, Statement.RETURN_GENERATED_KEYS)) {
+            stmt.setInt(1, userId);
+            int result = stmt.executeUpdate();
+            if (result != 1) {
+                throw new DsmInternalError("Error inserting user setting. Result count was " + result);
+            }
+            try (ResultSet rs = stmt.getGeneratedKeys()) {
+                if (rs.next()) {
+                    id = rs.getInt(1);
+                }
+            }
+        } catch (SQLException ex) {
+            throw new DsmInternalError("Error inserting user setting", ex);
         }
+        return id;
+    }
+
+    public static int deleteUserSettings(int userId) {
+        return inTransaction(conn -> {
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_DELETE_USER_SETTINGS)) {
+                stmt.setInt(1, userId);
+                return stmt.executeUpdate();
+            } catch (SQLException ex) {
+                String msg = String.format("Error deleting user settings: userId=%d", userId);
+                throw new DsmInternalError(msg, ex);
+            }
+        });
     }
 }

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/user/UserDao.java

@@ -5,25 +5,34 @@
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.sql.Statement;
 import java.util.Optional;
 
 import lombok.NonNull;
 import org.broadinstitute.dsm.db.dao.Dao;
+import org.broadinstitute.dsm.db.dao.util.DaoUtil;
 import org.broadinstitute.dsm.db.dto.user.UserDto;
+import org.broadinstitute.dsm.exception.DsmInternalError;
 import org.broadinstitute.lddp.db.SimpleResult;
+import spark.utils.StringUtils;
 
 public class UserDao implements Dao<UserDto> {
 
     public static final String USER_ID = "user_id";
     public static final String NAME = "name";
     public static final String EMAIL = "email";
     public static final String PHONE_NUMBER = "phone_number";
-    private static final String SQL_INSERT_USER = "INSERT INTO access_user (name, email) VALUES (?,?)";
+    public static final String IS_ACTIVE = "is_active";
+    private static final String SQL_INSERT_USER = "INSERT INTO access_user (name, email, phone_number, is_active) VALUES (?,?,?,?)";
+    private static final String SQL_UPDATE_USER =
+            "UPDATE access_user SET name = ?, phone_number = ?, is_active = ? WHERE user_id = ?";
     private static final String SQL_DELETE_USER_BY_ID = "DELETE FROM access_user WHERE user_id = ?";
     private static final String SQL_SELECT_USER_BY_EMAIL =
-            "SELECT user.user_id, user.name, user.email, user.phone_number FROM access_user user WHERE user.email = ?";
+            "SELECT user.user_id, user.name, user.email, user.phone_number, user.is_active FROM access_user user "
+                    + "WHERE user.email = ?";
     private static final String SQL_SELECT_USER_BY_ID =
-            "SELECT user.user_id, user.name, user.email, user.phone_number FROM access_user user WHERE user.user_id = ?";
+            "SELECT user.user_id, user.name, user.email, user.phone_number, user.is_active FROM access_user user "
+                    + "WHERE user.user_id = ?";
 
     public Optional<UserDto> getUserByEmail(@NonNull String email) {
         SimpleResult results = inTransaction((conn) -> {
@@ -35,7 +44,8 @@ public Optional<UserDto> getUserByEmail(@NonNull String email) {
                         dbVals.resultValue = new UserDto(rs.getInt(USER_ID),
                                 rs.getString(NAME),
                                 rs.getString(EMAIL),
-                                rs.getString(PHONE_NUMBER));
+                                rs.getString(PHONE_NUMBER),
+                                rs.getInt(IS_ACTIVE));
                     }
                 }
             } catch (SQLException ex) {
@@ -45,7 +55,7 @@ public Optional<UserDto> getUserByEmail(@NonNull String email) {
         });
 
         if (results.resultException != null) {
-            throw new RuntimeException("Error getting list of realms ", results.resultException);
+            throw new DsmInternalError("Error getting user by email " + email, results.resultException);
         }
         return Optional.ofNullable((UserDto) results.resultValue);
     }
@@ -61,7 +71,8 @@ public Optional<UserDto> get(long userId) {
                         dbVals.resultValue = new UserDto(rs.getInt(USER_ID),
                                 rs.getString(NAME),
                                 rs.getString(EMAIL),
-                                rs.getString(PHONE_NUMBER));
+                                rs.getString(PHONE_NUMBER),
+                                rs.getInt(IS_ACTIVE));
                     }
                 }
             } catch (SQLException ex) {
@@ -71,52 +82,63 @@ public Optional<UserDto> get(long userId) {
         });
 
         if (results.resultException != null) {
-            throw new RuntimeException("Error getting list of realms ", results.resultException);
+            throw new DsmInternalError("Error getting user by id " + userId, results.resultException);
         }
         return Optional.ofNullable((UserDto) results.resultValue);
     }
 
     @Override
     public int create(UserDto userDto) {
-        SimpleResult results = inTransaction((conn) -> {
-            SimpleResult execResult = new SimpleResult();
-            try (PreparedStatement stmt = conn.prepareStatement(SQL_INSERT_USER, PreparedStatement.RETURN_GENERATED_KEYS)) {
-                stmt.setString(1, userDto.getName().orElse(""));
-                stmt.setString(2, userDto.getEmail().orElse(""));
+        String email = userDto.getEmailOrThrow();
+        if (StringUtils.isBlank(email)) {
+            throw new DsmInternalError("Error inserting user: email is blank");
+        }
+        return inTransaction(conn -> {
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_INSERT_USER, Statement.RETURN_GENERATED_KEYS)) {
+                stmt.setString(1, userDto.getName().orElse(null));
+                stmt.setString(2, email);
+                stmt.setString(3, userDto.getPhoneNumber().orElse(null));
+                stmt.setInt(4, userDto.getIsActive().orElse(1));
                 stmt.executeUpdate();
                 try (ResultSet rs = stmt.getGeneratedKeys()) {
-                    if (rs.next()) {
-                        execResult.resultValue = rs.getInt(1);
+                    if (!rs.next()) {
+                        throw new DsmInternalError("Error inserting user " + email);
                     }
+                    return rs.getInt(1);
                 }
             } catch (SQLException ex) {
-                execResult.resultException = ex;
+                throw new DsmInternalError("Error inserting user " + email, ex);
             }
-            return execResult;
         });
-        if (results.resultException != null) {
-            throw new RuntimeException("Error inserting user with "
-                    + userDto.getEmail(), results.resultException);
-        }
-        return (int) results.resultValue;
     }
 
-    @Override
-    public int delete(int id) {
-        SimpleResult results = inTransaction((conn) -> {
-            SimpleResult execResult = new SimpleResult();
-            try (PreparedStatement stmt = conn.prepareStatement(SQL_DELETE_USER_BY_ID)) {
-                stmt.setInt(1, id);
-                execResult.resultValue = stmt.executeUpdate();
+    public static void update(int userId, UserDto userDto) {
+        String email = userDto.getEmailOrThrow();
+        String errorMsg = "Error updating user " + email;
+        int res = inTransaction(conn -> {
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_UPDATE_USER)) {
+                stmt.setString(1, userDto.getName().orElse(null));
+                stmt.setString(2, userDto.getPhoneNumber().orElse(null));
+                stmt.setInt(3, userDto.getIsActive().orElse(1));
+                stmt.setInt(4, userId);
+                int result = stmt.executeUpdate();
+                if (result != 1) {
+                    throw new DsmInternalError(errorMsg + " Result count was " + result);
+                }
+                return result;
             } catch (SQLException ex) {
-                execResult.resultException = ex;
+                throw new DsmInternalError(errorMsg, ex);
             }
-            return execResult;
         });
-        if (results.resultException != null) {
-            throw new RuntimeException("Error deleting user with "
-                    + id, results.resultException);
+    }
+
+    @Override
+    public int delete(int id) {
+        SimpleResult simpleResult = DaoUtil.deleteById(id, SQL_DELETE_USER_BY_ID);
+        if (simpleResult.resultException != null) {
+            throw new DsmInternalError("Error deleting user with ID: " + id,
+                    simpleResult.resultException);
         }
-        return (int) results.resultValue;
+        return (int) simpleResult.resultValue;
     }
 }

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dto/user/UserDto.java

@@ -2,25 +2,27 @@
 
 import java.util.Optional;
 
+import lombok.AllArgsConstructor;
 import lombok.Setter;
+import org.broadinstitute.dsm.exception.DsmInternalError;
 
 @Setter
+@AllArgsConstructor
 public class UserDto {
 
     private int id;
     private String name;
     private String email;
     private String phoneNumber;
+    private Integer isActive;
 
-    public UserDto(int id, String name, String email, String phoneNumber) {
-        this.id = id;
+    public UserDto(String name, String email, String phoneNumber) {
         this.name = name;
         this.email = email;
         this.phoneNumber = phoneNumber;
     }
 
     public UserDto() {
-
     }
 
     public int getId() {
@@ -35,7 +37,20 @@ public Optional<String> getEmail() {
         return Optional.ofNullable(email);
     }
 
+    // TODO: getEmail should always throw on a missing email since it is not nullable
+    // but there are a lot of callers. Feel free to chase them all down and rename this method -DC
+    public String getEmailOrThrow() {
+        return getEmail().orElseThrow(() -> new DsmInternalError("User email cannot be null"));
+    }
+
     public Optional<String> getPhoneNumber() {
         return Optional.ofNullable(phoneNumber);
     }
+    public Optional<Integer> getIsActive() {
+        return Optional.ofNullable(isActive);
+    }
+
+    public boolean isActive() {
+        return getIsActive().orElse(0) == 1;
+    }
 }

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/files/parser/AbstractRecordsParser.java

@@ -72,14 +72,27 @@ public Optional<String> findMissingHeaderIfAny(List<String> extractedHeaders) {
 
     List<T> transformRecordsToList(String[] records) {
         return Arrays.stream(records)
+                .filter(this::filterRecord)
                 .map(this::transformRecordToMap)
                 .map(this::transformMapToObject)
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Return false if the record has no content (but may have delimiters)
+     */
+    boolean filterRecord(String record) {
+        String regex = String.format("[%s]", regexSeparator);
+        return !cleanRecord(record).replaceAll(regex, "").isEmpty();
+    }
+
+    String cleanRecord(String record) {
+        return record.replaceAll("[\n\r]$", "");
+    }
+
     Map<String, String> transformRecordToMap(String record) {
         // split but keep trailing delimiters
-        List<String> records = Arrays.asList(record.replaceAll("[\n\r]$", "").split(regexSeparator, -1));
+        List<String> records = Arrays.asList(cleanRecord(record).split(regexSeparator, -1));
         int colDiff = actualHeaders.size() - records.size();
         if (colDiff > 0) {
             String row = String.join(", ", records);