From 99a8370fe7fc62a54cc894a41254916f8ca70f7b Mon Sep 17 00:00:00 2001 From: Urs Joss Date: Thu, 7 Dec 2023 22:48:04 +0100 Subject: [PATCH] Revert "chore: Update abstract from pubmed where missing (#621)" This reverts commit 1dcad1cb4b54586eab13f087d31159286958edbd. --- .../core/ScipamatoCoreApplication.kt | 55 ------------------- .../scipamato/core/web/AbstractWicketTest.kt | 5 -- 2 files changed, 60 deletions(-) diff --git a/core/core-web/src/main/java/ch/difty/scipamato/core/ScipamatoCoreApplication.kt b/core/core-web/src/main/java/ch/difty/scipamato/core/ScipamatoCoreApplication.kt index 013bdc01c..a9324feb3 100644 --- a/core/core-web/src/main/java/ch/difty/scipamato/core/ScipamatoCoreApplication.kt +++ b/core/core-web/src/main/java/ch/difty/scipamato/core/ScipamatoCoreApplication.kt @@ -2,10 +2,6 @@ package ch.difty.scipamato.core import ch.difty.scipamato.common.logger import ch.difty.scipamato.common.web.AbstractPage -import ch.difty.scipamato.core.config.ApplicationCoreProperties -import ch.difty.scipamato.core.db.tables.Paper -import ch.difty.scipamato.core.db.tables.ScipamatoUser -import ch.difty.scipamato.core.pubmed.PubmedArticleService import ch.difty.scipamato.core.web.sync.ISyncTask import ch.difty.scipamato.core.web.sync.TasksRunnable import com.giffing.wicket.spring.boot.starter.app.WicketBootSecuredWebApplication @@ -14,16 +10,12 @@ import org.apache.wicket.markup.head.filter.JavaScriptFilteredIntoFooterHeaderRe import org.apache.wicket.markup.html.SecurePackageResourceGuard import org.apache.wicket.request.Request import org.apache.wicket.request.Response -import org.jooq.DSLContext -import org.springframework.beans.factory.annotation.Autowired import org.springframework.boot.autoconfigure.SpringBootApplication import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration import org.springframework.boot.runApplication import org.springframework.cache.annotation.EnableCaching import org.springframework.cloud.openfeign.EnableFeignClients import org.springframework.context.annotation.ComponentScan -import java.sql.Timestamp -import java.time.LocalDateTime import java.util.concurrent.Executors import java.util.concurrent.TimeUnit @@ -37,15 +29,6 @@ open class ScipamatoCoreApplication : WicketBootSecuredWebApplication() { private val executorService = Executors.newSingleThreadExecutor() - @Autowired - private lateinit var dsl: DSLContext - - @Autowired - protected lateinit var properties: ApplicationCoreProperties - - @Autowired - private lateinit var pubmedArticleService: PubmedArticleService - override fun init() { // TODO consider making it CSP compliant cspSettings.blocking().disabled() @@ -54,14 +37,6 @@ open class ScipamatoCoreApplication : WicketBootSecuredWebApplication() { headerResponseDecorators.add { JavaScriptFilteredIntoFooterHeaderResponse(it, AbstractPage.FOOTER_CONTAINER) } registerJasperJrxmlFilesWithPackageResourceGuard() - - triggerStartupMigration(dsl) { pmId: Long -> - val id = pmId.toInt() - val result = properties.pubmedApiKey?.let { - pubmedArticleService.getPubmedArticleWithPmidAndApiKey(id, it) - } ?: pubmedArticleService.getPubmedArticleWithPmid(id) - result.pubmedArticleFacade?.originalAbstract - } } // Allow access to jrxml jasper report definition files @@ -71,36 +46,6 @@ open class ScipamatoCoreApplication : WicketBootSecuredWebApplication() { } } - @Suppress("MagicNumber") - private fun triggerStartupMigration(dsl: DSLContext, getAbstract: (Long) -> String?) { - val adminUserId = (dsl - .select(ScipamatoUser.SCIPAMATO_USER.ID) - .from(ScipamatoUser.SCIPAMATO_USER) - .where(ScipamatoUser.SCIPAMATO_USER.USER_NAME.eq("admin")) - .fetchOne()?.get(0) as? Int?) ?: 1 - log.info("Starting Migration (user $adminUserId) <----------------------") - val papersToEnrich: List = - dsl.select(Paper.PAPER.ID, Paper.PAPER.PM_ID) - .from(Paper.PAPER) - .where(Paper.PAPER.PM_ID.isNotNull.and(Paper.PAPER.ORIGINAL_ABSTRACT.isNull)) - .fetchInto(PaperIds::class.java).toList() - log.info("affected records with no abstract but PM_ID: ${papersToEnrich.size}") - papersToEnrich.forEach { paper -> - getAbstract(paper.pmId)?.let { abstract -> - log.info("Migrating paper $paper") - dsl.update(Paper.PAPER) - .set(Paper.PAPER.ORIGINAL_ABSTRACT, abstract) - .set(Paper.PAPER.LAST_MODIFIED, Timestamp.valueOf(LocalDateTime.now())) - .set(Paper.PAPER.LAST_MODIFIED_BY, adminUserId) - .set(Paper.PAPER.VERSION, Paper.PAPER.VERSION + 1) - .where(Paper.PAPER.ID.eq(paper.id).and(Paper.PAPER.ORIGINAL_ABSTRACT.isNull())).execute() - Thread.sleep(1000L) - } - } - } - - private data class PaperIds(val id: Long, val pmId: Long) - override fun newSession(request: Request, response: Response): Session = ScipamatoSession(request) @Suppress("MagicNumber") diff --git a/core/core-web/src/test/kotlin/ch/difty/scipamato/core/web/AbstractWicketTest.kt b/core/core-web/src/test/kotlin/ch/difty/scipamato/core/web/AbstractWicketTest.kt index 58e2b5aff..c72d56eed 100644 --- a/core/core-web/src/test/kotlin/ch/difty/scipamato/core/web/AbstractWicketTest.kt +++ b/core/core-web/src/test/kotlin/ch/difty/scipamato/core/web/AbstractWicketTest.kt @@ -22,11 +22,9 @@ import ch.difty.scipamato.core.persistence.UserService import ch.difty.scipamato.core.pubmed.PubmedArticleService import com.ninjasquad.springmockk.MockkBean import io.mockk.junit5.MockKExtension -import org.jooq.DSLContext import org.junit.jupiter.api.extension.ExtendWith import org.springframework.beans.factory.annotation.Autowired import org.springframework.boot.test.context.SpringBootTest -import org.springframework.boot.test.mock.mockito.MockBean import org.springframework.context.ApplicationContext import org.springframework.context.annotation.Bean import org.springframework.test.context.ActiveProfiles @@ -87,7 +85,4 @@ abstract class AbstractWicketTest { @MockkBean protected lateinit var userServiceMock: UserService - - @MockkBean(relaxed = true) - protected lateinit var dsl: DSLContext }