fix: migrate ids from liquibase migration table

Migration ids were wrongly set and not unique so
they've been changed on the following commit:
5a9fa8a

The issue is that the automatic migration is crashing
because ids have changed.

We added an automated raw SQL migration step (on the liquibase table)
in datashare that is fixing liquibase migrations.

So this commit could be reverted after the next stable release
(i.e. when all intalled users have been run once datashare with
this commit).

Co-authored-by: Maxime Vanza Lutonda <mvanzalu@users.noreply.github.com>

Author: bamthomas

datashare-api/src/main/java/org/icij/datashare/Repository.java

@@ -66,6 +66,9 @@ public interface Repository {
 
     boolean save(User user);
     User getUser(String userId);
+    // TODO: from version 21.0.3
+    //  remove this after version 22.0.0 (or in a few stable releases)
+    void temporaryFixLiquibaseIds();
 
     class AggregateList<T> {
         public final List<Aggregate<T>> aggregates;

datashare-app/src/main/java/org/icij/datashare/mode/CommonMode.java

@@ -328,7 +328,10 @@ public Routes addExtensionsConfiguration(Routes routes) {
 
     void configurePersistence() {
         RepositoryFactoryImpl repositoryFactory = new RepositoryFactoryImpl(propertiesProvider);
-        bind(Repository.class).toInstance(repositoryFactory.createRepository());
+        Repository repository = repositoryFactory.createRepository();
+        // TODO: remove this in few stable releases (cf git commit comment)
+        repository.temporaryFixLiquibaseIds();
+        bind(Repository.class).toInstance(repository);
         bind(ApiKeyRepository.class).toInstance(repositoryFactory.createApiKeyRepository());
         bind(BatchSearchRepository.class).toInstance(repositoryFactory.createBatchSearchRepository());
         bind(CasbinRuleAdapter.class).toInstance(repositoryFactory.createCasbinRuleRepository());

datashare-db/src/main/java/org/icij/datashare/db/JooqRepository.java

@@ -26,25 +26,8 @@
 import org.icij.datashare.text.Tag;
 import org.icij.datashare.text.nlp.Pipeline;
 import org.icij.datashare.user.User;
-import org.jooq.DSLContext;
-import org.jooq.Field;
-import org.jooq.InsertOnDuplicateSetMoreStep;
-import org.jooq.InsertValuesStep2;
-import org.jooq.InsertValuesStep3;
-import org.jooq.InsertValuesStep4;
-import org.jooq.InsertValuesStep5;
-import org.jooq.InsertValuesStep6;
-import org.jooq.InsertValuesStep9;
+import org.jooq.*;
 import org.jooq.Record;
-import org.jooq.Record1;
-import org.jooq.SQLDialect;
-import org.jooq.SelectConditionStep;
-import org.jooq.SelectJoinStep;
-import org.jooq.SelectOnConditionStep;
-import org.jooq.SelectSelectStep;
-import org.jooq.SortField;
-import org.jooq.UpdateConditionStep;
-import org.jooq.UpdateSetMoreStep;
 import org.jooq.exception.DataAccessException;
 import org.jooq.impl.DSL;
 import org.slf4j.LoggerFactory;
@@ -89,6 +72,7 @@
 import static org.jooq.impl.DSL.condition;
 import static org.jooq.impl.DSL.count;
 import static org.jooq.impl.DSL.countDistinct;
+import static org.jooq.impl.DSL.field;
 import static org.jooq.impl.DSL.using;
 import static org.jooq.impl.DSL.value;
 
@@ -534,8 +518,8 @@ public boolean save(Note note) {
 
     @Override
     public boolean save(Project project) {
-        LocalDateTime projectCreationDate = project.creationDate == null ? null : LocalDateTime.ofInstant(project.creationDate.toInstant(),ZoneOffset.UTC);
-        LocalDateTime projectUpdateDate = project.updateDate == null ? null : LocalDateTime.ofInstant(project.updateDate.toInstant(),ZoneOffset.UTC);
+        LocalDateTime projectCreationDate = project.creationDate == null ? null : LocalDateTime.ofInstant(project.creationDate.toInstant(), ZoneOffset.UTC);
+        LocalDateTime projectUpdateDate = project.updateDate == null ? null : LocalDateTime.ofInstant(project.updateDate.toInstant(), ZoneOffset.UTC);
         InsertOnDuplicateSetMoreStep<ProjectRecord> innerSet = using(connectionProvider, dialect).insertInto(
                         PROJECT, PROJECT.ID, PROJECT.LABEL, PROJECT.DESCRIPTION, PROJECT.PATH, PROJECT.SOURCE_URL,
                         PROJECT.MAINTAINER_NAME, PROJECT.PUBLISHER_NAME, PROJECT.LOGO_URL,
@@ -582,6 +566,28 @@ public User getUser(String uid) {
         return createUserFrom(ctx.selectFrom(USER_INVENTORY).where(USER_INVENTORY.ID.eq(uid)).fetchOne());
     }
 
+    @Override
+    public void temporaryFixLiquibaseIds() {
+        using(connectionProvider, dialect).transaction(configuration -> {
+            DSLContext inner = using(configuration);
+            Field<String> id = field("id", String.class);
+            Result<? extends Record1<String>> records = inner.select(id).from("databasechangelog").where("filename=?", "liquibase/changelog/changes/043-adds-user-policy-table.yml").fetch();
+            if (records.isNotEmpty()) {
+                inner.queries(
+                        inner.query("UPDATE databasechangelog set id='64' where filename='liquibase/changelog/changes/036-create_task.yml'"),
+                        inner.query("UPDATE databasechangelog set id='65' where filename='liquibase/changelog/changes/037-adds-task-result-and-error.yml'"),
+                        inner.query("UPDATE databasechangelog set id='66' where filename='liquibase/changelog/changes/038-adds-uri-column-batch-search.yml'"),
+                        inner.query("UPDATE databasechangelog set id='67' where filename='liquibase/changelog/changes/039-adds-column-nb-queries-without-results-batch-search.yml'"),
+                        inner.query("UPDATE databasechangelog set id='68' where filename='liquibase/changelog/changes/040-sqlite-pragma-journal-wal.yml'"),
+                        inner.query("UPDATE databasechangelog set id='69' where filename='liquibase/changelog/changes/041-adds-column-blur-sensitive-to-note.yml'"),
+                        inner.query("UPDATE databasechangelog set id='70' where id='42' and filename='liquibase/changelog/changes/042-task-result-batch-search-migration.yml'"),
+                        inner.query("UPDATE databasechangelog set id='71' where id='43' and filename='liquibase/changelog/changes/042-task-result-batch-search-migration.yml'"),
+                        inner.query("DELETE FROM databasechangelog where filename='liquibase/changelog/changes/043-adds-user-policy-table.yml'")
+                ).executeBatch();
+            }
+        });
+    }
+
     @Override
     public boolean getHealth() {
         DSLContext ctx = DSL.using(connectionProvider, dialect);
@@ -701,7 +707,8 @@ private Document createDocumentFrom(Record result) {
         DocumentRecord documentRecord = result.into(DOCUMENT);
         Map<String, Object> metadata;
         try {
-            metadata = JsonObjectMapper.readValue(documentRecord.getMetadata(), new TypeReference<>() {});
+            metadata = JsonObjectMapper.readValue(documentRecord.getMetadata(), new TypeReference<>() {
+            });
         } catch (IOException e) {
             throw new RuntimeException(e);
         }