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Add Dashboard Drawer feature
- Added `DashboardDrawerController` for new endpoints - Implemented `DashboardDrawerService` for business logic - Created `DashboardDrawerRepository` for database access - Defined new configuration properties - Included new record classes: `DashboardDrawer`, `DashboardDrawerList` - Updated SQL queries in `DashboardRepository.java` to include `dataset_id`
1 parent cd06343 commit 194f350

8 files changed

+222
-1
lines changed

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepository.java

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@@ -52,6 +52,7 @@ public List<Map<String, String>> getHackyBDCRows() {
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String sql =
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"""
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SELECT
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dataset.dataset_id as dataset_id,
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dataset.abbreviation AS abbreviation,
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dataset.full_name AS name,
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CASE

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawer.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import java.util.List;
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public record DashboardDrawer(
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int datasetId,
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String studyFullname,
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String studyAbbreviation,
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List<String> consentGroups,
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String studySummary,
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List<String> studyFocus,
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String studyDesign,
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String sponsor
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) {
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}

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerController.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.http.ResponseEntity;
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import org.springframework.stereotype.Controller;
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import org.springframework.web.bind.annotation.*;
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@Controller
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@RequestMapping("/dashboard-drawer")
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public class DashboardDrawerController {
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@Autowired
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private DashboardDrawerService dashboardDrawerService;
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@GetMapping
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public ResponseEntity<DashboardDrawerList> findAll() {
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return ResponseEntity.ok(dashboardDrawerService.findAll());
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}
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@GetMapping("/{id}")
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public ResponseEntity<DashboardDrawerList> findByDatasetId(@PathVariable Integer id) {
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return ResponseEntity.ok(dashboardDrawerService.findByDatasetId(id));
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}
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}

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerList.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import java.util.List;
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public record DashboardDrawerList(List<DashboardDrawer> dashboardDrawerList) {
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}

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRepository.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
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import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
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import org.springframework.stereotype.Repository;
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import java.util.*;
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@Repository
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public class DashboardDrawerRepository {
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private final NamedParameterJdbcTemplate template;
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private static final Logger log = LoggerFactory.getLogger(DashboardDrawerRepository.class);
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@Autowired
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public DashboardDrawerRepository(NamedParameterJdbcTemplate template) {
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this.template = template;
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}
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public List<DashboardDrawer> getDashboardDrawerRows() {
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String materializedViewSql = """
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select * from dictionary_db.dict.dataset_meta_materialized_view dmmv;
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""";
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String fallbackSql = """
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SELECT d.dataset_id,
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MAX(d.full_name) study_fullname,
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MAX(d.abbreviation) study_abbreviation,
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ARRAY_AGG(DISTINCT c.description) consent_groups,
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MAX(d.description) study_summary,
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ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus,
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MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design,
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MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor
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FROM dataset d
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JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id
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JOIN consent c ON d.dataset_id = c.dataset_id
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GROUP BY d.dataset_id
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""";
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try {
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return template.query(materializedViewSql, new DashboardDrawerRowMapper());
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} catch (Exception e) {
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log.debug("Materialized view not available, using fallback query. Error: {}", e.getMessage());
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return template.query (fallbackSql, new DashboardDrawerRowMapper());
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}
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}
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public List<DashboardDrawer> getDashboardDrawerRows(Integer datasetId) {
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String materializedViewSql = """
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select * from dictionary_db.dict.dataset_meta_materialized_view dmmv where dmmv.dataset_id = :datasetId;
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""";
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String fallbackSql = """
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SELECT d.dataset_id dataset_id,
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MAX(d.full_name) study_fullname,
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MAX(d.abbreviation) study_abbreviation,
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ARRAY_AGG(DISTINCT c.description) consent_groups,
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MAX(d.description) study_summary,
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ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus,
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MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design,
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MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor
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FROM dataset d
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JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id
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JOIN consent c ON d.dataset_id = c.dataset_id
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where d.dataset_id = :datasetId
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GROUP BY d.dataset_id
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""";
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MapSqlParameterSource params = new MapSqlParameterSource();
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params.addValue("datasetId", datasetId);
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try {
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return template.query(materializedViewSql, params, new DashboardDrawerRowMapper());
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} catch (Exception e) {
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log.debug("Materialized view not available, using fallback query. Error: {}", e.getMessage());
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return template.query(fallbackSql, params, new DashboardDrawerRowMapper());
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}
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}
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}

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerRowMapper.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import org.springframework.jdbc.core.RowMapper;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Array; // For handling SQL Array
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import java.util.Arrays;
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import java.util.List;
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public class DashboardDrawerRowMapper implements RowMapper<DashboardDrawer> {
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@Override
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public DashboardDrawer mapRow(ResultSet rs, int rowNum) throws SQLException {
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return new DashboardDrawer(
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rs.getInt("dataset_id"),
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rs.getString("study_fullname"),
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rs.getString("study_abbreviation"),
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convertSqlArrayToList(rs.getArray("consent_groups")),
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rs.getString("study_summary"),
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convertSqlArrayToList(rs.getArray("study_focus")),
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rs.getString("study_design"),
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rs.getString("sponsor")
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);
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}
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private List<String> convertSqlArrayToList(Array sqlArray) throws SQLException {
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if (sqlArray == null ) {
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return List.of();
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} else {
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Object[] arrayContents = (Object[]) sqlArray.getArray();
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// Check if the array contains a single empty value
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if (arrayContents.length == 1 && "".equals(arrayContents[0])) {
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return List.of();
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} else {
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return Arrays.asList((String[]) sqlArray.getArray());
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}
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}
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}
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}

‎src/main/java/edu/harvard/dbmi/avillach/dictionary/dashboarddrawer/DashboardDrawerService.java

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package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.stereotype.Service;
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import java.util.ArrayList;
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import java.util.List;
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@Service
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public class DashboardDrawerService {
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private final DashboardDrawerRepository repository;
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private final String dashboardLayout;
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@Autowired
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public DashboardDrawerService(DashboardDrawerRepository repository, @Value("${dashboard.layout.type}") String dashboardLayout) {
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this.repository = repository;
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this.dashboardLayout = dashboardLayout;
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}
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/**
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* Retrieves the Dashboard Drawer for all datasets.
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*
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* @return a Dashboard instance with drawer-specific columns and rows.
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*/
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public DashboardDrawerList findAll() {
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if (dashboardLayout.equalsIgnoreCase("bdc")) {
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List<DashboardDrawer> records = repository.getDashboardDrawerRows();
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return new DashboardDrawerList(records);
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}
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return new DashboardDrawerList(new ArrayList<>());
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}
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/**
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* Retrieves the Dashboard Drawer for a specific dataset.
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*
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* @param datasetId the ID of the dataset to fetch.
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* @return a Dashboard instance with drawer-specific columns and rows.
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*/
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public DashboardDrawerList findByDatasetId(Integer datasetId) {
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if (dashboardLayout.equalsIgnoreCase("bdc")) {
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List<DashboardDrawer> records = repository.getDashboardDrawerRows(datasetId);
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return new DashboardDrawerList(records);
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}
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return new DashboardDrawerList(new ArrayList<>());
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}
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}

‎src/main/resources/application-bdc.properties

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@@ -6,5 +6,8 @@ spring.datasource.username=${DATASOURCE_USERNAME}
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server.port=80
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dashboard.enable.extra_details=true
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dashboard.enable.bdc_hack=true
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dashboard.layout.type=bdc
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filtering.unfilterable_concepts=stigmatized
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filtering.unfilterable_concepts=stigmatized

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