Fix primary.idx corruption after delete mutation

dbms/src/Interpreters/MutationsInterpreter.cpp

@@ -18,6 +18,7 @@
 #include <Parsers/ASTExpressionList.h>
 #include <Parsers/ASTSelectQuery.h>
 #include <Parsers/formatAST.h>
+#include <Parsers/ASTOrderByElement.h>
 #include <IO/WriteHelpers.h>
 
 
@@ -525,6 +526,39 @@ ASTPtr MutationsInterpreter::prepareInterpreterSelectQuery(std::vector<Stage> &
         }
         select->setExpression(ASTSelectQuery::Expression::WHERE, std::move(where_expression));
     }
+    auto metadata = storage->getInMemoryMetadata();
+    /// We have to execute select in order of primary key
+    /// because we don't sort results additionaly and don't have
+    /// any guarantees on data order without ORDER BY. It's almost free, because we
+    /// have optimization for data read in primary key order.
+    if (metadata.order_by_ast)
+    {
+        ASTPtr dummy;
+
+        ASTPtr key_expr;
+        if (metadata.primary_key_ast)
+            key_expr = metadata.primary_key_ast;
+        else
+            key_expr = metadata.order_by_ast;
+
+        bool empty = false;
+        /// In all other cases we cannot have empty key
+        if (auto key_function = key_expr->as<ASTFunction>())
+            empty = key_function->arguments->children.size() == 0;
+
+        /// Not explicitely spicified empty key
+        if (!empty)
+        {
+            auto order_by_expr = std::make_shared<ASTOrderByElement>(1, 1, false, dummy, false, dummy, dummy, dummy);
+
+
+            order_by_expr->children.push_back(key_expr);
+            auto res = std::make_shared<ASTExpressionList>();
+            res->children.push_back(order_by_expr);
+
+            select->setExpression(ASTSelectQuery::Expression::ORDER_BY, std::move(res));
+        }
+    }
 
     return select;
 }

dbms/src/Storages/MergeTree/StorageFromMergeTreeDataPart.h

@@ -47,6 +47,12 @@ class StorageFromMergeTreeDataPart : public ext::shared_ptr_helper<StorageFromMe
         return part->storage.mayBenefitFromIndexForIn(left_in_operand, query_context);
     }
 
+    StorageInMemoryMetadata getInMemoryMetadata() const override
+    {
+        return part->storage.getInMemoryMetadata();
+    }
+
+
 protected:
     StorageFromMergeTreeDataPart(const MergeTreeData::DataPartPtr & part_)
         : IStorage(getIDFromPart(part_), part_->storage.getVirtuals())

dbms/src/Storages/StorageReplicatedMergeTree.cpp

@@ -3222,6 +3222,7 @@ void StorageReplicatedMergeTree::alter(
     /// metadata alter.
     if (params.isSettingsAlter())
     {
+        lockStructureExclusively(table_lock_holder, query_context.getCurrentQueryId());
         /// We don't replicate storage_settings_ptr ALTER. It's local operation.
         /// Also we don't upgrade alter lock to table structure lock.
         LOG_DEBUG(log, "ALTER storage_settings_ptr only");
@@ -3271,9 +3272,7 @@ void StorageReplicatedMergeTree::alter(
     std::vector<ChangedNode> changed_nodes;
 
     {
-        /// Just to read current structure. Alter will be done in separate thread.
-        auto table_lock = lockStructureForShare(false, query_context.getCurrentQueryId());
-
+        /// We can safely read structure, because we guarded with alter_intention_lock
         if (is_readonly)
             throw Exception("Can't ALTER readonly table", ErrorCodes::TABLE_IS_READ_ONLY);
 
@@ -3305,10 +3304,13 @@ void StorageReplicatedMergeTree::alter(
 
         /// Perform settings update locally
 
-        auto old_metadata = getInMemoryMetadata();
-        old_metadata.settings_ast = metadata.settings_ast;
-        changeSettings(metadata.settings_ast, table_lock_holder);
-        global_context.getDatabase(table_id.database_name)->alterTable(query_context, table_id.table_name, old_metadata);
+        {
+            lockStructureExclusively(table_lock_holder, query_context.getCurrentQueryId());
+            auto old_metadata = getInMemoryMetadata();
+            old_metadata.settings_ast = metadata.settings_ast;
+            changeSettings(metadata.settings_ast, table_lock_holder);
+            global_context.getDatabase(table_id.database_name)->alterTable(query_context, table_id.table_name, old_metadata);
+        }
 
         /// Modify shared metadata nodes in ZooKeeper.
         Coordination::Requests ops;

dbms/tests/queries/0_stateless/01077_mutations_index_consistency.reference

@@ -0,0 +1,4 @@
+43200
+0
+43200
+43200

dbms/tests/queries/0_stateless/01077_mutations_index_consistency.sh

@@ -0,0 +1,60 @@
+#!/usr/bin/env bash
+
+CURDIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+. $CURDIR/../shell_config.sh
+
+
+$CLICKHOUSE_CLIENT --query "DROP TABLE IF EXISTS movement"
+
+$CLICKHOUSE_CLIENT -n --query "CREATE TABLE movement (date DateTime('Europe/Moscow')) Engine = MergeTree ORDER BY (toStartOfHour(date));"
+
+$CLICKHOUSE_CLIENT --query "insert into movement select toDateTime('2020-01-22 00:00:00') + number%(23*3600) from numbers(1000000);"
+
+$CLICKHOUSE_CLIENT --query "OPTIMIZE TABLE movement FINAL"
+
+$CLICKHOUSE_CLIENT -n --query "
+SELECT
+    count(),
+    toStartOfHour(date) AS Hour
+FROM movement
+WHERE (date >= toDateTime('2020-01-22T10:00:00')) AND (date <= toDateTime('2020-01-22T23:00:00'))
+GROUP BY Hour
+ORDER BY Hour DESC
+" | grep "16:00:00" | cut -f1
+
+
+$CLICKHOUSE_CLIENT --query "alter table movement delete where date >= toDateTime('2020-01-22T16:00:00')  and date < toDateTime('2020-01-22T17:00:00') SETTINGS mutations_sync = 2"
+
+$CLICKHOUSE_CLIENT -n --query "
+SELECT
+    count(),
+    toStartOfHour(date) AS Hour
+FROM movement
+WHERE (date >= toDateTime('2020-01-22T10:00:00')) AND (date <= toDateTime('2020-01-22T23:00:00'))
+GROUP BY Hour
+ORDER BY Hour DESC
+" | grep "16:00:00" | wc -l
+
+
+$CLICKHOUSE_CLIENT -n --query "
+SELECT
+    count(),
+    toStartOfHour(date) AS Hour
+FROM movement
+WHERE (date >= toDateTime('2020-01-22T10:00:00')) AND (date <= toDateTime('2020-01-22T23:00:00'))
+GROUP BY Hour
+ORDER BY Hour DESC
+" | grep "22:00:00" | cut -f1
+
+
+$CLICKHOUSE_CLIENT -n --query "
+SELECT
+    count(),
+    toStartOfHour(date) AS Hour
+FROM movement
+GROUP BY Hour
+ORDER BY Hour DESC
+" | grep "22:00:00" | cut -f1
+
+
+$CLICKHOUSE_CLIENT --query "DROP TABLE IF EXISTS movement"