Fixes OHDSI#108 (OHDSI#163)

* ignore IntelliJ files
add'l characterization/summarization work
added SQL files for summary service from Achilles::ExportToJSON
added data transfer objects (DTOs)
modified CDMResultsService, made several sql translation changes, moved
mappers and DTOs to report package in preparation for refactoring.
added add'l DTOs to report package and stubbed out service and runner classes.
fixed imports in some DTOs and RowMappers

* Use same method (getTreemap) for all (non-temporal) treemaps
Add generic row mapper, text hack impls
made several sql translation-related changes
Use same method (getTreemap) for all (non-temporal) treemaps
Use AS keyword in all cdm report query aliases
Remove text hack and camel case column names in cdm report queries
Replace all treemap endpoints with a single generic implementation
 * Rename all treemap CDM report files to treemap.sql
 * Enquote aliases in CDM report queries to preserve case
 * Add GenericRowMapper ctor with ObjectMapper for performance
 * CDMResultsAnalysisRunner.getTreemap returns ArrayNode

Fix condition CDM results queries (by concept)

 * include conceptId parameter
 * rename sqlAgeAtFirstDiagnosis to sqlAgeAtFirstOccurrence
 * modify sqlConditionsByType to check vocabulary_id, not domain_id
 * cast xCalendarYear to INT in sqlPrevalenceByGenderAgeYear

added fixes to row mapping in /person and dashboard

implemented /achillesheel, /datadensity
started implementation of /death
refactored CohortAttributeMapper --> CDMAttributeMapper
created new report data objects
drop unused/superfluous CDMResultsAnalysisRunner

fixed /datadensity

Fix queries associated with generic drilldown reports

 * Data types include conditionera, drug, drugera, measurement, observation, procedure, visit
 * Queries include AgeAtFirstOccurrence, PrevalenceByGenderAgeYear, ByType, ByMonth
 * Include parameter @conceptId
 * Cast xCalendarYear to INT (where applicable)

Remove obsoleted code from CDMResultsService (activates observation reports)

Standardize names of "by type" query files for cdm reports to sqlByType.sql

Applies to condition, drug, measurement, observation, procedure

Add cdm_database_schema to CDMResultsAnalysisRunner standard columns (for measurement treemap)

Fix typo in sqlVisitDurationByType.sql

cleaned up and changes /achillesheel --> /heel

	Add cdm_database_schema to CDMResultsAnalysisRunner standard columns as per mark-velez/* #e862d53

changed endpoint signature (/heel -->/achillesheel), fixed summary yob and yob in person report

fixed null totalRecords element in Data Density report

added summary to dashboard report in CDM results service

implemented death report

removed superfluous code (imports, methods, etc)

Reorganize sql files for cdm drilldowns (to reduce text wrangling) (#2)

* Remove sql prefix from files names
 * Camel-case filename
 * Move drilldown files to folders
 * Delete treemap files that were reverted back

removed unused method - renderDrillDownSql()

changed access modifier on several fields and methods

removed unused test and related resource

made post-rebase reconciliations in prep for PR

.gitignore

@@ -1,4 +1,6 @@
 *application.properties
+.idea/
+*.iml
 sandbox/
 /target/
 .settings

src/main/java/org/ohdsi/webapi/DataAccessConfig.java

@@ -28,98 +28,97 @@
 @EnableTransactionManagement
 public class DataAccessConfig {
 
-  @Autowired
-  private Environment env;
-
+    @Autowired
+    private Environment env;
 
-  private Properties getJPAProperties() {
-    Properties properties = new Properties();
-    properties.setProperty("hibernate.default_schema", this.env.getProperty("spring.jpa.properties.hibernate.default_schema"));
-    properties.setProperty("hibernate.dialect", this.env.getProperty("spring.jpa.properties.hibernate.dialect"));
-    return properties;
-  }
+    private Properties getJPAProperties() {
+        Properties properties = new Properties();
+        properties.setProperty("hibernate.default_schema", this.env.getProperty("spring.jpa.properties.hibernate.default_schema"));
+        properties.setProperty("hibernate.dialect", this.env.getProperty("spring.jpa.properties.hibernate.dialect"));
+        return properties;
+    }
 
-  @Bean
-  @Primary
-  public DataSource primaryDataSource() {
+    @Bean
+    @Primary    
+    public DataSource primaryDataSource() {
+        String driver = this.env.getRequiredProperty("datasource.driverClassName");
+        String url = this.env.getRequiredProperty("datasource.url");
+        String user = this.env.getRequiredProperty("datasource.username");
+        String pass = this.env.getRequiredProperty("datasource.password");
+        boolean autoCommit = false;
 
-    String driver = this.env.getRequiredProperty("datasource.driverClassName");
-    String url = this.env.getRequiredProperty("datasource.url");
-    String user = this.env.getRequiredProperty("datasource.username");
-    String pass = this.env.getRequiredProperty("datasource.password");
-    boolean autoCommit = false;
 
         //pooling - currently issues with (at least) oracle with use of temp tables and "on commit preserve rows" instead of "on commit delete rows";
-    //http://forums.ohdsi.org/t/transaction-vs-session-scope-for-global-temp-tables-statements/333/2
+        //http://forums.ohdsi.org/t/transaction-vs-session-scope-for-global-temp-tables-statements/333/2
         /*final PoolConfiguration pc = new org.apache.tomcat.jdbc.pool.PoolProperties();
      pc.setDriverClassName(driver);
      pc.setUrl(url);
      pc.setUsername(user);
      pc.setPassword(pass);
      pc.setDefaultAutoCommit(autoCommit);*/
-    //non-pooling
-    DriverManagerDataSource ds = new DriverManagerDataSource(url, user, pass);
-    ds.setDriverClassName(driver);
+        //non-pooling
+        DriverManagerDataSource ds = new DriverManagerDataSource(url, user, pass);
+        ds.setDriverClassName(driver);
         //note autocommit defaults vary across vendors. use provided @Autowired TransactionTemplate
 
-    String[] supportedDrivers;
-    supportedDrivers = new String[]{"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver", "com.amazon.redshift.jdbc41.Driver"};
-
-    for (String driverName : supportedDrivers) {
-      try {
-        Class.forName(driverName);
-        System.out.println("driver loaded: " + driverName);
-      } catch (Exception ex) {
-        System.out.println("error loading " + driverName + " driver.");
-      }
+        String[] supportedDrivers;
+        supportedDrivers = new String[]{"org.postgresql.Driver", "com.microsoft.sqlserver.jdbc.SQLServerDriver", "oracle.jdbc.driver.OracleDriver", "com.amazon.redshift.jdbc41.Driver"};
+
+        for (String driverName : supportedDrivers) {
+            try {
+                Class.forName(driverName);
+                System.out.println("driver loaded: " + driverName);
+            } catch (Exception ex) {
+                System.out.println("error loading " + driverName + " driver.");
+            }
+        }
+        return ds;
+        //return new org.apache.tomcat.jdbc.pool.DataSource(pc);
     }
-    return ds;
-    //return new org.apache.tomcat.jdbc.pool.DataSource(pc);        
-  }
 
-  @Bean
-  public EntityManagerFactory entityManagerFactory() {
+    @Bean
+    public EntityManagerFactory entityManagerFactory() {
 
-    HibernateJpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
-    vendorAdapter.setGenerateDdl(false);
-    vendorAdapter.setShowSql(Boolean.valueOf(this.env.getRequiredProperty("spring.jpa.show-sql")));
+        HibernateJpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
+        vendorAdapter.setGenerateDdl(false);
+        vendorAdapter.setShowSql(Boolean.valueOf(this.env.getRequiredProperty("spring.jpa.show-sql")));
         //hibernate.dialect is resolved based on driver
-    //vendorAdapter.setDatabasePlatform(hibernateDialect);
-    
-    LocalContainerEntityManagerFactoryBean factory = new LocalContainerEntityManagerFactoryBean();
-    factory.setJpaVendorAdapter(vendorAdapter);
-    factory.setJpaProperties(getJPAProperties());
-    factory.setPackagesToScan("org.ohdsi.webapi");
-    factory.setDataSource(primaryDataSource());
-    factory.afterPropertiesSet();
-
-    return factory.getObject();
-  }
-
-  @Bean
-  @Primary
-  //This is needed so that JpaTransactionManager is used for autowiring, instead of DataSourceTransactionManager
-  public PlatformTransactionManager jpaTransactionManager() {//EntityManagerFactory entityManagerFactory) {
-
-    JpaTransactionManager txManager = new JpaTransactionManager();
-    txManager.setEntityManagerFactory(entityManagerFactory());
-    return txManager;
-  }
-
-  @Bean
-  public TransactionTemplate transactionTemplate(PlatformTransactionManager transactionManager) {
-    TransactionTemplate transactionTemplate = new TransactionTemplate();
-    transactionTemplate.setTransactionManager(transactionManager);
-    return transactionTemplate;
-  }
-
-  @Bean
-  public TransactionTemplate transactionTemplateRequiresNew(PlatformTransactionManager transactionManager) {
-    TransactionTemplate transactionTemplate = new TransactionTemplate();
-    transactionTemplate.setTransactionManager(transactionManager);
-    transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
-    return transactionTemplate;
-  }
+        //vendorAdapter.setDatabasePlatform(hibernateDialect);
+
+        LocalContainerEntityManagerFactoryBean factory = new LocalContainerEntityManagerFactoryBean();
+        factory.setJpaVendorAdapter(vendorAdapter);
+        factory.setJpaProperties(getJPAProperties());
+        factory.setPackagesToScan("org.ohdsi.webapi");
+        factory.setDataSource(primaryDataSource());
+        factory.afterPropertiesSet();
+
+        return factory.getObject();
+    }
+
+    @Bean
+    @Primary
+    //This is needed so that JpaTransactionManager is used for autowiring, instead of DataSourceTransactionManager
+    public PlatformTransactionManager jpaTransactionManager() {//EntityManagerFactory entityManagerFactory) {
+
+        JpaTransactionManager txManager = new JpaTransactionManager();
+        txManager.setEntityManagerFactory(entityManagerFactory());
+        return txManager;
+    }
+
+    @Bean
+    public TransactionTemplate transactionTemplate(PlatformTransactionManager transactionManager) {
+        TransactionTemplate transactionTemplate = new TransactionTemplate();
+        transactionTemplate.setTransactionManager(transactionManager);
+        return transactionTemplate;
+    }
+
+    @Bean
+    public TransactionTemplate transactionTemplateRequiresNew(PlatformTransactionManager transactionManager) {
+        TransactionTemplate transactionTemplate = new TransactionTemplate();
+        transactionTemplate.setTransactionManager(transactionManager);
+        transactionTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
+        return transactionTemplate;
+    }
 
   /*
   public String getSparqlEndpoint()