Mercurial > hg > orthanc-databases
annotate NOTES @ 478:0064a54745e1
todo
| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Wed, 06 Mar 2024 12:27:48 +0100 |
| parents | 0a8b34e3a337 |
| children | bf4b9c7cf338 |
| rev | line source |
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| 431 | 1 Resources: |
| 2 ********* | |
| 3 - PG transaction modes explained: https://www.postgresql.org/files/developer/concurrency.pdf | |
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4 - Isolation level explained (PG + MySQL): https://amirsoleimani.medium.com/understanding-database-isolation-level-via-examples-mysql-and-postgres-a86b5502d404 |
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5 - Message queuing in PG: https://www.crunchydata.com/blog/message-queuing-using-native-postgresql |
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6 |
| 431 | 7 |
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8 Create and delete instances Internals: |
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9 ************************************* |
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10 |
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11 isNewInstance = CreateInstance(...) |
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12 |
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13 if (!isNewInstance && overwriteInstances) |
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14 DeleteResource(instance) |
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15 -> ClearDeletedFiles(manager); |
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16 DELETE FROM DeletedFiles ------> this is not a temporary table in postgres but it is supposed to be empty before and after each transaction -> it is empty when taking a snapshot of the DB in READ COMMITTED mode!!! |
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17 ClearDeletedResources(manager); |
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18 DELETE FROM DeletedResources ------> this is not a temporary table in postgres but it is supposed to be empty before and after each transaction !!! |
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19 |
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20 DELETE FROM RemainingAncestor ------> this is not a temporary table in postgres but it is supposed to be empty before and after each transaction !!! |
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21 DELETE FROM Resources WHERE internalId=.. |
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22 -> cascades delete the MainDicomTags, the Metadata and the AttachedFiles |
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23 -> this triggers AttachedFileDeletedFunc |
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24 INSERT INTO DeletedFiles VALUES |
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25 (old.uuid, old.filetype, old.compressedSize, |
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26 old.uncompressedSize, old.compressionType, |
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27 old.uncompressedHash, old.compressedHash); |
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28 RETURN NULL; |
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29 -> this triggers a SQL trigger: ResourceDeletedFunc |
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30 INSERT INTO DeletedResources VALUES (old.resourceType, old.publicId); |
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31 IF EXISTS (SELECT 1 FROM Resources WHERE parentId = old.parentId) THEN |
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32 -- Signal that the deleted resource has a remaining parent |
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33 -- (a parent that must not be deleted but whose LastUpdate must be updated) |
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34 INSERT INTO RemainingAncestor |
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35 SELECT resourceType, publicId FROM Resources WHERE internalId = old.parentId; |
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36 ELSE |
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37 -- Delete a parent resource when its unique child is deleted |
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38 DELETE FROM Resources WHERE internalId = old.parentId; |
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39 END IF; |
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40 |
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41 SELECT * FROM RemainingAncestor |
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42 -> SignalRemainingAncestor() // There is at most 1 remaining ancestor |
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43 -> ServerIndex::TransactionContext::SignalRemainingAncestor() |
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44 -> stores remainingType and remainingPublicId (this is used in StatelessDatabaseOperations::DeleteResource to build the Rest Response of /delete |
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45 and to update the LastUpdate of all parent (only when deleted from /delete)) |
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46 |
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47 SignalDeletedFiles(output, manager); |
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48 SELECT * FROM DeletedFiles |
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49 -> SignalDeletedAttachment() |
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50 -> ServerIndex::TransactionContext::SignalAttachmentDeleted() |
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51 -> pendingFilesToRemove_.push_back(FileToRemove(info)) (files are deleted in CommitFilesToRemove in the ServerIndex::TransactionContext::Commit) |
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52 |
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53 SignalDeletedResources(output, manager); |
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54 SELECT resourceType, publicId FROM DeletedResources |
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55 -> SignalDeletedResource() |
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56 -> Emit DeletedResource event (lua) |
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57 |
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58 |
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59 if (!CreateInstance(...)) |
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60 Error: "No new instance while overwriting; this should not happen" |
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61 |
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62 if isNewInstance -> LogChange |
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63 if isNewSeries -> LogChange |
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64 .... |
| 431 | 65 |
| 66 Sample SQL code that you can execute in DBeaver to test new functions/procedures: | |
| 67 | |
| 68 CreateInstance | |
| 69 ************************************************************************ | |
| 70 | |
| 444 | 71 CREATE OR REPLACE FUNCTION CreateInstance( |
| 72 IN patient_public_id TEXT, | |
| 73 IN study_public_id TEXT, | |
| 74 IN series_public_id TEXT, | |
| 75 IN instance_public_id TEXT, | |
| 76 OUT is_new_patient BIGINT, | |
| 77 OUT is_new_study BIGINT, | |
| 78 OUT is_new_series BIGINT, | |
| 79 OUT is_new_instance BIGINT, | |
| 80 OUT patient_internal_id BIGINT, | |
| 81 OUT study_internal_id BIGINT, | |
| 82 OUT series_internal_id BIGINT, | |
| 83 OUT instance_internal_id BIGINT) AS $body$ | |
| 84 | |
| 85 BEGIN | |
| 86 is_new_patient := 1; | |
| 87 is_new_study := 1; | |
| 88 is_new_series := 1; | |
| 89 is_new_instance := 1; | |
| 90 | |
| 91 | |
| 92 BEGIN | |
| 93 INSERT INTO "resources" VALUES (DEFAULT, 0, patient_public_id, NULL); | |
| 94 EXCEPTION | |
| 95 WHEN unique_violation THEN | |
| 96 is_new_patient := 0; | |
| 97 END; | |
| 98 SELECT internalid INTO patient_internal_id FROM "resources" WHERE publicId = patient_public_id AND resourcetype = 0 FOR UPDATE; -- also locks the resource and its parent to prevent from deletion while we complete this transaction | |
| 431 | 99 |
| 100 BEGIN | |
| 444 | 101 INSERT INTO "resources" VALUES (DEFAULT, 1, study_public_id, patient_internal_id); |
| 102 EXCEPTION | |
| 103 WHEN unique_violation THEN | |
| 104 is_new_study := 0; | |
| 105 END; | |
| 106 SELECT internalid INTO study_internal_id FROM "resources" WHERE publicId = study_public_id AND resourcetype = 1 FOR UPDATE; -- also locks the resource and its parent to prevent from deletion while we complete this transaction | |
| 431 | 107 |
| 108 BEGIN | |
| 444 | 109 INSERT INTO "resources" VALUES (DEFAULT, 2, series_public_id, study_internal_id); |
| 110 EXCEPTION | |
| 111 WHEN unique_violation THEN | |
| 112 is_new_series := 0; | |
| 113 END; | |
| 114 SELECT internalid INTO series_internal_id FROM "resources" WHERE publicId = series_public_id AND resourcetype = 2 FOR UPDATE; -- also locks the resource and its parent to prevent from deletion while we complete this transaction | |
| 431 | 115 |
| 116 BEGIN | |
| 444 | 117 INSERT INTO "resources" VALUES (DEFAULT, 3, instance_public_id, series_internal_id); |
| 118 EXCEPTION | |
| 119 WHEN unique_violation THEN | |
| 120 is_new_instance := 0; | |
| 121 END; | |
| 122 SELECT internalid INTO instance_internal_id FROM "resources" WHERE publicId = instance_public_id AND resourcetype = 3 FOR UPDATE; -- also locks the resource and its parent to prevent from deletion while we complete this transaction | |
| 123 | |
| 124 IF is_new_instance > 0 THEN | |
| 125 -- Move the patient to the end of the recycling order. | |
| 126 PERFORM PatientAddedOrUpdated(patient_internal_id, 1); | |
| 127 END IF; | |
| 431 | 128 END; |
| 444 | 129 |
| 130 $body$ LANGUAGE plpgsql; | |
| 131 | |
| 431 | 132 |
| 133 DO $$ | |
| 134 DECLARE | |
| 135 result record; | |
| 136 begin | |
| 137 delete from "resources"; | |
| 138 | |
| 139 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance1'); | |
| 140 | |
| 444 | 141 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patient_internal_id, result.is_new_patient; |
| 142 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.study_internal_id, result.is_new_study; | |
| 143 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.series_internal_id, result.is_new_series; | |
| 144 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instance_internal_id, result.is_new_instance; | |
| 431 | 145 RAISE NOTICE '--------------'; |
| 146 | |
| 147 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance2'); | |
| 148 | |
| 444 | 149 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patient_internal_id, result.is_new_patient; |
| 150 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.study_internal_id, result.is_new_study; | |
| 151 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.series_internal_id, result.is_new_series; | |
| 152 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instance_internal_id, result.is_new_instance; | |
| 431 | 153 RAISE NOTICE '--------------'; |
| 154 | |
| 155 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance2'); | |
| 156 | |
| 444 | 157 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patient_internal_id, result.is_new_patient; |
| 158 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.study_internal_id, result.is_new_study; | |
| 159 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.series_internal_id, result.is_new_series; | |
| 160 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instance_internal_id, result.is_new_instance; | |
| 431 | 161 RAISE NOTICE '--------------'; |
| 162 | |
| 163 END $$; | |
| 164 | |
| 444 | 165 |
| 431 | 166 -- \set patient_key 'patient_key' |
| 167 -- SELECT CreateInstance('patient', 'study', 'series', 'instance', patient_key) ; | |
| 168 | |
| 169 -- drop function CreateInstance | |
| 170 -- select * from "resources"; | |
| 171 -- delete from "resources"; | |
| 172 -- INSERT INTO "resources" VALUES (DEFAULT, 0, 'patient', NULL) | |
| 173 | |
| 174 | |
| 175 | |
| 176 ************************************************************************ | |
| 177 | |
| 443 | 178 In debug, no verbose logs, 10 connections |
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179 Orthanc 1.12.1 + PG 5.1 (serializable mode) : test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 43.957 s |
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180 Orthanc mainline + PG mainline (read-committed mode) : test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 15.744 s |
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181 test_concurrent_anonymize_same_study deletion took: 18.8 s |
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182 |
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183 Orthanc 1.12.1 + PG 5.1 (serializable mode) : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 21.214 s |
| 446 | 184 Orthanc mainline + PG mainline (read-committed mode) : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 9.514 s |
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185 |
| 443 | 186 Orthanc 1.12.1 + PG 5.1 (serializable mode) : test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 23.016 s |
| 187 Orthanc mainline + PG mainline (read-committed mode) : test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 7.129 s | |
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188 |
| 444 | 189 Orthanc mainline + PG mainline (read-committed mode) : test_upload_multiple_studies_from_multiple_threads with 10 workers and 25 files and repeat 3x: 6.454 s |
| 190 | |
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191 With Docker with 10 connections SQL: |
| 446 | 192 osimis/orthanc:24.1.2 : test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 18.956 s FAIL !!! |
| 193 test_concurrent_anonymize_same_study deletion took: NA | |
| 194 osimis/orthanc:current: test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 6.867 s | |
| 195 test_concurrent_anonymize_same_study deletion took: 9.095 s | |
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f16faa1fdc46
InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
diff
changeset
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196 |
| 446 | 197 osimis/orthanc:24.1.2 : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 9.822 s |
| 198 osimis/orthanc:current: test_concurrent_uploads_same_study with 20 workers and 1x repeat: 16.027 s up to 38s ! (slower but the test is not representative of a real life scenario !!!!!) | |
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436
f16faa1fdc46
InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
diff
changeset
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199 |
| 446 | 200 osimis/orthanc:24.1.2 : test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 12.966 s |
| 201 osimis/orthanc:current: test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 4.196 s | |
| 202 | |
| 203 osimis/orthanc:24.1.2 : test_upload_multiple_studies_from_multiple_threads with 10 workers and 25 files and repeat 3x: 8.957 s | |
| 204 osimis/orthanc:current: test_upload_multiple_studies_from_multiple_threads with 10 workers and 25 files and repeat 3x: 2.671 s | |
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436
f16faa1fdc46
InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
diff
changeset
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205 |
| 443 | 206 Testing the connecions (note: Orthanc and PG server running on the same server) |
| 207 10 connections : test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 15.744 s | |
| 208 1 connection : test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 21.341 s | |
| 209 10 connections : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 6.57 s | |
| 210 1 connection : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 10.223 s | |
| 211 10 connections : test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 7.129 s | |
| 212 1 connection : test_upload_delete_same_study_from_multiple_threads with 5 workers and 3x repeat (10x): 11.172 s | |
| 213 | |
| 431 | 214 |
| 215 TODO: | |
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437
d979f25e60cf
Re-organized DB creation/upgrade into standalone files
Alain Mazy <am@osimis.io>
parents:
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216 - have a separate "thread" to UpdateStatistics ? |
| 453 | 217 |
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433
5964ce6385a5
use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
Alain Mazy <am@osimis.io>
parents:
432
diff
changeset
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218 - check https://discourse.orthanc-server.org/t/image-insert-are-too-slow-databse-performance-too-poor-when-using-mysql-mariadb/3820 |
| 443 | 219 |
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433
5964ce6385a5
use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
Alain Mazy <am@osimis.io>
parents:
432
diff
changeset
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220 DONE: |
| 453 | 221 - implement a downgrade script ? And test it in PotgresUpgrades integ tests |
| 222 - test the transfer plugin | |
| 223 - perf tests: upload generated data (different studies) | |
| 224 - In Docker images, re-enable MySQL & ODBC plugins + tests | |
| 443 | 225 - reenable PatientRecyclingOrder |
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432
8b7c1c423367
new 'TransactionMode' config + rewrote ResourceDeletedFunc to avoid IF/THEN/ELSE pattern
Alain Mazy <am@osimis.io>
parents:
431
diff
changeset
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226 - force the create/update DB transaction to be serializable (not needed: this is handled by POSTGRESQL_LOCK_DATABASE_SETUP) |
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437
d979f25e60cf
Re-organized DB creation/upgrade into standalone files
Alain Mazy <am@osimis.io>
parents:
436
diff
changeset
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227 - PatientAddedFunc contains an IF (check if other IF/THEN/ELSE pattern remains) |
| 443 | 228 - validate upgrade DB from previous Orthanc and from scratch |
| 229 - check minimal version of PG (9.5 - 9.6 ? for create index if not exists): seems to work with 9.5 cfr PotgresUpgrades integ tests | |
| 230 - test events generation StableSeries .... (count the NewSeries, NewInstances event and make sure they match the numb) |