Add condition entity for aou_synthetic underlay. Tests for entity queries. (#84)

* Add optional TableFilter to EntityMapping. Example in nautical underlay.

* Fix UnderlayConversionTest.

* New test for embedded SELECT in FROM clause.

* Check table filters in underlay conversion test.

* Resolve table with table filter defined to a nested select.

* Handle ints in column filter.

* Fix UnderlaysApiControllerTest.

* Make column filter value use oneof.

* Make table filter use oneof.

* Remove boolean from column value options because unsupported datatype.

* Check that binary table filter column is in same table as pk.

* Add tests for different value types and operators.

* Fix checkstyle errors.

* Replace System.out.println with logger.

* Add condition entity. Tests for queries against AoU synthetic underlay.

* Fix pmd error.

* Add procedure entity.

* Add measurement entity.

* Add visit entity.

* Add observation entity.

* Add device entity.

* Add ingredient entity.

* Add brand entity.

* Add Test suffix to test classes.

* Use golden files for SQL string comparison tests.

* Include gradle command to regenerate files in error msg.

Author: marikomedlock

.gitignore

@@ -4,6 +4,9 @@ build/
 !**/src/main/**
 !**/src/test/**
 
+### Jenv ###
+.java-version
+
 ### STS ###
 .apt_generated
 .classpath

.java-version

@@ -26,3 +26,11 @@ to regenerate the `gradle.lockfile` with the added dependencies. If this is not
 error about
 > Could not resolve all files for configuration...
 > Resolved foo.bar:lib:version which is not part of the dependency lock state
+
+## Generating SQL strings for tests
+Some tests compare the SQL string generated by the API code with an expected string, stored in a golden file.
+An example test is `bio.terra.tanagra.aousynthethic.BrandEntityQueriesTest.generateSqlForAllBrandEntities` and
+the accompanying golden file is `api/src/test/resources/aousynthetic.all-brand-entities.sql`.
+
+To regenerate the golden files, run the tests with the `generateSqlFiles` Gradle project property set. e.g.:
+`./gradlew cleanTest api:test --tests bio.terra.tanagra.aousynthetic.* --info -PgenerateSqlFiles=true`

api/README.md

@@ -89,6 +89,13 @@ dependencies {
 
 test {
     useJUnitPlatform()
+
+    // These System properties are used for the generated SQL strings to compare against during tests.
+    // See bio.terra.tanagra.aousynthetic.GeneratedSqlUtils for how they are used.
+    systemProperty("GRADLE_PROJECT_DIR", projectDir)
+    if (project.findProperty("generateSqlFiles")) {
+        systemProperty("GENERATE_SQL_FILES", "true")
+    }
 }
 
 // Apply Gradle Script Plugins for more modular gradle files.