Is_nullable JSON-path indexes used to lose is_nullable property
being defined on a space having format. This patch fixes this
problem.

Closes #4520

(cherry picked from commit 3d01b3af)

Functional index extractor code used to raise an invalid
error message when the user-defined extractor function
returns a scalar instead of a table.

Closes #4553

(cherry picked from commit 260a3b3a)

End recovery (which means building secondary indexes) just after
last known log file was read. This allows fast switch to hot standby
instance without any delay for secondary index to be built.
Due to engine_end_recovery carryover, xdir_collect_inprogress,
previously being called from it, is now moved to garbage collector.

Closes #4135

(cherry picked from commit 5aa243de)

Rows_per_wal option was deprecated because it can be covered by
wal_max_size. In order not to complicate WAL code with that
option's support this commit drops it completely.

In some tests the option was used to create several small xlog
files. Now the same is done via wal_max_size. Where it was
needed, number of rows per wal is estimated as wal_max_size / 50.
Because struct xrow_header size ~= 50 not counting paddings and
body.

Note, file box/configuration.result was deleted here, because it
is a stray result file, and it contained the rows_per_wal option
mentioning. Its test was dropped much earlier in
fdc3d1dd.

Closes #3762

(cherry picked from commit c6012920)

In patch c6bea65f I
added a bug - replication/misc leaves a bad value in
box.cfg.replication. Before that patch the test was
resetting this to empty replication. In my patch I
forgot about that, and left there the value

    {box.cfg.listen, "12345"}

This patch cleans it up.

Follow up #3760

(cherry picked from commit 399899a1)

Replication quorum 0 not only affects orphan status, but also,
according to documentation, makes box.cfg() return immediately
regardless of whether connections to upstreams are established.

It was not so before the patch. What is worse, even with non 0
quorum the instance was blocked on reconfiguration for connect
timeout seconds, if at least one node is not connected.

Now quorum is respected on reconfiguration. On a bootstrap it is
still impossible to return earlier than
replication_connect_timeout, because nodes need to choose some
cluster settings. Too early start would make it impossible -
cluster's participants will just start and choose different
cluster UUIDs.

Closes #3760

(cherry picked from commit c6bea65f)

A successfully fetched remote instance ballot isn't updated during
bootstrap procedure. This leads to a case when different instances
choose different masters as their bootstrap leaders.

Imagine such a situation.
You start instance A without replication set up. Instance A successfully
bootstraps.
You also have instances B and C both with replication set up to {A, B,
C} and replication_connect_quorum set to 3
You first start instance B. It doesn't proceed to choosing a leader
until one of the events happens: either the replication_connect_timeout
runs out, or instance C is up and starts listening on its port.
B has established connection to A and fetched its ballot, with some
vclock, say, {1: 1}.
B retries connection to C every replication_timeout seconds.
Then you start instance C. Instance C succeeds in connecting to A and B
right away and bootstraps from instance A. Instance A registers C in its
_cluster table. This registration is replicated to instance C.
Meanwhile, instance C is trying to sync with quorum instances (which is
3), and stays in orphan mode.
Now replication_timeout on instance B finally runs out. It retries a
previously unsuccessful connection to C and succeeds. C sends its ballot
to B with vclock = {1: 2, 2:0} (in our example), since it has already
incremented it after _cluster registration.
B sees that C has a greater vclock than A, and chooses to bootstrap from
C instead of A. C is orphan and rejects B's attempt to join. B dies.

To fix such ungentlemanlike behaviour of C, we should at least include
loading status in ballot and prefer fully bootstrapped instances to the
ones still syncing with other replicas.
We also need to use a separate flag instead of ballot's already existent
is_ro, since we still want to prefer loading instances over the ones
explicitly configured to be read-only.

Closes #4527

(cherry picked from commit dc1e4009)

(cherry picked from commit 0b9de586)

Count lines in the json parsing structure. It is needed to print
the number of line and column where a mistake was made.

Closes #3316

(cherry picked from commit 9f9bd3eb2d064129ff6b1a764140ebef242d7ff7)
(cherry picked from commit 53d43160)

Code to run main script (passed via command line args, or
interactive console) has a footer where it notifies systemd,
logs a happened error, and panics.

Before the patch that code was unreachable in case of any
exception in a main script, because panic happened earlier. Now a
happened exception is correctly carried to the footer with proper
error processing.

A first and obvious solution was replace all panics with diag_set
and use fiber_join on the script runner fiber. But appeared, that
the fiber running a main script can't be joined. This is because
normally it exits via os.exit() which never returns and therefore
its caller never dies = can't be joined.

The patch solves this problem by passing main fiber diag to the
script runner by pointer, eliminating fiber_join necessity.

Closes #4382

(cherry picked from commit 157a2d88)

Closes #4434
Follow-up #4366

@TarantoolBot document
Title: json/msgpack.cfg.encode_deep_as_nil option

Tarantool has several so called serializers to convert data
between Lua and another format: YAML, JSON, msgpack.

YAML is a crazy serializer without depth restrictions. But for
JSON, msgpack, and msgpackffi a user could set encode_max_depth
option. That option led to crop of a table when it had too many
nested levels. Sometimes such behaviour is undesirable.

Now an error is raised instead of data corruption:

    t = nil
    for i = 1, 100 do t = {t} end
    msgpack.encode(t) -- Here an exception is thrown.

To disable it and return the old behaviour back here is a new
option:

    <serializer>.cfg({encode_deep_as_nil = true})

Option encode_deep_as_nil works for JSON, msgpack, and msgpackffi
modules, and is false by default. It means, that now if some
existing users have cropping, even intentional, they will get the
exception.

(cherry picked from commit d7a8942a)

Tuple is a C library exposed to Lua. In Lua to translate Lua
objects into tuples and back luaL_serializer structure is used.

In Tarantool we have several global serializers, one of which is
for msgpack. Tuples store data in msgpack, and in theory should
have used that global msgpack serializer. But in fact the tuple
module had its own private serializer because of tuples encoding
specifics such as never encode sparse arrays as maps.

This patch makes tuple Lua module use global msgpack serializer
always. But how does tuple handle sparse arrays now? In fact,
the tuple module still has its own serializer, but it is updated
each time when the msgpack serializer is changed.

Part of #4434

(cherry picked from commit 676369b1)

Msgpack Lua module is not a simple set of functions. It is a
global serializer object used by plenty of other Lua and C
modules. Msgpack as a serializer can be configured, and in theory
its configuration updates should affect all other modules. For
example, a user could change encode_max_depth:

    require('msgpack').cfg({encode_max_depth = <new_value>})

And that would make tuple:update() accept tables with <new_value>
depth without a crop.

But in fact msgpack configuration didn't affect some places, such
as this one. And all the others who use msgpackffi.

This patch fixes it, for encode_max_depth option. Other options
are still ignored.

Part of #4434

(cherry picked from commit 4bb253f7)

There are some objects called serializers - msgpack, cjson, yaml,
maybe more. They are global objects affecting both Lua and C
modules.

A serializer have settings which can be updated. But before the
patch an update changed only C structure of the serializer. It
made impossible to use settings of the serializers from Lua.

Now any update of any serializer is reflected both in its C and
Lua structures.

Part of #4434

(cherry picked from commit fe4a8047)

Since ARRAY and MAP cannot be converted to SCALAR type, this
operation should throw an error. But when the error is raised in
SQL, it is displayed in unreadable form. The reason for this is
that the given array or map is not correctly converted to a
string. This patch fixes the problem by converting ARRAY or MAP to
their string representation.
For example:

box.execute('CREATE TABLE t1(i INT PRIMARY KEY, a SCALAR);')
format = {}
format[1] = {type = 'integer', name = 'I'}
format[2] = {type = 'array', name = 'A'}
s = box.schema.space.create('T2', {format=format})
i = s:create_index('ii')
s:insert({1, {1,2,3}})
box.execute('INSERT INTO t1 SELECT * FROM t2;')

Should return:
- error: 'Type mismatch: can not convert [1, 2, 3] to scalar'

Follow-up #4189

(cherry picked from commit 736cdd81)

Function mem_apply_type() implements implicit type conversion. As
a rule, tuple to be inserted to the space is exposed to this
conversion which is invoked during execution of OP_MakeRecord
opcode (which in turn forms tuple). This function was not adjusted
to operate on ARRAY, MAP and ANY field types since they are poorly
supported in current SQL implementation. Hence, when tuple to be
inserted in space having mentioned field types reaches this
function, it results in error. Note that we can't set ARRAY or MAP
types in SQL, but such situation may appear during UPDATE
operation on space created via Lua interface. This problem is
solved by extending implicit type conversions with obvious casts:
array field can be casted to array, map to map and any to any.

Closes #4189

(cherry picked from commit de79b714)

Method fio.mktree is used to create given path unconditionally -
without checking if it was a directory or something else. This
led to inappropriate error messages or even inconsistent behavior.
Now check the type of a given path.

Closes #4439

(cherry picked from commit 8ccfc691)

It was forgotten to swap old and new mask (holding fields involved into
foreign key relation) during space alteration (lists of object
representing FK metadata are swapped successfully). Since mask is vital
and depending on its value different byte-codes implementing SQL query
can be produced, this mistake resulted in assertion fault in debug build
and wrong constraint check in release build. Let's fix this bug and swap
masks as well as foreign key lists.

Closes #4495

(cherry picked from commit 33236ecc)

This patch provides a test suite that allows us to make sure that
the SQL BOOLEAN type works as intended.

Part of #4228

(cherry picked from commit 7cf84a54)

In a configuration with several read-only and read-write instances, if
replication_connect_quorum is not greater than the amount of read-only
instances and replication_connect_timeout happens to be small enough
for some read-only instances to form a quorum and exceed the timeout
before any of the read-write instaces start, all these read-only
instances will choose themselves a read-only bootstrap leader.
This 'leader' will successfully bootstrap itself, but will fail to
register any of the other instances in _cluster table, since it isn't
writeable. As a result, some of the read-only instances will just die
unable to bootstrap from a read-only bootstrap leader, and when the
read-write instances are finally up, they'll see a single read-only
instance which managed to bootstrap itself and now gets a
REPLICASET_UUID_MISMATCH error, since no read-write instance will
choose it as bootstrap leader, and will rather bootstrap from one of
its read-write mates.

The described situation is clearly not what user has hoped for, so
throw an error, when a read-only instance tries to initiate the
bootstrap. The error will give the user a cue that he should increase
replication_connect_timeout.

Closes #4321

@TarantoolBot document
Title: replication: forbid to bootstrap read-only masters.

It is no longer possible to bootstrap a read-only instance in an emply
data directory as a master. You will see the following error trying to
do so:
```
ER_BOOTSTRAP_READONLY: Trying to bootstrap a local read-only instance as master
```
Now if you have a fresh instance, which has
`read_only=true` in an initial `box.cfg` call, you need to set up
replication from an instance which is either read-write, or has your
local instance's uuid in its `_cluster` table.

In case you have multiple read-only and read-write instances with
replication set up, and you still see the aforementioned error message,
this means that none of your read-write instances managed to start
listening on their port before read_only instances have exceeded the
`replication_connect_timeout`. In this case you should raise
`replication_connect_timeout` to a greater value.

(cherry picked from commit 037bd58c)

* All test chunks related to luajit were moved from tarantool source
tree to the luajit repo
* Adjusted CMakeLists via creating a symlink to luajit test directory
to fix out-of-source tests

Closed #4478

(cherry picked from commit 43575303)

The json.encode() used to cause a segfault in case of recursive
table:
  tbl = {}
  tbl[1] = tbl
  json.encode(tbl)

Library doesn't test whether given object on Lua stack parsed
earlier, because it performs a lightweight in-depth traverse
of Lua stack. However it must stop when encode_max_depth is
reached (by design).

Tarantool's lua_cjson implementation has a bug introduced during
porting original library: it doesn't handle some corner cases:
entering into a map correctly increases a current depth, while
entering into an array didn't. This patch adopts author's
approach to check encode_max_depth limit. Thanks to handling this
constraint correctly the segfault no longer occurs.

Closes #4366

(cherry picked from commit d2641e66e65ab57317b8e70bb7115517ec81238e)

The test sql-tap/gh-3083-ephemeral-unref-tuples.test.lua took
too long runtime and failed to finish in timeout limit of 2
minutes when it runs near the end of the running queue:

No output during 120 seconds. Will abort after 120 seconds without output. List of workers not reporting the status:
- 012_sql-tap [sql-tap/gh-3083-ephemeral-unref-tuples.test.lua, vinyl] at var/012_sql-tap/gh-3083-ephemeral-unref-tuples.result:0
Test hung! Result content mismatch:
[File does not exists: sql-tap/gh-3083-ephemeral-unref-tuples.result]
[Main process] No output from workers. It seems that we hang. Send SIGKILL to workers; exiting...

Due to suggestion from Konstantin Osipov at gh-3845:
https://github.com/tarantool/tarantool/issues/3845#issue-385735959

The following tests:
  gh-3083-ephemeral-unref-tuples.test.lua
  gh-3332-tuple-format-leak.test.lua
where set to run only on memtx configuration.

Also the test:
  gh-3083-ephemeral-unref-tuples.test.lua
was removed from the test-run 'fragile' option flaky list.

Closed #4128

(cherry picked from commit 40c94af7)

Added "fragile" option to the flaky tests that are
not intended to be run in parallel with others.
Option set at the suite.ini file at the appropriate
suites with comments including the issue that stores
the fail.

(cherry picked from commit 165f8ee6)

It turned out that patch d0e38d59 wasn't accompanied
w/ a test. Add proper check.

(cherry picked from commit c80e9416)

Currently we only enter orphan mode when instance fails to connect to
replication_connect_quorum remote instances during local recovery.
On bootstrap and manual replication configuration change an error is
thrown. We better enter orphan mode on manual config change, and leave
it only in case we managed to sync with replication_connect_quorum
instances.

Closes #4424

@TarantoolBot document
Title: document reaction on error in replication configuration change.

Now when issuing `box.cfg{replication={uri1, uri2, ...}}` and failing to
sync with replication_connect_quorum remote instances, the server will
throw an error, if it is bootstrapping, and just set its state to orphan
in all other cases (recovering from existing xlog/snap files or manually
changing box.cfg.replication on the fly). To leave orphan mode, you may
wait until the server manages to sync with replication_connect_quorum
instances.
In order to leave orphan mode you need to make the server sync with
enough instances. To do so, you may either:
1) set replication_connect_quorum to a lower value
2) reset box.cfg.replication to exclude instances that cannot
   be reached or synced with
3) just set box.cfg.replication to "" (empty string)

(cherry picked from commit 5a0cfe02)

CentOS 6 and FreeBSD 12 implementations of getpwuid() rewind
setpwent()-{getpwent()}-endpwent() loop to a start that leads to a hang
during pwd.getpwall() invoke. The same is true for a getgrgid() call
during setgrent()-{getgrent()}-endgrent() loop.

The commit modifies pwd module to avoid getpwuid() calls during passwd
database traversal and to avoid getgrgid() calls when traversing groups.

The commit also fixes the important regression on CentOS 6 after
f5d8331e ('lua: workaround
pwd.getpwall() issue on Fedora 29'): tarantool hungs during startup due
to added getpwall() call. This made tarantool unusable on CentOS 6 at
all.

Aside of that the commit fixes another pwd.getgrall() problem: the
function gaves password entries instead of group entries.

Fixes #4428.
Fixes #4447.
Part of #4271.

(cherry picked from commit 7753d350)

app-tap.tarantoolctl.test.lua fails after
17df9edf ('tarantoolctl: allow to start
instances with delayed box.cfg{}').

The commit fixes the test case that did check that an error is reported
if box.cfg() was not called in an instance script.

Follows up #4435.
Fixes #4448.

(cherry picked from commit 6c627af3)

To compare floating point values and integers in SQL functions
compare_uint_float() and compare_int_float() are used. Unfortunately,
they contain bug connected with checking border case: that's not correct
to cast UINT64_MAX (2^64 - 1) to double. Proper way is to use exp2(2^64)
or predefined floating point constant. To not bother fixing function
which in turn may contain other tricky places, let's use instead already
verified double_compare_uint64(). So that we have unified way of
integer<->float comparison.

(cherry picked from commit 73a4a525)

Name duplicates are allowed for savepoints (both in our SQL
implementation and in ANSI specification). ANSI SQL states that previous
savepoint should be deleted. What is more, our doc confirms this fact
and says that "...it is released before the new savepoint is set."
Unfortunately, it's not true - currently old savepoint remains in the
list. For instance:

SAVEPOINT t;
SAVEPOINT t;
RELEASE SAVEPOINT t;
RELEASE SAVEPOINT t; -- no error is raised

Let's fix this and remove old savepoint from the list.

(cherry picked from commit 8b8b6895)

This procedure is processed in several steps. Firstly, we add name
to struct txn_savepoint since we should be capable of operating on named
savepoints (which in turn is SQL feature). Still, anonymous (in the sense
of name absence) savepoints are also valid. Then, we add list (as
implementation of stailq) of savepoints to struct txn: it allows us to
find savepoint by its name. Finally, we patch rollback to/release
savepoint routines: for rollback tail of the list containing savepoints
is cut (but subject of rollback routine remains in the list); for
release routine we cut tail including node being released.

(cherry picked from commit 56096ff2)

Hold libcurl-7.65.3. This version is not affected by the following
issues:

* #4180 ('httpc: redirects are broken with libcurl-7.30 and older');
* #4389 ('libcurl memory leak');
* #4397 ('HTTPS seem to be unstable').

After this patch libcurl will be statically linked when
ENABLE_BUNDLED_LIBCURL option is set. This option is set by default.

Closes #4318

@TarantoolBot document
Title: Tarantool dependency list was changed

* Added build dependencies: autoconf, automake, libtool, zlib-devel
  (zlib1g-dev on Debian).
* Added runtime dependencies: zlib (zlib1g on Debian).
* Removed build dependencies: libcurl-devel (libcurl4-openssl-dev on
  Debian).
* Removed runtime dependencies: curl.

The reason is that now we use compiled-in libcurl: so we don't depend on
a system libcurl, but inherit its dependencies.

(cherry picked from commit 7e51aebb)

It was forgotten to update result file of sql/bind.test.lua
in previous patch. Let's fix that and refresh sql/bind.result with
up-to-date results.

(cherry picked from commit 0894bec2)

It was decided that for all integer literals we would return "INTEGER"
type, not "UNSIGNED". Accidentally, after substitution of unsigned
binding value type was set to "UNSIGNED". Let's fix that and set
"INTEGER" type.

(cherry picked from commit b7d595ac)

https://github.com/LuaJIT/LuaJIT/issues/505
(cherry picked from commit 26303604)

In one place that test sends a packet and expects that it has
arrived two lines below. Under high load it may take more time.
The patch makes the test explicitly wait for the packet arrival.

Closes #4392

Found that on high loaded hosts the test flaky fails at:

[004] --- app/socket.result	Mon Jul 15 07:18:57 2019
[004] +++ app/socket.reject	Tue Jul 16 16:37:35 2019
[004] @@ -1118,7 +1118,7 @@
[004]  ...
[004]  ch:get(1)
[004]  ---
[004] -- true
[004] +- null
[004]  ...
[004]  s:error()
[004]  ---

Found that the test in previous was used for testing the
the channel get() function timeout and the error occurred
on it, but later the checking error changed to:
"builtin/socket.lua: attempt to use closed socket" and the
test became not correct. Because for now it passes when the
socket read function runs before the socket closing, but in
this way read call doesn't wait. In the other way on high
loaded hosts the close call may occure before read call and
in this way read call halts and socket get call returns
'null'. As seen both ways are not correct to check the error.
Decided to remove this subtest.

Check commit ba7a4fee ("Add tests for socket:close closes #360")

Fixes #4354

(cherry picked from commit 952d8d1d)

JSON paths has no a strict standard, but definitely there is no
an implementation, allowing to omit '.' after [], if a next token
is a key. For example:

    [1]key

is invalid. It should be written like that:

    [1].key

Strangely, but we even had tests on the invalid case.

Closes #4419

(cherry picked from commit ef64ee51)

In case an error occurs between relay_start() and cord_costart() in
relay_subscribe(), the relay status won't be reset to STOPPED. As a
result, any further attempt to re-subscribe will fail with ER_CFG:
duplicate connection with the same replica UUID. This may happen, for
example, if the WAL directory happens to be temporarily inaccessible on
the master.

Closes #4399

(cherry picked from commit 35ef3320)

It was decided that null value in SQL by default should be of type
boolean. Justification of such change is that according to ANSI boolean
type in fact has three different values: true, false and unknown. The
latter is basically an alias to null value.