[ALS-7694] Add DashboardDrawer feature with controller, service, and …

…repository (#55)

* Add Dashboard Drawer feature

- Introduce DashboardDrawerController for drawer-related endpoints
- Implement DashboardDrawerService to handle drawer logic
- Create DashboardDrawerRepository for database interactions
- Define DashboardDrawer and DashboardDrawerList records
- Add DashboardDrawerRowMapper for result set mapping
- Update DashboardRepository SQL to include dataset_id
- Modify application properties to include dashboard layout configuration

* Update application-bdc.properties with dashboard and filtering configs

- Added `dashboard.enable.bdc_hack` property
- Added `dashboard.layout.type` property
- Moved `filtering.unfilterable_concepts` property
- Ensured newline at end of file

* Add 'program_name' column to Dashboard repository

- Updated SQL query to include 'program_name' field.
- Joined 'dataset_meta' table for 'program_name' metadata.
- Added 'program_name' to the column list in DashboardService.

* Refactor service and controller to handle Optional returns

- Refactor `DashboardDrawerService` methods to return `Optional`
- Update controller methods to handle `Optional` results with appropriate HTTP responses
- Modify repository methods to return `Optional` for single item queries
- Ensure consistency and error handling improvements across the service and controller layers

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

@@ -52,6 +52,7 @@ public List<Map<String, String>> getHackyBDCRows() {
         String sql =
             """
                     SELECT
+                        dataset.dataset_id as dataset_id,
                         dataset.abbreviation AS abbreviation,
                         dataset.full_name AS name,
                         CASE
@@ -70,10 +71,11 @@ public List<Map<String, String>> getHackyBDCRows() {
                             END
                             AS samples,
                         CASE
-                                WHEN (consent.consent_code IS NOT NULL AND consent.consent_code != '') THEN concat(study_accession_meta.value, '.', consent.consent_code)
+                            WHEN (consent.consent_code IS NOT NULL AND consent.consent_code != '') THEN concat(study_accession_meta.value, '.', consent.consent_code)
                             ELSE study_accession_meta.value
                             END
                             AS accession,
+                        program_name.value as program_name,
                         study_focus_meta.value AS study_focus,
                         additional_info_meta.value AS additional_info_link
                     FROM
@@ -82,6 +84,7 @@ public List<Map<String, String>> getHackyBDCRows() {
                         LEFT JOIN dataset_meta AS study_focus_meta ON study_focus_meta.dataset_id = dataset.dataset_id AND study_focus_meta.KEY = 'study_focus'
                         LEFT JOIN dataset_meta AS study_accession_meta ON study_accession_meta.dataset_id = dataset.dataset_id AND study_accession_meta.KEY = 'study_accession'
                         LEFT JOIN dataset_meta AS additional_info_meta ON additional_info_meta.dataset_id = dataset.dataset_id AND additional_info_meta.KEY = 'study_link'
+                        LEFT JOIN dataset_meta AS program_name ON program_name.dataset_id = dataset.dataset_id AND program_name.KEY = 'program_name'
                         WHERE dataset.dataset_id NOT IN (select dataset_id from dataset_meta where KEY = 'show_dashboad' and VALUE = 'false')
                     ORDER BY name ASC, abbreviation ASC
                 """;

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

@@ -34,8 +34,9 @@ public Dashboard getDashboard() {
 
     private static final List<DashboardColumn> hackyBDCColumns = List.of(
         new DashboardColumn("abbreviation", "Abbreviation"), new DashboardColumn("name", "Name"),
-        new DashboardColumn("study_focus", "Study Focus"), new DashboardColumn("clinvars", "Clinical Variables"),
-        new DashboardColumn("participants", "Participants"), new DashboardColumn("samples", "Samples Sequenced"),
-        new DashboardColumn("accession", "Accession"), new DashboardColumn("additional_info_link", "Study Link")
+        new DashboardColumn("study_focus", "Study Focus"), new DashboardColumn("program_name", "Program"),
+        new DashboardColumn("participants", "Participants"), new DashboardColumn("clinvars", "Clinical Variables"),
+        new DashboardColumn("samples", "Samples Sequenced"), new DashboardColumn("accession", "Accession"),
+        new DashboardColumn("additional_info_link", "Study Link")
     );
 }

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

@@ -0,0 +1,9 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import java.util.List;
+
+public record DashboardDrawer(
+    int datasetId, String studyFullname, String studyAbbreviation, List<String> consentGroups, String studySummary, List<String> studyFocus,
+    String studyDesign, String sponsor
+) {
+}

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

@@ -0,0 +1,24 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.*;
+
+@Controller
+@RequestMapping("/dashboard-drawer")
+public class DashboardDrawerController {
+
+    @Autowired
+    private DashboardDrawerService dashboardDrawerService;
+
+    @GetMapping
+    public ResponseEntity<DashboardDrawerList> findAll() {
+        return dashboardDrawerService.findAll().map(ResponseEntity::ok).orElseGet(() -> ResponseEntity.notFound().build());
+    }
+
+    @GetMapping("/{id}")
+    public ResponseEntity<DashboardDrawer> findByDatasetId(@PathVariable Integer id) {
+        return dashboardDrawerService.findByDatasetId(id).map(ResponseEntity::ok).orElseGet(() -> ResponseEntity.notFound().build());
+    }
+}

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

@@ -0,0 +1,6 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import java.util.List;
+
+public record DashboardDrawerList(List<DashboardDrawer> dashboardDrawerList) {
+}

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

@@ -0,0 +1,82 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
+import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
+import org.springframework.stereotype.Repository;
+
+import java.util.*;
+
+@Repository
+public class DashboardDrawerRepository {
+
+    private final NamedParameterJdbcTemplate template;
+
+    private static final Logger log = LoggerFactory.getLogger(DashboardDrawerRepository.class);
+
+    @Autowired
+    public DashboardDrawerRepository(NamedParameterJdbcTemplate template) {
+        this.template = template;
+    }
+
+    public List<DashboardDrawer> getDashboardDrawerRows() {
+        String materializedViewSql = """
+            select * from dictionary_db.dict.dataset_meta_materialized_view dmmv;
+            """;
+
+        String fallbackSql = """
+            SELECT d.dataset_id,
+                MAX(d.full_name) study_fullname,
+                MAX(d.abbreviation) study_abbreviation,
+                ARRAY_AGG(DISTINCT c.description) consent_groups,
+                MAX(d.description) study_summary,
+                ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus,
+                MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design,
+                MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor
+            FROM dataset d
+            JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id
+            JOIN consent c ON d.dataset_id = c.dataset_id
+            GROUP BY d.dataset_id
+            """;
+
+        try {
+            return template.query(materializedViewSql, new DashboardDrawerRowMapper());
+        } catch (Exception e) {
+            log.debug("Materialized view not available, using fallback query. Error: {}", e.getMessage());
+            return template.query(fallbackSql, new DashboardDrawerRowMapper());
+        }
+    }
+
+    public Optional<DashboardDrawer> getDashboardDrawerRows(Integer datasetId) {
+        String materializedViewSql = """
+            select * from dictionary_db.dict.dataset_meta_materialized_view dmmv where dmmv.dataset_id = :datasetId;
+            """;
+
+        String fallbackSql = """
+            SELECT d.dataset_id dataset_id,
+                MAX(d.full_name) study_fullname,
+                MAX(d.abbreviation) study_abbreviation,
+                ARRAY_AGG(DISTINCT c.description) consent_groups,
+                MAX(d.description) study_summary,
+                ARRAY_AGG(DISTINCT dm.value) FILTER (where dm.key IN ('study_focus')) study_focus,
+                MAX(DISTINCT dm.value) FILTER (where dm.key IN ('study_design')) study_design,
+                MAX(DISTINCT dm.value) FILTER (where dm.key IN ('sponsor')) sponsor
+            FROM dataset d
+            JOIN dataset_meta dm ON d.dataset_id = dm.dataset_id
+            JOIN consent c ON d.dataset_id = c.dataset_id
+            where d.dataset_id = :datasetId
+            GROUP BY d.dataset_id
+            """;
+        MapSqlParameterSource params = new MapSqlParameterSource();
+        params.addValue("datasetId", datasetId);
+
+        try {
+            return template.query(materializedViewSql, params, new DashboardDrawerRowMapper()).stream().findFirst();
+        } catch (Exception e) {
+            log.debug("Materialized view not available, using fallback query. Error: {}", e.getMessage());
+            return template.query(fallbackSql, params, new DashboardDrawerRowMapper()).stream().findFirst();
+        }
+    }
+}

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

@@ -0,0 +1,35 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import org.springframework.jdbc.core.RowMapper;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Array; // For handling SQL Array
+import java.util.Arrays;
+import java.util.List;
+
+public class DashboardDrawerRowMapper implements RowMapper<DashboardDrawer> {
+
+    @Override
+    public DashboardDrawer mapRow(ResultSet rs, int rowNum) throws SQLException {
+        return new DashboardDrawer(
+            rs.getInt("dataset_id"), rs.getString("study_fullname"), rs.getString("study_abbreviation"),
+            convertSqlArrayToList(rs.getArray("consent_groups")), rs.getString("study_summary"),
+            convertSqlArrayToList(rs.getArray("study_focus")), rs.getString("study_design"), rs.getString("sponsor")
+        );
+    }
+
+    private List<String> convertSqlArrayToList(Array sqlArray) throws SQLException {
+        if (sqlArray == null) {
+            return List.of();
+        } else {
+            Object[] arrayContents = (Object[]) sqlArray.getArray();
+            // Check if the array contains a single empty value
+            if (arrayContents.length == 1 && "".equals(arrayContents[0])) {
+                return List.of();
+            } else {
+                return Arrays.asList((String[]) sqlArray.getArray());
+            }
+        }
+    }
+}

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

@@ -0,0 +1,50 @@
+package edu.harvard.dbmi.avillach.dictionary.dashboarddrawer;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Service;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class DashboardDrawerService {
+
+    private final DashboardDrawerRepository repository;
+    private final String dashboardLayout;
+
+    @Autowired
+    public DashboardDrawerService(DashboardDrawerRepository repository, @Value("${dashboard.layout.type}") String dashboardLayout) {
+        this.repository = repository;
+        this.dashboardLayout = dashboardLayout;
+    }
+
+    /**
+     * Retrieves the Dashboard Drawer for all datasets.
+     *
+     * @return All Dashboard Instances and their metadata.
+     */
+    public Optional<DashboardDrawerList> findAll() {
+        if (dashboardLayout.equalsIgnoreCase("bdc")) {
+            List<DashboardDrawer> records = repository.getDashboardDrawerRows();
+            return Optional.of(new DashboardDrawerList(records));
+        }
+
+        return Optional.of(new DashboardDrawerList(new ArrayList<>()));
+    }
+
+    /**
+     * Retrieves the Dashboard Drawer for a specific dataset.
+     *
+     *
+     * @param datasetId the ID of the dataset to fetch.
+     * @return a single Dashboard instance with drawer-specific metadata.
+     */
+    public Optional<DashboardDrawer> findByDatasetId(Integer datasetId) {
+        if ("bdc".equalsIgnoreCase(dashboardLayout)) {
+            return repository.getDashboardDrawerRows(datasetId);
+        }
+        return Optional.empty();
+    }
+}

src/main/resources/application-bdc.properties

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

src/main/resources/application.properties

@@ -3,12 +3,14 @@ spring.datasource.url=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB}?cur
 spring.datasource.username=${POSTGRES_USER}
 spring.datasource.password=${POSTGRES_PASSWORD}
 spring.datasource.driver-class-name=org.postgresql.Driver
+
 server.port=80
 
 dashboard.columns={abbreviation:'Abbreviation',name:'Name',clinvars:'Clinical Variables'}
 dashboard.column-order=abbreviation,name,clinvars
 dashboard.nonmeta-columns=abbreviation,name
 dashboard.enable.extra_details=true
-dashboard.enable.bdc_hack=true
+dashboard.enable.bdc_hack=false
+dashboard.layout.type=default
 
 filtering.unfilterable_concepts=stigmatized

src/test/resources/application.properties

@@ -7,8 +7,8 @@ spring.datasource.driver-class-name=org.postgresql.Driver
 dashboard.columns={abbreviation:'Abbreviation',melast:'This one goes last',name:'Name',clinvars:'Clinical Variables',participants:'Participants'}
 dashboard.column-order=abbreviation,name,clinvars
 dashboard.nonmeta-columns=abbreviation,name
-
 dashboard.enable.extra_details=true
 dashboard.enable.bdc_hack=false
+dashboard.layout.type=default
 
 filtering.unfilterable_concepts=stigmatized