SERVER-23299 When starting mongod, clear temp flags from collections if appropriate.

See the description in SERVER-23299 for the definition of appropriate.

(cherry picked from commit 5e11e4484b84c8f913a4b14b24fbb7c9c46ee40f)

6 files changed, 106 insertions, 6 deletions

diff --git a/src/mongo/db/catalog/collection_catalog_entry.h b/src/mongo/db/catalog/collection_catalog_entry.h
index e1261e6a409..a31843b3cce 100644
--- a/src/mongo/db/catalog/collection_catalog_entry.h
+++ b/src/mongo/db/catalog/collection_catalog_entry.h
@@ -98,6 +98,11 @@ public:
     virtual void updateFlags(OperationContext* txn, int newValue) = 0;
 
     /**
+     * Clears the "temp" flag from the CollectionOptions of this collection.
+     */
+    virtual void clearTempFlag(OperationContext* txn) = 0;
+
+    /**
      * Updates the validator for this collection.
      *
      * An empty validator removes all validation.
diff --git a/src/mongo/db/db.cpp b/src/mongo/db/db.cpp
index 583907c6619..b49310a0046 100644
--- a/src/mongo/db/db.cpp
+++ b/src/mongo/db/db.cpp
@@ -48,6 +48,7 @@
 #include "mongo/db/auth/authorization_manager.h"
 #include "mongo/db/auth/authorization_manager_global.h"
 #include "mongo/db/catalog/collection.h"
+#include "mongo/db/catalog/collection_catalog_entry.h"
 #include "mongo/db/catalog/database.h"
 #include "mongo/db/catalog/database_catalog_entry.h"
 #include "mongo/db/catalog/database_holder.h"
@@ -56,8 +57,11 @@
 #include "mongo/db/client.h"
 #include "mongo/db/clientcursor.h"
 #include "mongo/db/concurrency/d_concurrency.h"
+#include "mongo/db/concurrency/lock_state.h"
+#include "mongo/db/concurrency/write_conflict_exception.h"
 #include "mongo/db/db_raii.h"
 #include "mongo/db/dbdirectclient.h"
+#include "mongo/db/dbhelpers.h"
 #include "mongo/db/dbmessage.h"
 #include "mongo/db/dbwebserver.h"
 #include "mongo/db/ftdc/ftdc_mongod.h"
@@ -145,6 +149,8 @@ void (*snmpInit)() = NULL;
 
 extern int diagLogging;
 
+static const NamespaceString startupLogCollectionName("local.startup_log");
+
 #ifdef _WIN32
 ntservice::NtServiceDefaultStrings defaultServiceStrings = {
     L"MongoDB", L"MongoDB", L"MongoDB Server"};
@@ -232,18 +238,17 @@ static void logStartup(OperationContext* txn) {
 
     ScopedTransaction transaction(txn, MODE_X);
     Lock::GlobalWrite lk(txn->lockState());
-    AutoGetOrCreateDb autoDb(txn, "local", mongo::MODE_X);
+    AutoGetOrCreateDb autoDb(txn, startupLogCollectionName.db(), mongo::MODE_X);
     Database* db = autoDb.getDb();
-    const std::string ns = "local.startup_log";
-    Collection* collection = db->getCollection(ns);
+    Collection* collection = db->getCollection(startupLogCollectionName);
     WriteUnitOfWork wunit(txn);
     if (!collection) {
         BSONObj options = BSON("capped" << true << "size" << 10 * 1024 * 1024);
         bool shouldReplicateWrites = txn->writesAreReplicated();
         txn->setReplicatedWrites(false);
         ON_BLOCK_EXIT(&OperationContext::setReplicatedWrites, txn, shouldReplicateWrites);
-        uassertStatusOK(userCreateNS(txn, db, ns, options));
-        collection = db->getCollection(ns);
+        uassertStatusOK(userCreateNS(txn, db, startupLogCollectionName.ns(), options));
+        collection = db->getCollection(startupLogCollectionName);
     }
     invariant(collection);
     uassertStatusOK(collection->insertDocument(txn, o, false));
@@ -299,6 +304,76 @@ static unsigned long long checkIfReplMissingFromCommandLine(OperationContext* tx
     return 0;
 }
 
+/**
+ * Due to SERVER-23274, versions 3.2.0 through 3.2.4 of MongoDB incorrectly mark the final output
+ * collections of aggregations with $out stages as temporary on most replica set secondaries. Rather
+ * than risk deleting collections that the user did not intend to be temporary when newer nodes
+ * start up or get promoted to be replica set primaries, newer nodes clear the temp flags left by
+ * these versions.
+ */
+static bool isSubjectToSERVER23299(OperationContext* txn) {
+    dbHolder().openDb(txn, startupLogCollectionName.db());
+    AutoGetCollectionForRead autoColl(txn, startupLogCollectionName);
+    // No startup log or an empty one means either that the user was not running an affected
+    // version, or that they manually deleted the startup collection since they last started an
+    // affected version.
+    LOG(1) << "Checking node for SERVER-23299 eligibility";
+    if (!autoColl.getCollection()) {
+        LOG(1) << "Didn't find " << startupLogCollectionName;
+        return false;
+    }
+    LOG(1) << "Checking node for SERVER-23299 applicability - reading startup log";
+    BSONObj lastStartupLogDoc;
+    if (!Helpers::getLast(txn, startupLogCollectionName.ns().c_str(), lastStartupLogDoc)) {
+        return false;
+    }
+    std::vector<int> versionComponents;
+    try {
+        for (auto elem : lastStartupLogDoc["buildinfo"]["versionArray"].Obj()) {
+            versionComponents.push_back(elem.Int());
+        }
+        uassert(40050,
+                str::stream() << "Expected three elements in buildinfo.versionArray; found "
+                              << versionComponents.size(),
+                versionComponents.size() >= 3);
+    } catch (const DBException& ex) {
+        log() << "Last entry of " << startupLogCollectionName
+              << " has no well-formed  buildinfo.versionArray field; ignoring " << causedBy(ex);
+        return false;
+    }
+    LOG(1)
+        << "Checking node for SERVER-23299 applicability - checking version 3.2.x for x in [0, 4]";
+    if (versionComponents[0] != 3)
+        return false;
+    if (versionComponents[1] != 2)
+        return false;
+    if (versionComponents[2] > 4)
+        return false;
+    LOG(1) << "Node eligible for SERVER-23299";
+    return true;
+}
+
+static void handleSERVER23299ForDb(OperationContext* txn, Database* db) {
+    log() << "Scanning " << db->name() << " db for SERVER-23299 eligibility";
+    const auto dbEntry = db->getDatabaseCatalogEntry();
+    list<string> collNames;
+    dbEntry->getCollectionNamespaces(&collNames);
+    for (const auto& collName : collNames) {
+        const auto collEntry = dbEntry->getCollectionCatalogEntry(collName);
+        const auto collOptions = collEntry->getCollectionOptions(txn);
+        if (!collOptions.temp)
+            continue;
+        log() << "Marking collection " << collName << " as permanent per SERVER-23299";
+        MONGO_WRITE_CONFLICT_RETRY_LOOP_BEGIN {
+            WriteUnitOfWork wuow(txn);
+            collEntry->clearTempFlag(txn);
+            wuow.commit();
+        }
+        MONGO_WRITE_CONFLICT_RETRY_LOOP_END(txn, "repair SERVER-23299", collEntry->ns().ns());
+    }
+    log() << "Done scanning " << db->name() << " for SERVER-23299 eligibility";
+}
+
 static void repairDatabasesAndCheckVersion(OperationContext* txn) {
     LOG(1) << "enter repairDatabases (to check pdfile version #)" << endl;
 
@@ -307,7 +382,7 @@ static void repairDatabasesAndCheckVersion(OperationContext* txn) {
 
     vector<string> dbNames;
 
-    StorageEngine* storageEngine = getGlobalServiceContext()->getGlobalStorageEngine();
+    StorageEngine* storageEngine = txn->getServiceContext()->getGlobalStorageEngine();
     storageEngine->listDatabases(&dbNames);
 
     // Repair all databases first, so that we do not try to open them if they are in bad shape
@@ -330,6 +405,8 @@ static void repairDatabasesAndCheckVersion(OperationContext* txn) {
         !(checkIfReplMissingFromCommandLine(txn) || replSettings.usingReplSets() ||
           replSettings.isSlave());
 
+    const bool shouldDoCleanupForSERVER23299 = isSubjectToSERVER23299(txn);
+
     for (vector<string>::const_iterator i = dbNames.begin(); i != dbNames.end(); ++i) {
         const string dbName = *i;
         LOG(1) << "    Recovering database: " << dbName << endl;
@@ -398,6 +475,10 @@ static void repairDatabasesAndCheckVersion(OperationContext* txn) {
             checkForIdIndexes(txn, db);
         }
 
+        if (shouldDoCleanupForSERVER23299) {
+            handleSERVER23299ForDb(txn, db);
+        }
+
         if (shouldClearNonLocalTmpCollections || dbName == "local") {
             db->clearTmpCollections(txn);
         }
diff --git a/src/mongo/db/storage/kv/kv_collection_catalog_entry.cpp b/src/mongo/db/storage/kv/kv_collection_catalog_entry.cpp
index 2381a80fff6..38a9d2b3b09 100644
--- a/src/mongo/db/storage/kv/kv_collection_catalog_entry.cpp
+++ b/src/mongo/db/storage/kv/kv_collection_catalog_entry.cpp
@@ -163,6 +163,12 @@ void KVCollectionCatalogEntry::updateFlags(OperationContext* txn, int newValue)
     _catalog->putMetaData(txn, ns().toString(), md);
 }
 
+void KVCollectionCatalogEntry::clearTempFlag(OperationContext* txn) {
+    MetaData md = _getMetaData(txn);
+    md.options.temp = false;
+    _catalog->putMetaData(txn, ns().ns(), md);
+}
+
 void KVCollectionCatalogEntry::updateValidator(OperationContext* txn,
                                                const BSONObj& validator,
                                                StringData validationLevel,
diff --git a/src/mongo/db/storage/kv/kv_collection_catalog_entry.h b/src/mongo/db/storage/kv/kv_collection_catalog_entry.h
index 11cc4ecafc6..3a3704e82d5 100644
--- a/src/mongo/db/storage/kv/kv_collection_catalog_entry.h
+++ b/src/mongo/db/storage/kv/kv_collection_catalog_entry.h
@@ -68,6 +68,8 @@ public:
 
     void updateFlags(OperationContext* txn, int newValue) final;
 
+    void clearTempFlag(OperationContext* txn) final;
+
     void updateValidator(OperationContext* txn,
                          const BSONObj& validator,
                          StringData validationLevel,
diff --git a/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.cpp b/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.cpp
index 736c3c11acc..278474cabb0 100644
--- a/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.cpp
+++ b/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.cpp
@@ -372,6 +372,10 @@ void NamespaceDetailsCollectionCatalogEntry::updateFlags(OperationContext* txn,
     _updateSystemNamespaces(txn, BSON("$set" << BSON("options.flags" << newValue)));
 }
 
+void NamespaceDetailsCollectionCatalogEntry::clearTempFlag(OperationContext* txn) {
+    _updateSystemNamespaces(txn, BSON("$set" << BSON("options.temp" << false)));
+}
+
 void NamespaceDetailsCollectionCatalogEntry::updateValidator(OperationContext* txn,
                                                              const BSONObj& validator,
                                                              StringData validationLevel,
diff --git a/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.h b/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.h
index 4bdebf31d5e..89760adf99a 100644
--- a/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.h
+++ b/src/mongo/db/storage/mmap_v1/catalog/namespace_details_collection_entry.h
@@ -93,6 +93,8 @@ public:
 
     void updateFlags(OperationContext* txn, int newValue) final;
 
+    void clearTempFlag(OperationContext* txn) final;
+
     void updateValidator(OperationContext* txn,
                          const BSONObj& validator,
                          StringData validationLevel,