[BAD] - Temporary hack for BDC. Evil query for Dashboard

Author: Luke Sikina

db/schema.sql

@@ -24,9 +24,9 @@ CREATE TABLE dict.consent (
     DATASET_ID INT NOT NULL,
     CONSENT_CODE VARCHAR(512) NOT NULL,
     DESCRIPTION VARCHAR(512) NOT NULL,
-    PARTICIPANT_COUNT INT NOT NULL,
-    VARIABLE_COUNT INT NOT NULL,
-    SAMPLE_COUNT INT NOT NULL,
+    PARTICIPANT_COUNT INT NOT NULL DEFAULT 12,
+    VARIABLE_COUNT INT NOT NULL DEFAULT 99,
+    SAMPLE_COUNT INT NOT NULL DEFAULT 14,
     AUTHZ VARCHAR(512) NOT NULL,
     PRIMARY KEY (CONSENT_ID),
     UNIQUE (CONSENT_CODE, DATASET_ID)

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

@@ -2,13 +2,15 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.dao.DataAccessException;
+import org.springframework.jdbc.core.ResultSetExtractor;
 import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
 import org.springframework.stereotype.Repository;
 
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.*;
 import java.util.function.Predicate;
 
 @Repository
@@ -31,6 +33,49 @@ public DashboardRepository(
         this.extractor = extractor;
     }
 
+    private static final class ListMapExtractor implements ResultSetExtractor<List<Map<String,String>>> {
+
+        @Override
+        public List<Map<String, String>> extractData(ResultSet rs) throws SQLException, DataAccessException {
+            List<Map<String, String>> rows = new ArrayList<>();
+            while (rs.next()) {
+                Map<String, String> row = new HashMap<>();
+                for (int i = 0; i < rs.getMetaData().getColumnCount(); i++) {
+                    String key = rs.getMetaData().getColumnName(i + 1);
+                    row.put(key, rs.getString(key));
+                }
+                rows.add(row);
+            }
+            return rows;
+        }
+    }
+
+    public List<Map<String, String>> getHackyBDCRows() {
+        String sql = """
+                SELECT
+                    dataset.abbreviation AS abbreviation,
+                    dataset.full_name AS name,
+                    consent.variable_count AS clinvars,
+                    consent.participant_count AS participants,
+                    consent.sample_count AS samples,
+                    CASE
+                        WHEN consent.consent_code <> NULL THEN concat(study_accession_meta.value, '.', consent.consent_code)
+                        ELSE study_accession_meta.value
+                        END
+                    AS accession,
+                    study_focus_meta.value AS study_focus,
+                    additional_info_meta.value AS additional_info_link
+                FROM
+                    dataset
+                    LEFT JOIN consent ON consent.dataset_id = dataset.dataset_id
+                    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 = 'additional_info_link'
+                ORDER BY name ASC, abbreviation ASC
+            """;
+        return template.query(sql, new ListMapExtractor());
+    }
+
     public List<Map<String, String>> getRows() {
         String sql = """
             SELECT

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

@@ -1,5 +1,7 @@
 package edu.harvard.dbmi.avillach.dictionary.dashboard;
 
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
 import java.util.List;
@@ -10,17 +12,42 @@ public class DashboardService {
 
     private final DashboardRepository repository;
     private final List<DashboardColumn> columns;
+    private final boolean bdcHack;
 
-    public DashboardService(DashboardRepository repository, List<DashboardColumn> columns) {
+    @Autowired
+    public DashboardService(
+        DashboardRepository repository,
+        List<DashboardColumn> columns,
+        @Value("${dashboard.enable.bdc_hack}") boolean bdcHack
+    ) {
         this.repository = repository;
         this.columns = columns;
+        this.bdcHack = bdcHack;
     }
 
     public Dashboard getDashboard() {
+        if (bdcHack) {
+            List<Map<String, String>> rows = repository.getHackyBDCRows();
+            return new Dashboard(
+                hackyBDCColumns,
+                rows
+            );
+        }
         List<Map<String, String>> rows = repository.getRows();
         return new Dashboard(
             columns,
             rows
         );
     }
+
+    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")
+    );
 }

src/main/resources/application.properties

@@ -8,4 +8,5 @@ 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.extra_details=true
+dashboard.enable.bdc_hack=true

src/test/java/edu/harvard/dbmi/avillach/dictionary/dashboard/DashboardRepositoryTest.java

@@ -53,4 +53,10 @@ void shouldGetDashboardRows() {
         );
         Assertions.assertEquals(expected, actual);
     }
+
+    @Test
+    void shouldDoBDCHack() {
+        List<Map<String, String>> rows = subject.getHackyBDCRows();
+        Assertions.assertNotNull(rows);
+    }
 }

src/test/resources/application.properties

@@ -8,4 +8,5 @@ dashboard.columns={abbreviation:'Abbreviation',melast:'This one goes last',name:
 dashboard.column-order=abbreviation,name,clinvars
 dashboard.nonmeta-columns=abbreviation,name
 
-dashboard.enable.extra_details=true
+dashboard.enable.extra_details=true
+dashboard.enable.bdc_hack=false

src/test/resources/seed.sql

@@ -103,7 +103,10 @@ CREATE TABLE public.consent (
     dataset_id integer NOT NULL,
     consent_code character varying(512) NOT NULL,
     description character varying(512) NOT NULL,
-    authz character varying(512) NOT NULL
+    authz character varying(512) NOT NULL,
+    PARTICIPANT_COUNT INT NOT NULL DEFAULT 12,
+    VARIABLE_COUNT INT NOT NULL DEFAULT 99,
+    SAMPLE_COUNT INT NOT NULL DEFAULT 14
 );
 
 --