Add modification date to study (#25)

Author: dmgaldi

src/main/java/org/veupathdb/service/eda/ss/model/Study.java

@@ -14,7 +14,7 @@ public class Study extends StudyOverview {
   private final Map<String, Entity> _entityIdMap;
 
   public Study(StudyOverview overview, TreeNode<Entity> entityTree, Map<String, Entity> entityIdMap) {
-    super(overview.getStudyId(), overview.getInternalAbbrev(), overview.getStudySourceType());
+    super(overview.getStudyId(), overview.getInternalAbbrev(), overview.getStudySourceType(), overview.getLastModified());
     _entityTree = entityTree;
     _entityIdMap = entityIdMap;
     initEntities(entityTree);

src/main/java/org/veupathdb/service/eda/ss/model/StudyOverview.java

@@ -1,5 +1,7 @@
 package org.veupathdb.service.eda.ss.model;
 
+import java.util.Date;
+
 /* a brief version of the study */
 public class StudyOverview {
 
@@ -11,11 +13,16 @@ public enum StudySourceType {
   private final String id;
   private final String internalAbbrev;
   private final StudySourceType studySourceType;
+  private final Date lastModified;
 
-  public StudyOverview(String id, String internalAbbrev, StudySourceType studySourceType) {
+  public StudyOverview(String id,
+                       String internalAbbrev,
+                       StudySourceType studySourceType,
+                       Date lastModified) {
     this.id = id;
     this.internalAbbrev = internalAbbrev;
     this.studySourceType = studySourceType;
+    this.lastModified = lastModified;
   }
 
   public String getStudyId() {
@@ -29,4 +36,8 @@ public String getInternalAbbrev() {
   public StudySourceType getStudySourceType() {
     return studySourceType;
   }
+
+  public Date getLastModified() {
+    return lastModified;
+  }
 }

src/main/java/org/veupathdb/service/eda/ss/model/db/DB.java

@@ -20,6 +20,7 @@ interface Study {
       interface Columns extends ColumnCollection {
         String STUDY_ID_COL_NAME = "stable_id";
         String STUDY_ABBREV_COL_NAME = "internal_abbrev";
+        String STUDY_DATE_MODIFIED_COL_NAME = "modification_date";
       }
     }
 

src/main/java/org/veupathdb/service/eda/ss/model/db/StudyFactory.java

@@ -8,16 +8,17 @@
 import org.veupathdb.service.eda.ss.model.Study;
 import org.veupathdb.service.eda.ss.model.StudyOverview;
 import org.veupathdb.service.eda.ss.model.StudyOverview.StudySourceType;
-import org.veupathdb.service.eda.ss.model.reducer.BinaryMetadataProvider;
-import org.veupathdb.service.eda.ss.model.variable.binary.BinaryFilesManager;
 
 import javax.sql.DataSource;
+import java.time.Instant;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
 import static org.veupathdb.service.eda.ss.model.db.DB.Tables.Study.Columns.STUDY_ABBREV_COL_NAME;
+import static org.veupathdb.service.eda.ss.model.db.DB.Tables.Study.Columns.STUDY_DATE_MODIFIED_COL_NAME;
 import static org.veupathdb.service.eda.ss.model.db.DB.Tables.Study.Columns.STUDY_ID_COL_NAME;
 
 public class StudyFactory implements StudyProvider {
@@ -40,7 +41,7 @@ public StudyFactory(DataSource dataSource,
   }
 
   private static String getStudyOverviewSql(String appDbSchema) {
-    return "select s." + STUDY_ID_COL_NAME + ", s." + STUDY_ABBREV_COL_NAME +
+    return "select s." + STUDY_ID_COL_NAME + ", s." + STUDY_ABBREV_COL_NAME + ", s." + STUDY_DATE_MODIFIED_COL_NAME +
            " from " + appDbSchema + DB.Tables.Study.NAME + " s ";
   }
 
@@ -52,7 +53,8 @@ public List<StudyOverview> getStudyOverviews() {
       while (rs.next()) {
         String id = rs.getString(1);
         String abbrev = rs.getString(2);
-        StudyOverview study = new StudyOverview(id, abbrev, _sourceType);
+        Date lastModified = rs.getDate(3);
+        StudyOverview study = new StudyOverview(id, abbrev, _sourceType, lastModified);
         studyOverviews.add(study);
       }
       return studyOverviews;

src/main/java/org/veupathdb/service/eda/ss/test/MockModel.java

@@ -7,7 +7,6 @@
 import org.veupathdb.service.eda.ss.model.distribution.DateDistributionConfig;
 import org.veupathdb.service.eda.ss.model.distribution.NumberDistributionConfig;
 import org.veupathdb.service.eda.ss.model.variable.*;
-import org.veupathdb.service.eda.ss.model.variable.binary.EmptyBinaryProperties;
 
 import java.util.*;
 
@@ -42,7 +41,7 @@ public class MockModel {
 
   public MockModel() {
     createTestEntities();
-    StudyOverview overview = new StudyOverview("GEMS", "ds2324", StudyOverview.StudySourceType.CURATED);
+    StudyOverview overview = new StudyOverview("GEMS", "ds2324", StudyOverview.StudySourceType.CURATED, new Date());
     study = new Study(overview, constructEntityTree(), createIdMap());
     constructVariables();
   }

src/main/resources/org/veupathdb/service/eda/ss/stubdb/createDbSchema.sql

@@ -9,6 +9,7 @@ create table Study (
   stable_id varchar(50) not null,
   display_name varchar(30) not null,
   internal_abbrev varchar(30),
+  modification_date date,
   PRIMARY KEY (stable_id)
 );
 alter table Study add unique (display_name);

src/main/resources/org/veupathdb/service/eda/ss/stubdb/insertDbData.sql

@@ -10,7 +10,7 @@
 ------------------------------------------------------------
 
 --(stable_id, display_nme, internal_abbrev)
-insert into study values ('DS-2324', 'GEMS', 'ds2324');
+insert into study values ('DS-2324', 'GEMS', 'ds2324', '2023-01-01');
 
 insert into StudyIdDatasetId values('DS-2324', 'datasetid_2222');
 

src/test/java/org/veupathdb/service/eda/ss/testutil/TestDataProvider.java

@@ -9,6 +9,7 @@
 import org.veupathdb.service.eda.ss.model.variable.*;
 
 import java.util.Collections;
+import java.util.Date;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -72,7 +73,7 @@ public StudyBuilder addEntity(Entity entity, String parentId) {
     }
 
     public Study build() {
-      final StudyOverview studyOverview = new StudyOverview(studyId, internalAbbrev, StudyOverview.StudySourceType.CURATED);
+      final StudyOverview studyOverview = new StudyOverview(studyId, internalAbbrev, StudyOverview.StudySourceType.CURATED, new Date());
       return new Study(studyOverview, rootEntity, entityIdMap);
     }