SERVER-34482 Drop MMAP-specific system collections on wiredTiger

It is possible for a user to explicitly create MMAP-specific system
collections when using wiredTiger. The presence of these collections
may cause UUID checks to fail.

2 files changed, 106 insertions, 5 deletions

diff --git a/jstests/multiVersion/drop_mmap_system_collections_on_wt.js b/jstests/multiVersion/drop_mmap_system_collections_on_wt.js
new file mode 100644
index 00000000000..4335ef2650e
--- /dev/null
+++ b/jstests/multiVersion/drop_mmap_system_collections_on_wt.js
@@ -0,0 +1,73 @@
+// Ensure system.indexes created on wiredTiger 3.4 does not cause mongodb 4.0 to fail to start up
+// (see SERVER-34482). This test is to be removed after mongodb 4.0.
+(function() {
+    "use strict";
+
+    load("jstests/libs/feature_compatibility_version.js");
+    load("jstests/libs/check_uuids.js");
+    load("jstests/multiVersion/libs/multi_rs.js");
+
+    const UUIDCheckBinary = "latest";
+    const UUIDBinary = "3.6";
+    const noUUIDBinary = "3.4";
+    const systemIndexesDB = "systemIndexesDB";
+    const UUIDFCV = "3.6";
+
+    // Create system.indexes on wiredTiger, using a version of mongod that does not assign UUIDs.
+    let rst = new ReplSetTest({
+        nodes: 3,
+        nodeOptions: {binVersion: noUUIDBinary},
+    });
+    rst.startSet();
+    rst.initiate();
+    let primaryTestDB = rst.getPrimary().getDB(systemIndexesDB);
+    primaryTestDB.dropDatabase();
+    const systemIndexesColl = "system.indexes";
+    const createCmd = {create: systemIndexesColl, writeConcern: {w: "majority"}};
+    assert.commandWorked(primaryTestDB.runCommand(createCmd),
+                         "expected " + tojson(createCmd) + " to succeed");
+    rst.awaitReplication();
+    assert(primaryTestDB.getCollectionInfos().length == 1);
+    assert(primaryTestDB.getCollectionInfos()[0].name == systemIndexesColl);
+    let secondaries = rst.getSecondaries();
+    for (let j = 0; j < secondaries.length; j++) {
+        let secondaryTestDB = secondaries[j].getDB(systemIndexesDB);
+        assert(secondaryTestDB.getCollectionInfos().length == 1);
+        assert(secondaryTestDB.getCollectionInfos()[0].name == systemIndexesColl);
+    }
+
+    // Restart with mongodb 3.6 and set the FCV to 3.6, which will assign UUIDs to all
+    // collections except for system.indexes and system.namespaces.
+    rst.upgradeSet({binVersion: UUIDBinary});
+
+    let primaryAdminDB = rst.getPrimary().getDB("admin");
+    assert.commandWorked(primaryAdminDB.runCommand({setFeatureCompatibilityVersion: UUIDFCV}));
+    rst.awaitReplication();
+    checkFCV(primaryAdminDB, UUIDFCV);
+    secondaries = rst.getSecondaries();
+    for (let j = 0; j < secondaries.length; j++) {
+        let secondaryAdminDB = secondaries[j].getDB("admin");
+        checkFCV(secondaryAdminDB, UUIDFCV);
+    }
+
+    primaryTestDB = rst.getPrimary().getDB(systemIndexesDB);
+    assert(!primaryTestDB.getCollectionInfos()[0].info.uuid);
+
+    // Restart with mongodb 4.0. This will drop system.indexes and system.namespaces if they
+    // exist, allowing the UUID check on start up to pass.
+    rst.upgradeSet({binVersion: UUIDCheckBinary});
+
+    primaryTestDB = rst.getPrimary().getDB(systemIndexesDB);
+    assert(primaryTestDB.getCollectionInfos().length == 0);
+
+    primaryAdminDB = rst.getPrimary().getDB("admin");
+    secondaries = rst.getSecondaries();
+    checkCollectionUUIDs(primaryAdminDB);
+    for (let j = 0; j < secondaries.length; j++) {
+        let secondaryTestDB = secondaries[j].getDB(systemIndexesDB);
+        assert(secondaryTestDB.getCollectionInfos().length == 0);
+        let secondaryAdminDB = secondaries[j].getDB("admin");
+        checkCollectionUUIDs(secondaryAdminDB);
+    }
+    rst.stopSet();
+})();
diff --git a/src/mongo/db/repair_database_and_check_version.cpp b/src/mongo/db/repair_database_and_check_version.cpp
index 37baffa3ab4..90f5872adc6 100644
--- a/src/mongo/db/repair_database_and_check_version.cpp
+++ b/src/mongo/db/repair_database_and_check_version.cpp
@@ -36,6 +36,7 @@
 #include "mongo/db/catalog/database.h"
 #include "mongo/db/catalog/database_catalog_entry.h"
 #include "mongo/db/catalog/database_holder.h"
+#include "mongo/db/catalog/drop_collection.h"
 #include "mongo/db/catalog/index_catalog.h"
 #include "mongo/db/commands/feature_compatibility_version.h"
 #include "mongo/db/commands/feature_compatibility_version_documentation.h"
@@ -50,6 +51,7 @@
 #include "mongo/db/repl/replication_coordinator.h"
 #include "mongo/db/server_options.h"
 #include "mongo/db/storage/mmap_v1/mmap_v1_options.h"
+#include "mongo/util/exit.h"
 #include "mongo/util/log.h"
 #include "mongo/util/quick_exit.h"
 #include "mongo/util/version.h"
@@ -140,14 +142,40 @@ Status ensureAllCollectionsHaveUUIDs(OperationContext* opCtx,
         invariant(db);
         for (auto collectionIt = db->begin(); collectionIt != db->end(); ++collectionIt) {
             Collection* coll = *collectionIt;
-            if (!coll->uuid()) {
-                // system.indexes and system.namespaces don't currently have UUIDs in MMAP.
-                // SERVER-29926 and SERVER-30095 will address this problem.
-                if (isMmapV1 && (coll->ns().coll() == "system.indexes" ||
-                                 coll->ns().coll() == "system.namespaces")) {
+            // The presence of system.indexes or system.namespaces on wiredTiger may
+            // have undesirable results (see SERVER-32894, SERVER-34482). It is okay to
+            // drop these collections on wiredTiger because users are not permitted to
+            // store data in them.
+            if (coll->ns().coll() == "system.indexes" || coll->ns().coll() == "system.namespaces") {
+                if (isMmapV1) {
+                    // system.indexes and system.namespaces don't currently have UUIDs in MMAP.
+                    // SERVER-29926 and SERVER-30095 will address this problem.
                     continue;
                 }
+                const auto nssToDrop = coll->ns();
+                LOG(1) << "Attempting to drop invalid system collection " << nssToDrop;
+                if (coll->numRecords(opCtx)) {
+                    severe(LogComponent::kControl) << "Cannot drop non-empty collection "
+                                                   << nssToDrop.ns();
+                    exitCleanly(EXIT_NEED_DOWNGRADE);
+                }
+                repl::UnreplicatedWritesBlock uwb(opCtx);
+                writeConflictRetry(opCtx, "dropSystemIndexes", nssToDrop.ns(), [&] {
+                    WriteUnitOfWork wunit(opCtx);
+                    BSONObjBuilder unusedResult;
+                    fassert(50837,
+                            dropCollection(
+                                opCtx,
+                                nssToDrop,
+                                unusedResult,
+                                {},
+                                DropCollectionSystemCollectionMode::kAllowSystemCollectionDrops));
+                    wunit.commit();
+                });
+                continue;
+            }
 
+            if (!coll->uuid()) {
                 if (!coll->ns().isReplicated()) {
                     nonReplicatedCollNSSsWithoutUUIDs.push_back(coll->ns());
                     continue;