Peter Hambly 16th October 2017
The object of this document is to detail how to add a restful web service to the RIF. The RIF is structured with an HTML5/Javascript front end, using Angular.js and Leaflet. Middleware is implemented using Restfull web services written in Java and running in Apache Tomcat. All data is stored in a GeoSptial database, with a choice of MicroSoft SQL Server or Postgres.
The web services are thus the key interface in the software, and this document details who to create one. The example code is principally focused on the Middleware, with the interfacing with the front end and the database detailed.
This markdown document details the steps needed to create the latest Restful web service: getExtractStatus.
It should be noted that RIF web services come in Microsoft SQL Server and Postgres variants. The code in the data storage layer is separated into separate ms and pg path components with no common code. This causes substantial code duplication and will be rectified by the new Java Developer currently being hired (October 2017). These links will only work in a RIF browser session!
This returns the reposnse: STUDY_EXTRACTABLE_NEEDS_ZIPPING.
Get textual extract status of a study.
This function determines whether a study can be extracted from the database and the results returned to the user in a ZIP file.
It is intended that during 2018 this function be enhanced to support the information governance requirements that should an organisation wish, the (to be created) Informartion Governance tool will control none, one or both of:
The middleware export functionality will shortly be modified to use numbered directories (1-100 etc) to reduce the number of files/directories per directory to 100. This is to improve filesystem performance on Windows Tomcat servers. This will result in the code changing from this example.
The GetExtractStatus web service returns the following textual strings:
STUDY_EXTRACTABLE_NEEDS_ZIPPING: returned for the following rif40_studies.study_state code/meaning of: S: R success; when the ZIP extrsct file has not yet been created;
STUDY_EXTRABLE_ZIPPID: returned for the following rif40_studies.study_statu code/meaning of: S: R success; when the ZIP extrsct file has been created;
The GetExtractStatus web service is used by the export dashboard in the front end and on is one of three export related middleware calls:
The purpose of the GetExtractStatus web service is to manage what the download button does. The *export” button can:
Currently the user has to push the export button at least twice; firstly to create the extract and then again one or more time every time the extract is downloaded. I.e. the study export omnly needs to be created once! As exporting a large study may take some minutes it was decided not the “click” the completed download link for the user as the user may have moved onto other tasks.
Two screenshots of the process are shown below. Firstly, after an export has been requested, including showing the effect of clicking the download link:
And secondly, after the download the file is available for fresh download:
If the export is then saved to disk and unzipped, the R phase of the study can be re-run. This proves the validity of the extract and gives the investigator the basis of future analysis. The export will be enhanced to add maps over the winter of 2017:
C:\Users\Peter\Downloads\peter_s53a\data>rif40_run_R.bat
##########################################################################################
#
# Run R script on a study extract.
#
# USERID=peter
# DBNAME=sahsuland
# DBHOST=localhost\SQLEXPRESS
# DBPORT=1433
# DB_DRIVER_PREFIX=jdbc:sqlserver
# DB_DRIVER_CLASS_NAME=com.microsoft.sqlserver.jdbc.SQLServerDriver
# STUDYID=53
# INVESTIGATIONNAME=TEST_1002
# INVESTIGATIONID=53
# ODBCDATASOURCE=SQLServer11
# MODEL=HET
# COVARIATENAME=none
#
##########################################################################################
"C:\Program Files\R\R-3.4.0\bin\x64\RScript" Adj_Cov_Smooth_csv.R ^
--db_driver_prefix=jdbc:sqlserver --db_driver_class_name=com.microsoft.sqlserver.jdbc.SQLServerDriver --odbcDataSource=SQLServer11 ^
--dbHost=localhost\SQLEXPRESS --dbPort=1433 --dbName=sahsuland ^
--studyID=53 --investigationName=TEST_1002 --investigationId=53 ^
--model=HET --covariateName=none ^
--userID=peter --password=XXXXXXXXXXXXXXXXXXXXXX ^
--scratchspace=c:\rifDemo\scratchSpace\ --dumpframestocsv=FALSE
Warning message:
package 'pryr' was built under R version 3.4.2
Loading required package: sp
Loading required package: methods
Loading required package: Matrix
This is INLA 0.0-1485844051, dated 2017-01-31 (09:14:12+0300).
See www.r-inla.org/contact-us for how to get help.
Attaching package: 'INLA'
The following object is masked from 'package:pryr':
f
Checking rgeos availability: FALSE
Note: when rgeos is not available, polygon geometry computations in maptools depend on gpclib,
which has a restricted licence. It is disabled by default;
to enable gpclib, type gpclibPermit()
CATALINA_HOME=C:\Program Files\Apache Software Foundation\Tomcat 8.5
Source: C:\Program Files\Apache Software Foundation\Tomcat 8.5\webapps\rifServices\WEB-INF\classes\performSmoothingActivity.R
13 arguments were supplied
Parsing parameters
name value
1 db_driver_prefix jdbc:sqlserver
2 db_driver_class_name com.microsoft.sqlserver.jdbc.SQLServerDriver
3 odbcDataSource SQLServer11
4 dbHost localhost\\SQLEXPRESS
5 dbPort 1433
6 dbName sahsuland
7 studyID 53
8 investigationName TEST_1002
9 investigationId 53
10 model HET
11 covariateName none
12 scratchspace c:\\rifDemo\\scratchSpace\\
13 dumpframestocsv FALSE
Performing basic stats and smoothing
Covariates: NONE
Bayes smoothing with HET model type no adjustment
Posterior probability calculated
callPerformSmoothingActivity exitValue: 0
performSmoothingActivity() OK: 0
check.integer: 01.001.000100.1; as.numeric(str): 1; isNumeric: TRUE; isInteger: TRUE; isNotRounded: TRUE; isIntRegexp: FALSE; check.
integer.Result: FALSE
typeof(result$area_id[1]) ----> integer ; check.integer(result$area_id[1]): FALSE ; result$area_id[1]: 01.001.000100.1
check.integer: 01.001.000100.1; as.numeric(str): 1; isNumeric: TRUE; isInteger: TRUE; isNotRounded: TRUE; isIntRegexp: FALSE; check.
integer.Result: FALSE
.Primitive("return")
Total memory is use: 145322216
Memory by object:
AdjRowset: 309240
area_id_is_integer: 48
data: 4414272
errorTrace: 1048
ototal: 48
result: 746696
Garbage collection 169 = 133+15+21 (level 2) ...
103.1 Mbytes of cons cells used (34%)
30.6 Mbytes of vectors used (32%)
Free 5471352 memory; total memory is use: 140009424
Memory by object:
errorTrace: 1048
R script ran OK
Adj_Cov_Smooth_csv.R procedure OK for study: 53; investigation: 53
Tne web service has the following parameters:
The GetExtractStatus web service returns the textual extract status, e.g. STUDY_EXTRABLE_ZIPPID or a JSON error:
[{"errorMessages":["Record \"Study\" with value \"535\" not found in the database."]}]
The middleware consists of five class in three distinct layers:
The key PG/MSSQLRIFStudySubmissionWebServiceResource classes define the ms and pg family webservices:
In most cases, as in this example, this extends the PG/MSSQLAbstractRIFWebServiceResource class
@GET
@Produces({"application/json"})
@Path("/getExtractStatus")
public Response getExtractStatus(
@Context HttpServletRequest servletRequest,
@QueryParam("userID") String userID,
@QueryParam("studyID") String studyID) {
return super.getExtractStatus(
servletRequest,
userID,
studyID);
}
The function super.getExtractStatus() is analogous to PG/MSSQLAbstractRIFWebServiceResource.getExtractStatus()
This class hierarchy probably cannot be de-duplicated, but it does allow webservics to be disabled for one of the database ports.
protected Response getExtractStatus(
final HttpServletRequest servletRequest,
final String userID,
final String studyID) {
String result = null;
try {
User user = createUser(servletRequest, userID);
RIFStudySubmissionAPI studySubmissionService
= getRIFStudySubmissionService();
result=studySubmissionService.getExtractStatus(
user,
studyID);
}
catch(RIFServiceException rifServiceException) {
rifLogger.error(this.getClass(),
"MSSQLAbstractRIFWebServiceResource.getExtractStatus error", rifServiceException);
result
= serialiseException(
servletRequest,
rifServiceException);
}
return webServiceResponseGenerator.generateWebServiceResponse(
servletRequest,
result);
}
In virtually all cases the code is identical.. A new class AbstractRIFWebServiceResource should be extended by the PG/MSSQLAbstractRIFWebServiceResource class [PH suggestion - I may be wrong as I am not a Java programmer].
This defines PG/MSSQLAbstractRIFStudySubmissionService.getExtractStatus() in the data storage layer
public String getExtractStatus(
final User user,
final String studyID)
throws RIFServiceException;
This function is principally to set up the web service and the call the worker function in the Extract Manager:
/**
* Get textual extract status of a study.
* <p>
* This fucntion determines whether a study can be extracted from the database and the results returned to the user in a ZIP file
* </p>
* <p>
* Returns the following textual strings:
* <il>
* <li>STUDY_INCOMPLETE_NOT_ZIPPABLE: returned for the following rif40_studies.study_state codes/meanings:
* <ul>
* <li>C: created, not verified;</li>
* <li>V: verified, but no other work done; [NOT USED BY MIDDLEWARE]</li>
* <li>E: extracted imported or created, but no results or maps created;</li>
* <li>R: initial results population, create map table; [NOT USED BY MIDDLEWARE] design]</li>
* <li>W: R warning. [NOT USED BY MIDDLEWARE]</li>
* <ul>
* </li>
* <li>STUDY_FAILED_NOT_ZIPPABLE: returned for the following rif40_studies.study_state codes/meanings:
* <li>G: Extract failure, extract, results or maps not created;</li>
* <li>F: R failure, R has caught one or more exceptions [depends on the exception handler]</li>
* </li>
* <li>STUDY_EXTRACTABLE_NEEDS_ZIPPING: returned for the following rif40_studies.study_state code/meaning of: S: R success;
* when the ZIP extrsct file has not yet been created
* </il>
* <li>STUDY_EXTRABLE_ZIPPID: returned for the following rif40_studies.study_statu code/meaning of: S: R success;
* when the ZIP extrsct file has been created
* </il>
* </il>
* </p>
* <p>
* Calls MSSQLStudyExtractManager.getExtractStatus()
* </p>
*
* @param _user Database username of logged on user.
* @param studyID Integer study identifier (database study_id field).
*
* @return Textual extract status
* NULL on exception or permission denied by sqlConnectionManager
*/
public String getExtractStatus(
final User _user,
final String studyID)
throws RIFServiceException {
String result = null;
RIFLogger rifLogger = RIFLogger.getLogger();
//Defensively copy parameters and guard against blocked users
User user = User.createCopy(_user);
PGSQLConnectionManager sqlConnectionManager
= rifServiceResources.getSqlConnectionManager();
if (sqlConnectionManager.isUserBlocked(user) == true) {
return null;
}
Connection connection = null;
try {
//Part II: Check for empty parameter values
FieldValidationUtility fieldValidationUtility
= new FieldValidationUtility();
fieldValidationUtility.checkNullMethodParameter(
"getExtractStatus",
"user",
user);
fieldValidationUtility.checkNullMethodParameter(
"getExtractStatus",
"studyID",
studyID);
//Check for security violations
validateUser(user);
fieldValidationUtility.checkMaliciousMethodParameter(
"getExtractStatus",
"studyID",
studyID);
//Audit attempt to do operation
String auditTrailMessage
= RIFServiceMessages.getMessage("logging.getExtractStatus",
user.getUserID(),
user.getIPAddress(),
studyID);
rifLogger.info(
getClass(),
auditTrailMessage);
//Assign pooled connection
connection
= sqlConnectionManager.assignPooledWriteConnection(user);
PGSQLRIFSubmissionManager sqlRIFSubmissionManager
= rifServiceResources.getRIFSubmissionManager();
RIFStudySubmission rifStudySubmission
= sqlRIFSubmissionManager.getRIFStudySubmission(
connection,
user,
studyID);
PGSQLStudyExtractManager studyExtractManager
= rifServiceResources.getSQLStudyExtractManager();
result=studyExtractManager.getExtractStatus(
connection,
user,
rifStudySubmission,
studyID);
}
catch(RIFServiceException rifServiceException) {
//Audit failure of operation
logException(
user,
"getExtractStatus",
rifServiceException);
}
finally {
rifLogger.info(getClass(), "get ZIP file extract status: " + result);
//Reclaim pooled connection
sqlConnectionManager.reclaimPooledWriteConnection(
user,
connection);
}
return result;
}
In virtually all cases the code is identical..
This function does the principal work associated with the web service specification:
/**
* Get textual extract status of a study.
* <p>
* This fucntion determines whether a study can be extracted from the database and the results returned to the user in a ZIP file
* </p>
* <p>
* Returns the following textual strings:
* <il>
* <li>STUDY_INCOMPLETE_NOT_ZIPPABLE: returned for the following rif40_studies.study_state codes/meanings:
* <ul>
* <li>C: created, not verified;</li>
* <li>V: verified, but no other work done; [NOT USED BY MIDDLEWARE]</li>
* <li>E: extracted imported or created, but no results or maps created;</li>
* <li>R: initial results population, create map table; [NOT USED BY MIDDLEWARE] design]</li>
* <li>W: R warning. [NOT USED BY MIDDLEWARE]</li>
* <ul>
* </li>
* <li>STUDY_FAILED_NOT_ZIPPABLE: returned for the following rif40_studies.study_state codes/meanings:
* <li>G: Extract failure, extract, results or maps not created;</li>
* <li>F: R failure, R has caught one or more exceptions [depends on the exception handler]</li>
* </li>
* <li>STUDY_EXTRACTABLE_NEEDS_ZIPPING: returned for the following rif40_studies.study_state code/meaning of: S: R success;
* when the ZIP extrsct file has not yet been created
* </il>
* <li>STUDY_EXTRABLE_ZIPPID: returned for the following rif40_studies.study_status code/meaning of: S: R success;
* when the ZIP extrsct file has been created
* </il>
* </il>
* </p>
*
* @param connection Database specfic Connection object assigned from pool
* @param user Database username of logged on user.
* @param rifStudySubmission RIFStudySubmission object.
* @param studyID Study_id (as text!).
*
* @return Textual extract status
*
* @exception RIFServiceException Catches all exceptions, logs, and re-throws as RIFServiceException
*/
public String getExtractStatus(
final Connection connection,
final User user,
final RIFStudySubmission rifStudySubmission,
final String studyID
)
throws RIFServiceException {
String result=null;
File submissionZipFile = null;
String zipFileName="UNKNOWN";
try {
//Establish the phrase that will be used to help name the main zip
//file and data files within its directories
String studyStatus=getRif40StudyState(connection, studyID);
if (studyStatus == null) { // Study ID does not exist. You will not get this
// [this is raised as an exception in the calling function: RIFStudySubmission.getRIFStudySubmission()]
throw new Exception("STUDY_NOT_FOUND: " + studyID);
}
if (result != null && studyStatus != null) {
switch (studyStatus.charAt(0)) {
case 'C':
case 'V':
case 'E':
case 'R':
case 'W':
result="STUDY_INCOMPLETE_NOT_ZIPPABLE";
break;
case 'G':
case 'F':
result="STUDY_FAILED_NOT_ZIPPABLE";
break;
case 'S': /* R success */
break;
default:
throw new Exception("Invalid rif40_studies.study_state: " + studyStatus);
}
}
if (result == null) {
String baseStudyName
= createBaseStudyFileName(rifStudySubmission, studyID);
submissionZipFile = createSubmissionZipFile(
user,
baseStudyName);
zipFileName=submissionZipFile.getAbsolutePath();
if (submissionZipFile.isFile()) { // ZIP file exists - no need to recreate
result="STUDY_EXTRABLE_ZIPPID";
}
else { // No zip file
result="STUDY_EXTRACTABLE_NEEDS_ZIPPING";
}
}
}
catch(Exception exception) {
rifLogger.error(this.getClass(), "PGSQLStudyExtractManager ERROR", exception);
String errorMessage
= RIFServiceMessages.getMessage(
"sqlStudyStateManager.error.unableToGetExtractStatus",
user.getUserID(),
studyID,
zipFileName);
RIFServiceException rifServiceExeption
= new RIFServiceException(
RIFServiceError.ZIPFILE_GET_STATUS_FAILED,
errorMessage);
throw rifServiceExeption;
}
return result;
}
public String getRif40StudyState(
final Connection connection,
final String studyID)
throws Exception {
//get study_state
SQLGeneralQueryFormatter studyStatusQueryFormatter = new SQLGeneralQueryFormatter();
studyStatusQueryFormatter.addQueryLine(0, "SELECT a.study_state");
studyStatusQueryFormatter.addQueryLine(0, "FROM rif40.rif40_studies a");
studyStatusQueryFormatter.addQueryLine(0, "WHERE a.study_id = ?");
ResultSet studyStatusResultSet = null;
String studyStatus = null;
try {
logSQLQuery("getRif40StudyState", studyStatusQueryFormatter, studyID);
PreparedStatement studyStatusStatement = createPreparedStatement(connection, studyStatusQueryFormatter);
studyStatusStatement.setInt(1, Integer.parseInt(studyID));
studyStatusResultSet = studyStatusStatement.executeQuery();
studyStatusResultSet.next();
studyStatus = studyStatusResultSet.getString(1);
}
catch (Exception exception) {
rifLogger.error(this.getClass(), "Error in SQL Statement: >>> " + lineSeparator + studyStatusQueryFormatter.generateQuery(),
exception);
throw exception;
}
return studyStatus;
}
In some cases the code is identical. Principally Microsoft SQL Server has no concept on an object search path or SYNONYMs so requires the the table name to be prefixed with the schema name. The same code would work on Postgres, but this reduces deployment functionality.
Add messaage template for RIFServiceMessages.getMessage() messages to:
logging.getExtractStatus=User:\"{0}\" IP:\"{1}\" Cheking status of extract for study {2}.
sqlStudyStateManager.error.unableToGetExtractStatus=Unable to get extract zipfile status for user \"{0}\", study \"{1}\", zipfile \"{2}\".
Add error code to RIFServiceError enum to:
ZIPFILE_GET_STATUS_FAILED,/* Unable to get Zipfile status*/
Add logSQLQuery() SQL statment name to:
getRif40StudyState=true
//Get Extract Status - can Zip file be created/fetched
self.getExtractStatus = function (username, studyID) {
//http://localhost:8080/rifServices/studySubmission/pg/getExtractStatus=dwmorley&studyID=46
return studySubmissionURL + DatabaseService.getDatabase() + 'getExtractStatus?userID=' + username + '&studyID=' + studyID;
};
$scope.setupZipButton = function setupZipButton() {
$scope.extractStatus=user.getExtractStatus(user.currentUser, $scope.studyID["exportmap"].study_id).then(function (res) {
if (res.data === "STUDY_EXTRACTABLE_NEEDS_ZIPPING") {
$scope.exportTAG="Export Study Tables";
$scope.exportURL = undefined;
$scope.disableMapListButton=false;
}
else if (res.data === "STUDY_EXTRABLE_ZIPPID") {
$scope.exportURL = user.getZipFileURL(user.currentUser, $scope.studyID["exportmap"].study_id,
$scope.exportLevel); // Set mapListButtonExport URL
$scope.exportTAG="Download Study Export";
$scope.disableMapListButton=false;
}
else if (res.data === "STUDY_INCOMPLETE_NOT_ZIPPABLE") {
$scope.exportTAG="Study Incomplete";
$scope.exportURL = undefined;
$scope.disableMapListButton=true;
}
else if (res.data === "STUDY_FAILED_NOT_ZIPPABLE") {
$scope.exportTAG="Study Failed";
$scope.exportURL = undefined;
$scope.disableMapListButton=true;
}
else {
$scope.exportTAG="Study NOT Exportable";
$scope.exportURL = undefined;
$scope.disableMapListButton=true;
}
});
}
The function $scope.setupZipButton(); is then called at appropriate points in the controller so the export tag (button title), export
download URL and button disable/enable state is set appropriately. See github change:
https://github.com/smallAreaHealthStatisticsUnit/rapidInquiryFacility/commit/606fb25e5dd0745f8c26bdf91d27716e44cf11d0
In this case the study state column was deliberately missspelt to generate an error! (study_statey instead of study_state):
User:"peter" IP:"0:0:0:0:0:0:0:1" Cheking status of extract for study 53.
15:49:04.857 [http-nio-8080-exec-7] WARN rifGenericLibrary.util.RIFLogger : [rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager]:
MSSQLAbstractSQLManager checkIfQueryLoggingEnabled=FALSE property: getRif40StudyState NOT FOUND
15:49:04.889 [http-nio-8080-exec-7] ERROR rifGenericLibrary.util.RIFLogger : [rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager]:
Error in SQL Statement: >>>
SELECT a.study_statey
FROM rif40.rif40_studies a
WHERE a.study_id = ?
getMessage: SQLServerException: Invalid column name 'study_statey'.
getRootCauseMessage: SQLServerException: Invalid column name 'study_statey'.
getThrowableCount: 1
getRootCauseStackTrace >>>
com.microsoft.sqlserver.jdbc.SQLServerException: Invalid column name 'study_statey'.
at com.microsoft.sqlserver.jdbc.SQLServerException.makeFromDatabaseError(SQLServerException.java:232)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.getNextResult(SQLServerStatement.java:1672)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.doExecutePreparedStatement(SQLServerPreparedStatement.java:460)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement$PrepStmtExecCmd.doExecute(SQLServerPreparedStatement.java:405)
at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:7535)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:2438)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeCommand(SQLServerStatement.java:208)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeStatement(SQLServerStatement.java:183)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.executeQuery(SQLServerPreparedStatement.java:317)
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getRif40StudyState(MSSQLStudyExtractManager.java:773)
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getExtractStatus(MSSQLStudyExtractManager.java:263)
at rifServices.dataStorageLayer.ms.MSSQLAbstractRIFStudySubmissionService.getExtractStatus(MSSQLAbstractRIFStudySubmissionService.java:1190)
at rifServices.restfulWebServices.ms.MSSQLAbstractRIFWebServiceResource.getExtractStatus(MSSQLAbstractRIFWebServiceResource.java:972)
at rifServices.restfulWebServices.ms.MSSQLRIFStudySubmissionWebServiceResource.getExtractStatus(MSSQLRIFStudySubmissionWebServiceResource.java:1216)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:558)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:733)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:341)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1455)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
<<< End getRootCauseStackTrace.
15:49:04.891 [http-nio-8080-exec-7] ERROR rifGenericLibrary.util.RIFLogger : [rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager]:
MSSQLStudyExtractManager ERROR
getMessage: SQLServerException: Invalid column name 'study_statey'.
getRootCauseMessage: SQLServerException: Invalid column name 'study_statey'.
getThrowableCount: 1
getRootCauseStackTrace >>>
com.microsoft.sqlserver.jdbc.SQLServerException: Invalid column name 'study_statey'.
at com.microsoft.sqlserver.jdbc.SQLServerException.makeFromDatabaseError(SQLServerException.java:232)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.getNextResult(SQLServerStatement.java:1672)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.doExecutePreparedStatement(SQLServerPreparedStatement.java:460)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement$PrepStmtExecCmd.doExecute(SQLServerPreparedStatement.java:405)
at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:7535)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:2438)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeCommand(SQLServerStatement.java:208)
at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeStatement(SQLServerStatement.java:183)
at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.executeQuery(SQLServerPreparedStatement.java:317)
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getRif40StudyState(MSSQLStudyExtractManager.java:773)
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getExtractStatus(MSSQLStudyExtractManager.java:263)
at rifServices.dataStorageLayer.ms.MSSQLAbstractRIFStudySubmissionService.getExtractStatus(MSSQLAbstractRIFStudySubmissionService.java:1190)
at rifServices.restfulWebServices.ms.MSSQLAbstractRIFWebServiceResource.getExtractStatus(MSSQLAbstractRIFWebServiceResource.java:972)
at rifServices.restfulWebServices.ms.MSSQLRIFStudySubmissionWebServiceResource.getExtractStatus(MSSQLRIFStudySubmissionWebServiceResource.java:1216)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:558)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:733)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:341)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1455)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
<<< End getRootCauseStackTrace.
15:49:04.893 [http-nio-8080-exec-7] ERROR rifGenericLibrary.util.RIFLogger : [rifServices.dataStorageLayer.ms.MSSQLAbstractRIFService]:
getExtractStatus
getMessage: RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
getRootCauseMessage: RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
getThrowableCount: 1
getRootCauseStackTrace >>>
rifGenericLibrary.system.RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getExtractStatus(MSSQLStudyExtractManager.java:313)
at rifServices.dataStorageLayer.ms.MSSQLAbstractRIFStudySubmissionService.getExtractStatus(MSSQLAbstractRIFStudySubmissionService.java:1190)
at rifServices.restfulWebServices.ms.MSSQLAbstractRIFWebServiceResource.getExtractStatus(MSSQLAbstractRIFWebServiceResource.java:972)
at rifServices.restfulWebServices.ms.MSSQLRIFStudySubmissionWebServiceResource.getExtractStatus(MSSQLRIFStudySubmissionWebServiceResource.java:1216)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:558)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:733)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:341)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1455)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
<<< End getRootCauseStackTrace.
15:49:04.894 [http-nio-8080-exec-7] INFO rifGenericLibrary.util.RIFLogger : [rifServices.dataStorageLayer.ms.MSSQLProductionRIFStudySubmissionService]:
get ZIP file extract status: null
15:49:04.895 [http-nio-8080-exec-7] ERROR rifGenericLibrary.util.RIFLogger : [rifServices.restfulWebServices.ms.MSSQLRIFStudySubmissionWebServiceResource]:
MSSQLAbstractRIFWebServiceResource.getExtractStatus error
getMessage: RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
getRootCauseMessage: RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
getThrowableCount: 1
getRootCauseStackTrace >>>
rifGenericLibrary.system.RIFServiceException: Unable to get extract zipfile status for user "peter", study "53", zipfile "UNKNOWN".
at rifServices.dataStorageLayer.ms.MSSQLStudyExtractManager.getExtractStatus(MSSQLStudyExtractManager.java:313)
at rifServices.dataStorageLayer.ms.MSSQLAbstractRIFStudySubmissionService.getExtractStatus(MSSQLAbstractRIFStudySubmissionService.java:1190)
at rifServices.restfulWebServices.ms.MSSQLAbstractRIFWebServiceResource.getExtractStatus(MSSQLAbstractRIFWebServiceResource.java:972)
at rifServices.restfulWebServices.ms.MSSQLRIFStudySubmissionWebServiceResource.getExtractStatus(MSSQLRIFStudySubmissionWebServiceResource.java:1216)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:558)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:733)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:478)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:624)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:341)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:799)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:861)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1455)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
<<< End getRootCauseStackTrace.
Peter Hambly 16th October 2017