From a3680f736e25ff7608f7bd00969a2ec556c35a85 Mon Sep 17 00:00:00 2001 From: maverickstuder Date: Fri, 22 Mar 2024 17:06:59 +0100 Subject: [PATCH] RED-8702: Explore document databases to store entityLog * bugfix --- .../build.gradle.kts | 8 +- .../redaction/v1/server/Application.java | 4 +- .../server/mongo/EntityLogMongoService.java | 29 +- .../v1/server/MyMongoLiquibaseTest.java | 26 +- ...4b5d4e11211fc0d7732fd45b78.ENTITY_LOG.json | 65652 ++++++++++++++++ .../changelog/mongo.changelog-tenant.xml | 7 + ...ial-database.changelog-with-validation.xml | 224 + .../tenant/1-initial-database.changelog.xml | 17 + .../tenant/2-create-indices-for-entries.xml | 37 + ...ove-entry-number-of-comments.changelog.xml | 26 + .../mongo/liquibase/test.changelog.xml | 45 - 11 files changed, 66012 insertions(+), 63 deletions(-) create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/6f2a9d4b5d4e11211fc0d7732fd45b78.ENTITY_LOG.json create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/mongo.changelog-tenant.xml create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog-with-validation.xml create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog.xml create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/2-create-indices-for-entries.xml create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/example-remove-entry-number-of-comments.changelog.xml delete mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/test.changelog.xml diff --git a/redaction-service-v1/redaction-service-server-v1/build.gradle.kts b/redaction-service-v1/redaction-service-server-v1/build.gradle.kts index 04b95e8f..b5839535 100644 --- a/redaction-service-v1/redaction-service-server-v1/build.gradle.kts +++ b/redaction-service-v1/redaction-service-server-v1/build.gradle.kts @@ -42,7 +42,7 @@ dependencies { implementation("com.iqser.red.commons:dictionary-merge-commons:1.5.0") implementation("com.iqser.red.commons:storage-commons:2.45.0") implementation("com.knecon.fforesight:tenant-commons:maverick-mongo") - implementation("com.knecon.fforesight:mongo-database-commons:maverick-mongo3") + implementation("com.knecon.fforesight:mongo-database-commons:maverick-mongo6") implementation("com.knecon.fforesight:tracing-commons:0.5.0") implementation("com.fasterxml.jackson.module:jackson-module-afterburner:${jacksonVersion}") @@ -67,9 +67,9 @@ dependencies { implementation("org.reflections:reflections:0.10.2") - implementation("org.liquibase:liquibase-core:4.24.0") - - implementation("org.liquibase.ext:liquibase-mongodb:4.24.0") + //todo 8702: remove this + implementation("org.liquibase:liquibase-core:4.20.0") + implementation("org.liquibase.ext:liquibase-mongodb:4.20.0") testImplementation(project(":rules-management")) testImplementation("org.apache.pdfbox:pdfbox:${pdfBoxVersion}") diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/Application.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/Application.java index 8e1884d6..1892f9fa 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/Application.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/Application.java @@ -4,8 +4,10 @@ import org.springframework.boot.SpringApplication; import org.springframework.boot.actuate.autoconfigure.security.servlet.ManagementWebSecurityAutoConfiguration; import org.springframework.boot.autoconfigure.ImportAutoConfiguration; import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.autoconfigure.data.mongo.MongoDataAutoConfiguration; import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration; import org.springframework.boot.autoconfigure.liquibase.LiquibaseAutoConfiguration; +import org.springframework.boot.autoconfigure.mongo.MongoAutoConfiguration; import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration; import org.springframework.boot.context.properties.EnableConfigurationProperties; import org.springframework.cache.annotation.EnableCaching; @@ -31,7 +33,7 @@ import io.micrometer.observation.aop.ObservedAspect; @EnableFeignClients(basePackageClasses = RulesClient.class) @EnableConfigurationProperties(RedactionServiceSettings.class) @EnableMongoRepositories -@SpringBootApplication(exclude = {SecurityAutoConfiguration.class, ManagementWebSecurityAutoConfiguration.class, DataSourceAutoConfiguration.class, LiquibaseAutoConfiguration.class}) +@SpringBootApplication(exclude = {SecurityAutoConfiguration.class, ManagementWebSecurityAutoConfiguration.class, DataSourceAutoConfiguration.class, LiquibaseAutoConfiguration.class, MongoAutoConfiguration.class, MongoDataAutoConfiguration.class}) public class Application { public static void main(String[] args) { diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/mongo/EntityLogMongoService.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/mongo/EntityLogMongoService.java index 3f6a0188..0e925153 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/mongo/EntityLogMongoService.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/mongo/EntityLogMongoService.java @@ -13,6 +13,8 @@ import com.iqser.red.service.persistence.management.v1.processor.document.Entity import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogEntry; +import jakarta.transaction.Transactional; + @Service public class EntityLogMongoService { @@ -27,33 +29,40 @@ public class EntityLogMongoService { } + @Transactional public void insertEntityLog(String dossierId, String fileId, EntityLog entityLog) { EntityLogDocument entityLogDocument = entityLogDocumentRepository.insert(new EntityLogDocument(dossierId, fileId, entityLog)); entityLogEntryDocumentRepository.insert(entityLog.getEntityLogEntry() .stream() - .map(entityLogEntry -> new EntityLogEntryDocument(entityLogDocument.getId(), entityLogEntry)) + .map(entityLogEntry -> new EntityLogEntryDocument(entityLogDocument.getId(), entityLogEntry)).distinct() .toList()); } // this does everything : insert when not found and update if found // todo: remove and replace when services use insert,update,delete correctly + @Transactional public void saveEntityLog(String dossierId, String fileId, EntityLog entityLog) { Optional optionalEntityLogDocument = entityLogDocumentRepository.findById(EntityLogDocument.getDocumentId(dossierId, fileId)); + System.out.println("8702 DEBUG - save entity log"); if (optionalEntityLogDocument.isEmpty()) { + System.out.println("8702 DEBUG - executing insert"); // throw new EntityLogDocumentNotFoundException(String.format("Entity log for dossier %s and file %s not found.", dossierId, fileId)); insertEntityLog(dossierId, fileId, entityLog); return; } + System.out.println("8702 DEBUG - executing update"); EntityLogDocument oldEntityLogDocument = optionalEntityLogDocument.get(); List oldEntityLogEntryDocuments = oldEntityLogDocument.getEntityLogEntryDocument(); + System.out.println("8702 DEBUG - oldEntityLogEntryDocuments " + oldEntityLogEntryDocuments.size()); EntityLogDocument newEntityLogDocument = new EntityLogDocument(dossierId, fileId, entityLog); List newEntityLogEntryDocuments = newEntityLogDocument.getEntityLogEntryDocument(); + System.out.println("8702 DEBUG - newEntityLogEntryDocuments " + newEntityLogEntryDocuments.size()); List toUpdate = new ArrayList<>(newEntityLogEntryDocuments); toUpdate.retainAll(oldEntityLogEntryDocuments); @@ -64,24 +73,31 @@ public class EntityLogMongoService { List toInsert = new ArrayList<>(newEntityLogEntryDocuments); toInsert.removeAll(toUpdate); - entityLogEntryDocumentRepository.saveAll(toUpdate); - entityLogEntryDocumentRepository.deleteAll(toRemove); - entityLogEntryDocumentRepository.insert(toInsert); + toInsert.forEach(System.out::println); + System.out.println("8702 DEBUG - saving toUpdate " + toUpdate.size()); + entityLogEntryDocumentRepository.saveAll(toUpdate); + System.out.println("8702 DEBUG - deleting toRemove " + toRemove.size()); + entityLogEntryDocumentRepository.deleteAll(toRemove); + System.out.println("8702 DEBUG - inserting toInsert " + toInsert.size()); + System.out.println("8702 DEBUG - inserting toInsert " + toInsert.stream().distinct().toList()); + entityLogEntryDocumentRepository.insert(toInsert.stream().distinct().toList()); + + System.out.println("8702 DEBUG - saving newEntityLogDocument " + newEntityLogDocument.getEntityLogEntryDocument().size()); entityLogDocumentRepository.save(newEntityLogDocument); } + @Transactional public void deleteEntityLog(String dossierId, String fileId) { String entityLogId = EntityLogDocument.getDocumentId(dossierId, fileId); entityLogDocumentRepository.deleteById(entityLogId); - entityLogEntryDocumentRepository.deleteByEntityLogId(entityLogId); } - + @Transactional public void insertEntityLogEntries(String dossierId, String fileId, List entityLogEntries) { String entityLogId = EntityLogDocument.getDocumentId(dossierId, fileId); @@ -109,6 +125,7 @@ public class EntityLogMongoService { } + @Transactional public void deleteEntityLogEntries(String dossierId, String fileId, List entityLogEntries) { String entityLogId = EntityLogDocument.getDocumentId(dossierId, fileId); diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/MyMongoLiquibaseTest.java b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/MyMongoLiquibaseTest.java index 4243f6b4..0c224192 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/MyMongoLiquibaseTest.java +++ b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/MyMongoLiquibaseTest.java @@ -1,11 +1,19 @@ package com.iqser.red.service.redaction.v1.server; -import static com.mongodb.client.model.Filters.eq; +import java.io.File; -import org.junit.jupiter.api.Disabled; +import org.bson.Document; import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.core.io.ResourceLoader; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import com.mongodb.client.FindIterable; +import com.mongodb.client.MongoCollection; -import liquibase.Contexts; import liquibase.Liquibase; import liquibase.database.DatabaseFactory; import liquibase.ext.mongodb.database.MongoLiquibaseDatabase; @@ -18,18 +26,22 @@ public class MyMongoLiquibaseTest { private static final String PORT = "27017"; private static final String DATABASE = "redaction"; private static final String USERNAME = "root"; - private static final String PASSWORD = "AP8ckozpAl55JDAAFR4rxpbPj1WXdBTL"; + private static final String PASSWORD = "XaRIBExTr8JrCSfgaHek3dl7wJj7dKZm"; private static final String URL = String.format("mongodb://%s:%s/%s", HOSTNAME, PORT, DATABASE); @Test - @Disabled + //@Disabled @SneakyThrows public void testMongoDB() { try (MongoLiquibaseDatabase database = (MongoLiquibaseDatabase) DatabaseFactory.getInstance().openDatabase(URL, USERNAME, PASSWORD, null, null)) { - try (Liquibase liquibase = new Liquibase("mongo/liquibase/test.changelog.xml", new ClassLoaderResourceAccessor(), database)) { - liquibase.update(); + + //MongoCollection logs = database.getMongoDatabase().getCollection("entity-logs"); + //long count = logs.countDocuments(); + String path = "/mongo/liquibase/changelog/mongo.changelog-tenant.xml"; + try (Liquibase liquibase = new Liquibase(path, new ClassLoaderResourceAccessor(), database)) { + liquibase.update(""); } } } diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/6f2a9d4b5d4e11211fc0d7732fd45b78.ENTITY_LOG.json b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/6f2a9d4b5d4e11211fc0d7732fd45b78.ENTITY_LOG.json new file mode 100644 index 00000000..92cc6320 --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/6f2a9d4b5d4e11211fc0d7732fd45b78.ENTITY_LOG.json @@ -0,0 +1,65652 @@ +{ + "analysisVersion": 1, + "analysisNumber": 2, + "entityLogEntry": [ + { + "id": "8f4af72f01a7760290666d9b2237333d", + "type": "CBI_address", + "entryType": "RECOMMENDATION", + "state": "SKIPPED", + "value": "12852, Park One Drive, Sugar Land, Texas, USA", + "reason": "", + "matchedRule": "", + "legalBasis": "", + "imported": false, + "containingNodeId": [ + 518, + 3, + 0, + 0, + 1 + ], + "closestHeadline": "Table 7.1.3.1.2-619: KFOC and 1/n (Freundlich exponent) adsorption values of CGA192155 in different soils ", + "section": "[518, 3, 0, 0, 1]: Paragraph: K-IIA 7.1.2. 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the request, except for information which is relevant to the assessment of safety", + "reason": "Article 63(2)(a) of Regulation (EC) No 1107/2009 (making reference to Article 39 of Regulation EC No 178/2002)" + }, + { + "name": "6. specification of impurity", + "description": "the specification of impurity of the active substance and the related methods of analysis for impurities in the active substance as manufactured, except for the impurities that are considered to be toxicologically, ecotoxicologically or environmentally relevant and the related methods of analysis for such impurities", + "reason": "Article 63(2)(b) of Regulation (EC) No 1107/2009" + }, + { + "name": "7. results of production batches", + "description": "results of production batches of the active substance including impurities", + "reason": "Article 63(2)(c) of Regulation (EC) No 1107/2009" + }, + { + "name": "8. composition of a plant protection product", + "description": "information on the complete composition of a plant protection product", + "reason": "Article 63(2)(d) of Regulation (EC) No 1107/2009" + } + ], + "dictionaryVersion": 21, + "dossierDictionaryVersion": 6, + "rulesVersion": 1, + "legalBasisVersion": 2 +} \ No newline at end of file diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/mongo.changelog-tenant.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/mongo.changelog-tenant.xml new file mode 100644 index 00000000..9e049c40 --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/mongo.changelog-tenant.xml @@ -0,0 +1,7 @@ + + + + diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog-with-validation.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog-with-validation.xml new file mode 100644 index 00000000..c988f71a --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog-with-validation.xml @@ -0,0 +1,224 @@ + + + + + + + { + validator: { + $jsonSchema: { + bsonType: "object", + required: ["entryId", "entityLogId", "type", "entryType", "state", "value", "reason", "matchedRule", "legalBasis", "containingNodeId", "closestHeadline", "section", + "positions", "textBefore", "textAfter", "startOffset", "endOffset", "imageHasTransparency", "dictionaryEntry", "dossierDictionaryEntry", "excluded", "changes", + "manualChanges", "engines", "reference", "importedRedactionIntersections", "numberOfComments"], + properties: { + entryId: { + bsonType: "string", + description: "The Entry ID" + }, + entityLogId: { + bsonType: "string", + description: "The Entity Log ID" + }, + type: { + bsonType: "string", + description: "The Type" + }, + entryType: { + bsonType: "string", + description: "The Entry Type" + }, + state: { + bsonType: "string", + description: "The Entry State" + }, + value: { + bsonType: "string", + description: "The Value" + }, + reason: { + bsonType: "string", + description: "The Reason" + }, + matchedRule: { + bsonType: "string", + description: "The Matched Rule" + }, + legalBasis: { + bsonType: "string", + description: "The Legal Basis" + }, + containingNodeId: { + bsonType: "array", + items: { + bsonType: "int", + description: "The Containing Node ID" + } + }, + closestHeadline: { + bsonType: "string", + description: "The Closest Headline" + }, + section: { + bsonType: "string", + description: "The Section" + }, + positions: { + bsonType: "array", + description: "The Positions", + items: { + bsonType: "object" + } + }, + textBefore: { + bsonType: "string", + description: "Text before the entry" + }, + textAfter: { + bsonType: "string", + description: "Text after the entry" + }, + startOffset: { + bsonType: "int", + description: "Start offset of the entry" + }, + endOffset: { + bsonType: "int", + description: "End offset of the entry" + }, + imageHasTransparency: { + bsonType: "bool", + description: "Whether the image has transparency" + }, + dictionaryEntry: { + bsonType: "bool", + description: "Whether it's a dictionary entry" + }, + dossierDictionaryEntry: { + bsonType: "bool", + description: "Whether it's a dossier dictionary entry" + }, + excluded: { + bsonType: "bool", + description: "Whether it's excluded" + }, + changes: { + bsonType: "array", + description: "The Changes", + items: { + bsonType: "object" + } + }, + manualChanges: { + bsonType: "array", + description: "The Manual Changes", + items: { + bsonType: "object" + } + }, + engines: { + bsonType: "array", + description: "The Engines", + items: { + bsonType: "string" + } + }, + reference: { + bsonType: "array", + description: "The Reference", + items: { + bsonType: "string" + } + }, + importedRedactionIntersections: { + bsonType: "array", + description: "The Imported Redaction Intersections", + items: { + bsonType: "string" + } + }, + numberOfComments: { + bsonType: "int", + description: "The Number of Comments" + } + } + } + }, + validationAction: "warn", + validationLevel: "strict" + } + + + + + + { + validator: { + $jsonSchema: { + bsonType: "object", + required: ["dossierId", "fileId", "analysisVersion", "analysisNumber", "entityLogEntryDocument", "legalBasis"], + properties: { + dossierId: { + bsonType: "string", + description: "The Dossier ID" + }, + fileId: { + bsonType: "string", + description: "The File ID" + }, + analysisVersion: { + bsonType: "long", + description: "The Analysis Version" + }, + analysisNumber: { + bsonType: "int", + description: "The Analysis Number" + }, + entityLogEntryDocument: { + bsonType: "array", + description: "The Entity Log Entry Documents", + items: { + bsonType: "objectId" + } + }, + legalBasis: { + bsonType: "array", + description: "The Legal Basis", + items: { + bsonType: "object" + } + }, + dictionaryVersion: { + bsonType: "long", + description: "The Dictionary Version" + }, + dossierDictionaryVersion: { + bsonType: "long", + description: "The Dossier Dictionary Version" + }, + rulesVersion: { + bsonType: "long", + description: "The Rules Version" + }, + legalBasisVersion: { + bsonType: "long", + description: "The Legal Basis Version" + } + } + } + }, + validationAction: "warn", + validationLevel: "strict" + } + + + + + + + \ No newline at end of file diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog.xml new file mode 100644 index 00000000..c8e1cbce --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/1-initial-database.changelog.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/2-create-indices-for-entries.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/2-create-indices-for-entries.xml new file mode 100644 index 00000000..5fe9ed7c --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/2-create-indices-for-entries.xml @@ -0,0 +1,37 @@ + + + + + + + { + "_id": 1, + "positions.pageNumber": 1 + } + + + {name: "positions_pageNumber_index"} + + + + + + { + "_id": 1, + "changes.analysisNumber": -1 + } + + + {name: "changes_analysisNumber_index"} + + + + + + + \ No newline at end of file diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/example-remove-entry-number-of-comments.changelog.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/example-remove-entry-number-of-comments.changelog.xml new file mode 100644 index 00000000..9665c17b --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/changelog/tenant/example-remove-entry-number-of-comments.changelog.xml @@ -0,0 +1,26 @@ + + + + + + { + update: "entity-log-entries", + updates: [ + { + q: {}, + u: { $unset: { "numberOfComments": "" } }, + multi: true + } + ] + } + + + + + + \ No newline at end of file diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/test.changelog.xml b/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/test.changelog.xml deleted file mode 100644 index 23d67a7f..00000000 --- a/redaction-service-v1/redaction-service-server-v1/src/test/resources/mongo/liquibase/test.changelog.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - - - - - { - update: "entity-logs", - updates: [ - { - q: {}, - u: { $rename: { "dId": "dossierId" } }, - multi: true - } - ] - } - - - - - - \ No newline at end of file