Add created, created_by columns to artifacts (#305)

* cohort created

* created concept set

* created review study

* last modified, some cohort created_by

* finish cohort created_by

* concept set created_by

* review created_by

* study created_by

* move toApiObject back to controller

* spotbugs

* fix ui tests

* review fixes

* checkstyle

.run/Main.run.xml

@@ -0,0 +1,22 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Main" type="SpringBootApplicationConfigurationType" factoryName="Spring Boot">
+    <module name="tanagra.service.main" />
+    <option name="SPRING_BOOT_MAIN_CLASS" value="bio.terra.tanagra.app.Main" />
+    <option name="WORKING_DIRECTORY" value="file://$PROJECT_DIR$/service" />
+    <option name="ALTERNATIVE_JRE_PATH" />
+    <envs>
+      <env name="TANAGRA_DATABASE_NAME" value="tanagra_db" />
+      <env name="TANAGRA_DB_INITIALIZE_ON_START" value="false" />
+      <env name="TANAGRA_DB_USERNAME" value="dbuser" />
+      <env name="TANAGRA_DB_PASSWORD" value="dbpwd" />
+      <env name="TANAGRA_UNDERLAY_FILES" value="broad/aou_synthetic/expanded/aou_synthetic.json,broad/cms_synpuf/expanded/cms_synpuf.json" />
+      <env name="TANAGRA_FEATURE_ARTIFACT_STORAGE_ENABLED" value="true" />
+      <env name="TANAGRA_AUTH_IAP_GKE_JWT" value="false" />
+      <env name="TANAGRA_AUTH_BEARER_TOKEN" value="true" />
+      <env name="GOOGLE_APPLICATION_CREDENTIALS" value="$PROJECT_DIR$/rendered/tanagra_sa.json" />
+    </envs>
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>

service/src/main/java/bio/terra/tanagra/app/controller/CohortsV2ApiController.java

@@ -70,6 +70,7 @@ public ResponseEntity<ApiCohortV2> createCohort(String studyId, ApiCohortCreateI
             .underlayName(body.getUnderlayName())
             .cohortRevisionGroupId(newCohortRevisionGroupId)
             .version(Cohort.STARTING_VERSION)
+            .createdBy(UserId.currentUser().getEmail())
             .displayName(body.getDisplayName())
             .description(body.getDescription())
             .build();

service/src/main/java/bio/terra/tanagra/app/controller/ConceptSetsV2ApiController.java

@@ -67,6 +67,7 @@ public ResponseEntity<ApiConceptSetV2> createConceptSet(
             .conceptSetId(newConceptSetId)
             .underlayName(body.getUnderlayName())
             .entityName(body.getEntity())
+            .createdBy(UserId.currentUser().getEmail())
             .displayName(body.getDisplayName())
             .description(body.getDescription())
             .build();
@@ -153,15 +154,16 @@ public ResponseEntity<ApiConceptSetV2> updateConceptSet(
     return ResponseEntity.ok(toApiObject(updatedConceptSet));
   }
 
-  /** Convert the internal Concept Set object to an API Concept Set object. */
   private static ApiConceptSetV2 toApiObject(ConceptSet conceptSet) {
     return new ApiConceptSetV2()
         .id(conceptSet.getConceptSetId())
         .underlayName(conceptSet.getUnderlayName())
         .entity(conceptSet.getEntityName())
         .displayName(conceptSet.getDisplayName())
         .description(conceptSet.getDescription())
-        .lastModified(conceptSet.getLastModifiedUTC())
+        .created(conceptSet.getCreated())
+        .createdBy(conceptSet.getCreatedBy())
+        .lastModified(conceptSet.getLastModified())
         .criteria(
             conceptSet.getCriteria() == null
                 ? null

service/src/main/java/bio/terra/tanagra/app/controller/ReviewsV2ApiController.java

@@ -106,6 +106,7 @@ public ResponseEntity<ApiReviewV2> createReview(
             .displayName(body.getDisplayName())
             .description(body.getDescription())
             .size(body.getSize())
+            .createdBy(UserId.currentUser().getEmail())
             .build();
 
     // TODO: Move this to the ReviewService once we can build the EntityFilter from the Cohort on
@@ -309,7 +310,9 @@ private static ApiReviewV2 toApiObject(Review review) {
         .displayName(review.getDisplayName())
         .description(review.getDescription())
         .size(review.getSize())
-        .created(review.getCreatedUTC())
+        .created(review.getCreated())
+        .createdBy(review.getCreatedBy())
+        .lastModified(review.getLastModified())
         .cohort(ToApiConversionUtils.toApiObject(review.getCohort()));
   }
 

service/src/main/java/bio/terra/tanagra/app/controller/StudiesV2ApiController.java

@@ -55,6 +55,7 @@ public ResponseEntity<ApiStudyV2> createStudy(ApiStudyCreateInfoV2 body) {
             .displayName(body.getDisplayName())
             .description(body.getDescription())
             .properties(fromApiObject(body.getProperties()))
+            .createdBy(UserId.currentUser().getEmail())
             .build();
     studyService.createStudy(studyToCreate);
     return ResponseEntity.ok(toApiObject(studyToCreate));
@@ -133,7 +134,10 @@ private static ApiStudyV2 toApiObject(Study study) {
         .id(study.getStudyId())
         .displayName(study.getDisplayName())
         .description(study.getDescription())
-        .properties(apiProperties);
+        .properties(apiProperties)
+        .created(study.getCreated())
+        .createdBy(study.getCreatedBy())
+        .lastModified(study.getLastModified());
   }
 
   private static ImmutableMap<String, String> fromApiObject(

service/src/main/java/bio/terra/tanagra/db/CohortDao.java

@@ -38,7 +38,7 @@ public class CohortDao {
 
   // SQL query and row mapper for reading a cohort.
   private static final String COHORT_SELECT_SQL =
-      "SELECT study_id, cohort_id, underlay_name, cohort_revision_group_id, version, is_most_recent, is_editable, last_modified, display_name, description FROM cohort";
+      "SELECT study_id, cohort_id, underlay_name, cohort_revision_group_id, version, is_most_recent, is_editable, created, created_by, last_modified, display_name, description FROM cohort";
   private static final RowMapper<Cohort.Builder> COHORT_ROW_MAPPER =
       (rs, rowNum) ->
           Cohort.builder()
@@ -49,7 +49,9 @@ public class CohortDao {
               .version(rs.getInt("version"))
               .isMostRecent(rs.getBoolean("is_most_recent"))
               .isEditable(rs.getBoolean("is_editable"))
-              .lastModified(rs.getTimestamp("last_modified"))
+              .createdBy(rs.getString("created_by"))
+              .created(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("created")))
+              .lastModified(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("last_modified")))
               .displayName(rs.getString("display_name"))
               .description(rs.getString("description"));
 
@@ -342,15 +344,17 @@ public boolean updateCohortLatestVersion(
   private void createCohortHelper(Cohort cohort) {
     // Store the cohort. New cohort rows are always the most recent and editable.
     final String cohortSql =
-        "INSERT INTO cohort (study_id, cohort_id, underlay_name, cohort_revision_group_id, version, is_most_recent, is_editable, last_modified, display_name, description) "
-            + "VALUES (:study_id, :cohort_id, :underlay_name, :cohort_revision_group_id, :version, TRUE, TRUE, :last_modified, :display_name, :description)";
+        "INSERT INTO cohort (study_id, cohort_id, underlay_name, cohort_revision_group_id, version, is_most_recent, is_editable, created_by, last_modified, display_name, description) "
+            + "VALUES (:study_id, :cohort_id, :underlay_name, :cohort_revision_group_id, :version, TRUE, TRUE, :created_by, :last_modified, :display_name, :description)";
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("study_id", cohort.getStudyId())
             .addValue("cohort_id", cohort.getCohortId())
             .addValue("underlay_name", cohort.getUnderlayName())
             .addValue("cohort_revision_group_id", cohort.getCohortRevisionGroupId())
             .addValue("version", cohort.getVersion())
+            // Don't need to set created. Liquibase defaultValueComputed handles that.
+            .addValue("created_by", cohort.getCreatedBy())
             .addValue("last_modified", Timestamp.from(Instant.now()))
             .addValue("display_name", cohort.getDisplayName())
             .addValue("description", cohort.getDescription());

service/src/main/java/bio/terra/tanagra/db/ConceptSetDao.java

@@ -35,15 +35,17 @@ public class ConceptSetDao {
 
   // SQL query and row mapper for reading a concept set.
   private static final String CONCEPT_SET_SELECT_SQL =
-      "SELECT study_id, concept_set_id, underlay_name, entity_name, last_modified, display_name, description FROM concept_set";
+      "SELECT study_id, concept_set_id, underlay_name, entity_name, created, created_by, last_modified, display_name, description FROM concept_set";
   private static final RowMapper<ConceptSet.Builder> CONCEPT_SET_ROW_MAPPER =
       (rs, rowNum) ->
           ConceptSet.builder()
               .studyId(rs.getString("study_id"))
               .conceptSetId(rs.getString("concept_set_id"))
               .underlayName(rs.getString("underlay_name"))
               .entityName(rs.getString("entity_name"))
-              .lastModified(rs.getTimestamp("last_modified"))
+              .created(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("created")))
+              .createdBy(rs.getString("created_by"))
+              .lastModified(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("last_modified")))
               .displayName(rs.getString("display_name"))
               .description(rs.getString("description"));
 
@@ -170,14 +172,16 @@ private void populateCriteria(List<ConceptSet.Builder> conceptSets) {
   public void createConceptSet(ConceptSet conceptSet) {
     // Store the concept set.
     final String sql =
-        "INSERT INTO concept_set (study_id, concept_set_id, underlay_name, entity_name, last_modified, display_name, description) "
-            + "VALUES (:study_id, :concept_set_id, :underlay_name, :entity_name, :last_modified, :display_name, :description)";
+        "INSERT INTO concept_set (study_id, concept_set_id, underlay_name, entity_name, created_by, last_modified, display_name, description) "
+            + "VALUES (:study_id, :concept_set_id, :underlay_name, :entity_name, :created_by, :last_modified, :display_name, :description)";
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("study_id", conceptSet.getStudyId())
             .addValue("concept_set_id", conceptSet.getConceptSetId())
             .addValue("underlay_name", conceptSet.getUnderlayName())
             .addValue("entity_name", conceptSet.getEntityName())
+            // Don't need to set created. Liquibase defaultValueComputed handles that.
+            .addValue("created_by", conceptSet.getCreatedBy())
             .addValue("last_modified", Timestamp.from(Instant.now()))
             .addValue("display_name", conceptSet.getDisplayName())
             .addValue("description", conceptSet.getDescription());

service/src/main/java/bio/terra/tanagra/db/DbUtils.java

@@ -1,6 +1,9 @@
 package bio.terra.tanagra.db;
 
 import bio.terra.common.exception.MissingRequiredFieldException;
+import java.sql.Timestamp;
+import java.time.OffsetDateTime;
+import java.time.ZoneId;
 import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Set;
@@ -39,4 +42,8 @@ public static String setColumnsClause(MapSqlParameterSource columnParams, String
 
     return sb.toString();
   }
+
+  public static OffsetDateTime timestampToOffsetDateTime(Timestamp timestamp) {
+    return OffsetDateTime.ofInstant(timestamp.toInstant(), ZoneId.of("UTC"));
+  }
 }

service/src/main/java/bio/terra/tanagra/db/ReviewDao.java

@@ -10,8 +10,6 @@
 import bio.terra.tanagra.query.RowResult;
 import bio.terra.tanagra.service.artifact.Cohort;
 import bio.terra.tanagra.service.artifact.Review;
-import java.sql.Timestamp;
-import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
@@ -37,7 +35,7 @@ public class ReviewDao {
 
   // SQL query and row mapper for reading a review.
   private static final String REVIEW_SELECT_SQL =
-      "SELECT r.cohort_id, r.review_id, r.display_name, r.description, r.size, r.created FROM review AS r "
+      "SELECT r.cohort_id, r.review_id, r.display_name, r.description, r.size, r.created, r.created_by, r.last_modified FROM review AS r "
           + "JOIN cohort AS c ON c.cohort_id = r.cohort_id";
   private static final RowMapper<Review.Builder> REVIEW_ROW_MAPPER =
       (rs, rowNum) ->
@@ -47,7 +45,9 @@ public class ReviewDao {
               .displayName(rs.getString("display_name"))
               .description(rs.getString("description"))
               .size(rs.getInt("size"))
-              .created(rs.getTimestamp("created"));
+              .created(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("created")))
+              .createdBy(rs.getString("created_by"))
+              .lastModified(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("last_modified")));
 
   // SQL query and row mapper for reading a review instance.
   private static final String REVIEW_INSTANCE_SELECT_SQL =
@@ -79,16 +79,17 @@ public void createReview(
     cohortDao.freezeCohortLatestVersionOrThrow(studyId, cohort.getCohortRevisionGroupId());
 
     final String sql =
-        "INSERT INTO review (cohort_id, review_id, display_name, description, size, created) "
-            + "VALUES (:cohort_id, :review_id, :display_name, :description, :size, :created)";
+        "INSERT INTO review (cohort_id, review_id, display_name, description, size, created, created_by) "
+            + "VALUES (:cohort_id, :review_id, :display_name, :description, :size, :created, :created_by)";
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("cohort_id", cohort.getCohortId())
             .addValue("review_id", review.getReviewId())
             .addValue("display_name", review.getDisplayName())
             .addValue("description", review.getDescription())
             .addValue("size", review.getSize())
-            .addValue("created", Timestamp.from(Instant.now()));
+            // Don't need to set created. Liquibase defaultValueComputed handles that.
+            .addValue("created_by", review.getCreatedBy());
     try {
       jdbcTemplate.update(sql, params);
       LOGGER.info("Inserted record for review {}", review.getReviewId());

service/src/main/java/bio/terra/tanagra/db/StudyDao.java

@@ -30,7 +30,7 @@ public class StudyDao {
 
   // SQL query and row mapper for reading a study.
   private static final String STUDY_SELECT_SQL =
-      "SELECT study_id, display_name, description, properties FROM study";
+      "SELECT study_id, display_name, description, properties, created, created_by, last_modified FROM study";
   private static final RowMapper<Study> STUDY_ROW_MAPPER =
       (rs, rowNum) ->
           Study.builder()
@@ -41,6 +41,9 @@ public class StudyDao {
                   Optional.ofNullable(rs.getString("properties"))
                       .map(DbSerDes::jsonToProperties)
                       .orElse(null))
+              .created(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("created")))
+              .createdBy(rs.getString("created_by"))
+              .lastModified(DbUtils.timestampToOffsetDateTime(rs.getTimestamp("last_modified")))
               .build();
 
   private final NamedParameterJdbcTemplate jdbcTemplate;
@@ -58,15 +61,17 @@ public StudyDao(NamedParameterJdbcTemplate jdbcTemplate) {
   @WriteTransaction
   public void createStudy(Study study) {
     final String sql =
-        "INSERT INTO study (study_id, display_name, description, properties) "
-            + "VALUES (:study_id, :display_name, :description, CAST(:properties AS jsonb))";
+        "INSERT INTO study (study_id, display_name, description, properties, created_by) "
+            + "VALUES (:study_id, :display_name, :description, CAST(:properties AS jsonb), :created_by)";
 
     MapSqlParameterSource params =
         new MapSqlParameterSource()
             .addValue("study_id", study.getStudyId())
             .addValue("display_name", study.getDisplayName())
             .addValue("description", study.getDescription())
-            .addValue("properties", DbSerDes.propertiesToJson(study.getProperties()));
+            .addValue("properties", DbSerDes.propertiesToJson(study.getProperties()))
+            // Don't need to set created. Liquibase defaultValueComputed handles that.
+            .addValue("created_by", study.getCreatedBy());
     try {
       jdbcTemplate.update(sql, params);
       LOGGER.info("Inserted record for study {}", study.getStudyId());

service/src/main/java/bio/terra/tanagra/service/artifact/Cohort.java

@@ -1,9 +1,7 @@
 package bio.terra.tanagra.service.artifact;
 
 import bio.terra.tanagra.exception.SystemException;
-import java.sql.Timestamp;
 import java.time.OffsetDateTime;
-import java.time.ZoneOffset;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -19,7 +17,9 @@ public class Cohort {
   private final int version;
   private final boolean isMostRecent;
   private final boolean isEditable;
-  private final Timestamp lastModified;
+  private final OffsetDateTime created;
+  private final String createdBy;
+  private final OffsetDateTime lastModified;
   private final @Nullable String displayName;
   private final @Nullable String description;
   private final List<CriteriaGroup> criteriaGroups;
@@ -32,6 +32,8 @@ private Cohort(Builder builder) {
     this.version = builder.version;
     this.isMostRecent = builder.isMostRecent;
     this.isEditable = builder.isEditable;
+    this.created = builder.created;
+    this.createdBy = builder.createdBy;
     this.lastModified = builder.lastModified;
     this.displayName = builder.displayName;
     this.description = builder.description;
@@ -51,6 +53,8 @@ public Builder toBuilder() {
         .version(version)
         .isMostRecent(isMostRecent)
         .isEditable(isEditable)
+        .created(created)
+        .createdBy(createdBy)
         .lastModified(lastModified)
         .displayName(displayName)
         .description(description)
@@ -98,9 +102,19 @@ public boolean isEditable() {
     return isEditable;
   }
 
+  /** Timestamp of when this cohort was created. */
+  public OffsetDateTime getCreated() {
+    return created;
+  }
+
+  /** Email of user who created this cohort. */
+  public String getCreatedBy() {
+    return createdBy;
+  }
+
   /** Timestamp of when this cohort was last modified. */
-  public OffsetDateTime getLastModifiedUTC() {
-    return lastModified.toInstant().atOffset(ZoneOffset.UTC);
+  public OffsetDateTime getLastModified() {
+    return lastModified;
   }
 
   /** Optional display name for the cohort. */
@@ -130,7 +144,9 @@ public static class Builder {
     private int version;
     private boolean isMostRecent;
     private boolean isEditable;
-    private Timestamp lastModified;
+    private OffsetDateTime created;
+    private String createdBy;
+    private OffsetDateTime lastModified;
     private @Nullable String displayName;
     private @Nullable String description;
     private List<CriteriaGroup> criteriaGroups = new ArrayList<>();
@@ -170,8 +186,18 @@ public Builder isEditable(boolean isEditable) {
       return this;
     }
 
-    public Builder lastModified(Timestamp lastModified) {
-      this.lastModified = (Timestamp) lastModified.clone();
+    public Builder created(OffsetDateTime created) {
+      this.created = created;
+      return this;
+    }
+
+    public Builder createdBy(String createdBy) {
+      this.createdBy = createdBy;
+      return this;
+    }
+
+    public Builder lastModified(OffsetDateTime lastModified) {
+      this.lastModified = lastModified;
       return this;
     }