Revert "chore: Update abstract from pubmed where missing (#621)"

This reverts commit 1dcad1c.
ursjoss · Dec 7, 2023 · 99a8370 · 99a8370
1 parent 1dcad1c
commit 99a8370
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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
@@ -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<PaperIds> =
-            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
@@ -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
 }