Merge branch 'develop' into PEPPER-853_zeroSmIdFix

pepper-apis/dsm-core/pom.xml

@@ -57,6 +57,11 @@
             <!-- <version>1.4.11</version> -->
         </dependency>
 
+        <dependency>
+            <groupId>commons-validator</groupId>
+            <artifactId>commons-validator</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-dbcp2</artifactId>

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

@@ -647,7 +647,6 @@ protected void setupCustomRouting(@NonNull Config cfg) {
         setupDDPConfigurationLookup(cfg.getString(ApplicationConfigConstants.DDP));
 
         AuthenticationRoute authenticationRoute = new AuthenticationRoute(auth0Util,
-                userUtil,
                 cfg.getString(ApplicationConfigConstants.AUTH0_DOMAIN),
                 cfg.getString(ApplicationConfigConstants.AUTH0_MGT_SECRET),
                 cfg.getString(ApplicationConfigConstants.AUTH0_MGT_KEY),
@@ -930,11 +929,11 @@ private void setupAdminRoutes() {
         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());
+        put(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());
+        put(uiRoot + RoutePath.USER, userRoute, new JsonTransformer());
     }
 
 
@@ -1060,6 +1059,8 @@ private void setupRouteGenericErrorHandlers() {
             response.body(exception.getMessage());
         });
         exception(DsmInternalError.class, (exception, request, response) -> {
+            logger.error("Internal error {}", exception.toString());
+            exception.printStackTrace();
             response.status(500);
             response.body(exception.getMessage());
         });

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

@@ -24,10 +24,12 @@ public class UserDao implements Dao<UserDto> {
     public static final String PHONE_NUMBER = "phone_number";
     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, user.is_active FROM access_user user "
-                    + "WHERE user.email = ?";
+                    + "WHERE UPPER(user.email) = ?";
     private static final String SQL_SELECT_USER_BY_ID =
             "SELECT user.user_id, user.name, user.email, user.phone_number, user.is_active FROM access_user user "
                     + "WHERE user.user_id = ?";
@@ -36,7 +38,7 @@ public Optional<UserDto> getUserByEmail(@NonNull String email) {
         SimpleResult results = inTransaction((conn) -> {
             SimpleResult dbVals = new SimpleResult();
             try (PreparedStatement stmt = conn.prepareStatement(SQL_SELECT_USER_BY_EMAIL)) {
-                stmt.setString(1, email);
+                stmt.setString(1, email.toUpperCase());
                 try (ResultSet rs = stmt.executeQuery()) {
                     if (rs.next()) {
                         dbVals.resultValue = new UserDto(rs.getInt(USER_ID),
@@ -87,7 +89,7 @@ public Optional<UserDto> get(long userId) {
 
     @Override
     public int create(UserDto userDto) {
-        String email = userDto.getEmail().orElse(null);
+        String email = userDto.getEmailOrThrow();
         if (StringUtils.isBlank(email)) {
             throw new DsmInternalError("Error inserting user: email is blank");
         }
@@ -110,6 +112,26 @@ public int create(UserDto userDto) {
         });
     }
 
+    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) {
+                throw new DsmInternalError(errorMsg, ex);
+            }
+        });
+    }
+
     @Override
     public int delete(int id) {
         SimpleResult simpleResult = DaoUtil.deleteById(id, SQL_DELETE_USER_BY_ID);

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

@@ -4,6 +4,7 @@
 
 import lombok.AllArgsConstructor;
 import lombok.Setter;
+import org.broadinstitute.dsm.exception.DsmInternalError;
 
 @Setter
 @AllArgsConstructor
@@ -36,10 +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/model/dashboard/BasicChartStrategy.java

@@ -43,7 +43,7 @@ protected void fillLabelsValues() {
             MultiSearchResponse.Item response = msearch.getResponses()[i];
             long count = 0;
             if (response != null && response.getResponse() != null) {
-                count = response.getResponse().getHits().getTotalHits();
+                count = response.getResponse().getHits().getTotalHits().value;
             }
             fillData(values, labels, dashboardDto.getLabels().get(i), count);
         }

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/model/dashboard/CountStrategy.java

@@ -21,7 +21,7 @@ public DashboardData get() {
         if (response != null && response.getResponse() != null) {
             return new CountData(dashboardDto.getDisplayType(), Collections.emptyList(),
                     dashboardDto.getSize(), dashboardDto.getDisplayText(), dashboardDto.getOrder(),
-                    response.getResponse().getHits().getTotalHits()
+                    response.getResponse().getHits().getTotalHits().value
             );
         }
         return null;

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/model/elastic/mapping/FieldTypeExtractor.java

@@ -24,9 +24,9 @@ public class FieldTypeExtractor implements TypeExtractor<Map<String, String>> {
     @Override
     public Map<String, String> extract() {
         if (isFieldsNotCached()) {
-            Map<String, GetFieldMappingsResponse.FieldMappingMetaData> mapping = getMapping().get(index);
+            Map<String, GetFieldMappingsResponse.FieldMappingMetadata> mapping = getMapping().get(index);
             Map<String, String> fieldTypeMapping = new HashMap<>();
-            for (Map.Entry<String, GetFieldMappingsResponse.FieldMappingMetaData> entry : mapping.entrySet()) {
+            for (Map.Entry<String, GetFieldMappingsResponse.FieldMappingMetadata> entry : mapping.entrySet()) {
                 fieldTypeMapping.put(getRightMostFieldName(entry.getKey()), extractType(entry.getKey(), entry.getValue()));
             }
             cachedFieldTypes.putAll(fieldTypeMapping);
@@ -44,13 +44,13 @@ private List<String> notCachedFields() {
                 .collect(Collectors.toList());
     }
 
-    private String extractType(String fullFieldName, GetFieldMappingsResponse.FieldMappingMetaData value) {
+    private String extractType(String fullFieldName, GetFieldMappingsResponse.FieldMappingMetadata value) {
         String key = getRightMostFieldName(fullFieldName);
         return (String) ((Map<String, Object>) value.sourceAsMap().get(key)).get(MappingGenerator.TYPE);
     }
 
-    private Map<String, Map<String, GetFieldMappingsResponse.FieldMappingMetaData>> getMapping() {
-        Map<String, Map<String, GetFieldMappingsResponse.FieldMappingMetaData>> result = new HashMap<>();
+    private Map<String, Map<String, GetFieldMappingsResponse.FieldMappingMetadata>> getMapping() {
+        Map<String, Map<String, GetFieldMappingsResponse.FieldMappingMetadata>> result = new HashMap<>();
         GetFieldMappingsRequest request = new GetFieldMappingsRequest();
         request.indices(index);
         String[] fields = this.notCachedFields().toArray(new String[] {});

pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/model/elastic/search/ElasticSearch.java

@@ -175,7 +175,7 @@ public ElasticSearch getParticipantsWithinRange(String esParticipantsIndex, int
         }
         List<ElasticSearchParticipantDto> esParticipants = parseSourceMaps(response.getHits().getHits());
         logger.info("Got " + esParticipants.size() + " participants from ES for instance " + esParticipantsIndex);
-        return new ElasticSearch(esParticipants, response.getHits().getTotalHits());
+        return new ElasticSearch(esParticipants, response.getHits().getTotalHits().value);
     }
 
     @Override
@@ -199,7 +199,7 @@ public ElasticSearch getParticipantsByIds(String esIndex, List<String> participa
         List<ElasticSearchParticipantDto> esParticipants = parseSourceMaps(response.getHits().getHits());
 
         logger.info("Got " + esParticipants.size() + " participants from ES for instance " + esIndex);
-        return new ElasticSearch(esParticipants, response.getHits().getTotalHits());
+        return new ElasticSearch(esParticipants, response.getHits().getTotalHits().value);
     }
 
     @Override
@@ -247,7 +247,7 @@ public ElasticSearch getParticipantsByRangeAndFilter(String esParticipantsIndex,
         }
         List<ElasticSearchParticipantDto> esParticipants = parseSourceMaps(response.getHits().getHits());
         logger.info("Got " + esParticipants.size() + " participants from ES for instance " + esParticipantsIndex);
-        return new ElasticSearch(esParticipants, response.getHits().getTotalHits());
+        return new ElasticSearch(esParticipants, response.getHits().getTotalHits().value);
     }
 
     private AbstractQueryBuilder addOsteo2Filter(AbstractQueryBuilder queryBuilder) {
@@ -287,7 +287,7 @@ public ElasticSearch getParticipantsByRangeAndIds(String participantIndexES, int
         }
         List<ElasticSearchParticipantDto> esParticipants = parseSourceMaps(response.getHits().getHits());
         logger.info("Got " + esParticipants.size() + " participants from ES for instance " + participantIndexES);
-        return new ElasticSearch(esParticipants, response.getHits().getTotalHits());
+        return new ElasticSearch(esParticipants, response.getHits().getTotalHits().value);
     }
 
     @Override
@@ -331,7 +331,7 @@ public ElasticSearch getAllParticipantsDataByInstanceIndex(String esParticipants
         }
         List<ElasticSearchParticipantDto> elasticSearchParticipantDtos = parseSourceMaps(searchResponse.getHits().getHits());
         logger.info("Got " + elasticSearchParticipantDtos.size() + " participants from ES for instance " + esParticipantsIndex);
-        return new ElasticSearch(elasticSearchParticipantDtos, searchResponse.getHits().getTotalHits());
+        return new ElasticSearch(elasticSearchParticipantDtos, searchResponse.getHits().getTotalHits().value);
     }
 
     private BoolQueryBuilder getBoolQueryOfParticipantsId(List<String> participantIds) {