Skip to content

Commit

Permalink
Merge branch 'hackathon' of https://github.com/hms-dbmi/IRCT into hac…
Browse files Browse the repository at this point in the history 
…kathon
  • Loading branch information
Jason Stedman committed Sep 8, 2017
2 parents 53f19e4 + efd6994 commit b3eefea
Show file tree
Hide file tree
Showing 93 changed files with 1,091 additions and 14,430 deletions.
52 changes: 28 additions & 24 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/IRCTApplication.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.logging.Level;
import java.util.logging.Logger;

import javax.annotation.PostConstruct;
import javax.ejb.Singleton;
Expand All @@ -24,6 +22,8 @@
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Root;

import org.apache.log4j.Logger;

import edu.harvard.hms.dbmi.bd2k.irct.dataconverter.ResultDataConverter;
import edu.harvard.hms.dbmi.bd2k.irct.event.EventConverterImplementation;
import edu.harvard.hms.dbmi.bd2k.irct.event.IRCTEventListener;
Expand Down Expand Up @@ -52,8 +52,7 @@ public class IRCTApplication {
private Map<String, IRCTJoin> supportedJoinTypes;
private Map<ResultDataType, List<DataConverterImplementation>> resultDataConverters;

@Inject
Logger log;
Logger logger = Logger.getLogger(this.getClass());

@Inject
private EntityManagerFactory objectEntityManager;
Expand All @@ -70,27 +69,27 @@ public class IRCTApplication {
*/
@PostConstruct
public void init() {
log.info("Starting IRCT Application");
logger.info("Starting IRCT Application");
this.oem = objectEntityManager.createEntityManager();
this.oem.setFlushMode(FlushModeType.COMMIT);

log.info("Loading Data Converters");
logger.info("Loading Data Converters");
loadDataConverters();
log.info("Finished Data Converters");
logger.info("Finished Data Converters");

log.info("Loading Event Listeners");
logger.info("Loading Event Listeners");
loadIRCTEventListeners();
log.info("Finished Loading Event Listeners");
logger.info("Finished Loading Event Listeners");

log.info("Loading Join Types");
logger.info("Loading Join Types");
loadJoins();
log.info("Finished Loading Join Types");
logger.info("Finished Loading Join Types");

log.info("Loading Resources");
logger.info("Loading Resources");
loadResources();
log.info("Finished Loading Resources");
logger.info("Finished Loading Resources");

log.info("Finished Starting IRCT Application");
logger.info("Finished Starting IRCT Application");
}

public String getVersion() {
Expand All @@ -109,14 +108,13 @@ public String getVersion() {
version = p.getProperty("version", "");
}
} catch (Exception e) {
log.log(Level.INFO, "getVersion() ERROR:" + e.getMessage());
logger.error("getVersion() ERROR:" + e.getMessage());
}

if (version == null) {
// we could not compute the version so use a blank
version = "N/A";
}

return version;
}

Expand All @@ -136,7 +134,7 @@ private void loadIRCTEventListeners() {
irctEventListener.registerListener(irctEvent);
}

log.info("Loaded " + allEventListeners.size() + " IRCT Event listeners");
logger.info("Loaded " + allEventListeners.size() + " IRCT Event listeners");
}

/**
Expand All @@ -161,7 +159,7 @@ private void loadDataConverters() {

}

log.info("Loaded " + allDCI.size() + " result data converters");
logger.info("Loaded " + allDCI.size() + " result data converters");
}

/**
Expand All @@ -178,7 +176,7 @@ private void loadJoins() {
for (IRCTJoin jt : oem.createQuery(criteria).getResultList()) {
this.supportedJoinTypes.put(jt.getName(), jt);
}
log.info("Loaded " + this.supportedJoinTypes.size() + " joins");
logger.info("Loaded " + this.supportedJoinTypes.size() + " joins");
}

/**
Expand All @@ -194,19 +192,19 @@ private void loadResources() {
CriteriaQuery<Resource> criteria = cb.createQuery(Resource.class);
Root<Resource> load = criteria.from(Resource.class);
criteria.select(load);
log.info("loadResources() "+criteria.toString());
logger.info("loadResources() "+criteria.toString());
for (Resource resource : oem.createQuery(criteria).getResultList()) {
try {
log.info("loadResources() Setting up resource:"+resource.toString()+" "+resource.getId()+" "+resource.getClass().toString());
logger.info("loadResources() Setting up resource:"+resource.toString()+" "+resource.getId()+" "+resource.getClass().toString());
resource.setup();
log.info("loadResources() resource ```"+resource.getName()+"``` has been loaded");
logger.info("loadResources() resource ```"+resource.getName()+"``` has been loaded");
this.resources.put(resource.getName(), resource);
} catch (ResourceInterfaceException e) {
log.warning("loadResources() Exception: "+e.getMessage());
logger.error("loadResources() Exception: "+e.getMessage());
e.printStackTrace();
}
}
log.info("loadResources() Loaded " + this.resources.size() + " resources");
logger.info("loadResources() Loaded " + this.resources.size() + " resources");
}

/**
Expand Down Expand Up @@ -255,6 +253,12 @@ public boolean doesResourceExist(String name) {
* @return Resources
*/
public Map<String, Resource> getResources() {
logger.debug("getResources()");

//Map<String, Resource> resources
for (Map.Entry<String, Resource> entry : resources.entrySet()) {
logger.debug("getResources() resource key: " + entry.getKey() + " value:" + entry.getValue().getName());
}
return resources;
}

Expand Down
46 changes: 37 additions & 9 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/action/QueryAction.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,10 @@

import javax.naming.NamingException;

import org.apache.log4j.Logger;

import edu.harvard.hms.dbmi.bd2k.irct.event.IRCTEventListener;
import edu.harvard.hms.dbmi.bd2k.irct.exception.ResourceInterfaceException;
import edu.harvard.hms.dbmi.bd2k.irct.model.query.ClauseAbstract;
import edu.harvard.hms.dbmi.bd2k.irct.model.query.Query;
import edu.harvard.hms.dbmi.bd2k.irct.model.query.WhereClause;
Expand All @@ -18,8 +22,6 @@
import edu.harvard.hms.dbmi.bd2k.irct.model.result.ResultStatus;
import edu.harvard.hms.dbmi.bd2k.irct.model.security.SecureSession;
import edu.harvard.hms.dbmi.bd2k.irct.util.Utilities;
import edu.harvard.hms.dbmi.bd2k.irct.event.IRCTEventListener;
import edu.harvard.hms.dbmi.bd2k.irct.exception.ResourceInterfaceException;

/**
* Implements the Action interface to run a query on a specific instance
Expand All @@ -35,7 +37,8 @@ public class QueryAction implements Action {
private Result result;

private IRCTEventListener irctEventListener;

private Logger logger = Logger.getLogger(this.getClass());

/**
* Sets up the action to run a given query on a resource
*
Expand All @@ -45,14 +48,22 @@ public class QueryAction implements Action {
* Run the query
*/
public void setup(Resource resource, Query query) {
logger.debug("setup() Starting...");

if (resource == null) {
logger.warn("setup() resource is null");
}
this.query = query;
this.resource = resource;
this.status = ActionStatus.CREATED;
this.irctEventListener = Utilities.getIRCTEventListener();
logger.debug("setup() Finished.");
}

@Override
public void updateActionParams(Map<String, Result> updatedParams) {
logger.debug("updateActionParams() Starting...");

for (String key : updatedParams.keySet()) {
Long clauseId = Long.valueOf(key.split(".")[0]);
String parameterId = key.split(".")[1];
Expand All @@ -64,33 +75,50 @@ public void updateActionParams(Map<String, Result> updatedParams) {
updatedParams.get(key).getId().toString());
}
}
logger.debug("updateActionParams() Finished.");
}

@Override
public void run(SecureSession session) {
logger.debug("run() Starting...");

logger.debug("run() calling `beforeQuery`");
irctEventListener.beforeQuery(session, resource, query);
logger.debug("run() set status to "+ActionStatus.RUNNING);
this.status = ActionStatus.RUNNING;
try {
logger.debug("run() getting `QueryResourceImplementationInterface` object");
QueryResourceImplementationInterface queryInterface = (QueryResourceImplementationInterface) resource
.getImplementingInterface();

if (queryInterface == null) {
logger.error("run() `queryInterface` is not found for "+resource.getName()+" resource");
throw new RuntimeException("Unknown implementing interface for resource `"+resource.getName()+"`");
}

this.result = ActionUtilities.createResult(queryInterface
.getQueryDataType(query));
logger.debug("run() creating `result` field.");
this.result = ActionUtilities.createResult(queryInterface.getQueryDataType(query));

if (session != null) {
logger.debug("run() setting `user` field of the `result`.");
this.result.setUser(session.getUser());
}



logger.debug("run() calling runQuery() on the interface.");
this.result = queryInterface.runQuery(session, query, result);

// Update the result in the database
logger.debug("run() calling ActionUtilities.mergeResult(). This would persist the result in the database.");
ActionUtilities.mergeResult(this.result);
} catch (Exception e) {
this.result.setResultStatus(ResultStatus.ERROR);
this.result.setMessage(e.getMessage());
logger.error("run() Exception: "+e.getMessage());
this.status = ActionStatus.ERROR;
if (this.result == null) {
throw new RuntimeException(e);
} else {
this.result.setResultStatus(ResultStatus.ERROR);
this.result.setMessage(e.getMessage());
}
}
irctEventListener.afterQuery(session, resource, query);
}
Expand Down
56 changes: 45 additions & 11 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/controller/ExecutionController.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@

import java.util.Date;
import java.util.concurrent.Callable;
import java.util.logging.Logger;

import javax.annotation.Resource;
import javax.ejb.Asynchronous;
Expand All @@ -18,6 +17,8 @@
import javax.persistence.PersistenceContext;
import javax.transaction.UserTransaction;

import org.apache.log4j.Logger;

import edu.harvard.hms.dbmi.bd2k.irct.action.JoinAction;
import edu.harvard.hms.dbmi.bd2k.irct.action.ProcessAction;
import edu.harvard.hms.dbmi.bd2k.irct.action.QueryAction;
Expand All @@ -44,8 +45,7 @@
@Stateless
public class ExecutionController {

@Inject
Logger log;
Logger logger = Logger.getLogger(this.getClass());

@PersistenceContext(unitName = "primary")
EntityManager entityManager;
Expand Down Expand Up @@ -103,31 +103,49 @@ public Long runProcess(IRCTProcess process, SecureSession secureSession)
*/
public Long runQuery(Query query, SecureSession secureSession)
throws PersistableException {
logger.debug("runQuery() Starting...");

Result newResult = new Result();
newResult.setJobType("EXECUTION");
logger.debug("runQuery() Set `newResult` as type:EXECUTION");

// Add the current user to the query.
newResult.setUser(secureSession.getUser());

logger.debug("runQuery() Set `newResult` as user:"+newResult.getUser().getUserId());

newResult.setResultStatus(ResultStatus.RUNNING);
logger.debug("runQuery() Set `newResult` as type:EXECUTION");

entityManager.persist(newResult);
logger.debug("runQuery() persited `newResult`");

QueryAction qa = new QueryAction();

edu.harvard.hms.dbmi.bd2k.irct.model.resource.Resource resource = (edu.harvard.hms.dbmi.bd2k.irct.model.resource.Resource) query.getResources().toArray()[0];
logger.debug("runQuery() `QueryAction` and `Resource` are set.");

if(!resource.isSetup()) {
logger.debug("runQuery() Resource `"+resource.getName()+"` is not set up, yet.");
resource = rc.getResource(resource.getName());
} else {
logger.debug("runQuery() Resource is already set up. "+resource.getName());
}
logger.debug("runQuery() Resource `"+resource.getName()+"` is now should be all set.");

logger.debug("runQuery() Setting up queryaction with resource and query.");
qa.setup(resource, query);
logger.debug("runQuery() `QueryAction` setup is now complete.");

ExecutableLeafNode eln = new ExecutableLeafNode();
eln.setAction(qa);
logger.debug("runQuery() Added `QueryAction` to `ExecutableLeafNode`.");

ExecutionPlan exp = new ExecutionPlan();
exp.setup(eln, secureSession);

logger.debug("runQuery() `ExecutionPlan` is all set up. Try runExecutionPlan() now");

runExecutionPlan(exp, newResult);

logger.debug("runQuery() returning `newResult.id` as "+newResult.getId());
return newResult.getId();
}

Expand Down Expand Up @@ -178,12 +196,16 @@ public Long runJoin(Join join, SecureSession secureSession)
@Asynchronous
public void runExecutionPlan(final ExecutionPlan executionPlan,
final Result result) throws PersistableException {


logger.debug("runExectionPlan() Starting...");
Callable<Result> runPlan = new Callable<Result>() {
@Override
public Result call() {
logger.debug("Callable.call() starting in inner class");

try {
result.setStartTime(new Date());
logger.debug("Callable.call() Calling run() on `executionPlan` "+executionPlan.getClass().getName());
executionPlan.run();

Result finalResult = executionPlan.getResults();
Expand All @@ -206,25 +228,37 @@ public Result call() {
}

result.setEndTime(new Date());

UserTransaction userTransaction = lookup();

userTransaction.begin();
entityManager.merge(result);
userTransaction.commit();

} catch (PersistableException e) {
logger.error("Callable.call() PersistableException:"+e.getMessage());

result.setResultStatus(ResultStatus.ERROR);
result.setMessage(e.getMessage());
} catch (Exception e) {
e.printStackTrace();
log.info(e.getMessage());
logger.error("Callable.call() Exception:"+e.getMessage());
result.setResultStatus(ResultStatus.ERROR);
} finally {

logger.debug("Callable.call() done with the method");
}
logger.debug("Callable.call() returning `result` with status "+result.getResultStatus().toString());
return result;
}
};

mes.submit(runPlan);
logger.debug("runExecutionPlan() created `Callable`. calling submit() of ManagedExecutionService");
try {
mes.submit(runPlan);
} catch (Exception e) {
logger.error("runExecutionPlan() >>>Exception: "+e.getMessage());
} finally {
logger.debug("runExecutionPlan() Finished.");
}
}

private UserTransaction lookup() throws NamingException {
Expand Down
Loading

0 comments on commit b3eefea

Please sign in to comment.