Local fork at gpMgmt/bin/ext/yaml was removed by
03960e45333c3a7d8fe677b9015ce2a7c33c502b. Unpack
it from gpMgmt/bin/pythonSrc/ext just like pygresql.

Use yaml.safe_load rather than yaml.load as yaml.load is deprecated
Co-authored-by: NTyler Ramer <tramer@vmware.com>
Co-authored-by: NJamie McAtamney <jmcatamney@vmware.com>

Yaml was imported but unused in several locations.
gpMgmt/test/behave/mgmt_utils/steps/mgmt_utils.py had numerous unused
or duplicated imports.
Co-authored-by: NTyler Ramer <tramer@vmware.com>
Co-authored-by: NJamie McAtamney <jmcatamney@vmware.com>

It seems this yaml class is dead code. Removing it for this reason.
Co-authored-by: NTyler Ramer <tramer@vmware.com>
Co-authored-by: NJamie McAtamney <jmcatamney@vmware.com>

The version of PyYAML vendored in gpMgmt/bin/ext is old, unmaintained,
and does not support python3. Actually, it does not even contain a
`__version__` attribute, so it is not possible to know the version.

We need to unvendor yaml and address CVEs that have been found in the
library since the version vendored in source.

Also update yaml.load to use yaml.safe_load instead.
Co-authored-by: NTyler Ramer <tramer@vmware.com>
Co-authored-by: NJamie McAtamney <jmcatamney@vmware.com>

Currently GPDB tries to pull up EXPR sublinks to inner joins. For query

select * from foo where foo.a >
    (select avg(bar.a) from bar where foo.b = bar.b);

GPDB would transform it to:

select * from foo inner join
    (select bar.b, avg(bar.a) as avg from bar group by bar.b) sub
on foo.b = sub.b and foo.a > sub.avg;

To do that, GPDB needs to recurse through the quals in sub-select and
extract quals of form 'outervar = innervar' and then build new
SortGroupClause items and TargetEntry items based on these quals for
sub-select.

But for quals of form 'function(outervar, innervar1) = innvervar2', GPDB
handles them incorrectly and will cause wrong results issues as
described in issue #9615.

This patch fixes this issue by treating these kinds of quals as not
compatible correlated and thus the sub-select would not be converted to
join.
Reviewed-by: NHeikki Linnakangas <hlinnakangas@pivotal.io>
Reviewed-by: NAsim R P <apraveen@pivotal.io>
(cherry picked from commit dcdc6c0b)

Remove the set `gp_fts_probe_retries to 1` which may cause FTS probe failed.
This was first added to reduce the test time, but set a lower retry
value may cause the test failed to probe FTS update segment
configuration. Since reduce the `gp_fts_replication_attempt_count` also
save the test time, so skip alter ``gp_fts_probe_retries`.

Also find an assertion may not match when mark mirror down happens before
walsender exit, which will free the replication status before walsender
exit and try to record disconnect time and failure count. Which lead the
segment crash and starts recover.

When alter table add a column to AOCS table, the storage setting (compresstype,
compresslevel and blocksize) of the new column can be specified in the ENCODING
clause; it inherits the setting from the table if ENCODING is not specified; it
will use the value from GUC 'gp_default_storage_options' when the table dosen't
have the compression configuration.

Currently, replicated tables are not allowed to inherit a parent
table. But ALTER TABLE .. INHERIT can pass around the restriction.

On the other hand, a replicated table is allowed to be inherited
by a hash distributed table. It makes things much complicated.
When the parent table is declared as a replicated table inherited by
a hash distributed table, its data on the parent is replicated
but the data on the child is hash distributed. When running
`select * from parent;`, the generated plan is:
```
gpadmin=# explain select * from parent;
                                 QUERY PLAN
-----------------------------------------------------------------------------
 Gather Motion 3:1  (slice1; segments: 3)  (cost=0.00..4.42 rows=14 width=6)
   ->  Append  (cost=0.00..4.14 rows=5 width=6)
         ->  Result  (cost=0.00..1.20 rows=4 width=7)
               One-Time Filter: (gp_execution_segment() = 1)
               ->  Seq Scan on parent  (cost=0.00..1.10 rows=4 width=7)
         ->  Seq Scan on child  (cost=0.00..3.04 rows=2 width=4)
 Optimizer: Postgres query optimizer
(7 rows)
```
It's not particularly useful for the parent table to be replicated.
So, we disallow the replicated table to be inherited.
Reported-by: NHeikki Linnakangas <hlinnakangas@pivotal.io>
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>
(cherry picked from commit dc4b839e)

When there is a big lag between primary and mirror replay, gp_replica_check
will fail if the checkpoint is not replayed in about 60 seconds. Extend the
timeout to 600 seconds to reduce the chance of flaky.

[Lockfile](https://pypi.org/project/lockfile/) has not been maintained
since around 2015. Further, the functionality it provided seems poor - a
review of the code indicated that it used the presence of the PID file
itself as the lock - in Unix, using a file's existence followed by a
creation is not atomic, so a lock could be prone to race conditions.

The lockfile package also did not clean up after itself - a process
which was destroyed unexpectedly would not clear the created locks, so
some faulty logic was added to mainUtils.py, which checked to see if a
process with the same PID as the lockfile's creator was running. This
is obviously failure prone, as a new process might be assigned the same
PID as the old lockfile's owner, without actually being the same process.

(Of note, the SIG_DFL argument to os.kill() is not a signal at all, but
rather of type signal.handler. It appears that the python cast this
handler to the int 0, which, according to man 2 kill, leads to no signal
being sent, but existance and permission checks are still performed. So
it is a happy accident that this code worked at all)

This commit removes lockfile from the codebase entirely.

It also adds a "PIDLockFile" class which provides an atomic-guarenteed
lock via the mkdir and rmdir commands on Unix - thus, it is not safely
portable to Windows, but this should not be an issue as only Unix-based
utilities use the "simple_main()" function.

PIDLockFile provides API compatible classes to replace most of the
functionality from lockfile.PidLockFile, but does remove any timeout
logic as it was not used in any meaningful sense - a hard-coded timeout
of 1 second was used, but an immediate result of if the lock is held is
sufficient.

PIDLockFile also includes appropriate __enter__, __exit__, and __del__
attributes, so that, should we extend this class in the future, with
syntax is functional, and __del__ calls release, so a process reaped
unexpectedly should still clean its own locks as part of the garbage
collection process.
Authored-by: NTyler Ramer <tramer@pivotal.io>

Do not remove PYLIB_SRC_EXT during make clean/distclean

Commit 8190ed40 removed lockfile from
mainUtils, but did not remove a reference to its source directory in the
make clean/distclean target. As a result, because LOCKFILE_DIR is no
longer defined, the make clean/distclean target removes the
PYLIB_SRC_EXT directory.

Previously, the PdrgpcrsAddEquivClass function would modify the input
colref set. This does not appear intentional, as this same reference may
be accessed in other places. This caused Orca to fall back to planner in
some cases during translation with "Attribute number 0 not found in
project list".
Co-authored-by: Nmubo.fy <mubo.fy@alibaba-inc.com>
Co-authored-by: NChris Hajas <chajas@pivotal.io>
Co-authored-by: NHans Zeller <hzeller@vmware.com>
(cherry picked from commit 84c027afdff13f1d91447a5a88809f6e85399a1b)

The entry in aocsseg table might be compacted and waiting for drop, so we
should use 'state' to filter the unused entry.

column 'vpinfo' in pg_aoseg.pg_aocsseg_xxx record the 'eof' of each attribute
in the AOCS table. Add a new check 'aoseg_table' in gpcheckcat, it checks the
number of attributes in 'vpinfo' is the same as the number of attributes in
'pg_attribute'. This check is performed in parallel and independently on each
segment, and it checks aoseg table and pg_attribute in different transaction,
so it should be run 'offline' to avoid false alarm.

When ExecReScanBitmapHeapScan get executed, bitmap state (tbmiterator
and tbmres) gets freed in freeBitmapState. So the tbmres is NULL, and we
need to reinit bitmap state to start scan from the beginning and reset AO/AOCS
bitmap pages' flags(baos_gotpage, baos_lossy, baos_cindex and baos_ntuples).

Especially when ExecReScan happens on the bitmap append only scan and
not all the matched tuples in bitmap are consumed, for example, Bitmap
Heap Scan as inner plan of the Nest Loop Semi Join. If tbmres not get init,
and not read all tuples in last bitmap, BitmapAppendOnlyNext will assume the
current bitmap page still has data to return. but bitmap state already freed.

From the code, for Nest Loop Semi Join, when a match find, a new outer slot is
requested, and then `ExecReScanBitmapHeapScan` get called, `node->tbmres` and
`node->tbmiterator` set to NULL. `node->baos_gotpage` still keeps true.
When execute `BitmapAppendOnlyNext`, it skip create new `node->tbmres`.
And jump to access `tbmres->recheck`.
Reviewed-by: NJinbao Chen <jinchen@pivotal.io>
Reviewed-by: NAsim R P <pasim@vmware.com>
(cherry picked from commit cb5d18d1)

Make some utilities search path safe, so it'll not calling any external
functions that has the same name with our built-in functions.

This fix does not guarantee to fix CVE-2018-1058.

Backport from 070d6221.

Co-authored-by: Jamie McAtamney jmcatamney@pivotal.io
Co-authored-by: Jacob Champion pchampion@pivotal.io
Co-authored-by: Shoaib Lari slari@pivotal.io

The path constructed in OpenAOSegmentFile() didn't take into account
"t_" semantic of filename. Ideally, the correct filename is passed to
function, so no need to construct the same.

Would be better if can move MakeAOSegmentFileName() inside
OpenAOSegmentFile(), as all callers call it except
truncate_ao_perFile(), which doesn't fit that model.

(cherry picked from commit 327abdb5)

* docs - gphdfs2pxf migration pxf supports avro compression

* missing plural

We've moved the repo that holds trigger commits to a private repo since
there wasn't anything interesting there.

- generate-greenplum-path.sh use second parameter `yes` to generate
PYTHONHOME
- ONLY gpAux need to run this script with second parameter `yes`, since
in GPDB6 we always vendor python.
- developer build on their box won't be impacted by this change, since
regular build doesn't have second parameter, hence PYTHONHOME will be
skipped.

We added test-generate-greeplum-path.bash to verify the correctness of
the script.

[#173567726]
Co-authored-by: NBradford D. Boyle <bradfordb@vmware.com>
Co-authored-by: NTingFang Bao <bbob@vmware.com>
Co-authored-by: NXin Zhang <zhxin@vmware.com>
Co-authored-by: NBradford D. Boyle <bradfordb@vmware.com>
Co-authored-by: NTingFang Bao <bbob@vmware.com>

Force to update checkpoint timeline id in control data after promotion and before pg_rewind. (#10402)

After promotion there is a checkpoint but not an immediate one, so the
checkpoint timeline id in pg_control data might not be updated in time when
running pg_rewind which depends on that to decide the necessity of incremental
recovery.  Let's run checkpoint after promotion in tests so that later
pg_rewind will not bypass the incremental recovery.

This should be able to fix some long-existing annoying flaky pg_rewind tests.
Reviewed-by: N(Jerome)Junfeng Yang <jeyang@pivotal.io>
(cherry picked from commit e072dff7)

This reverts commit b0afc59b.

--Also, add some links to other topics.

For GPDB FTS, if the primary, mirror replication keeps crash
continuously and attempt to crate replication connection too many times,
FTS should mark the mirror down. Otherwise, it may block other
processes.
If the WAL starts streaming, clear the attempt count to 0. This is because the blocked
transaction can only be released once the WAL in streaming state.

The solution for this is:

1. Use ` FTSReplicationStatus` which under `gp_replication.c`  to track current primary-mirror
replication status. This includes:
    - A continuous failure counter. The counter gets reset once the replication
    starts streaming, or replication restarted.
    - A record of the last disconnect timestamp which is refactored from
    `WalSnd` slot.
    The reason for moving this is: When FTS probe happens, the `WalSnd`
    slot may already get freed. And `WalSnd` slot is designed reusable.
    It's hacky to read value from a freed slot in shared memory.

2. When handling each probe query, `GetMirrorStatus` will check the current
mirror status and the failure count from walsender's application ` FTSReplicationStatus`.
If the count exceeds the limit, the retry test will ignore the last replication
disconnect time since it gets refreshed when new walsender starts. (Since
in the current case, the walsender keeps restart.)

3. On FTS bgworker. If mirror down and retry set to false, mark the mirror
down.

A `gp_fts_replication_attempt_count` GUC is added. When the replication failure count
exceed this GUC, ignore the last replication disconnect time when checking for mirror
probe retry.

The life cycle of a ` FTSReplicationStatus`:
1. It gets created when first enable replication during the replication
start phase. Each replication's sender should have a unique
`application_name`, which also used to specify the replication priority
in multi-mirror env. So ` FTSReplicationStatus` uses the `application_name` mark
itself.

2. The ` FTSReplicationStatus` for replication will exist until FTS detects
failure and stop the replication between primary and mirror. Then
` FTSReplicationStatus` for that `application_name` will be dropped.

Now the `FTSReplicationStatus` is used only for GPDB primary-mirror replication.

(cherry picked from commit 252ba888)

Reviewed-by: Ashwin Agrawal aagrawal@pivotal.io

If the directory of tablespace does not exist, we should got a
error on commit transaction. But error on commit transaction will
cause a panic. So the directory of tablespace should be checked
so that we can avoid panic.

Previously, there are some code executed in QEs that will check
the value of the GUC gp_enable_global_deadlock_detector. The
historical reason is that:
  Before we have GDD, UPDATE|DELETE operations cannot be
  concurrently executed, and we do not meet the EvalPlanQual
  issue and concurrent split update issue. After we have GDD,
  we meet such issues and add code to resolve them, and we
  add the code `if (gp_enable_global_deadlock_detector)` at
  the very first. It is just like habitual thinking.

In fact, we do not rely on it in QEs and I tried to remove this
in the context: #9992 (review).
I tried to add an assert there but could not handle utility mode
as Heikki's comments. To continue that idea, we can just remove
the check of gp_enable_global_deadlock_detector. This brings two
benefits:
  1. Some users only change this GUC on master. By removing the usage
     in QEs, it is safe now to make the GUC master only.
  2. We can bring back the skills to only restart master node's postmaster
     to enable GDD, this save a lot of time in pipeline. This commit
     also do this for the isolation2 test cases: lockmodes and gdd/.

The Github issue #10030  is gone after this commit.

Also, this commit backports lockmodes test from master branch and
refactor concurrent_update test cases.

While installing ORCA in Ubuntu 18.04 I ran into some issues while
trying to install gp-xerces. During the build, Greenplum was trying to
link against the installed xerces `libxerces-c-dev`, which is installed
by running the `./README.ubuntu.bash` script. By default, Ubuntu 18.04
will install xerces 3.2, which is incompatible with the version used by
Greenplum 6.

The pg_get_viewdef() function was fixed to properly show views define.
Should remove the view which not supported in old version before the
binary swap test.

For non partition table, we will skip gpexpand external tables,
but for partition table, when one of its child parition is a
external table, we error out when gpexpand. This is not a correct
behavior.
Since data of foreign table is located outside gpdb, skip these
tables when gpexpand is enough.

Co-Authored-by: Ning Yu nyu@pivotal.io

(cherry picked from commit b9691eba)

The clause 'CASE WHEN (arg1) IS NOT DISTINCT FROM (arg2)' dump will miss
the arg1. For example:
```
CREATE OR REPLACE VIEW xxxtest AS
SELECT
    CASE
    WHEN 'I will disappear' IS NOT DISTINCT FROM ''::text
    THEN 'A'::text
    ELSE 'B'::text
    END AS t;
```
The dump will lose 'I will disappear'.

```
SELECT
    CASE
    WHEN IS NOT DISTINCT FROM ''::text
    THEN 'A'::text
    ELSE 'B'::text
    END AS t;
```

For below example:
```
CREATE TABLE mytable2 (
    key character varying(20) NOT NULL,
    key_value character varying(50)
) DISTRIBUTED BY (key);

CREATE VIEW aaa AS
SELECT
    CASE mytable2.key_value
        WHEN IS NOT DISTINCT FROM 'NULL'::text THEN 'now'::text::date
        ELSE to_date(mytable2.key_value::text, 'YYYYMM'::text)
        END AS t
    FROM mytable2;

```

mytable2.key_value will cast to type date. For clause `(ARG1) IS NOT
DISTINCT FROM (ARG2)`, this leads ARG1 become a RelabelType node and
contains CaseTestExpr node in RelabelType->arg.

So when dumping the view, it'll mark dump as

```
select pg_get_viewdef('notdisview3',false);
                               pg_get_viewdef
-----------------------------------------------------------------------------
  SELECT                                                                    +
         CASE mytable2.key_value                                            +
             WHEN (CASE_TEST_EXPR) IS NOT DISTINCT FROM 'NULL'::text THEN ('now'::text)::date+
             ELSE to_date((mytable2.key_value)::text, 'YYYYMM'::text)       +
         END AS t                                                           +
    FROM mytable2;
(1 row)
```

I dig into commit a453004e, if left-hand argument for `IS NOT DISTINCT
FROM` contains any `CaseTestExpr` node, the left-hand arg should be omitted.
`CaseTestExpr` is a placeholder for CASE expression.

Resource group we does not distinguish the per segment cpu usage, the
cpu usage reported by a segment is actually the total cpu usage of all
the segments on the host.  This is by design, not a bug.  However, in
the gp_toolkit.gp_resgroup_status_per_host view it reports the cpu usage
as the sum of all the segments on the same host, so the reported per
host cpu usage is actually N times of the actual usage, where N is the
count of the segments on that host.

Fixed by reporting the avg() instead of the sum().

Tests are not provided as the resgroup/resgroup_views did not verify cpu
usages since the beginning, because the cpu usage is unstable on
pipelines.  However, I have verified manually.
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>
(cherry picked from commit e0d78729)

It could be called in utility mode, however we should avoid calling into
FtsNotifyProber() for such case. Ideally we could do that if we access the
master node and postgres is no in single mode, but it seems that we do not that
need.

Here is the stack of the issue I encountered.

0  0x0000003397e32625 in raise () from /lib64/libc.so.6
1  0x0000003397e33e05 in abort () from /lib64/libc.so.6
2  0x0000000000b39844 in ExceptionalCondition (conditionName=0xeebac0 "!(Gp_role == GP_ROLE_DISPATCH)", errorType=0xeebaaf "FailedAssertion",
    fileName=0xeeba67 "cdbfts.c", lineNumber=101) at assert.c:66
3  0x0000000000bffb1e in FtsNotifyProber () at cdbfts.c:101
4  0x0000000000c389a4 in cdbcomponent_getCdbComponents () at cdbutil.c:714
5  0x0000000000c26e3a in gp_pgdatabase__ (fcinfo=0x7ffd7b009c10) at cdbpgdatabase.c:74
6  0x000000000076dbd6 in ExecMakeTableFunctionResult (funcexpr=0x3230fc0, econtext=0x3230988, argContext=0x3232b68, expectedDesc=0x3231df8, randomAccess=0 '\000',
	    operatorMemKB=32768) at execQual.c:2275
......
18 0x00000000009afeb2 in exec_simple_query (query_string=0x316ce20 "select * from gp_pgdatabase") at postgres.c:1778
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>

Cherry-picked from 06d7fe0a

* Doc updates to cover packaging changes/additions for versions 7/6

* Removing nav link to non-default steps

* Add missing chown examples; add note about symbolic link update in upgrade procedure

* Typo fix

Analyze error'd with "ERROR: unsupported table type" if external table
is part of partition hierarchy. Also, that blocks analyzing database
wide as can't analyze such partitions. This commit adds check to skip
external tables during acquire_inherited_sample_rows().

Fixes #9506 github issue.
Co-authored-by: NAlexandra Wang <lewang@pivotal.io>

This problem manifests itself with HashAgg on the top of
DynamicIndexScan node and can cause a segmentation fault.

1. A HashAgg node initializes a tuple descriptor for its hash
slot using a reference from input tuples (coming from
DynamicIndexScan through a Sequence node).
2. At the end of every partition index scan in DynamicIndexScan
we unlink and free unused memory chunks and reset partition's
memory context. It causes a total destruction of all objects in
the context including partition index tuple descriptor used in a
HashAgg node.
As a result we get a dangling pointer in HashAgg on switching to
a new index partition during DynamicIndexScan that can cause a
segfault.

This backports from commit: 41ce55bf.
Co-authored-by: NDenis Smirnov <sd@arenadata.io>

When cleaning up the master-only files on the new segments we used to do
the job one by one, when there are tens or hundreds of segments it can
be very slow.

Now we cleanup in parallel.

(cherry picked from commit 857763ae)
Reviewed-by: NZhenghua Lyu <zlv@pivotal.io>

For the Python testing artifacts used by the CLI tools, utilize the
Concourse cached directories feature to create and use a pip cache dir
shared between task runs.

Be aware, the cache is scoped to the worker the task is run on. We do
not get a cache hit when subsequent builds run on different workers.

* The environment variable PIP_CACHE_DIR is used to store the cache
directory.

* Add "--retries 10" to Behave test dependency pip install commands.

Mirror registration passes through several steps at the moment:
1. CREATE_QE_ARRAY (QE_MIRROR_ARRAY is ordered by content)
2. ARRAY_REORDER (QE_MIRROR_ARRAY is ordered by port)
3. CREATE_ARRAY_SORTED_ON_CONTENT_ID (form QE_MIRROR_ARRAY_SORTED_ON_CONTENT_ID
   on a base of QE_MIRROR_ARRAY)
4. REGISTER_MIRRORS (walk through QE_MIRROR_ARRAY, register mirrors with
   pg_catalog.gp_add_segment_mirror on master's gp_segment_configuration
   and update QE_MIRROR_ARRAY with returned dbids)
5. CREATE_SEGMENT (walk through QE_MIRROR_ARRAY_SORTED_ON_CONTENT_ID with old
   dbids and create mirrors on segment hosts with pg_basebackup)
The problem is in a step 4 - we update the wrong array (QE_MIRROR_ARRAY instead
of QE_MIRROR_ARRAY_SORTED_ON_CONTENT_ID). Because of that we get inconsistency
between mirror dbids on gp_segment_configuration and internal.auto.conf files.
This can cause inoperable cluster state in some situations when we promote a
failed primary from a mirror with wrong dbids (FTS can't solve this issue).

Also fixed column indexes in array used for segment arrray ordering.
It was not done after commit https://github.com/greenplum-db/gpdb/commit/03c7d557720c5a78af1e2574ac385d10a0797f5e
which prepend array with new hostname column.
Co-authored-by: NVasiliy Ivanov <ivi@arenadata.io>
(cherry picked from commit 8d008792)