Add missing precision to DATETIME columns

Hibernate 4 uses that information to truncate fractional seconds accordingly. We want to preserve the milliseconds of the java.util.Date object, so 3 is adequate.
PavlidisLab · Dec 3, 2022 · 2bce979 · 2bce979
1 parent 5658b1e
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diff --git a/gemma-core/src/main/resources/sql/migrations/db.1.29.0.sql b/gemma-core/src/main/resources/sql/migrations/db.1.29.0.sql
@@ -41,4 +41,18 @@ alter table GENE_SET modify column AUDIT_TRAIL_FK BIGINT not null;
 alter table EXTERNAL_DATABASE
     add column EXTERNAL_DATABASE_FK BIGINT after DATABASE_SUPPLIER_FK;
 alter table EXTERNAL_DATABASE
-    add constraint EXTERNAL_DATABASE_FKC foreign key (EXTERNAL_DATABASE_FK) references EXTERNAL_DATABASE (ID);
+    add constraint EXTERNAL_DATABASE_FKC foreign key (EXTERNAL_DATABASE_FK) references EXTERNAL_DATABASE (ID);
+
+-- add precision to our datetime to match that of java.util.Date
+alter table PHENOTYPE_ASSOCIATION modify column LAST_UPDATED DATETIME(3);
+alter table AUDIT_EVENT modify column DATE DATETIME(3);
+alter table CONTACT modify column SIGNUP_TOKEN_DATESTAMP DATETIME(3);
+alter table JOB_INFO
+    modify column START_TIME DATETIME(3),
+    modify column END_TIME DATETIME(3);
+alter table CURATION_DETAILS modify column LAST_UPDATED DATETIME(3);
+alter table EXTERNAL_DATABASE modify column LAST_UPDATED DATETIME(3);
+alter table BIO_ASSAY modify column PROCESSING_DATE DATETIME(3);
+
+-- initially stored as a DATETIME, but publication time is just not a thing
+alter table BIBLIOGRAPHIC_REFERENCE modify column PUBLICATION_DATE DATE;
diff --git a/...re/src/main/resources/ubic/gemma/model/association/phenotype/PhenotypeAssociation.hbm.xml b/...re/src/main/resources/ubic/gemma/model/association/phenotype/PhenotypeAssociation.hbm.xml
@@ -51,7 +51,7 @@
             <column name="STRENGTH" not-null="false" unique="false" sql-type="DOUBLE"/>
         </property>
         <property name="lastUpdated" type="java.util.Date">
-            <column name="LAST_UPDATED" not-null="true" unique="false" sql-type="DATETIME"/>
+            <column name="LAST_UPDATED" not-null="true" unique="false" sql-type="DATETIME(3)"/>
         </property>
         <many-to-one name="gene" class="ubic.gemma.model.genome.Gene" cascade="none" lazy="false" fetch="join">
             <column name="GENE_FK" not-null="false" sql-type="BIGINT"/>

diff --git a/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/AuditEvent.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/AuditEvent.hbm.xml
@@ -10,7 +10,7 @@
             <generator class="native"/>
         </id>
         <property access="field" name="date" type="java.util.Date">
-            <column name="DATE" not-null="true" sql-type="DATETIME"/>
+            <column name="DATE" not-null="true" sql-type="DATETIME(3)"/>
         </property>
         <property access="field" name="action"
                   type="ubic.gemma.model.common.auditAndSecurity.AuditActionEnum">

diff --git a/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/Contact.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/Contact.hbm.xml
@@ -42,7 +42,7 @@
                     <column name="SIGNUP_TOKEN" not-null="false" unique="false" sql-type="VARCHAR(255)"/>
                 </property>
                 <property name="signupTokenDatestamp" type="java.util.Date">
-                    <column name="SIGNUP_TOKEN_DATESTAMP" not-null="false" unique="false" sql-type="DATETIME"/>
+                    <column name="SIGNUP_TOKEN_DATESTAMP" not-null="false" unique="false" sql-type="DATETIME(3)"/>
                 </property>
                 <set name="jobs" lazy="true" fetch="select" inverse="true">
                     <cache usage="read-write"/>

diff --git a/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/JobInfo.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/common/auditAndSecurity/JobInfo.hbm.xml
@@ -18,10 +18,10 @@
             <column name="FAILED_MESSAGE" not-null="false" unique="false" sql-type="text"/>
         </property>
         <property name="startTime" type="java.util.Date">
-            <column name="START_TIME" not-null="true" unique="false" sql-type="DATETIME"/>
+            <column name="START_TIME" not-null="true" unique="false" sql-type="DATETIME(3)"/>
         </property>
         <property name="endTime" type="java.util.Date">
-            <column name="END_TIME" not-null="false" unique="false" sql-type="DATETIME"/>
+            <column name="END_TIME" not-null="false" unique="false" sql-type="DATETIME(3)"/>
         </property>
         <property name="phases" type="java.lang.Integer">
             <column name="PHASES" not-null="true" unique="false" sql-type="INTEGER"/>

diff --git a/.../main/resources/ubic/gemma/model/common/auditAndSecurity/curation/CurationDetails.hbm.xml b/.../main/resources/ubic/gemma/model/common/auditAndSecurity/curation/CurationDetails.hbm.xml
@@ -26,7 +26,7 @@
             <column name="NOTE_AUDIT_EVENT_FK" not-null="false" sql-type="BIGINT" unique="true"/>
         </many-to-one>
         <property name="lastUpdated" type="java.util.Date">
-            <column name="LAST_UPDATED" not-null="false" unique="false" sql-type="DATETIME"/>
+            <column name="LAST_UPDATED" not-null="false" unique="false" sql-type="DATETIME(3)"/>
         </property>
         <property name="troubled" type="java.lang.Boolean">
             <column name="TROUBLED" not-null="true" unique="false" sql-type="TINYINT"/>

diff --git a/...ore/src/main/resources/ubic/gemma/model/common/description/BibliographicReference.hbm.xml b/...ore/src/main/resources/ubic/gemma/model/common/description/BibliographicReference.hbm.xml
@@ -51,7 +51,7 @@
             <column name="CITATION" not-null="false" unique="false" sql-type="text"/>
         </property>
         <property name="publicationDate" type="java.util.Date">
-            <column name="PUBLICATION_DATE" not-null="false" unique="false" sql-type="DATETIME"/>
+            <column name="PUBLICATION_DATE" not-null="false" unique="false" sql-type="DATE"/>
         </property>
         <property name="annotatedAbstract" type="org.hibernate.type.MaterializedClobType">
             <column name="ANNOTATED_ABSTRACT" not-null="false" unique="false" sql-type="text"/>

diff --git a/gemma-core/src/main/resources/ubic/gemma/model/common/description/ExternalDatabase.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/common/description/ExternalDatabase.hbm.xml
@@ -35,8 +35,8 @@
         <property name="releaseUrl" type="java.net.URL">
             <column name="RELEASE_URL" not-null="false" unique="false" sql-type="VARCHAR(255)"/>
         </property>
-        <property name="lastUpdated" type="java.util.Date">
-            <column name="LAST_UPDATED" not-null="false" unique="false" sql-type="DATETIME"/>
+        <property name="lastUpdated" type="java.util.Date" precision="4">
+            <column name="LAST_UPDATED" not-null="false" unique="false" sql-type="DATETIME(3)"/>
         </property>
         <many-to-one name="databaseSupplier" class="ubic.gemma.model.common.auditAndSecurity.Contact" cascade="none"
                      lazy="proxy" fetch="select">

diff --git a/gemma-core/src/main/resources/ubic/gemma/model/expression/bioAssay/BioAssay.hbm.xml b/gemma-core/src/main/resources/ubic/gemma/model/expression/bioAssay/BioAssay.hbm.xml
@@ -18,7 +18,7 @@
          <column name="DESCRIPTION" not-null="false" unique="false" sql-type="text"/>
       </property>
       <property name="processingDate" type="java.util.Date">
-         <column name="PROCESSING_DATE" not-null="false" unique="false" sql-type="DATETIME"/>
+         <column name="PROCESSING_DATE" not-null="false" unique="false" sql-type="DATETIME(3)"/>
       </property>
       <property name="sequenceReadCount" type="java.lang.Integer">
          <column name="SEQUENCE_READ_COUNT" not-null="false" unique="false" sql-type="INTEGER"/>

diff --git a/...st/java/ubic/gemma/core/analysis/service/GeneMultifunctionalityPopulationServiceTest.java b/...st/java/ubic/gemma/core/analysis/service/GeneMultifunctionalityPopulationServiceTest.java
@@ -139,7 +139,7 @@ public void test() {
         assertThat( ed ).isNotNull();
         assertThat( ed.getLastUpdated() )
                 .isNotNull()
-                .isBetween( DateUtils.round( beforeUpdateDate, Calendar.SECOND ), DateUtils.round( new Date(), Calendar.SECOND ), true, true );
+                .isBetween( beforeUpdateDate, new Date(), true, true );
 
         List<AuditEvent> auditEvents = ed.getAuditTrail().getEvents();
         assertThat( auditEvents ).hasSizeGreaterThanOrEqualTo( 2 );

diff --git a/...t/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseServiceTest.java b/...t/java/ubic/gemma/persistence/service/common/description/ExternalDatabaseServiceTest.java
@@ -75,6 +75,14 @@ public void testUpdateReleaseDetails() throws MalformedURLException {
                         tuple( AuditAction.UPDATE, currentUser ) ); // from AuditAdvice on update()
         assertThat( externalDatabase.getAuditTrail().getEvents().get( 1 ).getNote() )
                 .isEqualTo( "Yep" );
+        // make sure that the last updated date is properly stored
+        Date lastUpdated = externalDatabase.getLastUpdated();
+        assertThat( lastUpdated ).isNotNull();
+        externalDatabase = externalDatabaseService.find( externalDatabase );
+        assertThat( externalDatabase ).isNotNull();
+        assertThat( externalDatabase.getLastUpdated() ).isNotNull();
+        assertThat( externalDatabase.getLastUpdated().getTime() )
+                .isEqualTo( lastUpdated.getTime() );
     }
 
     @Test