grnsight 6.0.4 → 7.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1245) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/database/README.md +224 -79
  3. package/database/constants.py +42 -0
  4. package/database/expression-database/README.md +2 -2
  5. package/database/expression-database/schema.sql +14 -14
  6. package/database/expression-database/scripts/loader.py +6 -6
  7. package/database/filter_update.py +168 -0
  8. package/database/grnsettings-database/README.md +52 -0
  9. package/database/grnsettings-database/schema.sql +4 -0
  10. package/database/loader.py +30 -0
  11. package/database/loader_update.py +36 -0
  12. package/database/network-database/README.md +36 -4
  13. package/database/network-database/schema.sql +7 -7
  14. package/database/network-database/scripts/generate_network.py +16 -24
  15. package/database/network-database/scripts/generate_new_network_version.py +216 -0
  16. package/database/protein-protein-database/README.md +71 -0
  17. package/database/protein-protein-database/schema.sql +37 -0
  18. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  19. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  20. package/database/utils.py +418 -0
  21. package/package.json +2 -2
  22. package/server/app.js +2 -0
  23. package/server/config/config.js +4 -4
  24. package/server/controllers/additional-sheet-parser.js +2 -1
  25. package/server/controllers/constants.js +5 -0
  26. package/server/controllers/custom-workbook-controller.js +8 -6
  27. package/server/controllers/demo-workbooks.js +1460 -4
  28. package/server/controllers/export-constants.js +3 -2
  29. package/server/controllers/exporters/sif.js +6 -1
  30. package/server/controllers/exporters/xlsx.js +8 -3
  31. package/server/controllers/expression-sheet-parser.js +0 -6
  32. package/server/controllers/grnsettings-database-controller.js +17 -0
  33. package/server/controllers/importers/sif.js +29 -11
  34. package/server/controllers/network-database-controller.js +2 -2
  35. package/server/controllers/network-sheet-parser.js +54 -12
  36. package/server/controllers/protein-database-controller.js +18 -0
  37. package/server/controllers/sif-constants.js +4 -4
  38. package/server/controllers/spreadsheet-controller.js +44 -1
  39. package/server/controllers/workbook-constants.js +21 -4
  40. package/server/dals/expression-dal.js +8 -7
  41. package/server/dals/grnsetting-dal.js +49 -0
  42. package/server/dals/network-dal.js +13 -12
  43. package/server/dals/protein-dal.js +106 -0
  44. package/test/export-tests.js +136 -9
  45. package/test/import-sif-tests.js +54 -13
  46. package/test/test.js +1 -1
  47. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  48. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  49. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  50. package/web-client/config/config.js +4 -4
  51. package/web-client/public/js/api/grnsight-api.js +72 -56
  52. package/web-client/public/js/constants.js +26 -12
  53. package/web-client/public/js/generateNetwork.js +173 -67
  54. package/web-client/public/js/graph.js +420 -150
  55. package/web-client/public/js/grnsight.js +25 -4
  56. package/web-client/public/js/grnstate.js +3 -1
  57. package/web-client/public/js/iframe-coordination.js +3 -3
  58. package/web-client/public/js/setup-handlers.js +28 -32
  59. package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
  60. package/web-client/public/js/update-app.js +84 -17
  61. package/web-client/public/js/upload.js +193 -157
  62. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  63. package/web-client/public/stylesheets/grnsight.styl +40 -16
  64. package/web-client/views/components/demo.pug +7 -5
  65. package/web-client/views/upload.pug +63 -49
  66. package/.bundle/config +0 -3
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  68. package/Gemfile.lock +0 -259
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@@ -1,796 +0,0 @@
1
- # -----------------------------
2
- # PostgreSQL configuration file
3
- # -----------------------------
4
- #
5
- # This file consists of lines of the form:
6
- #
7
- # name = value
8
- #
9
- # (The "=" is optional.) Whitespace may be used. Comments are introduced with
10
- # "#" anywhere on a line. The complete list of parameter names and allowed
11
- # values can be found in the PostgreSQL documentation.
12
- #
13
- # The commented-out settings shown in this file represent the default values.
14
- # Re-commenting a setting is NOT sufficient to revert it to the default value;
15
- # you need to reload the server.
16
- #
17
- # This file is read on server startup and when the server receives a SIGHUP
18
- # signal. If you edit the file on a running system, you have to SIGHUP the
19
- # server for the changes to take effect, run "pg_ctl reload", or execute
20
- # "SELECT pg_reload_conf()". Some parameters, which are marked below,
21
- # require a server shutdown and restart to take effect.
22
- #
23
- # Any parameter can also be given as a command-line option to the server, e.g.,
24
- # "postgres -c log_connections=on". Some parameters can be changed at run time
25
- # with the "SET" SQL command.
26
- #
27
- # Memory units: B = bytes Time units: us = microseconds
28
- # kB = kilobytes ms = milliseconds
29
- # MB = megabytes s = seconds
30
- # GB = gigabytes min = minutes
31
- # TB = terabytes h = hours
32
- # d = days
33
-
34
-
35
- #------------------------------------------------------------------------------
36
- # FILE LOCATIONS
37
- #------------------------------------------------------------------------------
38
-
39
- # The default values of these variables are driven from the -D command-line
40
- # option or PGDATA environment variable, represented here as ConfigDir.
41
-
42
- #data_directory = 'ConfigDir' # use data in another directory
43
- # (change requires restart)
44
- #hba_file = 'ConfigDir/pg_hba.conf' # host-based authentication file
45
- # (change requires restart)
46
- #ident_file = 'ConfigDir/pg_ident.conf' # ident configuration file
47
- # (change requires restart)
48
-
49
- # If external_pid_file is not explicitly set, no extra PID file is written.
50
- #external_pid_file = '' # write an extra PID file
51
- # (change requires restart)
52
-
53
-
54
- #------------------------------------------------------------------------------
55
- # CONNECTIONS AND AUTHENTICATION
56
- #------------------------------------------------------------------------------
57
-
58
- # - Connection Settings -
59
-
60
- #listen_addresses = 'localhost' # what IP address(es) to listen on;
61
- # comma-separated list of addresses;
62
- # defaults to 'localhost'; use '*' for all
63
- # (change requires restart)
64
- #port = 5432 # (change requires restart)
65
- max_connections = 100 # (change requires restart)
66
- #superuser_reserved_connections = 3 # (change requires restart)
67
- #unix_socket_directories = '/tmp' # comma-separated list of directories
68
- # (change requires restart)
69
- #unix_socket_group = '' # (change requires restart)
70
- #unix_socket_permissions = 0777 # begin with 0 to use octal notation
71
- # (change requires restart)
72
- #bonjour = off # advertise server via Bonjour
73
- # (change requires restart)
74
- #bonjour_name = '' # defaults to the computer name
75
- # (change requires restart)
76
-
77
- # - TCP settings -
78
- # see "man tcp" for details
79
-
80
- #tcp_keepalives_idle = 0 # TCP_KEEPIDLE, in seconds;
81
- # 0 selects the system default
82
- #tcp_keepalives_interval = 0 # TCP_KEEPINTVL, in seconds;
83
- # 0 selects the system default
84
- #tcp_keepalives_count = 0 # TCP_KEEPCNT;
85
- # 0 selects the system default
86
- #tcp_user_timeout = 0 # TCP_USER_TIMEOUT, in milliseconds;
87
- # 0 selects the system default
88
-
89
- #client_connection_check_interval = 0 # time between checks for client
90
- # disconnection while running queries;
91
- # 0 for never
92
-
93
- # - Authentication -
94
-
95
- #authentication_timeout = 1min # 1s-600s
96
- #password_encryption = scram-sha-256 # scram-sha-256 or md5
97
- #db_user_namespace = off
98
-
99
- # GSSAPI using Kerberos
100
- #krb_server_keyfile = 'FILE:${sysconfdir}/krb5.keytab'
101
- #krb_caseins_users = off
102
-
103
- # - SSL -
104
-
105
- #ssl = off
106
- #ssl_ca_file = ''
107
- #ssl_cert_file = 'server.crt'
108
- #ssl_crl_file = ''
109
- #ssl_crl_dir = ''
110
- #ssl_key_file = 'server.key'
111
- #ssl_ciphers = 'HIGH:MEDIUM:+3DES:!aNULL' # allowed SSL ciphers
112
- #ssl_prefer_server_ciphers = on
113
- #ssl_ecdh_curve = 'prime256v1'
114
- #ssl_min_protocol_version = 'TLSv1.2'
115
- #ssl_max_protocol_version = ''
116
- #ssl_dh_params_file = ''
117
- #ssl_passphrase_command = ''
118
- #ssl_passphrase_command_supports_reload = off
119
-
120
-
121
- #------------------------------------------------------------------------------
122
- # RESOURCE USAGE (except WAL)
123
- #------------------------------------------------------------------------------
124
-
125
- # - Memory -
126
-
127
- shared_buffers = 128MB # min 128kB
128
- # (change requires restart)
129
- #huge_pages = try # on, off, or try
130
- # (change requires restart)
131
- #huge_page_size = 0 # zero for system default
132
- # (change requires restart)
133
- #temp_buffers = 8MB # min 800kB
134
- #max_prepared_transactions = 0 # zero disables the feature
135
- # (change requires restart)
136
- # Caution: it is not advisable to set max_prepared_transactions nonzero unless
137
- # you actively intend to use prepared transactions.
138
- #work_mem = 4MB # min 64kB
139
- #hash_mem_multiplier = 1.0 # 1-1000.0 multiplier on hash table work_mem
140
- #maintenance_work_mem = 64MB # min 1MB
141
- #autovacuum_work_mem = -1 # min 1MB, or -1 to use maintenance_work_mem
142
- #logical_decoding_work_mem = 64MB # min 64kB
143
- #max_stack_depth = 2MB # min 100kB
144
- #shared_memory_type = mmap # the default is the first option
145
- # supported by the operating system:
146
- # mmap
147
- # sysv
148
- # windows
149
- # (change requires restart)
150
- dynamic_shared_memory_type = posix # the default is the first option
151
- # supported by the operating system:
152
- # posix
153
- # sysv
154
- # windows
155
- # mmap
156
- # (change requires restart)
157
- #min_dynamic_shared_memory = 0MB # (change requires restart)
158
-
159
- # - Disk -
160
-
161
- #temp_file_limit = -1 # limits per-process temp file space
162
- # in kilobytes, or -1 for no limit
163
-
164
- # - Kernel Resources -
165
-
166
- #max_files_per_process = 1000 # min 64
167
- # (change requires restart)
168
-
169
- # - Cost-Based Vacuum Delay -
170
-
171
- #vacuum_cost_delay = 0 # 0-100 milliseconds (0 disables)
172
- #vacuum_cost_page_hit = 1 # 0-10000 credits
173
- #vacuum_cost_page_miss = 2 # 0-10000 credits
174
- #vacuum_cost_page_dirty = 20 # 0-10000 credits
175
- #vacuum_cost_limit = 200 # 1-10000 credits
176
-
177
- # - Background Writer -
178
-
179
- #bgwriter_delay = 200ms # 10-10000ms between rounds
180
- #bgwriter_lru_maxpages = 100 # max buffers written/round, 0 disables
181
- #bgwriter_lru_multiplier = 2.0 # 0-10.0 multiplier on buffers scanned/round
182
- #bgwriter_flush_after = 0 # measured in pages, 0 disables
183
-
184
- # - Asynchronous Behavior -
185
-
186
- #backend_flush_after = 0 # measured in pages, 0 disables
187
- #effective_io_concurrency = 0 # 1-1000; 0 disables prefetching
188
- #maintenance_io_concurrency = 10 # 1-1000; 0 disables prefetching
189
- #max_worker_processes = 8 # (change requires restart)
190
- #max_parallel_workers_per_gather = 2 # taken from max_parallel_workers
191
- #max_parallel_maintenance_workers = 2 # taken from max_parallel_workers
192
- #max_parallel_workers = 8 # maximum number of max_worker_processes that
193
- # can be used in parallel operations
194
- #parallel_leader_participation = on
195
- #old_snapshot_threshold = -1 # 1min-60d; -1 disables; 0 is immediate
196
- # (change requires restart)
197
-
198
-
199
- #------------------------------------------------------------------------------
200
- # WRITE-AHEAD LOG
201
- #------------------------------------------------------------------------------
202
-
203
- # - Settings -
204
-
205
- #wal_level = replica # minimal, replica, or logical
206
- # (change requires restart)
207
- #fsync = on # flush data to disk for crash safety
208
- # (turning this off can cause
209
- # unrecoverable data corruption)
210
- #synchronous_commit = on # synchronization level;
211
- # off, local, remote_write, remote_apply, or on
212
- #wal_sync_method = fsync # the default is the first option
213
- # supported by the operating system:
214
- # open_datasync
215
- # fdatasync (default on Linux and FreeBSD)
216
- # fsync
217
- # fsync_writethrough
218
- # open_sync
219
- #full_page_writes = on # recover from partial page writes
220
- #wal_log_hints = off # also do full page writes of non-critical updates
221
- # (change requires restart)
222
- #wal_compression = off # enable compression of full-page writes
223
- #wal_init_zero = on # zero-fill new WAL files
224
- #wal_recycle = on # recycle WAL files
225
- #wal_buffers = -1 # min 32kB, -1 sets based on shared_buffers
226
- # (change requires restart)
227
- #wal_writer_delay = 200ms # 1-10000 milliseconds
228
- #wal_writer_flush_after = 1MB # measured in pages, 0 disables
229
- #wal_skip_threshold = 2MB
230
-
231
- #commit_delay = 0 # range 0-100000, in microseconds
232
- #commit_siblings = 5 # range 1-1000
233
-
234
- # - Checkpoints -
235
-
236
- #checkpoint_timeout = 5min # range 30s-1d
237
- #checkpoint_completion_target = 0.9 # checkpoint target duration, 0.0 - 1.0
238
- #checkpoint_flush_after = 0 # measured in pages, 0 disables
239
- #checkpoint_warning = 30s # 0 disables
240
- max_wal_size = 1GB
241
- min_wal_size = 80MB
242
-
243
- # - Archiving -
244
-
245
- #archive_mode = off # enables archiving; off, on, or always
246
- # (change requires restart)
247
- #archive_command = '' # command to use to archive a logfile segment
248
- # placeholders: %p = path of file to archive
249
- # %f = file name only
250
- # e.g. 'test ! -f /mnt/server/archivedir/%f && cp %p /mnt/server/archivedir/%f'
251
- #archive_timeout = 0 # force a logfile segment switch after this
252
- # number of seconds; 0 disables
253
-
254
- # - Archive Recovery -
255
-
256
- # These are only used in recovery mode.
257
-
258
- #restore_command = '' # command to use to restore an archived logfile segment
259
- # placeholders: %p = path of file to restore
260
- # %f = file name only
261
- # e.g. 'cp /mnt/server/archivedir/%f %p'
262
- #archive_cleanup_command = '' # command to execute at every restartpoint
263
- #recovery_end_command = '' # command to execute at completion of recovery
264
-
265
- # - Recovery Target -
266
-
267
- # Set these only when performing a targeted recovery.
268
-
269
- #recovery_target = '' # 'immediate' to end recovery as soon as a
270
- # consistent state is reached
271
- # (change requires restart)
272
- #recovery_target_name = '' # the named restore point to which recovery will proceed
273
- # (change requires restart)
274
- #recovery_target_time = '' # the time stamp up to which recovery will proceed
275
- # (change requires restart)
276
- #recovery_target_xid = '' # the transaction ID up to which recovery will proceed
277
- # (change requires restart)
278
- #recovery_target_lsn = '' # the WAL LSN up to which recovery will proceed
279
- # (change requires restart)
280
- #recovery_target_inclusive = on # Specifies whether to stop:
281
- # just after the specified recovery target (on)
282
- # just before the recovery target (off)
283
- # (change requires restart)
284
- #recovery_target_timeline = 'latest' # 'current', 'latest', or timeline ID
285
- # (change requires restart)
286
- #recovery_target_action = 'pause' # 'pause', 'promote', 'shutdown'
287
- # (change requires restart)
288
-
289
-
290
- #------------------------------------------------------------------------------
291
- # REPLICATION
292
- #------------------------------------------------------------------------------
293
-
294
- # - Sending Servers -
295
-
296
- # Set these on the primary and on any standby that will send replication data.
297
-
298
- #max_wal_senders = 10 # max number of walsender processes
299
- # (change requires restart)
300
- #max_replication_slots = 10 # max number of replication slots
301
- # (change requires restart)
302
- #wal_keep_size = 0 # in megabytes; 0 disables
303
- #max_slot_wal_keep_size = -1 # in megabytes; -1 disables
304
- #wal_sender_timeout = 60s # in milliseconds; 0 disables
305
- #track_commit_timestamp = off # collect timestamp of transaction commit
306
- # (change requires restart)
307
-
308
- # - Primary Server -
309
-
310
- # These settings are ignored on a standby server.
311
-
312
- #synchronous_standby_names = '' # standby servers that provide sync rep
313
- # method to choose sync standbys, number of sync standbys,
314
- # and comma-separated list of application_name
315
- # from standby(s); '*' = all
316
- #vacuum_defer_cleanup_age = 0 # number of xacts by which cleanup is delayed
317
-
318
- # - Standby Servers -
319
-
320
- # These settings are ignored on a primary server.
321
-
322
- #primary_conninfo = '' # connection string to sending server
323
- #primary_slot_name = '' # replication slot on sending server
324
- #promote_trigger_file = '' # file name whose presence ends recovery
325
- #hot_standby = on # "off" disallows queries during recovery
326
- # (change requires restart)
327
- #max_standby_archive_delay = 30s # max delay before canceling queries
328
- # when reading WAL from archive;
329
- # -1 allows indefinite delay
330
- #max_standby_streaming_delay = 30s # max delay before canceling queries
331
- # when reading streaming WAL;
332
- # -1 allows indefinite delay
333
- #wal_receiver_create_temp_slot = off # create temp slot if primary_slot_name
334
- # is not set
335
- #wal_receiver_status_interval = 10s # send replies at least this often
336
- # 0 disables
337
- #hot_standby_feedback = off # send info from standby to prevent
338
- # query conflicts
339
- #wal_receiver_timeout = 60s # time that receiver waits for
340
- # communication from primary
341
- # in milliseconds; 0 disables
342
- #wal_retrieve_retry_interval = 5s # time to wait before retrying to
343
- # retrieve WAL after a failed attempt
344
- #recovery_min_apply_delay = 0 # minimum delay for applying changes during recovery
345
-
346
- # - Subscribers -
347
-
348
- # These settings are ignored on a publisher.
349
-
350
- #max_logical_replication_workers = 4 # taken from max_worker_processes
351
- # (change requires restart)
352
- #max_sync_workers_per_subscription = 2 # taken from max_logical_replication_workers
353
-
354
-
355
- #------------------------------------------------------------------------------
356
- # QUERY TUNING
357
- #------------------------------------------------------------------------------
358
-
359
- # - Planner Method Configuration -
360
-
361
- #enable_async_append = on
362
- #enable_bitmapscan = on
363
- #enable_gathermerge = on
364
- #enable_hashagg = on
365
- #enable_hashjoin = on
366
- #enable_incremental_sort = on
367
- #enable_indexscan = on
368
- #enable_indexonlyscan = on
369
- #enable_material = on
370
- #enable_memoize = on
371
- #enable_mergejoin = on
372
- #enable_nestloop = on
373
- #enable_parallel_append = on
374
- #enable_parallel_hash = on
375
- #enable_partition_pruning = on
376
- #enable_partitionwise_join = off
377
- #enable_partitionwise_aggregate = off
378
- #enable_seqscan = on
379
- #enable_sort = on
380
- #enable_tidscan = on
381
-
382
- # - Planner Cost Constants -
383
-
384
- #seq_page_cost = 1.0 # measured on an arbitrary scale
385
- #random_page_cost = 4.0 # same scale as above
386
- #cpu_tuple_cost = 0.01 # same scale as above
387
- #cpu_index_tuple_cost = 0.005 # same scale as above
388
- #cpu_operator_cost = 0.0025 # same scale as above
389
- #parallel_setup_cost = 1000.0 # same scale as above
390
- #parallel_tuple_cost = 0.1 # same scale as above
391
- #min_parallel_table_scan_size = 8MB
392
- #min_parallel_index_scan_size = 512kB
393
- #effective_cache_size = 4GB
394
-
395
- #jit_above_cost = 100000 # perform JIT compilation if available
396
- # and query more expensive than this;
397
- # -1 disables
398
- #jit_inline_above_cost = 500000 # inline small functions if query is
399
- # more expensive than this; -1 disables
400
- #jit_optimize_above_cost = 500000 # use expensive JIT optimizations if
401
- # query is more expensive than this;
402
- # -1 disables
403
-
404
- # - Genetic Query Optimizer -
405
-
406
- #geqo = on
407
- #geqo_threshold = 12
408
- #geqo_effort = 5 # range 1-10
409
- #geqo_pool_size = 0 # selects default based on effort
410
- #geqo_generations = 0 # selects default based on effort
411
- #geqo_selection_bias = 2.0 # range 1.5-2.0
412
- #geqo_seed = 0.0 # range 0.0-1.0
413
-
414
- # - Other Planner Options -
415
-
416
- #default_statistics_target = 100 # range 1-10000
417
- #constraint_exclusion = partition # on, off, or partition
418
- #cursor_tuple_fraction = 0.1 # range 0.0-1.0
419
- #from_collapse_limit = 8
420
- #jit = on # allow JIT compilation
421
- #join_collapse_limit = 8 # 1 disables collapsing of explicit
422
- # JOIN clauses
423
- #plan_cache_mode = auto # auto, force_generic_plan or
424
- # force_custom_plan
425
-
426
-
427
- #------------------------------------------------------------------------------
428
- # REPORTING AND LOGGING
429
- #------------------------------------------------------------------------------
430
-
431
- # - Where to Log -
432
-
433
- #log_destination = 'stderr' # Valid values are combinations of
434
- # stderr, csvlog, syslog, and eventlog,
435
- # depending on platform. csvlog
436
- # requires logging_collector to be on.
437
-
438
- # This is used when logging to stderr:
439
- #logging_collector = off # Enable capturing of stderr and csvlog
440
- # into log files. Required to be on for
441
- # csvlogs.
442
- # (change requires restart)
443
-
444
- # These are only used if logging_collector is on:
445
- #log_directory = 'log' # directory where log files are written,
446
- # can be absolute or relative to PGDATA
447
- #log_filename = 'postgresql-%Y-%m-%d_%H%M%S.log' # log file name pattern,
448
- # can include strftime() escapes
449
- #log_file_mode = 0600 # creation mode for log files,
450
- # begin with 0 to use octal notation
451
- #log_rotation_age = 1d # Automatic rotation of logfiles will
452
- # happen after that time. 0 disables.
453
- #log_rotation_size = 10MB # Automatic rotation of logfiles will
454
- # happen after that much log output.
455
- # 0 disables.
456
- #log_truncate_on_rotation = off # If on, an existing log file with the
457
- # same name as the new log file will be
458
- # truncated rather than appended to.
459
- # But such truncation only occurs on
460
- # time-driven rotation, not on restarts
461
- # or size-driven rotation. Default is
462
- # off, meaning append to existing files
463
- # in all cases.
464
-
465
- # These are relevant when logging to syslog:
466
- #syslog_facility = 'LOCAL0'
467
- #syslog_ident = 'postgres'
468
- #syslog_sequence_numbers = on
469
- #syslog_split_messages = on
470
-
471
- # This is only relevant when logging to eventlog (Windows):
472
- # (change requires restart)
473
- #event_source = 'PostgreSQL'
474
-
475
- # - When to Log -
476
-
477
- #log_min_messages = warning # values in order of decreasing detail:
478
- # debug5
479
- # debug4
480
- # debug3
481
- # debug2
482
- # debug1
483
- # info
484
- # notice
485
- # warning
486
- # error
487
- # log
488
- # fatal
489
- # panic
490
-
491
- #log_min_error_statement = error # values in order of decreasing detail:
492
- # debug5
493
- # debug4
494
- # debug3
495
- # debug2
496
- # debug1
497
- # info
498
- # notice
499
- # warning
500
- # error
501
- # log
502
- # fatal
503
- # panic (effectively off)
504
-
505
- #log_min_duration_statement = -1 # -1 is disabled, 0 logs all statements
506
- # and their durations, > 0 logs only
507
- # statements running at least this number
508
- # of milliseconds
509
-
510
- #log_min_duration_sample = -1 # -1 is disabled, 0 logs a sample of statements
511
- # and their durations, > 0 logs only a sample of
512
- # statements running at least this number
513
- # of milliseconds;
514
- # sample fraction is determined by log_statement_sample_rate
515
-
516
- #log_statement_sample_rate = 1.0 # fraction of logged statements exceeding
517
- # log_min_duration_sample to be logged;
518
- # 1.0 logs all such statements, 0.0 never logs
519
-
520
-
521
- #log_transaction_sample_rate = 0.0 # fraction of transactions whose statements
522
- # are logged regardless of their duration; 1.0 logs all
523
- # statements from all transactions, 0.0 never logs
524
-
525
- # - What to Log -
526
-
527
- #debug_print_parse = off
528
- #debug_print_rewritten = off
529
- #debug_print_plan = off
530
- #debug_pretty_print = on
531
- #log_autovacuum_min_duration = -1 # log autovacuum activity;
532
- # -1 disables, 0 logs all actions and
533
- # their durations, > 0 logs only
534
- # actions running at least this number
535
- # of milliseconds.
536
- #log_checkpoints = off
537
- #log_connections = off
538
- #log_disconnections = off
539
- #log_duration = off
540
- #log_error_verbosity = default # terse, default, or verbose messages
541
- #log_hostname = off
542
- #log_line_prefix = '%m [%p] ' # special values:
543
- # %a = application name
544
- # %u = user name
545
- # %d = database name
546
- # %r = remote host and port
547
- # %h = remote host
548
- # %b = backend type
549
- # %p = process ID
550
- # %P = process ID of parallel group leader
551
- # %t = timestamp without milliseconds
552
- # %m = timestamp with milliseconds
553
- # %n = timestamp with milliseconds (as a Unix epoch)
554
- # %Q = query ID (0 if none or not computed)
555
- # %i = command tag
556
- # %e = SQL state
557
- # %c = session ID
558
- # %l = session line number
559
- # %s = session start timestamp
560
- # %v = virtual transaction ID
561
- # %x = transaction ID (0 if none)
562
- # %q = stop here in non-session
563
- # processes
564
- # %% = '%'
565
- # e.g. '<%u%%%d> '
566
- #log_lock_waits = off # log lock waits >= deadlock_timeout
567
- #log_recovery_conflict_waits = off # log standby recovery conflict waits
568
- # >= deadlock_timeout
569
- #log_parameter_max_length = -1 # when logging statements, limit logged
570
- # bind-parameter values to N bytes;
571
- # -1 means print in full, 0 disables
572
- #log_parameter_max_length_on_error = 0 # when logging an error, limit logged
573
- # bind-parameter values to N bytes;
574
- # -1 means print in full, 0 disables
575
- #log_statement = 'none' # none, ddl, mod, all
576
- #log_replication_commands = off
577
- #log_temp_files = -1 # log temporary files equal or larger
578
- # than the specified size in kilobytes;
579
- # -1 disables, 0 logs all temp files
580
- log_timezone = 'America/Los_Angeles'
581
-
582
-
583
- #------------------------------------------------------------------------------
584
- # PROCESS TITLE
585
- #------------------------------------------------------------------------------
586
-
587
- #cluster_name = '' # added to process titles if nonempty
588
- # (change requires restart)
589
- #update_process_title = on
590
-
591
-
592
- #------------------------------------------------------------------------------
593
- # STATISTICS
594
- #------------------------------------------------------------------------------
595
-
596
- # - Query and Index Statistics Collector -
597
-
598
- #track_activities = on
599
- #track_activity_query_size = 1024 # (change requires restart)
600
- #track_counts = on
601
- #track_io_timing = off
602
- #track_wal_io_timing = off
603
- #track_functions = none # none, pl, all
604
- #stats_temp_directory = 'pg_stat_tmp'
605
-
606
-
607
- # - Monitoring -
608
-
609
- #compute_query_id = auto
610
- #log_statement_stats = off
611
- #log_parser_stats = off
612
- #log_planner_stats = off
613
- #log_executor_stats = off
614
-
615
-
616
- #------------------------------------------------------------------------------
617
- # AUTOVACUUM
618
- #------------------------------------------------------------------------------
619
-
620
- #autovacuum = on # Enable autovacuum subprocess? 'on'
621
- # requires track_counts to also be on.
622
- #autovacuum_max_workers = 3 # max number of autovacuum subprocesses
623
- # (change requires restart)
624
- #autovacuum_naptime = 1min # time between autovacuum runs
625
- #autovacuum_vacuum_threshold = 50 # min number of row updates before
626
- # vacuum
627
- #autovacuum_vacuum_insert_threshold = 1000 # min number of row inserts
628
- # before vacuum; -1 disables insert
629
- # vacuums
630
- #autovacuum_analyze_threshold = 50 # min number of row updates before
631
- # analyze
632
- #autovacuum_vacuum_scale_factor = 0.2 # fraction of table size before vacuum
633
- #autovacuum_vacuum_insert_scale_factor = 0.2 # fraction of inserts over table
634
- # size before insert vacuum
635
- #autovacuum_analyze_scale_factor = 0.1 # fraction of table size before analyze
636
- #autovacuum_freeze_max_age = 200000000 # maximum XID age before forced vacuum
637
- # (change requires restart)
638
- #autovacuum_multixact_freeze_max_age = 400000000 # maximum multixact age
639
- # before forced vacuum
640
- # (change requires restart)
641
- #autovacuum_vacuum_cost_delay = 2ms # default vacuum cost delay for
642
- # autovacuum, in milliseconds;
643
- # -1 means use vacuum_cost_delay
644
- #autovacuum_vacuum_cost_limit = -1 # default vacuum cost limit for
645
- # autovacuum, -1 means use
646
- # vacuum_cost_limit
647
-
648
-
649
- #------------------------------------------------------------------------------
650
- # CLIENT CONNECTION DEFAULTS
651
- #------------------------------------------------------------------------------
652
-
653
- # - Statement Behavior -
654
-
655
- #client_min_messages = notice # values in order of decreasing detail:
656
- # debug5
657
- # debug4
658
- # debug3
659
- # debug2
660
- # debug1
661
- # log
662
- # notice
663
- # warning
664
- # error
665
- #search_path = '"$user", public' # schema names
666
- #row_security = on
667
- #default_table_access_method = 'heap'
668
- #default_tablespace = '' # a tablespace name, '' uses the default
669
- #default_toast_compression = 'pglz' # 'pglz' or 'lz4'
670
- #temp_tablespaces = '' # a list of tablespace names, '' uses
671
- # only default tablespace
672
- #check_function_bodies = on
673
- #default_transaction_isolation = 'read committed'
674
- #default_transaction_read_only = off
675
- #default_transaction_deferrable = off
676
- #session_replication_role = 'origin'
677
- #statement_timeout = 0 # in milliseconds, 0 is disabled
678
- #lock_timeout = 0 # in milliseconds, 0 is disabled
679
- #idle_in_transaction_session_timeout = 0 # in milliseconds, 0 is disabled
680
- #idle_session_timeout = 0 # in milliseconds, 0 is disabled
681
- #vacuum_freeze_table_age = 150000000
682
- #vacuum_freeze_min_age = 50000000
683
- #vacuum_failsafe_age = 1600000000
684
- #vacuum_multixact_freeze_table_age = 150000000
685
- #vacuum_multixact_freeze_min_age = 5000000
686
- #vacuum_multixact_failsafe_age = 1600000000
687
- #bytea_output = 'hex' # hex, escape
688
- #xmlbinary = 'base64'
689
- #xmloption = 'content'
690
- #gin_pending_list_limit = 4MB
691
-
692
- # - Locale and Formatting -
693
-
694
- datestyle = 'iso, mdy'
695
- #intervalstyle = 'postgres'
696
- timezone = 'America/Los_Angeles'
697
- #timezone_abbreviations = 'Default' # Select the set of available time zone
698
- # abbreviations. Currently, there are
699
- # Default
700
- # Australia (historical usage)
701
- # India
702
- # You can create your own file in
703
- # share/timezonesets/.
704
- #extra_float_digits = 1 # min -15, max 3; any value >0 actually
705
- # selects precise output mode
706
- #client_encoding = sql_ascii # actually, defaults to database
707
- # encoding
708
-
709
- # These settings are initialized by initdb, but they can be changed.
710
- lc_messages = 'C' # locale for system error message
711
- # strings
712
- lc_monetary = 'C' # locale for monetary formatting
713
- lc_numeric = 'C' # locale for number formatting
714
- lc_time = 'C' # locale for time formatting
715
-
716
- # default configuration for text search
717
- default_text_search_config = 'pg_catalog.english'
718
-
719
- # - Shared Library Preloading -
720
-
721
- #local_preload_libraries = ''
722
- #session_preload_libraries = ''
723
- #shared_preload_libraries = '' # (change requires restart)
724
- #jit_provider = 'llvmjit' # JIT library to use
725
-
726
- # - Other Defaults -
727
-
728
- #dynamic_library_path = '$libdir'
729
- #gin_fuzzy_search_limit = 0
730
-
731
-
732
- #------------------------------------------------------------------------------
733
- # LOCK MANAGEMENT
734
- #------------------------------------------------------------------------------
735
-
736
- #deadlock_timeout = 1s
737
- #max_locks_per_transaction = 64 # min 10
738
- # (change requires restart)
739
- #max_pred_locks_per_transaction = 64 # min 10
740
- # (change requires restart)
741
- #max_pred_locks_per_relation = -2 # negative values mean
742
- # (max_pred_locks_per_transaction
743
- # / -max_pred_locks_per_relation) - 1
744
- #max_pred_locks_per_page = 2 # min 0
745
-
746
-
747
- #------------------------------------------------------------------------------
748
- # VERSION AND PLATFORM COMPATIBILITY
749
- #------------------------------------------------------------------------------
750
-
751
- # - Previous PostgreSQL Versions -
752
-
753
- #array_nulls = on
754
- #backslash_quote = safe_encoding # on, off, or safe_encoding
755
- #escape_string_warning = on
756
- #lo_compat_privileges = off
757
- #quote_all_identifiers = off
758
- #standard_conforming_strings = on
759
- #synchronize_seqscans = on
760
-
761
- # - Other Platforms and Clients -
762
-
763
- #transform_null_equals = off
764
-
765
-
766
- #------------------------------------------------------------------------------
767
- # ERROR HANDLING
768
- #------------------------------------------------------------------------------
769
-
770
- #exit_on_error = off # terminate session on any error?
771
- #restart_after_crash = on # reinitialize after backend crash?
772
- #data_sync_retry = off # retry or panic on failure to fsync
773
- # data?
774
- # (change requires restart)
775
- #recovery_init_sync_method = fsync # fsync, syncfs (Linux 5.8+)
776
-
777
-
778
- #------------------------------------------------------------------------------
779
- # CONFIG FILE INCLUDES
780
- #------------------------------------------------------------------------------
781
-
782
- # These options allow settings to be loaded from files other than the
783
- # default postgresql.conf. Note that these are directives, not variable
784
- # assignments, so they can usefully be given more than once.
785
-
786
- #include_dir = '...' # include files ending in '.conf' from
787
- # a directory, e.g., 'conf.d'
788
- #include_if_exists = '...' # include file only if it exists
789
- #include = '...' # include file
790
-
791
-
792
- #------------------------------------------------------------------------------
793
- # CUSTOMIZED OPTIONS
794
- #------------------------------------------------------------------------------
795
-
796
- # Add settings for extensions here