* docs - update postGIS 2.5.4 docs

Updates for Greenplum PostGIS 2.5.4 v2

--Add list of PostGIS extensions
--Add support for PostGIS TIGER geocoder, address standardizer and address rules files.
--Update install/uninstall instructions to use CREATE EXTENSION command
--Remove postgis_manager.sh script
--Remove PostGIS Raster limitation.

* docs updated PostGIS 2.5.4 docs based on review comments.

* docs - removed postgis_raster extension.

* docs - review comment updates  -Added section for installing the PostGIS package
-Updated section on removing PostGIS package
-Fix typos.

* docs - updated platform requirements for PostGIS 2.5.4 v2
-also removed "beta" from GreenplumR

PyGreSQL may now be installed via pip or via Ubuntu apt.

Update the travis pipeline as well, using submodules to pull the
necessary python dependencies. Thus, they are removed from PIP as well.
Authored-by: NTyler Ramer <tramer@pivotal.io>

This patch fixes the issue: https://github.com/greenplum-db/gpdb/issues/10224
Replicated table is not allowed to be a partition table.
So an existing partition table must not be altered its
distribution policy to REPLICATED.
Reported-by: NHeikki Linnakangas <hlinnakangas@pivotal.io>
Reviewed-by: NZhenghua Lyu <zlv@pivotal.io>

Greenplum tests the visibility of heap tuples firstly using
distributed snapshot. Distributed snapshot is generated on
QD and then dispatched to QEs. Some utility statement needs
to work under the latest snapshot when executing, so that they
invoke the function `GetLatestSnapshot` in QEs. But remember
we cannot get the latest distributed snapshot.

Subtle cases are: Alter Table or Alter Domain statements on QD
get snapshot in Portal Run and then try to hold locks on the
target table in ProcessUtilitySlow. Here is the key point:
  1. try to hold lock ==> it might be blocked by other transactions
  2. then it will be waked up to continue
  3. when it can continue, the world has changed because other transactions
     then blocks it has been over

Previously, on QD we do not getsnapshot before we dispatch utility
statement to QEs which leads to the distributed snapshot does not
reflect the "world change". This will lead to some bugs. For example,
if the first transaction is to rewrite the whole heap, and then
the second Alter Table or Alter Domain statements continues with
the distributed snapshot that txn1 does not commit yet, it will
see no tuples in the new heap!

This commit fixes the issue by getting a local snapshot when
invoking `GetLatestSnapshot` when in QEs.

See Github issue: https://github.com/greenplum-db/gpdb/issues/10216Co-authored-by: NHubert Zhang <hzhang@pivotal.io>

We encounted a bug in escaping dbname and connection options in pygresql
5.1.2, which we submitted a patch for here:
https://github.com/PyGreSQL/PyGreSQL/pull/40

This has been merged, but it will take time to be added to a tagged
release. For this reason, we have downloaded the source using this
commit,
https://github.com/PyGreSQL/PyGreSQL/commit/b1e040e989b5b1b75f42c1103562bfe8f09f93c3
to install.
Co-authored-by: NTyler Ramer <tramer@pivotal.io>
Co-authored-by: NJamie McAtamney <jmcatamney@pivotal.io>

The test addressed in this commit was added in commit f3df8b18, fails
for the entirely unrelated reason that, due to a modification of
sql_isolation_testcase.py, the line numbers are different.

I find this test very fragile for this reason, and for the fact that
we're relying on an execution failure in isolation2 python code to test
the database code. This means that any refactoring of isolation2 will
cause this test to fail - which should not be.

I looked into adding an ignore to the exact lines, but isolation2 wants
there to be a matched ignore in the input sql file - which makes the
test useless, because we're looking for some exact exception from
isolation2 from a valid sql input. Isolation2 doesn't give us the
framework to ignore just some messages on the output side. Using a
isolation2 init modification still just ignores the actual problem, but
in a different file.

This fix should just be considered a tempory work to get the pipeline
green while a better solution is determined later.
Authored-by: NTyler Ramer <tramer@pivotal.io>

The update to pygresql pg connection allows the output of sql isolation2
testing to be more similar to psql. Thus, we are reverting some of the
changes made in commits 20b3aa3a to instead be more inline with the
usual psql output. Notably, trailing zeroes on floats are trimmed.
Co-authored-by: NTyler Ramer <tramer@pivotal.io>
Co-authored-by: NJamie McAtamney <jmcatamney@pivotal.io>

Due to refactor of dbconn and newer versions of pygresql, using
`with dbconn.connect() as conn` no longer attempts to close a
connection, even if it did prior. Instead, this syntax uses the
connection itself as context and, as noted in execSQL, overrides the
autocommit functionality of execSQL.

Therefore, close the connection manually to ensure that execSQL is
auto-commited, and the connection is closed.
Co-authored-by: NTyler Ramer <tramer@pivotal.io>
Co-authored-by: NJamie McAtamney <jmcatamney@pivotal.io>

One reason pygresql was previously modified was that it did not handle
closing a connection very gracefully. In the process of updating
pygresql, we've wrapped the connection it provides with a
ClosingConnection function, which should handle gracefully closing the
connection when the "with dbconn.connect as conn" syntax is used.

This did, however, illustrate issues where a cursor might have been
created as the result of a dbconn.execSQL() call, which seems to hold
the connection open if not specifically closed.

It is therefore necessary to remove the ability to get a cursor from
dbconn.execSQL(). To highlight this difference, and to ensure that
future calls to this library is easy to use, I've cleaned up and
clarified the dbconn execution code, to include the following features.

- dbconn.execSQL() closes the cursor as part of the function. It returns
  no rows
- functions dbconn.query() is added, which behaves like dbconn.execSQL()
  except that it now returns a cursor
- function dbconn.execQueryforSingleton() is renamed
  dconn.querySingleton()
- function dbconn.execQueryforSingletonRow() is renamed
  dconn.queryRow()
Authored-by: NTyler Ramer <tramer@pivotal.io>

This commit updates pygresql from 4.0.0 to 5.1.2, which requires
numerous changes to take advantages of the major result syntax change
that pygresql5 implemented. Of note, cursors or query objects
automatically cast returned values as appropriate python types - list of
ints, for example, instead of a string like "{1,2}". This is the bulk of
the changes.

Updating to pygresql 5.1.2 provides numerous benfits, including the
following:

- CVE-2018-1058 was addressed in pygresql 5.1.1

- We can save notices in the pgdb module, rather than relying on importing
the pg module, thanks to the new "set_notices()"

- pygresql 5 supports python3

- Thanks to a change in the cursor, using a "with" syntax guarentees a
  "commit" on the close of the with block.

This commit is a starting point for additional changes, including
refactoring the dbconn module.

Additionally, since isolation2 uses pygresql, some pl/python scripts
were updated, and isolation2 SQL output is further decoupled from
pygresql. The output of a psql command should be similar enough to
isolation2's pg output that minimal or no modification is needed to
ensure gpdiff can recognize the output.
Co-Authored-by: NTyler Ramer <tramer@pivotal.io>
Co-authored-by: NJamie McAtamney <jmcatamney@pivotal.io>

We had a bug in a few of the combine functions where if the combine
function returned a NULL, it didn't set fcinfo->isnull = true. This led
to a segfault when we would spill in the final hashagg of a two-stage
agg inside the serial function. So, properly mark NULL outputs from the
combine functions.
Co-authored-by: NDenis Smirnov <sd@arenadata.io>
Co-authored-by: NSoumyadeep Chakraborty <sochakraborty@pivotal.io>

Earlier, we always deducted FREEABLE_BATCHFILE_METADATA inside
closeSpillFile() regardless of whether the spill file was already
suspended. This deduction, is already performed inside
suspendSpillFiles(). This double accounting leads to
hashtable->mem_for_metadata becoming negative and we get:

FailedAssertion("!(hashtable->mem_for_metadata > 0)", File: "execHHashagg.c", Line: 2141)
Co-authored-by: NSoumyadeep Chakraborty <sochakraborty@pivotal.io>

This commit fixes the following assertion failure message reported in:
(#9902) https://github.com/greenplum-db/gpdb/issues/9902

FailedAssertion("!(hashtable->nbuckets > spill_set->num_spill_files)", File: "execHHashagg.c", Line: 1355)

hashtable->nbuckets can actually end up being equal to
spill_set->num_spill_files, which causes the failure. This is because:

hashtable->nbuckets is set with HashAggTableSizes->nbuckets, which can
end up being equal to: gp_hashagg_default_nbatches. Refer:
nbuckets = Max(nbuckets, gp_hashagg_default_nbatches);

Also, spill_set->num_spill_files is set with
HashAggTableSizes->nbatches, which is further set to
gp_hashagg_default_nbatches.

Thus, these two entities can be equal.
Co-authored-by: NSoumyadeep Chakraborty <sochakraborty@pivotal.io>

Increase the retry count to prevent test failed. Most of the time, the
failure is because slow processing.

We need to ignore the output when enabling/disabling an Orca xform, as
if the server is not compiled with Orca there will be a diff (and we
don't really care about this output).

Additionally, clean up unnecessaary/excessive setting of GUCs

Some of these gucs were on by default or only intended for a specific
test. Explicitly setting them caused them to appear at the end of
`explain verbose` plans, making the expected output more difficult to
match with if the server was built with/without Orca.

Some test cases have been failing due to too few retries. Let's increase them and also
create some common UDF for use.
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>
Reviewed-by: NAshwin Agrawal <aagrawal@pivotal.io>

Fix flakiness of "select 1" output after master reset due to injected panic fault before_read_command (#10275)

Several tests inject panic in before_read_command to trigger master reset.
Previous we run "select 1" after the fault inject query to verify, but the
output is not deterministic sometimes. i.e. sometimes we do not see the line

PANIC:  fault triggered, fault name:'before_read_command' fault type:'panic'

This was actually observed in test crash_recovery_redundant_dtx per commit
message and test comment.  It ignores the output of "select 1", but probably
we still want the output to verify the fault is encountered.

It's still mysterious why sometimes the PANIC message is missing. I spent some
time on digging but reckon that I can not root cause in short time. One guess
is that the PANIC message was although sent to the frontend in errfinish() but
the kernel buffer-ed data was dropped after abort() due to ereport(PANIC);
Another guess is something wrong related to libpq protocol (not saying it's a
libpq bug).  In any case, it does not deserve much time to work on the tests
only, so simply mask the PANIC message to make the test result deterministic
and also not affect the test purpose.
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>

When move a query to a resource group whose memory_limit is 0, the available
memory is the current available global shared memory.

When the error happens after ProcArrayEndTransaction, it will recurse back to
AbortTransaction, we need to make sure it will not generate extra WAL record
and not fail the assertions.

The flaky case happens when select an external table with option
"fill missing fields". By gdb the qe, this value is not false
on QE sometimes. When ProcessCopyOptions, we use intVal(defel->arg)
to parse the boolean value, which is not correct. Using defGetBoolean
to replace it.
Also fix a pxf_fdw test case, which should set fill_missing_fields to true
explicitly.

Remove pg_exttable.h since the catalog is no longer exist anymore.
Move function declaration in pg_exttable.h into external.h.
Extract related code into external.c which maintains all codes that
can not be moved into an external table fdw extension.

Also, move the external table orca interface into external.c as a workaround.
Maybe provide orca fdw routine in the future.

Extract the external table's execution logic into external table fdw
extension.

Create the gp_exttable_fdw extension during gpinitsystem to allow
creating system external tables.

This reverts commit 026e4595.
This commit break pxf test case. We need to handle it firstly.

The test case restarts all primaries and expects the old session
would fail for the next query since gangs are cached.
But the restart may last more than 18s which is the max idle
time QEs could exist. In this case, the new query in the old
session will just fetch a new gang without expected errors.
Just set gp_vmem_idle_resource_timeout to 0 to fix this flaky test.
Reviewed-by: NPaul Guo <pguo@pivotal.io>

The flaky case happens when select an external table with option
"fill missing fields". By gdb the qe, this value is not false
on QE sometimes. When ProcessCopyOptions, we use intVal(defel->arg)
to parse the boolean value, which is not correct. Using defGetBoolean
to replace it.

* clarifying pg_upgrade note

* graph edits

* graph analytics updates

* menu edits and code spacing

* graph further edits

* insert links for modules

* Add GUC write_to_gpfdist_timeout

write_to_gpfdist_timeout controls timeout value (in seconds) for writing data to gpfdist server. Default value is 300, valid scope is [1, 7200]

Set CURLOPT_TIMEOUT as write_to_gpfdist_timeout
For any error, retry with double interval time, returns SQL ERROR if write_to_gpfdist_timeout is reached

Add regression test for GUC writable_external_table_timeout

The python changes required new images, so we now need a separate
pipeline for slack commands from 6X. We also no longer need libsigar.

* clarifying pg_upgrade note

* gpinitsystem -O clarification

* further reviews

After gprecoverseg, need to wait until the cluster is synchronized before
running subsequent tests.
Reviewed-by: NHubert Zhang <hzhang@pivotal.io>
Reviewed-by: NReviewed-by: Ashwin Agrawal <aagrawal@pivotal.io>

* Update statement about mirroring recommendations & support

* Updates based on k8s feedback

Was left unused by commit e4b499aa that removed the pg_exttable catalog
table.

Previous commit 62579728 fixes a lateral panic issue but does
not handle all the bad cases because it only check if the query
tree contains limit clause. Bad cases for example: if the subquery
is like `q1 union all (q2 limit 1)` then the whole query tree
does not contain limit clause.

Another bad case is the lateral subquery may contain groupby.
like:

    select * from t1_lateral_limit t1 cross join lateral
    (select (c).x+t2.a, sum(t2.a+t2.b) from t2_lateral_limit t2
     group by (c).x+t2.a)x;

When planning the lateraled subquery we do not know where is
the param in the subquery's query tree. Thus it is a bit complicated
to precisely and efficiently resolve this issue.

This commit adopts a simple method to fix panic issue: it justs
check the subquery's query tree to see if there is any group-by
or limit clause, if so, force gather each relation and materialize
them. This is not the best plan we might get. But let's make it
correct first and I think in future we should seriously consider
how to fully and efficiently support lateral.

Use guc gp_role only now and replace the functionality of guc gp_session_role with it
also. Previously we have both gucs. The difference of the two gucs are (copied
from code comment):

 * gp_session_role
 *
 * - does not affect the operation of the backend, and
 * - does not change during the lifetime of PostgreSQL session.
 *
 * gp_role
 *
 * - determines the operating role of the backend, and
 * - may be changed by a superuser via the SET command.

This is not friendly for coding. For example, You could find Gp_role and
Gp_session_role are set as GP_ROLE_DISPATCH on Postmaster & many aux processes
on all nodes (even QE nodes) in a cluster, so you can see that to differ from
QD postmaster and QE postmaster, current gpdb uses an additional -E option in
postmaster arguments. These makes developers confusing when writing role branch
related code given we have three related variables.  Also some related code is
even buggy now (e.g. 'set gp_role' even FATAL quits).

With this patch we just have gp_role now. Some changes which might be
interesting in the patch are:

1. For postmaster, we should specify '-c gp_role=' (e.g. via pg_ctl argument) to
   determine the role else we assume the utility role.

2. For stand-alone backend, utility role is enforced (no need to specify by
   users).

3. Could still connect QE/QD nodes using utility mode with PGOPTIONS, etc as
   before.

4. Remove the '-E' gpdb hacking and align the '-E' usage with upstream.

5. Move pm_launch_walreceiver out of the fts related shmem given the later is
   not used on QE.
Reviewed-by: NBhuvnesh Chaudhary <bchaudhary@pivotal.io>
Reviewed-by: NGang Xiong <gxiong@pivotal.io>
Reviewed-by: NHao Wu <gfphoenix78@gmail.com>
Reviewed-by: NYandong Yao <yyao@pivotal.io>

* docs - add info about moving a query to a different resource group

* need to be superuser

* remove upgrade/downgrade info for master