Mercurial > hg > orthanc-databases
annotate NOTES @ 437:d979f25e60cf pg-transactions
Re-organized DB creation/upgrade into standalone files
| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Mon, 18 Dec 2023 18:50:01 +0100 |
| parents | f16faa1fdc46 |
| children | 2a48f8fcec6e |
| rev | line source |
|---|---|
| 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 | |
| 71 CREATE OR replace FUNCTION CreateInstance( | |
| 72 IN patient TEXT, | |
| 73 IN study TEXT, | |
| 74 IN series TEXT, | |
| 75 IN instance TEXT, | |
| 76 OUT isNewPatient BIGINT, | |
| 77 OUT isNewStudy BIGINT, | |
| 78 OUT isNewSeries BIGINT, | |
| 79 OUT isNewInstance BIGINT, | |
| 80 OUT patientKey BIGINT, | |
| 81 OUT studyKey BIGINT, | |
| 82 OUT seriesKey BIGINT, | |
| 83 OUT instanceKey BIGINT) | |
| 84 AS $$ | |
| 85 begin | |
| 86 isNewPatient := 1; | |
| 87 isNewStudy := 1; | |
| 88 isNewSeries := 1; | |
| 89 isNewInstance := 1; | |
| 90 | |
| 91 BEGIN | |
| 92 INSERT INTO "resources" VALUES (DEFAULT, 0, patient, NULL); | |
| 93 exception | |
| 94 when unique_violation then | |
| 95 isNewPatient := 0; | |
| 96 end; | |
| 97 select internalid into patientKey from "resources" where publicId=patient and resourcetype = 0; | |
| 98 | |
| 99 BEGIN | |
| 100 INSERT INTO "resources" VALUES (DEFAULT, 1, study, patientKey); | |
| 101 exception | |
| 102 when unique_violation then | |
| 103 isNewStudy := 0; | |
| 104 end; | |
| 105 select internalid into studyKey from "resources" where publicId=study and resourcetype = 1; | |
| 106 | |
| 107 BEGIN | |
| 108 INSERT INTO "resources" VALUES (DEFAULT, 2, series, studyKey); | |
| 109 exception | |
| 110 when unique_violation then | |
| 111 isNewSeries := 0; | |
| 112 end; | |
| 113 select internalid into seriesKey from "resources" where publicId=series and resourcetype = 2; | |
| 114 | |
| 115 BEGIN | |
| 116 INSERT INTO "resources" VALUES (DEFAULT, 3, instance, seriesKey); | |
| 117 exception | |
| 118 when unique_violation then | |
| 119 isNewInstance := 0; | |
| 120 end; | |
| 121 select internalid into instanceKey from "resources" where publicId=instance and resourcetype = 3; | |
| 122 | |
| 123 END; | |
| 124 $$ LANGUAGE plpgsql; | |
| 125 | |
| 126 DO $$ | |
| 127 DECLARE | |
| 128 result record; | |
| 129 begin | |
| 130 delete from "resources"; | |
| 131 | |
| 132 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance1'); | |
| 133 | |
| 134 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patientKey, result.isNewPatient; | |
| 135 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.studyKey, result.isNewStudy; | |
| 136 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.seriesKey, result.isNewSeries; | |
| 137 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instanceKey, result.isNewInstance; | |
| 138 RAISE NOTICE '--------------'; | |
| 139 | |
| 140 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance2'); | |
| 141 | |
| 142 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patientKey, result.isNewPatient; | |
| 143 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.studyKey, result.isNewStudy; | |
| 144 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.seriesKey, result.isNewSeries; | |
| 145 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instanceKey, result.isNewInstance; | |
| 146 RAISE NOTICE '--------------'; | |
| 147 | |
| 148 SELECT * INTO result from CreateInstance('patient1', 'study1', 'series1', 'instance2'); | |
| 149 | |
| 150 RAISE NOTICE 'Value patientInternalId: %, is_new: %', result.patientKey, result.isNewPatient; | |
| 151 RAISE NOTICE 'Value studyInternalId: %, is_new: %', result.studyKey, result.isNewStudy; | |
| 152 RAISE NOTICE 'Value seriesInternalId: %, is_new: %', result.seriesKey, result.isNewSeries; | |
| 153 RAISE NOTICE 'Value instanceInternalId: %, is_new: %', result.instanceKey, result.isNewInstance; | |
| 154 RAISE NOTICE '--------------'; | |
| 155 | |
| 156 END $$; | |
| 157 | |
| 158 -- \set patient_key 'patient_key' | |
| 159 -- SELECT CreateInstance('patient', 'study', 'series', 'instance', patient_key) ; | |
| 160 | |
| 161 -- drop function CreateInstance | |
| 162 -- select * from "resources"; | |
| 163 -- delete from "resources"; | |
| 164 -- INSERT INTO "resources" VALUES (DEFAULT, 0, 'patient', NULL) | |
| 165 | |
| 166 | |
| 167 | |
| 168 ************************************************************************ | |
| 169 | |
| 170 In debug, no verbose logs | |
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171 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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172 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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173 test_concurrent_anonymize_same_study deletion took: 18.8 s |
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435
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174 |
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175 Orthanc 1.12.1 + PG 5.1 (serializable mode) : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 21.214 s |
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176 Orthanc mainline + PG mainline (read-committed mode) : test_concurrent_uploads_same_study with 20 workers and 1x repeat: 6.57 s (with temporary tables) |
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177 |
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178 Orthanc 1.12.1 + PG 5.1 (serializable mode) : test_upload_delete_same_study_from_multiple_threads with 5 workers and 30x repeat: 23.016 s |
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179 Orthanc mainline + PG mainline (read-committed mode) : test_upload_delete_same_study_from_multiple_threads with 5 workers and 30x repeat: 7.129 s |
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180 |
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181 With Docker with 10 connections SQL: |
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182 osimis/orthanc:23.11.0: TIMING test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 25.047 s |
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183 osimis/orthanc:current: TIMING test_concurrent_anonymize_same_study with 4 workers and 10x repeat: 8.649 s |
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184 |
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185 osimis/orthanc:23.11.0: TIMING test_concurrent_anonymize_same_study deletion took: 11.807 s |
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186 osimis/orthanc:current: TIMING test_concurrent_anonymize_same_study deletion took: 10.620 s |
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
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187 |
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f16faa1fdc46
InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
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188 osimis/orthanc:23.11.0: TIMING test_concurrent_uploads_same_study with 20 workers and 1x repeat: 10.736 s |
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
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189 osimis/orthanc:current: TIMING test_concurrent_uploads_same_study with 20 workers and 1x repeat: 3.465 s |
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
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changeset
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190 |
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f16faa1fdc46
InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
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191 osimis/orthanc:23.11.0: TIMING test_upload_delete_same_study_from_multiple_threads with 5 workers and 30x repeat: 11.966 s |
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
435
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192 osimis/orthanc:current: TIMING test_upload_delete_same_study_from_multiple_threads with 5 workers and 30x repeat: 5.092 s |
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
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193 |
| 431 | 194 |
| 195 TODO: | |
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437
d979f25e60cf
Re-organized DB creation/upgrade into standalone files
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196 - reenable PatientRecyclingOrder |
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197 - have a separate "thread" to UpdateStatistics ? |
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433
5964ce6385a5
use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
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198 - test events generation StableSeries .... |
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use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
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199 - check https://discourse.orthanc-server.org/t/image-insert-are-too-slow-databse-performance-too-poor-when-using-mysql-mariadb/3820 |
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432
8b7c1c423367
new 'TransactionMode' config + rewrote ResourceDeletedFunc to avoid IF/THEN/ELSE pattern
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200 - validate upgrade DB from previous Orthanc and from scratch |
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201 - check minimal version of PG (9.5 - 9.6 ? for create index if not exists) |
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202 - implement a downgrade script ? |
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432
8b7c1c423367
new 'TransactionMode' config + rewrote ResourceDeletedFunc to avoid IF/THEN/ELSE pattern
Alain Mazy <am@osimis.io>
parents:
431
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203 - test with older version of PG |
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436
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InsertOrUpdateMetadata function + UpdateAndGetStatistics
Alain Mazy <am@osimis.io>
parents:
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204 - In Docker images, re-enable MySQL & ODBC plugins + tests |
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433
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use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
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parents:
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205 |
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use temporary tables for DeletedFiles, RemainingAncestor and DeletedResources
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parents:
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206 DONE: |
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432
8b7c1c423367
new 'TransactionMode' config + rewrote ResourceDeletedFunc to avoid IF/THEN/ELSE pattern
Alain Mazy <am@osimis.io>
parents:
431
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207 - force the create/update DB transaction to be serializable (not needed: this is handled by POSTGRESQL_LOCK_DATABASE_SETUP) |
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437
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parents:
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208 - PatientAddedFunc contains an IF (check if other IF/THEN/ELSE pattern remains) |