@Override
public void onReferencesRequired(final Long dbId) {
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryReferences/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONArray list = JSONParser.parseStrict(response.getText()).isArray();
List<LiteratureReference> references = new ArrayList<LiteratureReference>();
for (int i = 0; i < list.size(); ++i) {
JSONObject object = list.get(i).isObject();
references.add((LiteratureReference) ModelFactory.getDatabaseObject(object));
}
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, references);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received References object for 'DbId="
+ dbId
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for 'DbId="
+ dbId
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested references data for 'DbId="
+ dbId
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
}
@Override
public void onMoleculeDataRequired(final Molecule molecule) {
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryById/ReferenceEntity/" + molecule.getDbId();
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONObject json = JSONParser.parseStrict(response.getText()).isObject();
Molecule molecule =
new Molecule(ModelFactory.getDatabaseObject(json).getSchemaClass(), json);
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for Molecule '"
+ molecule.getDisplayName()
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for Molecule '"
+ molecule.getDisplayName()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested detailed data for Molecule \n'"
+ molecule.getDisplayName()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
}
@Override
public void onDataRequired(final DatabaseObject databaseObject) {
final long dbId = databaseObject.getDbId();
String url = "/ReactomeRESTfulAPI/RESTfulWS/detailedView/DatabaseObject/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONObject json = JSONParser.parseStrict(response.getText()).isObject();
DatabaseObject databaseObject = ModelFactory.getDatabaseObject(json);
DataRequiredListener.getDataRequiredListener()
.setRequiredData(dbId, databaseObject);
eventBus.fireELVEvent(ELVEventType.DETAILED_VIEW_LOADED, databaseObject);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for 'DbId="
+ databaseObject.getDbId()
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for 'DbId="
+ databaseObject.getDbId()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested data for 'DbId="
+ databaseObject.getDbId()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onPathRequired(final Event event) {
/* TODO Testing
but never used because DataRequiredListener is used by DetailsPanel and there ancestorsRequired is unused */
final long dbId = event.getDbId();
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryEventAncestors/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONArray list = JSONParser.parseStrict(response.getText()).isArray();
Ancestors ancestors = new Ancestors(list);
DataRequiredListener.getDataRequiredListener()
.setRequiredAncestors(dbId, ancestors);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for 'DbId="
+ event.getDbId()
+ "' is empty or faulty and could not be parsed into a path or hierarchy.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The PathRequired request for 'DbId="
+ event.getDbId()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested data for 'DbId="
+ event.getDbId()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onResourceChosen(final String resource) {
String url = AnalysisHelper.URL_PREFIX + "/token/" + token + "?page=1&resource=" + resource;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
AnalysisResult result =
AnalysisModelFactory.getModelObject(AnalysisResult.class, response.getText());
// We have to do this here because there is no name coming from the RESTFul service
result
.getSummary()
.setSpeciesName(speciesMap.get(result.getSummary().getSpecies()));
view.clearSelection();
view.showResult(result, resource);
view.selectPathway(selected);
} catch (AnalysisModelException e) {
MessageObject msgObj =
new MessageObject(
"The received object for '"
+ resource
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ e.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + e.getMessage());
view.setInitialState();
}
}
@Override
public void onError(Request request, Throwable exception) {
// TODO Check before commit - not yet tested
MessageObject msgObj =
new MessageObject(
"The request for '"
+ resource
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + exception.getMessage());
view.setInitialState();
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested detailed data for '"
+ resource
+ "'\nin the Analysis could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
view.setInitialState();
}
}