Merge pull request #50 from OHDSI/release-1.9.0

Release 1.9.0

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>com.odysseusinc.athena</groupId>
     <artifactId>athena</artifactId>
-    <version>1.8.0</version>
+    <version>1.9.0</version>
     <packaging>jar</packaging>
 
 
@@ -34,7 +34,7 @@
         <javax.mail.version>1.4</javax.mail.version>
         <spring.context.support>4.3.7.RELEASE</spring.context.support>
         <dockerImagePrefix>hub.arachnenetwork.com</dockerImagePrefix>
-        <arachne.version>1.13.0-SNAPSHOT</arachne.version>
+        <arachne.version>1.13.0</arachne.version>
         <disruptor.version>3.3.6</disruptor.version>
         <commons-lang3.version>3.0</commons-lang3.version>
         <build.number>${BUILD_NUMBER}</build.number>

properties/dev/application.properties

@@ -107,6 +107,8 @@ athena.security.saml.attributes.middle_name=middleName
 
 arachne.portal.url=https://localhost:8080
 arachne.portal.professionalTypesPath=/api/v1/user-management/professional-types
+arachne.portal.countriesPath=/api/v1/user-management/countries/search
+arachne.portal.provincePath=/api/v1/user-management/state-province/search
 arachne.portal.registerPath=/api/v1/auth/registration
 arachne.portal.remindPasswordPath=/api/v1/auth/remind-password
 arachne.portal.resetPasswordPath=/api/v1/auth/reset-password

properties/prod/application.properties

@@ -103,6 +103,8 @@ athena.security.saml.attributes.middle_name=middleName
 
 arachne.portal.url=
 arachne.portal.professionalTypesPath=/api/v1/user-management/professional-types
+arachne.portal.countriesPath=/api/v1/user-management/countries/search
+arachne.portal.provincePath=/api/v1/user-management/state-province/search
 arachne.portal.registerPath=/api/v1/auth/registration
 arachne.portal.remindPasswordPath=/api/v1/auth/remind-password
 arachne.portal.resetPasswordPath=/api/v1/auth/reset-password

properties/qa/application.properties

@@ -103,6 +103,8 @@ athena.security.saml.attributes.middle_name=middleName
 
 arachne.portal.url=
 arachne.portal.professionalTypesPath=/api/v1/user-management/professional-types
+arachne.portal.countriesPath=/api/v1/user-management/countries/search
+arachne.portal.provincePath=/api/v1/user-management/state-province/search
 arachne.portal.registerPath=/api/v1/auth/registration
 arachne.portal.remindPasswordPath=/api/v1/auth/remind-password
 arachne.portal.resetPasswordPath=/api/v1/auth/reset-password

properties/test/application.properties

@@ -103,6 +103,8 @@ athena.security.saml.attributes.middle_name=middleName
 
 arachne.portal.url=https://test.arachnenetwork.com
 arachne.portal.professionalTypesPath=/api/v1/user-management/professional-types
+arachne.portal.countriesPath=/api/v1/user-management/countries/search
+arachne.portal.provincePath=/api/v1/user-management/state-province/search
 arachne.portal.registerPath=/api/v1/auth/registration
 arachne.portal.remindPasswordPath=/api/v1/auth/remind-password
 arachne.portal.resetPasswordPath=/api/v1/auth/reset-password

src/main/docker/cpt4_4_5/cpt.bat

@@ -1,2 +1,29 @@
 @echo off
-java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 4
+rem Argument counting code from http://www.testdeveloper.com/2010/09/26/how-to-count-arguments-to-a-dos-batch-file-without-using-your-fingers-and-toes
+set _exitStatus=0
+set _argcActual=0
+set _argcExpected=2
+for %%i in (%*) do set /A _argcActual+=1
+if %_argcActual% NEQ %_argcExpected% ( 
+  call :_ShowUsage %0%, "Need to include login name and password for UMLS Terminology Services."  
+  set _exitStatus=1  
+  goto:_EOF
+)
+
+FOR /f tokens^=2-5^ delims^=.-_^" %%j IN ('java -fullversion 2^>^&1') DO SET "jver=%%j%%k"
+IF %jver% GTR 18 (
+java -Dumls-user=%1 -Dumls-password=%2 --add-modules=java.xml.ws  -jar cpt4.jar 4
+) ELSE (
+java -Dumls-user=%1 -Dumls-password=%2 -jar cpt4.jar 4
+)
+set _exitStatus=%ERRORLEVEL%
+goto:_EOF
+:_ShowUsage  
+echo [USAGE]: %~1 login password 
+if NOT "%~2" == "" (   
+  echo %~2      
+)  
+goto:eof
+:_EOF
+echo The exit status is %_exitStatus%
+cmd /c exit %_exitStatus%

src/main/docker/cpt4_5/cpt.bat

@@ -1,2 +1,29 @@
 @echo off
-java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 5
+rem Argument counting code from http://www.testdeveloper.com/2010/09/26/how-to-count-arguments-to-a-dos-batch-file-without-using-your-fingers-and-toes
+set _exitStatus=0
+set _argcActual=0
+set _argcExpected=2
+for %%i in (%*) do set /A _argcActual+=1
+if %_argcActual% NEQ %_argcExpected% ( 
+  call :_ShowUsage %0%, "Need to include login name and password for UMLS Terminology Services."  
+  set _exitStatus=1  
+  goto:_EOF
+)
+
+FOR /f tokens^=2-5^ delims^=.-_^" %%j IN ('java -fullversion 2^>^&1') DO SET "jver=%%j%%k"
+IF %jver% GTR 18 (
+java -Dumls-user=%1 -Dumls-password=%2 --add-modules=java.xml.ws  -jar cpt4.jar 5
+) ELSE (
+java -Dumls-user=%1 -Dumls-password=%2 -jar cpt4.jar 5
+)
+set _exitStatus=%ERRORLEVEL%
+goto:_EOF
+:_ShowUsage  
+echo [USAGE]: %~1 login password 
+if NOT "%~2" == "" (   
+  echo %~2      
+)  
+goto:eof
+:_EOF
+echo The exit status is %_exitStatus%
+cmd /c exit %_exitStatus%

src/main/java/com/odysseusinc/athena/api/v1/controller/UserController.java

@@ -71,6 +71,12 @@ public class UserController {
     @Value("${arachne.portal.professionalTypesPath}")
     private String professionalTypesPath;
 
+    @Value("${arachne.portal.countriesPath}")
+    private String countriesPath;
+
+    @Value("${arachne.portal.provincePath}")
+    private String provincePath;
+
     @Value("${arachne.portal.registerPath}")
     private String registerPath;
 
@@ -128,6 +134,51 @@ public JsonResult listProfessionalTypes() throws URISyntaxException {
         return responseEntity.getBody();
     }
 
+    @RequestMapping(value = "/countries", method = GET)
+    public JsonResult searchCountries(
+						@RequestParam("query") String query,
+						@RequestParam("limit") Integer limit,
+						@RequestParam(value = "includeId", required = false) Long includeId
+		) {
+    		String uri = UriComponentsBuilder
+								.fromUriString(arachneUrl)
+								.replacePath(countriesPath)
+								.queryParam("query", query)
+								.queryParam("limit", limit)
+								.queryParam("includeId", includeId)
+								.toUriString();
+    		ResponseEntity<JsonResult> responseEntity = restTemplate.exchange(
+    						uri,
+								HttpMethod.GET,
+								null,
+								JsonResult.class
+				);
+    		return responseEntity.getBody();
+		}
+
+		@RequestMapping(value = "/provinces", method = GET)
+		public JsonResult searchProvinces(
+						@RequestParam("countryId") String countryIdParam,
+						@RequestParam("query") String query,
+						@RequestParam("limit") Integer limit,
+						@RequestParam(value = "includeId", required = false) String includeIdParam
+		) {
+    		String uri = UriComponentsBuilder
+								.fromUriString(arachneUrl)
+								.replacePath(provincePath)
+								.queryParam("countryId", countryIdParam)
+								.queryParam("query", query)
+								.queryParam("limit", limit)
+								.queryParam("includeId", includeIdParam)
+								.toUriString();
+    		ResponseEntity<JsonResult> responseEntity = restTemplate.exchange(
+    						uri,
+								HttpMethod.GET,
+								null,
+								JsonResult.class);
+    		return responseEntity.getBody();
+		}
+
     @RequestMapping(method = RequestMethod.POST)
     public ResponseEntity register(@RequestBody CommonUserRegistrationDTO dto) throws PermissionDeniedException {
 

src/main/java/com/odysseusinc/athena/service/saver/v4/InvalidConceptCPT4V4Saver.java

@@ -47,7 +47,7 @@ public String fileName() {
     @Override
     protected String query() {
 
-        return "SELECT * FROM concept WHERE vocabulary_id in (?) AND invalid_reason is not null";
+        return "SELECT * FROM concept WHERE vocabulary_id in (?) AND valid_end_date <= now()";
     }
 
     @Override

src/main/java/com/odysseusinc/athena/service/saver/v5/InvalidConceptCPT4V5Saver.java

@@ -45,7 +45,7 @@ public String fileName() {
     @Override
     protected String query() {
 
-        return "SELECT * FROM concept WHERE vocabulary_id in (?) AND invalid_reason is not null";
+        return "SELECT * FROM concept WHERE vocabulary_id in (?) AND valid_end_date <= now()";
     }
 
     @Override