Add REST endpoint, which generates DDL for Result schema (#285)

pom.xml

@@ -254,7 +254,7 @@
       <dependency>
         <groupId>com.amazon.redshift</groupId>
         <artifactId>redshift-jdbc4-no-awssdk</artifactId>
-        <version>1.2.8.1005</version>
+        <version>1.2.10.1009</version>
       </dependency>
     </dependencies>
   </dependencyManagement>

src/main/java/org/ohdsi/webapi/service/AbstractDaoService.java

@@ -23,6 +23,9 @@
 import org.springframework.jdbc.datasource.DriverManagerDataSource;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import java.sql.Connection;
+import java.util.Properties;
+
 /**
  *
  */
@@ -112,6 +115,7 @@ public JdbcTemplate getJdbcTemplate() {
   }
 
   public JdbcTemplate getSourceJdbcTemplate(Source source) {
+
     DriverManagerDataSource dataSource = new DriverManagerDataSource(source.getSourceConnection());
     JdbcTemplate template = new JdbcTemplate(dataSource);
     return template;

src/main/java/org/ohdsi/webapi/service/DDLService.java

@@ -0,0 +1,80 @@
+/*
+ *
+ * Copyright 2017 Observational Health Data Sciences and Informatics
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Authors: Maria Pozhidaeva
+ *
+ */
+package org.ohdsi.webapi.service;
+
+import static org.ohdsi.webapi.service.SqlRenderService.translateSQL;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import javax.ws.rs.DefaultValue;
+import javax.ws.rs.GET;
+import javax.ws.rs.Path;
+import javax.ws.rs.Produces;
+import javax.ws.rs.QueryParam;
+import org.ohdsi.circe.helper.ResourceHelper;
+import org.ohdsi.webapi.sqlrender.SourceStatement;
+import org.ohdsi.webapi.sqlrender.TranslatedStatement;
+import org.springframework.stereotype.Component;
+
+@Path("/ddl/")
+@Component
+public class DDLService {
+
+    private static final Collection<String> COMMON_COHORT_RESULT_FILE_PATHS = Arrays.asList(
+            "/db/cohort_results/cohort_feasiblity.sql",
+            "/db/cohort_results/cohort_features_results.sql",
+            "/db/cohort_results/ir_analysis.sql",
+            "/db/cohort_results/createHeraclesTables.sql");
+
+    private static final String INDEXES_COHORT_RESULT_FILE_PATHS = "/db/cohort_results/heracles_indexes.sql";
+    private static final Collection<String> DBMS_NO_INDEXES = Arrays.asList("redshift", "impala", "netezza");
+
+    @GET
+    @Path("results")
+    @Produces("text/plain")
+    public String generateResultSQL(@QueryParam("dialect") String dialect, @DefaultValue("results") @QueryParam("schema") String schema) {
+
+        StringBuilder sqlBuilder = new StringBuilder();
+        for (String fileName : COMMON_COHORT_RESULT_FILE_PATHS){
+            sqlBuilder.append("\n").append(ResourceHelper.GetResourceAsString(fileName));
+        }
+        if (dialect == null || DBMS_NO_INDEXES.stream().noneMatch(dbms -> dbms.equals(dialect.toLowerCase()))) {
+            sqlBuilder.append("\n").append(ResourceHelper.GetResourceAsString(INDEXES_COHORT_RESULT_FILE_PATHS));
+        }
+        String result = sqlBuilder.toString();
+        if(dialect != null){
+           result = translateSqlFile(result, dialect, schema);
+        }
+        return result.replaceAll(";", ";\n");
+    }
+
+    private String translateSqlFile(String sql, String dialect, String schema) {
+
+        SourceStatement statement = new SourceStatement();
+        statement.targetDialect = dialect.toLowerCase();
+        statement.sql = sql;
+        HashMap<String, String> parameters = new HashMap<>();
+        parameters.put("results_schema", schema);
+        statement.parameters = parameters;
+        TranslatedStatement translatedStatement = translateSQL(statement);
+        return translatedStatement.targetSQL;
+    }
+
+}

src/main/java/org/ohdsi/webapi/service/SqlRenderService.java

@@ -1,45 +1,53 @@
 package org.ohdsi.webapi.service;
 
-import java.util.HashMap;
 import java.util.ArrayList;
+import java.util.HashMap;
 import javax.servlet.ServletContext;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.POST;
 import javax.ws.rs.Path;
 import javax.ws.rs.Produces;
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.MediaType;
-
 import org.ohdsi.sql.SqlRender;
 import org.ohdsi.sql.SqlTranslate;
 import org.ohdsi.webapi.sqlrender.SourceStatement;
 import org.ohdsi.webapi.sqlrender.TranslatedStatement;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
 
 /**
  *
  * @author Lee Evans
  */
 @Path("/sqlrender/")
 public class SqlRenderService {
-    
+
     @Context
     ServletContext context;
+    @Autowired
+    ApplicationContext applicationContext;
 
     @Path("translate")
     @POST
     @Produces(MediaType.APPLICATION_JSON)
     @Consumes(MediaType.APPLICATION_JSON)
-    public TranslatedStatement translateSQL(SourceStatement sourceStatement) {
+    public TranslatedStatement translateSQLFromSourceStatement(SourceStatement sourceStatement) {
+
+        return translateSQL(sourceStatement);
+    }
+
+    static TranslatedStatement translateSQL(SourceStatement sourceStatement) {
 
         TranslatedStatement translated = new TranslatedStatement();
- 
+
         try {
-            
+
             String parameterKeys[] = getMapKeys(sourceStatement.parameters);
             String parameterValues[] = getMapValues(sourceStatement.parameters, parameterKeys);
 
-            String renderedSQL = SqlRender.renderSql(sourceStatement.sql, parameterKeys, parameterValues );
-            
+            String renderedSQL = SqlRender.renderSql(sourceStatement.sql, parameterKeys, parameterValues);
+
             if ((sourceStatement.targetDialect == null) || ("sql server".equals(sourceStatement.targetDialect))) {
                 translated.targetSQL = renderedSQL;
             } else {
@@ -49,28 +57,28 @@ public TranslatedStatement translateSQL(SourceStatement sourceStatement) {
         } catch (Exception exception) {
             throw new RuntimeException(exception);
         }
-        
+
         return translated;
     }
-    
-    private String[] getMapKeys(HashMap<String,String> parameters) {
+
+    private static String[] getMapKeys(HashMap<String, String> parameters) {
         if (parameters == null) {
             return null;
         } else {
             return parameters.keySet().toArray(new String[parameters.keySet().size()]);
         }
     }
 
-    private String[] getMapValues(HashMap<String,String> parameters, String[] parameterKeys) {
+    private static String[] getMapValues(HashMap<String, String> parameters, String[] parameterKeys) {
         ArrayList<String> parameterValues = new ArrayList<>();
         if (parameters == null) {
             return null;
         } else {
             for (String parameterKey : parameterKeys) {
-                parameterValues.add((String) parameters.get(parameterKey));
+                parameterValues.add(parameters.get(parameterKey));
             }
             return parameterValues.toArray(new String[parameterValues.size()]);
         }
     }
-    
+
 }

src/main/resources/db/cohort_results/cohort_feasiblity.sql

@@ -0,0 +1,54 @@
+IF OBJECT_ID('@results_schema.cohort_inclusion', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_inclusion(
+  cohort_definition_id int NOT NULL,
+  rule_sequence int NOT NULL,
+  name varchar(255) NULL,
+  description varchar(1000) NULL
+);
+
+IF OBJECT_ID('@results_schema.cohort_inclusion_result', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_inclusion_result(
+  cohort_definition_id int NOT NULL,
+  inclusion_rule_mask bigint NOT NULL,
+  person_count bigint NOT NULL
+);
+
+IF OBJECT_ID('@results_schema.cohort_inclusion_stats', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_inclusion_stats(
+  cohort_definition_id int NOT NULL,
+  rule_sequence int NOT NULL,
+  person_count bigint NOT NULL,
+  gain_count bigint NOT NULL,
+  person_total bigint NOT NULL
+);
+
+IF OBJECT_ID('@results_schema.cohort_summary_stats', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_summary_stats(
+  cohort_definition_id int NOT NULL,
+  base_count bigint NOT NULL,
+  final_count bigint NOT NULL
+);
+
+IF OBJECT_ID('@results_schema.feas_study_result', 'U') IS NULL
+CREATE TABLE $results_schema.feas_study_result(
+  study_id int NOT NULL,
+  inclusion_rule_mask bigint NOT NULL,
+  person_count bigint NOT NULL
+);
+
+IF OBJECT_ID('@results_schema.feas_study_inclusion_stats', 'U') IS NULL
+CREATE TABLE $results_schema.feas_study_inclusion_stats(
+  study_id int NOT NULL,
+  rule_sequence int NOT NULL,
+  name varchar(255) NOT NULL,
+  person_count bigint NOT NULL,
+  gain_count bigint NOT NULL,
+  person_total bigint NOT NULL
+);
+
+IF OBJECT_ID('@results_schema.feas_study_index_stats', 'U') IS NULL
+CREATE TABLE $results_schema.feas_study_index_stats(
+  study_id int NOT NULL,
+  person_count bigint NOT NULL,
+  match_count bigint NOT NULL
+);

src/main/resources/db/cohort_results/cohort_features_results.sql

@@ -0,0 +1,48 @@
+IF OBJECT_ID('@results_schema.cohort_features_dist', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_features_dist
+(
+  cohort_definition_id bigint,   
+  covariate_id bigint, 
+  count_value float, 
+  min_value float, 
+  max_value float, 
+  average_value float, 
+  standard_deviation float, 
+  median_value float, 
+  p10_value float, 
+  p25_value float, 
+  p75_value float, 
+  p90_value float
+);
+
+IF OBJECT_ID('@results_schema.cohort_features', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_features
+(
+  cohort_definition_id bigint,
+  covariate_id bigint, 
+  sum_value bigint, 
+  average_value float
+);
+
+IF OBJECT_ID('@results_schema.cohort_features_ref', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_features_ref
+(
+  cohort_definition_id bigint,
+  covariate_id bigint, 
+  covariate_name varchar(1000), 
+  analysis_id int, 
+  concept_id int
+);
+
+IF OBJECT_ID('@results_schema.cohort_features_analysis_ref', 'U') IS NULL
+CREATE TABLE @results_schema.cohort_features_analysis_ref
+(
+  cohort_definition_id bigint,
+  analysis_id int, 
+  analysis_name varchar(1000), 
+  domain_id varchar(100), 
+  start_day int, 
+  end_day int, 
+  is_binary char,
+  missing_means_zero char
+);