Vacuum dropped columns during checkpoint

[ray6080]

Description

The PR is to fix a bug due to not vacuum dropped columns during checkpoint. The bug happens when we recover after dropped a column and performed checkpoint. During the recovery, we will have some columns as nullptr, which lead to seg faults when we collect data types from table columns.

This PR solves the issue by always vacuuming dropped columns from storage during checkpoint. Note that the column ID inside property will be reset due to the vacuuming, that's why the checkpoint of catalog now happens after the checkpoint of tables. Letting storage modifies catalog may not be a good practice, alternatively, we can let TableCatalogEntry reset its column ids during checkpoint independently, which sounds like a better idea to me.

In the future, we should also reclaim disk pages of persistent column chunks being dropped during checkpoint.

A minor refactoring:

• aligned columnID for rel table properties (nextColumnID starts from 1 to skip the anonymous NBR_ID column inside RelTableCatalogEntry). thus removed the special implementation of RelTableCatalogEntry::getColumnID.

[codecov]

Codecov Report

Attention: Patch coverage is 97.29730% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.53%. Comparing base (95d338e) to head (93840bb).

Files	Patch %	Lines
src/storage/store/csr_node_group.cpp	66.66%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #4074      +/-   ##
==========================================
+ Coverage   84.52%   84.53%   +0.01%     
==========================================
  Files        1300     1300              
  Lines       51024    51048      +24     
  Branches     7051     7058       +7     
==========================================
+ Hits        43127    43153      +26     
+ Misses       7758     7755       -3     
- Partials      139      140       +1     

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[github-actions]

Benchmark Result

Master commit hash: 95d338e22f58405ebc255286f8f6594c01e9f0b0
Branch commit hash: a4de5b2712556e88541aebbd808bd4e5c6eeab3b

Query Group	Query Name	Mean Time - Commit (ms)	Mean Time - Master (ms)	Diff
aggregation	q24	677.57	675.04	2.53 (0.38%)
aggregation	q28	11764.08	11363.26	400.81 (3.53%)
filter	q14	153.99	150.84	3.15 (2.09%)
filter	q15	151.16	152.91	-1.75 (-1.14%)
filter	q16	331.38	328.89	2.49 (0.76%)
filter	q17	471.55	471.30	0.25 (0.05%)
filter	q18	1941.75	1941.45	0.30 (0.02%)
fixed_size_expr_evaluator	q07	564.69	577.38	-12.69 (-2.20%)
fixed_size_expr_evaluator	q08	773.10	779.19	-6.09 (-0.78%)
fixed_size_expr_evaluator	q09	771.32	782.45	-11.13 (-1.42%)
fixed_size_expr_evaluator	q10	264.56	267.65	-3.09 (-1.15%)
fixed_size_expr_evaluator	q11	259.23	262.35	-3.12 (-1.19%)
fixed_size_expr_evaluator	q12	259.43	261.64	-2.22 (-0.85%)
fixed_size_expr_evaluator	q13	1493.75	1497.71	-3.96 (-0.26%)
fixed_size_seq_scan	q23	142.63	146.35	-3.72 (-2.54%)
join	q31	12.37	12.28	0.09 (0.72%)
ldbc_snb_ic	q35	775.77	1087.33	-311.56 (-28.65%)
ldbc_snb_ic	q36	46.74	41.66	5.08 (12.19%)
ldbc_snb_is	q32	8.93	8.51	0.42 (4.92%)
ldbc_snb_is	q33	19.17	18.52	0.65 (3.52%)
ldbc_snb_is	q34	7.93	8.90	-0.97 (-10.90%)
multi-rel	multi-rel-large-scan	2767.03	2849.47	-82.44 (-2.89%)
multi-rel	multi-rel-lookup	57.29	60.15	-2.86 (-4.76%)
multi-rel	multi-rel-small-scan	50.55	63.32	-12.76 (-20.16%)
order_by	q25	151.22	153.82	-2.61 (-1.69%)
order_by	q26	470.88	475.39	-4.50 (-0.95%)
order_by	q27	1424.71	1434.29	-9.58 (-0.67%)
scan_after_filter	q01	201.56	198.20	3.35 (1.69%)
scan_after_filter	q02	187.42	186.16	1.26 (0.68%)
shortest_path_ldbc100	q39	156.99	155.86	1.12 (0.72%)
var_size_expr_evaluator	q03	2072.47	2086.81	-14.34 (-0.69%)
var_size_expr_evaluator	q04	2254.53	2263.25	-8.72 (-0.39%)
var_size_expr_evaluator	q05	2677.69	2640.74	36.95 (1.40%)
var_size_expr_evaluator	q06	1358.60	1346.79	11.82 (0.88%)
var_size_seq_scan	q19	1481.62	1490.11	-8.49 (-0.57%)
var_size_seq_scan	q20	3168.07	3153.42	14.65 (0.46%)
var_size_seq_scan	q21	2419.20	2455.25	-36.05 (-1.47%)
var_size_seq_scan	q22	135.41	134.86	0.54 (0.40%)